diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
index 0eaeef28b..72926a77d 100644
--- a/.github/workflows/build_and_test.yml
+++ b/.github/workflows/build_and_test.yml
@@ -8,7 +8,7 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.config.name }} (Python ${{ matrix.python-version}})
+    name: ${{ matrix.config.name }} (Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.config.os }}
     strategy:
       fail-fast: false
@@ -65,15 +65,24 @@ jobs:
         conda install -y --override-channels -c conda-forge --file tomviz/tests/python/requirements-dev.txt
         pip install --no-build-isolation --no-deps -U tomviz/tomviz/python
         pip install --no-build-isolation --no-deps -U tomviz/acquisition
+        # These do not have to be in the same environment as Tomviz, but the dependencies
+        # are so far compatible and we'll just let it go for the tests.
+        conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/pyxrf_requirements.txt
+        pip install --no-build-isolation --no-deps -U tomviz/tomviz/python/tomviz/pyxrf/pyxrf-utils
 
     - name: Run Tests
+      env:
+          # Make sure the Qt tests run offscreen
+          QT_QPA_PLATFORM: offscreen
+          TOMVIZ_REQUIRE_PYXRF: true
       run: |
         cd tomviz-build
-        TOMVIZ_TEST_PYTHON_EXECUTABLE=$(which python3) ctest --output-on-failure
+        export TOMVIZ_TEST_PYTHON_EXECUTABLE=$(which python3)
+        ctest --output-on-failure
 
     - name: Upload CTest Log (On Failure Only)
       if: ${{ failure() }}
       uses: actions/upload-artifact@v4
       with:
-        name: TomvizCTestLog.log
+        name: TomvizCTestLog_${{ matrix.config.name }}_Py${{ matrix.python-version }}.log
         path: tomviz-build/Testing/Temporary/LastTest.log
diff --git a/.github/workflows/build_requirements.txt b/.github/workflows/build_requirements.txt
index 86b5d9343..b46c1aece 100644
--- a/.github/workflows/build_requirements.txt
+++ b/.github/workflows/build_requirements.txt
@@ -6,3 +6,5 @@ vtk
 libxml2-devel=2.14*
 # This is needed for building the tests
 gtest
+# This is needed for installing stuff on Python3.13
+setuptools
diff --git a/.github/workflows/pyxrf_requirements.txt b/.github/workflows/pyxrf_requirements.txt
new file mode 100644
index 000000000..3208689d9
--- /dev/null
+++ b/.github/workflows/pyxrf_requirements.txt
@@ -0,0 +1,9 @@
+# These are PyXRF workflow dependencies
+hxntools
+pyxrf
+xrf-tomo
+xraylib
+scikit-beam
+tomopy
+# These are required for installing the pyxrf-utils environment
+hatchling
diff --git a/.github/workflows/runtime_requirements.txt b/.github/workflows/runtime_requirements.txt
index 0b5ec89a3..7eaa60237 100644
--- a/.github/workflows/runtime_requirements.txt
+++ b/.github/workflows/runtime_requirements.txt
@@ -7,10 +7,4 @@ jsonpointer
 pyfftw
 pygments
 pystackreg
-# These are PyXRF workflow dependencies
 h5py
-pyxrf
-xrf-tomo
-xraylib
-scikit-beam
-tomopy
diff --git a/BUILDING.md b/BUILDING.md
index c28906414..b87a0d051 100644
--- a/BUILDING.md
+++ b/BUILDING.md
@@ -1,8 +1,8 @@
 Building Tomviz
 ===============
 
-Building Tomviz is an advanced process that requires compiling ParaView,
-as well as ensuring all necessary dependencies are in place. Most users
+Building Tomviz can be an advanced process that requires
+ensuring that all necessary dependencies are in place. Most users
 ought to install Tomviz from the conda-forge packages rather than
 building it. These instructions are primarily for developers who wish
 to make contributions.
@@ -16,14 +16,10 @@ conda create -n tomviz -y
 conda activate tomviz
 ```
 
-First, we need to ensure that ParaView and tomviz are cloned into the
-current repository. Run the following bash code to do so:
+First, we need to ensure that tomviz is cloned into the current repository.
+Run the following bash code to do so:
 
 ```bash
-if ! [ -e "paraview" ]; then
-  git clone -b v6.0.1 --recursive https://gitlab.kitware.com/paraview/paraview
-fi
-
 if ! [ -e "tomviz" ]; then
   git clone --recursive https://github.com/NSLS2/tomviz
 fi
@@ -36,12 +32,6 @@ conda-forge. Thus we will use those lists for installation.
 conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/build_requirements.txt
 ```
 
-Next, build ParaView. This may take some time.
-
-```bash
-bash tomviz/.github/workflows/scripts/build_paraview.sh
-```
-
 Now, build Tomviz.
 
 ```bash
@@ -65,10 +55,6 @@ Tomviz may then be ran as follows:
 All of the build instructions above put into a single script are as follows:
 
 ```bash
-if ! [ -e "paraview" ]; then
-  git clone -b v6.0.1 --recursive https://gitlab.kitware.com/paraview/paraview
-fi
-
 if ! [ -e "tomviz" ]; then
   git clone --recursive https://github.com/NSLS2/tomviz
 fi
@@ -76,8 +62,7 @@ fi
 # Install build requirements
 conda install -y --override-channels -c conda-forge --file tomviz/.github/workflows/build_requirements.txt
 
-# Build ParaView and Tomviz
-bash tomviz/.github/workflows/scripts/build_paraview.sh
+# Build Tomviz
 bash tomviz/.github/workflows/scripts/build_tomviz.sh
 
 # Install runtime dependencies
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fe010df77..102412bcd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -89,7 +89,7 @@ file(RELATIVE_PATH
 set(CMAKE_MODULE_PATH "${tomviz_SOURCE_DIR}/cmake")
 
 # Request C++11 standard, using new CMake variables.
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 set(CMAKE_CXX_EXTENSIONS False)
 
@@ -146,7 +146,7 @@ endif()
 
 find_package(ITK 4.9)
 
-set(PYBIND11_CPP_STANDARD "-std=c++11" CACHE STRING "")
+set(PYBIND11_CPP_STANDARD "-std=c++17" CACHE STRING "")
 add_subdirectory(${PROJECT_SOURCE_DIR}/thirdparty/pybind11)
 
 option(tomviz_ENABLE_LOOKING_GLASS "Enable the looking glass plugin" OFF)
diff --git a/acquisition/requirements-dev.txt b/acquisition/requirements-dev.txt
index 3db2e5bff..f583c9fc4 100644
--- a/acquisition/requirements-dev.txt
+++ b/acquisition/requirements-dev.txt
@@ -1,9 +1,10 @@
-pytest==3.0.6
-requests==2.20.0
-Pillow==8.3.2
+pytest>=8.3
+requests>=2.32.4
+Pillow==10.3.0
 # Need this for testing so we can stop there server, change when the required
 # get into a release.
-https://github.com/bottlepy/bottle/archive/41ed6965.zip
+# https://github.com/bottlepy/bottle/archive/41ed6965.zip
+bottle>=0.13.2
 mock==2.0.0
 diskcache==3.0.1
 -e git+https://cjh1@bitbucket.org/cjh1/pydm3reader.git@filelike#egg=dm3_lib
diff --git a/acquisition/setup.py b/acquisition/setup.py
index a245bd207..bffe55ca9 100644
--- a/acquisition/setup.py
+++ b/acquisition/setup.py
@@ -30,7 +30,7 @@
     },
     entry_points={
         'console_scripts': [
-            'tomviz-acquisition = tomviz.acquisition.cli:main',
+            'tomviz-acquisition = tomviz_acquisition.acquisition.cli:main',
             'tomviz-tiltseries-writer = tests.mock.tiltseries.writer:main'
         ]
     }
diff --git a/acquisition/tests/conftest.py b/acquisition/tests/conftest.py
index bc5a54149..7f490307d 100644
--- a/acquisition/tests/conftest.py
+++ b/acquisition/tests/conftest.py
@@ -4,7 +4,7 @@
 from threading import Thread
 from bottle import default_app, WSGIRefServer
 
-from tomviz.acquisition import server
+from tomviz_acquisition.acquisition import server
 from .mock.tiltseries import TIFFWriter, DM3Writer
 
 
diff --git a/acquisition/tests/fei_test.py b/acquisition/tests/fei_test.py
index 9e560f094..2c2ebbcb2 100644
--- a/acquisition/tests/fei_test.py
+++ b/acquisition/tests/fei_test.py
@@ -4,17 +4,17 @@
 import sys
 import os
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 
 # Add mock modules to path
-mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz',
+mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz_acquisition',
                         'acquisition', 'vendors', 'fei', 'mock')
 sys.path.append(mock_dir)
 
 
 @pytest.fixture(scope="module")
 def fei_acquisition_server(acquisition_server):
-    acquisition_server.setup('tomviz.acquisition.vendors.fei.FeiAdapter')
+    acquisition_server.setup('tomviz_acquisition.acquisition.vendors.fei.FeiAdapter')
     yield acquisition_server
 
 
diff --git a/acquisition/tests/fixtures/source1.py b/acquisition/tests/fixtures/source1.py
index c07cfdc10..5f1eb985a 100644
--- a/acquisition/tests/fixtures/source1.py
+++ b/acquisition/tests/fixtures/source1.py
@@ -1,6 +1,6 @@
 import tempfile
 import os
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 
 
 class ApiAdapter1(AbstractSource):
diff --git a/acquisition/tests/fixtures/source2.py b/acquisition/tests/fixtures/source2.py
index 821b225c2..b702208c5 100644
--- a/acquisition/tests/fixtures/source2.py
+++ b/acquisition/tests/fixtures/source2.py
@@ -1,6 +1,6 @@
 import tempfile
 import os
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 
 
 class ApiAdapter2(AbstractSource):
diff --git a/acquisition/tests/jsonrpc_test.py b/acquisition/tests/jsonrpc_test.py
index f1746b8d8..bb1f1fc07 100644
--- a/acquisition/tests/jsonrpc_test.py
+++ b/acquisition/tests/jsonrpc_test.py
@@ -1,6 +1,6 @@
 import pytest
 
-from tomviz.jsonrpc import JsonRpcHandler, jsonrpc_message
+from tomviz_acquisition.jsonrpc import JsonRpcHandler, jsonrpc_message
 
 
 @pytest.fixture
diff --git a/acquisition/tests/mock/mock_api.py b/acquisition/tests/mock/mock_api.py
index 047776f6c..b20947bea 100644
--- a/acquisition/tests/mock/mock_api.py
+++ b/acquisition/tests/mock/mock_api.py
@@ -1,7 +1,7 @@
 import time
 from PIL import Image
 from . import test_image, test_black_image, angle_to_page
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition.utility import tobytes
 
 img = Image.open(test_image())
 black = test_black_image().read()
diff --git a/acquisition/tests/mock/source.py b/acquisition/tests/mock/source.py
index 9d449b46b..2f35664cf 100644
--- a/acquisition/tests/mock/source.py
+++ b/acquisition/tests/mock/source.py
@@ -1,6 +1,6 @@
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import AbstractSource
 from . import mock_api
-from tomviz.acquisition import describe
+from tomviz_acquisition.acquisition import describe
 
 
 class ApiAdapter(AbstractSource):
diff --git a/acquisition/tests/passive_test.py b/acquisition/tests/passive_test.py
index 4d35d7764..e0b61ad77 100644
--- a/acquisition/tests/passive_test.py
+++ b/acquisition/tests/passive_test.py
@@ -7,9 +7,9 @@
 from PIL import Image
 import dm3_lib as dm3
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 from .mock import test_image, test_dm3_tilt_series
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition.utility import tobytes
 
 # Add mock modules to path
 mock_dir = os.path.join(os.path.dirname(__file__), '..', 'tomviz',
@@ -19,7 +19,7 @@
 
 @pytest.fixture(scope="module")
 def passive_acquisition_server(acquisition_server):
-    source = 'tomviz.acquisition.vendors.passive.PassiveWatchSource'
+    source = 'tomviz_acquisition.acquisition.vendors.passive.PassiveWatchSource'
     acquisition_server.setup(source)
     yield acquisition_server
 
diff --git a/acquisition/tests/server_test.py b/acquisition/tests/server_test.py
index b8cd30847..870d8f774 100644
--- a/acquisition/tests/server_test.py
+++ b/acquisition/tests/server_test.py
@@ -5,7 +5,7 @@
 import pytest
 import inspect
 
-from tomviz.jsonrpc import jsonrpc_message
+from tomviz_acquisition.jsonrpc import jsonrpc_message
 from tests.mock.source import ApiAdapter
 
 
diff --git a/acquisition/tomviz/__init__.py b/acquisition/tomviz/__init__.py
deleted file mode 100644
index 69e3be50d..000000000
--- a/acquisition/tomviz/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-__path__ = __import__('pkgutil').extend_path(__path__, __name__)
diff --git a/acquisition/tomviz/acquisition/vendors/__init__.py b/acquisition/tomviz_acquisition/__init__.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/__init__.py
rename to acquisition/tomviz_acquisition/__init__.py
diff --git a/acquisition/tomviz/acquisition/__init__.py b/acquisition/tomviz_acquisition/acquisition/__init__.py
similarity index 100%
rename from acquisition/tomviz/acquisition/__init__.py
rename to acquisition/tomviz_acquisition/acquisition/__init__.py
diff --git a/acquisition/tomviz/acquisition/cli/__init__.py b/acquisition/tomviz_acquisition/acquisition/cli/__init__.py
similarity index 91%
rename from acquisition/tomviz/acquisition/cli/__init__.py
rename to acquisition/tomviz_acquisition/acquisition/cli/__init__.py
index 79ee22b3d..c2ccc0b4f 100644
--- a/acquisition/tomviz/acquisition/cli/__init__.py
+++ b/acquisition/tomviz_acquisition/acquisition/cli/__init__.py
@@ -1,5 +1,5 @@
 import argparse
-from tomviz.utility import logging
+from tomviz_acquisition.utility import logging
 
 
 def main():
@@ -23,7 +23,7 @@ def main():
     if args.redirect:
         logging.setup_std_loggers()
 
-    from tomviz.acquisition import server
+    from tomviz_acquisition.acquisition import server
 
     logging.setup_loggers(args.debug, args.redirect)
     server_params = vars(args)
diff --git a/acquisition/tomviz/acquisition/cli/__main__.py b/acquisition/tomviz_acquisition/acquisition/cli/__main__.py
similarity index 100%
rename from acquisition/tomviz/acquisition/cli/__main__.py
rename to acquisition/tomviz_acquisition/acquisition/cli/__main__.py
diff --git a/acquisition/tomviz/acquisition/server.py b/acquisition/tomviz_acquisition/acquisition/server.py
similarity index 97%
rename from acquisition/tomviz/acquisition/server.py
rename to acquisition/tomviz_acquisition/acquisition/server.py
index 96c359198..29e0e9b26 100644
--- a/acquisition/tomviz/acquisition/server.py
+++ b/acquisition/tomviz_acquisition/acquisition/server.py
@@ -8,10 +8,9 @@
 import bottle
 from bottle import run, route, request, HTTPResponse, Bottle
 
-import tomviz
-from tomviz import jsonrpc
-from tomviz.utility import inject
-from tomviz.acquisition import AbstractSource
+from tomviz_acquisition import jsonrpc
+from tomviz_acquisition.utility import inject
+from tomviz_acquisition.acquisition import AbstractSource
 import shutil
 
 # For python 3
@@ -26,7 +25,7 @@
 PORT = 8080
 LOG_BUF_SIZE = 65536
 
-logger = logging.getLogger('tomviz')
+logger = logging.getLogger('tomviz_acquisition')
 app = Bottle()
 
 
diff --git a/acquisition/tomviz/acquisition/utility.py b/acquisition/tomviz_acquisition/acquisition/utility.py
similarity index 100%
rename from acquisition/tomviz/acquisition/utility.py
rename to acquisition/tomviz_acquisition/acquisition/utility.py
diff --git a/acquisition/tomviz/acquisition/vendors/fei/mock/win32com/__init__.py b/acquisition/tomviz_acquisition/acquisition/vendors/__init__.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/fei/mock/win32com/__init__.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/__init__.py
diff --git a/acquisition/tomviz/acquisition/vendors/fei/__init__.py b/acquisition/tomviz_acquisition/acquisition/vendors/fei/__init__.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/fei/__init__.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/fei/__init__.py
diff --git a/acquisition/tomviz/acquisition/vendors/fei/mock/TemScripting.py b/acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/TemScripting.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/fei/mock/TemScripting.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/TemScripting.py
diff --git a/acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/win32com/__init__.py b/acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/win32com/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/acquisition/tomviz/acquisition/vendors/fei/mock/win32com/client.py b/acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/win32com/client.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/fei/mock/win32com/client.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/fei/mock/win32com/client.py
diff --git a/acquisition/tomviz/acquisition/vendors/passive/__init__.py b/acquisition/tomviz_acquisition/acquisition/vendors/passive/__init__.py
similarity index 97%
rename from acquisition/tomviz/acquisition/vendors/passive/__init__.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/passive/__init__.py
index 2166348ad..055163a79 100644
--- a/acquisition/tomviz/acquisition/vendors/passive/__init__.py
+++ b/acquisition/tomviz_acquisition/acquisition/vendors/passive/__init__.py
@@ -5,9 +5,9 @@
 import os
 import dm3_lib as dm3
 
-from tomviz.acquisition import AbstractSource
-from tomviz.acquisition import describe
-from tomviz.acquisition.utility import tobytes
+from tomviz_acquisition.acquisition import AbstractSource
+from tomviz_acquisition.acquisition import describe
+from tomviz_acquisition.acquisition.utility import tobytes
 from .filesystem import Monitor
 
 try:
diff --git a/acquisition/tomviz/acquisition/vendors/passive/filesystem.py b/acquisition/tomviz_acquisition/acquisition/vendors/passive/filesystem.py
similarity index 100%
rename from acquisition/tomviz/acquisition/vendors/passive/filesystem.py
rename to acquisition/tomviz_acquisition/acquisition/vendors/passive/filesystem.py
diff --git a/acquisition/tomviz/jsonrpc/__init__.py b/acquisition/tomviz_acquisition/jsonrpc/__init__.py
similarity index 100%
rename from acquisition/tomviz/jsonrpc/__init__.py
rename to acquisition/tomviz_acquisition/jsonrpc/__init__.py
diff --git a/acquisition/tomviz/utility/__init__.py b/acquisition/tomviz_acquisition/utility/__init__.py
similarity index 100%
rename from acquisition/tomviz/utility/__init__.py
rename to acquisition/tomviz_acquisition/utility/__init__.py
diff --git a/acquisition/tomviz/utility/logging.py b/acquisition/tomviz_acquisition/utility/logging.py
similarity index 97%
rename from acquisition/tomviz/utility/logging.py
rename to acquisition/tomviz_acquisition/utility/logging.py
index 29aa228b6..a05ecaef7 100644
--- a/acquisition/tomviz/utility/logging.py
+++ b/acquisition/tomviz_acquisition/utility/logging.py
@@ -60,7 +60,7 @@ def setup_std_loggers():
 
 
 def setup_loggers(debug=False, redirect=False):
-    logger = logging.getLogger('tomviz')
+    logger = logging.getLogger('tomviz_acquisition')
     logger.setLevel(logging.DEBUG if debug else logging.INFO)
 
     file_handler = logging.handlers.RotatingFileHandler(
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..822f03730
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,6813 @@
+version: 6
+environments:
+  default:
+    channels:
+    - url: https://conda.anaconda.org/conda-forge/
+    indexes:
+    - https://pypi.org/simple
+    packages:
+      linux-64:
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-5_kmp_llvm.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/aiohappyeyeballs-2.6.1-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aiohttp-3.13.2-py312h27b7581_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/aiosignal-1.4.0-pyhd8ed1ab_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.2-h39aace5_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/attrs-25.4.0-pyh71513ae_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/backports-datetime-fromisoformat-2.0.3-py312h7900ff3_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.2.0-h41a2e66_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.2.0-hf2c8021_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/brunsli-0.1-hd1e3526_2.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.22.0-h4cfbee9_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
+      - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
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+  md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=13
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  purls: []
+  size: 567578
+  timestamp: 1742433379869
diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 000000000..0df287926
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,37 @@
+[project]
+name = "tomviz"
+description = "Environment to run tomviz"
+version = "0.1.0"
+channels = ["conda-forge"]
+platforms = ["linux-64"]
+
+[dependencies]
+python = "==3.12"
+tomviz = ">=2.1.3"
+h5py = "*"
+tomopy = "*"
+
+[tasks]
+# Launch Tomviz from the pixi environment
+tomviz = "tomviz"
+
+# -------------------------
+# Environments
+# -------------------------
+[environments]
+default = { solve-group = "default" }
+dev     = { features = ["dev"], solve-group = "default" }
+
+# -------------------------
+# Features
+# -------------------------
+# Dev-only tools and tasks (enabled when -e dev is used)
+[feature.dev.dependencies]
+pytest = "*"
+ruff = "*"
+ipython = "*"
+matplotlib-base = "*"
+
+[feature.dev.tasks]
+lint = "ruff check"
+
diff --git a/tests/cxx/.gitignore b/tests/cxx/.gitignore
new file mode 100644
index 000000000..1269488f7
--- /dev/null
+++ b/tests/cxx/.gitignore
@@ -0,0 +1 @@
+data
diff --git a/tests/cxx/AcquisitionClientTest.cxx b/tests/cxx/AcquisitionClientTest.cxx
index 4e886af64..55f48844b 100644
--- a/tests/cxx/AcquisitionClientTest.cxx
+++ b/tests/cxx/AcquisitionClientTest.cxx
@@ -39,7 +39,7 @@ private slots:
 
     QStringList arguments;
     arguments << "-m"
-              << "tomviz.acquisition.cli";
+              << "tomviz_acquisition.acquisition.cli";
 
     server = new QProcess();
     server->start(python, arguments, QIODevice::ReadWrite);
diff --git a/tests/cxx/CMakeLists.txt b/tests/cxx/CMakeLists.txt
index e88a9527d..0acbd9d0f 100644
--- a/tests/cxx/CMakeLists.txt
+++ b/tests/cxx/CMakeLists.txt
@@ -52,7 +52,8 @@ add_cxx_test(Variant)
 
 add_cxx_qtest(DockerUtilities)
 add_cxx_qtest(AcquisitionClient PYTHONPATH "${CMAKE_SOURCE_DIR}/acquisition")
-
+add_cxx_qtest(PtychoWorkflow)
+add_cxx_qtest(PyXRFWorkflow)
 
 # Generate the executable
 create_test_executable(tomvizTests)
diff --git a/tests/cxx/CxxTests.cmake b/tests/cxx/CxxTests.cmake
index a2b2519d6..e03285b9b 100644
--- a/tests/cxx/CxxTests.cmake
+++ b/tests/cxx/CxxTests.cmake
@@ -26,6 +26,9 @@ macro(add_cxx_qtest name)
   set(_executable_name "qtest${name}")
   add_executable(${_executable_name} ${_test_src})
   target_link_libraries(${_executable_name} tomvizlib Qt6::Test)
+  # Need to set this property so that in stack traces, tomviz symbols
+  # can be resolved.
+  set_target_properties(${_executable_name} PROPERTIES ENABLE_EXPORTS TRUE)
 
   add_test(NAME "${name}" COMMAND ${_executable_name})
   if(_pythonpath)
@@ -51,6 +54,10 @@ macro(create_test_executable name)
   target_link_libraries(${name} tomvizlib
     GTest::gtest GTest::gtest_main ${EXTRA_LINK_LIB})
 
+  # Need to set this property so that in stack traces, tomviz symbols
+  # can be resolved.
+  set_target_properties(${_executable_name} PROPERTIES ENABLE_EXPORTS TRUE)
+
   foreach(_test_name ${_tomviz_cxx_tests})
     add_test(NAME "${_test_name}"
         COMMAND ${name} "--gtest_filter=${_test_name}Test.*")
diff --git a/tests/cxx/OperatorPythonTest.cxx b/tests/cxx/OperatorPythonTest.cxx
index a05ac81da..dfe652749 100644
--- a/tests/cxx/OperatorPythonTest.cxx
+++ b/tests/cxx/OperatorPythonTest.cxx
@@ -74,7 +74,7 @@ TEST_F(OperatorPythonTest, transform_function)
 TEST_F(OperatorPythonTest, operator_transform)
 {
   pythonOperator->setLabel("operator_transform");
-  QFile file(QString("%1/fixtures/operator.py").arg(SOURCE_DIR));
+  QFile file(QString("%1/fixtures/test_operator.py").arg(SOURCE_DIR));
   if (file.open(QIODevice::ReadOnly)) {
     QByteArray array = file.readAll();
     QString script(array);
diff --git a/tests/cxx/PtychoWorkflowTest.cxx b/tests/cxx/PtychoWorkflowTest.cxx
new file mode 100644
index 000000000..3f0e94452
--- /dev/null
+++ b/tests/cxx/PtychoWorkflowTest.cxx
@@ -0,0 +1,153 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#include <QApplication>
+#include <QDebug>
+#include <QDir>
+#include <QFileInfo>
+#include <QLineEdit>
+#include <QProcess>
+#include <QProcessEnvironment>
+#include <QTest>
+#include <QThread>
+
+#include <pqPVApplicationCore.h>
+
+#include "PythonUtilities.h"
+#include "PtychoDialog.h"
+#include "PtychoRunner.h"
+
+#include "TomvizTest.h"
+
+using namespace tomviz;
+
+const QDir ROOT_DATA_DIR = QString(SOURCE_DIR) + "/data";
+const QDir DATA_DIR = ROOT_DATA_DIR.absolutePath() + "/Pt_Zn_Phase";
+
+template <typename T>
+T* findWidget()
+{
+  for (auto* widget : QApplication::topLevelWidgets()) {
+    if (qobject_cast<T*>(widget)) {
+      return qobject_cast<T*>(widget);
+    }
+  }
+
+  return nullptr;
+}
+
+class PtychoWorkflowTest : public QObject
+{
+  Q_OBJECT
+
+private:
+  void downloadDataIfMissing()
+  {
+    if (DATA_DIR.exists()) {
+      // Nothing to do
+      return;
+    }
+    // Download the data if it is not present
+    QString python = "python";
+    QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
+    if (env.contains("TOMVIZ_TEST_PYTHON_EXECUTABLE")) {
+      python = env.value("TOMVIZ_TEST_PYTHON_EXECUTABLE");
+    }
+
+    auto scriptFile = QFileInfo(QString(SOURCE_DIR) + "/fixtures/download_and_unzip.py");
+    QString scriptPath = scriptFile.absoluteFilePath();
+
+    QString url = "https://data.kitware.com/api/v1/file/6914aad883abdcd84d150c91/download";
+
+    // We unzip into the parent directory, which will then have `Pt_Zn_Phase`
+    // after unzipping.
+    QStringList arguments;
+    arguments << scriptPath << url << ROOT_DATA_DIR.absolutePath();
+
+    QProcess process;
+    process.setProcessChannelMode(QProcess::ForwardedChannels);
+    process.start(python, arguments);
+
+    // Timeout in seconds
+    int timeout = 60 * 10;
+    QVERIFY(process.waitForFinished(timeout * 1000));
+    QVERIFY(process.exitCode() == 0);
+  }
+
+private slots:
+  void initTestCase()
+  {
+    downloadDataIfMissing();
+  }
+
+  void cleanupTestCase() {}
+
+  void runTest()
+  {
+    QString ptychoDir = DATA_DIR.absolutePath() + "/Ptycho/recon_result/";
+    QString outputDir = DATA_DIR.absolutePath() + "/output/";
+
+    auto* runner = new PtychoRunner(this);
+    runner->setAutoLoadFinalData(false);
+    runner->start();
+
+    auto* dialog = findWidget<PtychoDialog>();
+    QVERIFY(dialog);
+
+    auto* ptychoDirEdit = dialog->findChild<QLineEdit*>("ptychoDirectory");
+    QVERIFY(ptychoDirEdit);
+    ptychoDirEdit->setText(ptychoDir);
+
+    // Trigger the necessary changes
+    emit ptychoDirEdit->editingFinished();
+
+    auto* outputDirEdit = dialog->findChild<QLineEdit*>("outputDirectory");
+    QVERIFY(outputDirEdit);
+    outputDirEdit->setText(outputDir);
+
+    dialog->accept();
+
+    QStringList outputFileNames = {"ptycho_object.emd", "ptycho_probe.emd"};
+
+    auto checkAllExist = [&outputDir, &outputFileNames]() {
+      for (const auto& filename : outputFileNames) {
+        if (!QFile::exists(outputDir + filename)) {
+          return false;
+        }
+
+      }
+      return true;
+    };
+
+    // Wait for it to finish, and verify the output files were written
+    int timeout = 30;
+    int waitTime = 0;
+    bool found = false;
+
+    while (waitTime < timeout) {
+      if (checkAllExist()) {
+        found = true;
+        break;
+      }
+      QThread::sleep(1);
+      ++waitTime;
+    }
+    // Verify everything was found
+    QVERIFY(found);
+  }
+
+};
+
+int main(int argc, char** argv)
+{
+  QApplication app(argc, argv);
+
+  pqPVApplicationCore appCore(argc, argv);
+
+  Python::initialize();
+
+  PtychoWorkflowTest tc;
+  return QTest::qExec(&tc, argc, argv);
+}
+
+#include "PtychoWorkflowTest.moc"
diff --git a/tests/cxx/PyXRFWorkflowTest.cxx b/tests/cxx/PyXRFWorkflowTest.cxx
new file mode 100644
index 000000000..ed30515af
--- /dev/null
+++ b/tests/cxx/PyXRFWorkflowTest.cxx
@@ -0,0 +1,182 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#include <QApplication>
+#include <QComboBox>
+#include <QDebug>
+#include <QDir>
+#include <QFileInfo>
+#include <QLineEdit>
+#include <QProcess>
+#include <QProcessEnvironment>
+#include <QTest>
+#include <QThread>
+#include <QTimer>
+
+#include <pqPVApplicationCore.h>
+
+#include "PythonUtilities.h"
+#include "PyXRFRunner.h"
+#include "PyXRFMakeHDF5Dialog.h"
+#include "PyXRFProcessDialog.h"
+#include "SelectItemsDialog.h"
+
+#include "TomvizTest.h"
+
+using namespace tomviz;
+
+const QDir ROOT_DATA_DIR = QString(SOURCE_DIR) + "/data";
+const QDir DATA_DIR = ROOT_DATA_DIR.absolutePath() + "/Pt_Zn_XRF";
+
+template <typename T>
+T* findWidget()
+{
+  for (auto* widget : QApplication::topLevelWidgets()) {
+    if (qobject_cast<T*>(widget)) {
+      return qobject_cast<T*>(widget);
+    }
+  }
+
+  return nullptr;
+}
+
+class PyXRFWorkflowTest : public QObject
+{
+  Q_OBJECT
+
+private:
+  void downloadDataIfMissing()
+  {
+    if (DATA_DIR.exists()) {
+      // Nothing to do
+      return;
+    }
+    // Download the data if it is not present
+    QString python = "python";
+    QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
+    if (env.contains("TOMVIZ_TEST_PYTHON_EXECUTABLE")) {
+      python = env.value("TOMVIZ_TEST_PYTHON_EXECUTABLE");
+    }
+
+    auto scriptFile = QFileInfo(QString(SOURCE_DIR) + "/fixtures/download_and_unzip.py");
+    QString scriptPath = scriptFile.absoluteFilePath();
+
+    QString url = "https://data.kitware.com/api/v1/file/6914b15783abdcd84d150c97/download";
+
+    // We unzip into the parent directory, which will then have `Pt_Zn_XRF`
+    // after unzipping.
+    QStringList arguments;
+    arguments << scriptPath << url << ROOT_DATA_DIR.absolutePath();
+
+    QProcess process;
+    process.setProcessChannelMode(QProcess::ForwardedChannels);
+    process.start(python, arguments);
+
+    // Timeout in seconds
+    int timeout = 60 * 10;
+    QVERIFY(process.waitForFinished(timeout * 1000));
+    QVERIFY(process.exitCode() == 0);
+  }
+
+private slots:
+  void initTestCase()
+  {
+    downloadDataIfMissing();
+  }
+
+  void cleanupTestCase() {}
+
+  void runTest()
+  {
+    QString workingDir = DATA_DIR.absolutePath() + "/";
+
+    auto* runner = new PyXRFRunner(this);
+    runner->setAutoLoadFinalData(false);
+    runner->start();
+
+    auto* makeHDF5Dialog = findWidget<PyXRFMakeHDF5Dialog>();
+    QVERIFY(makeHDF5Dialog);
+
+    // Set the method to already existing
+    auto* method = makeHDF5Dialog->findChild<QComboBox*>("method");
+    QVERIFY(method);
+    method->setCurrentText("Already Existing");
+
+    auto* workingDirEdit = makeHDF5Dialog->findChild<QLineEdit*>("workingDirectory");
+    QVERIFY(workingDirEdit);
+    workingDirEdit->setText(workingDir);
+
+    makeHDF5Dialog->accept();
+
+    auto* processDialog = findWidget<PyXRFProcessDialog>();
+    QVERIFY(processDialog);
+
+    auto* logFile = processDialog->findChild<QLineEdit*>("logFile");
+    QVERIFY(logFile);
+    logFile->setText(workingDir + "log.csv");
+
+    auto* paramsFile = processDialog->findChild<QLineEdit*>("parametersFile");
+    QVERIFY(paramsFile);
+    paramsFile->setText(workingDir + "pyxrf_model_parameters_157397.json");
+
+    auto* outputDir = processDialog->findChild<QLineEdit*>("outputDirectory");
+    QVERIFY(outputDir);
+    outputDir->setText(workingDir + "recon");
+
+    auto* icName = processDialog->findChild<QComboBox*>("icName");
+    QVERIFY(icName);
+    icName->setCurrentText("sclr1_ch4");
+
+    // After accepting, a modal dialog will appear. Start posting
+    // events to check it and accept it when it appears.
+    bool found = false;
+
+    std::function<void()> checkFunc;
+    checkFunc = [&found, &checkFunc](){
+      auto* dialog = findWidget<SelectItemsDialog>();
+      if (!dialog) {
+        QTimer::singleShot(1000, checkFunc);
+        return;
+      }
+
+      // Just accept the dialog
+      found = true;
+      dialog->accept();
+    };
+
+    QTimer::singleShot(0, checkFunc);
+    processDialog->accept();
+
+    // Keep processing events until all dialogs have
+    // been found and accepted/rejected.
+    int timeElapsed = 0;
+    int maxTime = 30;
+    while (!found && timeElapsed < maxTime) {
+      QThread::sleep(1);
+      QApplication::processEvents();
+      timeElapsed += 1;
+    }
+
+    // Verify everything was found
+    QVERIFY(found);
+
+    // Verify that one of the output files now exist
+    auto exampleFile = workingDir + "recon/extracted_elements/Cl_K.emd";
+    QVERIFY(QFileInfo::exists(exampleFile));
+  }
+
+};
+
+int main(int argc, char** argv)
+{
+  QApplication app(argc, argv);
+
+  pqPVApplicationCore appCore(argc, argv);
+
+  Python::initialize();
+
+  PyXRFWorkflowTest tc;
+  return QTest::qExec(&tc, argc, argv);
+}
+
+#include "PyXRFWorkflowTest.moc"
diff --git a/tests/cxx/fixtures/download_and_unzip.py b/tests/cxx/fixtures/download_and_unzip.py
new file mode 100644
index 000000000..2001dbb59
--- /dev/null
+++ b/tests/cxx/fixtures/download_and_unzip.py
@@ -0,0 +1,37 @@
+import os
+from pathlib import Path
+import sys
+import urllib.request
+import zipfile
+
+if len(sys.argv) < 3:
+    sys.exit('Usage: <script> <url> <extract_dir>')
+
+url = sys.argv[1]
+extract_dir = Path(sys.argv[2])
+
+filename = Path('downloaded_file.zip')
+if filename.exists():
+    filename.unlink()
+
+last_progress = -1
+
+def download_progress_hook(block_num, block_size, total_size):
+    global last_progress
+    downloaded = block_num * block_size
+    downloaded_mb = downloaded / 1024 / 1024
+    total_size_mb = total_size / 1024 / 1024
+    progress = int((downloaded / total_size) * 100) if total_size > 0 else 0
+    if progress > last_progress:
+        last_progress = progress
+        print(f"\rDownload Progress: {progress}% ({downloaded_mb:.2f}/{total_size_mb:.2f} MB)")
+
+print(f'Downloading "{url}" to "{filename}"')
+urllib.request.urlretrieve(url, filename, reporthook=download_progress_hook)
+print('\n')
+
+extract_dir.mkdir(parents=True, exist_ok=True)
+
+print(f'Unzipping "{filename}" to "{extract_dir}"')
+with zipfile.ZipFile(filename, 'r') as zip_ref:
+    zip_ref.extractall(extract_dir)
diff --git a/tests/cxx/fixtures/operator.py b/tests/cxx/fixtures/test_operator.py
similarity index 100%
rename from tests/cxx/fixtures/operator.py
rename to tests/cxx/fixtures/test_operator.py
diff --git a/tests/python/.gitignore b/tests/python/.gitignore
new file mode 100644
index 000000000..3eeb4c030
--- /dev/null
+++ b/tests/python/.gitignore
@@ -0,0 +1,3 @@
+data
+downloaded_file.zip
+downloaded_file
diff --git a/tests/python/CMakeLists.txt b/tests/python/CMakeLists.txt
index 3d407bd35..33cd12e5a 100644
--- a/tests/python/CMakeLists.txt
+++ b/tests/python/CMakeLists.txt
@@ -2,3 +2,8 @@ include(PythonTests.cmake)
 
 add_python_test(operator)
 add_python_test(external)
+add_python_test(pystackreg)
+add_python_test(multi_array)
+add_python_test(xcorr)
+add_python_test(tilt_axis_shift)
+add_python_test(constraint_dft)
diff --git a/tests/python/PythonTests.cmake b/tests/python/PythonTests.cmake
index 11bb1fb81..ee118c72a 100644
--- a/tests/python/PythonTests.cmake
+++ b/tests/python/PythonTests.cmake
@@ -25,14 +25,18 @@ function(add_python_test case)
     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
     COMMAND "${_python_executable}" -m pytest -k ${module}
   )
-  set(_pythonpath "${tomviz_python_binary_dir}")
-  set(_pythonpath "${_pythonpath}${_separator}${fn_PYTHONPATH}")
-  set(_pythonpath "$ENV{PYTHONPATH}${_separator}${_pythonpath}")
-  if (WIN32)
-    string(REPLACE "\\;" ";" _pythonpath "${_pythonpath}")
-    string(REPLACE ";" "\\;" _pythonpath "${_pythonpath}")
+
+  # Don't modify the PYTHONPATH if we are in a conda environment
+  if (NOT DEFINED ENV{CONDA_PREFIX})
+    set(_pythonpath "${tomviz_python_binary_dir}")
+    set(_pythonpath "${_pythonpath}${_separator}${fn_PYTHONPATH}")
+    set(_pythonpath "$ENV{PYTHONPATH}${_separator}${_pythonpath}")
+    if (WIN32)
+      string(REPLACE "\\;" ";" _pythonpath "${_pythonpath}")
+      string(REPLACE ";" "\\;" _pythonpath "${_pythonpath}")
+    endif()
+    set_property(TEST ${name} PROPERTY ENVIRONMENT
+      "PYTHONPATH=${_pythonpath}"
+    )
   endif()
-  set_property(TEST ${name} PROPERTY ENVIRONMENT
-    "PYTHONPATH=${_pythonpath}"
-  )
 endfunction()
diff --git a/tests/python/conftest.py b/tests/python/conftest.py
index b42949c19..d8c1429f6 100644
--- a/tests/python/conftest.py
+++ b/tests/python/conftest.py
@@ -3,12 +3,99 @@
 import diskcache
 import tempfile
 import os
+from pathlib import Path
 import tarfile
 import shutil
 
+import numpy as np
+
+from tomviz.executor import load_dataset
+from tomviz.external_dataset import Dataset
+
+from utils import download_file, download_and_unzip_file
+
 DATA_URL = 'https://data.kitware.com/api/v1/file'
 
 
+@pytest.fixture
+def data_dir() -> Path:
+    return Path(__file__).parent / 'data'
+
+
+@pytest.fixture
+def hxn_xrf_example_output_dir(data_dir: Path) -> Path:
+    output_dir = data_dir / 'Pt_Zn_XRF_recon_output'
+    if not output_dir.exists():
+        # Download it
+        url = DATA_URL + '/6914b90283abdcd84d150c9e/download'
+        download_and_unzip_file(url, output_dir.parent)
+
+    return output_dir
+
+
+@pytest.fixture(scope='function')
+def hxn_xrf_example_dataset(hxn_xrf_example_output_dir: Path) -> Dataset:
+    example_files = [
+        'Pt_L.h5',
+        'Zn_K.h5',
+    ]
+    example_files = [
+        hxn_xrf_example_output_dir / 'extracted_elements' / name
+        for name in example_files
+    ]
+    dataset = load_dataset(example_files[0])
+    for new_file in example_files[1:]:
+        new_dataset = load_dataset(new_file)
+        new_name = new_dataset.active_name
+        dataset.arrays[new_name] = new_dataset.active_scalars
+
+    return dataset
+
+
+@pytest.fixture
+def pystackreg_reference_output(data_dir: Path) -> dict[str, np.ndarray]:
+    filepath = data_dir / 'test_pystackreg_reference_output.npz'
+    if not filepath.exists():
+        # Download it
+        url = DATA_URL + '/690e69aa83abdcd84d150c7e/download'
+        download_file(url, filepath)
+
+    return np.load(filepath)
+
+
+@pytest.fixture
+def xcorr_reference_output(data_dir: Path) -> dict[str, np.ndarray]:
+    filepath = data_dir / 'test_xcorr_reference_output.npz'
+    if not filepath.exists():
+        # Download it
+        url = DATA_URL + '/6920b212cdb169d7a021d769/download'
+        download_file(url, filepath)
+
+    return np.load(filepath)
+
+
+@pytest.fixture
+def tilt_axis_shift_reference_output(data_dir: Path) -> dict[str, np.ndarray]:
+    filepath = data_dir / 'test_tilt_axis_shift_reference_output.npz'
+    if not filepath.exists():
+        # Download it
+        url = DATA_URL + '/6920b333cdb169d7a021d76c/download'
+        download_file(url, filepath)
+
+    return np.load(filepath)
+
+
+@pytest.fixture
+def constraint_dft_reference_output(data_dir: Path) -> dict[str, np.ndarray]:
+    filepath = data_dir / 'test_constraint_dft_reference_output.npz'
+    if not filepath.exists():
+        # Download it
+        url = DATA_URL + '/6920b750cdb169d7a021d773/download'
+        download_file(url, filepath)
+
+    return np.load(filepath)
+
+
 @pytest.fixture(scope="module")
 def test_state_file(tmpdir_factory):
     tmpdir = tmpdir_factory.mktemp('state')
diff --git a/tests/python/constraint_dft_test.py b/tests/python/constraint_dft_test.py
new file mode 100644
index 000000000..a9bd8ce03
--- /dev/null
+++ b/tests/python/constraint_dft_test.py
@@ -0,0 +1,48 @@
+import numpy as np
+
+from utils import load_operator_class, load_operator_module
+
+from tomviz.external_dataset import Dataset
+
+
+def test_constraint_dft(hxn_xrf_example_dataset: Dataset,
+                        constraint_dft_reference_output: dict[str, np.ndarray]):
+    dataset = hxn_xrf_example_dataset
+    reference_output = constraint_dft_reference_output
+
+    # Load the operator module
+    module = load_operator_module('Recon_DFT_constraint')
+    operator = load_operator_class(module)
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # But the arrays should not match. In fact, the shapes should not match.
+    assert not all(
+        np.array_equal(reference_output[key].shape, dataset.arrays[key].shape)
+        for key in reference_output
+    )
+
+    # Apply the transformation
+    results = operator.transform(
+        dataset,
+        Niter=10,
+        Niter_update_support=50,
+        supportSigma=0.1,
+        supportThreshold=10,
+        seed=0,
+    )
+
+    recon_dataset = results['reconstruction']
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(recon_dataset.arrays))
+
+    # Arrays should now match
+    assert all(
+        np.allclose(reference_output[key], recon_dataset.arrays[key], atol=1e-2)
+        for key in reference_output
+    )
+
+    # Save a new reference output:
+    # np.savez_compressed('test_constraint_dft_reference_output.npz', **recon_dataset.arrays)
diff --git a/tests/python/multi_array_test.py b/tests/python/multi_array_test.py
new file mode 100644
index 000000000..b9ed035f0
--- /dev/null
+++ b/tests/python/multi_array_test.py
@@ -0,0 +1,68 @@
+import numpy as np
+
+from utils import load_operator_class, load_operator_module
+
+from tomviz.external_dataset import Dataset
+
+
+def test_multi_arrays(hxn_xrf_example_dataset: Dataset):
+    dataset = hxn_xrf_example_dataset
+
+    # Test a few operators that use `@apply_to_each_array`, and verify
+    # that they do indeed apply to each array.
+    # Load the operator module
+    bin_module = load_operator_module('BinTiltSeriesByTwo')
+
+    # Verify the tilt angles won't change, but image shape decreases by 2x
+    orig_shapes = {k: v.shape for k, v in dataset.arrays.items()}
+    orig_tilt_angles = dataset.tilt_angles
+
+    # Apply the transformation
+    bin_module.transform(dataset)
+
+    # New shapes should be binned by 2 in x and y, but not z
+    # Tilt angles should be unaffected
+    binned_shapes = {k: v.shape for k, v in dataset.arrays.items()}
+    expected_shapes = {k: (shape[0] // 2, shape[1] // 2, shape[2])
+                       for k, shape in orig_shapes.items()}
+
+    assert binned_shapes == expected_shapes
+    assert np.allclose(orig_tilt_angles, dataset.tilt_angles)
+
+    # Delete 3 slices. This will delete tilt angles too.
+    delete_slices_module = load_operator_module('DeleteSlices')
+
+    first_slice = 3
+    last_slice = 5
+    num_deleted = last_slice - first_slice + 1
+    delete_slices_module.transform(dataset,
+                                   firstSlice=first_slice,
+                                   lastSlice=last_slice,
+                                   axis=2)
+
+    # New shapes should be the same, other than 3 less in Z
+    expected_shapes = {k: (shape[0], shape[1], shape[2] - num_deleted)
+                       for k, shape in binned_shapes.items()}
+    deleted_shapes = {k: v.shape for k, v in dataset.arrays.items()}
+
+    expected_angles = np.hstack((orig_tilt_angles[:first_slice],
+                                 orig_tilt_angles[last_slice + 1:]))
+
+    assert deleted_shapes == expected_shapes
+    assert np.allclose(dataset.tilt_angles, expected_angles)
+
+    # Now run a reconstruction and verify we get all results
+    recon_sirt_module = load_operator_module('Recon_SIRT')
+    operator = load_operator_class(recon_sirt_module)
+
+    results = operator.transform(dataset, Niter=2)
+
+    recon_dataset = results['reconstruction']
+
+    # We should have the same scalar names
+    assert sorted(recon_dataset.scalars_names) == sorted(dataset.scalars_names)
+
+    # Verify the output appears valid. We are not testing the actual
+    # reconstruction operator here, just that it ran on multiple arrays.
+    means = [np.mean(array) for array in recon_dataset.arrays.values()]
+    assert np.all(np.array(means) > 0)
diff --git a/tests/python/pystackreg_test.py b/tests/python/pystackreg_test.py
new file mode 100644
index 000000000..6e5b91600
--- /dev/null
+++ b/tests/python/pystackreg_test.py
@@ -0,0 +1,51 @@
+import numpy as np
+
+from utils import load_operator_module
+
+from tomviz.external_dataset import Dataset
+
+
+def test_pystackreg(hxn_xrf_example_dataset: Dataset,
+                    pystackreg_reference_output: dict[str, np.ndarray]):
+    dataset = hxn_xrf_example_dataset
+    reference_output = pystackreg_reference_output
+
+    # Load the operator module
+    module = load_operator_module('PyStackRegImageAlignment')
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # But the arrays should not match
+    assert not all(
+        np.allclose(reference_output[key], dataset.arrays[key])
+        for key in reference_output
+    )
+
+    # Apply the transformation
+    module.transform(
+        dataset,
+        transform_source='generate',
+        padding=10,
+        apply_to_all_arrays=True,
+        # Only used if `transform_source` is `generate`
+        transform_type='translation',
+        reference='slice_index',
+        transforms_save_file='',
+        # Only used if `transform_type` is `slice_index`
+        ref_slice_index=90,
+        # Only used if `transform_source` is `from_file`.
+        transform_file=None,
+    )
+
+    # Verify the keys match
+    assert list(sorted(pystackreg_reference_output)) == list(sorted(dataset.arrays))
+
+    # Arrays should now match
+    assert all(
+        np.allclose(pystackreg_reference_output[key], dataset.arrays[key])
+        for key in pystackreg_reference_output
+    )
+
+    # Save a new reference output:
+    # np.savez_compressed('test_pystackreg_reference_output.npz', **dataset.arrays)
diff --git a/tests/python/tilt_axis_shift_test.py b/tests/python/tilt_axis_shift_test.py
new file mode 100644
index 000000000..1d2eef16a
--- /dev/null
+++ b/tests/python/tilt_axis_shift_test.py
@@ -0,0 +1,46 @@
+import numpy as np
+
+from utils import load_operator_class, load_operator_module
+
+from tomviz.external_dataset import Dataset
+
+
+def test_tilt_axis_shift(hxn_xrf_example_dataset: Dataset,
+                         tilt_axis_shift_reference_output: dict[str, np.ndarray]):
+    dataset = hxn_xrf_example_dataset
+    reference_output = tilt_axis_shift_reference_output
+
+    # Load the operator module
+    module = load_operator_module('AutoTiltAxisShiftAlignment')
+    operator = load_operator_class(module)
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # But the arrays should not match
+    assert not all(
+        np.allclose(reference_output[key], dataset.arrays[key])
+        for key in reference_output
+    )
+
+    # Apply the transformation
+    operator.transform(
+        dataset,
+        transform_source='generate',
+        padding=10,
+        num_slices=5,
+        seed=0,
+        apply_to_all_arrays=True,
+    )
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # Arrays should now match
+    assert all(
+        np.allclose(reference_output[key], dataset.arrays[key])
+        for key in reference_output
+    )
+
+    # Save a new reference output:
+    # np.savez_compressed('test_tilt_axis_shift_reference_output.npz', **dataset.arrays)
diff --git a/tests/python/utils.py b/tests/python/utils.py
new file mode 100644
index 000000000..b7ba753da
--- /dev/null
+++ b/tests/python/utils.py
@@ -0,0 +1,64 @@
+import importlib.util
+import inspect
+from pathlib import Path
+import shutil
+from types import ModuleType
+import urllib.request
+import zipfile
+
+from tomviz.executor import OperatorWrapper
+from tomviz.operators import Operator
+
+OPERATOR_PATH = Path(__file__).parent.parent.parent / 'tomviz/python'
+
+
+def load_operator_module(operator_name: str) -> ModuleType:
+    module_path = OPERATOR_PATH / f'{operator_name}.py'
+    spec = importlib.util.spec_from_file_location(operator_name, module_path)
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+    return module
+
+
+def load_operator_class(operator_module: ModuleType) -> Operator | None:
+    # Locate the operator class
+    for v in operator_module.__dict__.values():
+        if inspect.isclass(v) and issubclass(v, Operator):
+            # Instantiate and set up wrapper
+            operator = v()
+            operator._operator_wrapper = OperatorWrapper()
+            return operator
+
+
+def download_file(url: str, destination: str):
+    filename = Path('downloaded_file')
+    if filename.exists():
+        filename.unlink()
+
+    last_progress = -1
+
+    def download_progress_hook(block_num, block_size, total_size):
+        nonlocal last_progress
+        downloaded = block_num * block_size
+        downloaded_mb = downloaded / 1024 / 1024
+        total_size_mb = total_size / 1024 / 1024
+        progress = int((downloaded / total_size) * 100) if total_size > 0 else 0
+        if progress > last_progress:
+            last_progress = progress
+            print(f"\rDownload Progress: {progress}% ({downloaded_mb:.2f}/{total_size_mb:.2f} MB)")
+
+    print(f'Downloading "{url}" to "{filename}"')
+    urllib.request.urlretrieve(url, filename, reporthook=download_progress_hook)
+    print('\n')
+
+    shutil.copy(filename, destination)
+
+
+def download_and_unzip_file(url: str, extract_dir: str):
+    filename = Path('downloaded_file.zip')
+    download_file(url, filename)
+    extract_dir.mkdir(parents=True, exist_ok=True)
+
+    print(f'Unzipping "{filename}" to "{extract_dir}"')
+    with zipfile.ZipFile(filename, 'r') as zip_ref:
+        zip_ref.extractall(extract_dir)
diff --git a/tests/python/xcorr_test.py b/tests/python/xcorr_test.py
new file mode 100644
index 000000000..c56ab2851
--- /dev/null
+++ b/tests/python/xcorr_test.py
@@ -0,0 +1,43 @@
+import numpy as np
+
+from utils import load_operator_class, load_operator_module
+
+from tomviz.external_dataset import Dataset
+
+
+def test_xcorr(hxn_xrf_example_dataset: Dataset,
+               xcorr_reference_output: dict[str, np.ndarray]):
+    dataset = hxn_xrf_example_dataset
+    reference_output = xcorr_reference_output
+
+    # Load the operator module
+    module = load_operator_module('AutoCrossCorrelationTiltImageAlignment')
+    operator = load_operator_class(module)
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # But the arrays should not match
+    assert not all(
+        np.allclose(reference_output[key], dataset.arrays[key])
+        for key in reference_output
+    )
+
+    # Apply the transformation
+    operator.transform(
+        dataset,
+        transform_source='generate',
+        apply_to_all_arrays=True,
+    )
+
+    # Verify the keys match
+    assert list(sorted(reference_output)) == list(sorted(dataset.arrays))
+
+    # Arrays should now match
+    assert all(
+        np.allclose(reference_output[key], dataset.arrays[key])
+        for key in reference_output
+    )
+
+    # Save a new reference output:
+    # np.savez_compressed('test_xcorr_reference_output.npz', **dataset.arrays)
diff --git a/tomviz/AddPythonTransformReaction.cxx b/tomviz/AddPythonTransformReaction.cxx
index 91ab9c7bf..4e8fb887e 100644
--- a/tomviz/AddPythonTransformReaction.cxx
+++ b/tomviz/AddPythonTransformReaction.cxx
@@ -6,6 +6,8 @@
 #include "ActiveObjects.h"
 #include "DataSource.h"
 #include "EditOperatorDialog.h"
+#include "ModuleManager.h"
+#include "ModuleSlice.h"
 #include "OperatorDialog.h"
 #include "OperatorFactory.h"
 #include "OperatorPython.h"
@@ -36,108 +38,6 @@
 
 #include <cassert>
 
-namespace {
-
-class SelectSliceRangeWidget : public QWidget
-{
-  Q_OBJECT
-  typedef QWidget Superclass;
-
-public:
-  SelectSliceRangeWidget(int* ext, bool showAxisSelector = true,
-                         QWidget* p = nullptr)
-    : Superclass(p), firstSlice(new tomviz::SpinBox(this)),
-      lastSlice(new tomviz::SpinBox(this)), axisSelect(new QComboBox(this))
-  {
-    for (int i = 0; i < 6; ++i) {
-      this->Extent[i] = ext[i];
-    }
-    QHBoxLayout* rangeLayout = new QHBoxLayout;
-    QLabel* startLabel = new QLabel("Start:", this);
-    QLabel* endLabel = new QLabel("End:", this);
-
-    this->firstSlice->setRange(0, ext[5] - ext[4]);
-    this->firstSlice->setValue(0);
-    this->lastSlice->setRange(0, ext[5] - ext[4]);
-    this->lastSlice->setValue(0);
-
-    rangeLayout->addWidget(startLabel);
-    rangeLayout->addWidget(this->firstSlice);
-    rangeLayout->addWidget(endLabel);
-    rangeLayout->addWidget(this->lastSlice);
-
-    QHBoxLayout* axisSelectLayout = new QHBoxLayout;
-    QLabel* axisLabel = new QLabel("Axis:", this);
-    this->axisSelect->addItem("X");
-    this->axisSelect->addItem("Y");
-    this->axisSelect->addItem("Z");
-    this->axisSelect->setCurrentIndex(2);
-
-    axisSelectLayout->addWidget(axisLabel);
-    axisSelectLayout->addWidget(this->axisSelect);
-
-    QVBoxLayout* widgetLayout = new QVBoxLayout;
-    widgetLayout->addLayout(rangeLayout);
-    widgetLayout->addLayout(axisSelectLayout);
-
-    if (!showAxisSelector) {
-      axisLabel->hide();
-      this->axisSelect->hide();
-    }
-
-    this->setLayout(widgetLayout);
-
-    QObject::connect(this->firstSlice, SIGNAL(editingFinished()), this,
-                     SLOT(onMinimumChanged()));
-    QObject::connect(this->lastSlice, SIGNAL(editingFinished()), this,
-                     SLOT(onMaximumChanged()));
-    this->connect(axisSelect, SIGNAL(currentIndexChanged(int)),
-                  SLOT(onAxisChanged(int)));
-  }
-
-  ~SelectSliceRangeWidget() {}
-
-  int startSlice() const { return this->firstSlice->value(); }
-
-  int endSlice() const { return this->lastSlice->value(); }
-
-  int axis() const { return this->axisSelect->currentIndex(); }
-
-public slots:
-  void onMinimumChanged()
-  {
-    int val = this->firstSlice->value();
-    if (this->lastSlice->value() < val) {
-      this->lastSlice->setValue(val);
-    }
-  }
-
-  void onMaximumChanged()
-  {
-    int val = this->lastSlice->value();
-    if (this->firstSlice->value() > val) {
-      this->firstSlice->setValue(val);
-    }
-  }
-
-  void onAxisChanged(int newAxis)
-  {
-    int newSliceMax = this->Extent[2 * newAxis + 1] - this->Extent[2 * newAxis];
-    this->firstSlice->setMaximum(newSliceMax);
-    this->lastSlice->setMaximum(newSliceMax);
-  }
-
-private:
-  Q_DISABLE_COPY(SelectSliceRangeWidget)
-  tomviz::SpinBox* firstSlice; // delete slices starting at this slice index
-  tomviz::SpinBox* lastSlice;  // delete slices ending at this slice index
-  QComboBox* axisSelect;
-  int Extent[6];
-};
-} // namespace
-
-#include "AddPythonTransformReaction.moc"
-
 namespace tomviz {
 
 AddPythonTransformReaction::AddPythonTransformReaction(
@@ -211,11 +111,30 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
   }
 
   bool hasJson = this->jsonSource.size() > 0;
+
   if (hasJson) {
     OperatorPython* opPython = new OperatorPython(source);
     opPython->setJSONDescription(jsonSource);
     opPython->setLabel(scriptLabel);
     opPython->setScript(scriptSource);
+    if (scriptLabel == "Auto Tilt Image Align (PyStackReg)") {
+      // If there are any slice modules on this data source, use the
+      // slice index as the default value for the slice index.
+      int defaultSliceIdx = 0;
+      // Use the output data source of the pipeline if it is available. If
+      // one is not available, this just defaults to the root data source.
+      auto tSource = source->pipeline()->transformedDataSource();
+      auto sliceModules = ModuleManager::instance().findModules<ModuleSlice*>(
+          tSource, nullptr);
+      if (sliceModules.size() > 0 && sliceModules[0]) {
+        defaultSliceIdx = std::max(sliceModules[0]->slice(), 0);
+      }
+
+      QMap<QString, QVariant> arguments{{"ref_slice_index", defaultSliceIdx}};
+      QMap<QString, QString> typeInfo{{"ref_slice_index", "int"}};
+      opPython->setArguments(arguments);
+      opPython->setTypeInfo(typeInfo);
+    }
 
     // Use JSON to build the interface via the EditOperatorDialog
     // If the operator doesn't have parameters, don't show the dialog on first
@@ -372,40 +291,6 @@ OperatorPython* AddPythonTransformReaction::addExpression(DataSource* source)
       addPythonOperator(source, this->scriptLabel, this->scriptSource,
                         arguments, typeInfo);
     }
-  } else if (scriptLabel == "Delete Slices") {
-    auto t = source->producer();
-    auto data = vtkImageData::SafeDownCast(t->GetOutputDataObject(0));
-    int* shape = data->GetExtent();
-
-    QDialog dialog(tomviz::mainWidget());
-
-    SelectSliceRangeWidget* sliceRange =
-      new SelectSliceRangeWidget(shape, true, &dialog);
-
-    QVBoxLayout* v = new QVBoxLayout;
-    QDialogButtonBox* buttons = new QDialogButtonBox(
-      QDialogButtonBox::Ok | QDialogButtonBox::Cancel, Qt::Horizontal, &dialog);
-    connect(buttons, SIGNAL(accepted()), &dialog, SLOT(accept()));
-    connect(buttons, SIGNAL(rejected()), &dialog, SLOT(reject()));
-    v->addWidget(sliceRange);
-    v->addWidget(buttons);
-    dialog.setLayout(v);
-    dialog.setWindowTitle("Delete Slices");
-    dialog.layout()->setSizeConstraint(
-      QLayout::SetFixedSize); // Make the UI non-resizeable
-
-    if (dialog.exec() == QDialog::Accepted) {
-      QMap<QString, QVariant> arguments;
-      arguments.insert("firstSlice", sliceRange->startSlice());
-      arguments.insert("lastSlice", sliceRange->endSlice());
-      arguments.insert("axis", sliceRange->axis());
-      QMap<QString, QString> typeInfo;
-      typeInfo["firstSlice"] = "int";
-      typeInfo["lastSlice"] = "int";
-      typeInfo["axis"] = "int";
-      addPythonOperator(source, this->scriptLabel, this->scriptSource,
-                        arguments, typeInfo);
-    }
   } else if (scriptLabel == "Clear Volume") {
     QDialog* dialog = new QDialog(tomviz::mainWidget());
     dialog->setWindowTitle("Select Volume to Clear");
diff --git a/tomviz/CMakeLists.txt b/tomviz/CMakeLists.txt
index 24fadfcbb..8ef8abd09 100644
--- a/tomviz/CMakeLists.txt
+++ b/tomviz/CMakeLists.txt
@@ -172,6 +172,10 @@ set(SOURCES
   ProgressDialog.h
   ProgressDialogManager.cxx
   ProgressDialogManager.h
+  PtychoDialog.cxx
+  PtychoDialog.h
+  PtychoRunner.cxx
+  PtychoRunner.h
   PythonGeneratedDatasetReaction.cxx
   PythonGeneratedDatasetReaction.h
   PythonReader.cxx
@@ -271,12 +275,16 @@ set(SOURCES
   vtkOMETiffReader.h
   vtkTriangleBar.cxx
   vtkTriangleBar.h
-  vtkVolumeScaleRepresentation.h
-  vtkVolumeScaleRepresentation.cxx
   WebExportWidget.cxx
   WebExportWidget.h
 )
 
+list(APPEND SOURCES
+  loguru/loguru.cpp
+  loguru/loguru.hpp
+)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/loguru)
+
 list(APPEND SOURCES
   modules/Module.cxx
   modules/Module.h
@@ -446,6 +454,7 @@ set(python_files
   AutoTiltAxisShiftAlignment.py
   AutoCenterOfMassTiltImageAlignment.py
   AutoCrossCorrelationTiltImageAlignment.py
+  PyStackRegImageAlignment.py
   ctf_correct.py
   Recon_DFT.py
   Recon_DFT_constraint.py
@@ -475,7 +484,7 @@ set(python_files
   PeronaMalikAnisotropicDiffusion.py
   MedianFilter.py
   Resample.py
-  deleteSlices.py
+  DeleteSlices.py
   ClearVolume.py
   ConstantDataset.py
   RandomParticles.py
@@ -506,6 +515,8 @@ set(json_files
   AddPoissonNoise.json
   AutoCenterOfMassTiltImageAlignment.json
   AutoCrossCorrelationTiltImageAlignment.json
+  AutoTiltAxisShiftAlignment.json
+  PyStackRegImageAlignment.json
   BinaryThreshold.json
   CircleMask.json
   ConnectedComponents.json
@@ -524,6 +535,7 @@ set(json_files
   Shift_Stack_Uniformly.json
   Pad_Data.json
   Resample.json
+  DeleteSlices.json
   GaussianFilter.json
   GaussianFilterTiltSeries.json
   PeronaMalikAnisotropicDiffusion.json
@@ -613,6 +625,7 @@ endforeach()
 set(tomviz_python_modules
   __init__.py
   _internal.py
+  fix_pdb.py
   operators.py
   internal_dataset.py
   itkutils.py
@@ -665,9 +678,9 @@ endforeach()
 
 set(tomviz_python_pyxrf_modules
   __init__.py
+  ic_names.py
   load_output.py
-  make_hdf5.py
-  process_projections.py
+  sids.py
 )
 
 file(MAKE_DIRECTORY "${tomviz_python_binary_dir}/tomviz/pyxrf")
@@ -677,6 +690,18 @@ foreach(file ${tomviz_python_pyxrf_modules})
     "${tomviz_python_binary_dir}/tomviz/pyxrf/${file}")
 endforeach()
 
+set(tomviz_python_ptycho_modules
+  __init__.py
+  ptycho.py
+)
+
+file(MAKE_DIRECTORY "${tomviz_python_binary_dir}/tomviz/ptycho")
+foreach(file ${tomviz_python_ptycho_modules})
+  execute_process(COMMAND ${CMAKE_COMMAND} -E ${script_cmd}
+    "${tomviz_SOURCE_DIR}/tomviz/python/tomviz/ptycho/${file}"
+    "${tomviz_python_binary_dir}/tomviz/ptycho/${file}")
+endforeach()
+
 file(GLOB tomviz_python_state_modules "${tomviz_SOURCE_DIR}/tomviz/python/tomviz/state/*.py")
 file(MAKE_DIRECTORY "${tomviz_python_binary_dir}/tomviz/state")
 foreach(file_ ${tomviz_python_state_modules})
@@ -726,10 +751,18 @@ configure_file(tomvizPythonConfig.h.in tomvizPythonConfig.h @ONLY)
 add_library(tomvizlib STATIC ${SOURCES} ${accel_srcs})
 set_target_properties(tomvizlib PROPERTIES OUTPUT_NAME tomviz)
 
+# Need to set this property so that in stack traces, tomviz symbols
+# can be resolved.
+set_target_properties(tomvizlib PROPERTIES ENABLE_EXPORTS TRUE)
+
 set_property(TARGET tomvizlib PROPERTY POSITION_INDEPENDENT_CODE TRUE)
 
 add_executable(tomviz WIN32 MACOSX_BUNDLE ${exec_sources} resources.qrc)
-target_link_libraries(tomviz PRIVATE tomvizlib ${OPENGL_LIBRARIES})
+target_link_libraries(tomviz PRIVATE tomvizlib ${OPENGL_LIBRARIES} ${extra_link_libraries})
+
+# Need to set this property so that in stack traces, tomviz symbols
+# can be resolved.
+set_target_properties(tomviz PROPERTIES ENABLE_EXPORTS TRUE)
 
 target_link_libraries(tomvizlib
   PUBLIC
diff --git a/tomviz/DataPropertiesPanel.cxx b/tomviz/DataPropertiesPanel.cxx
index 8473fd59f..68e39c526 100644
--- a/tomviz/DataPropertiesPanel.cxx
+++ b/tomviz/DataPropertiesPanel.cxx
@@ -53,6 +53,9 @@ DataPropertiesPanel::DataPropertiesPanel(QWidget* parentObject)
   m_ui->xLengthBox->setValidator(new QDoubleValidator(m_ui->xLengthBox));
   m_ui->yLengthBox->setValidator(new QDoubleValidator(m_ui->yLengthBox));
   m_ui->zLengthBox->setValidator(new QDoubleValidator(m_ui->zLengthBox));
+  m_ui->xVoxelSizeBox->setValidator(new QDoubleValidator(m_ui->xVoxelSizeBox));
+  m_ui->yVoxelSizeBox->setValidator(new QDoubleValidator(m_ui->yVoxelSizeBox));
+  m_ui->zVoxelSizeBox->setValidator(new QDoubleValidator(m_ui->zVoxelSizeBox));
   m_ui->TiltAnglesTable->installEventFilter(this);
   m_ui->ScalarsTable->setModel(&m_scalarsTableModel);
 
@@ -103,6 +106,13 @@ DataPropertiesPanel::DataPropertiesPanel(QWidget* parentObject)
   connect(m_ui->zLengthBox, &QLineEdit::editingFinished,
           [this]() { this->updateLength(m_ui->zLengthBox, 2); });
 
+  connect(m_ui->xVoxelSizeBox, &QLineEdit::editingFinished,
+          [this]() { this->updateVoxelSize(m_ui->xVoxelSizeBox, 0); });
+  connect(m_ui->yVoxelSizeBox, &QLineEdit::editingFinished,
+          [this]() { this->updateVoxelSize(m_ui->yVoxelSizeBox, 1); });
+  connect(m_ui->zVoxelSizeBox, &QLineEdit::editingFinished,
+          [this]() { this->updateVoxelSize(m_ui->zVoxelSizeBox, 2); });
+
   connect(m_ui->xOriginBox, &QLineEdit::editingFinished,
           [this]() { this->updateOrigin(m_ui->xOriginBox, 0); });
   connect(m_ui->yOriginBox, &QLineEdit::editingFinished,
@@ -194,11 +204,16 @@ void DataPropertiesPanel::onDataPropertiesChanged()
   m_currentDataSource->getPhysicalDimensions(length);
   auto origin = m_currentDataSource->displayPosition();
   auto orientation = m_currentDataSource->displayOrientation();
+  auto* spacing = m_currentDataSource->getSpacing();
 
   m_ui->xLengthBox->setText(QString("%1").arg(length[0]));
   m_ui->yLengthBox->setText(QString("%1").arg(length[1]));
   m_ui->zLengthBox->setText(QString("%1").arg(length[2]));
 
+  m_ui->xVoxelSizeBox->setText(QString("%1").arg(spacing[0]));
+  m_ui->yVoxelSizeBox->setText(QString("%1").arg(spacing[1]));
+  m_ui->zVoxelSizeBox->setText(QString("%1").arg(spacing[2]));
+
   m_ui->xOriginBox->setText(QString("%1").arg(origin[0]));
   m_ui->yOriginBox->setText(QString("%1").arg(origin[1]));
   m_ui->zOriginBox->setText(QString("%1").arg(origin[2]));
@@ -277,10 +292,30 @@ QList<ArrayInfo> DataPropertiesPanel::getArraysInfo(DataSource* dataSource)
     }
   }
 
+  // Remove any invalid scalar indices to prevent a crash
+  QList<int> toRemove;
+  for (auto i : m_scalarIndexes) {
+    // name, type, data range, data type, active
+    auto arrayName = dataSource->scalarsName(i);
+    auto array = dataSource->getScalarsArray(arrayName);
+    if (!array) {
+      toRemove.append(i);
+    }
+  }
+
+  while (toRemove.size() != 0) {
+    m_scalarIndexes.remove(toRemove[0]);
+    toRemove.removeAt(0);
+  }
+
   for (auto i : m_scalarIndexes) {
     // name, type, data range, data type, active
     auto arrayName = dataSource->scalarsName(i);
     auto array = dataSource->getScalarsArray(arrayName);
+    if (!array) {
+      continue;
+    }
+
     QString dataType = vtkImageScalarTypeNameMacro(array->GetDataType());
     int numComponents = array->GetNumberOfComponents();
     QString dataRange;
@@ -640,6 +675,29 @@ void DataPropertiesPanel::updateLength(QLineEdit* widget, int axis)
   emit dsource->dataPropertiesChanged();
 }
 
+void DataPropertiesPanel::updateVoxelSize(QLineEdit* widget, int axis)
+{
+  double newSize;
+  bool ok = DataPropertiesPanel::parseField(widget, newSize);
+
+  if (!ok) {
+    return;
+  }
+
+  double spacing[3];
+  m_currentDataSource->getSpacing(spacing);
+  spacing[axis] = newSize;
+  m_currentDataSource->setSpacing(spacing);
+
+  updateData();
+  DataSource* dsource = m_currentDataSource;
+  if (!dsource) {
+    return;
+  }
+  resetCamera();
+  emit dsource->dataPropertiesChanged();
+}
+
 void DataPropertiesPanel::updateOrigin(QLineEdit* widget, int axis)
 {
   double newValue;
diff --git a/tomviz/DataPropertiesPanel.h b/tomviz/DataPropertiesPanel.h
index f46a23761..2453da6d3 100644
--- a/tomviz/DataPropertiesPanel.h
+++ b/tomviz/DataPropertiesPanel.h
@@ -47,6 +47,7 @@ class DataPropertiesPanel : public QWidget
   void updateComponentsCombo();
   static bool parseField(QLineEdit* widget, double& value);
   void updateLength(QLineEdit* widget, int axis);
+  void updateVoxelSize(QLineEdit* widget, int axis);
   void updateOrigin(QLineEdit* widget, int axis);
   void updateOrientation(QLineEdit* widget, int axis);
 
diff --git a/tomviz/DataPropertiesPanel.ui b/tomviz/DataPropertiesPanel.ui
index 5ba9fdfe0..02e401d0a 100644
--- a/tomviz/DataPropertiesPanel.ui
+++ b/tomviz/DataPropertiesPanel.ui
@@ -150,22 +150,36 @@
         <property name="spacing">
          <number>2</number>
         </property>
-        <item row="1" column="0">
-         <widget class="QLabel" name="leftBracketLabel">
+        <item row="0" column="7" alignment="Qt::AlignHCenter">
+         <widget class="QLabel" name="unitLabel">
           <property name="text">
-           <string>(</string>
+           <string>Units</string>
           </property>
          </widget>
         </item>
-        <item row="1" column="1">
-         <widget class="QLineEdit" name="xLengthBox">
+        <item row="1" column="2">
+         <widget class="QLabel" name="multiplyLabel1">
+          <property name="text">
+           <string>x</string>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="5">
+         <widget class="QLineEdit" name="zVoxelSizeBox">
           <property name="alignment">
            <set>Qt::AlignCenter</set>
           </property>
          </widget>
         </item>
-        <item row="1" column="7">
-         <widget class="QLineEdit" name="unitBox">
+        <item row="1" column="0">
+         <widget class="QLabel" name="leftBracketLabel">
+          <property name="text">
+           <string>(</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="5">
+         <widget class="QLineEdit" name="zLengthBox">
           <property name="alignment">
            <set>Qt::AlignCenter</set>
           </property>
@@ -178,6 +192,13 @@
           </property>
          </widget>
         </item>
+        <item row="1" column="7">
+         <widget class="QLineEdit" name="unitBox">
+          <property name="alignment">
+           <set>Qt::AlignCenter</set>
+          </property>
+         </widget>
+        </item>
         <item row="1" column="6">
          <widget class="QLabel" name="rightBracketLabel">
           <property name="text">
@@ -185,8 +206,29 @@
           </property>
          </widget>
         </item>
-        <item row="1" column="5">
-         <widget class="QLineEdit" name="zLengthBox">
+        <item row="1" column="4">
+         <widget class="QLabel" name="multiplyLabel2">
+          <property name="text">
+           <string>x</string>
+          </property>
+         </widget>
+        </item>
+        <item row="0" column="1" alignment="Qt::AlignHCenter">
+         <widget class="QLabel" name="xLabel">
+          <property name="text">
+           <string>X</string>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="1">
+         <widget class="QLineEdit" name="xVoxelSizeBox">
+          <property name="alignment">
+           <set>Qt::AlignCenter</set>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="1">
+         <widget class="QLineEdit" name="xLengthBox">
           <property name="alignment">
            <set>Qt::AlignCenter</set>
           </property>
@@ -199,6 +241,13 @@
           </property>
          </widget>
         </item>
+        <item row="3" column="3">
+         <widget class="QLineEdit" name="yVoxelSizeBox">
+          <property name="alignment">
+           <set>Qt::AlignCenter</set>
+          </property>
+         </widget>
+        </item>
         <item row="1" column="3">
          <widget class="QLineEdit" name="yLengthBox">
           <property name="alignment">
@@ -206,31 +255,48 @@
           </property>
          </widget>
         </item>
-        <item row="1" column="4">
-         <widget class="QLabel" name="multiplyLabel2">
+        <item row="2" column="0" colspan="8">
+         <widget class="Line" name="line">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="7">
+         <widget class="QLabel" name="voxelSizesLabel">
+          <property name="text">
+           <string>voxel sizes</string>
+          </property>
+          <property name="alignment">
+           <set>Qt::AlignCenter</set>
+          </property>
+         </widget>
+        </item>
+        <item row="3" column="2">
+         <widget class="QLabel" name="label_4">
           <property name="text">
            <string>x</string>
           </property>
          </widget>
         </item>
-        <item row="0" column="1" alignment="Qt::AlignHCenter">
-         <widget class="QLabel" name="xLabel">
+        <item row="3" column="4">
+         <widget class="QLabel" name="label_5">
           <property name="text">
-           <string>X</string>
+           <string>x</string>
           </property>
          </widget>
         </item>
-        <item row="0" column="7" alignment="Qt::AlignHCenter">
-         <widget class="QLabel" name="unitLabel">
+        <item row="3" column="0">
+         <widget class="QLabel" name="label_6">
           <property name="text">
-           <string>Units</string>
+           <string>(</string>
           </property>
          </widget>
         </item>
-        <item row="1" column="2">
-         <widget class="QLabel" name="multiplyLabel1">
+        <item row="3" column="6">
+         <widget class="QLabel" name="label_7">
           <property name="text">
-           <string>x</string>
+           <string>)</string>
           </property>
          </widget>
         </item>
@@ -438,12 +504,17 @@
  <tabstops>
   <tabstop>FileName</tabstop>
   <tabstop>ActiveScalars</tabstop>
+  <tabstop>showTimeSeriesLabel</tabstop>
+  <tabstop>editTimeSeries</tabstop>
   <tabstop>componentNamesEditor</tabstop>
   <tabstop>ScalarsTable</tabstop>
   <tabstop>xLengthBox</tabstop>
   <tabstop>yLengthBox</tabstop>
   <tabstop>zLengthBox</tabstop>
   <tabstop>unitBox</tabstop>
+  <tabstop>xVoxelSizeBox</tabstop>
+  <tabstop>yVoxelSizeBox</tabstop>
+  <tabstop>zVoxelSizeBox</tabstop>
   <tabstop>xOriginBox</tabstop>
   <tabstop>yOriginBox</tabstop>
   <tabstop>zOriginBox</tabstop>
diff --git a/tomviz/DataTransformMenu.cxx b/tomviz/DataTransformMenu.cxx
index 4ae55f12f..ee8b7dc24 100644
--- a/tomviz/DataTransformMenu.cxx
+++ b/tomviz/DataTransformMenu.cxx
@@ -103,7 +103,9 @@ void DataTransformMenu::buildTransforms()
     readInPythonScript("Shift_Stack_Uniformly"), false, false, false,
     readInJSONDescription("Shift_Stack_Uniformly"));
   new AddPythonTransformReaction(deleteSliceAction, "Delete Slices",
-                                 readInPythonScript("deleteSlices"));
+                                 readInPythonScript("DeleteSlices"),
+                                 false, false, false,
+                                 readInJSONDescription("DeleteSlices"));
   new AddPythonTransformReaction(padVolumeAction, "Pad Volume",
                                  readInPythonScript("Pad_Data"), false, false,
                                  false, readInJSONDescription("Pad_Data"));
diff --git a/tomviz/InterfaceBuilder.cxx b/tomviz/InterfaceBuilder.cxx
index 787446fda..166b06b01 100644
--- a/tomviz/InterfaceBuilder.cxx
+++ b/tomviz/InterfaceBuilder.cxx
@@ -137,6 +137,51 @@ QWidget* getNumericWidget(double defaultValue, double rangeMin, double rangeMax,
   return spinBox;
 }
 
+template<typename T>
+bool isWidgetType(const QWidget* widget) {
+  return qobject_cast<const T*>(widget) != nullptr;
+}
+
+bool isWidgetNumeric(const QWidget* widget) {
+  return isWidgetType<QDoubleSpinBox>(widget) || isWidgetType<QSpinBox>(widget);
+}
+
+template <typename T>
+auto changedSignal()
+{
+  // Get a generic symbol a widget has changed
+  if constexpr (std::is_same_v<T, QComboBox>) {
+    return QOverload<int>::of(&QComboBox::currentIndexChanged);
+  } else if constexpr (std::is_same_v<T, QCheckBox>) {
+    return &QCheckBox::toggled;
+  } else if constexpr (std::is_same_v<T, QDoubleSpinBox>) {
+    return QOverload<double>::of(&QDoubleSpinBox::valueChanged);
+  } else if constexpr (std::is_same_v<T, QSpinBox>) {
+    return QOverload<int>::of(&QSpinBox::valueChanged);
+  } else if constexpr (std::is_same_v<T, QLineEdit>) {
+    return &QLineEdit::textChanged;
+  }
+}
+
+template <typename T>
+auto widgetValue(const T* w)
+{
+  // Get the widget value.
+  // This will be an int for QSpinBox, double for QDoubleSpinBox,
+  // string for QComboBox, etc.
+  if constexpr (std::is_same_v<T, QComboBox>) {
+    return w->currentData().toString();
+  } else if constexpr (std::is_same_v<T, QCheckBox>) {
+    return w->isChecked();
+  } else if constexpr (std::is_same_v<T, QDoubleSpinBox>) {
+    return w->value();
+  } else if constexpr (std::is_same_v<T, QSpinBox>) {
+    return w->value();
+  } else if constexpr (std::is_same_v<T, QLineEdit>) {
+    return w->text();
+  }
+}
+
 void addBoolWidget(QGridLayout* layout, int row, QJsonObject& parameterNode)
 {
   QJsonValueRef nameValue = parameterNode["name"];
@@ -165,6 +210,7 @@ void addBoolWidget(QGridLayout* layout, int row, QJsonObject& parameterNode)
   QCheckBox* checkBox = new QCheckBox();
   checkBox->setObjectName(nameValue.toString());
   checkBox->setCheckState(defaultValue ? Qt::Checked : Qt::Unchecked);
+  label->setBuddy(checkBox);
   layout->addWidget(checkBox, row, 1, 1, 1);
 }
 
@@ -260,6 +306,7 @@ void addNumericWidget(QGridLayout* layout, int row, QJsonObject& parameterNode,
   horizontalLayout->setContentsMargins(0, 0, 0, 0);
   QWidget* horizontalWidget = new QWidget;
   horizontalWidget->setLayout(horizontalLayout);
+  label->setBuddy(horizontalWidget);
   layout->addWidget(horizontalWidget, row, 1, 1, 1);
 
   for (size_t i = 0; i < defaultValues.size(); ++i) {
@@ -298,14 +345,9 @@ void addEnumerationWidget(QGridLayout* layout, int row,
   }
   layout->addWidget(label, row, 0, 1, 1);
 
-  int defaultOption = 0;
-  QJsonValueRef defaultNode = parameterNode["default"];
-  if (!defaultNode.isUndefined() && isType<int>(defaultNode)) {
-    defaultOption = getAs<int>(defaultNode);
-  }
-
   QComboBox* comboBox = new QComboBox();
   comboBox->setObjectName(nameValue.toString());
+  label->setBuddy(comboBox);
   QJsonValueRef optionsNode = parameterNode["options"];
   if (!optionsNode.isUndefined()) {
     QJsonArray optionsArray = optionsNode.toArray();
@@ -325,7 +367,19 @@ void addEnumerationWidget(QGridLayout* layout, int row,
     }
   }
 
-  comboBox->setCurrentIndex(defaultOption);
+  // Set the default if present
+  QJsonValueRef defaultNode = parameterNode["default"];
+  if (!defaultNode.isUndefined()) {
+    if (isType<int>(defaultNode)) {
+      comboBox->setCurrentIndex(getAs<int>(defaultNode));
+    } else if (defaultNode.isString()) {
+      // Find the data that matches, and set it
+      int defaultIndex = comboBox->findData(getAs<QString>(defaultNode));
+      if (defaultIndex >= 0) {
+        comboBox->setCurrentIndex(defaultIndex);
+      }
+    }
+  }
 
   layout->addWidget(comboBox, row, 1, 1, 1);
 }
@@ -376,6 +430,7 @@ void addPathWidget(QGridLayout* layout, int row, QJsonObject& pathNode)
 
   QJsonValueRef labelValue = pathNode["label"];
   QLabel* label = new QLabel(nameValue.toString());
+  label->setBuddy(horizontalWidget);
   if (!labelValue.isUndefined()) {
     label->setText(labelValue.toString());
   }
@@ -387,11 +442,20 @@ void addPathWidget(QGridLayout* layout, int row, QJsonObject& pathNode)
   pathField->setProperty("type", type);
   pathField->setObjectName(nameValue.toString());
   pathField->setMinimumWidth(500);
+
+  // Set default if present
+  QJsonValueRef defaultNode = pathNode["default"];
+  if (!defaultNode.isUndefined() && defaultNode.isString()) {
+    auto defaultValue = getAs<QString>(defaultNode);
+    pathField->setText(defaultValue);
+  }
+
   horizontalLayout->addWidget(pathField);
+  auto filter = pathNode["filter"].toString();
 
   QPushButton* browseButton = new QPushButton("Browse");
   horizontalLayout->addWidget(browseButton);
-  QObject::connect(browseButton, &QPushButton::clicked, [type, pathField]() {
+  QObject::connect(browseButton, &QPushButton::clicked, [type, pathField, filter]() {
     // Determine the directory we should open the file browser at.
     QString browseDir;
     if (!pathField->text().isEmpty()) {
@@ -406,7 +470,10 @@ void addPathWidget(QGridLayout* layout, int row, QJsonObject& pathNode)
     QString path;
     if (type == "file") {
       path = QFileDialog::getOpenFileName(tomviz::mainWidget(), "Select File",
-                                          browseDir);
+                                          browseDir, filter);
+    } else if (type == "save_file") {
+      path = QFileDialog::getSaveFileName(tomviz::mainWidget(), "Save File Path",
+                                          browseDir, filter);
     } else {
       path = QFileDialog::getExistingDirectory(tomviz::mainWidget(),
                                                "Select Directory", browseDir);
@@ -458,6 +525,7 @@ void addStringWidget(QGridLayout* layout, int row, QJsonObject& pathNode)
   stringField->setProperty("type", type);
   stringField->setObjectName(nameValue.toString());
   stringField->setMinimumWidth(500);
+  label->setBuddy(stringField);
   horizontalLayout->addWidget(stringField);
 
   QJsonValueRef defaultNode = pathNode["default"];
@@ -488,6 +556,7 @@ void addDatasetWidget(QGridLayout* layout, int row, QJsonObject& parameterNode)
 
   QComboBox* comboBox = new QComboBox();
   comboBox->setObjectName(nameValue.toString());
+  labelWidget->setBuddy(comboBox);
   QStringList addedLabels;
   auto dataSources =
     tomviz::ModuleManager::instance().allDataSourcesDepthFirst();
@@ -514,10 +583,17 @@ void addDatasetWidget(QGridLayout* layout, int row, QJsonObject& parameterNode)
   layout->addWidget(comboBox, row, 1, 1, 1);
 }
 
+static const QStringList PATH_TYPES = { "file", "save_file", "directory" };
+
 } // end anonymous namespace
 
 namespace tomviz {
 
+bool setupEnableTriggerAbstract(QWidget* refWidget, QWidget* widget,
+                                const QString& comparator,
+                                const QVariant& compareValue,
+                                bool visibility);
+
 InterfaceBuilder::InterfaceBuilder(QObject* parentObject, DataSource* ds)
   : QObject(parentObject), m_dataSource(ds)
 {}
@@ -589,7 +665,7 @@ QLayout* InterfaceBuilder::buildParameterInterface(QGridLayout* layout,
       addEnumerationWidget(layout, i + 1, parameterObject);
     } else if (typeString == "xyz_header") {
       addXYZHeaderWidget(layout, i + 1, parameterObject);
-    } else if (typeString == "file" || typeString == "directory") {
+    } else if (PATH_TYPES.contains(typeString)) {
       addPathWidget(layout, i + 1, parameterObject);
     } else if (typeString == "string") {
       addStringWidget(layout, i + 1, parameterObject);
@@ -598,12 +674,81 @@ QLayout* InterfaceBuilder::buildParameterInterface(QGridLayout* layout,
     }
   }
 
+  setupEnableAndVisibleStates(layout->parentWidget(), parameters);
+
   return layout;
 }
 
+void InterfaceBuilder::setupEnableAndVisibleStates(
+  const QObject* parent,
+  QJsonArray& parameters) const
+{
+  setupEnableStates(parent, parameters, true);
+  setupEnableStates(parent, parameters, false);
+}
+
+void InterfaceBuilder::setupEnableStates(const QObject* parent,
+                                         QJsonArray& parameters,
+                                         bool visible) const
+{
+  static const QStringList validComparators = {
+    "==", "!=", ">", ">=", "<", "<="
+  };
+
+  QJsonObject::size_type numParameters = parameters.size();
+  for (QJsonObject::size_type i = 0; i < numParameters; ++i) {
+    QJsonValueRef parameterNode = parameters[i];
+    QJsonObject parameterObject = parameterNode.toObject();
+
+    QString text = visible ? "visible_if" : "enable_if";
+    QString enableIfValue = parameterObject[text].toString("");
+    if (enableIfValue.isEmpty()) {
+      continue;
+    }
+
+    QString widgetName = parameterObject["name"].toString("");
+    if (widgetName.isEmpty()) {
+      qCritical() << text << "parameters must have a name. Ignoring...";
+      continue;
+    }
+    auto* widget = parent->findChild<QWidget*>(widgetName);
+    if (!widget) {
+      qCritical() << "Failed to find widget with name:" << widgetName;
+      continue;
+    }
+
+    auto split = enableIfValue.simplified().split(" ");
+    if (split.size() != 3) {
+      qCritical() << "Invalid" << text << "string:" << enableIfValue;
+      continue;
+    }
+
+    auto refWidgetName = split[0];
+    auto comparator = split[1];
+    auto compareValue = split[2];
+    auto* refWidget = parent->findChild<QWidget*>(refWidgetName);
+
+    if (!refWidget) {
+      qCritical() << "Invalid widget name in" << text << "string:" << enableIfValue;
+      continue;
+    }
+
+    if (!validComparators.contains(comparator)) {
+      qCritical() << "Invalid comparator in" << text << "string:" << enableIfValue;
+      continue;
+    }
+
+    if (!setupEnableTriggerAbstract(refWidget, widget, comparator,
+                                    compareValue, visible)) {
+      qCritical() << "Failed to set up" << text << "trigger for" << widgetName;
+    }
+  }
+}
+
 QLayout* InterfaceBuilder::buildInterface() const
 {
   QWidget* widget = new QWidget;
+  widget->setProperty("isRootInterfaceWidget", true);
 
   QVBoxLayout* verticalLayout = new QVBoxLayout;
   verticalLayout->addWidget(widget);
@@ -774,14 +919,13 @@ QVariantMap InterfaceBuilder::parameterValues(const QObject* parent)
     }
   }
 
-  // QLineEdit's ( currently 'file' and 'directory' types ).
-  QStringList pathTypes = { "file", "directory" };
+  // QLineEdit's ( currently 'file', 'save_file', and 'directory' types ).
   QList<QLineEdit*> lineEdits = parent->findChildren<QLineEdit*>();
   for (int i = 0; i < lineEdits.size(); ++i) {
     auto lineEdit = lineEdits[i];
     QVariant type = lineEdit->property("type");
     bool canConvertTypeToString = QMetaType::canConvert(type.metaType(), QMetaType(QMetaType::QString));
-    if (canConvertTypeToString && pathTypes.contains(type.toString())) {
+    if (canConvertTypeToString && PATH_TYPES.contains(type.toString())) {
       map[lineEdit->objectName()] = lineEdit->text();
     } else if (canConvertTypeToString && type.toString() == "string") {
       map[lineEdit->objectName()] = lineEdit->text();
@@ -791,4 +935,163 @@ QVariantMap InterfaceBuilder::parameterValues(const QObject* parent)
   return map;
 }
 
+QWidget* findRootInterfaceWidget(const QWidget* widget)
+{
+  auto* parent = widget->parent();
+  while (parent and not parent->property("isRootInterfaceWidget").toBool()) {
+    parent = parent->parent();
+  }
+
+  if (parent and parent->property("isRootInterfaceWidget").toBool()) {
+    return qobject_cast<QWidget*>(parent);
+  }
+
+  return nullptr;
+}
+
+QLabel* findLabelForWidget(const QWidget* widget)
+{
+  // We use the buddy system to keep track of which label is for
+  // which widget.
+  auto* parent = findRootInterfaceWidget(widget);
+  if (!parent) {
+    return nullptr;
+  }
+
+  for (auto* child : parent->findChildren<QLabel*>()) {
+    if (child->buddy() == widget) {
+      return child;
+    }
+  }
+
+  return nullptr;
+}
+
+void setWidgetProperty(QWidget* widget, const char* property, QVariant value)
+{
+  if (isWidgetNumeric(widget) || isWidgetType<QLineEdit>(widget)) {
+    // These types actually want the parent widget instead, because there
+    // is some parent widget holding everything (spinboxes, path button, etc.).
+    widget = widget->parentWidget();
+    if (!widget) {
+      // This hopefully should't happen.
+      return;
+    }
+  }
+
+  // First, set the property on the widget
+  widget->setProperty(property, value);
+
+  // Next, see if we can find the label corresponding to this widget, and
+  // set the property there as well.
+  auto* label = findLabelForWidget(widget);
+  if (label) {
+    label->setProperty(property, value);
+  }
+}
+
+template <typename T>
+bool compareGeneric(T value, T ref, const QString& comparator)
+{
+  // The generic one, for bools and strings, can only do `==` and `!=`.
+  if (comparator == "==") {
+    return value == ref;
+  } else if (comparator == "!=") {
+    return value != ref;
+  }
+
+  return false;
+}
+
+template <typename T>
+bool compareNumbers(T value, T ref, const QString& comparator)
+{
+  // This is for ints and floats. We can do inequality comparisons.
+  if (comparator == "==") {
+    return value == ref;
+  } else if (comparator == "!=") {
+    return value != ref;
+  } else if (comparator == ">") {
+    return value > ref;
+  } else if (comparator == "<") {
+    return value < ref;
+  } else if (comparator == ">=") {
+    return value >= ref;
+  } else if (comparator == "<=") {
+    return value <= ref;
+  }
+
+  return false;
+}
+
+template <typename T>
+bool compare(const T* widget, const QVariant& compareValue,
+             const QString& comparator)
+{
+  auto value = widgetValue(widget);
+  if constexpr (std::is_same_v<T, QComboBox> || std::is_same_v<T, QLineEdit>) {
+    QString ref = compareValue.toString();
+    if (ref.startsWith("'") || ref.startsWith("\"")) {
+      // Remove the first and last characters
+      ref = ref.mid(1, ref.length() - 2);
+    }
+    return compareGeneric(value, ref, comparator);
+  } else if constexpr (std::is_same_v<T, QCheckBox>) {
+    return compareGeneric(value, compareValue.toBool(), comparator);
+  } else if constexpr (std::is_same_v<T, QSpinBox>) {
+    return compareNumbers(value, compareValue.toInt(), comparator);
+  } else if constexpr (std::is_same_v<T, QDoubleSpinBox>) {
+    return compareNumbers(value, compareValue.toDouble(), comparator);
+  }
+
+  return false;
+}
+
+template <typename T>
+bool setupEnableTrigger(T* refWidget, QWidget* widget,
+                        const QString& comparator, const QVariant& compareValue,
+                        const char* property)
+{
+  // Set up the callback function
+  auto func = [=](){
+    auto result = compare(refWidget, compareValue, comparator);
+    setWidgetProperty(widget, property, result);
+  };
+  // Make the connection
+  widget->connect(refWidget, changedSignal<T>(), widget, func);
+
+  // Trigger the update one time, since defaults are already set.
+  func();
+
+  return true;
+}
+
+bool setupEnableTriggerAbstract(QWidget* refWidget, QWidget* widget,
+                                const QString& comparator,
+                                const QVariant& compareValue,
+                                bool visibility)
+{
+  const char* property = visibility ? "visible" : "enabled";
+  if (isWidgetType<QSpinBox>(refWidget)) {
+    return setupEnableTrigger(qobject_cast<QSpinBox*>(refWidget), widget,
+                              comparator, compareValue, property);
+  } else if (isWidgetType<QDoubleSpinBox>(refWidget)) {
+    return setupEnableTrigger(qobject_cast<QDoubleSpinBox*>(refWidget), widget,
+                              comparator, compareValue, property);
+  } else if (isWidgetType<QCheckBox>(refWidget)) {
+    return setupEnableTrigger(qobject_cast<QCheckBox*>(refWidget), widget,
+                              comparator, compareValue, property);
+  } else if (isWidgetType<QComboBox>(refWidget)) {
+    return setupEnableTrigger(qobject_cast<QComboBox*>(refWidget), widget,
+                              comparator, compareValue, property);
+  } else if (isWidgetType<QLineEdit>(refWidget)) {
+    return setupEnableTrigger(qobject_cast<QLineEdit*>(refWidget), widget,
+                              comparator, compareValue, property);
+  }
+
+  qCritical() << "Unhandled widget type for object: "
+              << refWidget->objectName();
+  return false;
+}
+
 } // namespace tomviz
diff --git a/tomviz/InterfaceBuilder.h b/tomviz/InterfaceBuilder.h
index c8bfa32f4..0d3c026b8 100644
--- a/tomviz/InterfaceBuilder.h
+++ b/tomviz/InterfaceBuilder.h
@@ -40,6 +40,13 @@ class InterfaceBuilder : public QObject
 
   void updateWidgetValues(const QObject* parent);
 
+  void setupEnableAndVisibleStates(const QObject* parent,
+                                   QJsonArray& parameters) const;
+  void setupEnableStates(const QObject* parent, QJsonArray& parameters,
+                         bool visible) const;
+
+  QWidget* findWidgetByName(const QObject* parent, const QString& name) const;
+
 private:
   Q_DISABLE_COPY(InterfaceBuilder)
 
diff --git a/tomviz/MainWindow.cxx b/tomviz/MainWindow.cxx
index 8f51dd588..4f6da8816 100644
--- a/tomviz/MainWindow.cxx
+++ b/tomviz/MainWindow.cxx
@@ -48,6 +48,7 @@
 #include "PipelineProxy.h"
 #include "PipelineSettingsDialog.h"
 #include "ProgressDialogManager.h"
+#include "PtychoRunner.h"
 #include "PyXRFRunner.h"
 #include "PythonGeneratedDatasetReaction.h"
 #include "PythonUtilities.h"
@@ -109,13 +110,6 @@ namespace tomviz {
 MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
   : QMainWindow(parent, flags), m_ui(new Ui::MainWindow)
 {
-  // Override the default setting for showing full messages. This needs to be
-  // done prior to calling m_ui->setupUi(this) which sets the default to false.
-  pqSettings* qtSettings = pqApplicationCore::instance()->settings();
-  if (!qtSettings->contains("pqOutputWidget.ShowFullMessages")) {
-    qtSettings->setValue("pqOutputWidget.ShowFullMessages", true);
-  }
-
   VolumeManager::instance();
   connect(&ModuleManager::instance(), &ModuleManager::enablePythonConsole, this,
           &MainWindow::setEnabledPythonConsole);
@@ -137,12 +131,14 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
 
   // checkOpenGL();
   m_ui->setupUi(this);
+  // Force full messages to be shown
+  m_ui->outputWidget->showFullMessages(true);
   m_timer = new QTimer(this);
   connect(m_timer, SIGNAL(timeout()), SLOT(autosave()));
   m_timer->start(5 /*minutes*/ * 60 /*seconds per minute*/ *
                  1000 /*msec per second*/);
 
-  qSetMessagePattern("%{type}: %{message}");
+  qSetMessagePattern("[%{type}] %{message}");
 
   QString version(TOMVIZ_VERSION);
   if (QString(TOMVIZ_VERSION_EXTRA).size() > 0)
@@ -258,6 +254,14 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
   auto dataBrokerSaveReaction =
     new DataBrokerSaveReaction(m_ui->actionExportToDataBroker, this);
 
+  // Workflows menu
+  auto pyXRFRunner = new PyXRFRunner(this);
+  connect(m_ui->actionPyXRFWorkflow, &QAction::triggered, pyXRFRunner,
+          &PyXRFRunner::start);
+  auto ptychoRunner = new PtychoRunner(this);
+  connect(m_ui->actionPtychoWorkflow, &QAction::triggered, ptychoRunner,
+          &PtychoRunner::start);
+
   // Build Data Transforms menu
   new DataTransformMenu(this, m_ui->menuData, m_ui->menuSegmentation);
 
@@ -318,6 +322,8 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
     "Image Alignment (Auto: Cross Correlation)");
   QAction* autoAlignCOMAction =
     m_ui->menuTomography->addAction("Image Alignment (Auto: Center of Mass)");
+  QAction* autoAlignPyStackRegAction =
+    m_ui->menuTomography->addAction("Image Alignment (Auto: PyStackReg)");
   QAction* alignAction =
     m_ui->menuTomography->addAction("Image Alignment (Manual)");
   QAction* autoRotateAlignAction =
@@ -411,7 +417,8 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
     readInPythonScript("AutoTiltAxisRotationAlignment"), true);
   new AddPythonTransformReaction(
     autoRotateAlignShiftAction, "Auto Tilt Axis Shift Align",
-    readInPythonScript("AutoTiltAxisShiftAlignment"), true);
+    readInPythonScript("AutoTiltAxisShiftAlignment"), true, false, false,
+    readInJSONDescription("AutoTiltAxisShiftAlignment"));
 
   new AddPythonTransformReaction(
     autoAlignCCAction, "Auto Tilt Image Align (XCORR)",
@@ -421,6 +428,11 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
     autoAlignCOMAction, "Auto Tilt Image Align (CoM)",
     readInPythonScript("AutoCenterOfMassTiltImageAlignment"), false, false,
     false, readInJSONDescription("AutoCenterOfMassTiltImageAlignment"));
+  new AddPythonTransformReaction(
+    autoAlignPyStackRegAction, "Auto Tilt Image Align (PyStackReg)",
+    readInPythonScript("PyStackRegImageAlignment"), false, false,
+    false, readInJSONDescription("PyStackRegImageAlignment"));
+
   new AddPythonTransformReaction(reconDFMAction, "Reconstruct (Direct Fourier)",
                                  readInPythonScript("Recon_DFT"), true, false,
                                  false, readInJSONDescription("Recon_DFT"));
@@ -556,10 +568,6 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
   connect(m_ui->actionPipelineSettings, &QAction::triggered,
           pipelineSettingsDialog, &QWidget::show);
 
-  auto pyXRFRunner = new PyXRFRunner(this);
-  connect(m_ui->actionPyXRFWorkflow, &QAction::triggered, pyXRFRunner,
-          &PyXRFRunner::start);
-
   // Prepopulate the previously seen python readers/writers
   // This operation is fast since it fetches the readers description
   // from the settings, without really invoking python
@@ -570,7 +578,7 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
   statusBar()->showMessage("Initializing python...");
   auto pythonWatcher = new QFutureWatcher<std::vector<OperatorDescription>>;
   connect(pythonWatcher, &QFutureWatcherBase::finished, this,
-          [this, pyXRFRunner, pythonWatcher, dataBrokerSaveReaction]() {
+          [this, pyXRFRunner, ptychoRunner, pythonWatcher, dataBrokerSaveReaction]() {
             m_ui->actionAcquisition->setEnabled(true);
             m_ui->actionPassiveAcquisition->setEnabled(true);
             registerCustomOperators(pythonWatcher->result());
@@ -595,6 +603,16 @@ MainWindow::MainWindow(QWidget* parent, Qt::WindowFlags flags)
               m_ui->actionPyXRFWorkflow->setToolTip(tooltip);
             }
 
+            installed = ptychoRunner->isInstalled();
+            m_ui->actionPtychoWorkflow->setEnabled(installed);
+            if (!installed) {
+              // Grab the import error and show it in the tooltip
+              QString tooltip = "Failed to import required modules. "
+                                "Error message was:\n\n" +
+                                ptychoRunner->importError();
+              m_ui->actionPtychoWorkflow->setToolTip(tooltip);
+            }
+
             delete pythonWatcher;
             statusBar()->showMessage("Initialization complete", 1500);
           });
diff --git a/tomviz/MainWindow.ui b/tomviz/MainWindow.ui
index 41e8ba308..d0e8e4539 100644
--- a/tomviz/MainWindow.ui
+++ b/tomviz/MainWindow.ui
@@ -82,7 +82,6 @@
     <addaction name="actionAnimationHelper"/>
     <addaction name="actionPassiveAcquisition"/>
     <addaction name="actionPipelineSettings"/>
-    <addaction name="actionPyXRFWorkflow"/>
    </widget>
    <widget class="QMenu" name="menuData">
     <property name="title">
@@ -111,7 +110,15 @@
      <string>Segmentation</string>
     </property>
    </widget>
+   <widget class="QMenu" name="menuWorkflows">
+    <property name="title">
+     <string>Workflows</string>
+    </property>
+    <addaction name="actionPyXRFWorkflow"/>
+    <addaction name="actionPtychoWorkflow"/>
+   </widget>
    <addaction name="menu_File"/>
+   <addaction name="menuWorkflows"/>
    <addaction name="menuData"/>
    <addaction name="menuSegmentation"/>
    <addaction name="menuTomography"/>
@@ -408,7 +415,7 @@
     <string>&amp;Passive Acquisition</string>
    </property>
    <property name="toolTip">
-    <string> </string>
+    <string>Passive Acquisition</string>
    </property>
   </action>
   <action name="actionSaveData">
@@ -481,7 +488,7 @@
     <string>Pipeline Settings</string>
    </property>
    <property name="toolTip">
-    <string> </string>
+    <string>Pipeline Settings</string>
    </property>
   </action>
   <action name="actionAcquisition">
@@ -489,7 +496,7 @@
     <string>Acquisition</string>
    </property>
    <property name="toolTip">
-    <string> </string>
+    <string>Acquisition</string>
    </property>
   </action>
   <action name="actionReadTheDocs">
@@ -526,13 +533,18 @@
    </property>
   </action>
   <action name="actionPyXRFWorkflow">
-   <property name="enabled">
-    <bool>false</bool>
-   </property>
    <property name="text">
+    <string>PyXRF</string>
+   </property>
+   <property name="toolTip">
     <string>PyXRF Workflow</string>
    </property>
   </action>
+  <action name="actionPtychoWorkflow">
+   <property name="text">
+    <string>Ptycho</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>
diff --git a/tomviz/Pipeline.cxx b/tomviz/Pipeline.cxx
index 4864cf414..345c9b035 100644
--- a/tomviz/Pipeline.cxx
+++ b/tomviz/Pipeline.cxx
@@ -372,7 +372,8 @@ void Pipeline::branchFinished()
       lastOp->setChildDataSource(newChildDataSource);
       auto rootDataSource = dataSource();
       // connect signal to flow units and spacing to child data source.
-      connect(dataSource(), &DataSource::dataPropertiesChanged,
+      connect(rootDataSource, &DataSource::dataPropertiesChanged,
+              newChildDataSource,
               [rootDataSource, newChildDataSource]() {
                 // Only flow the properties if no user modifications have been
                 // made.
@@ -606,12 +607,11 @@ Pipeline::Future* Pipeline::emptyFuture()
 
 void Pipeline::moveModulesDown(DataSource* newChildDataSource)
 {
-  auto view = ActiveObjects::instance().activeView();
   foreach (Module* module, ModuleManager::instance().findModules<Module*>(
            dataSource(), nullptr)) {
     // TODO: We should really copy the module properties as well.
     auto newModule = ModuleManager::instance().createAndAddModule(
-      module->label(), newChildDataSource, view);
+      module->label(), newChildDataSource, module->view());
     // Copy over properties using the serialization code.
     newModule->deserialize(module->serialize());
     ModuleManager::instance().removeModule(module);
diff --git a/tomviz/ProgressDialog.cxx b/tomviz/ProgressDialog.cxx
index 3b3cf2552..2319fe0d1 100644
--- a/tomviz/ProgressDialog.cxx
+++ b/tomviz/ProgressDialog.cxx
@@ -14,6 +14,12 @@ ProgressDialog::ProgressDialog(const QString& title, const QString& msg,
   : QDialog(parent), m_ui(new Ui::ProgressDialog)
 {
   m_ui->setupUi(this);
+
+  // Override the pqOutputWidget message pattern that was just set.
+  qSetMessagePattern("[%{type}] %{message}");
+
+  // Force full messages to be shown
+  m_ui->outputWidget->showFullMessages(true);
   setWindowTitle(title);
   m_ui->label->setText(msg);
 
diff --git a/tomviz/PtychoDialog.cxx b/tomviz/PtychoDialog.cxx
new file mode 100644
index 000000000..75e70199e
--- /dev/null
+++ b/tomviz/PtychoDialog.cxx
@@ -0,0 +1,863 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#include "PtychoDialog.h"
+#include "ui_PtychoDialog.h"
+
+#include "PythonUtilities.h"
+
+#include <pqApplicationCore.h>
+#include <pqSettings.h>
+
+#include <QCheckBox>
+#include <QComboBox>
+#include <QBrush>
+#include <QDebug>
+#include <QDir>
+#include <QFileDialog>
+#include <QFileInfo>
+#include <QLabel>
+#include <QMessageBox>
+#include <QPointer>
+#include <QProcess>
+#include <QProcessEnvironment>
+#include <QScrollBar>
+
+namespace tomviz {
+
+class PtychoDialog::Internal : public QObject
+{
+  Q_OBJECT
+
+public:
+  Ui::PtychoDialog ui;
+  QPointer<PtychoDialog> parent;
+
+  bool ptychoguiIsRunning = false;
+
+  // Key is SID
+  QMap<long, QStringList> versionOptions;
+  // First key for these is the SID. Second key is the version.
+  QMap<long, QMap<QString, double>> angleOptions;
+  QMap<long, QMap<QString, QString>> allErrorLists;
+
+  QList<long> sidList;
+  QList<double> angleList;
+  QStringList versionList;
+  QList<bool> useList;
+  QStringList errorReasonList;
+
+  QList<long> filteredSidList;
+
+  QMap<int, QString> tableColumns;
+
+  Python::Module ptychoModule;
+
+  Internal(PtychoDialog* p)
+    : parent(p)
+  {
+    ui.setupUi(p);
+    setParent(p);
+
+    importModule();
+
+    setupTable();
+    setupConnections();
+  }
+
+  void setupConnections()
+  {
+    connect(ui.startPtychoGUI, &QPushButton::clicked, this,
+            &Internal::startPtychoGUI);
+
+    connect(ui.ptychoDirectory, &QLineEdit::editingFinished,
+            this, &Internal::ptychoDirEdited);
+    connect(ui.selectPtychoDirectory, &QPushButton::clicked, this,
+            &Internal::selectPtychoDirectory);
+
+    connect(ui.loadFromCSVFile, &QLineEdit::editingFinished,
+            this, &Internal::setUseAndVersionsFromCSV);
+    connect(ui.selectLoadFromCSVFile, &QPushButton::clicked, this,
+            &Internal::selectLoadFromCSV);
+
+    connect(ui.filterSIDsString, &QLineEdit::editingFinished,
+            this, &Internal::updateFilteredSidList);
+    connect(ui.selectOutputDirectory, &QPushButton::clicked, this,
+            &Internal::selectOutputDirectory);
+
+    connect(ui.buttonBox, &QDialogButtonBox::accepted, this,
+            &Internal::accepted);
+  }
+
+  void setupTable()
+  {
+    auto* table = ui.table;
+    auto& columns = tableColumns;
+
+    columns.clear();
+    columns[0] = "SID";
+    columns[1] = "Angle";
+    columns[2] = "Version";
+    columns[3] = "Use";
+    columns[4] = "Error Reason";
+
+    table->setColumnCount(columns.size());
+    for (int i = 0; i < columns.size(); ++i) {
+      auto* header = new QTableWidgetItem(columns[i]);
+      table->setHorizontalHeaderItem(i, header);
+    }
+  }
+
+  void importModule()
+  {
+    Python python;
+
+    if (ptychoModule.isValid()) {
+      return;
+    }
+
+    ptychoModule = python.import("tomviz.ptycho");
+    if (!ptychoModule.isValid()) {
+      qCritical() << "Failed to import \"tomviz.ptycho\" module";
+    }
+  }
+
+  void accepted()
+  {
+    QString reason;
+    if (!validate(reason)) {
+      QString title = "Invalid Settings";
+      QMessageBox::critical(parent.data(), title, reason);
+      parent->show();
+      return;
+    }
+
+    writeSettings();
+    parent->accept();
+  }
+
+  QList<long> selectedSids()
+  {
+    // Only include the filtered ones
+    QList<long> ret;
+    for (auto& sid : filteredSidList) {
+      auto idx = sidList.indexOf(sid);
+      auto use = useList[idx];
+      if (use) {
+        ret.append(sid);
+      }
+    }
+
+    return ret;
+  }
+
+  QStringList selectedVersions()
+  {
+    QStringList versions;
+    for (auto sid : selectedSids()) {
+      auto idx = sidList.indexOf(sid);
+      versions.append(versionList[idx]);
+    }
+    return versions;
+  }
+
+  QList<double> selectedAngles()
+  {
+    QList<double> angles;
+    for (auto sid : selectedSids()) {
+      auto idx = sidList.indexOf(sid);
+      angles.append(angleList[idx]);
+    }
+    return angles;
+  }
+
+  QList<long> invalidSidsSelected()
+  {
+    QList<long> invalid;
+    for (auto sid : selectedSids()) {
+      auto idx = sidList.indexOf(sid);
+      if (!errorReasonList[idx].isEmpty()) {
+        invalid.append(sid);
+      }
+    }
+    return invalid;
+  }
+
+  bool validate(QString& reason)
+  {
+    // Validate settings
+    if (ptychoDirectory().isEmpty() || !QDir(ptychoDirectory()).exists()) {
+      reason = "Ptycho directory does not exist: " + ptychoDirectory();
+      return false;
+    }
+
+    if (sidList.isEmpty()) {
+      reason = "No SIDs found in ptycho directory: " + ptychoDirectory();
+      return false;
+    }
+
+    auto invalid = invalidSidsSelected();
+    if (!invalid.isEmpty()) {
+      QString title = "Invalid SID and version combinations selected";
+      QString text = "Invalid SIDs were selected. ";
+      text += "Do you wish to automatically deselect them and continue?";
+      if (QMessageBox::question(parent, title, text) == QMessageBox::No) {
+        reason = "Invalid SIDs were selected";
+        return false;
+      }
+
+      for (auto sid : invalid) {
+        auto idx = sidList.indexOf(sid);
+        useList[idx] = false;
+        updateTable();
+      }
+    }
+
+    if (!QDir(outputDirectory()).exists()) {
+      // First ask if the user wants to make it.
+      QString title = "Directory does not exist";
+      auto text = QString("Output directory \"%1\" does not exist. Create it?")
+                    .arg(outputDirectory());
+      if (QMessageBox::question(parent, title, text) == QMessageBox::Yes) {
+        QDir().mkpath(outputDirectory());
+      }
+    }
+
+    if (outputDirectory().isEmpty() || !QDir(outputDirectory()).exists()) {
+      reason = "Output directory does not exist: " + outputDirectory();
+      return false;
+    }
+
+    return true;
+  }
+
+  void updateTable()
+  {
+    auto* table = ui.table;
+
+    int scrollbarPosition = 0;
+    auto scrollbar = table->verticalScrollBar();
+    if (scrollbar) {
+      scrollbarPosition = scrollbar->value();
+    }
+
+    table->clearContents();
+
+    table->setRowCount(filteredSidList.size());
+    for (int i = 0; i < filteredSidList.size(); ++i) {
+      auto sid = filteredSidList[i];
+      bool invalid = false;
+      for (auto j : tableColumns.keys()) {
+        auto column = tableColumns[j];
+        auto value = tableValue(sid, column);
+        if (column == "Version") {
+          auto* cb = createVersionComboBox(sid, value);
+          table->setCellWidget(i, j, cb);
+          continue;
+        } else if (column == "Use") {
+          auto* w = createUseCheckBox(sid, value);
+          table->setCellWidget(i, j, w);
+          continue;
+        } else if (column == "Error Reason") {
+          invalid = !value.isEmpty();
+        }
+
+        auto* item = new QTableWidgetItem(value);
+        item->setTextAlignment(Qt::AlignCenter);
+        table->setItem(i, j, item);
+      }
+
+      if (invalid) {
+        // Make every item have a red background
+        for (int j = 0; j < tableColumns.size(); ++j) {
+          auto* item = table->item(i, j);
+          if (item) {
+            item->setBackground(QBrush(Qt::red));
+          } else {
+            auto* cw = table->cellWidget(i, j);
+            if (cw) {
+              cw->setStyleSheet("background-color: red");
+            }
+          }
+        }
+      }
+    }
+
+    if (scrollbar) {
+      scrollbar->setValue(scrollbarPosition);
+    }
+  }
+
+  QWidget* createVersionComboBox(long sid, QString value)
+  {
+    if (versionOptions[sid].size() < 2) {
+      // If there aren't any options, the item will just be a label
+      QString text = "None";
+      if (versionOptions[sid].size() == 1) {
+        text = versionOptions[sid][0];
+      }
+      return createTableWidget(new QLabel(text, parent));
+    }
+
+    auto cb = new QComboBox(parent);
+    for (auto& option: versionOptions[sid]) {
+      cb->addItem(option);
+    }
+    cb->setCurrentText(value);
+
+    connect(cb, &QComboBox::currentIndexChanged, this, [this, sid, cb]() {
+      auto idx = sidList.indexOf(sid);
+      versionList[idx] = cb->currentText();
+      onSelectedVersionsChanged();
+      // Update the table, because the angle and error reason likely changed
+      updateTable();
+    });
+
+    return createTableWidget(cb);
+  }
+
+  QWidget* createUseCheckBox(long sid, QString value)
+  {
+    auto cb = new QCheckBox(parent);
+    cb->setChecked(value == "x" || value == "1");
+    connect(cb, &QCheckBox::toggled, this, [this, sid](bool b) {
+      auto idx = sidList.indexOf(sid);
+      useList[idx] = b;
+    });
+
+    return createTableWidget(cb);
+  }
+
+  QWidget* createTableWidget(QWidget* w)
+  {
+    // This is required to center the widget
+    auto* tw = new QWidget(ui.table);
+    auto* layout = new QHBoxLayout(tw);
+    layout->addWidget(w);
+    layout->setAlignment(Qt::AlignCenter);
+    layout->setContentsMargins(0, 0, 0, 0);
+    return tw;
+  }
+
+  QString tableValue(long sid, QString column)
+  {
+    auto idx = sidList.indexOf(sid);
+    if (column == "SID") {
+      return QString::number(sidList[idx]);
+    } else if (column == "Version") {
+      return versionList[idx];
+    } else if (column == "Angle") {
+      return QString::number(angleList[idx]);
+    } else if (column == "Use") {
+      return useList[idx] ? "x" : "";
+    } else if (column == "Error Reason") {
+      return errorReasonList[idx];
+    }
+
+    qCritical() << "Unknown table column: " << column;
+    return "";
+  }
+
+  QString defaultOutputDirectory() { return QDir::home().filePath("ptycho_output"); }
+
+  void readSettings()
+  {
+    auto settings = pqApplicationCore::instance()->settings();
+    settings->beginGroup("ptycho");
+    settings->beginGroup("process");
+
+    setPtychoGUICommand(
+      settings->value("ptychoGUICommand", "run-ptycho").toString());
+
+    setPtychoDirectory(settings->value("ptychoDirectory", "").toString());
+    setCsvFile(settings->value("loadFromCSVFile", "").toString());
+    setFilterSIDsString(settings->value("filterSIDsString", "").toString());
+
+    setOutputDirectory(
+      settings->value("outputDirectory", defaultOutputDirectory()).toString());
+    setRotateDatasets(
+      settings->value("rotateDatasets", true).toBool());
+
+    QVariantList sidListV = settings->value("sidListV").toList();
+    QVariantList versionListV = settings->value("versionListV").toList();
+    QVariantList useListV = settings->value("useListV").toList();
+
+    QList<long> savedSidList;
+    for (const auto& var : sidListV) {
+      savedSidList.append(var.value<long>());
+    }
+
+    QStringList savedVersionList;
+    for (const auto& var : versionListV) {
+      savedVersionList.append(var.value<QString>());
+    }
+
+    QList<bool> savedUseList;
+    for (const auto& var : useListV) {
+      savedUseList.append(var.value<bool>());
+    }
+
+    settings->endGroup();
+    settings->endGroup();
+
+    if (!ptychoDirectory().isEmpty()) {
+      // Trigger a load
+      loadPtychoDir();
+
+      if (!csvFile().isEmpty()) {
+        // Trigger applying the CSV file
+        setUseAndVersionsFromCSV();
+      }
+
+      if (!filterSIDsString().isEmpty()) {
+        // Trigger an update via the filters
+        updateFilteredSidList();
+      }
+
+      if (savedSidList == sidList) {
+        // If the saved SID list matches, we can also load the settings
+        // for "use" and "version"
+        versionList = savedVersionList;
+        useList = savedUseList;
+        onSelectedVersionsChanged();
+        updateTable();
+      }
+    }
+  }
+
+  void writeSettings()
+  {
+    auto settings = pqApplicationCore::instance()->settings();
+    settings->beginGroup("ptycho");
+    settings->beginGroup("process");
+
+    // Save general settings
+    settings->setValue("ptychoGUICommand", ptychoGUICommand());
+    settings->setValue("ptychoDirectory", ptychoDirectory());
+    settings->setValue("loadFromCSVFile", csvFile());
+
+    settings->setValue("filterSIDsString", filterSIDsString());
+
+    settings->setValue("outputDirectory", outputDirectory());
+    settings->setValue("rotateDatasets", rotateDatasets());
+
+    // Save out our lists
+    QVariantList sidListV;
+    for (auto v: sidList) {
+      sidListV.append(QVariant::fromValue(v));
+    }
+
+    QVariantList versionListV;
+    for (auto v: versionList) {
+      versionListV.append(QVariant::fromValue(v));
+    }
+
+    QVariantList useListV;
+    for (auto b: useList) {
+      useListV.append(QVariant::fromValue(b));
+    }
+
+    settings->setValue("sidListV", sidListV);
+    settings->setValue("versionListV", versionListV);
+    settings->setValue("useListV", useListV);
+
+    settings->endGroup();
+    settings->endGroup();
+  }
+
+  void startPtychoGUI()
+  {
+    if (ptychoguiIsRunning) {
+      // It's already running. Just return.
+      return;
+    }
+
+    QString program = ptychoGUICommand();
+    QStringList args;
+
+    auto* process = new QProcess(this);
+
+    auto processEnv = QProcessEnvironment::systemEnvironment();
+
+    // Remove variables related to python environment
+    processEnv.remove("PYTHONHOME");
+    processEnv.remove("PYTHONPATH");
+
+    process->setProcessEnvironment(processEnv);
+
+    // Forward stdout/stderr to this process
+    process->setProcessChannelMode(QProcess::ForwardedChannels);
+
+    process->start(program, args);
+
+    ptychoguiIsRunning = true;
+
+    connect(process,
+            QOverload<int, QProcess::ExitStatus>::of(&QProcess::finished), this,
+            [this]() {
+      ptychoguiIsRunning = false;
+      loadPtychoDir();
+    });
+
+    connect(
+      process, &QProcess::errorOccurred, this,
+      [this, process](QProcess::ProcessError err) {
+        ptychoguiIsRunning = false;
+
+        QString title;
+        QString msg;
+
+        if (err == QProcess::FailedToStart) {
+          title = "Ptycho GUI failed to start";
+          msg = QString("The program \"%1\" failed to start.\n\n")
+                  .arg(process->program());
+        } else {
+          QString output = process->readAllStandardOutput();
+          QString error = process->readAllStandardError();
+          title = "Ptycho GUI exited with an error";
+          msg =
+            QString("stdout: \"%1\"\n\nstderr: \"%2\"").arg(output).arg(error);
+        }
+        QMessageBox::critical(parent.data(), title, msg);
+      });
+  }
+
+  void selectPtychoDirectory()
+  {
+    QString caption = "Select Ptycho GUI Directory";
+    auto file =
+      QFileDialog::getExistingDirectory(parent.data(), caption,
+                                        ptychoDirectory());
+    if (file.isEmpty()) {
+      return;
+    }
+
+    setPtychoDirectory(file);
+    ptychoDirEdited();
+  }
+
+  void ptychoDirEdited()
+  {
+    // Whenever this is called, make sure we clear the CSV file and SID filters
+    setCsvFile("");
+    setFilterSIDsString("");
+
+    loadPtychoDir();
+  }
+
+  void loadPtychoDir()
+  {
+    clearTable();
+
+    Python python;
+
+    auto func = ptychoModule.findFunction("gather_ptycho_info");
+    if (!func.isValid()) {
+      QString msg = "Failed to import \"tomviz.ptycho.gather_ptycho_info\"";
+      qCritical() << msg;
+      return;
+    }
+
+    Python::Dict kwargs;
+    kwargs.set("ptycho_dir", ptychoDirectory());
+    auto result = func.call(kwargs);
+
+    if (!result.isValid() || !result.isDict()) {
+      QString msg = "Error calling \"tomviz.ptycho.gather_ptycho_info\"";
+      qCritical() << msg;
+      return;
+    }
+
+    auto resultDict = result.toDict();
+
+    auto sidListV = resultDict["sid_list"].toVariant().toList();
+    auto versionDictV = resultDict["version_list"].toVariant().toList();
+    auto angleDictV = resultDict["angle_list"].toVariant().toList();
+    auto errorDictV = resultDict["error_list"].toVariant().toList();
+
+    sidList.clear();
+    versionOptions.clear();
+    angleOptions.clear();
+    allErrorLists.clear();
+    for (size_t i = 0; i < sidListV.size(); ++i) {
+      auto sid = sidListV[i].toLong();
+      sidList.append(sid);
+
+      auto versionOptionsV = versionDictV[i].toList();
+      auto theseAnglesV = angleDictV[i].toList();
+      auto theseErrorsV = errorDictV[i].toList();
+
+      QStringList versions;
+      QMap<QString, double> angles;
+      QMap<QString, QString> errors;
+      for (size_t j = 0; j < versionOptionsV.size(); ++j) {
+        auto version = QString::fromStdString(versionOptionsV[j].toString());
+        versions.append(version);
+        angles[version] = theseAnglesV[j].toDouble();
+        errors[version] = QString::fromStdString(theseErrorsV[j].toString());
+      }
+      versionOptions[sid] = versions;
+      angleOptions[sid] = angles;
+      allErrorLists[sid] = errors;
+    }
+
+    resetSelectedVersionsAndUseList();
+    updateFilteredSidList();
+  }
+
+  void resetSelectedVersionsAndUseList()
+  {
+    versionList.clear();
+    useList.clear();
+
+    for (auto sid: sidList) {
+      bool set = false;
+      for (auto& version: versionOptions[sid]) {
+        if (allErrorLists[sid][version].isEmpty()) {
+          // This one is valid.
+          versionList.append(version);
+          useList.append(true);
+          set = true;
+          break;
+        }
+      }
+      if (!set) {
+        // Do the first one and don't set it to be used.
+        versionList.append(versionOptions[sid][0]);
+        useList.append(false);
+      }
+    }
+
+    onSelectedVersionsChanged();
+  }
+
+  void onSelectedVersionsChanged()
+  {
+    angleList.clear();
+    errorReasonList.clear();
+
+    for (int i = 0; i < sidList.size(); ++i) {
+      auto sid = sidList[i];
+      auto version = versionList[i];
+      angleList.append(angleOptions[sid][version]);
+      errorReasonList.append(allErrorLists[sid][version]);
+    }
+  }
+
+  void updateFilteredSidList()
+  {
+    auto filterString = filterSIDsString();
+
+    Python python;
+
+    auto func = ptychoModule.findFunction("filter_sid_list");
+    if (!func.isValid()) {
+      qCritical() << "Failed to find function \"filter_sid_list\"";
+      return;
+    }
+
+    Python::Dict kwargs;
+    kwargs.set("sid_list", sidList);
+    kwargs.set("filter_string", filterString);
+    auto result = func.call(kwargs);
+    if (!result.isValid() || !result.isList()) {
+      qCritical() << "Failed to call function \"filter_sid_list\"";
+      return;
+    }
+
+    filteredSidList.clear();
+    auto resultList = result.toList();
+    for (int i = 0; i < resultList.length(); ++i) {
+      filteredSidList.append(resultList[i].toLong());
+    }
+
+    updateTable();
+  }
+
+  void selectLoadFromCSV()
+  {
+    QString caption = "Select CSV file to load Use and Version settings";
+    auto startPath = !csvFile().isEmpty() ? csvFile() : ptychoDirectory();
+    auto file =
+      QFileDialog::getOpenFileName(parent.data(), caption, startPath);
+    if (file.isEmpty()) {
+      return;
+    }
+    ui.loadFromCSVFile->setText(file);
+
+    setUseAndVersionsFromCSV();
+  }
+
+  void setUseAndVersionsFromCSV()
+  {
+    Python python;
+
+    auto func = ptychoModule.findFunction("get_use_and_versions_from_csv");
+    if (!func.isValid()) {
+      qCritical() << "Failed to find function \"get_use_and_versions_from_csv\"";
+      return;
+    }
+
+    Python::Dict kwargs;
+    kwargs.set("csv_path", csvFile());
+    auto result = func.call(kwargs);
+    if (!result.isValid() || !result.isDict()) {
+      qCritical() << "Failed to call function \"get_use_and_versions_from_csv\"";
+      return;
+    }
+
+    auto resultDict = result.toDict();
+
+    QList<long> sids;
+    QList<bool> use;
+    QStringList versions;
+
+    auto sidsPy = resultDict["sids"].toList();
+    auto usePy = resultDict["use"].toList();
+    auto versionsPy = resultDict["versions"].toList();
+
+    for (auto i = 0; i < sidsPy.length(); ++i) {
+      sids.append(sidsPy[i].toLong());
+      if (i < usePy.length()) {
+        use.append(usePy[i].toBool());
+      }
+      if (i < versionsPy.length()) {
+        versions.append(versionsPy[i].toString());
+      }
+    }
+
+    if (sids.size() == 0) {
+      qCritical() << "No SIDs found in CSV file. Aborting";
+      return;
+    }
+
+    if (use.size() != 0) {
+      // Set the "Use" for every current one to "false";
+      for (int i = 0; i < useList.size(); ++i) {
+        useList[i] = false;
+      }
+    }
+
+    for (int i = 0; i < sids.size(); ++i) {
+      auto sid = sids[i];
+      auto idx = sidList.indexOf(sid);
+      if (i < use.size()) {
+        useList[idx] = use[i];
+      }
+
+      if (i < versions.size()) {
+        // Verify it is a valid version
+        auto newVersion = versions[i];
+        if (!versionOptions[sid].contains(newVersion)) {
+          qCritical() << "SID \"" << sid << "\" from CSV file "
+                      << "indicated a version of " << newVersion << ", "
+                      << "but that did not match the available versions "
+                      << "found within the ptycho directory for that SID. "
+                      << "Skipping...";
+        } else {
+          versionList[idx] = newVersion;
+        }
+      }
+    }
+
+    updateTable();
+  }
+
+  void selectOutputDirectory()
+  {
+    QString caption = "Select output directory";
+    auto dir = QFileDialog::getExistingDirectory(parent.data(), caption,
+                                                 outputDirectory());
+    if (dir.isEmpty()) {
+      return;
+    }
+
+    setOutputDirectory(dir);
+  }
+
+  void clearTable()
+  {
+    versionOptions.clear();
+    angleOptions.clear();
+    allErrorLists.clear();
+
+    sidList.clear();
+    angleList.clear();
+    versionList.clear();
+    useList.clear();
+    errorReasonList.clear();
+
+    filteredSidList.clear();
+  }
+
+  QString ptychoGUICommand() const { return ui.ptychoGUICommand->text(); }
+
+  void setPtychoGUICommand(QString s) { ui.ptychoGUICommand->setText(s); }
+
+  QString ptychoDirectory() const { return ui.ptychoDirectory->text(); }
+
+  void setPtychoDirectory(QString s) { ui.ptychoDirectory->setText(s); }
+
+  QString csvFile() const { return ui.loadFromCSVFile->text(); }
+
+  void setCsvFile(QString s) { ui.loadFromCSVFile->setText(s); }
+
+  QString filterSIDsString() const { return ui.filterSIDsString->text().trimmed(); }
+
+  void setFilterSIDsString(QString s) const { ui.filterSIDsString->setText(s); }
+
+  QString outputDirectory() const { return ui.outputDirectory->text(); }
+
+  void setOutputDirectory(QString s) { ui.outputDirectory->setText(s); }
+
+  bool rotateDatasets() const { return ui.rotateDatasets->isChecked(); }
+
+  void setRotateDatasets(bool b) { ui.rotateDatasets->setChecked(b); }
+};
+
+PtychoDialog::PtychoDialog(QWidget* parent)
+  : QDialog(parent), m_internal(new Internal(this))
+{
+}
+
+PtychoDialog::~PtychoDialog() = default;
+
+void PtychoDialog::show()
+{
+  m_internal->readSettings();
+  QDialog::show();
+}
+
+QString PtychoDialog::ptychoDirectory() const
+{
+  return m_internal->ptychoDirectory();
+}
+
+QList<long> PtychoDialog::selectedSids() const
+{
+  return m_internal->selectedSids();
+}
+
+QStringList PtychoDialog::selectedVersions() const
+{
+  return m_internal->selectedVersions();
+}
+
+QList<double> PtychoDialog::selectedAngles() const
+{
+  return m_internal->selectedAngles();
+}
+
+QString PtychoDialog::outputDirectory() const
+{
+  return m_internal->outputDirectory();
+}
+
+bool PtychoDialog::rotateDatasets() const
+{
+  return m_internal->rotateDatasets();
+}
+
+} // namespace tomviz
+
+#include "PtychoDialog.moc"
diff --git a/tomviz/PtychoDialog.h b/tomviz/PtychoDialog.h
new file mode 100644
index 000000000..585ed2530
--- /dev/null
+++ b/tomviz/PtychoDialog.h
@@ -0,0 +1,37 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#ifndef tomvizPtychoDialog_h
+#define tomvizPtychoDialog_h
+
+#include <QDialog>
+#include <QScopedPointer>
+
+namespace tomviz {
+
+class PtychoDialog : public QDialog
+{
+  Q_OBJECT
+
+public:
+  explicit PtychoDialog(QWidget* parent);
+  ~PtychoDialog() override;
+
+  virtual void show();
+
+  QString ptychoDirectory() const;
+  QString outputDirectory() const;
+  bool rotateDatasets() const;
+
+  QList<long> selectedSids() const;
+  QStringList selectedVersions() const;
+  QList<double> selectedAngles() const;
+
+private:
+  class Internal;
+  QScopedPointer<Internal> m_internal;
+};
+
+} // namespace tomviz
+
+#endif
diff --git a/tomviz/PtychoDialog.ui b/tomviz/PtychoDialog.ui
new file mode 100644
index 000000000..749e118fe
--- /dev/null
+++ b/tomviz/PtychoDialog.ui
@@ -0,0 +1,237 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>PtychoDialog</class>
+ <widget class="QDialog" name="PtychoDialog">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>669</width>
+    <height>732</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Ptycho Dialog</string>
+  </property>
+  <layout class="QGridLayout" name="gridLayout">
+   <property name="leftMargin">
+    <number>6</number>
+   </property>
+   <property name="topMargin">
+    <number>6</number>
+   </property>
+   <property name="rightMargin">
+    <number>6</number>
+   </property>
+   <property name="bottomMargin">
+    <number>6</number>
+   </property>
+   <item row="10" column="1">
+    <widget class="QLineEdit" name="outputDirectory">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output files will be written. If one is not specified, the Ptycho directory will be used.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+    </widget>
+   </item>
+   <item row="11" column="0" colspan="3">
+    <widget class="QCheckBox" name="rotateDatasets">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The orientation of the tilt series does match what Tomviz expects internally. Rotating the data ensures that the later Tomviz operators will be able to run properly.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Rotate datasets to Tomviz convention?</string>
+     </property>
+     <property name="checked">
+      <bool>true</bool>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="0">
+    <widget class="QLabel" name="filterSIDsLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Filter out SIDs using numpy-like slice syntax. For example: &lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This would only allow every third number between 157394 (inclusive) and 157413 (exclusive) to be shown.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The filtered out SIDs are hidden and won't be used in the next step.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This also supports separate sets of comma-delimited slices, for example:&lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3, 157420:157500:2&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Filter SIDs:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="1" colspan="2">
+    <widget class="QLineEdit" name="filterSIDsString">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Filter out SIDs using numpy-like slice syntax. For example: &lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This would only allow every third number between 157394 (inclusive) and 157413 (exclusive) to be shown.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The filtered out SIDs are hidden and won't be used in the next step.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This also supports separate sets of comma-delimited slices, for example:&lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3, 157420:157500:2&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="1">
+    <widget class="QLineEdit" name="ptychoDirectory">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The Ptycho directory should contain data organized as created from the Ptycho GUI output. It will be used to determine the contents of the table below.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho directory is expected to have, at its top level, a list of scan directories all starting with 'S'. For example, 'S157391' is the directory for scan number 157391.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the scan directory are version directories. For example, 't1'.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the version directories are 'recon_data' and 'recon_pic'. The 'recon_data' should contain all the necessary datasets from the ptychography reconstruction.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+    </widget>
+   </item>
+   <item row="0" column="0" colspan="3">
+    <layout class="QHBoxLayout" name="ptychoGUICommandLayout">
+     <item>
+      <widget class="QLabel" name="ptychoGUICommandLabel">
+       <property name="toolTip">
+        <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Command used when &amp;quot;Start Ptycho GUI&amp;quot; is clicked.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho GUI should be used to download the data and produce image stacks within what will be the &amp;quot;Ptycho Directory&amp;quot;.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+       </property>
+       <property name="text">
+        <string>Start Ptycho GUI Command:</string>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QLineEdit" name="ptychoGUICommand">
+       <property name="toolTip">
+        <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Command used when &amp;quot;Start Ptycho GUI&amp;quot; is clicked.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho GUI should be used to download the data and produce image stacks within what will be the &amp;quot;Ptycho Directory&amp;quot;.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+       </property>
+       <property name="text">
+        <string>run-ptycho</string>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item row="12" column="0" colspan="3">
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
+     </property>
+    </widget>
+   </item>
+   <item row="2" column="0" colspan="3">
+    <widget class="QPushButton" name="startPtychoGUI">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Run the command to start the Ptycho GUI.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho GUI should be used to download the data and produce image stacks within what will be the &amp;quot;Ptycho Directory&amp;quot;.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Start Ptycho GUI</string>
+     </property>
+    </widget>
+   </item>
+   <item row="10" column="0">
+    <widget class="QLabel" name="outputDirectoryLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output files will be written. If one is not specified, the Ptycho directory will be used.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Output Directory:</string>
+     </property>
+     <property name="buddy">
+      <cstring>outputDirectory</cstring>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="2">
+    <widget class="QPushButton" name="selectPtychoDirectory">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The Ptycho directory should contain data organized as created from the Ptycho GUI output. It will be used to determine the contents of the table below.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho directory is expected to have, at its top level, a list of scan directories all starting with 'S'. For example, 'S157391' is the directory for scan number 157391.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the scan directory are version directories. For example, 't1'.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the version directories are 'recon_data' and 'recon_pic'. The 'recon_data' should contain all the necessary datasets from the ptychography reconstruction.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Select</string>
+     </property>
+    </widget>
+   </item>
+   <item row="3" column="0">
+    <widget class="QLabel" name="ptychoDirectoryLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The Ptycho directory should contain data organized as created from the Ptycho GUI output. It will be used to determine the contents of the table below.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The Ptycho directory is expected to have, at its top level, a list of scan directories all starting with 'S'. For example, 'S157391' is the directory for scan number 157391.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the scan directory are version directories. For example, 't1'.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Within the version directories are 'recon_data' and 'recon_pic'. The 'recon_data' should contain all the necessary datasets from the ptychography reconstruction.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Ptycho Directory:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="7" column="0" colspan="3">
+    <widget class="QTableWidget" name="table">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select which SIDs to use for each version.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The list of SIDs to use can be specified via numpy slice syntax (for example, '157391:157637'), a comma-delimited list (for example, '157391, 157394'), or loaded from a txt/csv file.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Any SIDs which are missing data or angles will be automatically ignored. A list of the ones ignored may be seen from the console and messages output.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="editTriggers">
+      <set>QAbstractItemView::NoEditTriggers</set>
+     </property>
+     <property name="selectionMode">
+      <enum>QAbstractItemView::NoSelection</enum>
+     </property>
+     <attribute name="horizontalHeaderStretchLastSection">
+      <bool>true</bool>
+     </attribute>
+    </widget>
+   </item>
+   <item row="10" column="2">
+    <widget class="QPushButton" name="selectOutputDirectory">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output files will be written. If one is not specified, the Ptycho directory will be used.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Select</string>
+     </property>
+    </widget>
+   </item>
+   <item row="4" column="0">
+    <widget class="QLabel" name="loadFromCSVFileLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select a pyxrf-style CSV file from which the &amp;quot;Use&amp;quot; and &amp;quot;Version&amp;quot; settings will be loaded.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This expects columns of &amp;quot;Scan ID&amp;quot;, &amp;quot;Use&amp;quot;, and &amp;quot;Version&amp;quot; to be within the file. If it indeed has these columns (except for &amp;quot;Version&amp;quot;, which is optional), all current SID &amp;quot;Use&amp;quot; settings will be checked off, and only SIDs marked for &amp;quot;Use&amp;quot; within the CSV file will be checked back on.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Additionally, if &amp;quot;Version&amp;quot; is present as well, the version will be automatically selected for each SID, assuming that the version is indeed a viable option within the ptycho directory for that SID.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The user may still modify settings afterwards.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Load settings from CSV:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="4" column="1">
+    <widget class="QLineEdit" name="loadFromCSVFile">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select a pyxrf-style CSV file from which the &amp;quot;Use&amp;quot; and &amp;quot;Version&amp;quot; settings will be loaded.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This expects columns of &amp;quot;Scan ID&amp;quot;, &amp;quot;Use&amp;quot;, and &amp;quot;Version&amp;quot; to be within the file. If it indeed has these columns (except for &amp;quot;Version&amp;quot;, which is optional), all current SID &amp;quot;Use&amp;quot; settings will be checked off, and only SIDs marked for &amp;quot;Use&amp;quot; within the CSV file will be checked back on.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Additionally, if &amp;quot;Version&amp;quot; is present as well, the version will be automatically selected for each SID, assuming that the version is indeed a viable option within the ptycho directory for that SID.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The user may still modify settings afterwards.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+    </widget>
+   </item>
+   <item row="4" column="2">
+    <widget class="QPushButton" name="selectLoadFromCSVFile">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select a pyxrf-style CSV file from which the &amp;quot;Use&amp;quot; and &amp;quot;Version&amp;quot; settings will be loaded.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This expects columns of &amp;quot;Scan ID&amp;quot;, &amp;quot;Use&amp;quot;, and &amp;quot;Version&amp;quot; to be within the file. If it indeed has these columns (except for &amp;quot;Version&amp;quot;, which is optional), all current SID &amp;quot;Use&amp;quot; settings will be checked off, and only SIDs marked for &amp;quot;Use&amp;quot; within the CSV file will be checked back on.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;Additionally, if &amp;quot;Version&amp;quot; is present as well, the version will be automatically selected for each SID, assuming that the version is indeed a viable option within the ptycho directory for that SID.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The user may still modify settings afterwards.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Select</string>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <tabstops>
+  <tabstop>ptychoGUICommand</tabstop>
+  <tabstop>startPtychoGUI</tabstop>
+  <tabstop>ptychoDirectory</tabstop>
+  <tabstop>selectPtychoDirectory</tabstop>
+  <tabstop>loadFromCSVFile</tabstop>
+  <tabstop>selectLoadFromCSVFile</tabstop>
+  <tabstop>filterSIDsString</tabstop>
+  <tabstop>table</tabstop>
+  <tabstop>outputDirectory</tabstop>
+  <tabstop>selectOutputDirectory</tabstop>
+  <tabstop>rotateDatasets</tabstop>
+ </tabstops>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>rejected()</signal>
+   <receiver>PtychoDialog</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>316</x>
+     <y>260</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>
diff --git a/tomviz/PtychoRunner.cxx b/tomviz/PtychoRunner.cxx
new file mode 100644
index 000000000..79d65d3c5
--- /dev/null
+++ b/tomviz/PtychoRunner.cxx
@@ -0,0 +1,324 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#include "PtychoRunner.h"
+
+#include "DataSource.h"
+#include "LoadDataReaction.h"
+#include "ProgressDialog.h"
+#include "PtychoDialog.h"
+#include "PythonUtilities.h"
+#include "Utilities.h"
+
+#include <QDebug>
+#include <QDir>
+#include <QFileInfo>
+#include <QFutureWatcher>
+#include <QMessageBox>
+#include <QPointer>
+#include <QtConcurrent>
+
+namespace tomviz {
+
+class PtychoRunner::Internal : public QObject
+{
+public:
+  QPointer<PtychoRunner> parent;
+  QPointer<QWidget> parentWidget;
+  QPointer<PtychoDialog> ptychoDialog;
+  QPointer<ProgressDialog> progressDialog;
+  QFutureWatcher<bool> ptychoFutureWatcher;
+
+  // Python modules and functions
+  Python::Module ptychoModule;
+  Python::Function stackPtychoFunc;
+
+  // Ptycho options
+  QString ptychoDirectory;
+  QString outputDirectory;
+  bool rotateDatasets = true;
+
+  // These will be generated by calling functions
+  QStringList versionList;
+  QList<long> sidList;
+  QList<double> angleList;
+
+  QStringList outputFiles;
+
+  // Recon options
+  QStringList selectedArrays;
+
+  bool autoLoadFinalData = true;
+
+  Internal(PtychoRunner* p) : parent(p)
+  {
+    setParent(p);
+    parentWidget = mainWidget();
+
+    progressDialog = new ProgressDialog(parentWidget);
+    progressDialog->setWindowTitle("Tomviz");
+    progressDialog->showOutputWidget(true);
+    progressDialog->resize(progressDialog->width(), 500);
+
+    setupConnections();
+  }
+
+  void setupConnections()
+  {
+    connect(&ptychoFutureWatcher, &QFutureWatcher<bool>::finished, this,
+            &Internal::stackPtychoFinished);
+  }
+
+  void importModule()
+  {
+    Python python;
+
+    if (ptychoModule.isValid()) {
+      return;
+    }
+
+    ptychoModule = python.import("tomviz.ptycho");
+    if (!ptychoModule.isValid()) {
+      qCritical() << "Failed to import \"tomviz.ptycho\" module";
+    }
+  }
+
+  bool isInstalled()
+  {
+    importModule();
+
+    Python python;
+
+    auto installed = ptychoModule.findFunction("installed");
+    if (!installed.isValid()) {
+      qCritical() << "Failed to import \"tomviz.ptycho.installed\"";
+      return false;
+    }
+
+    auto res = installed.call();
+
+    if (!res.isValid()) {
+      qCritical() << "Error calling \"tomviz.ptycho.installed\"";
+      return false;
+    }
+
+    return res.toBool();
+  }
+
+  bool onFailure(const QString& msg)
+  {
+    qCritical() << msg;
+    QMessageBox::critical(parentWidget, "Tomviz", msg);
+    return false;
+  }
+
+  QString importError()
+  {
+    importModule();
+
+    Python python;
+
+    auto func = ptychoModule.findFunction("import_error");
+    if (!func.isValid()) {
+      qCritical() << "Failed to import \"tomviz.ptycho.import_error\"";
+      return "import_error not found";
+    }
+
+    auto res = func.call();
+
+    if (!res.isValid()) {
+      qCritical() << "Error calling \"tomviz.ptycho.import_error\"";
+      return "import_error not found";
+    }
+
+    return res.toString();
+  }
+
+  void importFunctions()
+  {
+    importModule();
+
+    Python python;
+
+    if (!stackPtychoFunc.isValid()) {
+      stackPtychoFunc = ptychoModule.findFunction("load_stack_ptycho");
+      if (!stackPtychoFunc.isValid()) {
+        qCritical() << "Failed to find function \"load_stack_ptycho\"";
+      }
+    }
+  }
+
+  template <typename T>
+  void clearWidget(QPointer<T> d)
+  {
+    if (!d) {
+      return;
+    }
+
+    d->hide();
+    d->deleteLater();
+    d.clear();
+  }
+
+  void clear()
+  {
+    clearWidget(ptychoDialog);
+  }
+
+  void start()
+  {
+    clear();
+    importFunctions();
+    showPtychoDialog();
+  }
+
+  void showPtychoDialog()
+  {
+    clearWidget(ptychoDialog);
+
+    ptychoDialog = new PtychoDialog(parentWidget);
+    connect(ptychoDialog.data(), &QDialog::accepted, this,
+            &Internal::ptychoDialogAccepted);
+    ptychoDialog->show();
+  }
+
+  void ptychoDialogAccepted()
+  {
+    // Gather the settings and decide what to do
+    ptychoDirectory = ptychoDialog->ptychoDirectory();
+    sidList = ptychoDialog->selectedSids();
+    versionList = ptychoDialog->selectedVersions();
+    angleList = ptychoDialog->selectedAngles();
+    outputDirectory = ptychoDialog->outputDirectory();
+    rotateDatasets = ptychoDialog->rotateDatasets();
+
+    runStackPtycho();
+  }
+
+  void runStackPtycho()
+  {
+    progressDialog->clearOutputWidget();
+    progressDialog->setText("Stacking ptychography datasets...");
+    progressDialog->show();
+    auto future = QtConcurrent::run(std::bind(&Internal::_runStackPtycho, this));
+    ptychoFutureWatcher.setFuture(future);
+  }
+
+  bool _runStackPtycho()
+  {
+    Python python;
+
+    // Reset the output files
+    outputFiles.clear();
+
+    if (!stackPtychoFunc.isValid()) {
+      qCritical() << "Failed to find function \"load_stack_ptycho\"";
+      return false;
+    }
+
+    Python::Dict kwargs;
+    kwargs.set("version_list", versionList);
+    kwargs.set("sid_list", sidList);
+    kwargs.set("angle_list", angleList);
+    kwargs.set("ptycho_dir", ptychoDirectory);
+    kwargs.set("output_dir", outputDirectory);
+    kwargs.set("rotate_datasets", rotateDatasets);
+    auto result = stackPtychoFunc.call(kwargs);
+
+    if (!result.isValid() || !result.isList()) {
+      qCritical() << "Error calling tomviz.ptycho.load_stack_ptycho";
+      return false;
+    }
+
+    auto resultList = result.toList();
+    for (int i = 0; i < resultList.length(); ++i) {
+      outputFiles.append(resultList[i].toString());
+    }
+
+    return true;
+  }
+
+  void stackPtychoFinished()
+  {
+    progressDialog->accept();
+
+    auto success = ptychoFutureWatcher.result();
+    if (!success || !validateResult()) {
+      QString msg = "Stack ptycho failed";
+      onFailure(msg);
+      // Show the dialog again
+      showPtychoDialog();
+      return;
+    }
+
+    qDebug() << "Results written to:";
+    for (const auto& filePath : outputFiles) {
+      qDebug() << "  " << filePath;
+    }
+
+    if (autoLoadFinalData) {
+      loadOutputFiles();
+    }
+  }
+
+  bool validateResult() const
+  {
+    if (outputFiles.isEmpty()) {
+      return false;
+    }
+
+    for (auto& filePath: outputFiles) {
+      if (!QFile::exists(filePath)) {
+        return false;
+      }
+    }
+
+    return true;
+  }
+
+  void loadOutputFiles()
+  {
+    for (auto& filePath: outputFiles) {
+      auto* dataSource = LoadDataReaction::loadData(filePath);
+      if (!dataSource || !dataSource->imageData()) {
+        qCritical() << "Failed to load file:" << filePath;
+        return;
+      }
+    }
+
+    QString title = "Loading ptycho data complete";
+    auto text =
+      QString("Ptycho data in \"%1\" was written and loaded into Tomviz")
+        .arg(outputDirectory);
+    QMessageBox::information(parentWidget, title, text);
+  }
+};
+
+PtychoRunner::PtychoRunner(QObject* parent)
+  : QObject(parent), m_internal(new Internal(this))
+{
+}
+
+PtychoRunner::~PtychoRunner() = default;
+
+bool PtychoRunner::isInstalled()
+{
+  return m_internal->isInstalled();
+}
+
+QString PtychoRunner::importError()
+{
+  return m_internal->importError();
+}
+
+void PtychoRunner::start()
+{
+  m_internal->start();
+}
+
+void PtychoRunner::setAutoLoadFinalData(bool b)
+{
+  m_internal->autoLoadFinalData = b;
+}
+
+} // namespace tomviz
diff --git a/tomviz/PtychoRunner.h b/tomviz/PtychoRunner.h
new file mode 100644
index 000000000..c3b1da447
--- /dev/null
+++ b/tomviz/PtychoRunner.h
@@ -0,0 +1,37 @@
+/* This source file is part of the Tomviz project, https://tomviz.org/.
+   It is released under the 3-Clause BSD License, see "LICENSE". */
+
+#ifndef tomvizPtychoRunner_h
+#define tomvizPtychoRunner_h
+
+#include <QDialog>
+#include <QScopedPointer>
+
+namespace tomviz {
+
+class PtychoRunner : public QObject
+{
+  Q_OBJECT
+
+public:
+  explicit PtychoRunner(QObject* parent);
+  ~PtychoRunner() override;
+
+  // Returns True if the necessary dependencies are installed
+  bool isInstalled();
+
+  void start();
+
+  // Whether to auto-load the final dataset after it finishes
+  void setAutoLoadFinalData(bool b);
+
+  // Get the import error if the needed modules are not installed
+  QString importError();
+
+private:
+  class Internal;
+  QScopedPointer<Internal> m_internal;
+};
+} // namespace tomviz
+
+#endif
diff --git a/tomviz/PyXRFMakeHDF5Dialog.cxx b/tomviz/PyXRFMakeHDF5Dialog.cxx
index 18c6094db..027dc10c9 100644
--- a/tomviz/PyXRFMakeHDF5Dialog.cxx
+++ b/tomviz/PyXRFMakeHDF5Dialog.cxx
@@ -28,6 +28,7 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
     // Hide the tab bar. We will change pages automatically.
     ui.methodWidget->tabBar()->hide();
 
+    updateEnableStates();
     setupConnections();
   }
 
@@ -35,6 +36,8 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
   {
     connect(ui.method, QOverload<int>::of(&QComboBox::currentIndexChanged),
             this, &Internal::methodChanged);
+    connect(ui.remakeCsvFile, &QCheckBox::toggled, this,
+            &Internal::updateEnableStates);
     connect(ui.selectWorkingDirectory, &QPushButton::clicked, this,
             &Internal::selectWorkingDirectory);
 
@@ -42,6 +45,16 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
             &Internal::accepted);
   }
 
+  QString command() const
+  {
+    return ui.command->text();
+  }
+
+  void setCommand(const QString& cmd)
+  {
+    ui.command->setText(cmd);
+  }
+
   bool useAlreadyExistingData() const
   {
     return ui.method->currentText() == "Already Existing";
@@ -62,6 +75,10 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
 
   void setSuccessfulScansOnly(bool b) { ui.successfulScansOnly->setChecked(b); }
 
+  bool remakeCsvFile() const { return ui.remakeCsvFile->isChecked(); }
+
+  void setRemakeCsvFile(bool b) { ui.remakeCsvFile->setChecked(b); }
+
   QString method() const { return ui.method->currentText(); }
 
   void setMethod(QString s) { ui.method->setCurrentText(s); }
@@ -70,6 +87,7 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
   {
     // The indices match
     ui.methodWidget->setCurrentIndex(i);
+    updateEnableStates();
   }
 
   QString workingDirectory() const { return ui.workingDirectory->text(); }
@@ -150,12 +168,21 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
     return true;
   }
 
+  void updateEnableStates()
+  {
+    bool enable = method() == "New" || remakeCsvFile();
+    ui.scanNumbersGroup->setEnabled(enable);
+  }
+
   void readSettings()
   {
     auto settings = pqApplicationCore::instance()->settings();
     settings->beginGroup("pyxrf");
-    settings->beginGroup("makeHDF5");
 
+    // Do this in the general pyxrf settings
+    setCommand(settings->value("pyxrfUtilsCommand", "pyxrf-utils").toString());
+
+    settings->beginGroup("makeHDF5");
     setMethod(settings->value("method", "New").toString());
     setWorkingDirectory(
       settings->value("workingDirectory", defaultWorkingDirectory())
@@ -164,24 +191,30 @@ class PyXRFMakeHDF5Dialog::Internal : public QObject
     setScanStop(settings->value("scanStop", 0).toInt());
     setSuccessfulScansOnly(
       settings->value("successfulScansOnly", true).toBool());
-
+    setRemakeCsvFile(settings->value("remakeCsvFile", false).toBool());
     settings->endGroup();
+
     settings->endGroup();
+    updateEnableStates();
   }
 
   void writeSettings()
   {
     auto settings = pqApplicationCore::instance()->settings();
     settings->beginGroup("pyxrf");
-    settings->beginGroup("makeHDF5");
 
+    // Do this in the general pyxrf settings
+    settings->setValue("pyxrfUtilsCommand", command());
+
+    settings->beginGroup("makeHDF5");
     settings->setValue("method", method());
     settings->setValue("workingDirectory", workingDirectory());
     settings->setValue("scanStart", scanStart());
     settings->setValue("scanStop", scanStop());
     settings->setValue("successfulScansOnly", successfulScansOnly());
-
+    settings->setValue("remakeCsvFile", remakeCsvFile());
     settings->endGroup();
+
     settings->endGroup();
   }
 };
@@ -199,6 +232,11 @@ void PyXRFMakeHDF5Dialog::show()
   QDialog::show();
 }
 
+QString PyXRFMakeHDF5Dialog::command() const
+{
+  return m_internal->command();
+}
+
 bool PyXRFMakeHDF5Dialog::useAlreadyExistingData() const
 {
   return m_internal->useAlreadyExistingData();
@@ -224,4 +262,9 @@ bool PyXRFMakeHDF5Dialog::successfulScansOnly() const
   return m_internal->successfulScansOnly();
 }
 
+bool PyXRFMakeHDF5Dialog::remakeCsvFile() const
+{
+  return m_internal->remakeCsvFile();
+}
+
 } // namespace tomviz
diff --git a/tomviz/PyXRFMakeHDF5Dialog.h b/tomviz/PyXRFMakeHDF5Dialog.h
index 05e295eae..9e689def7 100644
--- a/tomviz/PyXRFMakeHDF5Dialog.h
+++ b/tomviz/PyXRFMakeHDF5Dialog.h
@@ -19,11 +19,13 @@ class PyXRFMakeHDF5Dialog : public QDialog
 
   void show();
 
+  QString command() const;
   bool useAlreadyExistingData() const;
   QString workingDirectory() const;
   int scanStart() const;
   int scanStop() const;
   bool successfulScansOnly() const;
+  bool remakeCsvFile() const;
 
 private:
   class Internal;
diff --git a/tomviz/PyXRFMakeHDF5Dialog.ui b/tomviz/PyXRFMakeHDF5Dialog.ui
index 0c3500e91..e490abf6c 100644
--- a/tomviz/PyXRFMakeHDF5Dialog.ui
+++ b/tomviz/PyXRFMakeHDF5Dialog.ui
@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>595</width>
-    <height>305</height>
+    <height>341</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -26,50 +26,38 @@
    <property name="bottomMargin">
     <number>6</number>
    </property>
-   <item row="3" column="0">
-    <widget class="QLabel" name="workingDirectoryLabel">
-     <property name="text">
-      <string>Working directory:</string>
-     </property>
-     <property name="buddy">
-      <cstring>workingDirectory</cstring>
-     </property>
-    </widget>
-   </item>
-   <item row="3" column="1">
-    <widget class="QLineEdit" name="workingDirectory"/>
-   </item>
-   <item row="6" column="0" colspan="2">
-    <spacer name="verticalSpacer">
+   <item row="7" column="0" colspan="3">
+    <widget class="QDialogButtonBox" name="buttonBox">
      <property name="orientation">
-      <enum>Qt::Vertical</enum>
+      <enum>Qt::Horizontal</enum>
      </property>
-     <property name="sizeHint" stdset="0">
-      <size>
-       <width>20</width>
-       <height>40</height>
-      </size>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
      </property>
-    </spacer>
+    </widget>
    </item>
-   <item row="3" column="2">
+   <item row="5" column="2">
     <widget class="QPushButton" name="selectWorkingDirectory">
      <property name="text">
       <string>Select</string>
      </property>
     </widget>
    </item>
-   <item row="5" column="0" colspan="3">
-    <widget class="QDialogButtonBox" name="buttonBox">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
-     </property>
-     <property name="standardButtons">
-      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
-     </property>
+   <item row="1" column="1" colspan="2">
+    <widget class="QComboBox" name="method">
+     <item>
+      <property name="text">
+       <string>New</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string>Already Existing</string>
+      </property>
+     </item>
     </widget>
    </item>
-   <item row="1" column="0" colspan="3">
+   <item row="3" column="0" colspan="3">
     <widget class="QTabWidget" name="methodWidget">
      <property name="currentIndex">
       <number>0</number>
@@ -79,49 +67,6 @@
        <string>New Data</string>
       </attribute>
       <layout class="QGridLayout" name="gridLayout_2">
-       <item row="0" column="0" colspan="3">
-        <widget class="QGroupBox" name="scanNumbersGroup">
-         <property name="title">
-          <string>Scan Numbers</string>
-         </property>
-         <layout class="QHBoxLayout" name="horizontalLayout">
-          <item>
-           <widget class="QLabel" name="scanStartLabel">
-            <property name="text">
-             <string>Start:</string>
-            </property>
-            <property name="buddy">
-             <cstring>scanStart</cstring>
-            </property>
-           </widget>
-          </item>
-          <item>
-           <widget class="QSpinBox" name="scanStart">
-            <property name="maximum">
-             <number>100000000</number>
-            </property>
-           </widget>
-          </item>
-          <item>
-           <widget class="QLabel" name="scanStopLabel">
-            <property name="text">
-             <string>Stop:</string>
-            </property>
-            <property name="buddy">
-             <cstring>scanStop</cstring>
-            </property>
-           </widget>
-          </item>
-          <item>
-           <widget class="QSpinBox" name="scanStop">
-            <property name="maximum">
-             <number>100000000</number>
-            </property>
-           </widget>
-          </item>
-         </layout>
-        </widget>
-       </item>
        <item row="2" column="0" colspan="3">
         <widget class="QCheckBox" name="successfulScansOnly">
          <property name="text">
@@ -135,10 +80,22 @@
       <attribute name="title">
        <string>Already Existing</string>
       </attribute>
+      <layout class="QGridLayout" name="gridLayout_3">
+       <item row="0" column="0">
+        <widget class="QCheckBox" name="remakeCsvFile">
+         <property name="text">
+          <string>Remake CSV file?</string>
+         </property>
+        </widget>
+       </item>
+      </layout>
      </widget>
     </widget>
    </item>
-   <item row="0" column="0">
+   <item row="5" column="1">
+    <widget class="QLineEdit" name="workingDirectory"/>
+   </item>
+   <item row="1" column="0">
     <widget class="QLabel" name="methodLabel">
      <property name="text">
       <string>Method:</string>
@@ -149,22 +106,95 @@
     </widget>
    </item>
    <item row="0" column="1" colspan="2">
-    <widget class="QComboBox" name="method">
-     <item>
-      <property name="text">
-       <string>New</string>
-      </property>
-     </item>
-     <item>
-      <property name="text">
-       <string>Already Existing</string>
-      </property>
-     </item>
+    <widget class="QLineEdit" name="command">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Command for running pyxrf-utils, which will be used to run the make-hdf5 command.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>pyxrf-utils</string>
+     </property>
+    </widget>
+   </item>
+   <item row="8" column="0" colspan="2">
+    <spacer name="verticalSpacer">
+     <property name="orientation">
+      <enum>Qt::Vertical</enum>
+     </property>
+     <property name="sizeHint" stdset="0">
+      <size>
+       <width>20</width>
+       <height>40</height>
+      </size>
+     </property>
+    </spacer>
+   </item>
+   <item row="5" column="0">
+    <widget class="QLabel" name="workingDirectoryLabel">
+     <property name="text">
+      <string>Working directory:</string>
+     </property>
+     <property name="buddy">
+      <cstring>workingDirectory</cstring>
+     </property>
+    </widget>
+   </item>
+   <item row="0" column="0">
+    <widget class="QLabel" name="commandLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Command for running pyxrf-utils, which will be used to run the make-hdf5 command.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>PyXRF Utils Command:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="4" column="0" colspan="3">
+    <widget class="QGroupBox" name="scanNumbersGroup">
+     <property name="title">
+      <string>Scan Numbers</string>
+     </property>
+     <layout class="QHBoxLayout" name="horizontalLayout">
+      <item>
+       <widget class="QLabel" name="scanStartLabel">
+        <property name="text">
+         <string>Start:</string>
+        </property>
+        <property name="buddy">
+         <cstring>scanStart</cstring>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QSpinBox" name="scanStart">
+        <property name="maximum">
+         <number>100000000</number>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QLabel" name="scanStopLabel">
+        <property name="text">
+         <string>Stop:</string>
+        </property>
+        <property name="buddy">
+         <cstring>scanStop</cstring>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <widget class="QSpinBox" name="scanStop">
+        <property name="maximum">
+         <number>100000000</number>
+        </property>
+       </widget>
+      </item>
+     </layout>
     </widget>
    </item>
   </layout>
  </widget>
  <tabstops>
+  <tabstop>command</tabstop>
   <tabstop>method</tabstop>
   <tabstop>methodWidget</tabstop>
   <tabstop>scanStart</tabstop>
diff --git a/tomviz/PyXRFProcessDialog.cxx b/tomviz/PyXRFProcessDialog.cxx
index 55c0b66a2..d74de1bf7 100644
--- a/tomviz/PyXRFProcessDialog.cxx
+++ b/tomviz/PyXRFProcessDialog.cxx
@@ -37,6 +37,12 @@ class PyXRFProcessDialog::Internal : public QObject
   QList<QStringList> logFileData;
   QMap<QString, int> logFileColumnIndices;
   QMap<int, QString> tableColumns;
+  QMap<QString, int> sidToRow;
+
+  QStringList filteredSidList;
+
+  double pixelSizeX = -1;
+  double pixelSizeY = -1;
 
   Python::Module pyxrfModule;
 
@@ -46,11 +52,7 @@ class PyXRFProcessDialog::Internal : public QObject
     ui.setupUi(p);
     setParent(p);
 
-    // Our embedded python in conda doesn't seem to have its paths set up
-    // correctly. No idea why. Fix it.
-    fixPythonPaths();
-
-    setupTable();
+    setupTableColumns();
     setupComboBoxes();
     setupConnections();
 
@@ -66,6 +68,8 @@ class PyXRFProcessDialog::Internal : public QObject
     connect(ui.startPyXRFGUI, &QPushButton::clicked, this,
             &Internal::startPyXRFGUI);
     connect(ui.logFile, &QLineEdit::textChanged, this, &Internal::updateTable);
+    connect(ui.filterSidsString, &QLineEdit::editingFinished, this,
+            &Internal::onFilterSidsStringChanged);
 
     connect(ui.selectLogFile, &QPushButton::clicked, this,
             &Internal::selectLogFile);
@@ -78,7 +82,7 @@ class PyXRFProcessDialog::Internal : public QObject
             &Internal::accepted);
   }
 
-  void setupTable()
+  void setupTableColumns()
   {
     auto* table = ui.logFileTable;
     auto& columns = tableColumns;
@@ -126,6 +130,8 @@ class PyXRFProcessDialog::Internal : public QObject
       return;
     }
 
+    setHiddenRowsToUnused();
+    readPixelSizes();
     writeLogFile();
     writeSettings();
     parent->accept();
@@ -167,31 +173,67 @@ class PyXRFProcessDialog::Internal : public QObject
       return false;
     }
 
+    if (filteredSidList.isEmpty()) {
+      reason = "No SIDs were selected";
+      return false;
+    }
+
+    // Check if there are any duplicate angles selected
+    QStringList anglesUsed;
+    QStringList anglesDuplicated;
+    for (int i = 0; i < logFileData.size(); ++i) {
+      auto use = logFileValue(i, "Use");
+      if (use != "x" && use != "1") {
+        // This angle wasn't used.
+        continue;
+      }
+
+      auto angle = logFileValue(i, "Theta");
+      if (anglesUsed.contains(angle) && !anglesDuplicated.contains(angle)) {
+        anglesDuplicated.append(angle);
+      }
+
+      anglesUsed.append(angle);
+    }
+
+    if (anglesDuplicated.size() != 0) {
+      QString title = "Duplicate angles detected";
+      QString text = "The following duplicate angles were detected. Proceed anyways?";
+      text += ("\n\n" + anglesDuplicated.join(", "));
+      if (QMessageBox::question(parent, title, text) == QMessageBox::No) {
+        reason = "Rejected proceeding with duplicate angles.";
+        return false;
+      }
+    }
+
     return true;
   }
 
   void updateTable()
   {
     auto* table = ui.logFileTable;
-    table->clearContents();
+    table->clear();
 
     readLogFile();
 
-    table->setRowCount(logFileData.size());
-    for (int i = 0; i < logFileData.size(); ++i) {
-      for (auto j : tableColumns.keys()) {
-        auto column = tableColumns[j];
-        auto value = logFileValue(i, column);
-        if (column == "Use") {
+    setupTableColumns();
+    table->setRowCount(filteredSidList.size());
+    for (int row = 0; row < filteredSidList.size(); ++row) {
+      auto sid = filteredSidList[row];
+      int logFileRow = sidToRow[sid];
+      for (auto col : tableColumns.keys()) {
+        auto columnName = tableColumns[col];
+        auto value = logFileValue(logFileRow, columnName);
+        if (columnName == "Use") {
           // Special case
-          auto* cb = createUseCheckbox(i, value);
-          table->setCellWidget(i, j, cb);
+          auto* cb = createUseCheckbox(row, value);
+          table->setCellWidget(row, col, cb);
           continue;
         }
 
         auto* item = new QTableWidgetItem(value);
         item->setTextAlignment(Qt::AlignCenter);
-        table->setItem(i, j, item);
+        table->setItem(row, col, item);
       }
     }
   }
@@ -201,7 +243,7 @@ class PyXRFProcessDialog::Internal : public QObject
     auto cb = new QCheckBox(parent);
     cb->setChecked(value == "x" || value == "1");
     connect(cb, &QCheckBox::toggled, this, [this, row](bool b) {
-      QString val = b ? "x" : "0";
+      QString val = b ? "1" : "0";
       setLogFileValue(row, "Use", val);
     });
 
@@ -223,6 +265,7 @@ class PyXRFProcessDialog::Internal : public QObject
   {
     logFileData.clear();
     logFileColumnIndices.clear();
+    sidToRow.clear();
 
     QFile file(logFile());
     if (!file.exists()) {
@@ -249,6 +292,101 @@ class PyXRFProcessDialog::Internal : public QObject
       auto line = reader.readLine();
       logFileData.append(line.split(','));
     }
+
+    for (int row = 0; row < logFileData.size(); ++row) {
+      auto sid = logFileValue(row, "Scan ID");
+      sidToRow[sid] = row;
+    }
+
+    updateFilteredSidList();
+  }
+
+  QMap<QString, bool> sidVisibleMap()
+  {
+    QMap<QString, bool> ret;
+    for (auto s : allSids()) {
+      ret[s] = false;
+    }
+
+    for (auto s : filteredSidList) {
+      ret[s] = true;
+    }
+
+    return ret;
+  }
+
+  void setHiddenRowsToUnused()
+  {
+    auto visibleMap = sidVisibleMap();
+    for (int row = 0; row < logFileData.size(); ++row) {
+      auto sid = logFileValue(row, "Scan ID");
+      if (!visibleMap[sid]) {
+        // Make sure "Use" is turned off
+        setLogFileValue(row, "Use", "0");
+      }
+    }
+  }
+
+  void readPixelSizes()
+  {
+    pixelSizeX = -1;
+    pixelSizeY = -1;
+
+    // Find the first selected scan index
+    int firstScanIdx = -1;
+    for (int i = 0; i < logFileData.size(); ++i) {
+      auto use = logFileValue(i, "Use");
+      if (use == "x" || use == "1") {
+        firstScanIdx = i;
+        break;
+      }
+    }
+
+    if (firstScanIdx == -1) {
+      // Don't need to print an error message here, because we have
+      // bigger problems that will be reported elsewhere.
+      return;
+    }
+
+    auto scanId = logFileValue(firstScanIdx, "Scan ID");
+    qInfo() << "Reading pixel sizes from the first checked scan: " << scanId;
+
+    static QStringList columnsNeeded = {
+      "X Start",
+      "X Stop",
+      "Num X",
+      "Y Start",
+      "Y Stop",
+      "Num Y"
+    };
+
+    // We will store the values in here
+    QMap<QString, double> values;
+    for (const auto& colName : columnsNeeded) {
+      auto value = logFileValue(firstScanIdx, colName);
+      if (value.isEmpty()) {
+        qCritical() << "Failed to locate value for column:" << colName;
+        qCritical() << "Pixel sizes will not be set.";
+        return;
+      }
+
+      bool ok;
+      auto valueD = value.toDouble(&ok);
+      if (!ok) {
+        qCritical() << "Failed to convert column value for column" << colName
+                    << "to double. Column value was:" << value;
+        qCritical() << "Pixel sizes will not be set.";
+        return;
+      }
+      values[colName] = valueD;
+    }
+
+    // If we made it here, we must have all column values we need.
+    // Compute and set.
+    pixelSizeX = (values["X Stop"] - values["X Start"]) / values["Num X"] * 1e3;
+    pixelSizeY = (values["Y Stop"] - values["Y Start"]) / values["Num Y"] * 1e3;
+
+    qInfo() << "Pixel sizes determined to be: " << pixelSizeX << pixelSizeY;
   }
 
   void writeLogFile()
@@ -338,59 +476,109 @@ class PyXRFProcessDialog::Internal : public QObject
     logFileData[row][col] = value;
   }
 
-  QString defaultOutputDirectory() { return QDir::home().filePath("recon"); }
+  QStringList allSids()
+  {
+    return sidToRow.keys();
+  }
 
-  void readSettings()
+  void onFilterSidsStringChanged()
   {
-    auto settings = pqApplicationCore::instance()->settings();
-    settings->beginGroup("pyxrf");
-    settings->beginGroup("process");
+    updateTable();
+  }
 
-    // Only set the log file if it isn't already set
-    if (logFile().isEmpty() || !QFile::exists(logFile())) {
-      setLogFile(settings->value("logFile", "").toString());
+  void updateFilteredSidList()
+  {
+    auto filterString = filterSidsString().trimmed();
+    if (filterString.isEmpty()) {
+      filteredSidList = allSids();
+      return;
     }
 
-    setParametersFile(settings->value("parametersFile", "").toString());
-    setIcName(settings->value("icName", "").toString());
-    setOutputDirectory(
-      settings->value("outputDirectory", defaultOutputDirectory()).toString());
+    // Otherwise, run the Python function to filter out the list
+    importModule();
+
+    Python python;
 
-    settings->endGroup();
-    settings->endGroup();
+    auto func = pyxrfModule.findFunction("filter_sids");
+    if (!func.isValid()) {
+      qCritical() << "Failed to import tomviz.pyxrf.filter_sids";
+      return;
+    }
+
+    Python::Dict kwargs;
+    kwargs.set("all_sids", allSids());
+    kwargs.set("filter_string", filterString);
+    auto res = func.call(kwargs);
+
+    if (!res.isValid() || !res.isList()) {
+      qCritical() << "Error calling tomviz.pyxrf.filter_sids";
+      return;
+    }
+
+    filteredSidList.clear();
+    auto resList = res.toList();
+    for (int i = 0; i < resList.length(); ++i) {
+      filteredSidList.append(resList[i].toString());
+    }
   }
 
-  void writeSettings()
+  QString defaultOutputDirectory() { return QDir::home().filePath("recon"); }
+
+  void readSettings()
   {
     auto settings = pqApplicationCore::instance()->settings();
     settings->beginGroup("pyxrf");
-    settings->beginGroup("process");
 
-    settings->setValue("parametersFile", parametersFile());
-    settings->setValue("logFile", logFile());
-    settings->setValue("icName", icName());
-    settings->setValue("outputDirectory", outputDirectory());
+    setCommand(settings->value("pyxrfUtilsCommand", "pyxrf-utils").toString());
 
+    settings->beginGroup("process");
+    // Only load these settings if we are re-using the same previous
+    // working directory. Otherwise, use all new settings
+    auto previousWorkingDir = settings->value("previousProcessWorkingDir", "");
+    setPyxrfGUICommand(
+      settings->value("pyxrfGUICommand", "pyxrf").toString());
+    if (workingDirectory == previousWorkingDir) {
+      if (logFile().isEmpty()) {
+        setLogFile(settings->value("logFile", "").toString());
+      }
+      setFilterSidsString(settings->value("filterSidsString", "").toString());
+      setParametersFile(settings->value("parametersFile", "").toString());
+      setOutputDirectory(
+        settings->value("outputDirectory", defaultOutputDirectory()).toString());
+    }
+    setIcName(settings->value("icName", "sclr1_ch4").toString());
+    setSkipProcessed(settings->value("skipProcessed", true).toBool());
+    setRotateDatasets(
+      settings->value("rotateDatasets", true).toBool());
     settings->endGroup();
+
     settings->endGroup();
+
+    // Table might have been modified from the settings
+    updateTable();
   }
 
-  void fixPythonPaths()
+  void writeSettings()
   {
-    importModule();
+    auto settings = pqApplicationCore::instance()->settings();
+    settings->beginGroup("pyxrf");
 
-    Python python;
+    // Do this in the general pyxrf settings
+    settings->setValue("pyxrfUtilsCommand", command());
 
-    auto func = pyxrfModule.findFunction("fix_python_paths");
-    if (!func.isValid()) {
-      qCritical() << "Failed to import tomviz.pyxrf.fix_python_paths";
-      return;
-    }
+    settings->beginGroup("process");
+    settings->setValue("previousProcessWorkingDir", workingDirectory);
+    settings->setValue("logFile", logFile());
+    settings->setValue("filterSidsString", filterSidsString());
+    settings->setValue("pyxrfGUICommand", pyxrfGUICommand());
+    settings->setValue("parametersFile", parametersFile());
+    settings->setValue("outputDirectory", outputDirectory());
+    settings->setValue("icName", icName());
+    settings->setValue("skipProcessed", skipProcessed());
+    settings->setValue("rotateDatasets", rotateDatasets());
+    settings->endGroup();
 
-    auto res = func.call();
-    if (!res.isValid()) {
-      qCritical() << "Error calling tomviz.pyxrf.fix_python_paths";
-    }
+    settings->endGroup();
   }
 
   QStringList icNames()
@@ -430,7 +618,7 @@ class PyXRFProcessDialog::Internal : public QObject
       return;
     }
 
-    QString program = "pyxrf";
+    QString program = pyxrfGUICommand();
     auto environment = QProcessEnvironment::systemEnvironment();
     if (environment.contains("TOMVIZ_PYXRF_EXECUTABLE")) {
       program = environment.value("TOMVIZ_PYXRF_EXECUTABLE");
@@ -439,6 +627,10 @@ class PyXRFProcessDialog::Internal : public QObject
     QStringList args;
 
     auto* process = new QProcess(this);
+
+    // Forward stdout/stderr to this process
+    process->setProcessChannelMode(QProcess::ForwardedChannels);
+
     process->start(program, args);
 
     pyxrfIsRunning = true;
@@ -477,8 +669,9 @@ class PyXRFProcessDialog::Internal : public QObject
   {
     QString caption = "Select log file";
     QString filter = "*.csv";
+    auto startPath = logFile() != "" ? logFile() : workingDirectory;
     auto file =
-      QFileDialog::getOpenFileName(parent.data(), caption, logFile(), filter);
+      QFileDialog::getOpenFileName(parent.data(), caption, startPath, filter);
     if (file.isEmpty()) {
       return;
     }
@@ -490,8 +683,9 @@ class PyXRFProcessDialog::Internal : public QObject
   {
     QString caption = "Select parameters file";
     QString filter = "*.json";
+    auto startPath = parametersFile() != "" ? parametersFile() : workingDirectory;
     auto file = QFileDialog::getOpenFileName(parent.data(), caption,
-                                             parametersFile(), filter);
+                                             startPath, filter);
     if (file.isEmpty()) {
       return;
     }
@@ -502,8 +696,9 @@ class PyXRFProcessDialog::Internal : public QObject
   void selectOutputDirectory()
   {
     QString caption = "Select output directory";
+    auto startPath = outputDirectory() != "" ? outputDirectory() : workingDirectory;
     auto dir = QFileDialog::getExistingDirectory(parent.data(), caption,
-                                                 outputDirectory());
+                                                 startPath);
     if (dir.isEmpty()) {
       return;
     }
@@ -511,6 +706,14 @@ class PyXRFProcessDialog::Internal : public QObject
     setOutputDirectory(dir);
   }
 
+  QString command() const { return ui.command->text(); }
+
+  void setCommand(const QString& s) { ui.command->setText(s); }
+
+  QString pyxrfGUICommand() const { return ui.pyxrfGUICommand->text(); }
+
+  void setPyxrfGUICommand(const QString& s) { ui.pyxrfGUICommand->setText(s); }
+
   QString parametersFile() const { return ui.parametersFile->text(); }
 
   void setParametersFile(QString s) { ui.parametersFile->setText(s); }
@@ -519,6 +722,10 @@ class PyXRFProcessDialog::Internal : public QObject
 
   void setLogFile(QString s) { ui.logFile->setText(s); }
 
+  QString filterSidsString() const { return ui.filterSidsString->text(); }
+
+  void setFilterSidsString(QString s) const { ui.filterSidsString->setText(s); }
+
   QString icName() const { return ui.icName->currentText(); }
 
   void setIcName(QString s) { ui.icName->setCurrentText(s); }
@@ -526,6 +733,14 @@ class PyXRFProcessDialog::Internal : public QObject
   QString outputDirectory() const { return ui.outputDirectory->text(); }
 
   void setOutputDirectory(QString s) { ui.outputDirectory->setText(s); }
+
+  bool skipProcessed() const { return ui.skipProcessed->isChecked(); }
+
+  void setSkipProcessed(bool b) { ui.skipProcessed->setChecked(b); }
+
+  bool rotateDatasets() const { return ui.rotateDatasets->isChecked(); }
+
+  void setRotateDatasets(bool b) { ui.rotateDatasets->setChecked(b); }
 };
 
 PyXRFProcessDialog::PyXRFProcessDialog(QString workingDirectory,
@@ -542,6 +757,11 @@ void PyXRFProcessDialog::show()
   QDialog::show();
 }
 
+QString PyXRFProcessDialog::command() const
+{
+  return m_internal->command();
+}
+
 QString PyXRFProcessDialog::parametersFile() const
 {
   return m_internal->parametersFile();
@@ -562,4 +782,24 @@ QString PyXRFProcessDialog::outputDirectory() const
   return m_internal->outputDirectory();
 }
 
+double PyXRFProcessDialog::pixelSizeX() const
+{
+  return m_internal->pixelSizeX;
+}
+
+double PyXRFProcessDialog::pixelSizeY() const
+{
+  return m_internal->pixelSizeY;
+}
+
+bool PyXRFProcessDialog::skipProcessed() const
+{
+  return m_internal->skipProcessed();
+}
+
+bool PyXRFProcessDialog::rotateDatasets() const
+{
+  return m_internal->rotateDatasets();
+}
+
 } // namespace tomviz
diff --git a/tomviz/PyXRFProcessDialog.h b/tomviz/PyXRFProcessDialog.h
index 2222962ef..281921236 100644
--- a/tomviz/PyXRFProcessDialog.h
+++ b/tomviz/PyXRFProcessDialog.h
@@ -19,10 +19,15 @@ class PyXRFProcessDialog : public QDialog
 
   virtual void show();
 
+  QString command() const;
   QString parametersFile() const;
   QString logFile() const;
   QString icName() const;
   QString outputDirectory() const;
+  double pixelSizeX() const;
+  double pixelSizeY() const;
+  bool skipProcessed() const;
+  bool rotateDatasets() const;
 
 private:
   class Internal;
diff --git a/tomviz/PyXRFProcessDialog.ui b/tomviz/PyXRFProcessDialog.ui
index 9e73e0235..c7877b7a2 100644
--- a/tomviz/PyXRFProcessDialog.ui
+++ b/tomviz/PyXRFProcessDialog.ui
@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>595</width>
-    <height>377</height>
+    <height>494</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -26,37 +26,84 @@
    <property name="bottomMargin">
     <number>6</number>
    </property>
-   <item row="6" column="2">
-    <widget class="QPushButton" name="selectOutputDirectory">
+   <item row="9" column="1">
+    <widget class="QLineEdit" name="outputDirectory">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output will be written.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+    </widget>
+   </item>
+   <item row="9" column="0">
+    <widget class="QLabel" name="outputDirectoryLabel">
      <property name="toolTip">
       <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output will be written.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="text">
-      <string>Select</string>
+      <string>Output Directory:</string>
+     </property>
+     <property name="buddy">
+      <cstring>outputDirectory</cstring>
      </property>
     </widget>
    </item>
-   <item row="3" column="0" colspan="3">
-    <widget class="QTableWidget" name="logFileTable">
-     <property name="editTriggers">
-      <set>QAbstractItemView::NoEditTriggers</set>
+   <item row="13" column="0" colspan="3">
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
      </property>
-     <property name="selectionMode">
-      <enum>QAbstractItemView::NoSelection</enum>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
      </property>
-     <attribute name="horizontalHeaderStretchLastSection">
+    </widget>
+   </item>
+   <item row="4" column="0">
+    <widget class="QLabel" name="filterSidsLabel">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Filter out SIDs using numpy-like slice syntax. For example: &lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This would only allow every third number between 157394 (inclusive) and 157413 (exclusive) to be shown.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The filtered out SIDs are hidden and won't be used in the next step.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This also supports separate sets of comma-delimited slices, for example:&lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3, 157420:157500:2&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Filter SIDs:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="11" column="0" colspan="3">
+    <widget class="QCheckBox" name="skipProcessed">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;xrf-tomo will store the output from processed scans within the input HDF5 files. If this is checked, any HDF5 files that have already been processed will be skipped over, and their old output re-used.&lt;/p&gt;&lt;p&gt;&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This should be unchecked if you change the parameters file or the normalization channel - otherwise, previously processed files will not be processed with the updated values.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Skip already processed scans?</string>
+     </property>
+     <property name="checked">
       <bool>true</bool>
-     </attribute>
+     </property>
     </widget>
    </item>
-   <item row="7" column="1" colspan="2">
-    <widget class="QComboBox" name="icName">
+   <item row="8" column="2">
+    <widget class="QPushButton" name="selectParametersFile">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Name of the scalar for normalization of fluorescence data.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select the parameters file that was generated using the PyXRF GUI on one of the datasets.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+     </property>
+     <property name="text">
+      <string>Select</string>
      </property>
     </widget>
    </item>
-   <item row="0" column="0" colspan="3">
+   <item row="1" column="0">
+    <widget class="QLabel" name="commandLabel">
+     <property name="text">
+      <string>PyXRF Utils Command:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="1" column="1" colspan="2">
+    <widget class="QLineEdit" name="command">
+     <property name="text">
+      <string>pyxrf-utils</string>
+     </property>
+    </widget>
+   </item>
+   <item row="2" column="0" colspan="3">
     <layout class="QHBoxLayout" name="logFileLayout">
      <item>
       <widget class="QLabel" name="logFileLabel">
@@ -90,101 +137,130 @@
      </item>
     </layout>
    </item>
-   <item row="5" column="0">
-    <widget class="QLabel" name="parametersFileLabel">
+   <item row="6" column="0">
+    <widget class="QLabel" name="pyxrfGUICommandLabel">
+     <property name="text">
+      <string>PyXRF GUI Command:</string>
+     </property>
+    </widget>
+   </item>
+   <item row="10" column="0">
+    <widget class="QLabel" name="icNameLabel">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select the parameters file that was generated using the PyXRF GUI on one of the datasets.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Name of the scalar for normalization of fluorescence data.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="text">
-      <string>Parameters File:</string>
+      <string>Normalization Channel:</string>
      </property>
      <property name="buddy">
-      <cstring>parametersFile</cstring>
+      <cstring>icName</cstring>
      </property>
     </widget>
    </item>
-   <item row="8" column="0" colspan="3">
-    <widget class="QDialogButtonBox" name="buttonBox">
-     <property name="orientation">
-      <enum>Qt::Horizontal</enum>
+   <item row="7" column="0" colspan="3">
+    <widget class="QPushButton" name="startPyXRFGUI">
+     <property name="toolTip">
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Use the PyXRF GUI to generate a parameters file with one of the datasets. Then, select the parameters file below.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
-     <property name="standardButtons">
-      <set>QDialogButtonBox::Close|QDialogButtonBox::Ok</set>
+     <property name="text">
+      <string>Start PyXRF GUI</string>
      </property>
     </widget>
    </item>
-   <item row="5" column="2">
-    <widget class="QPushButton" name="selectParametersFile">
+   <item row="10" column="1" colspan="2">
+    <widget class="QComboBox" name="icName">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select the parameters file that was generated using the PyXRF GUI on one of the datasets.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Name of the scalar for normalization of fluorescence data.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
+    </widget>
+   </item>
+   <item row="6" column="1" colspan="2">
+    <widget class="QLineEdit" name="pyxrfGUICommand">
      <property name="text">
-      <string>Select</string>
+      <string>pyxrf</string>
      </property>
     </widget>
    </item>
-   <item row="6" column="0">
-    <widget class="QLabel" name="outputDirectoryLabel">
+   <item row="9" column="2">
+    <widget class="QPushButton" name="selectOutputDirectory">
      <property name="toolTip">
       <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output will be written.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="text">
-      <string>Output Directory:</string>
-     </property>
-     <property name="buddy">
-      <cstring>outputDirectory</cstring>
+      <string>Select</string>
      </property>
     </widget>
    </item>
-   <item row="4" column="0" colspan="3">
-    <widget class="QPushButton" name="startPyXRFGUI">
+   <item row="8" column="0">
+    <widget class="QLabel" name="parametersFileLabel">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Use the PyXRF GUI to generate a parameters file with one of the datasets. Then, select the parameters file below.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select the parameters file that was generated using the PyXRF GUI on one of the datasets.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="text">
-      <string>Start PyXRF GUI</string>
+      <string>Parameters File:</string>
+     </property>
+     <property name="buddy">
+      <cstring>parametersFile</cstring>
      </property>
     </widget>
    </item>
-   <item row="7" column="0">
-    <widget class="QLabel" name="icNameLabel">
+   <item row="12" column="0" colspan="3">
+    <widget class="QCheckBox" name="rotateDatasets">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Name of the scalar for normalization of fluorescence data.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The orientation of the tilt series from PyXRF does match what Tomviz expects internally. Rotating the data ensures that the later Tomviz operators will be able to run properly.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
      <property name="text">
-      <string>IC Name:</string>
+      <string>Rotate datasets to Tomviz convention?</string>
      </property>
-     <property name="buddy">
-      <cstring>icName</cstring>
+     <property name="checked">
+      <bool>true</bool>
      </property>
     </widget>
    </item>
-   <item row="5" column="1">
+   <item row="8" column="1">
     <widget class="QLineEdit" name="parametersFile">
      <property name="toolTip">
       <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Select the parameters file that was generated using the PyXRF GUI on one of the datasets.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
     </widget>
    </item>
-   <item row="6" column="1">
-    <widget class="QLineEdit" name="outputDirectory">
+   <item row="5" column="0" colspan="3">
+    <widget class="QTableWidget" name="logFileTable">
+     <property name="editTriggers">
+      <set>QAbstractItemView::NoEditTriggers</set>
+     </property>
+     <property name="selectionMode">
+      <enum>QAbstractItemView::NoSelection</enum>
+     </property>
+     <attribute name="horizontalHeaderStretchLastSection">
+      <bool>true</bool>
+     </attribute>
+    </widget>
+   </item>
+   <item row="4" column="1" colspan="2">
+    <widget class="QLineEdit" name="filterSidsString">
      <property name="toolTip">
-      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The directory where the output will be written.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+      <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;Filter out SIDs using numpy-like slice syntax. For example: &lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This would only allow every third number between 157394 (inclusive) and 157413 (exclusive) to be shown.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;The filtered out SIDs are hidden and won't be used in the next step.&lt;br/&gt;&lt;/p&gt;&lt;p&gt;This also supports separate sets of comma-delimited slices, for example:&lt;br/&gt;&lt;/p&gt;&lt;p&gt;157394:157413:3, 157420:157500:2&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
      </property>
     </widget>
    </item>
   </layout>
  </widget>
  <tabstops>
+  <tabstop>command</tabstop>
   <tabstop>logFile</tabstop>
   <tabstop>selectLogFile</tabstop>
+  <tabstop>filterSidsString</tabstop>
   <tabstop>logFileTable</tabstop>
+  <tabstop>pyxrfGUICommand</tabstop>
   <tabstop>startPyXRFGUI</tabstop>
   <tabstop>parametersFile</tabstop>
   <tabstop>selectParametersFile</tabstop>
   <tabstop>outputDirectory</tabstop>
   <tabstop>selectOutputDirectory</tabstop>
   <tabstop>icName</tabstop>
+  <tabstop>skipProcessed</tabstop>
+  <tabstop>rotateDatasets</tabstop>
  </tabstops>
  <resources/>
  <connections>
diff --git a/tomviz/PyXRFRunner.cxx b/tomviz/PyXRFRunner.cxx
index 42b8af5db..66f377d98 100644
--- a/tomviz/PyXRFRunner.cxx
+++ b/tomviz/PyXRFRunner.cxx
@@ -3,6 +3,8 @@
 
 #include "PyXRFRunner.h"
 
+#include "DataSource.h"
+#include "EmdFormat.h"
 #include "LoadDataReaction.h"
 #include "ProgressDialog.h"
 #include "PyXRFMakeHDF5Dialog.h"
@@ -13,11 +15,17 @@
 
 #include <QDebug>
 #include <QDir>
-#include <QFutureWatcher>
+#include <QFileInfo>
 #include <QMessageBox>
 #include <QPointer>
+#include <QProcess>
 #include <QtConcurrent>
 
+#include <vtkDataArray.h>
+#include <vtkImageData.h>
+#include <vtkNew.h>
+#include <vtkPointData.h>
+
 namespace tomviz {
 
 class PyXRFRunner::Internal : public QObject
@@ -28,23 +36,24 @@ class PyXRFRunner::Internal : public QObject
   QPointer<PyXRFMakeHDF5Dialog> makeHDF5Dialog;
   QPointer<PyXRFProcessDialog> processDialog;
   QPointer<ProgressDialog> progressDialog;
-  QFutureWatcher<bool> makeHDF5FutureWatcher;
-  QFutureWatcher<bool> processFutureWatcher;
+  QProcess makeHDF5Process;
+  QProcess remakeCsvFileProcess;
+  QProcess processProjectionsProcess;
 
   // Python modules and functions
   Python::Module pyxrfModule;
-  Python::Function makeHDF5Func;
-  Python::Function processProjectionsFunc;
 
   // Options we will use as arguments to various pieces
 
   // General options
   QString workingDirectory;
+  QString pyxrfUtilsCommand;
 
   // Make HDF5 options
   int scanStart = 0;
   int scanStop = 0;
   bool successfulScansOnly = true;
+  bool remakeCsvFile = false;
   QString defaultLogFileName = "tomo_info.csv";
 
   // Process projection options
@@ -53,10 +62,15 @@ class PyXRFRunner::Internal : public QObject
   QString icName;
   QString outputDirectory;
   bool skipProcessed = true;
+  double pixelSizeX = -1;
+  double pixelSizeY = -1;
+  bool rotateDatasets = true;
 
   // Recon options
   QStringList selectedElements;
 
+  bool autoLoadFinalData = true;
+
   Internal(PyXRFRunner* p) : parent(p)
   {
     setParent(p);
@@ -72,10 +86,27 @@ class PyXRFRunner::Internal : public QObject
 
   void setupConnections()
   {
-    connect(&makeHDF5FutureWatcher, &QFutureWatcher<bool>::finished, this,
+    connect(&makeHDF5Process, &QProcess::finished, this,
             &Internal::makeHDF5Finished);
-    connect(&processFutureWatcher, &QFutureWatcher<bool>::finished, this,
+    connect(&makeHDF5Process, &QProcess::readyReadStandardOutput, this,
+            &Internal::_printProcStdout);
+    connect(&makeHDF5Process, &QProcess::readyReadStandardError, this,
+            &Internal::_printProcStderr);
+
+    connect(&remakeCsvFileProcess, &QProcess::finished, this,
+            &Internal::remakeCsvFileFinished);
+    connect(&remakeCsvFileProcess, &QProcess::readyReadStandardOutput, this,
+            &Internal::_printProcStdout);
+    connect(&remakeCsvFileProcess, &QProcess::readyReadStandardError, this,
+            &Internal::_printProcStderr);
+
+
+    connect(&processProjectionsProcess, &QProcess::finished, this,
             &Internal::processProjectionsFinished);
+    connect(&processProjectionsProcess, &QProcess::readyReadStandardOutput, this,
+            &Internal::_printProcStdout);
+    connect(&processProjectionsProcess, &QProcess::readyReadStandardError, this,
+            &Internal::_printProcStderr);
   }
 
   void importModule()
@@ -139,22 +170,6 @@ class PyXRFRunner::Internal : public QObject
   void importFunctions()
   {
     importModule();
-
-    Python python;
-
-    if (!makeHDF5Func.isValid()) {
-      makeHDF5Func = pyxrfModule.findFunction("make_hdf5");
-      if (!makeHDF5Func.isValid()) {
-        qCritical() << "Failed to find function \"make_hdf5\"";
-      }
-    }
-
-    if (!processProjectionsFunc.isValid()) {
-      processProjectionsFunc = pyxrfModule.findFunction("process_projections");
-      if (!processProjectionsFunc.isValid()) {
-        qCritical() << "Failed to find function \"process_projections\"";
-      }
-    }
   }
 
   template <typename T>
@@ -178,7 +193,7 @@ class PyXRFRunner::Internal : public QObject
   void start()
   {
     clear();
-    importFunctions();
+    importModule();
     showMakeHDF5Dialog();
   }
 
@@ -195,15 +210,21 @@ class PyXRFRunner::Internal : public QObject
   void makeHDF5DialogAccepted()
   {
     // Gather the settings and decide what to do
+    pyxrfUtilsCommand = makeHDF5Dialog->command();
     workingDirectory = makeHDF5Dialog->workingDirectory();
     scanStart = makeHDF5Dialog->scanStart();
     scanStop = makeHDF5Dialog->scanStop();
     successfulScansOnly = makeHDF5Dialog->successfulScansOnly();
+    remakeCsvFile = makeHDF5Dialog->remakeCsvFile();
 
     auto useAlreadyExistingData = makeHDF5Dialog->useAlreadyExistingData();
     if (useAlreadyExistingData) {
-      // Proceed to the next step
-      showProcessProjectionsDialog();
+      if (remakeCsvFile) {
+        runRemakeCsvFile();
+      } else {
+        // Proceed to the next step
+        showProcessProjectionsDialog();
+      }
     } else {
       runMakeHDF5();
     }
@@ -214,44 +235,71 @@ class PyXRFRunner::Internal : public QObject
     progressDialog->clearOutputWidget();
     progressDialog->setText("Generating HDF5 Files...");
     progressDialog->show();
-    auto future = QtConcurrent::run(std::bind(&Internal::_runMakeHDF5, this));
-    makeHDF5FutureWatcher.setFuture(future);
+
+    QString program = pyxrfUtilsCommand;
+    QStringList args;
+
+    args << "make-hdf5" << workingDirectory
+         << "-s" << QString::number(scanStart)
+         << "-e" << QString::number(scanStop)
+         << "-l" << defaultLogFileName;
+
+    if (successfulScansOnly) {
+      args.append("-b");
+    }
+
+    qInfo() << "Running:" << program + " " + args.join(" ");
+    makeHDF5Process.start(program, args);
   }
 
-  bool _runMakeHDF5()
+  void makeHDF5Finished()
   {
-    Python python;
+    progressDialog->accept();
 
-    if (!makeHDF5Func.isValid()) {
-      qCritical() << "Failed to find function \"make_hdf5\"";
-      return false;
+    auto success = makeHDF5Process.exitStatus() == QProcess::NormalExit;
+    if (!success) {
+      QString msg = "Make HDF5 failed";
+      qCritical() << msg;
+      QMessageBox::critical(parentWidget, "Tomviz", msg);
+      // Show the dialog again
+      showMakeHDF5Dialog();
+      return;
     }
 
-    Python::Dict kwargs;
-    kwargs.set("start_scan", scanStart);
-    kwargs.set("stop_scan", scanStop);
-    kwargs.set("successful_scans_only", successfulScansOnly);
-    kwargs.set("working_directory", workingDirectory);
-    kwargs.set("log_file_name", defaultLogFileName);
-    auto res = makeHDF5Func.call(kwargs);
+    showProcessProjectionsDialog();
+  }
 
-    if (!res.isValid()) {
-      qCritical() << "Error calling tomviz.pyxrf.make_hdf5";
-      return false;
-    }
+  void runRemakeCsvFile()
+  {
+    progressDialog->clearOutputWidget();
+    progressDialog->setText("Remaking CSV file...");
+    progressDialog->show();
 
-    return true;
+    QString program = pyxrfUtilsCommand;
+    QStringList args;
+
+    QString rangeString = QString::number(scanStart) +
+                          ":" + QString::number(scanStop + 1);
+    args << "make-csv" << "-i"
+         << "-w" << workingDirectory
+         << "-s" << rangeString
+         << defaultLogFileName;
+
+    qInfo() << "Running:" << program + " " + args.join(" ");
+    remakeCsvFileProcess.start(program, args);
   }
 
-  void makeHDF5Finished()
+  void remakeCsvFileFinished()
   {
     progressDialog->accept();
 
-    auto success = makeHDF5FutureWatcher.result();
+    auto success = remakeCsvFileProcess.exitStatus() == QProcess::NormalExit;
     if (!success) {
-      QString msg = "Make HDF5 failed";
+      QString msg = "Remake CSV file failed";
       qCritical() << msg;
       QMessageBox::critical(parentWidget, "Tomviz", msg);
+      // Show the dialog again
+      showMakeHDF5Dialog();
       return;
     }
 
@@ -271,6 +319,10 @@ class PyXRFRunner::Internal : public QObject
     processDialog = new PyXRFProcessDialog(workingDirectory, parentWidget);
     connect(processDialog.data(), &QDialog::accepted, this,
             &Internal::processDialogAccepted);
+    // If the user rejects the process dialog, go back to
+    // the make HDF5 dialog.
+    connect(processDialog.data(), &QDialog::rejected, this,
+            &Internal::showMakeHDF5Dialog);
     processDialog->show();
   }
 
@@ -291,10 +343,18 @@ class PyXRFRunner::Internal : public QObject
   void processDialogAccepted()
   {
     // Pull out the options that were chosen
+    pyxrfUtilsCommand = processDialog->command();
     parametersFile = processDialog->parametersFile();
     logFile = processDialog->logFile();
     icName = processDialog->icName();
     outputDirectory = processDialog->outputDirectory();
+    pixelSizeX = processDialog->pixelSizeX();
+    pixelSizeY = processDialog->pixelSizeY();
+    skipProcessed = processDialog->skipProcessed();
+    rotateDatasets = processDialog->rotateDatasets();
+
+    // Make sure the output directory exists
+    QDir().mkpath(outputDirectory);
 
     // Run process projections
     runProcessProjections();
@@ -305,45 +365,77 @@ class PyXRFRunner::Internal : public QObject
     progressDialog->clearOutputWidget();
     progressDialog->setText("Processing projections...");
     progressDialog->show();
-    auto future = QtConcurrent::run(std::bind(&Internal::_runProcessProjections, this));
-    processFutureWatcher.setFuture(future);
+
+    QString program = pyxrfUtilsCommand;
+    QStringList args;
+
+    args << "process-projections" << workingDirectory
+         << "-p" << parametersFile
+         << "-l" << logFile
+         << "-i" << icName
+         << "-o" << outputDirectory;
+
+    if (skipProcessed) {
+      args << "-s";
+    }
+
+    qInfo() << "Running:" << program + " " + args.join(" ");
+    processProjectionsProcess.start(program, args);
   }
 
-  bool _runProcessProjections()
+  void _printProcStdout()
   {
-    Python python;
+    auto* proc = qobject_cast<QProcess*>(sender());
+    if (!proc) {
+      return;
+    }
 
-    if (!processProjectionsFunc.isValid()) {
-      qCritical() << "Failed to find function \"process_projections\"";
-      return false;
+    auto output = proc->readAllStandardOutput();
+    if (output.size() == 0) {
+      return;
     }
 
-    Python::Dict kwargs;
-    kwargs.set("working_directory", workingDirectory);
-    kwargs.set("parameters_file_name", parametersFile);
-    kwargs.set("log_file_name", logFile);
-    kwargs.set("ic_name", icName);
-    kwargs.set("skip_processed", skipProcessed);
-    kwargs.set("output_directory", outputDirectory);
-    auto res = processProjectionsFunc.call(kwargs);
+    // Remove the ending newline because qInfo() will add one
+    if (output.endsWith("\r\n")) {
+      output.chop(2);
+    } else if (output.endsWith('\n')) {
+      output.chop(1);
+    }
+    qInfo() << output.constData();
+  }
 
-    if (!res.isValid()) {
-      qCritical() << "Error calling tomviz.pyxrf.process_projections";
-      return false;
+  void _printProcStderr()
+  {
+    auto* proc = qobject_cast<QProcess*>(sender());
+    if (!proc) {
+      return;
     }
 
-    return true;
+    auto output = proc->readAllStandardError();
+    if (output.size() == 0) {
+      return;
+    }
+
+    // Remove the ending newline because qWarning() will add one
+    if (output.endsWith("\r\n")) {
+      output.chop(2);
+    } else if (output.endsWith('\n')) {
+      output.chop(1);
+    }
+    qWarning() << output.constData();
   }
 
   void processProjectionsFinished()
   {
     progressDialog->accept();
 
-    auto success = processFutureWatcher.result();
+    auto success = processProjectionsProcess.exitStatus() == QProcess::NormalExit;
     if (!success || !validateOutputDirectory()) {
       QString msg = "Process projections failed";
       qCritical() << msg;
       QMessageBox::critical(parentWidget, "Tomviz", msg);
+      // Show the dialog again
+      showProcessProjectionsDialog();
       return;
     }
 
@@ -448,6 +540,9 @@ class PyXRFRunner::Internal : public QObject
     kwargs.set("filename", outputFile());
     kwargs.set("elements", variantList);
     kwargs.set("output_path", outputPath);
+    kwargs.set("rotate_datasets", rotateDatasets);
+    kwargs.set("pixel_size_x", pixelSizeX);
+    kwargs.set("pixel_size_y", pixelSizeY);
     auto res = extractElementsFunc.call(kwargs);
 
     if (!res.isValid()) {
@@ -460,16 +555,66 @@ class PyXRFRunner::Internal : public QObject
       ret.append(item.toString().c_str());
     }
 
-    QString title = "Element extraction complete";
-    auto text =
-      QString("Elements were extracted to \"%1\".\n\nLoad the first one "
-              "(\"%2\") into Tomviz?")
-        .arg(outputPath)
-        .arg(ret[0]);
-    if (QMessageBox::question(parentWidget, title, text) == QMessageBox::Yes) {
-      // Load the first one
-      LoadDataReaction::loadData(ret[0]);
+    if (ret.size() == 0) {
+      qCritical("No elements were extracted");
+      return;
+    }
+
+    if (autoLoadFinalData) {
+      loadElementsIntoArray(ret);
+      QString title = "Element extraction complete";
+      auto text =
+        QString("Elements were extracted to \"%1\" and loaded into Tomviz")
+          .arg(outputPath);
+      QMessageBox::information(parentWidget, title, text);
+    }
+  }
+
+  void loadElementsIntoArray(const QStringList& fileList) {
+    // Load the first file into a DataSource
+    auto* dataSource = LoadDataReaction::loadData(fileList[0]);
+    if (!dataSource || !dataSource->imageData()) {
+      qCritical() << "Failed to load file:" << fileList[0];
+      return;
+    }
+
+    auto* rootImageData = dataSource->imageData();
+    auto* rootPointData = rootImageData->GetPointData();
+    auto newRootName = QFileInfo(fileList[0]).baseName();
+    rootPointData->GetScalars()->SetName(newRootName.toStdString().c_str());
+
+    // The other files should have identical metadata. We'll just load
+    // the image data for those, and add them to the point data.
+    EmdFormat format;
+    for (int i = 1; i < fileList.size(); ++i) {
+      vtkNew<vtkImageData> imageData;
+      format.read(fileList[i].toStdString(), imageData);
+      if (!imageData || !imageData->GetPointData()->GetScalars()) {
+        qCritical() << "Failed to read image data for file:" << fileList[i];
+        continue;
+      }
+
+      auto* scalars = imageData->GetPointData()->GetScalars();
+      auto newName = QFileInfo(fileList[i]).baseName();
+      scalars->SetName(newName.toStdString().c_str());
+
+      // Add the array to the root image data
+      rootPointData->AddArray(scalars);
     }
+
+    // Sort the list, and make the first one alphabetically be selected
+    auto sortedList = fileList;
+    sortedList.sort();
+    auto firstName = QFileInfo(sortedList[0]).baseName();
+
+    dataSource->setActiveScalars(firstName.toStdString().c_str());
+    dataSource->setLabel("Extracted Elements");
+    dataSource->dataModified();
+
+    // Write this to an EMD format
+    QString saveFile = QFileInfo(sortedList[0]).dir().absoluteFilePath("extracted_elements.emd");
+    EmdFormat::write(saveFile.toStdString(), dataSource);
+    dataSource->setFileName(saveFile);
   }
 };
 
@@ -495,4 +640,9 @@ void PyXRFRunner::start()
   m_internal->start();
 }
 
+void PyXRFRunner::setAutoLoadFinalData(bool b)
+{
+  m_internal->autoLoadFinalData = b;
+}
+
 } // namespace tomviz
diff --git a/tomviz/PyXRFRunner.h b/tomviz/PyXRFRunner.h
index 8058bce1a..0d900ac56 100644
--- a/tomviz/PyXRFRunner.h
+++ b/tomviz/PyXRFRunner.h
@@ -22,6 +22,9 @@ class PyXRFRunner : public QObject
 
   void start();
 
+  // Whether to auto-load the final dataset after it finishes
+  void setAutoLoadFinalData(bool b);
+
   // Get the import error if the needed modules are not installed
   QString importError();
 
diff --git a/tomviz/PythonUtilities.cxx b/tomviz/PythonUtilities.cxx
index db8d8248a..2e828951e 100644
--- a/tomviz/PythonUtilities.cxx
+++ b/tomviz/PythonUtilities.cxx
@@ -59,6 +59,33 @@ Python::Object::Object(const QString& str)
   m_smartPyObject = new vtkSmartPyObject(toPyObject(str.toStdString()));
 }
 
+Python::Object::Object(const QStringList& list)
+{
+  std::vector<Variant> l;
+  for (const auto& s: list) {
+    l.push_back(s.toStdString());
+  }
+  m_smartPyObject = new vtkSmartPyObject(toPyObject(l));
+}
+
+Python::Object::Object(const QList<long>& list)
+{
+  std::vector<Variant> l;
+  for (const auto& i: list) {
+    l.push_back(i);
+  }
+  m_smartPyObject = new vtkSmartPyObject(toPyObject(l));
+}
+
+Python::Object::Object(const QList<double>& list)
+{
+  std::vector<Variant> l;
+  for (const auto& f: list) {
+    l.push_back(f);
+  }
+  m_smartPyObject = new vtkSmartPyObject(toPyObject(l));
+}
+
 Python::Object::Object(const Variant& value)
 {
   m_smartPyObject = new vtkSmartPyObject(toPyObject(value));
@@ -319,6 +346,14 @@ Python::Object Python::Dict::operator[](const char* key)
   return item;
 }
 
+Python::Object Python::Dict::operator[](const Object& key)
+{
+  PyObject* item = PyDict_GetItem(m_smartPyObject->GetPointer(), key);
+  // Increment ref count as our destructor will decrement it.
+  Py_XINCREF(item);
+  return item;
+}
+
 void Python::Dict::set(const QString& key, const Object& value)
 {
   Python::Object pyKey(key);
diff --git a/tomviz/PythonUtilities.h b/tomviz/PythonUtilities.h
index 14aee9714..22350d78f 100644
--- a/tomviz/PythonUtilities.h
+++ b/tomviz/PythonUtilities.h
@@ -56,6 +56,9 @@ class Python
     Object();
     Object(const Object& other);
     Object(const QString& str);
+    Object(const QStringList& str);
+    Object(const QList<long>& intList);
+    Object(const QList<double>& floatList);
     Object(const Variant& value);
     Object(const DataSourceBase& source);
     Object(PyObject* obj);
@@ -119,6 +122,7 @@ class Python
     Object operator[](const QString& key);
     Object operator[](const std::string& key);
     Object operator[](const char* key);
+    Object operator[](const Object& obj);
     void set(const QString& key, const Object& value);
     void set(const QString& key, const Variant& value);
     QString toString();
diff --git a/tomviz/Tvh5Format.cxx b/tomviz/Tvh5Format.cxx
index 9514d6bb5..6e295d743 100644
--- a/tomviz/Tvh5Format.cxx
+++ b/tomviz/Tvh5Format.cxx
@@ -67,6 +67,11 @@ bool Tvh5Format::write(const std::string& fileName)
   writer.createGroup("/tomviz_datasources");
   auto sources = ModuleManager::instance().allDataSources();
   for (auto* ds : sources) {
+    if (!ds) {
+      // Somehow, invalid data sources ended up in here...
+      continue;
+    }
+
     // Name the group after its id
     auto id = ds->id().toStdString();
 
diff --git a/tomviz/Utilities.cxx b/tomviz/Utilities.cxx
index 8b6d38966..e61bd1210 100644
--- a/tomviz/Utilities.cxx
+++ b/tomviz/Utilities.cxx
@@ -1338,9 +1338,6 @@ double getVoxelValue(vtkImageData* data, const vtkVector3d& point,
     return 0;
   }
 
-  vtkVector3d position;
-  data->GetPoint(pointId, position.GetData());
-
   vtkVector3d origin;
   data->GetOrigin(origin.GetData());
 
@@ -1348,7 +1345,7 @@ double getVoxelValue(vtkImageData* data, const vtkVector3d& point,
   data->GetSpacing(spacing.GetData());
 
   for (int i = 0; i < 3; ++i) {
-    indices[i] = round((position[i] - origin[i]) / spacing[i]);
+    indices[i] = round((point[i] - origin[i]) / spacing[i]);
   }
 
   double scalar = data->GetScalarComponentAsDouble(
diff --git a/tomviz/core/Variant.h b/tomviz/core/Variant.h
index f745c16e3..e2e60b195 100644
--- a/tomviz/core/Variant.h
+++ b/tomviz/core/Variant.h
@@ -4,11 +4,13 @@
 #ifndef tomvizVariant_h
 #define tomvizVariant_h
 
+#ifndef TOMVIZCORE_EXPORT
 #ifdef IS_TOMVIZ_CORE_BUILD
 #include "tomvizcore_export.h"
 #else
 #define TOMVIZCORE_EXPORT
 #endif
+#endif
 
 #include <iostream>
 #include <map>
diff --git a/tomviz/loguru/LICENSE_LOGURU.txt b/tomviz/loguru/LICENSE_LOGURU.txt
new file mode 100644
index 000000000..fdddb29aa
--- /dev/null
+++ b/tomviz/loguru/LICENSE_LOGURU.txt
@@ -0,0 +1,24 @@
+This is free and unencumbered software released into the public domain.
+
+Anyone is free to copy, modify, publish, use, compile, sell, or
+distribute this software, either in source code form or as a compiled
+binary, for any purpose, commercial or non-commercial, and by any
+means.
+
+In jurisdictions that recognize copyright laws, the author or authors
+of this software dedicate any and all copyright interest in the
+software to the public domain. We make this dedication for the benefit
+of the public at large and to the detriment of our heirs and
+successors. We intend this dedication to be an overt act of
+relinquishment in perpetuity of all present and future rights to this
+software under copyright law.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+For more information, please refer to <https://unlicense.org>
diff --git a/tomviz/loguru/README b/tomviz/loguru/README
new file mode 100644
index 000000000..97a6494b7
--- /dev/null
+++ b/tomviz/loguru/README
@@ -0,0 +1,3 @@
+VTK contains loguru, but it does not appear to be compiled with the
+correct settings to print a stack trace. Thus, we have to include and
+compile it on our own...
diff --git a/tomviz/loguru/loguru.cpp b/tomviz/loguru/loguru.cpp
new file mode 100644
index 000000000..431a97159
--- /dev/null
+++ b/tomviz/loguru/loguru.cpp
@@ -0,0 +1,2039 @@
+// Loguru obtained from: https://github.com/emilk/loguru
+// License is: The Unlicense
+#if defined(__GNUC__) || defined(__clang__)
+// Disable all warnings from gcc/clang:
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wpragmas"
+
+#pragma GCC diagnostic ignored "-Wc++98-compat"
+#pragma GCC diagnostic ignored "-Wc++98-compat-pedantic"
+#pragma GCC diagnostic ignored "-Wexit-time-destructors"
+#pragma GCC diagnostic ignored "-Wformat-nonliteral"
+#pragma GCC diagnostic ignored "-Wglobal-constructors"
+#pragma GCC diagnostic ignored "-Wgnu-zero-variadic-macro-arguments"
+#pragma GCC diagnostic ignored "-Wmissing-prototypes"
+#pragma GCC diagnostic ignored "-Wpadded"
+#pragma GCC diagnostic ignored "-Wsign-conversion"
+#pragma GCC diagnostic ignored "-Wunknown-pragmas"
+#pragma GCC diagnostic ignored "-Wunused-macros"
+#pragma GCC diagnostic ignored "-Wzero-as-null-pointer-constant"
+#elif defined(_MSC_VER)
+#pragma warning(push)
+#pragma warning(disable:4365) // conversion from 'X' to 'Y', signed/unsigned mismatch
+#endif
+
+#include "loguru.hpp"
+
+#ifndef LOGURU_HAS_BEEN_IMPLEMENTED
+#define LOGURU_HAS_BEEN_IMPLEMENTED
+
+#define LOGURU_PREAMBLE_WIDTH (53 + LOGURU_THREADNAME_WIDTH + LOGURU_FILENAME_WIDTH)
+
+#undef min
+#undef max
+
+#include <algorithm>
+#include <atomic>
+#include <cctype>
+#include <chrono>
+#include <cstdarg>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <mutex>
+#include <regex>
+#include <string>
+#include <thread>
+#include <vector>
+
+#if LOGURU_SYSLOG
+#include <syslog.h>
+#else
+#define LOG_USER 0
+#endif
+
+#ifdef _WIN32
+	#include <direct.h>
+
+	#define localtime_r(a, b) localtime_s(b, a) // No localtime_r with MSVC, but arguments are swapped for localtime_s
+#else
+	#include <signal.h>
+	#include <sys/stat.h> // mkdir
+	#include <unistd.h>   // STDERR_FILENO
+#endif
+
+#ifdef __linux__
+	#include <linux/limits.h> // PATH_MAX
+#elif !defined(_WIN32)
+	#include <limits.h> // PATH_MAX
+#endif
+
+#ifndef PATH_MAX
+	#define PATH_MAX 1024
+#endif
+
+#ifdef __APPLE__
+	#include "TargetConditionals.h"
+#endif
+
+// TODO: use defined(_POSIX_VERSION) for some of these things?
+
+#if defined(_WIN32) || defined(__CYGWIN__)
+	#define LOGURU_PTHREADS    0
+	#define LOGURU_WINTHREADS  1
+	#ifndef LOGURU_STACKTRACES
+		#define LOGURU_STACKTRACES 0
+	#endif
+#else
+	#define LOGURU_PTHREADS    1
+	#define LOGURU_WINTHREADS  0
+	#ifdef __GLIBC__
+		#ifndef LOGURU_STACKTRACES
+			#define LOGURU_STACKTRACES 1
+		#endif
+	#else
+		#ifndef LOGURU_STACKTRACES
+			#define LOGURU_STACKTRACES 0
+		#endif
+	#endif
+#endif
+
+#if LOGURU_STACKTRACES
+	#include <cxxabi.h>    // for __cxa_demangle
+	#include <dlfcn.h>     // for dladdr
+	#include <execinfo.h>  // for backtrace
+#endif // LOGURU_STACKTRACES
+
+#if LOGURU_PTHREADS
+	#include <pthread.h>
+	#if defined(__FreeBSD__)
+		#include <pthread_np.h>
+		#include <sys/thr.h>
+	#elif defined(__OpenBSD__)
+		#include <pthread_np.h>
+	#endif
+
+	#ifdef __linux__
+		/* On Linux, the default thread name is the same as the name of the binary.
+		   Additionally, all new threads inherit the name of the thread it got forked from.
+		   For this reason, Loguru use the pthread Thread Local Storage
+		   for storing thread names on Linux. */
+		#ifndef LOGURU_PTLS_NAMES
+			#define LOGURU_PTLS_NAMES 1
+		#endif
+	#endif
+#endif
+
+#if LOGURU_WINTHREADS
+	#ifndef _WIN32_WINNT
+		#define _WIN32_WINNT 0x0502
+	#endif
+	#define WIN32_LEAN_AND_MEAN
+	#define NOMINMAX
+	#include <windows.h>
+#endif
+
+#ifndef LOGURU_PTLS_NAMES
+   #define LOGURU_PTLS_NAMES 0
+#endif
+
+LOGURU_ANONYMOUS_NAMESPACE_BEGIN
+
+namespace loguru
+{
+	using namespace std::chrono;
+
+#if LOGURU_WITH_FILEABS
+	struct FileAbs
+	{
+		char path[PATH_MAX];
+		char mode_str[4];
+		Verbosity verbosity;
+		struct stat st;
+		FILE* fp;
+		bool is_reopening = false; // to prevent recursive call in file_reopen.
+		decltype(steady_clock::now()) last_check_time = steady_clock::now();
+	};
+#else
+	typedef FILE* FileAbs;
+#endif
+
+	struct Callback
+	{
+		std::string     id;
+		log_handler_t   callback;
+		void*           user_data;
+		Verbosity       verbosity; // Does not change!
+		close_handler_t close;
+		flush_handler_t flush;
+		unsigned        indentation;
+	};
+
+	using CallbackVec = std::vector<Callback>;
+
+	using StringPair     = std::pair<std::string, std::string>;
+	using StringPairList = std::vector<StringPair>;
+
+	const auto s_start_time = steady_clock::now();
+
+	Verbosity g_stderr_verbosity  = Verbosity_0;
+	bool      g_colorlogtostderr  = true;
+	unsigned  g_flush_interval_ms = 0;
+	bool      g_preamble_header   = true;
+	bool      g_preamble          = true;
+
+	Verbosity g_internal_verbosity = Verbosity_0;
+
+	// Preamble details
+	bool      g_preamble_date     = true;
+	bool      g_preamble_time     = true;
+	bool      g_preamble_uptime   = true;
+	bool      g_preamble_thread   = true;
+	bool      g_preamble_file     = true;
+	bool      g_preamble_verbose  = true;
+	bool      g_preamble_pipe     = true;
+
+	static std::recursive_mutex  s_mutex;
+	static Verbosity             s_max_out_verbosity = Verbosity_OFF;
+	static std::string           s_argv0_filename;
+	static std::string           s_arguments;
+	static char                  s_current_dir[PATH_MAX];
+	static CallbackVec           s_callbacks;
+	static fatal_handler_t       s_fatal_handler   = nullptr;
+	static verbosity_to_name_t   s_verbosity_to_name_callback = nullptr;
+	static name_to_verbosity_t   s_name_to_verbosity_callback = nullptr;
+	static StringPairList        s_user_stack_cleanups;
+	static bool                  s_strip_file_path = true;
+	static std::atomic<unsigned> s_stderr_indentation { 0 };
+
+	// For periodic flushing:
+	static std::thread* s_flush_thread   = nullptr;
+	static bool         s_needs_flushing = false;
+
+	static SignalOptions s_signal_options = SignalOptions::none();
+
+	static const bool s_terminal_has_color = [](){
+		#ifdef _WIN32
+			#ifndef ENABLE_VIRTUAL_TERMINAL_PROCESSING
+			#define ENABLE_VIRTUAL_TERMINAL_PROCESSING  0x0004
+			#endif
+
+			HANDLE hOut = GetStdHandle(STD_OUTPUT_HANDLE);
+			if (hOut != INVALID_HANDLE_VALUE) {
+				DWORD dwMode = 0;
+				GetConsoleMode(hOut, &dwMode);
+				dwMode |= ENABLE_VIRTUAL_TERMINAL_PROCESSING;
+				return SetConsoleMode(hOut, dwMode) != 0;
+			}
+			return false;
+		#else
+			if (!isatty(STDERR_FILENO)) {
+				return false;
+			}
+			if (const char* term = getenv("TERM")) {
+				return 0 == strcmp(term, "cygwin")
+					|| 0 == strcmp(term, "linux")
+					|| 0 == strcmp(term, "rxvt-unicode-256color")
+					|| 0 == strcmp(term, "screen")
+					|| 0 == strcmp(term, "screen-256color")
+					|| 0 == strcmp(term, "screen.xterm-256color")
+					|| 0 == strcmp(term, "tmux-256color")
+					|| 0 == strcmp(term, "xterm")
+					|| 0 == strcmp(term, "xterm-256color")
+					|| 0 == strcmp(term, "xterm-termite")
+					|| 0 == strcmp(term, "xterm-color");
+			} else {
+				return false;
+			}
+		#endif
+	}();
+
+	static void print_preamble_header(char* out_buff, size_t out_buff_size);
+
+	// ------------------------------------------------------------------------------
+	// Colors
+
+	bool terminal_has_color() { return s_terminal_has_color; }
+
+	// Colors
+
+#ifdef _WIN32
+#define VTSEQ(ID) ("\x1b[1;" #ID "m")
+#else
+#define VTSEQ(ID) ("\x1b[" #ID "m")
+#endif
+
+	const char* terminal_black()      { return s_terminal_has_color ? VTSEQ(30) : ""; }
+	const char* terminal_red()        { return s_terminal_has_color ? VTSEQ(31) : ""; }
+	const char* terminal_green()      { return s_terminal_has_color ? VTSEQ(32) : ""; }
+	const char* terminal_yellow()     { return s_terminal_has_color ? VTSEQ(33) : ""; }
+	const char* terminal_blue()       { return s_terminal_has_color ? VTSEQ(34) : ""; }
+	const char* terminal_purple()     { return s_terminal_has_color ? VTSEQ(35) : ""; }
+	const char* terminal_cyan()       { return s_terminal_has_color ? VTSEQ(36) : ""; }
+	const char* terminal_light_gray() { return s_terminal_has_color ? VTSEQ(37) : ""; }
+	const char* terminal_white()      { return s_terminal_has_color ? VTSEQ(37) : ""; }
+	const char* terminal_light_red()  { return s_terminal_has_color ? VTSEQ(91) : ""; }
+	const char* terminal_dim()        { return s_terminal_has_color ? VTSEQ(2)  : ""; }
+
+	// Formating
+	const char* terminal_bold()       { return s_terminal_has_color ? VTSEQ(1) : ""; }
+	const char* terminal_underline()  { return s_terminal_has_color ? VTSEQ(4) : ""; }
+
+	// You should end each line with this!
+	const char* terminal_reset()      { return s_terminal_has_color ? VTSEQ(0) : ""; }
+
+	// ------------------------------------------------------------------------------
+#if LOGURU_WITH_FILEABS
+	void file_reopen(void* user_data);
+	inline FILE* to_file(void* user_data) { return reinterpret_cast<FileAbs*>(user_data)->fp; }
+#else
+	inline FILE* to_file(void* user_data) { return reinterpret_cast<FILE*>(user_data); }
+#endif
+
+	void file_log(void* user_data, const Message& message)
+	{
+#if LOGURU_WITH_FILEABS
+		FileAbs* file_abs = reinterpret_cast<FileAbs*>(user_data);
+		if (file_abs->is_reopening) {
+			return;
+		}
+		// It is better checking file change every minute/hour/day,
+		// instead of doing this every time we log.
+		// Here check_interval is set to zero to enable checking every time;
+		const auto check_interval = seconds(0);
+		if (duration_cast<seconds>(steady_clock::now() - file_abs->last_check_time) > check_interval) {
+			file_abs->last_check_time = steady_clock::now();
+			file_reopen(user_data);
+		}
+		FILE* file = to_file(user_data);
+		if (!file) {
+			return;
+		}
+#else
+		FILE* file = to_file(user_data);
+#endif
+		fprintf(file, "%s%s%s%s\n",
+			message.preamble, message.indentation, message.prefix, message.message);
+		if (g_flush_interval_ms == 0) {
+			fflush(file);
+		}
+	}
+
+	void file_close(void* user_data)
+	{
+		FILE* file = to_file(user_data);
+		if (file) {
+			fclose(file);
+		}
+#if LOGURU_WITH_FILEABS
+		delete reinterpret_cast<FileAbs*>(user_data);
+#endif
+	}
+
+	void file_flush(void* user_data)
+	{
+		FILE* file = to_file(user_data);
+		fflush(file);
+	}
+
+#if LOGURU_WITH_FILEABS
+	void file_reopen(void* user_data)
+	{
+		FileAbs * file_abs = reinterpret_cast<FileAbs*>(user_data);
+		struct stat st;
+		int ret;
+		if (!file_abs->fp || (ret = stat(file_abs->path, &st)) == -1 || (st.st_ino != file_abs->st.st_ino)) {
+			file_abs->is_reopening = true;
+			if (file_abs->fp) {
+				fclose(file_abs->fp);
+			}
+			if (!file_abs->fp) {
+				VLOG_F(g_internal_verbosity, "Reopening file '" LOGURU_FMT(s) "' due to previous error", file_abs->path);
+			}
+			else if (ret < 0) {
+				const auto why = errno_as_text();
+				VLOG_F(g_internal_verbosity, "Reopening file '" LOGURU_FMT(s) "' due to '" LOGURU_FMT(s) "'", file_abs->path, why.c_str());
+			} else {
+				VLOG_F(g_internal_verbosity, "Reopening file '" LOGURU_FMT(s) "' due to file changed", file_abs->path);
+			}
+			// try reopen current file.
+			if (!create_directories(file_abs->path)) {
+				LOG_F(ERROR, "Failed to create directories to '" LOGURU_FMT(s) "'", file_abs->path);
+			}
+			file_abs->fp = fopen(file_abs->path, file_abs->mode_str);
+			if (!file_abs->fp) {
+				LOG_F(ERROR, "Failed to open '" LOGURU_FMT(s) "'", file_abs->path);
+			} else {
+				stat(file_abs->path, &file_abs->st);
+			}
+			file_abs->is_reopening = false;
+		}
+	}
+#endif
+	// ------------------------------------------------------------------------------
+	// ------------------------------------------------------------------------------
+#if LOGURU_SYSLOG
+	void syslog_log(void* /*user_data*/, const Message& message)
+	{
+		/*
+			Level 0: Is reserved for kernel panic type situations.
+			Level 1: Is for Major resource failure.
+			Level 2->7 Application level failures
+		*/
+		int level;
+		if (message.verbosity < Verbosity_FATAL) {
+			level = 1; // System Alert
+		} else {
+			switch(message.verbosity) {
+				case Verbosity_FATAL:   level = 2; break;	// System Critical
+				case Verbosity_ERROR:   level = 3; break;	// System Error
+				case Verbosity_WARNING: level = 4; break;	// System Warning
+				case Verbosity_INFO:    level = 5; break;	// System Notice
+				case Verbosity_1:       level = 6; break;	// System Info
+				default:                level = 7; break;	// System Debug
+			}
+		}
+
+		// Note: We don't add the time info.
+		// This is done automatically by the syslog deamon.
+		// Otherwise log all information that the file log does.
+		syslog(level, "%s%s%s", message.indentation, message.prefix, message.message);
+	}
+
+	void syslog_close(void* /*user_data*/)
+	{
+		closelog();
+	}
+
+	void syslog_flush(void* /*user_data*/)
+	{}
+#endif
+// ------------------------------------------------------------------------------
+	// Helpers:
+
+	Text::~Text() { free(_str); }
+
+#if LOGURU_USE_FMTLIB
+	Text vtextprintf(const char* format, fmt::format_args args)
+	{
+		return Text(STRDUP(fmt::vformat(format, args).c_str()));
+	}
+#else
+	LOGURU_PRINTF_LIKE(1, 0)
+	static Text vtextprintf(const char* format, va_list vlist)
+	{
+#ifdef _WIN32
+		int bytes_needed = _vscprintf(format, vlist);
+		CHECK_F(bytes_needed >= 0, "Bad string format: '%s'", format);
+		char* buff = (char*)malloc(bytes_needed+1);
+		vsnprintf(buff, bytes_needed+1, format, vlist);
+		return Text(buff);
+#else
+		char* buff = nullptr;
+		int result = vasprintf(&buff, format, vlist);
+		CHECK_F(result >= 0, "Bad string format: '" LOGURU_FMT(s) "'", format);
+		return Text(buff);
+#endif
+	}
+
+	Text textprintf(const char* format, ...)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		auto result = vtextprintf(format, vlist);
+		va_end(vlist);
+		return result;
+	}
+#endif
+
+	// Overloaded for variadic template matching.
+	Text textprintf()
+	{
+		return Text(static_cast<char*>(calloc(1, 1)));
+	}
+
+	static const char* indentation(unsigned depth)
+	{
+		static const char buff[] =
+		".   .   .   .   .   .   .   .   .   .   " ".   .   .   .   .   .   .   .   .   .   "
+		".   .   .   .   .   .   .   .   .   .   " ".   .   .   .   .   .   .   .   .   .   "
+		".   .   .   .   .   .   .   .   .   .   " ".   .   .   .   .   .   .   .   .   .   "
+		".   .   .   .   .   .   .   .   .   .   " ".   .   .   .   .   .   .   .   .   .   "
+		".   .   .   .   .   .   .   .   .   .   " ".   .   .   .   .   .   .   .   .   .   ";
+		static const size_t INDENTATION_WIDTH = 4;
+		static const size_t NUM_INDENTATIONS = (sizeof(buff) - 1) / INDENTATION_WIDTH;
+		depth = std::min<unsigned>(depth, NUM_INDENTATIONS);
+		return buff + INDENTATION_WIDTH * (NUM_INDENTATIONS - depth);
+	}
+
+	static void parse_args(int& argc, char* argv[], const char* verbosity_flag)
+	{
+		int arg_dest = 1;
+		int out_argc = argc;
+
+		for (int arg_it = 1; arg_it < argc; ++arg_it) {
+			auto cmd = argv[arg_it];
+			auto arg_len = strlen(verbosity_flag);
+
+			bool last_is_alpha = false;
+			#if LOGURU_USE_LOCALE
+			try {  // locale variant of isalpha will throw on error
+				last_is_alpha = std::isalpha(cmd[arg_len], std::locale(""));
+			}
+			catch (...) {
+				last_is_alpha = std::isalpha(static_cast<int>(cmd[arg_len]));
+			}
+			#else
+			last_is_alpha = std::isalpha(static_cast<int>(cmd[arg_len]));
+			#endif
+
+			if (strncmp(cmd, verbosity_flag, arg_len) == 0 && !last_is_alpha) {
+				out_argc -= 1;
+				auto value_str = cmd + arg_len;
+				if (value_str[0] == '\0') {
+					// Value in separate argument
+					arg_it += 1;
+					CHECK_LT_F(arg_it, argc, "Missing verbosiy level after " LOGURU_FMT(s) "", verbosity_flag);
+					value_str = argv[arg_it];
+					out_argc -= 1;
+				}
+				if (*value_str == '=') { value_str += 1; }
+
+				auto req_verbosity = get_verbosity_from_name(value_str);
+				if (req_verbosity != Verbosity_INVALID) {
+					g_stderr_verbosity = req_verbosity;
+				} else {
+					char* end = 0;
+					g_stderr_verbosity = static_cast<int>(strtol(value_str, &end, 10));
+					CHECK_F(end && *end == '\0',
+						"Invalid verbosity. Expected integer, INFO, WARNING, ERROR or OFF, got '" LOGURU_FMT(s) "'", value_str);
+				}
+			} else {
+				argv[arg_dest++] = argv[arg_it];
+			}
+		}
+
+		argc = out_argc;
+		argv[argc] = nullptr;
+	}
+
+	static long long now_ns()
+	{
+		return duration_cast<nanoseconds>(high_resolution_clock::now().time_since_epoch()).count();
+	}
+
+	// Returns the part of the path after the last / or \ (if any).
+	const char* filename(const char* path)
+	{
+		for (auto ptr = path; *ptr; ++ptr) {
+			if (*ptr == '/' || *ptr == '\\') {
+				path = ptr + 1;
+			}
+		}
+		return path;
+	}
+
+	// ------------------------------------------------------------------------------
+
+	static void on_atexit()
+	{
+		VLOG_F(g_internal_verbosity, "atexit");
+		flush();
+	}
+
+	static void install_signal_handlers(const SignalOptions& signal_options);
+
+	static void write_hex_digit(std::string& out, unsigned num)
+	{
+		DCHECK_LT_F(num, 16u);
+		if (num < 10u) { out.push_back(char('0' + num)); }
+		else { out.push_back(char('A' + num - 10)); }
+	}
+
+	static void write_hex_byte(std::string& out, uint8_t n)
+	{
+		write_hex_digit(out, n >> 4u);
+		write_hex_digit(out, n & 0x0f);
+	}
+
+	static void escape(std::string& out, const std::string& str)
+	{
+		for (char c : str) {
+			/**/ if (c == '\a') { out += "\\a";  }
+			else if (c == '\b') { out += "\\b";  }
+			else if (c == '\f') { out += "\\f";  }
+			else if (c == '\n') { out += "\\n";  }
+			else if (c == '\r') { out += "\\r";  }
+			else if (c == '\t') { out += "\\t";  }
+			else if (c == '\v') { out += "\\v";  }
+			else if (c == '\\') { out += "\\\\"; }
+			else if (c == '\'') { out += "\\\'"; }
+			else if (c == '\"') { out += "\\\""; }
+			else if (c == ' ')  { out += "\\ ";  }
+			else if (0 <= c && c < 0x20) { // ASCI control character:
+			// else if (c < 0x20 || c != (c & 127)) { // ASCII control character or UTF-8:
+				out += "\\x";
+				write_hex_byte(out, static_cast<uint8_t>(c));
+			} else { out += c; }
+		}
+	}
+
+	Text errno_as_text()
+	{
+		char buff[256];
+	#if defined(__GLIBC__) && defined(_GNU_SOURCE)
+		// GNU Version
+		return Text(STRDUP(strerror_r(errno, buff, sizeof(buff))));
+	#elif defined(__APPLE__) || _POSIX_C_SOURCE >= 200112L
+		// XSI Version
+		strerror_r(errno, buff, sizeof(buff));
+		return Text(strdup(buff));
+	#elif defined(_WIN32)
+		strerror_s(buff, sizeof(buff), errno);
+		return Text(STRDUP(buff));
+	#else
+		// Not thread-safe.
+		return Text(STRDUP(strerror(errno)));
+	#endif
+	}
+
+	void init(int& argc, char* argv[], const Options& options)
+	{
+		CHECK_GT_F(argc,       0,       "Expected proper argc/argv");
+		CHECK_EQ_F(argv[argc], nullptr, "Expected proper argc/argv");
+
+		s_argv0_filename = filename(argv[0]);
+
+		#ifdef _WIN32
+			#define getcwd _getcwd
+		#endif
+
+		if (!getcwd(s_current_dir, sizeof(s_current_dir))) {
+			const auto error_text = errno_as_text();
+			LOG_F(WARNING, "Failed to get current working directory: " LOGURU_FMT(s) "", error_text.c_str());
+		}
+
+		s_arguments = "";
+		for (int i = 0; i < argc; ++i) {
+			escape(s_arguments, argv[i]);
+			if (i + 1 < argc) {
+				s_arguments += " ";
+			}
+		}
+
+		if (options.verbosity_flag) {
+			parse_args(argc, argv, options.verbosity_flag);
+		}
+
+		if (const auto main_thread_name = options.main_thread_name) {
+			#if LOGURU_PTLS_NAMES || LOGURU_WINTHREADS
+				set_thread_name(main_thread_name);
+			#elif LOGURU_PTHREADS
+				char old_thread_name[16] = {0};
+				auto this_thread = pthread_self();
+				#if defined(__APPLE__) || defined(__linux__) || defined(__sun)
+					pthread_getname_np(this_thread, old_thread_name, sizeof(old_thread_name));
+				#endif
+				if (old_thread_name[0] == 0) {
+					#ifdef __APPLE__
+						pthread_setname_np(main_thread_name);
+					#elif defined(__FreeBSD__) || defined(__OpenBSD__)
+						pthread_set_name_np(this_thread, main_thread_name);
+					#elif defined(__linux__) || defined(__sun)
+						pthread_setname_np(this_thread, main_thread_name);
+					#endif
+				}
+			#endif // LOGURU_PTHREADS
+		}
+
+		if (g_stderr_verbosity >= Verbosity_INFO) {
+			if (g_preamble_header) {
+				char preamble_explain[LOGURU_PREAMBLE_WIDTH];
+				print_preamble_header(preamble_explain, sizeof(preamble_explain));
+				if (g_colorlogtostderr && s_terminal_has_color) {
+					fprintf(stderr, "%s%s%s\n", terminal_reset(), terminal_dim(), preamble_explain);
+				} else {
+					fprintf(stderr, "%s\n", preamble_explain);
+				}
+			}
+			fflush(stderr);
+		}
+		VLOG_F(g_internal_verbosity, "arguments: " LOGURU_FMT(s) "", s_arguments.c_str());
+		if (strlen(s_current_dir) != 0)
+		{
+			VLOG_F(g_internal_verbosity, "Current dir: " LOGURU_FMT(s) "", s_current_dir);
+		}
+		VLOG_F(g_internal_verbosity, "stderr verbosity: " LOGURU_FMT(d) "", g_stderr_verbosity);
+		VLOG_F(g_internal_verbosity, "-----------------------------------");
+
+		install_signal_handlers(options.signal_options);
+
+		atexit(on_atexit);
+	}
+
+	void shutdown()
+	{
+		VLOG_F(g_internal_verbosity, "loguru::shutdown()");
+		remove_all_callbacks();
+		set_fatal_handler(nullptr);
+		set_verbosity_to_name_callback(nullptr);
+		set_name_to_verbosity_callback(nullptr);
+	}
+
+	void write_date_time(char* buff, unsigned long long buff_size)
+	{
+		auto now = system_clock::now();
+		long long ms_since_epoch = duration_cast<milliseconds>(now.time_since_epoch()).count();
+		time_t sec_since_epoch = time_t(ms_since_epoch / 1000);
+		tm time_info;
+		localtime_r(&sec_since_epoch, &time_info);
+		snprintf(buff, buff_size, "%04d%02d%02d_%02d%02d%02d.%03lld",
+			1900 + time_info.tm_year, 1 + time_info.tm_mon, time_info.tm_mday,
+			time_info.tm_hour, time_info.tm_min, time_info.tm_sec, ms_since_epoch % 1000);
+	}
+
+	const char* argv0_filename()
+	{
+		return s_argv0_filename.c_str();
+	}
+
+	const char* arguments()
+	{
+		return s_arguments.c_str();
+	}
+
+	const char* current_dir()
+	{
+		return s_current_dir;
+	}
+
+	const char* home_dir()
+	{
+		#ifdef __MINGW32__
+			auto home = getenv("USERPROFILE");
+			CHECK_F(home != nullptr, "Missing USERPROFILE");
+			return home;
+		#elif defined(_WIN32)
+			char* user_profile;
+			size_t len;
+			errno_t err = _dupenv_s(&user_profile, &len, "USERPROFILE");
+			CHECK_F(err == 0, "Missing USERPROFILE");
+			return user_profile;
+		#else // _WIN32
+			auto home = getenv("HOME");
+			CHECK_F(home != nullptr, "Missing HOME");
+			return home;
+		#endif // _WIN32
+	}
+
+	void suggest_log_path(const char* prefix, char* buff, unsigned long long buff_size)
+	{
+		if (prefix[0] == '~') {
+			snprintf(buff, buff_size - 1, "%s%s", home_dir(), prefix + 1);
+		} else {
+			snprintf(buff, buff_size - 1, "%s", prefix);
+		}
+
+		// Check for terminating /
+		size_t n = strlen(buff);
+		if (n != 0) {
+			if (buff[n - 1] != '/') {
+				CHECK_F(n + 2 < buff_size, "Filename buffer too small");
+				buff[n] = '/';
+				buff[n + 1] = '\0';
+			}
+		}
+
+	#ifdef _WIN32
+		strncat_s(buff, buff_size - strlen(buff) - 1, s_argv0_filename.c_str(), buff_size - strlen(buff) - 1);
+		strncat_s(buff, buff_size - strlen(buff) - 1, "/",                      buff_size - strlen(buff) - 1);
+		write_date_time(buff + strlen(buff),    buff_size - strlen(buff));
+		strncat_s(buff, buff_size - strlen(buff) - 1, ".log",                   buff_size - strlen(buff) - 1);
+	#else
+		strncat(buff, s_argv0_filename.c_str(), buff_size - strlen(buff) - 1);
+		strncat(buff, "/", buff_size - strlen(buff) - 1);
+		write_date_time(buff + strlen(buff), buff_size - strlen(buff));
+		strncat(buff, ".log", buff_size - strlen(buff) - 1);
+	#endif
+	}
+
+	bool create_directories(const char* file_path_const)
+	{
+		CHECK_F(file_path_const && *file_path_const);
+		char* file_path = STRDUP(file_path_const);
+		for (char* p = strchr(file_path + 1, '/'); p; p = strchr(p + 1, '/')) {
+			*p = '\0';
+
+	#ifdef _WIN32
+			if (_mkdir(file_path) == -1) {
+	#else
+			if (mkdir(file_path, 0755) == -1) {
+	#endif
+				if (errno != EEXIST) {
+					LOG_F(ERROR, "Failed to create directory '" LOGURU_FMT(s) "'", file_path);
+					LOG_IF_F(ERROR, errno == EACCES,       "EACCES");
+					LOG_IF_F(ERROR, errno == ENAMETOOLONG, "ENAMETOOLONG");
+					LOG_IF_F(ERROR, errno == ENOENT,       "ENOENT");
+					LOG_IF_F(ERROR, errno == ENOTDIR,      "ENOTDIR");
+					LOG_IF_F(ERROR, errno == ELOOP,        "ELOOP");
+
+					*p = '/';
+					free(file_path);
+					return false;
+				}
+			}
+			*p = '/';
+		}
+		free(file_path);
+		return true;
+	}
+	bool add_file(const char* path_in, FileMode mode, Verbosity verbosity)
+	{
+		char path[PATH_MAX];
+		if (path_in[0] == '~') {
+			snprintf(path, sizeof(path) - 1, "%s%s", home_dir(), path_in + 1);
+		} else {
+			snprintf(path, sizeof(path) - 1, "%s", path_in);
+		}
+
+		if (!create_directories(path)) {
+			LOG_F(ERROR, "Failed to create directories to '" LOGURU_FMT(s) "'", path);
+		}
+
+		const char* mode_str = (mode == FileMode::Truncate ? "w" : "a");
+		FILE* file;
+	#ifdef _WIN32
+		file = _fsopen(path, mode_str, _SH_DENYNO);
+	#else
+		file = fopen(path, mode_str);
+	#endif
+		if (!file) {
+			LOG_F(ERROR, "Failed to open '" LOGURU_FMT(s) "'", path);
+			return false;
+		}
+#if LOGURU_WITH_FILEABS
+		FileAbs* file_abs = new FileAbs(); // this is deleted in file_close;
+		snprintf(file_abs->path, sizeof(file_abs->path) - 1, "%s", path);
+		snprintf(file_abs->mode_str, sizeof(file_abs->mode_str) - 1, "%s", mode_str);
+		stat(file_abs->path, &file_abs->st);
+		file_abs->fp = file;
+		file_abs->verbosity = verbosity;
+		add_callback(path_in, file_log, file_abs, verbosity, file_close, file_flush);
+#else
+		add_callback(path_in, file_log, file, verbosity, file_close, file_flush);
+#endif
+
+		if (mode == FileMode::Append) {
+			fprintf(file, "\n\n\n\n\n");
+		}
+		if (!s_arguments.empty()) {
+			fprintf(file, "arguments: %s\n", s_arguments.c_str());
+		}
+		if (strlen(s_current_dir) != 0) {
+			fprintf(file, "Current dir: %s\n", s_current_dir);
+		}
+		fprintf(file, "File verbosity level: %d\n", verbosity);
+		if (g_preamble_header) {
+			char preamble_explain[LOGURU_PREAMBLE_WIDTH];
+			print_preamble_header(preamble_explain, sizeof(preamble_explain));
+			fprintf(file, "%s\n", preamble_explain);
+		}
+		fflush(file);
+
+		VLOG_F(g_internal_verbosity, "Logging to '" LOGURU_FMT(s) "', mode: '" LOGURU_FMT(s) "', verbosity: " LOGURU_FMT(d) "", path, mode_str, verbosity);
+		return true;
+	}
+
+	/*
+		Will add syslog as a standard sink for log messages
+		Any logging message with a verbosity lower or equal to
+		the given verbosity will be included.
+
+		This works for Unix like systems (i.e. Linux/Mac)
+		There is no current implementation for Windows (as I don't know the
+		equivalent calls or have a way to test them). If you know please
+		add and send a pull request.
+
+		The code should still compile under windows but will only generate
+		a warning message that syslog is unavailable.
+
+		Search for LOGURU_SYSLOG to find and fix.
+	*/
+	bool add_syslog(const char* app_name, Verbosity verbosity)
+	{
+		return add_syslog(app_name, verbosity, LOG_USER);
+	}
+	bool add_syslog(const char* app_name, Verbosity verbosity, int facility)
+	{
+#if LOGURU_SYSLOG
+		if (app_name == nullptr) {
+			app_name = argv0_filename();
+		}
+		openlog(app_name, 0, facility);
+		add_callback("'syslog'", syslog_log, nullptr, verbosity, syslog_close, syslog_flush);
+
+		VLOG_F(g_internal_verbosity, "Logging to 'syslog' , verbosity: " LOGURU_FMT(d) "", verbosity);
+		return true;
+#else
+		(void)app_name;
+		(void)verbosity;
+		(void)facility;
+		VLOG_F(g_internal_verbosity, "syslog not implemented on this system. Request to install syslog logging ignored.");
+		return false;
+#endif
+	}
+	// Will be called right before abort().
+	void set_fatal_handler(fatal_handler_t handler)
+	{
+		s_fatal_handler = handler;
+	}
+
+	fatal_handler_t get_fatal_handler()
+	{
+		return s_fatal_handler;
+	}
+
+	void set_verbosity_to_name_callback(verbosity_to_name_t callback)
+	{
+		s_verbosity_to_name_callback = callback;
+	}
+
+	void set_name_to_verbosity_callback(name_to_verbosity_t callback)
+	{
+		s_name_to_verbosity_callback = callback;
+	}
+
+	void add_stack_cleanup(const char* find_this, const char* replace_with_this)
+	{
+		if (strlen(find_this) <= strlen(replace_with_this)) {
+			LOG_F(WARNING, "add_stack_cleanup: the replacement should be shorter than the pattern!");
+			return;
+		}
+
+		s_user_stack_cleanups.push_back(StringPair(find_this, replace_with_this));
+	}
+
+	static void on_callback_change()
+	{
+		s_max_out_verbosity = Verbosity_OFF;
+		for (const auto& callback : s_callbacks) {
+			s_max_out_verbosity = std::max(s_max_out_verbosity, callback.verbosity);
+		}
+	}
+
+	void add_callback(
+		const char*     id,
+		log_handler_t   callback,
+		void*           user_data,
+		Verbosity       verbosity,
+		close_handler_t on_close,
+		flush_handler_t on_flush)
+	{
+		std::lock_guard<std::recursive_mutex> lock(s_mutex);
+		s_callbacks.push_back(Callback{id, callback, user_data, verbosity, on_close, on_flush, 0});
+		on_callback_change();
+	}
+
+	// Returns a custom verbosity name if one is available, or nullptr.
+	// See also set_verbosity_to_name_callback.
+	const char* get_verbosity_name(Verbosity verbosity)
+	{
+		auto name = s_verbosity_to_name_callback
+				? (*s_verbosity_to_name_callback)(verbosity)
+				: nullptr;
+
+		// Use standard replacements if callback fails:
+		if (!name)
+		{
+			if (verbosity <= Verbosity_FATAL) {
+				name = "FATL";
+			} else if (verbosity == Verbosity_ERROR) {
+				name = "ERR";
+			} else if (verbosity == Verbosity_WARNING) {
+				name = "WARN";
+			} else if (verbosity == Verbosity_INFO) {
+				name = "INFO";
+			}
+		}
+
+		return name;
+	}
+
+	// Returns Verbosity_INVALID if the name is not found.
+	// See also set_name_to_verbosity_callback.
+	Verbosity get_verbosity_from_name(const char* name)
+	{
+		auto verbosity = s_name_to_verbosity_callback
+				? (*s_name_to_verbosity_callback)(name)
+				: Verbosity_INVALID;
+
+		// Use standard replacements if callback fails:
+		if (verbosity == Verbosity_INVALID) {
+			if (strcmp(name, "OFF") == 0) {
+				verbosity = Verbosity_OFF;
+			} else if (strcmp(name, "INFO") == 0) {
+				verbosity = Verbosity_INFO;
+			} else if (strcmp(name, "WARNING") == 0) {
+				verbosity = Verbosity_WARNING;
+			} else if (strcmp(name, "ERROR") == 0) {
+				verbosity = Verbosity_ERROR;
+			} else if (strcmp(name, "FATAL") == 0) {
+				verbosity = Verbosity_FATAL;
+			}
+		}
+
+		return verbosity;
+	}
+
+	bool remove_callback(const char* id)
+	{
+		std::lock_guard<std::recursive_mutex> lock(s_mutex);
+		auto it = std::find_if(begin(s_callbacks), end(s_callbacks), [&](const Callback& c) { return c.id == id; });
+		if (it != s_callbacks.end()) {
+			if (it->close) { it->close(it->user_data); }
+			s_callbacks.erase(it);
+			on_callback_change();
+			return true;
+		} else {
+			LOG_F(ERROR, "Failed to locate callback with id '" LOGURU_FMT(s) "'", id);
+			return false;
+		}
+	}
+
+	void remove_all_callbacks()
+	{
+		std::lock_guard<std::recursive_mutex> lock(s_mutex);
+		for (auto& callback : s_callbacks) {
+			if (callback.close) {
+				callback.close(callback.user_data);
+			}
+		}
+		s_callbacks.clear();
+		on_callback_change();
+	}
+
+	// Returns the maximum of g_stderr_verbosity and all file/custom outputs.
+	Verbosity current_verbosity_cutoff()
+	{
+		return g_stderr_verbosity > s_max_out_verbosity ?
+			   g_stderr_verbosity : s_max_out_verbosity;
+	}
+
+	// ------------------------------------------------------------------------
+	// Threads names
+
+#if LOGURU_PTLS_NAMES
+	static pthread_once_t s_pthread_key_once = PTHREAD_ONCE_INIT;
+	static pthread_key_t  s_pthread_key_name;
+
+	void make_pthread_key_name()
+	{
+		(void)pthread_key_create(&s_pthread_key_name, free);
+	}
+#endif
+
+#if LOGURU_WINTHREADS
+	// Where we store the custom thread name set by `set_thread_name`
+	char* thread_name_buffer()
+	{
+		__declspec( thread ) static char thread_name[LOGURU_THREADNAME_WIDTH + 1] = {0};
+		return &thread_name[0];
+	}
+#endif // LOGURU_WINTHREADS
+
+	void set_thread_name(const char* name)
+	{
+		#if LOGURU_PTLS_NAMES
+			// Store thread name in thread-local storage at `s_pthread_key_name`
+			(void)pthread_once(&s_pthread_key_once, make_pthread_key_name);
+			(void)pthread_setspecific(s_pthread_key_name, STRDUP(name));
+		#elif LOGURU_PTHREADS
+			// Tell the OS the thread name
+			#ifdef __APPLE__
+				pthread_setname_np(name);
+			#elif defined(__FreeBSD__) || defined(__OpenBSD__)
+				pthread_set_name_np(pthread_self(), name);
+			#elif defined(__linux__) || defined(__sun)
+				pthread_setname_np(pthread_self(), name);
+			#endif
+		#elif LOGURU_WINTHREADS
+			// Store thread name in a thread-local storage:
+			strncpy_s(thread_name_buffer(), LOGURU_THREADNAME_WIDTH + 1, name, _TRUNCATE);
+		#else // LOGURU_PTHREADS
+			// TODO: on these weird platforms we should also store the thread name
+			// in a generic thread-local storage.
+			(void)name;
+		#endif // LOGURU_PTHREADS
+	}
+
+	void get_thread_name(char* buffer, unsigned long long length, bool right_align_hex_id)
+	{
+		CHECK_NE_F(length, 0u, "Zero length buffer in get_thread_name");
+		CHECK_NOTNULL_F(buffer, "nullptr in get_thread_name");
+
+		#if LOGURU_PTLS_NAMES
+			(void)pthread_once(&s_pthread_key_once, make_pthread_key_name);
+			if (const char* name = static_cast<const char*>(pthread_getspecific(s_pthread_key_name))) {
+				snprintf(buffer, static_cast<size_t>(length), "%s", name);
+			} else {
+				buffer[0] = 0;
+			}
+		#elif LOGURU_PTHREADS
+			// Ask the OS about the thread name.
+			// This is what we *want* to do on all platforms, but
+			// only some platforms support it (currently).
+			pthread_getname_np(pthread_self(), buffer, length);
+		#elif LOGURU_WINTHREADS
+			snprintf(buffer, static_cast<size_t>(length), "%s", thread_name_buffer());
+		#else
+			// Thread names unsupported
+			buffer[0] = 0;
+		#endif
+
+		if (buffer[0] == 0) {
+			// We failed to get a readable thread name.
+			// Write a HEX thread ID instead.
+			// We try to get an ID that is the same as the ID you could
+			// read in your debugger, system monitor etc.
+
+			#ifdef __APPLE__
+				uint64_t thread_id;
+				pthread_threadid_np(pthread_self(), &thread_id);
+			#elif defined(__FreeBSD__)
+				long thread_id;
+				(void)thr_self(&thread_id);
+			#elif LOGURU_PTHREADS
+				uint64_t thread_id = pthread_self();
+			#else
+				// This ID does not correllate to anything we can get from the OS,
+				// so this is the worst way to get the ID.
+				const auto thread_id = std::hash<std::thread::id>{}(std::this_thread::get_id());
+			#endif
+
+			if (right_align_hex_id) {
+				snprintf(buffer, static_cast<size_t>(length), "%*X", static_cast<int>(length - 1), static_cast<unsigned>(thread_id));
+			} else {
+				snprintf(buffer, static_cast<size_t>(length), "%X", static_cast<unsigned>(thread_id));
+			}
+		}
+	}
+
+	// ------------------------------------------------------------------------
+	// Stack traces
+
+#if LOGURU_STACKTRACES
+	Text demangle(const char* name)
+	{
+		int status = -1;
+		char* demangled = abi::__cxa_demangle(name, 0, 0, &status);
+		Text result{status == 0 ? demangled : STRDUP(name)};
+		return result;
+	}
+
+	#if LOGURU_RTTI
+		template <class T>
+		std::string type_name()
+		{
+			auto demangled = demangle(typeid(T).name());
+			return demangled.c_str();
+		}
+	#endif // LOGURU_RTTI
+
+	static const StringPairList REPLACE_LIST = {
+		#if LOGURU_RTTI
+			{ type_name<std::string>(),    "std::string"    },
+			{ type_name<std::wstring>(),   "std::wstring"   },
+			{ type_name<std::u16string>(), "std::u16string" },
+			{ type_name<std::u32string>(), "std::u32string" },
+		#endif // LOGURU_RTTI
+		{ "std::__1::",                "std::"          },
+		{ "__thiscall ",               ""               },
+		{ "__cdecl ",                  ""               },
+	};
+
+	void do_replacements(const StringPairList& replacements, std::string& str)
+	{
+		for (auto&& p : replacements) {
+			if (p.first.size() <= p.second.size()) {
+				// On gcc, "type_name<std::string>()" is "std::string"
+				continue;
+			}
+
+			size_t it;
+			while ((it=str.find(p.first)) != std::string::npos) {
+				str.replace(it, p.first.size(), p.second);
+			}
+		}
+	}
+
+	std::string prettify_stacktrace(const std::string& input)
+	{
+		std::string output = input;
+
+		do_replacements(s_user_stack_cleanups, output);
+		do_replacements(REPLACE_LIST, output);
+
+		try {
+			std::regex std_allocator_re(R"(,\s*std::allocator<[^<>]+>)");
+			output = std::regex_replace(output, std_allocator_re, std::string(""));
+
+			std::regex template_spaces_re(R"(<\s*([^<> ]+)\s*>)");
+			output = std::regex_replace(output, template_spaces_re, std::string("<$1>"));
+		} catch (std::regex_error&) {
+			// Probably old GCC.
+		}
+
+		return output;
+	}
+
+	std::string stacktrace_as_stdstring(int skip)
+	{
+		// From https://gist.github.com/fmela/591333
+		void* callstack[128];
+		const auto max_frames = sizeof(callstack) / sizeof(callstack[0]);
+		int num_frames = backtrace(callstack, max_frames);
+		char** symbols = backtrace_symbols(callstack, num_frames);
+
+		std::string result;
+		// Print stack traces so the most relevant ones are written last
+		// Rationale: http://yellerapp.com/posts/2015-01-22-upside-down-stacktraces.html
+		for (int i = num_frames - 1; i >= skip; --i) {
+			char buf[1024];
+			Dl_info info;
+			if (dladdr(callstack[i], &info) && info.dli_sname) {
+				char* demangled = NULL;
+				int status = -1;
+				if (info.dli_sname[0] == '_') {
+					demangled = abi::__cxa_demangle(info.dli_sname, 0, 0, &status);
+				}
+				snprintf(buf, sizeof(buf), "%-3d %*p %s + %zd\n",
+						 i - skip, int(2 + sizeof(void*) * 2), callstack[i],
+						 status == 0 ? demangled :
+						 info.dli_sname == 0 ? symbols[i] : info.dli_sname,
+						 static_cast<char*>(callstack[i]) - static_cast<char*>(info.dli_saddr));
+				free(demangled);
+			} else {
+				snprintf(buf, sizeof(buf), "%-3d %*p %s\n",
+						 i - skip, int(2 + sizeof(void*) * 2), callstack[i], symbols[i]);
+			}
+			result += buf;
+		}
+		free(symbols);
+
+		if (num_frames == max_frames) {
+			result = "[truncated]\n" + result;
+		}
+
+		if (!result.empty() && result[result.size() - 1] == '\n') {
+			result.resize(result.size() - 1);
+		}
+
+		return prettify_stacktrace(result);
+	}
+
+#else // LOGURU_STACKTRACES
+	Text demangle(const char* name)
+	{
+		return Text(STRDUP(name));
+	}
+
+	std::string stacktrace_as_stdstring(int)
+	{
+		// No stacktraces available on this platform"
+		return "";
+	}
+
+#endif // LOGURU_STACKTRACES
+
+	Text stacktrace(int skip)
+	{
+		auto str = stacktrace_as_stdstring(skip + 1);
+		return Text(STRDUP(str.c_str()));
+	}
+
+	// ------------------------------------------------------------------------
+
+	static void print_preamble_header(char* out_buff, size_t out_buff_size)
+	{
+		if (out_buff_size == 0) { return; }
+		out_buff[0] = '\0';
+		size_t pos = 0;
+		if (g_preamble_date && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "date       ");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_time && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "time         ");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_uptime && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "( uptime  ) ");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_thread && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "[%-*s]", LOGURU_THREADNAME_WIDTH, " thread name/id");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_file && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "%*s:line  ", LOGURU_FILENAME_WIDTH, "file");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_verbose && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "   v");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_pipe && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "| ");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+	}
+
+	static void print_preamble(char* out_buff, size_t out_buff_size, Verbosity verbosity, const char* file, unsigned line)
+	{
+		if (out_buff_size == 0) { return; }
+		out_buff[0] = '\0';
+		if (!g_preamble) { return; }
+		long long ms_since_epoch = duration_cast<milliseconds>(system_clock::now().time_since_epoch()).count();
+		time_t sec_since_epoch = time_t(ms_since_epoch / 1000);
+		tm time_info;
+		localtime_r(&sec_since_epoch, &time_info);
+
+		auto uptime_ms = duration_cast<milliseconds>(steady_clock::now() - s_start_time).count();
+		auto uptime_sec = static_cast<double> (uptime_ms) / 1000.0;
+
+		char thread_name[LOGURU_THREADNAME_WIDTH + 1] = {0};
+		get_thread_name(thread_name, LOGURU_THREADNAME_WIDTH + 1, true);
+
+		if (s_strip_file_path) {
+			file = filename(file);
+		}
+
+		char level_buff[6];
+		const char* custom_level_name = get_verbosity_name(verbosity);
+		if (custom_level_name) {
+			snprintf(level_buff, sizeof(level_buff) - 1, "%s", custom_level_name);
+		} else {
+			snprintf(level_buff, sizeof(level_buff) - 1, "% 4d", static_cast<int8_t>(verbosity));
+		}
+
+		size_t pos = 0;
+
+		if (g_preamble_date && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "%04d-%02d-%02d ",
+				                 1900 + time_info.tm_year, 1 + time_info.tm_mon, time_info.tm_mday);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_time && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "%02d:%02d:%02d.%03lld ",
+			                     time_info.tm_hour, time_info.tm_min, time_info.tm_sec, ms_since_epoch % 1000);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_uptime && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "(%8.3fs) ",
+			                     uptime_sec);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_thread && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "[%-*s]",
+			                     LOGURU_THREADNAME_WIDTH, thread_name);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_file && pos < out_buff_size) {
+			char shortened_filename[LOGURU_FILENAME_WIDTH + 1];
+			snprintf(shortened_filename, LOGURU_FILENAME_WIDTH + 1, "%s", file);
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "%*s:%-5u ",
+			                     LOGURU_FILENAME_WIDTH, shortened_filename, line);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_verbose && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "%4s",
+			                     level_buff);
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+		if (g_preamble_pipe && pos < out_buff_size) {
+			int bytes = snprintf(out_buff + pos, out_buff_size - pos, "| ");
+			if (bytes > 0) {
+				pos += bytes;
+			}
+		}
+	}
+
+	// stack_trace_skip is just if verbosity == FATAL.
+	static void log_message(int stack_trace_skip, Message& message, bool with_indentation, bool abort_if_fatal)
+	{
+		const auto verbosity = message.verbosity;
+		std::lock_guard<std::recursive_mutex> lock(s_mutex);
+
+		if (message.verbosity == Verbosity_FATAL) {
+			auto st = loguru::stacktrace(stack_trace_skip + 2);
+			if (!st.empty()) {
+				RAW_LOG_F(ERROR, "Stack trace:\n" LOGURU_FMT(s) "", st.c_str());
+			}
+
+			auto ec = loguru::get_error_context();
+			if (!ec.empty()) {
+				RAW_LOG_F(ERROR, "" LOGURU_FMT(s) "", ec.c_str());
+			}
+		}
+
+		if (with_indentation) {
+			message.indentation = indentation(s_stderr_indentation);
+		}
+
+		if (verbosity <= g_stderr_verbosity) {
+			if (g_colorlogtostderr && s_terminal_has_color) {
+				if (verbosity > Verbosity_WARNING) {
+					fprintf(stderr, "%s%s%s%s%s%s%s%s\n",
+						terminal_reset(),
+						terminal_dim(),
+						message.preamble,
+						message.indentation,
+						verbosity == Verbosity_INFO ? terminal_reset() : "", // un-dim for info
+						message.prefix,
+						message.message,
+						terminal_reset());
+				} else {
+					fprintf(stderr, "%s%s%s%s%s%s%s\n",
+						terminal_reset(),
+						verbosity == Verbosity_WARNING ? terminal_yellow() : terminal_red(),
+						message.preamble,
+						message.indentation,
+						message.prefix,
+						message.message,
+						terminal_reset());
+				}
+			} else {
+				fprintf(stderr, "%s%s%s%s\n",
+					message.preamble, message.indentation, message.prefix, message.message);
+			}
+
+			if (g_flush_interval_ms == 0) {
+				fflush(stderr);
+			} else {
+				s_needs_flushing = true;
+			}
+		}
+
+		for (auto& p : s_callbacks) {
+			if (verbosity <= p.verbosity) {
+				if (with_indentation) {
+					message.indentation = indentation(p.indentation);
+				}
+				p.callback(p.user_data, message);
+				if (g_flush_interval_ms == 0) {
+					if (p.flush) { p.flush(p.user_data); }
+				} else {
+					s_needs_flushing = true;
+				}
+			}
+		}
+
+		if (g_flush_interval_ms > 0 && !s_flush_thread) {
+			s_flush_thread = new std::thread([](){
+				for (;;) {
+					if (s_needs_flushing) {
+						flush();
+					}
+					std::this_thread::sleep_for(std::chrono::milliseconds(g_flush_interval_ms));
+				}
+			});
+		}
+
+		if (message.verbosity == Verbosity_FATAL) {
+			flush();
+
+			if (s_fatal_handler) {
+				s_fatal_handler(message);
+				flush();
+			}
+
+			if (abort_if_fatal) {
+#if !defined(_WIN32)
+				if (s_signal_options.sigabrt) {
+					// Make sure we don't catch our own abort:
+					signal(SIGABRT, SIG_DFL);
+				}
+#endif
+				abort();
+			}
+		}
+	}
+
+	// stack_trace_skip is just if verbosity == FATAL.
+	void log_to_everywhere(int stack_trace_skip, Verbosity verbosity,
+	                       const char* file, unsigned line,
+	                       const char* prefix, const char* buff)
+	{
+		char preamble_buff[LOGURU_PREAMBLE_WIDTH];
+		print_preamble(preamble_buff, sizeof(preamble_buff), verbosity, file, line);
+		auto message = Message{verbosity, file, line, preamble_buff, "", prefix, buff};
+		log_message(stack_trace_skip + 1, message, true, true);
+	}
+
+#if LOGURU_USE_FMTLIB
+	void vlog(Verbosity verbosity, const char* file, unsigned line, const char* format, fmt::format_args args)
+	{
+		auto formatted = fmt::vformat(format, args);
+		log_to_everywhere(1, verbosity, file, line, "", formatted.c_str());
+	}
+
+	void raw_vlog(Verbosity verbosity, const char* file, unsigned line, const char* format, fmt::format_args args)
+	{
+		auto formatted = fmt::vformat(format, args);
+		auto message = Message{verbosity, file, line, "", "", "", formatted.c_str()};
+		log_message(1, message, false, true);
+	}
+#else
+	void log(Verbosity verbosity, const char* file, unsigned line, const char* format, ...)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		vlog(verbosity, file, line, format, vlist);
+		va_end(vlist);
+	}
+
+	void vlog(Verbosity verbosity, const char* file, unsigned line, const char* format, va_list vlist)
+	{
+		auto buff = vtextprintf(format, vlist);
+		log_to_everywhere(1, verbosity, file, line, "", buff.c_str());
+	}
+
+	void raw_log(Verbosity verbosity, const char* file, unsigned line, const char* format, ...)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		auto buff = vtextprintf(format, vlist);
+		auto message = Message{verbosity, file, line, "", "", "", buff.c_str()};
+		log_message(1, message, false, true);
+		va_end(vlist);
+	}
+#endif
+
+	void flush()
+	{
+		std::lock_guard<std::recursive_mutex> lock(s_mutex);
+		fflush(stderr);
+		for (const auto& callback : s_callbacks)
+		{
+			if (callback.flush) {
+				callback.flush(callback.user_data);
+			}
+		}
+		s_needs_flushing = false;
+	}
+
+	LogScopeRAII::LogScopeRAII(Verbosity verbosity, const char* file, unsigned line, const char* format, va_list vlist) :
+		_verbosity(verbosity), _file(file), _line(line)
+	{
+		this->Init(format, vlist);
+	}
+
+	LogScopeRAII::LogScopeRAII(Verbosity verbosity, const char* file, unsigned line, const char* format, ...) :
+		_verbosity(verbosity), _file(file), _line(line)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		this->Init(format, vlist);
+		va_end(vlist);
+	}
+
+	LogScopeRAII::~LogScopeRAII()
+	{
+		if (_file) {
+			std::lock_guard<std::recursive_mutex> lock(s_mutex);
+			if (_indent_stderr && s_stderr_indentation > 0) {
+				--s_stderr_indentation;
+			}
+			for (auto& p : s_callbacks) {
+				// Note: Callback indentation cannot change!
+				if (_verbosity <= p.verbosity) {
+					// in unlikely case this callback is new
+					if (p.indentation > 0) {
+						--p.indentation;
+					}
+				}
+			}
+#if LOGURU_VERBOSE_SCOPE_ENDINGS
+			auto duration_sec = static_cast<double>(now_ns() - _start_time_ns) / 1e9;
+#if LOGURU_USE_FMTLIB
+			auto buff = textprintf("{:.{}f} s: {:s}", duration_sec, LOGURU_SCOPE_TIME_PRECISION, _name);
+#else
+			auto buff = textprintf("%.*f s: %s", LOGURU_SCOPE_TIME_PRECISION, duration_sec, _name);
+#endif
+			log_to_everywhere(1, _verbosity, _file, _line, "} ", buff.c_str());
+#else
+			log_to_everywhere(1, _verbosity, _file, _line, "}", "");
+#endif
+		}
+	}
+
+	void LogScopeRAII::Init(const char* format, va_list vlist)
+	{
+		if (_verbosity <= current_verbosity_cutoff()) {
+			std::lock_guard<std::recursive_mutex> lock(s_mutex);
+			_indent_stderr = (_verbosity <= g_stderr_verbosity);
+			_start_time_ns = now_ns();
+			vsnprintf(_name, sizeof(_name), format, vlist);
+			log_to_everywhere(1, _verbosity, _file, _line, "{ ", _name);
+
+			if (_indent_stderr) {
+				++s_stderr_indentation;
+			}
+
+			for (auto& p : s_callbacks) {
+				if (_verbosity <= p.verbosity) {
+					++p.indentation;
+				}
+			}
+		} else {
+			_file = nullptr;
+		}
+	}
+
+#if LOGURU_USE_FMTLIB
+	void vlog_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line, const char* format, fmt::format_args args)
+	{
+		auto formatted = fmt::vformat(format, args);
+		log_to_everywhere(stack_trace_skip + 1, Verbosity_FATAL, file, line, expr, formatted.c_str());
+		abort(); // log_to_everywhere already does this, but this makes the analyzer happy.
+	}
+#else
+	void log_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line, const char* format, ...)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		auto buff = vtextprintf(format, vlist);
+		log_to_everywhere(stack_trace_skip + 1, Verbosity_FATAL, file, line, expr, buff.c_str());
+		va_end(vlist);
+		abort(); // log_to_everywhere already does this, but this makes the analyzer happy.
+	}
+#endif
+
+	void log_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line)
+	{
+		log_and_abort(stack_trace_skip + 1, expr, file, line, " ");
+	}
+
+	// ----------------------------------------------------------------------------
+	// Streams:
+
+#if LOGURU_USE_FMTLIB
+	template<typename... Args>
+	std::string vstrprintf(const char* format, const Args&... args)
+	{
+		auto text = textprintf(format, args...);
+		std::string result = text.c_str();
+		return result;
+	}
+
+	template<typename... Args>
+	std::string strprintf(const char* format, const Args&... args)
+	{
+		return vstrprintf(format, args...);
+	}
+#else
+	std::string vstrprintf(const char* format, va_list vlist)
+	{
+		auto text = vtextprintf(format, vlist);
+		std::string result = text.c_str();
+		return result;
+	}
+
+	std::string strprintf(const char* format, ...)
+	{
+		va_list vlist;
+		va_start(vlist, format);
+		auto result = vstrprintf(format, vlist);
+		va_end(vlist);
+		return result;
+	}
+#endif
+
+	#if LOGURU_WITH_STREAMS
+
+	StreamLogger::~StreamLogger() noexcept(false)
+	{
+		auto message = _ss.str();
+		log(_verbosity, _file, _line, LOGURU_FMT(s), message.c_str());
+	}
+
+	AbortLogger::~AbortLogger() noexcept(false)
+	{
+		auto message = _ss.str();
+		loguru::log_and_abort(1, _expr, _file, _line, LOGURU_FMT(s), message.c_str());
+	}
+
+	#endif // LOGURU_WITH_STREAMS
+
+	// ----------------------------------------------------------------------------
+	// 888888 88""Yb 88""Yb  dP"Yb  88""Yb      dP""b8  dP"Yb  88b 88 888888 888888 Yb  dP 888888
+	// 88__   88__dP 88__dP dP   Yb 88__dP     dP   `" dP   Yb 88Yb88   88   88__    YbdP    88
+	// 88""   88"Yb  88"Yb  Yb   dP 88"Yb      Yb      Yb   dP 88 Y88   88   88""    dPYb    88
+	// 888888 88  Yb 88  Yb  YbodP  88  Yb      YboodP  YbodP  88  Y8   88   888888 dP  Yb   88
+	// ----------------------------------------------------------------------------
+
+	struct StringStream
+	{
+		std::string str;
+	};
+
+	// Use this in your EcPrinter implementations.
+	void stream_print(StringStream& out_string_stream, const char* text)
+	{
+		out_string_stream.str += text;
+	}
+
+	// ----------------------------------------------------------------------------
+
+	using ECPtr = EcEntryBase*;
+
+#if defined(_WIN32) || (defined(__APPLE__) && !TARGET_OS_IPHONE)
+	#ifdef __APPLE__
+		#define LOGURU_THREAD_LOCAL __thread
+	#else
+		#define LOGURU_THREAD_LOCAL thread_local
+	#endif
+	static LOGURU_THREAD_LOCAL ECPtr thread_ec_ptr = nullptr;
+
+	ECPtr& get_thread_ec_head_ref()
+	{
+		return thread_ec_ptr;
+	}
+#else // !thread_local
+	static pthread_once_t s_ec_pthread_once = PTHREAD_ONCE_INIT;
+	static pthread_key_t  s_ec_pthread_key;
+
+	void free_ec_head_ref(void* io_error_context)
+	{
+		delete reinterpret_cast<ECPtr*>(io_error_context);
+	}
+
+	void ec_make_pthread_key()
+	{
+		(void)pthread_key_create(&s_ec_pthread_key, free_ec_head_ref);
+	}
+
+	ECPtr& get_thread_ec_head_ref()
+	{
+		(void)pthread_once(&s_ec_pthread_once, ec_make_pthread_key);
+		auto ec = reinterpret_cast<ECPtr*>(pthread_getspecific(s_ec_pthread_key));
+		if (ec == nullptr) {
+			ec = new ECPtr(nullptr);
+			(void)pthread_setspecific(s_ec_pthread_key, ec);
+		}
+		return *ec;
+	}
+#endif // !thread_local
+
+	// ----------------------------------------------------------------------------
+
+	EcHandle get_thread_ec_handle()
+	{
+		return get_thread_ec_head_ref();
+	}
+
+	Text get_error_context()
+	{
+		return get_error_context_for(get_thread_ec_head_ref());
+	}
+
+	Text get_error_context_for(const EcEntryBase* ec_head)
+	{
+		std::vector<const EcEntryBase*> stack;
+		while (ec_head) {
+			stack.push_back(ec_head);
+			ec_head = ec_head->_previous;
+		}
+		std::reverse(stack.begin(), stack.end());
+
+		StringStream result;
+		if (!stack.empty()) {
+			result.str += "------------------------------------------------\n";
+			for (auto entry : stack) {
+				const auto description = std::string(entry->_descr) + ":";
+#if LOGURU_USE_FMTLIB
+				auto prefix = textprintf("[ErrorContext] {.{}s}:{:-5u} {:-20s} ",
+					filename(entry->_file), LOGURU_FILENAME_WIDTH, entry->_line, description.c_str());
+#else
+				auto prefix = textprintf("[ErrorContext] %*s:%-5u %-20s ",
+					LOGURU_FILENAME_WIDTH, filename(entry->_file), entry->_line, description.c_str());
+#endif
+				result.str += prefix.c_str();
+				entry->print_value(result);
+				result.str += "\n";
+			}
+			result.str += "------------------------------------------------";
+		}
+		return Text(STRDUP(result.str.c_str()));
+	}
+
+	EcEntryBase::EcEntryBase(const char* file, unsigned line, const char* descr)
+		: _file(file), _line(line), _descr(descr)
+	{
+		EcEntryBase*& ec_head = get_thread_ec_head_ref();
+		_previous = ec_head;
+		ec_head = this;
+	}
+
+	EcEntryBase::~EcEntryBase()
+	{
+		get_thread_ec_head_ref() = _previous;
+	}
+
+	// ------------------------------------------------------------------------
+
+	Text ec_to_text(const char* value)
+	{
+		// Add quotes around the string to make it obvious where it begin and ends.
+		// This is great for detecting erroneous leading or trailing spaces in e.g. an identifier.
+		auto str = "\"" + std::string(value) + "\"";
+		return Text{STRDUP(str.c_str())};
+	}
+
+	Text ec_to_text(char c)
+	{
+		// Add quotes around the character to make it obvious where it begin and ends.
+		std::string str = "'";
+
+		auto write_hex_digit = [&](unsigned num)
+		{
+			if (num < 10u) { str += char('0' + num); }
+			else           { str += char('a' + num - 10); }
+		};
+
+		auto write_hex_16 = [&](uint16_t n)
+		{
+			write_hex_digit((n >> 12u) & 0x0f);
+			write_hex_digit((n >>  8u) & 0x0f);
+			write_hex_digit((n >>  4u) & 0x0f);
+			write_hex_digit((n >>  0u) & 0x0f);
+		};
+
+		if      (c == '\\') { str += "\\\\"; }
+		else if (c == '\"') { str += "\\\""; }
+		else if (c == '\'') { str += "\\\'"; }
+		else if (c == '\0') { str += "\\0";  }
+		else if (c == '\b') { str += "\\b";  }
+		else if (c == '\f') { str += "\\f";  }
+		else if (c == '\n') { str += "\\n";  }
+		else if (c == '\r') { str += "\\r";  }
+		else if (c == '\t') { str += "\\t";  }
+		else if (0 <= c && c < 0x20) {
+			str += "\\u";
+			write_hex_16(static_cast<uint16_t>(c));
+		} else { str += c; }
+
+		str += "'";
+
+		return Text{STRDUP(str.c_str())};
+	}
+
+	#define DEFINE_EC(Type)                        \
+		Text ec_to_text(Type value)                \
+		{                                          \
+			auto str = std::to_string(value);      \
+			return Text{STRDUP(str.c_str())};      \
+		}
+
+	DEFINE_EC(int)
+	DEFINE_EC(unsigned int)
+	DEFINE_EC(long)
+	DEFINE_EC(unsigned long)
+	DEFINE_EC(long long)
+	DEFINE_EC(unsigned long long)
+	DEFINE_EC(float)
+	DEFINE_EC(double)
+	DEFINE_EC(long double)
+
+	#undef DEFINE_EC
+
+	Text ec_to_text(EcHandle ec_handle)
+	{
+		Text parent_ec = get_error_context_for(ec_handle);
+		size_t buffer_size = strlen(parent_ec.c_str()) + 2;
+		char* with_newline = reinterpret_cast<char*>(malloc(buffer_size));
+		with_newline[0] = '\n';
+	#ifdef _WIN32
+		strncpy_s(with_newline + 1, buffer_size, parent_ec.c_str(), buffer_size - 2);
+	#else
+		strcpy(with_newline + 1, parent_ec.c_str());
+	#endif
+		return Text(with_newline);
+	}
+
+	// ----------------------------------------------------------------------------
+
+} // namespace loguru
+
+// ----------------------------------------------------------------------------
+// .dP"Y8 88  dP""b8 88b 88    db    88     .dP"Y8
+// `Ybo." 88 dP   `" 88Yb88   dPYb   88     `Ybo."
+// o.`Y8b 88 Yb  "88 88 Y88  dP__Yb  88  .o o.`Y8b
+// 8bodP' 88  YboodP 88  Y8 dP""""Yb 88ood8 8bodP'
+// ----------------------------------------------------------------------------
+
+#ifdef _WIN32
+namespace loguru {
+	void install_signal_handlers(const SignalOptions& signal_options)
+	{
+		(void)signal_options;
+		// TODO: implement signal handlers on windows
+	}
+} // namespace loguru
+
+#else // _WIN32
+
+namespace loguru
+{
+	void write_to_stderr(const char* data, size_t size)
+	{
+		auto result = write(STDERR_FILENO, data, size);
+		(void)result; // Ignore errors.
+	}
+
+	void write_to_stderr(const char* data)
+	{
+		write_to_stderr(data, strlen(data));
+	}
+
+	void call_default_signal_handler(int signal_number)
+	{
+		struct sigaction sig_action;
+		memset(&sig_action, 0, sizeof(sig_action));
+		sigemptyset(&sig_action.sa_mask);
+		sig_action.sa_handler = SIG_DFL;
+		sigaction(signal_number, &sig_action, NULL);
+		kill(getpid(), signal_number);
+	}
+
+	void signal_handler(int signal_number, siginfo_t*, void*)
+	{
+		const char* signal_name = "UNKNOWN SIGNAL";
+
+		if (signal_number == SIGABRT) { signal_name = "SIGABRT"; }
+		if (signal_number == SIGBUS)  { signal_name = "SIGBUS";  }
+		if (signal_number == SIGFPE)  { signal_name = "SIGFPE";  }
+		if (signal_number == SIGILL)  { signal_name = "SIGILL";  }
+		if (signal_number == SIGINT)  { signal_name = "SIGINT";  }
+		if (signal_number == SIGSEGV) { signal_name = "SIGSEGV"; }
+		if (signal_number == SIGTERM) { signal_name = "SIGTERM"; }
+
+		// --------------------------------------------------------------------
+		/* There are few things that are safe to do in a signal handler,
+		   but writing to stderr is one of them.
+		   So we first print out what happened to stderr so we're sure that gets out,
+		   then we do the unsafe things, like logging the stack trace.
+		*/
+
+		if (g_colorlogtostderr && s_terminal_has_color) {
+			write_to_stderr(terminal_reset());
+			write_to_stderr(terminal_bold());
+			write_to_stderr(terminal_light_red());
+		}
+		write_to_stderr("\n");
+		write_to_stderr("Loguru caught a signal: ");
+		write_to_stderr(signal_name);
+		write_to_stderr("\n");
+		if (g_colorlogtostderr && s_terminal_has_color) {
+			write_to_stderr(terminal_reset());
+		}
+
+		// --------------------------------------------------------------------
+
+		if (s_signal_options.unsafe_signal_handler) {
+			// --------------------------------------------------------------------
+			/* Now we do unsafe things. This can for example lead to deadlocks if
+			   the signal was triggered from the system's memory management functions
+			   and the code below tries to do allocations.
+			*/
+
+			flush();
+			char preamble_buff[LOGURU_PREAMBLE_WIDTH];
+			print_preamble(preamble_buff, sizeof(preamble_buff), Verbosity_FATAL, "", 0);
+			auto message = Message{Verbosity_FATAL, "", 0, preamble_buff, "", "Signal: ", signal_name};
+			try {
+				log_message(1, message, false, false);
+			} catch (...) {
+				// This can happed due to s_fatal_handler.
+				write_to_stderr("Exception caught and ignored by Loguru signal handler.\n");
+			}
+			flush();
+
+			// --------------------------------------------------------------------
+		}
+
+		call_default_signal_handler(signal_number);
+	}
+
+	void install_signal_handlers(const SignalOptions& signal_options)
+	{
+		s_signal_options = signal_options;
+
+		struct sigaction sig_action;
+		memset(&sig_action, 0, sizeof(sig_action));
+		sigemptyset(&sig_action.sa_mask);
+		sig_action.sa_flags |= SA_SIGINFO;
+		sig_action.sa_sigaction = &signal_handler;
+
+		if (signal_options.sigabrt) {
+			CHECK_F(sigaction(SIGABRT, &sig_action, NULL) != -1, "Failed to install handler for SIGABRT");
+		}
+		if (signal_options.sigbus) {
+			CHECK_F(sigaction(SIGBUS, &sig_action, NULL) != -1, "Failed to install handler for SIGBUS");
+		}
+		if (signal_options.sigfpe) {
+			CHECK_F(sigaction(SIGFPE, &sig_action, NULL) != -1, "Failed to install handler for SIGFPE");
+		}
+		if (signal_options.sigill) {
+			CHECK_F(sigaction(SIGILL, &sig_action, NULL) != -1, "Failed to install handler for SIGILL");
+		}
+		if (signal_options.sigint) {
+			CHECK_F(sigaction(SIGINT, &sig_action, NULL) != -1, "Failed to install handler for SIGINT");
+		}
+		if (signal_options.sigsegv) {
+			CHECK_F(sigaction(SIGSEGV, &sig_action, NULL) != -1, "Failed to install handler for SIGSEGV");
+		}
+		if (signal_options.sigterm) {
+			CHECK_F(sigaction(SIGTERM, &sig_action, NULL) != -1, "Failed to install handler for SIGTERM");
+		}
+	}
+} // namespace loguru
+
+#endif // _WIN32
+
+
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic pop
+#elif defined(_MSC_VER)
+#pragma warning(pop)
+#endif
+
+LOGURU_ANONYMOUS_NAMESPACE_END
+
+#endif // LOGURU_IMPLEMENTATION
diff --git a/tomviz/loguru/loguru.hpp b/tomviz/loguru/loguru.hpp
new file mode 100644
index 000000000..94d5964ba
--- /dev/null
+++ b/tomviz/loguru/loguru.hpp
@@ -0,0 +1,1482 @@
+/*
+Loguru logging library for C++, by Emil Ernerfeldt.
+www.github.com/emilk/loguru
+If you find Loguru useful, please let me know on twitter or in a mail!
+Twitter: @ernerfeldt
+Mail:    emil.ernerfeldt@gmail.com
+Website: www.ilikebigbits.com
+
+# License
+	This software is in the public domain. Where that dedication is not
+	recognized, you are granted a perpetual, irrevocable license to
+	copy, modify and distribute it as you see fit.
+
+# Inspiration
+	Much of Loguru was inspired by GLOG, https://code.google.com/p/google-glog/.
+	The choice of public domain is fully due Sean T. Barrett
+	and his wonderful stb libraries at https://github.com/nothings/stb.
+
+# Version history
+	* Version 0.1.0 - 2015-03-22 - Works great on Mac.
+	* Version 0.2.0 - 2015-09-17 - Removed the only dependency.
+	* Version 0.3.0 - 2015-10-02 - Drop-in replacement for most of GLOG
+	* Version 0.4.0 - 2015-10-07 - Single-file!
+	* Version 0.5.0 - 2015-10-17 - Improved file logging
+	* Version 0.6.0 - 2015-10-24 - Add stack traces
+	* Version 0.7.0 - 2015-10-27 - Signals
+	* Version 0.8.0 - 2015-10-30 - Color logging.
+	* Version 0.9.0 - 2015-11-26 - ABORT_S and proper handling of FATAL
+	* Version 1.0.0 - 2016-02-14 - ERROR_CONTEXT
+	* Version 1.1.0 - 2016-02-19 - -v OFF, -v INFO etc
+	* Version 1.1.1 - 2016-02-20 - textprintf vs strprintf
+	* Version 1.1.2 - 2016-02-22 - Remove g_alsologtostderr
+	* Version 1.1.3 - 2016-02-29 - ERROR_CONTEXT as linked list
+	* Version 1.2.0 - 2016-03-19 - Add get_thread_name()
+	* Version 1.2.1 - 2016-03-20 - Minor fixes
+	* Version 1.2.2 - 2016-03-29 - Fix issues with set_fatal_handler throwing an exception
+	* Version 1.2.3 - 2016-05-16 - Log current working directory in loguru::init().
+	* Version 1.2.4 - 2016-05-18 - Custom replacement for -v in loguru::init() by bjoernpollex
+	* Version 1.2.5 - 2016-05-18 - Add ability to print ERROR_CONTEXT of parent thread.
+	* Version 1.2.6 - 2016-05-19 - Bug fix regarding VLOG verbosity argument lacking ().
+	* Version 1.2.7 - 2016-05-23 - Fix PATH_MAX problem.
+	* Version 1.2.8 - 2016-05-26 - Add shutdown() and remove_all_callbacks()
+	* Version 1.2.9 - 2016-06-09 - Use a monotonic clock for uptime.
+	* Version 1.3.0 - 2016-07-20 - Fix issues with callback flush/close not being called.
+	* Version 1.3.1 - 2016-07-20 - Add LOGURU_UNSAFE_SIGNAL_HANDLER to toggle stacktrace on signals.
+	* Version 1.3.2 - 2016-07-20 - Add loguru::arguments()
+	* Version 1.4.0 - 2016-09-15 - Semantic versioning + add loguru::create_directories
+	* Version 1.4.1 - 2016-09-29 - Customize formating with LOGURU_FILENAME_WIDTH
+	* Version 1.5.0 - 2016-12-22 - LOGURU_USE_FMTLIB by kolis and LOGURU_WITH_FILEABS by scinart
+	* Version 1.5.1 - 2017-08-08 - Terminal colors on Windows 10 thanks to looki
+	* Version 1.6.0 - 2018-01-03 - Add LOGURU_RTTI and LOGURU_STACKTRACES settings
+	* Version 1.7.0 - 2018-01-03 - Add ability to turn off the preamble with loguru::g_preamble
+	* Version 1.7.1 - 2018-04-05 - Add function get_fatal_handler
+	* Version 1.7.2 - 2018-04-22 - Fix a bug where large file names could cause stack corruption (thanks @ccamporesi)
+	* Version 1.8.0 - 2018-04-23 - Shorten long file names to keep preamble fixed width
+	* Version 1.9.0 - 2018-09-22 - Adjust terminal colors, add LOGURU_VERBOSE_SCOPE_ENDINGS, add LOGURU_SCOPE_TIME_PRECISION, add named log levels
+	* Version 2.0.0 - 2018-09-22 - Split loguru.hpp into loguru.hpp and loguru.cpp
+	* Version 2.1.0 - 2019-09-23 - Update fmtlib + add option to loguru::init to NOT set main thread name.
+	* Version 2.2.0 - 2020-07-31 - Replace LOGURU_CATCH_SIGABRT with struct SignalOptions
+
+# Compiling
+	Just include <loguru.hpp> where you want to use Loguru.
+	Then, in one .cpp file #include <loguru.cpp>
+	Make sure you compile with -std=c++11 -lstdc++ -lpthread -ldl
+
+# Usage
+	For details, please see the official documentation at emilk.github.io/loguru
+
+	#include <loguru.hpp>
+
+	int main(int argc, char* argv[]) {
+		loguru::init(argc, argv);
+
+		// Put every log message in "everything.log":
+		loguru::add_file("everything.log", loguru::Append, loguru::Verbosity_MAX);
+
+		LOG_F(INFO, "The magic number is %d", 42);
+	}
+
+*/
+
+#if defined(LOGURU_IMPLEMENTATION)
+	#error "You are defining LOGURU_IMPLEMENTATION. This is for older versions of Loguru. You should now instead include loguru.cpp (or build it and link with it)"
+#endif
+
+// Disable all warnings from gcc/clang:
+#if defined(__clang__)
+	#pragma clang system_header
+#elif defined(__GNUC__)
+	#pragma GCC system_header
+#endif
+
+#ifndef LOGURU_HAS_DECLARED_FORMAT_HEADER
+#define LOGURU_HAS_DECLARED_FORMAT_HEADER
+
+// Semantic versioning. Loguru version can be printed with printf("%d.%d.%d", LOGURU_VERSION_MAJOR, LOGURU_VERSION_MINOR, LOGURU_VERSION_PATCH);
+#define LOGURU_VERSION_MAJOR 2
+#define LOGURU_VERSION_MINOR 1
+#define LOGURU_VERSION_PATCH 0
+
+#if defined(_MSC_VER)
+#include <sal.h>	// Needed for _In_z_ etc annotations
+#endif
+
+#if defined(__linux__) || defined(__APPLE__)
+#define LOGURU_SYSLOG 1
+#else
+#define LOGURU_SYSLOG 0
+#endif
+
+// ----------------------------------------------------------------------------
+
+#ifndef LOGURU_EXPORT
+	// Define to your project's export declaration if needed for use in a shared library.
+	#define LOGURU_EXPORT
+#endif
+
+#ifndef LOGURU_SCOPE_TEXT_SIZE
+	// Maximum length of text that can be printed by a LOG_SCOPE.
+	// This should be long enough to get most things, but short enough not to clutter the stack.
+	#define LOGURU_SCOPE_TEXT_SIZE 196
+#endif
+
+#ifndef LOGURU_FILENAME_WIDTH
+	// Width of the column containing the file name
+	#define LOGURU_FILENAME_WIDTH 23
+#endif
+
+#ifndef LOGURU_THREADNAME_WIDTH
+	// Width of the column containing the thread name
+	#define LOGURU_THREADNAME_WIDTH 16
+#endif
+
+#ifndef LOGURU_SCOPE_TIME_PRECISION
+	// Resolution of scope timers. 3=ms, 6=us, 9=ns
+	#define LOGURU_SCOPE_TIME_PRECISION 3
+#endif
+
+#ifdef LOGURU_CATCH_SIGABRT
+	#error "You are defining LOGURU_CATCH_SIGABRT. This is for older versions of Loguru. You should now instead set the options passed to loguru::init"
+#endif
+
+#ifndef LOGURU_VERBOSE_SCOPE_ENDINGS
+	// Show milliseconds and scope name at end of scope.
+	#define LOGURU_VERBOSE_SCOPE_ENDINGS 1
+#endif
+
+#ifndef LOGURU_REDEFINE_ASSERT
+	#define LOGURU_REDEFINE_ASSERT 0
+#endif
+
+#ifndef LOGURU_WITH_STREAMS
+	#define LOGURU_WITH_STREAMS 0
+#endif
+
+#ifndef LOGURU_REPLACE_GLOG
+	#define LOGURU_REPLACE_GLOG 0
+#endif
+
+#if LOGURU_REPLACE_GLOG
+	#undef LOGURU_WITH_STREAMS
+	#define LOGURU_WITH_STREAMS 1
+#endif
+
+#if defined(LOGURU_UNSAFE_SIGNAL_HANDLER)
+	#error "You are defining LOGURU_UNSAFE_SIGNAL_HANDLER. This is for older versions of Loguru. You should now instead set the unsafe_signal_handler option when you call loguru::init."
+#endif
+
+#if LOGURU_IMPLEMENTATION
+	#undef LOGURU_WITH_STREAMS
+	#define LOGURU_WITH_STREAMS 1
+#endif
+
+#ifndef LOGURU_USE_FMTLIB
+	#define LOGURU_USE_FMTLIB 0
+#endif
+
+#ifndef LOGURU_USE_LOCALE
+        #define LOGURU_USE_LOCALE 0
+#endif
+
+#ifndef LOGURU_WITH_FILEABS
+	#define LOGURU_WITH_FILEABS 0
+#endif
+
+#ifndef LOGURU_RTTI
+#if defined(__clang__)
+	#if __has_feature(cxx_rtti)
+		#define LOGURU_RTTI 1
+	#endif
+#elif defined(__GNUG__)
+	#if defined(__GXX_RTTI)
+		#define LOGURU_RTTI 1
+	#endif
+#elif defined(_MSC_VER)
+	#if defined(_CPPRTTI)
+		#define LOGURU_RTTI 1
+	#endif
+#endif
+#endif
+
+#ifdef LOGURU_USE_ANONYMOUS_NAMESPACE
+	#define LOGURU_ANONYMOUS_NAMESPACE_BEGIN namespace {
+	#define LOGURU_ANONYMOUS_NAMESPACE_END }
+#else
+	#define LOGURU_ANONYMOUS_NAMESPACE_BEGIN
+	#define LOGURU_ANONYMOUS_NAMESPACE_END
+#endif
+
+// --------------------------------------------------------------------
+// Utility macros
+
+#define LOGURU_CONCATENATE_IMPL(s1, s2) s1 ## s2
+#define LOGURU_CONCATENATE(s1, s2) LOGURU_CONCATENATE_IMPL(s1, s2)
+
+#ifdef __COUNTER__
+#   define LOGURU_ANONYMOUS_VARIABLE(str) LOGURU_CONCATENATE(str, __COUNTER__)
+#else
+#   define LOGURU_ANONYMOUS_VARIABLE(str) LOGURU_CONCATENATE(str, __LINE__)
+#endif
+
+#if defined(__clang__) || defined(__GNUC__)
+	// Helper macro for declaring functions as having similar signature to printf.
+	// This allows the compiler to catch format errors at compile-time.
+	#define LOGURU_PRINTF_LIKE(fmtarg, firstvararg) __attribute__((__format__ (__printf__, fmtarg, firstvararg)))
+	#define LOGURU_FORMAT_STRING_TYPE const char*
+#elif defined(_MSC_VER)
+	#define LOGURU_PRINTF_LIKE(fmtarg, firstvararg)
+	#define LOGURU_FORMAT_STRING_TYPE _In_z_ _Printf_format_string_ const char*
+#else
+	#define LOGURU_PRINTF_LIKE(fmtarg, firstvararg)
+	#define LOGURU_FORMAT_STRING_TYPE const char*
+#endif
+
+// Used to mark log_and_abort for the benefit of the static analyzer and optimizer.
+#if defined(_MSC_VER)
+#define LOGURU_NORETURN __declspec(noreturn)
+#else
+#define LOGURU_NORETURN __attribute__((noreturn))
+#endif
+
+#if defined(_MSC_VER)
+#define LOGURU_PREDICT_FALSE(x) (x)
+#define LOGURU_PREDICT_TRUE(x)  (x)
+#else
+#define LOGURU_PREDICT_FALSE(x) (__builtin_expect(x,     0))
+#define LOGURU_PREDICT_TRUE(x)  (__builtin_expect(!!(x), 1))
+#endif
+
+#if LOGURU_USE_FMTLIB
+	#include <fmt/format.h>
+	#define LOGURU_FMT(x) "{:" #x "}"
+#else
+	#define LOGURU_FMT(x) "%" #x
+#endif
+
+#ifdef _WIN32
+	#define STRDUP(str) _strdup(str)
+#else
+	#define STRDUP(str) strdup(str)
+#endif
+
+#include <stdarg.h>
+
+// --------------------------------------------------------------------
+LOGURU_ANONYMOUS_NAMESPACE_BEGIN
+
+namespace loguru
+{
+	// Simple RAII ownership of a char*.
+	class LOGURU_EXPORT Text
+	{
+	public:
+		explicit Text(char* owned_str) : _str(owned_str) {}
+		~Text();
+		Text(Text&& t)
+		{
+			_str = t._str;
+			t._str = nullptr;
+		}
+		Text(Text& t) = delete;
+		Text& operator=(Text& t) = delete;
+		void operator=(Text&& t) = delete;
+
+		const char* c_str() const { return _str; }
+		bool empty() const { return _str == nullptr || *_str == '\0'; }
+
+		char* release()
+		{
+			auto result = _str;
+			_str = nullptr;
+			return result;
+		}
+
+	private:
+		char* _str;
+	};
+
+	// Like printf, but returns the formated text.
+#if LOGURU_USE_FMTLIB
+	LOGURU_EXPORT
+	Text vtextprintf(const char* format, fmt::format_args args);
+
+	template<typename... Args>
+	LOGURU_EXPORT
+	Text textprintf(LOGURU_FORMAT_STRING_TYPE format, const Args&... args) {
+		return vtextprintf(format, fmt::make_format_args(args...));
+	}
+#else
+	LOGURU_EXPORT
+	Text textprintf(LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(1, 2);
+#endif
+
+	// Overloaded for variadic template matching.
+	LOGURU_EXPORT
+	Text textprintf();
+
+	using Verbosity = int;
+
+#undef FATAL
+#undef ERROR
+#undef WARNING
+#undef INFO
+#undef MAX
+
+	enum NamedVerbosity : Verbosity
+	{
+		// Used to mark an invalid verbosity. Do not log to this level.
+		Verbosity_INVALID = -10, // Never do LOG_F(INVALID)
+
+		// You may use Verbosity_OFF on g_stderr_verbosity, but for nothing else!
+		Verbosity_OFF     = -9, // Never do LOG_F(OFF)
+
+		// Prefer to use ABORT_F or ABORT_S over LOG_F(FATAL) or LOG_S(FATAL).
+		Verbosity_FATAL   = -3,
+		Verbosity_ERROR   = -2,
+		Verbosity_WARNING = -1,
+
+		// Normal messages. By default written to stderr.
+		Verbosity_INFO    =  0,
+
+		// Same as Verbosity_INFO in every way.
+		Verbosity_0       =  0,
+
+		// Verbosity levels 1-9 are generally not written to stderr, but are written to file.
+		Verbosity_1       = +1,
+		Verbosity_2       = +2,
+		Verbosity_3       = +3,
+		Verbosity_4       = +4,
+		Verbosity_5       = +5,
+		Verbosity_6       = +6,
+		Verbosity_7       = +7,
+		Verbosity_8       = +8,
+		Verbosity_9       = +9,
+
+		// Do not use higher verbosity levels, as that will make grepping log files harder.
+		Verbosity_MAX     = +9,
+	};
+
+	struct Message
+	{
+		// You would generally print a Message by just concatenating the buffers without spacing.
+		// Optionally, ignore preamble and indentation.
+		Verbosity   verbosity;   // Already part of preamble
+		const char* filename;    // Already part of preamble
+		unsigned    line;        // Already part of preamble
+		const char* preamble;    // Date, time, uptime, thread, file:line, verbosity.
+		const char* indentation; // Just a bunch of spacing.
+		const char* prefix;      // Assertion failure info goes here (or "").
+		const char* message;     // User message goes here.
+	};
+
+	/* Everything with a verbosity equal or greater than g_stderr_verbosity will be
+	written to stderr. You can set this in code or via the -v argument.
+	Set to loguru::Verbosity_OFF to write nothing to stderr.
+	Default is 0, i.e. only log ERROR, WARNING and INFO are written to stderr.
+	*/
+	LOGURU_EXPORT extern Verbosity g_stderr_verbosity;
+	LOGURU_EXPORT extern bool      g_colorlogtostderr; // True by default.
+	LOGURU_EXPORT extern unsigned  g_flush_interval_ms; // 0 (unbuffered) by default.
+	LOGURU_EXPORT extern bool      g_preamble_header; // Prepend each log start by a descriptions line with all columns name? True by default.
+	LOGURU_EXPORT extern bool      g_preamble; // Prefix each log line with date, time etc? True by default.
+
+	/* Specify the verbosity used by loguru to log its info messages including the header
+	logged when logged::init() is called or on exit. Default is 0 (INFO).
+	*/
+	LOGURU_EXPORT extern Verbosity g_internal_verbosity;
+
+	// Turn off individual parts of the preamble
+	LOGURU_EXPORT extern bool      g_preamble_date; // The date field
+	LOGURU_EXPORT extern bool      g_preamble_time; // The time of the current day
+	LOGURU_EXPORT extern bool      g_preamble_uptime; // The time since init call
+	LOGURU_EXPORT extern bool      g_preamble_thread; // The logging thread
+	LOGURU_EXPORT extern bool      g_preamble_file; // The file from which the log originates from
+	LOGURU_EXPORT extern bool      g_preamble_verbose; // The verbosity field
+	LOGURU_EXPORT extern bool      g_preamble_pipe; // The pipe symbol right before the message
+
+	// May not throw!
+	typedef void (*log_handler_t)(void* user_data, const Message& message);
+	typedef void (*close_handler_t)(void* user_data);
+	typedef void (*flush_handler_t)(void* user_data);
+
+	// May throw if that's how you'd like to handle your errors.
+	typedef void (*fatal_handler_t)(const Message& message);
+
+	// Given a verbosity level, return the level's name or nullptr.
+	typedef const char* (*verbosity_to_name_t)(Verbosity verbosity);
+
+	// Given a verbosity level name, return the verbosity level or
+	// Verbosity_INVALID if name is not recognized.
+	typedef Verbosity (*name_to_verbosity_t)(const char* name);
+
+	struct SignalOptions
+	{
+		/// Make Loguru try to do unsafe but useful things,
+		/// like printing a stack trace, when catching signals.
+		/// This may lead to bad things like deadlocks in certain situations.
+		bool unsafe_signal_handler = true;
+
+		/// Should Loguru catch SIGABRT ?
+		bool sigabrt = true;
+
+		/// Should Loguru catch SIGBUS ?
+		bool sigbus = true;
+
+		/// Should Loguru catch SIGFPE ?
+		bool sigfpe = true;
+
+		/// Should Loguru catch SIGILL ?
+		bool sigill = true;
+
+		/// Should Loguru catch SIGINT ?
+		bool sigint = true;
+
+		/// Should Loguru catch SIGSEGV ?
+		bool sigsegv = true;
+
+		/// Should Loguru catch SIGTERM ?
+		bool sigterm = true;
+
+		static SignalOptions none()
+		{
+			SignalOptions options;
+			options.unsafe_signal_handler = false;
+			options.sigabrt = false;
+			options.sigbus = false;
+			options.sigfpe = false;
+			options.sigill = false;
+			options.sigint = false;
+			options.sigsegv = false;
+			options.sigterm = false;
+			return options;
+		}
+	};
+
+	// Runtime options passed to loguru::init
+	struct Options
+	{
+		// This allows you to use something else instead of "-v" via verbosity_flag.
+		// Set to nullptr if you don't want Loguru to parse verbosity from the args.
+		const char* verbosity_flag = "-v";
+
+		// loguru::init will set the name of the calling thread to this.
+		// If you don't want Loguru to set the name of the main thread,
+		// set this to nullptr.
+		// NOTE: on SOME platforms loguru::init will only overwrite the thread name
+		// if a thread name has not already been set.
+		// To always set a thread name, use loguru::set_thread_name instead.
+		const char* main_thread_name = "main thread";
+
+		SignalOptions signal_options;
+	};
+
+	/*  Should be called from the main thread.
+		You don't *need* to call this, but if you do you get:
+			* Signal handlers installed
+			* Program arguments logged
+			* Working dir logged
+			* Optional -v verbosity flag parsed
+			* Main thread name set to "main thread"
+			* Explanation of the preamble (date, thread name, etc) logged
+
+		loguru::init() will look for arguments meant for loguru and remove them.
+		Arguments meant for loguru are:
+			-v n   Set loguru::g_stderr_verbosity level. Examples:
+				-v 3        Show verbosity level 3 and lower.
+				-v 0        Only show INFO, WARNING, ERROR, FATAL (default).
+				-v INFO     Only show INFO, WARNING, ERROR, FATAL (default).
+				-v WARNING  Only show WARNING, ERROR, FATAL.
+				-v ERROR    Only show ERROR, FATAL.
+				-v FATAL    Only show FATAL.
+				-v OFF      Turn off logging to stderr.
+
+		Tip: You can set g_stderr_verbosity before calling loguru::init.
+		That way you can set the default but have the user override it with the -v flag.
+		Note that -v does not affect file logging (see loguru::add_file).
+
+		You can you something other than the -v flag by setting the verbosity_flag option.
+	*/
+	LOGURU_EXPORT
+	void init(int& argc, char* argv[], const Options& options = {});
+
+	// Will call remove_all_callbacks(). After calling this, logging will still go to stderr.
+	// You generally don't need to call this.
+	LOGURU_EXPORT
+	void shutdown();
+
+	// What ~ will be replaced with, e.g. "/home/your_user_name/"
+	LOGURU_EXPORT
+	const char* home_dir();
+
+	/* Returns the name of the app as given in argv[0] but without leading path.
+	   That is, if argv[0] is "../foo/app" this will return "app".
+	*/
+	LOGURU_EXPORT
+	const char* argv0_filename();
+
+	// Returns all arguments given to loguru::init(), but escaped with a single space as separator.
+	LOGURU_EXPORT
+	const char* arguments();
+
+	// Returns the path to the current working dir when loguru::init() was called.
+	LOGURU_EXPORT
+	const char* current_dir();
+
+	// Returns the part of the path after the last / or \ (if any).
+	LOGURU_EXPORT
+	const char* filename(const char* path);
+
+	// e.g. "foo/bar/baz.ext" will create the directories "foo/" and "foo/bar/"
+	LOGURU_EXPORT
+	bool create_directories(const char* file_path_const);
+
+	// Writes date and time with millisecond precision, e.g. "20151017_161503.123"
+	LOGURU_EXPORT
+	void write_date_time(char* buff, unsigned long long buff_size);
+
+	// Helper: thread-safe version strerror
+	LOGURU_EXPORT
+	Text errno_as_text();
+
+	/* Given a prefix of e.g. "~/loguru/" this might return
+	   "/home/your_username/loguru/app_name/20151017_161503.123.log"
+
+	   where "app_name" is a sanitized version of argv[0].
+	*/
+	LOGURU_EXPORT
+	void suggest_log_path(const char* prefix, char* buff, unsigned long long buff_size);
+
+	enum FileMode { Truncate, Append };
+
+	/*  Will log to a file at the given path.
+		Any logging message with a verbosity lower or equal to
+		the given verbosity will be included.
+		The function will create all directories in 'path' if needed.
+		If path starts with a ~, it will be replaced with loguru::home_dir()
+		To stop the file logging, just call loguru::remove_callback(path) with the same path.
+	*/
+	LOGURU_EXPORT
+	bool add_file(const char* path, FileMode mode, Verbosity verbosity);
+
+	LOGURU_EXPORT
+	// Send logs to syslog with LOG_USER facility (see next call)
+	bool add_syslog(const char* app_name, Verbosity verbosity);
+	LOGURU_EXPORT
+	// Send logs to syslog with your own choice of facility (LOG_USER, LOG_AUTH, ...)
+	// see loguru.cpp: syslog_log() for more details.
+	bool add_syslog(const char* app_name, Verbosity verbosity, int facility);
+
+	/*  Will be called right before abort().
+		You can for instance use this to print custom error messages, or throw an exception.
+		Feel free to call LOG:ing function from this, but not FATAL ones! */
+	LOGURU_EXPORT
+	void set_fatal_handler(fatal_handler_t handler);
+
+	// Get the current fatal handler, if any. Default value is nullptr.
+	LOGURU_EXPORT
+	fatal_handler_t get_fatal_handler();
+
+	/*  Will be called on each log messages with a verbosity less or equal to the given one.
+		Useful for displaying messages on-screen in a game, for example.
+		The given on_close is also expected to flush (if desired).
+	*/
+	LOGURU_EXPORT
+	void add_callback(
+		const char*     id,
+		log_handler_t   callback,
+		void*           user_data,
+		Verbosity       verbosity,
+		close_handler_t on_close = nullptr,
+		flush_handler_t on_flush = nullptr);
+
+	/*  Set a callback that returns custom verbosity level names. If callback
+		is nullptr or returns nullptr, default log names will be used.
+	*/
+	LOGURU_EXPORT
+	void set_verbosity_to_name_callback(verbosity_to_name_t callback);
+
+	/*  Set a callback that returns the verbosity level matching a name. The
+		callback should return Verbosity_INVALID if the name is not
+		recognized.
+	*/
+	LOGURU_EXPORT
+	void set_name_to_verbosity_callback(name_to_verbosity_t callback);
+
+	/*  Get a custom name for a specific verbosity, if one exists, or nullptr. */
+	LOGURU_EXPORT
+	const char* get_verbosity_name(Verbosity verbosity);
+
+	/*  Get the verbosity enum value from a custom 4-character level name, if one exists.
+		If the name does not match a custom level name, Verbosity_INVALID is returned.
+	*/
+	LOGURU_EXPORT
+	Verbosity get_verbosity_from_name(const char* name);
+
+	// Returns true iff the callback was found (and removed).
+	LOGURU_EXPORT
+	bool remove_callback(const char* id);
+
+	// Shut down all file logging and any other callback hooks installed.
+	LOGURU_EXPORT
+	void remove_all_callbacks();
+
+	// Returns the maximum of g_stderr_verbosity and all file/custom outputs.
+	LOGURU_EXPORT
+	Verbosity current_verbosity_cutoff();
+
+#if LOGURU_USE_FMTLIB
+	// Internal functions
+    LOGURU_EXPORT
+	void vlog(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, fmt::format_args args);
+    LOGURU_EXPORT
+	void raw_vlog(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, fmt::format_args args);
+
+	// Actual logging function. Use the LOG macro instead of calling this directly.
+	template <typename... Args>
+	LOGURU_EXPORT
+	void log(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, const Args &... args) {
+	    vlog(verbosity, file, line, format, fmt::make_format_args(args...));
+	}
+
+	// Log without any preamble or indentation.
+	template <typename... Args>
+	LOGURU_EXPORT
+	void raw_log(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, const Args &... args) {
+	    raw_vlog(verbosity, file, line, format, fmt::make_format_args(args...));
+	}
+#else // LOGURU_USE_FMTLIB?
+	// Actual logging function. Use the LOG macro instead of calling this directly.
+	LOGURU_EXPORT
+	void log(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(4, 5);
+
+	// Actual logging function.
+	LOGURU_EXPORT
+	void vlog(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, va_list) LOGURU_PRINTF_LIKE(4, 0);
+
+	// Log without any preamble or indentation.
+	LOGURU_EXPORT
+	void raw_log(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(4, 5);
+#endif // !LOGURU_USE_FMTLIB
+
+	// Helper class for LOG_SCOPE_F
+	class LOGURU_EXPORT LogScopeRAII
+	{
+	public:
+		LogScopeRAII() : _file(nullptr) {} // No logging
+		LogScopeRAII(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, va_list vlist) LOGURU_PRINTF_LIKE(5, 0);
+		LogScopeRAII(Verbosity verbosity, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(5, 6);
+		~LogScopeRAII();
+
+		void Init(LOGURU_FORMAT_STRING_TYPE format, va_list vlist) LOGURU_PRINTF_LIKE(2, 0);
+
+#if defined(_MSC_VER) && _MSC_VER > 1800
+		// older MSVC default move ctors close the scope on move. See
+		// issue #43
+		LogScopeRAII(LogScopeRAII&& other)
+			: _verbosity(other._verbosity)
+			, _file(other._file)
+			, _line(other._line)
+			, _indent_stderr(other._indent_stderr)
+			, _start_time_ns(other._start_time_ns)
+		{
+			// Make sure the tmp object's destruction doesn't close the scope:
+			other._file = nullptr;
+
+			for (unsigned int i = 0; i < LOGURU_SCOPE_TEXT_SIZE; ++i) {
+				_name[i] = other._name[i];
+			}
+		}
+#else
+		LogScopeRAII(LogScopeRAII&&) = default;
+#endif
+
+	private:
+		LogScopeRAII(const LogScopeRAII&) = delete;
+		LogScopeRAII& operator=(const LogScopeRAII&) = delete;
+		void operator=(LogScopeRAII&&) = delete;
+
+		Verbosity   _verbosity;
+		const char* _file; // Set to null if we are disabled due to verbosity
+		unsigned    _line;
+		bool        _indent_stderr; // Did we?
+		long long   _start_time_ns;
+		char        _name[LOGURU_SCOPE_TEXT_SIZE];
+	};
+
+	// Marked as 'noreturn' for the benefit of the static analyzer and optimizer.
+	// stack_trace_skip is the number of extrace stack frames to skip above log_and_abort.
+#if LOGURU_USE_FMTLIB
+	LOGURU_EXPORT
+	LOGURU_NORETURN void vlog_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, fmt::format_args);
+	template <typename... Args>
+	LOGURU_EXPORT
+	LOGURU_NORETURN void log_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, const Args&... args) {
+	    vlog_and_abort(stack_trace_skip, expr, file, line, format, fmt::make_format_args(args...));
+	}
+#else
+	LOGURU_EXPORT
+	LOGURU_NORETURN void log_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line, LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(5, 6);
+#endif
+	LOGURU_EXPORT
+	LOGURU_NORETURN void log_and_abort(int stack_trace_skip, const char* expr, const char* file, unsigned line);
+
+	// Flush output to stderr and files.
+	// If g_flush_interval_ms is set to non-zero, this will be called automatically this often.
+	// If not set, you do not need to call this at all.
+	LOGURU_EXPORT
+	void flush();
+
+	template<class T> inline Text format_value(const T&)                    { return textprintf("N/A");     }
+	template<>        inline Text format_value(const char& v)               { return textprintf(LOGURU_FMT(c),   v); }
+	template<>        inline Text format_value(const int& v)                { return textprintf(LOGURU_FMT(d),   v); }
+	template<>        inline Text format_value(const float& v)              { return textprintf(LOGURU_FMT(f),   v); }
+	template<>        inline Text format_value(const double& v)             { return textprintf(LOGURU_FMT(f),   v); }
+
+#if LOGURU_USE_FMTLIB
+	template<>        inline Text format_value(const unsigned int& v)       { return textprintf(LOGURU_FMT(d), v); }
+	template<>        inline Text format_value(const long& v)               { return textprintf(LOGURU_FMT(d), v); }
+	template<>        inline Text format_value(const unsigned long& v)      { return textprintf(LOGURU_FMT(d), v); }
+	template<>        inline Text format_value(const long long& v)          { return textprintf(LOGURU_FMT(d), v); }
+	template<>        inline Text format_value(const unsigned long long& v) { return textprintf(LOGURU_FMT(d), v); }
+#else
+	template<>        inline Text format_value(const unsigned int& v)       { return textprintf(LOGURU_FMT(u),   v); }
+	template<>        inline Text format_value(const long& v)               { return textprintf(LOGURU_FMT(lu),  v); }
+	template<>        inline Text format_value(const unsigned long& v)      { return textprintf(LOGURU_FMT(ld),  v); }
+	template<>        inline Text format_value(const long long& v)          { return textprintf(LOGURU_FMT(llu), v); }
+	template<>        inline Text format_value(const unsigned long long& v) { return textprintf(LOGURU_FMT(lld), v); }
+#endif
+
+	/* Thread names can be set for the benefit of readable logs.
+	   If you do not set the thread name, a hex id will be shown instead.
+	   These thread names may or may not be the same as the system thread names,
+	   depending on the system.
+	   Try to limit the thread name to 15 characters or less. */
+	LOGURU_EXPORT
+	void set_thread_name(const char* name);
+
+	/* Returns the thread name for this thread.
+	   On most *nix systems this will return the system thread name (settable from both within and without Loguru).
+	   On other systems it will return whatever you set in `set_thread_name()`;
+	   If no thread name is set, this will return a hexadecimal thread id.
+	   `length` should be the number of bytes available in the buffer.
+	   17 is a good number for length.
+	   `right_align_hex_id` means any hexadecimal thread id will be written to the end of buffer.
+	*/
+	LOGURU_EXPORT
+	void get_thread_name(char* buffer, unsigned long long length, bool right_align_hex_id);
+
+	/* Generates a readable stacktrace as a string.
+	   'skip' specifies how many stack frames to skip.
+	   For instance, the default skip (1) means:
+	   don't include the call to loguru::stacktrace in the stack trace. */
+	LOGURU_EXPORT
+	Text stacktrace(int skip = 1);
+
+	/*  Add a string to be replaced with something else in the stack output.
+
+		For instance, instead of having a stack trace look like this:
+			0x41f541 some_function(std::basic_ofstream<char, std::char_traits<char> >&)
+		You can clean it up with:
+			auto verbose_type_name = loguru::demangle(typeid(std::ofstream).name());
+			loguru::add_stack_cleanup(verbose_type_name.c_str(); "std::ofstream");
+		So the next time you will instead see:
+			0x41f541 some_function(std::ofstream&)
+
+		`replace_with_this` must be shorter than `find_this`.
+	*/
+	LOGURU_EXPORT
+	void add_stack_cleanup(const char* find_this, const char* replace_with_this);
+
+	// Example: demangle(typeid(std::ofstream).name()) -> "std::basic_ofstream<char, std::char_traits<char> >"
+	LOGURU_EXPORT
+	Text demangle(const char* name);
+
+	// ------------------------------------------------------------------------
+	/*
+	Not all terminals support colors, but if they do, and g_colorlogtostderr
+	is set, Loguru will write them to stderr to make errors in red, etc.
+
+	You also have the option to manually use them, via the function below.
+
+	Note, however, that if you do, the color codes could end up in your logfile!
+
+	This means if you intend to use them functions you should either:
+		* Use them on the stderr/stdout directly (bypass Loguru).
+		* Don't add file outputs to Loguru.
+		* Expect some \e[1m things in your logfile.
+
+	Usage:
+		printf("%sRed%sGreen%sBold green%sClear again\n",
+			   loguru::terminal_red(), loguru::terminal_green(),
+			   loguru::terminal_bold(), loguru::terminal_reset());
+
+	If the terminal at hand does not support colors the above output
+	will just not have funky \e[1m things showing.
+	*/
+
+	// Do the output terminal support colors?
+	LOGURU_EXPORT
+	bool terminal_has_color();
+
+	// Colors
+	LOGURU_EXPORT const char* terminal_black();
+	LOGURU_EXPORT const char* terminal_red();
+	LOGURU_EXPORT const char* terminal_green();
+	LOGURU_EXPORT const char* terminal_yellow();
+	LOGURU_EXPORT const char* terminal_blue();
+	LOGURU_EXPORT const char* terminal_purple();
+	LOGURU_EXPORT const char* terminal_cyan();
+	LOGURU_EXPORT const char* terminal_light_gray();
+	LOGURU_EXPORT const char* terminal_light_red();
+	LOGURU_EXPORT const char* terminal_white();
+
+	// Formating
+	LOGURU_EXPORT const char* terminal_bold();
+	LOGURU_EXPORT const char* terminal_underline();
+
+	// You should end each line with this!
+	LOGURU_EXPORT const char* terminal_reset();
+
+	// --------------------------------------------------------------------
+	// Error context related:
+
+	struct StringStream;
+
+	// Use this in your EcEntryBase::print_value overload.
+	LOGURU_EXPORT
+	void stream_print(StringStream& out_string_stream, const char* text);
+
+	class LOGURU_EXPORT EcEntryBase
+	{
+	public:
+		EcEntryBase(const char* file, unsigned line, const char* descr);
+		~EcEntryBase();
+		EcEntryBase(const EcEntryBase&) = delete;
+		EcEntryBase(EcEntryBase&&) = delete;
+		EcEntryBase& operator=(const EcEntryBase&) = delete;
+		EcEntryBase& operator=(EcEntryBase&&) = delete;
+
+		virtual void print_value(StringStream& out_string_stream) const = 0;
+
+		EcEntryBase* previous() const { return _previous; }
+
+	// private:
+		const char*  _file;
+		unsigned     _line;
+		const char*  _descr;
+		EcEntryBase* _previous;
+	};
+
+	template<typename T>
+	class EcEntryData : public EcEntryBase
+	{
+	public:
+		using Printer = Text(*)(T data);
+
+		EcEntryData(const char* file, unsigned line, const char* descr, T data, Printer&& printer)
+			: EcEntryBase(file, line, descr), _data(data), _printer(printer) {}
+
+		virtual void print_value(StringStream& out_string_stream) const override
+		{
+			const auto str = _printer(_data);
+			stream_print(out_string_stream, str.c_str());
+		}
+
+	private:
+		T       _data;
+		Printer _printer;
+	};
+
+	// template<typename Printer>
+	// class EcEntryLambda : public EcEntryBase
+	// {
+	// public:
+	// 	EcEntryLambda(const char* file, unsigned line, const char* descr, Printer&& printer)
+	// 		: EcEntryBase(file, line, descr), _printer(std::move(printer)) {}
+
+	// 	virtual void print_value(StringStream& out_string_stream) const override
+	// 	{
+	// 		const auto str = _printer();
+	// 		stream_print(out_string_stream, str.c_str());
+	// 	}
+
+	// private:
+	// 	Printer _printer;
+	// };
+
+	// template<typename Printer>
+	// EcEntryLambda<Printer> make_ec_entry_lambda(const char* file, unsigned line, const char* descr, Printer&& printer)
+	// {
+	// 	return {file, line, descr, std::move(printer)};
+	// }
+
+	template <class T>
+	struct decay_char_array { using type = T; };
+
+	template <unsigned long long  N>
+	struct decay_char_array<const char(&)[N]> { using type = const char*; };
+
+	template <class T>
+	struct make_const_ptr { using type = T; };
+
+	template <class T>
+	struct make_const_ptr<T*> { using type = const T*; };
+
+	template <class T>
+	struct make_ec_type { using type = typename make_const_ptr<typename decay_char_array<T>::type>::type; };
+
+	/* 	A stack trace gives you the names of the function at the point of a crash.
+		With ERROR_CONTEXT, you can also get the values of select local variables.
+		Usage:
+
+		void process_customers(const std::string& filename)
+		{
+			ERROR_CONTEXT("Processing file", filename.c_str());
+			for (int customer_index : ...)
+			{
+				ERROR_CONTEXT("Customer index", customer_index);
+				...
+			}
+		}
+
+		The context is in effect during the scope of the ERROR_CONTEXT.
+		Use loguru::get_error_context() to get the contents of the active error contexts.
+
+		Example result:
+
+		------------------------------------------------
+		[ErrorContext]                main.cpp:416   Processing file:    "customers.json"
+		[ErrorContext]                main.cpp:417   Customer index:     42
+		------------------------------------------------
+
+		Error contexts are printed automatically on crashes, and only on crashes.
+		This makes them much faster than logging the value of a variable.
+	*/
+	#define ERROR_CONTEXT(descr, data)                                             \
+		const loguru::EcEntryData<loguru::make_ec_type<decltype(data)>::type>      \
+			LOGURU_ANONYMOUS_VARIABLE(error_context_scope_)(                       \
+				__FILE__, __LINE__, descr, data,                                   \
+				static_cast<loguru::EcEntryData<loguru::make_ec_type<decltype(data)>::type>::Printer>(loguru::ec_to_text) ) // For better error messages
+
+/*
+	#define ERROR_CONTEXT(descr, data)                                 \
+		const auto LOGURU_ANONYMOUS_VARIABLE(error_context_scope_)(    \
+			loguru::make_ec_entry_lambda(__FILE__, __LINE__, descr,    \
+				[=](){ return loguru::ec_to_text(data); }))
+*/
+
+	using EcHandle = const EcEntryBase*;
+
+	/*
+		Get a light-weight handle to the error context stack on this thread.
+		The handle is valid as long as the current thread has no changes to its error context stack.
+		You can pass the handle to loguru::get_error_context on another thread.
+		This can be very useful for when you have a parent thread spawning several working threads,
+		and you want the error context of the parent thread to get printed (too) when there is an
+		error on the child thread. You can accomplish this thusly:
+
+		void foo(const char* parameter)
+		{
+			ERROR_CONTEXT("parameter", parameter)
+			const auto parent_ec_handle = loguru::get_thread_ec_handle();
+
+			std::thread([=]{
+				loguru::set_thread_name("child thread");
+				ERROR_CONTEXT("parent context", parent_ec_handle);
+				dangerous_code();
+			}.join();
+		}
+
+	*/
+	LOGURU_EXPORT
+	EcHandle get_thread_ec_handle();
+
+	// Get a string describing the current stack of error context. Empty string if there is none.
+	LOGURU_EXPORT
+	Text get_error_context();
+
+	// Get a string describing the error context of the given thread handle.
+	LOGURU_EXPORT
+	Text get_error_context_for(EcHandle ec_handle);
+
+	// ------------------------------------------------------------------------
+
+	LOGURU_EXPORT Text ec_to_text(const char* data);
+	LOGURU_EXPORT Text ec_to_text(char data);
+	LOGURU_EXPORT Text ec_to_text(int data);
+	LOGURU_EXPORT Text ec_to_text(unsigned int data);
+	LOGURU_EXPORT Text ec_to_text(long data);
+	LOGURU_EXPORT Text ec_to_text(unsigned long data);
+	LOGURU_EXPORT Text ec_to_text(long long data);
+	LOGURU_EXPORT Text ec_to_text(unsigned long long data);
+	LOGURU_EXPORT Text ec_to_text(float data);
+	LOGURU_EXPORT Text ec_to_text(double data);
+	LOGURU_EXPORT Text ec_to_text(long double data);
+	LOGURU_EXPORT Text ec_to_text(EcHandle);
+
+	/*
+	You can add ERROR_CONTEXT support for your own types by overloading ec_to_text. Here's how:
+
+	some.hpp:
+		namespace loguru {
+			Text ec_to_text(MySmallType data)
+			Text ec_to_text(const MyBigType* data)
+		} // namespace loguru
+
+	some.cpp:
+		namespace loguru {
+			Text ec_to_text(MySmallType small_value)
+			{
+				// Called only when needed, i.e. on a crash.
+				std::string str = small_value.as_string(); // Format 'small_value' here somehow.
+				return Text{STRDUP(str.c_str())};
+			}
+
+			Text ec_to_text(const MyBigType* big_value)
+			{
+				// Called only when needed, i.e. on a crash.
+				std::string str = big_value->as_string(); // Format 'big_value' here somehow.
+				return Text{STRDUP(str.c_str())};
+			}
+		} // namespace loguru
+
+	Any file that include some.hpp:
+		void foo(MySmallType small, const MyBigType& big)
+		{
+			ERROR_CONTEXT("Small", small); // Copy ´small` by value.
+			ERROR_CONTEXT("Big",   &big);  // `big` should not change during this scope!
+			....
+		}
+	*/
+} // namespace loguru
+
+LOGURU_ANONYMOUS_NAMESPACE_END
+
+// --------------------------------------------------------------------
+// Logging macros
+
+// LOG_F(2, "Only logged if verbosity is 2 or higher: %d", some_number);
+#define VLOG_F(verbosity, ...)                                                                     \
+	((verbosity) > loguru::current_verbosity_cutoff()) ? (void)0                                   \
+									  : loguru::log(verbosity, __FILE__, __LINE__, __VA_ARGS__)
+
+// LOG_F(INFO, "Foo: %d", some_number);
+#define LOG_F(verbosity_name, ...) VLOG_F(loguru::Verbosity_ ## verbosity_name, __VA_ARGS__)
+
+#define VLOG_IF_F(verbosity, cond, ...)                                                            \
+	((verbosity) > loguru::current_verbosity_cutoff() || (cond) == false)                          \
+		? (void)0                                                                                  \
+		: loguru::log(verbosity, __FILE__, __LINE__, __VA_ARGS__)
+
+#define LOG_IF_F(verbosity_name, cond, ...)                                                        \
+	VLOG_IF_F(loguru::Verbosity_ ## verbosity_name, cond, __VA_ARGS__)
+
+#define VLOG_SCOPE_F(verbosity, ...)                                                               \
+	loguru::LogScopeRAII LOGURU_ANONYMOUS_VARIABLE(error_context_RAII_) =                          \
+	((verbosity) > loguru::current_verbosity_cutoff()) ? loguru::LogScopeRAII() :                  \
+	loguru::LogScopeRAII(verbosity, __FILE__, __LINE__, __VA_ARGS__)
+
+// Raw logging - no preamble, no indentation. Slightly faster than full logging.
+#define RAW_VLOG_F(verbosity, ...)                                                                 \
+	((verbosity) > loguru::current_verbosity_cutoff()) ? (void)0                                   \
+									  : loguru::raw_log(verbosity, __FILE__, __LINE__, __VA_ARGS__)
+
+#define RAW_LOG_F(verbosity_name, ...) RAW_VLOG_F(loguru::Verbosity_ ## verbosity_name, __VA_ARGS__)
+
+// Use to book-end a scope. Affects logging on all threads.
+#define LOG_SCOPE_F(verbosity_name, ...)                                                           \
+	VLOG_SCOPE_F(loguru::Verbosity_ ## verbosity_name, __VA_ARGS__)
+
+#define LOG_SCOPE_FUNCTION(verbosity_name) LOG_SCOPE_F(verbosity_name, __func__)
+
+// -----------------------------------------------
+// ABORT_F macro. Usage:  ABORT_F("Cause of error: %s", error_str);
+
+// Message is optional
+#define ABORT_F(...) loguru::log_and_abort(0, "ABORT: ", __FILE__, __LINE__, __VA_ARGS__)
+
+// --------------------------------------------------------------------
+// CHECK_F macros:
+
+#define CHECK_WITH_INFO_F(test, info, ...)                                                         \
+	LOGURU_PREDICT_TRUE((test) == true) ? (void)0 : loguru::log_and_abort(0, "CHECK FAILED:  " info "  ", __FILE__,      \
+													   __LINE__, ##__VA_ARGS__)
+
+/* Checked at runtime too. Will print error, then call fatal_handler (if any), then 'abort'.
+   Note that the test must be boolean.
+   CHECK_F(ptr); will not compile, but CHECK_F(ptr != nullptr); will. */
+#define CHECK_F(test, ...) CHECK_WITH_INFO_F(test, #test, ##__VA_ARGS__)
+
+#define CHECK_NOTNULL_F(x, ...) CHECK_WITH_INFO_F((x) != nullptr, #x " != nullptr", ##__VA_ARGS__)
+
+#define CHECK_OP_F(expr_left, expr_right, op, ...)                                                 \
+	do                                                                                             \
+	{                                                                                              \
+		auto val_left = expr_left;                                                                 \
+		auto val_right = expr_right;                                                               \
+		if (! LOGURU_PREDICT_TRUE(val_left op val_right))                                          \
+		{                                                                                          \
+			auto str_left = loguru::format_value(val_left);                                        \
+			auto str_right = loguru::format_value(val_right);                                      \
+			auto fail_info = loguru::textprintf("CHECK FAILED:  " LOGURU_FMT(s) " " LOGURU_FMT(s) " " LOGURU_FMT(s) "  (" LOGURU_FMT(s) " " LOGURU_FMT(s) " " LOGURU_FMT(s) ")  ",           \
+				#expr_left, #op, #expr_right, str_left.c_str(), #op, str_right.c_str());           \
+			auto user_msg = loguru::textprintf(__VA_ARGS__);                                       \
+			loguru::log_and_abort(0, fail_info.c_str(), __FILE__, __LINE__,                        \
+			                      LOGURU_FMT(s), user_msg.c_str());                                         \
+		}                                                                                          \
+	} while (false)
+
+#ifndef LOGURU_DEBUG_LOGGING
+	#ifndef NDEBUG
+		#define LOGURU_DEBUG_LOGGING 1
+	#else
+		#define LOGURU_DEBUG_LOGGING 0
+	#endif
+#endif
+
+#if LOGURU_DEBUG_LOGGING
+	// Debug logging enabled:
+	#define DLOG_F(verbosity_name, ...)     LOG_F(verbosity_name, __VA_ARGS__)
+	#define DVLOG_F(verbosity, ...)         VLOG_F(verbosity, __VA_ARGS__)
+	#define DLOG_IF_F(verbosity_name, ...)  LOG_IF_F(verbosity_name, __VA_ARGS__)
+	#define DVLOG_IF_F(verbosity, ...)      VLOG_IF_F(verbosity, __VA_ARGS__)
+	#define DRAW_LOG_F(verbosity_name, ...) RAW_LOG_F(verbosity_name, __VA_ARGS__)
+	#define DRAW_VLOG_F(verbosity, ...)     RAW_VLOG_F(verbosity, __VA_ARGS__)
+#else
+	// Debug logging disabled:
+	#define DLOG_F(verbosity_name, ...)
+	#define DVLOG_F(verbosity, ...)
+	#define DLOG_IF_F(verbosity_name, ...)
+	#define DVLOG_IF_F(verbosity, ...)
+	#define DRAW_LOG_F(verbosity_name, ...)
+	#define DRAW_VLOG_F(verbosity, ...)
+#endif
+
+#define CHECK_EQ_F(a, b, ...) CHECK_OP_F(a, b, ==, ##__VA_ARGS__)
+#define CHECK_NE_F(a, b, ...) CHECK_OP_F(a, b, !=, ##__VA_ARGS__)
+#define CHECK_LT_F(a, b, ...) CHECK_OP_F(a, b, < , ##__VA_ARGS__)
+#define CHECK_GT_F(a, b, ...) CHECK_OP_F(a, b, > , ##__VA_ARGS__)
+#define CHECK_LE_F(a, b, ...) CHECK_OP_F(a, b, <=, ##__VA_ARGS__)
+#define CHECK_GE_F(a, b, ...) CHECK_OP_F(a, b, >=, ##__VA_ARGS__)
+
+#ifndef LOGURU_DEBUG_CHECKS
+	#ifndef NDEBUG
+		#define LOGURU_DEBUG_CHECKS 1
+	#else
+		#define LOGURU_DEBUG_CHECKS 0
+	#endif
+#endif
+
+#if LOGURU_DEBUG_CHECKS
+	// Debug checks enabled:
+	#define DCHECK_F(test, ...)             CHECK_F(test, ##__VA_ARGS__)
+	#define DCHECK_NOTNULL_F(x, ...)        CHECK_NOTNULL_F(x, ##__VA_ARGS__)
+	#define DCHECK_EQ_F(a, b, ...)          CHECK_EQ_F(a, b, ##__VA_ARGS__)
+	#define DCHECK_NE_F(a, b, ...)          CHECK_NE_F(a, b, ##__VA_ARGS__)
+	#define DCHECK_LT_F(a, b, ...)          CHECK_LT_F(a, b, ##__VA_ARGS__)
+	#define DCHECK_LE_F(a, b, ...)          CHECK_LE_F(a, b, ##__VA_ARGS__)
+	#define DCHECK_GT_F(a, b, ...)          CHECK_GT_F(a, b, ##__VA_ARGS__)
+	#define DCHECK_GE_F(a, b, ...)          CHECK_GE_F(a, b, ##__VA_ARGS__)
+#else
+	// Debug checks disabled:
+	#define DCHECK_F(test, ...)
+	#define DCHECK_NOTNULL_F(x, ...)
+	#define DCHECK_EQ_F(a, b, ...)
+	#define DCHECK_NE_F(a, b, ...)
+	#define DCHECK_LT_F(a, b, ...)
+	#define DCHECK_LE_F(a, b, ...)
+	#define DCHECK_GT_F(a, b, ...)
+	#define DCHECK_GE_F(a, b, ...)
+#endif // NDEBUG
+
+
+#if LOGURU_REDEFINE_ASSERT
+	#undef assert
+	#ifndef NDEBUG
+		// Debug:
+		#define assert(test) CHECK_WITH_INFO_F(!!(test), #test) // HACK
+	#else
+		#define assert(test)
+	#endif
+#endif // LOGURU_REDEFINE_ASSERT
+
+#endif // LOGURU_HAS_DECLARED_FORMAT_HEADER
+
+// ----------------------------------------------------------------------------
+// .dP"Y8 888888 88""Yb 888888    db    8b    d8 .dP"Y8
+// `Ybo."   88   88__dP 88__     dPYb   88b  d88 `Ybo."
+// o.`Y8b   88   88"Yb  88""    dP__Yb  88YbdP88 o.`Y8b
+// 8bodP'   88   88  Yb 888888 dP""""Yb 88 YY 88 8bodP'
+
+#if LOGURU_WITH_STREAMS
+#ifndef LOGURU_HAS_DECLARED_STREAMS_HEADER
+#define LOGURU_HAS_DECLARED_STREAMS_HEADER
+
+/* This file extends loguru to enable std::stream-style logging, a la Glog.
+   It's an optional feature behind the LOGURU_WITH_STREAMS settings
+   because including it everywhere will slow down compilation times.
+*/
+
+#include <cstdarg>
+#include <sstream> // Adds about 38 kLoC on clang.
+#include <string>
+
+LOGURU_ANONYMOUS_NAMESPACE_BEGIN
+
+namespace loguru
+{
+	// Like sprintf, but returns the formated text.
+	LOGURU_EXPORT
+	std::string strprintf(LOGURU_FORMAT_STRING_TYPE format, ...) LOGURU_PRINTF_LIKE(1, 2);
+
+	// Like vsprintf, but returns the formated text.
+	LOGURU_EXPORT
+	std::string vstrprintf(LOGURU_FORMAT_STRING_TYPE format, va_list) LOGURU_PRINTF_LIKE(1, 0);
+
+	class LOGURU_EXPORT StreamLogger
+	{
+	public:
+		StreamLogger(Verbosity verbosity, const char* file, unsigned line) : _verbosity(verbosity), _file(file), _line(line) {}
+		~StreamLogger() noexcept(false);
+
+		template<typename T>
+		StreamLogger& operator<<(const T& t)
+		{
+			_ss << t;
+			return *this;
+		}
+
+		// std::endl and other iomanip:s.
+		StreamLogger& operator<<(std::ostream&(*f)(std::ostream&))
+		{
+			f(_ss);
+			return *this;
+		}
+
+	private:
+		Verbosity   _verbosity;
+		const char* _file;
+		unsigned    _line;
+		std::ostringstream _ss;
+	};
+
+	class LOGURU_EXPORT AbortLogger
+	{
+	public:
+		AbortLogger(const char* expr, const char* file, unsigned line) : _expr(expr), _file(file), _line(line) { }
+		LOGURU_NORETURN ~AbortLogger() noexcept(false);
+
+		template<typename T>
+		AbortLogger& operator<<(const T& t)
+		{
+			_ss << t;
+			return *this;
+		}
+
+		// std::endl and other iomanip:s.
+		AbortLogger& operator<<(std::ostream&(*f)(std::ostream&))
+		{
+			f(_ss);
+			return *this;
+		}
+
+	private:
+		const char*        _expr;
+		const char*        _file;
+		unsigned           _line;
+		std::ostringstream _ss;
+	};
+
+	class LOGURU_EXPORT Voidify
+	{
+	public:
+		Voidify() {}
+		// This has to be an operator with a precedence lower than << but higher than ?:
+		void operator&(const StreamLogger&) { }
+		void operator&(const AbortLogger&)  { }
+	};
+
+	/*  Helper functions for CHECK_OP_S macro.
+		GLOG trick: The (int, int) specialization works around the issue that the compiler
+		will not instantiate the template version of the function on values of unnamed enum type. */
+	#define DEFINE_CHECK_OP_IMPL(name, op)                                                             \
+		template <typename T1, typename T2>                                                            \
+		inline std::string* name(const char* expr, const T1& v1, const char* op_str, const T2& v2)     \
+		{                                                                                              \
+			if (LOGURU_PREDICT_TRUE(v1 op v2)) { return NULL; }                                        \
+			std::ostringstream ss;                                                                     \
+			ss << "CHECK FAILED:  " << expr << "  (" << v1 << " " << op_str << " " << v2 << ")  ";     \
+			return new std::string(ss.str());                                                          \
+		}                                                                                              \
+		inline std::string* name(const char* expr, int v1, const char* op_str, int v2)                 \
+		{                                                                                              \
+			return name<int, int>(expr, v1, op_str, v2);                                               \
+		}
+
+	DEFINE_CHECK_OP_IMPL(check_EQ_impl, ==)
+	DEFINE_CHECK_OP_IMPL(check_NE_impl, !=)
+	DEFINE_CHECK_OP_IMPL(check_LE_impl, <=)
+	DEFINE_CHECK_OP_IMPL(check_LT_impl, < )
+	DEFINE_CHECK_OP_IMPL(check_GE_impl, >=)
+	DEFINE_CHECK_OP_IMPL(check_GT_impl, > )
+	#undef DEFINE_CHECK_OP_IMPL
+
+	/*  GLOG trick: Function is overloaded for integral types to allow static const integrals
+		declared in classes and not defined to be used as arguments to CHECK* macros. */
+	template <class T>
+	inline const T&           referenceable_value(const T&           t) { return t; }
+	inline char               referenceable_value(char               t) { return t; }
+	inline unsigned char      referenceable_value(unsigned char      t) { return t; }
+	inline signed char        referenceable_value(signed char        t) { return t; }
+	inline short              referenceable_value(short              t) { return t; }
+	inline unsigned short     referenceable_value(unsigned short     t) { return t; }
+	inline int                referenceable_value(int                t) { return t; }
+	inline unsigned int       referenceable_value(unsigned int       t) { return t; }
+	inline long               referenceable_value(long               t) { return t; }
+	inline unsigned long      referenceable_value(unsigned long      t) { return t; }
+	inline long long          referenceable_value(long long          t) { return t; }
+	inline unsigned long long referenceable_value(unsigned long long t) { return t; }
+} // namespace loguru
+
+LOGURU_ANONYMOUS_NAMESPACE_END
+
+// -----------------------------------------------
+// Logging macros:
+
+// usage:  LOG_STREAM(INFO) << "Foo " << std::setprecision(10) << some_value;
+#define VLOG_IF_S(verbosity, cond)                                                                 \
+	((verbosity) > loguru::current_verbosity_cutoff() || (cond) == false)                          \
+		? (void)0                                                                                  \
+		: loguru::Voidify() & loguru::StreamLogger(verbosity, __FILE__, __LINE__)
+#define LOG_IF_S(verbosity_name, cond) VLOG_IF_S(loguru::Verbosity_ ## verbosity_name, cond)
+#define VLOG_S(verbosity)              VLOG_IF_S(verbosity, true)
+#define LOG_S(verbosity_name)          VLOG_S(loguru::Verbosity_ ## verbosity_name)
+
+// -----------------------------------------------
+// ABORT_S macro. Usage:  ABORT_S() << "Causo of error: " << details;
+
+#define ABORT_S() loguru::Voidify() & loguru::AbortLogger("ABORT: ", __FILE__, __LINE__)
+
+// -----------------------------------------------
+// CHECK_S macros:
+
+#define CHECK_WITH_INFO_S(cond, info)                                                              \
+	LOGURU_PREDICT_TRUE((cond) == true)                                                            \
+		? (void)0                                                                                  \
+		: loguru::Voidify() & loguru::AbortLogger("CHECK FAILED:  " info "  ", __FILE__, __LINE__)
+
+#define CHECK_S(cond) CHECK_WITH_INFO_S(cond, #cond)
+#define CHECK_NOTNULL_S(x) CHECK_WITH_INFO_S((x) != nullptr, #x " != nullptr")
+
+#define CHECK_OP_S(function_name, expr1, op, expr2)                                                \
+	while (auto error_string = loguru::function_name(#expr1 " " #op " " #expr2,                    \
+													 loguru::referenceable_value(expr1), #op,      \
+													 loguru::referenceable_value(expr2)))          \
+		loguru::AbortLogger(error_string->c_str(), __FILE__, __LINE__)
+
+#define CHECK_EQ_S(expr1, expr2) CHECK_OP_S(check_EQ_impl, expr1, ==, expr2)
+#define CHECK_NE_S(expr1, expr2) CHECK_OP_S(check_NE_impl, expr1, !=, expr2)
+#define CHECK_LE_S(expr1, expr2) CHECK_OP_S(check_LE_impl, expr1, <=, expr2)
+#define CHECK_LT_S(expr1, expr2) CHECK_OP_S(check_LT_impl, expr1, < , expr2)
+#define CHECK_GE_S(expr1, expr2) CHECK_OP_S(check_GE_impl, expr1, >=, expr2)
+#define CHECK_GT_S(expr1, expr2) CHECK_OP_S(check_GT_impl, expr1, > , expr2)
+
+#if LOGURU_DEBUG_LOGGING
+	// Debug logging enabled:
+	#define DVLOG_IF_S(verbosity, cond)     VLOG_IF_S(verbosity, cond)
+	#define DLOG_IF_S(verbosity_name, cond) LOG_IF_S(verbosity_name, cond)
+	#define DVLOG_S(verbosity)              VLOG_S(verbosity)
+	#define DLOG_S(verbosity_name)          LOG_S(verbosity_name)
+#else
+	// Debug logging disabled:
+	#define DVLOG_IF_S(verbosity, cond)                                                     \
+		(true || (verbosity) > loguru::current_verbosity_cutoff() || (cond) == false)       \
+			? (void)0                                                                       \
+			: loguru::Voidify() & loguru::StreamLogger(verbosity, __FILE__, __LINE__)
+
+	#define DLOG_IF_S(verbosity_name, cond) DVLOG_IF_S(loguru::Verbosity_ ## verbosity_name, cond)
+	#define DVLOG_S(verbosity)              DVLOG_IF_S(verbosity, true)
+	#define DLOG_S(verbosity_name)          DVLOG_S(loguru::Verbosity_ ## verbosity_name)
+#endif
+
+#if LOGURU_DEBUG_CHECKS
+	// Debug checks enabled:
+	#define DCHECK_S(cond)                  CHECK_S(cond)
+	#define DCHECK_NOTNULL_S(x)             CHECK_NOTNULL_S(x)
+	#define DCHECK_EQ_S(a, b)               CHECK_EQ_S(a, b)
+	#define DCHECK_NE_S(a, b)               CHECK_NE_S(a, b)
+	#define DCHECK_LT_S(a, b)               CHECK_LT_S(a, b)
+	#define DCHECK_LE_S(a, b)               CHECK_LE_S(a, b)
+	#define DCHECK_GT_S(a, b)               CHECK_GT_S(a, b)
+	#define DCHECK_GE_S(a, b)               CHECK_GE_S(a, b)
+#else
+// Debug checks disabled:
+	#define DCHECK_S(cond)                  CHECK_S(true || (cond))
+	#define DCHECK_NOTNULL_S(x)             CHECK_S(true || (x) != nullptr)
+	#define DCHECK_EQ_S(a, b)               CHECK_S(true || (a) == (b))
+	#define DCHECK_NE_S(a, b)               CHECK_S(true || (a) != (b))
+	#define DCHECK_LT_S(a, b)               CHECK_S(true || (a) <  (b))
+	#define DCHECK_LE_S(a, b)               CHECK_S(true || (a) <= (b))
+	#define DCHECK_GT_S(a, b)               CHECK_S(true || (a) >  (b))
+	#define DCHECK_GE_S(a, b)               CHECK_S(true || (a) >= (b))
+#endif
+
+#if LOGURU_REPLACE_GLOG
+	#undef LOG
+	#undef VLOG
+	#undef LOG_IF
+	#undef VLOG_IF
+	#undef CHECK
+	#undef CHECK_NOTNULL
+	#undef CHECK_EQ
+	#undef CHECK_NE
+	#undef CHECK_LT
+	#undef CHECK_LE
+	#undef CHECK_GT
+	#undef CHECK_GE
+	#undef DLOG
+	#undef DVLOG
+	#undef DLOG_IF
+	#undef DVLOG_IF
+	#undef DCHECK
+	#undef DCHECK_NOTNULL
+	#undef DCHECK_EQ
+	#undef DCHECK_NE
+	#undef DCHECK_LT
+	#undef DCHECK_LE
+	#undef DCHECK_GT
+	#undef DCHECK_GE
+	#undef VLOG_IS_ON
+
+	#define LOG            LOG_S
+	#define VLOG           VLOG_S
+	#define LOG_IF         LOG_IF_S
+	#define VLOG_IF        VLOG_IF_S
+	#define CHECK(cond)    CHECK_S(!!(cond))
+	#define CHECK_NOTNULL  CHECK_NOTNULL_S
+	#define CHECK_EQ       CHECK_EQ_S
+	#define CHECK_NE       CHECK_NE_S
+	#define CHECK_LT       CHECK_LT_S
+	#define CHECK_LE       CHECK_LE_S
+	#define CHECK_GT       CHECK_GT_S
+	#define CHECK_GE       CHECK_GE_S
+	#define DLOG           DLOG_S
+	#define DVLOG          DVLOG_S
+	#define DLOG_IF        DLOG_IF_S
+	#define DVLOG_IF       DVLOG_IF_S
+	#define DCHECK         DCHECK_S
+	#define DCHECK_NOTNULL DCHECK_NOTNULL_S
+	#define DCHECK_EQ      DCHECK_EQ_S
+	#define DCHECK_NE      DCHECK_NE_S
+	#define DCHECK_LT      DCHECK_LT_S
+	#define DCHECK_LE      DCHECK_LE_S
+	#define DCHECK_GT      DCHECK_GT_S
+	#define DCHECK_GE      DCHECK_GE_S
+	#define VLOG_IS_ON(verbosity) ((verbosity) <= loguru::current_verbosity_cutoff())
+
+#endif // LOGURU_REPLACE_GLOG
+
+#endif // LOGURU_WITH_STREAMS
+
+#endif // LOGURU_HAS_DECLARED_STREAMS_HEADER
diff --git a/tomviz/main.cxx b/tomviz/main.cxx
index 4710bd9d6..f7f142efa 100644
--- a/tomviz/main.cxx
+++ b/tomviz/main.cxx
@@ -14,7 +14,9 @@
 #include <vtkNew.h>
 #include <vtkObjectFactory.h>
 
+#include "loguru.hpp"
 #include "MainWindow.h"
+#include "PythonUtilities.h"
 #include "tomvizConfig.h"
 #include "tomvizPythonConfig.h"
 
@@ -22,6 +24,10 @@
 
 int main(int argc, char** argv)
 {
+  // Set up loguru, for printing stack traces on crashes
+  loguru::g_stderr_verbosity = loguru::Verbosity_ERROR;
+  loguru::init(argc, argv);
+
   QSurfaceFormat::setDefaultFormat(QVTKOpenGLStereoWidget::defaultFormat());
 
   QCoreApplication::setApplicationName("tomviz");
@@ -49,6 +55,10 @@ int main(int argc, char** argv)
   // modules.
   qputenv("TOMVIZ_APPLICATION", "1");
 
+  // If we don't initialize Python here, the application freezes when exiting
+  // at the very end, during Py_Finalize().
+  tomviz::Python::initialize();
+
   setlocale(LC_NUMERIC, "C");
   pqPVApplicationCore appCore(argc, argv);
   tomviz::MainWindow window;
diff --git a/tomviz/modules/ModuleManager.cxx b/tomviz/modules/ModuleManager.cxx
index 37a79eead..72733fd27 100644
--- a/tomviz/modules/ModuleManager.cxx
+++ b/tomviz/modules/ModuleManager.cxx
@@ -222,6 +222,36 @@ class ModuleManager::MMInternals
     auto root = rootDataSourceDependency(dep, dataSources);
     return root.value("id").toString() != dep;
   }
+
+  void removeInvalidDataSources()
+  {
+    int i = 0;
+    while (i < DataSources.size()) {
+      if (DataSources[i]) {
+        // Valid
+        i += 1;
+        continue;
+      } else {
+        // Invalid. Remove.
+        DataSources.removeAt(i);
+      }
+    }
+  }
+
+  void removeInvalidChildDataSources()
+  {
+    int i = 0;
+    while (i < ChildDataSources.size()) {
+      if (ChildDataSources[i]) {
+        // Valid
+        i += 1;
+        continue;
+      } else {
+        // Invalid. Remove.
+        ChildDataSources.removeAt(i);
+      }
+    }
+  }
 };
 
 ModuleManager::ModuleManager(QObject* parentObject)
@@ -249,6 +279,7 @@ void ModuleManager::reset()
 
 bool ModuleManager::hasRunningOperators()
 {
+  d->removeInvalidDataSources();
   for (QPointer<DataSource> dsource : d->DataSources) {
     if (dsource->pipeline()->isRunning()) {
       return true;
@@ -259,6 +290,9 @@ bool ModuleManager::hasRunningOperators()
 
 QList<DataSource*> ModuleManager::dataSources()
 {
+  // Somehow we have invalid data sources around. Make sure
+  // those are removed.
+  d->removeInvalidDataSources();
   QList<DataSource*> ret;
   std::copy(d->DataSources.begin(), d->DataSources.end(),
             std::back_inserter(ret));
@@ -267,6 +301,9 @@ QList<DataSource*> ModuleManager::dataSources()
 
 QList<DataSource*> ModuleManager::childDataSources()
 {
+  // Somehow we have invalid data sources around. Make sure
+  // those are removed.
+  d->removeInvalidChildDataSources();
   QList<DataSource*> ret;
   std::copy(d->ChildDataSources.begin(), d->ChildDataSources.end(),
             std::back_inserter(ret));
@@ -321,6 +358,7 @@ QStringList ModuleManager::createUniqueLabels(const QList<DataSource*>& sources)
 
 void ModuleManager::addDataSource(DataSource* dataSource)
 {
+  d->removeInvalidDataSources();
   if (dataSource && !d->DataSources.contains(dataSource)) {
     d->DataSources.push_back(dataSource);
     emit dataSourceAdded(dataSource);
@@ -329,6 +367,7 @@ void ModuleManager::addDataSource(DataSource* dataSource)
 
 void ModuleManager::addChildDataSource(DataSource* dataSource)
 {
+  d->removeInvalidChildDataSources();
   if (dataSource && !d->ChildDataSources.contains(dataSource)) {
     d->ChildDataSources.push_back(dataSource);
     emit childDataSourceAdded(dataSource);
@@ -337,6 +376,8 @@ void ModuleManager::addChildDataSource(DataSource* dataSource)
 
 void ModuleManager::removeDataSource(DataSource* dataSource)
 {
+  d->removeInvalidDataSources();
+  d->removeInvalidChildDataSources();
   if (d->DataSources.removeOne(dataSource) ||
       d->ChildDataSources.removeOne(dataSource)) {
     emit dataSourceRemoved(dataSource);
@@ -346,6 +387,7 @@ void ModuleManager::removeDataSource(DataSource* dataSource)
 
 void ModuleManager::removeChildDataSource(DataSource* dataSource)
 {
+  d->removeInvalidChildDataSources();
   if (d->ChildDataSources.removeOne(dataSource)) {
     emit childDataSourceRemoved(dataSource);
     dataSource->deleteLater();
@@ -354,6 +396,7 @@ void ModuleManager::removeChildDataSource(DataSource* dataSource)
 
 void ModuleManager::removeAllDataSources()
 {
+  d->removeInvalidDataSources();
   foreach (DataSource* dataSource, d->DataSources) {
     emit dataSourceRemoved(dataSource);
     dataSource->deleteLater();
@@ -394,6 +437,7 @@ void ModuleManager::removeOperator(Operator* op)
 
 bool ModuleManager::isChild(DataSource* source) const
 {
+  d->removeInvalidChildDataSources();
   return (d->ChildDataSources.indexOf(source) >= 0);
 }
 
@@ -577,6 +621,9 @@ QJsonArray jsonArrayFromXmlDouble(pugi::xml_node node)
 bool ModuleManager::serialize(QJsonObject& doc, const QDir& stateDir,
                               bool interactive) const
 {
+  d->removeInvalidDataSources();
+  d->removeInvalidChildDataSources();
+
   QJsonObject tvObj;
   tvObj["version"] = QString(TOMVIZ_VERSION);
   if (QString(TOMVIZ_VERSION_EXTRA).size() > 0) {
@@ -1274,6 +1321,7 @@ vtkSMViewProxy* ModuleManager::lookupView(int id)
 
 bool ModuleManager::hasDataSources()
 {
+  d->removeInvalidDataSources();
   return !d->DataSources.empty();
 }
 
diff --git a/tomviz/modules/ModuleSlice.h b/tomviz/modules/ModuleSlice.h
index b21e94ca1..9f6594722 100644
--- a/tomviz/modules/ModuleSlice.h
+++ b/tomviz/modules/ModuleSlice.h
@@ -76,6 +76,7 @@ class ModuleSlice : public Module
   bool updateClippingPlane(vtkPlane* plane, bool newFilter) override;
 
   bool isOrtho() const;
+  int slice() const { return m_slice; }
   int maxSlice() const;
 
   void onDirectionChanged(Direction direction);
diff --git a/tomviz/operators/OperatorPropertiesPanel.cxx b/tomviz/operators/OperatorPropertiesPanel.cxx
index 59a80b85a..af10dc559 100644
--- a/tomviz/operators/OperatorPropertiesPanel.cxx
+++ b/tomviz/operators/OperatorPropertiesPanel.cxx
@@ -49,7 +49,7 @@ void OperatorPropertiesPanel::setOperator(Operator* op)
     } else {
       auto description = new QLabel(op->label());
       layout()->addWidget(description);
-      connect(op, &Operator::labelModified, [this, description]() {
+      connect(op, &Operator::labelModified, m_activeOperator, [this, description]() {
         description->setText(m_activeOperator->label());
       });
     }
diff --git a/tomviz/operators/OperatorPython.cxx b/tomviz/operators/OperatorPython.cxx
index 2ccb4c4a7..a2af5ed3a 100644
--- a/tomviz/operators/OperatorPython.cxx
+++ b/tomviz/operators/OperatorPython.cxx
@@ -668,8 +668,9 @@ QJsonObject OperatorPython::serialize() const
   }
 
   if (!helpUrl().isEmpty()) {
-    json["help"] = QJsonObject();
-    json["help"].toObject()["url"] = helpUrl();
+    auto helpObj = QJsonObject();
+    helpObj["url"] = helpUrl();
+    json["help"] = helpObj;
   }
 
   return json;
@@ -856,7 +857,9 @@ void OperatorPython::setHelpFromJson(const QJsonObject& json)
   setHelpUrl("");
   auto helpNode = json["help"];
   if (!helpNode.isUndefined() && !helpNode.isNull()) {
-    auto helpNodeUrl = helpNode.toObject()["url"];
+    // Need to keep a reference to the object or it gets deleted
+    auto obj = helpNode.toObject();
+    auto helpNodeUrl = obj["url"];
     if (!helpNodeUrl.isUndefined() && !helpNodeUrl.isNull()) {
       setHelpUrl(helpNodeUrl.toString());
     }
diff --git a/tomviz/python/AutoCrossCorrelationTiltImageAlignment.json b/tomviz/python/AutoCrossCorrelationTiltImageAlignment.json
index c6a791b39..91c39a39c 100644
--- a/tomviz/python/AutoCrossCorrelationTiltImageAlignment.json
+++ b/tomviz/python/AutoCrossCorrelationTiltImageAlignment.json
@@ -1,10 +1,41 @@
 {
-  "externalCompatible": false,
-  "results" : [
+  "name" : "AutoCrossCorrelationTiltImageAlignment",
+  "label" : "Auto Tilt Image Align (XCORR)",
+  "description" : "Automatically align tilt images by cross-correlation",
+  "parameters" : [
     {
-      "name" : "alignments",
-      "label" : "Alignments",
-      "type" : "table"
+      "name" : "transform_source",
+      "label" : "Transformation Source",
+      "description" : "The source of the transformation shifts (i. e., generate them, load them from a file, etc.)",
+      "type" : "enumeration",
+      "default" : 0,
+      "options" : [
+        {"Generate" : "generate"},
+        {"Load From File": "from_file"}
+      ]
+    },
+    {
+      "name" : "transform_file",
+      "label" : "Transformations File",
+      "description": "Transformation file (npz format) to apply",
+      "type" : "file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'from_file'"
+    },
+    {
+      "name" : "transforms_save_file",
+      "label" : "Save Transformations File",
+      "description": "Save transformations file to apply to other datasets later. Leave this blank to not save it.",
+      "type" : "save_file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "apply_to_all_arrays",
+      "label": "Apply to All Arrays",
+      "description": "Apply the transformation shifts to all arrays within this data source (not just the currently selected one). The transformation is computed only using the currently selected array.",
+      "type" : "bool",
+      "default": true
     }
   ]
 }
diff --git a/tomviz/python/AutoCrossCorrelationTiltImageAlignment.py b/tomviz/python/AutoCrossCorrelationTiltImageAlignment.py
index 85c1c24d7..54fdcb7a6 100644
--- a/tomviz/python/AutoCrossCorrelationTiltImageAlignment.py
+++ b/tomviz/python/AutoCrossCorrelationTiltImageAlignment.py
@@ -1,11 +1,41 @@
 from tomviz import utils
-import numpy as np
 import tomviz.operators
 
+from scipy import ndimage
+import numpy as np
+
 
 class CrossCorrelationAlignmentOperator(tomviz.operators.CancelableOperator):
 
-    def transform(self, dataset):
+    def transform(
+        self,
+        dataset,
+        transform_source='generate',
+        apply_to_all_arrays=True,
+        transforms_save_file='',
+        transform_file=None,
+    ):
+        kwargs = {
+            'dataset': dataset,
+            'apply_to_all_arrays': apply_to_all_arrays,
+        }
+        if transform_source == 'generate':
+            kwargs = {
+                **kwargs,
+                'transforms_save_file': transforms_save_file,
+            }
+            return self.transform_generate(**kwargs)
+        elif transform_source == 'from_file':
+            kwargs = {
+                **kwargs,
+                'transform_file': transform_file,
+            }
+            return self.transform_from_file(**kwargs)
+
+        raise NotImplementedError(transform_source)
+
+    def transform_generate(self, dataset, apply_to_all_arrays,
+                           transforms_save_file):
         """Automatically align tilt images by cross-correlation"""
         self.progress.maximum = 1
 
@@ -65,20 +95,50 @@ def transform(self, dataset):
             self.progress.value = step
 
         dataset.active_scalars = tiltSeries
-
-        # Assign Negative Shifts when Shift > N/2.
-        indices_X = np.where(offsets[:, 0] > tiltSeries.shape[0] / 2)
-        offsets[indices_X, 0] -= tiltSeries.shape[0]
-        indices_Y = np.where(offsets[:, 1] > tiltSeries.shape[1] / 2)
-        offsets[indices_Y, 1] -= tiltSeries.shape[1]
-
-        # Create a spreadsheet data set from table data
-        column_names = ["X Offset", "Y Offset"]
-        offsetsTable = utils.make_spreadsheet(column_names, offsets)
-        # Set up dictionary to return operator results
-        returnValues = {}
-        returnValues["alignments"] = offsetsTable
-        return returnValues
+        if apply_to_all_arrays:
+            names = [name for name in dataset.scalars_names
+                     if name != dataset.active_name]
+            self.apply_offsets_to_scalar_names(dataset, offsets, names)
+
+        if transforms_save_file:
+            np.savez(
+                transforms_save_file,
+                offsets=offsets,
+                spacing=dataset.spacing,
+            )
+            print('Saved transforms to:', transforms_save_file)
+
+    def apply_offsets_to_scalar_names(self, dataset, offsets, names):
+        # Now apply the same offsets to all other arrays
+        for name in names:
+            print(f'Applying shifts to {name}...')
+            array = dataset.scalars(name)
+            for i in range(len(offsets)):
+                shifts = offsets[i]
+                array[:, :, i] = ndimage.shift(array[:, :, i],
+                                               shift=shifts,
+                                               order=1,
+                                               mode='wrap')
+
+            dataset.set_scalars(name, array)
+
+    def transform_from_file(self, dataset, apply_to_all_arrays,
+                            transform_file):
+        if not apply_to_all_arrays:
+            names = [dataset.active_name]
+        else:
+            names = dataset.scalars_names
+
+        with np.load(transform_file) as f:
+            transform_offsets = f['offsets']
+            transform_spacing = f['spacing']
+
+        # The true shift will depend on the voxel size ratio, along
+        # the shift direction, which is Y.
+        offsets = transform_offsets.astype(float)
+        offsets[:, 0] *= transform_spacing[0] / dataset.spacing[0]
+        offsets[:, 1] *= transform_spacing[1] / dataset.spacing[1]
+        return self.apply_offsets_to_scalar_names(dataset, offsets, names)
 
 
 def crossCorrelationAlign(image, reference, rFilter, kFilter):
diff --git a/tomviz/python/AutoTiltAxisShiftAlignment.json b/tomviz/python/AutoTiltAxisShiftAlignment.json
new file mode 100644
index 000000000..987253757
--- /dev/null
+++ b/tomviz/python/AutoTiltAxisShiftAlignment.json
@@ -0,0 +1,71 @@
+{
+  "name" : "AutoTiltAxisShiftAlignment",
+  "label" : "Auto Tilt Axis Shift Align",
+  "description" : "Automatically center images along the tilt axis",
+  "parameters" : [
+    {
+      "name" : "transform_source",
+      "label" : "Transformation Source",
+      "description" : "The source of the shift transformation value (i. e., generate it, load it from a file, etc.)",
+      "type" : "enumeration",
+      "default" : 0,
+      "options" : [
+        {"Generate" : "generate"},
+        {"Load From File": "from_file"}
+      ]
+    },
+    {
+      "name" : "transform_file",
+      "label" : "Transform File",
+      "description": "Transformation file (npz format) to apply",
+      "type" : "file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'from_file'"
+    },
+    {
+      "name" : "padding",
+      "label" : "Padding",
+      "description" : "Array padding along non-tilt axes when determining the shift",
+      "type" : "int",
+      "default" : 10,
+      "minimum" : 0,
+      "maximum" : 1000000,
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "num_slices",
+      "label" : "Number of Test Slices",
+      "description" : "Number of slices to randomly sample to determine ideal recon shift.",
+      "type" : "int",
+      "default" : 5,
+      "minimum" : 2,
+      "maximum" : 1000000,
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "seed",
+      "label" : "Random Number Generator Seed",
+      "description" : "Seed for the random number generator used to select slices. The seed is kept here so that when the pipeline is re-ran, the results are reproducible",
+      "type" : "int",
+      "default" : 0,
+      "minimum" : 0,
+      "maximum" : 10000000000000,
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "apply_to_all_arrays",
+      "label": "Apply to All Arrays",
+      "description": "Apply the shift alignment to all arrays within this data source (not just the currently selected one). The shift is computed only using the currently selected array.",
+      "type" : "bool",
+      "default": true
+    },
+    {
+      "name" : "transforms_save_file",
+      "label" : "Save Transformations File",
+      "description": "Save transformations file to apply to other datasets later. Leave this blank to not save it.",
+      "type" : "save_file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'generate'"
+    }
+  ]
+}
diff --git a/tomviz/python/AutoTiltAxisShiftAlignment.py b/tomviz/python/AutoTiltAxisShiftAlignment.py
index 7198c35d6..a7c4040f6 100644
--- a/tomviz/python/AutoTiltAxisShiftAlignment.py
+++ b/tomviz/python/AutoTiltAxisShiftAlignment.py
@@ -1,12 +1,45 @@
 import numpy as np
 from scipy.interpolate import interp1d
+from scipy import ndimage
+
 import tomviz.operators
+from tomviz.utils import pad_array
 
 
 class AutoTiltAxisShiftAlignmentOperator(tomviz.operators.CancelableOperator):
 
-    def transform(self, dataset):
+    def transform(self, dataset, transform_source: str = 'generate',
+                  transform_file: str = '', padding: int = 0,
+                  num_slices: int = 5, seed: int = 0,
+                  apply_to_all_arrays: bool = True,
+                  transforms_save_file: str = ''):
         """Automatic align the tilt axis to the center of images"""
+        shared_kwargs = {
+            'dataset': dataset,
+            'apply_to_all_arrays': apply_to_all_arrays,
+        }
+        if transform_source == 'generate':
+            kwargs = {
+                **shared_kwargs,
+                'padding': padding,
+                'num_slices': num_slices,
+                'seed': seed,
+                'transforms_save_file': transforms_save_file,
+            }
+            f = self.transform_generate
+        elif transform_source == 'from_file':
+            kwargs = {
+                **shared_kwargs,
+                'transform_file': transform_file,
+            }
+            f = self.transform_from_file
+
+        return f(**kwargs)
+
+    def transform_generate(self, dataset, padding: int = 0,
+                           num_slices: int = 5, seed: int = 0,
+                           apply_to_all_arrays: bool = True,
+                           transforms_save_file: str = ''):
         self.progress.maximum = 1
 
         # Get Tilt angles
@@ -16,16 +49,26 @@ def transform(self, dataset):
         if tiltSeries is None:
             raise RuntimeError("No scalars found!")
 
+        axis = 2
+        tiltSeries = pad_array(tiltSeries, padding, axis)
+
         Nx, Ny, Nz = tiltSeries.shape
 
         shifts = (np.linspace(-20, 20, 41)).astype('int')
-        numberOfSlices = 5  # number of slices used for recon
 
         # randomly choose slices with top 50% total intensities
         tiltSeriesSum = np.sum(tiltSeries, axis=(1, 2))
         temp = tiltSeriesSum.argsort()[Nx // 2:]
-        slices = temp[np.random.permutation(temp.size)[:numberOfSlices]]
-        print('Reconstruction slices:')
+
+        if num_slices > temp.size:
+            print(f'Warning: number of slices selected, "{num_slices}", '
+                  f'exceeded the max size of "{temp.size}". '
+                  f'Reducing the number of slices to "{temp.size}"')
+            num_slices = temp.size
+
+        random_state = np.random.RandomState(seed=seed)
+        slices = np.sort(temp[random_state.permutation(temp.size)[:num_slices]])
+        print('Trial reconstruction slices:')
         print(slices)
 
         I = np.zeros(shifts.size)
@@ -38,10 +81,10 @@ def transform(self, dataset):
                 return
             shiftedTiltSeries = np.roll(
                 tiltSeries[slices, :, :, ], shifts[i], axis=1)
-            for s in range(numberOfSlices):
+            for s in range(num_slices):
                 self.progress.message = ('Reconstructing slice No.%d/%d with a '
                                          'shift of %d pixels' %
-                                         (s, numberOfSlices, shifts[i]))
+                                         (s, num_slices, shifts[i]))
 
                 recon = wbp2(shiftedTiltSeries[s, :, :],
                              tilt_angles, Ny, 'ramp', 'linear')
@@ -50,13 +93,48 @@ def transform(self, dataset):
             step += 1
             self.progress.value = step
 
-        print('shift: %d' % shifts[np.argmax(I)])
+        shift = shifts[np.argmax(I)]
+        print(f'shift: {shift}')
+
+        if transforms_save_file:
+            np.savez(
+                transforms_save_file,
+                shift=shift,
+                spacing=dataset.spacing,
+            )
+            print('Saved transforms file to:', transforms_save_file)
+
+        return self.apply_shift_to_arrays(dataset, shift, apply_to_all_arrays)
+
+    def transform_from_file(self, dataset, transform_file: str = '',
+                            apply_to_all_arrays: bool = True):
+
+        with np.load(transform_file) as f:
+            transform_shift = f['shift']
+            transform_spacing = f['spacing']
+
+        # The true shift will depend on the voxel size ratio, along
+        # the shift direction, which is Y.
+        axis = 1
+        shift = (
+            transform_shift * transform_spacing[axis] / dataset.spacing[axis]
+        )
+        return self.apply_shift_to_arrays(dataset, shift, apply_to_all_arrays)
+
+    def apply_shift_to_arrays(self, dataset, shift,
+                              apply_to_all_arrays: bool = True):
+        if apply_to_all_arrays:
+            names = dataset.scalars_names
+        else:
+            names = [dataset.active_name]
 
-        result = np.roll(tiltSeries, shifts[np.argmax(I)], axis=1)
-        result = np.asfortranarray(result)
+        for name in names:
+            array = dataset.scalars(name)
+            result = ndimage.shift(array, shift=(0, shift, 0), order=1)
+            result = np.asfortranarray(result)
 
-        # Set the result as the new scalars.
-        dataset.active_scalars = result
+            # Set the result as the new scalars.
+            dataset.set_scalars(name, result)
 
 
 def wbp2(sinogram, angles, N=None, filter="ramp", interp="linear"):
@@ -76,8 +154,8 @@ def wbp2(sinogram, angles, N=None, filter="ramp", interp="linear"):
     # Create Fourier filter
     F = makeFilter(Nray, filter)
     # Pad sinogram for filtering
-    s = np.lib.pad(sinogram, ((0, F.size - Nray), (0, 0)),
-                   'constant', constant_values=(0, 0))
+    s = np.pad(sinogram, ((0, F.size - Nray), (0, 0)),
+               'constant', constant_values=(0, 0))
     # Apply Fourier filter
     s = np.fft.fft(s, axis=0) * F
     s = np.real(np.fft.ifft(s, axis=0))
diff --git a/tomviz/python/BinTiltSeriesByTwo.py b/tomviz/python/BinTiltSeriesByTwo.py
index febbc434a..e8139da93 100644
--- a/tomviz/python/BinTiltSeriesByTwo.py
+++ b/tomviz/python/BinTiltSeriesByTwo.py
@@ -1,7 +1,10 @@
+from tomviz import utils
+
+
+@utils.apply_to_each_array
 def transform(dataset):
     """Downsample tilt images by a factor of 2"""
 
-    from tomviz import utils
     import scipy.ndimage
     import numpy as np
     import warnings
diff --git a/tomviz/python/BinVolumeByTwo.py b/tomviz/python/BinVolumeByTwo.py
index 3c213f07c..f1020a5c7 100644
--- a/tomviz/python/BinVolumeByTwo.py
+++ b/tomviz/python/BinVolumeByTwo.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset):
     """Downsample volume by a factor of 2"""
 
diff --git a/tomviz/python/CircleMask.py b/tomviz/python/CircleMask.py
index ac434285b..ee16eeb6e 100644
--- a/tomviz/python/CircleMask.py
+++ b/tomviz/python/CircleMask.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, axis, ratio, value):
     try:
         import tomopy
diff --git a/tomviz/python/ClearVolume.py b/tomviz/python/ClearVolume.py
index ead713510..2c8366a69 100644
--- a/tomviz/python/ClearVolume.py
+++ b/tomviz/python/ClearVolume.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset,  XRANGE=None, YRANGE=None, ZRANGE=None):
     """Define this method for Python operators that
     transform input scalars"""
diff --git a/tomviz/python/DeleteSlices.json b/tomviz/python/DeleteSlices.json
new file mode 100644
index 000000000..d6cf5adfb
--- /dev/null
+++ b/tomviz/python/DeleteSlices.json
@@ -0,0 +1,38 @@
+{
+  "name" : "DeleteSlices",
+  "label" : "Delete Slices",
+  "description" : "Delete slices, including associated tilt angles, from a dataset",
+  "parameters" : [
+    {
+      "name" : "firstSlice",
+      "label" : "First Slice",
+      "description" : "The first slice in the slice range (inclusive)",
+      "type" : "int",
+      "default": 0,
+      "minimum": 0,
+      "maximum": 1000000
+    },
+    {
+      "name" : "lastSlice",
+      "label" : "Last Slice",
+      "description" : "The last slice in the slice range (inclusive)",
+      "type" : "int",
+      "default": 0,
+      "minimum": 0,
+      "maximum": 1000000
+    },
+    {
+      "name" : "axis",
+      "label" : "Axis",
+      "description" : "Axis along which to delete slices",
+      "type" : "enumeration",
+      "default" : 2,
+      "options" : [
+        {"X" : 0},
+        {"Y" : 1},
+        {"Z" : 2}
+      ]
+    }
+  ]
+}
+
diff --git a/tomviz/python/deleteSlices.py b/tomviz/python/DeleteSlices.py
similarity index 67%
rename from tomviz/python/deleteSlices.py
rename to tomviz/python/DeleteSlices.py
index d244e13df..51be004a6 100644
--- a/tomviz/python/deleteSlices.py
+++ b/tomviz/python/DeleteSlices.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, firstSlice=None, lastSlice=None, axis=2):
     """Delete Slices in Dataset"""
 
@@ -6,6 +10,15 @@ def transform(dataset, firstSlice=None, lastSlice=None, axis=2):
     # Get the current dataset.
     array = dataset.active_scalars
 
+    if lastSlice >= array.shape[axis]:
+        new_value = array.shape[axis] - 1
+        print('WARNING: the lastSlice is past the end of the array. '
+              f'Truncating the lastSlice value to {new_value}')
+        lastSlice = new_value
+
+    if lastSlice < firstSlice:
+        raise Exception(f'Last slice cannot be less than first slice')
+
     # Get indices of the slices to be deleted.
     indices = np.linspace(firstSlice, lastSlice,
                           lastSlice - firstSlice + 1).astype(int)
diff --git a/tomviz/python/GenerateTiltSeries.py b/tomviz/python/GenerateTiltSeries.py
index b7b015f83..2faccafaf 100644
--- a/tomviz/python/GenerateTiltSeries.py
+++ b/tomviz/python/GenerateTiltSeries.py
@@ -27,7 +27,7 @@ def transform(self, dataset, start_angle=-90.0, angle_increment=3.0,
         pad_y_post = int(np.floor((N - Ny) / 2.0))
         pad_z_pre = int(np.ceil((N - Nz) / 2.0))
         pad_z_post = int(np.floor((N - Nz) / 2.0))
-        volume_pad = np.lib.pad(
+        volume_pad = np.pad(
             volume, ((0, 0), (pad_y_pre, pad_y_post), (pad_z_pre, pad_z_post)),
             'constant')
 
diff --git a/tomviz/python/Pad_Data.py b/tomviz/python/Pad_Data.py
index a7a011e9a..2649d16d3 100644
--- a/tomviz/python/Pad_Data.py
+++ b/tomviz/python/Pad_Data.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, pad_size_before=[0, 0, 0], pad_size_after=[0, 0, 0],
               pad_mode_index=0):
     """Pad dataset"""
@@ -24,7 +28,7 @@ def transform(dataset, pad_size_before=[0, 0, 0], pad_size_after=[0, 0, 0],
     result = np.empty(result_shape, array.dtype, order='F')
 
     # pad the data.
-    result[:] = np.lib.pad(array, pad_width, padMode)
+    result[:] = np.pad(array, pad_width, padMode)
 
     dataset.active_scalars = result
 
@@ -32,7 +36,7 @@ def transform(dataset, pad_size_before=[0, 0, 0], pad_size_after=[0, 0, 0],
     if padWidthZ[0] + padWidthZ[1] > 0:
         try:
             tilt_angles = dataset.tilt_angles
-            tilt_angles = np.lib.pad(tilt_angles, padWidthZ, padMode)
+            tilt_angles = np.pad(tilt_angles, padWidthZ, padMode)
             dataset.tilt_angles = tilt_angles
         except: # noqa
             # TODO What exception are we ignoring?
diff --git a/tomviz/python/PyStackRegImageAlignment.json b/tomviz/python/PyStackRegImageAlignment.json
new file mode 100644
index 000000000..6eb65897e
--- /dev/null
+++ b/tomviz/python/PyStackRegImageAlignment.json
@@ -0,0 +1,91 @@
+{
+  "name" : "PyStackReg",
+  "label" : "Auto Tilt Image Align (PyStackReg)",
+  "description" : "Perform image alignment using PyStackReg.",
+  "parameters" : [
+    {
+      "name" : "transform_source",
+      "label" : "Transformation Source",
+      "description" : "The source of the transformation matrices (i. e., generate them, load them from a file, etc.)",
+      "type" : "enumeration",
+      "default" : 0,
+      "options" : [
+        {"Generate" : "generate"},
+        {"Load From File": "from_file"}
+      ]
+    },
+    {
+      "name" : "transform_type",
+      "label" : "Transformation Type",
+      "description" : "Transformation type for the registration",
+      "type" : "enumeration",
+      "default" : 0,
+      "options" : [
+        {"Translation" : "translation"},
+        {"Rigid Body" : "rigid body"},
+        {"Scaled Rotation" : "scaled rotation"},
+        {"Affine" : "affine"},
+        {"Bilinear": "bilinear"}
+      ],
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "transform_file",
+      "label" : "Transformations File",
+      "description": "Transformation file (npz format) to apply",
+      "type" : "file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'from_file'"
+    },
+    {
+      "name" : "padding",
+      "label" : "Padding",
+      "description" : "Array padding along non-tilt axes before registration",
+      "type" : "int",
+      "default" : 10,
+      "minimum" : 0,
+      "maximum" : 1000000,
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "reference",
+      "label" : "Reference",
+      "description" : "The reference slice to use when determining the registration transformation for each slice.",
+      "type" : "enumeration",
+      "default" : 3,
+      "options" : [
+        {"Previous" : "previous"},
+        {"First" : "first"},
+        {"Mean" : "mean"},
+        {"SliceIndex" : "slice_index"}
+      ],
+      "visible_if" : "transform_source == 'generate'"
+    },
+    {
+      "name" : "ref_slice_index",
+      "label" : "Slice Index",
+      "description": "Slice index to use for the reference",
+      "type" : "int",
+      "default" : 0,
+      "minimum" : 0,
+      "maximum" : 1000000,
+      "visible_if" : "transform_source == 'generate'",
+      "enable_if" : "reference == 'slice_index'"
+    },
+    {
+      "name" : "apply_to_all_arrays",
+      "label": "Apply to All Arrays",
+      "description": "Apply the registration transformation to all arrays within this data source (not just the currently selected one). The registration transformation is computed only using the currently selected array.",
+      "type" : "bool",
+      "default": true
+    },
+    {
+      "name" : "transforms_save_file",
+      "label" : "Save Transformations File",
+      "description": "Save transformations file to apply to other datasets later. Leave this blank to not save it.",
+      "type" : "save_file",
+      "filter": "NPZ files (*npz)",
+      "visible_if" : "transform_source == 'generate'"
+    }
+  ]
+}
diff --git a/tomviz/python/PyStackRegImageAlignment.py b/tomviz/python/PyStackRegImageAlignment.py
new file mode 100644
index 000000000..cd0114985
--- /dev/null
+++ b/tomviz/python/PyStackRegImageAlignment.py
@@ -0,0 +1,227 @@
+import numpy as np
+
+from tomviz.utils import pad_array, depad_array
+
+
+def transform(
+    dataset,
+    transform_source='generate',
+    padding=0,
+    apply_to_all_arrays=True,
+    # Only used if `transform_source` is `generate`
+    transform_type='translation',
+    reference='previous',
+    transforms_save_file='',
+    # Only used if `transform_type` is `slice_index`
+    ref_slice_index=0,
+    # Only used if `transform_source` is `from_file`.
+    transform_file=None,
+):
+    kwargs = {
+        'dataset': dataset,
+        'apply_to_all_arrays': apply_to_all_arrays,
+        'axis': 2,  # axis hard-coded to two for now
+    }
+    if transform_source == 'generate':
+        # Call the 'generate' version of this
+        return transform_generate(
+            transform_type=transform_type,
+            reference=reference,
+            ref_slice_index=ref_slice_index,
+            transforms_save_file=transforms_save_file,
+            padding=padding,
+            **kwargs,
+        )
+    elif transform_source == 'from_file':
+        # Call the 'from_file' version of this
+        return transform_from_file(
+            transform_file=transform_file,
+            **kwargs,
+        )
+
+    raise Exception(f'Unknown transform source: {transform_source}')
+
+
+def transform_generate(dataset, transform_type='translation', padding=0,
+                       reference='previous', ref_slice_index=0,
+                       apply_to_all_arrays=True, axis=0,
+                       transforms_save_file=''):
+    from pystackreg import StackReg
+
+    array = dataset.active_scalars
+    sr = StackReg(transform_type_map()[transform_type])
+
+    # Apply padding if specified
+    array = pad_array(array, padding, axis)
+
+    # First, determine the transform matrices
+    if reference != 'slice_index':
+        tmats = sr.register_stack(
+            array,
+            axis=axis,
+            reference=reference,
+        )
+    else:
+        # We have to do our own special magic to handle this
+        tmats = register_stack_from_slice(
+            sr,
+            array,
+            ref_idx=ref_slice_index,
+            axis=axis,
+        )
+
+    if transforms_save_file:
+        np.savez_compressed(
+            transforms_save_file,
+            transform_type=transform_type,
+            transform_matrices=tmats,
+            spacing=[x for i, x in enumerate(dataset.spacing) if i != axis],
+            shape=[x for i, x in enumerate(array.shape) if i != axis],
+            padding=padding,
+        )
+
+    # Now apply the transform to all specified scalars
+    apply_tmats(sr, dataset, tmats, padding, axis, apply_to_all_arrays)
+
+
+def apply_tmats(sr, dataset, tmats, padding, axis, apply_to_all_arrays):
+    if apply_to_all_arrays:
+        names = dataset.scalars_names
+    else:
+        names = [dataset.active_name]
+
+    for name in names:
+        array = dataset.scalars(name)
+        array = pad_array(array, padding, axis)
+        output = sr.transform_stack(array, axis=axis, tmats=tmats)
+
+        # Now remove the padding, if there was any
+        output = depad_array(output, padding, axis)
+
+        # Convert to Fortran to help VTK
+        dataset.set_scalars(name, output)
+
+
+def transform_from_file(dataset, transform_file, apply_to_all_arrays=True,
+                        axis=0):
+    array = dataset.active_scalars
+
+    # Padding should be zero if we transform from a file
+    padding = 0
+
+    # See if we need to rescale the transform matrices
+    frame_shape = [x for i, x in enumerate(array.shape) if i != axis]
+    spacing = [x for i, x in enumerate(dataset.spacing) if i != axis]
+
+    with np.load(transform_file) as f:
+        tmats = f['transform_matrices']
+        transform_type = f['transform_type'].item()
+        tmat_spacing = f['spacing']
+        tmat_shape = f['shape']
+        tmat_padding = f['padding']
+
+    # Rescale the tmats so they can be applied to an image with different
+    # physical extents (i. e., tmats generated from XRF can be applied to
+    # ptychography, which has a higher resolution in voxel space).
+    tmats = rescale_tmats(tmats, transform_type, tmat_shape, tmat_spacing,
+                          tmat_padding, frame_shape, spacing)
+
+    from pystackreg import StackReg
+    sr = StackReg(transform_type_map()[transform_type])
+    apply_tmats(sr, dataset, tmats, padding, axis, apply_to_all_arrays)
+
+
+def transform_type_map():
+    from pystackreg import StackReg
+
+    return {
+        'translation': StackReg.TRANSLATION,
+        'rigid body': StackReg.RIGID_BODY,
+        'scaled rotation': StackReg.SCALED_ROTATION,
+        'affine': StackReg.AFFINE,
+        'bilinear': StackReg.BILINEAR,
+    }
+
+
+def register_stack_from_slice(sr, image_stack, ref_idx, axis):
+    # PyStackReg doesn't allow us to pick an arbitrary slice to use
+    # as the reference, but it does allow us to use the first slice.
+    # To get around this, we'll swap whatever slice we want to use
+    # as the reference with the first slice, then perform the registration,
+    # then swap it back before we exit.
+    # Swap the first row with the ref_idx. We'll unswap when we exit.
+    if ref_idx == 0:
+        # We don't have to do anything special actually...
+        return sr.register_stack(image_stack, axis=axis, reference='first')
+
+    slices = [slice(None)] * 3
+    slices[axis] = [0, ref_idx]
+    reversed_slices = slices.copy()
+    reversed_slices[axis] = list(reversed(slices[axis]))
+    image_stack[tuple(slices)] = image_stack[tuple(reversed_slices)]
+    try:
+        tmats = sr.register_stack(
+            image_stack,
+            axis=axis,
+            reference='first',
+        )
+        # The first and reference idx are out of place. Swap them.
+        tmats[[0, ref_idx]] = tmats[[ref_idx, 0]]
+        return tmats
+    finally:
+        # Undo the row swap
+        image_stack[tuple(slices)] = image_stack[tuple(reversed_slices)]
+
+
+def rescale_tmats(tmats, transform_type, shape1, spacing1, padding1,
+                  shape2, spacing2):
+    if np.allclose(spacing1, spacing2) and padding1 == 0:
+        # No rescaling needed
+        return tmats
+
+    if transform_type == 'bilinear':
+        msg = (
+            'Transformation matrix rescaling is not yet supported for '
+            'bilinear transformations.'
+        )
+        raise Exception(msg)
+
+    # Account for changes to padding
+    pad_x_orig = padding1
+    pad_y_orig = padding1
+    pad_x_new = 0
+    pad_y_new = 0
+
+    # Account for pixel size changes
+    pixel_ratio_x = spacing2[1] / spacing1[1]
+    pixel_ratio_y = spacing2[0] / spacing1[0]
+
+    # We need to account for the padding and pixel resizing changes
+    translate_to_orig = np.array([
+        [1, 0, pad_x_orig - pad_x_new],
+        [0, 1, pad_y_orig - pad_y_new],
+        [0, 0, 1],
+    ])
+    scale_to_orig = np.array([
+        [pixel_ratio_x, 0, 0],
+        [0, pixel_ratio_y, 0],
+        [0, 0, 1],
+    ])
+    scale_to_new = np.array([
+        [1 / pixel_ratio_x, 0, 0],
+        [0, 1 / pixel_ratio_y, 0],
+        [0, 0, 1],
+    ])
+    translate_to_new = np.array([
+        [1, 0, -(pad_x_orig - pad_x_new)],
+        [0, 1, -(pad_y_orig - pad_y_new)],
+        [0, 0, 1],
+    ])
+
+    return (
+        translate_to_new @
+        scale_to_new @
+        tmats @
+        scale_to_orig @
+        translate_to_orig
+    )
diff --git a/tomviz/python/Recon_DFT.py b/tomviz/python/Recon_DFT.py
index f1f94fa84..6373ce341 100644
--- a/tomviz/python/Recon_DFT.py
+++ b/tomviz/python/Recon_DFT.py
@@ -14,105 +14,114 @@ def transform(self, dataset):
         # Get Tilt angles
         tiltAngles = dataset.tilt_angles
 
-        tiltSeries = dataset.active_scalars
-        if tiltSeries is None:
+        if dataset.active_scalars is None:
             raise RuntimeError("No scalars found!")
 
-        tiltSeries = np.double(tiltSeries)
-        (Nx, Ny, Nproj) = tiltSeries.shape
-        Npad = Ny * 2
-
-        tiltAngles = np.double(tiltAngles)
-        pad_pre = int(np.ceil((Npad - Ny) / 2.0))
-        pad_post = int(np.floor((Npad - Ny) / 2.0))
-
-        # Initialization
-        self.progress.message = 'Initialization'
-        Nz = Ny
-        w = np.zeros((Nx, Ny, Nz // 2 + 1)) #store weighting factors
-        v = pyfftw.empty_aligned(
-            (Nx, Ny, Nz // 2 + 1), dtype='complex64', n=16)
-
-        p = pyfftw.empty_aligned((Nx, Npad), dtype='float32', n=16)
-        pF = pyfftw.empty_aligned(
-            (Nx, Npad // 2 + 1), dtype='complex64', n=16)
-        p_fftw_object = pyfftw.FFTW(p, pF, axes=(0, 1))
-
-        dk = np.double(Ny) / np.double(Npad)
-
-        self.progress.maximum = Nproj + 1
-        step = 0
-
-        t0 = time.time()
-        etcMessage = 'Estimated time to complete: n/a'
-        counter = 1
-        for a in range(Nproj):
-            if self.canceled:
-                return
-            self.progress.message = 'Tilt image No.%d/%d. ' % (
-                a + 1, Nproj) + etcMessage
-
-            ang = tiltAngles[a] * np.pi / 180
-            projection = tiltSeries[:, :, a] #2D projection image
-            p = np.lib.pad(projection, ((0, 0), (pad_pre, pad_post)),
+        num_scalars = dataset.num_scalars
+        scalars_names = dataset.scalars_names
+        child_dataset = None
+
+        self.progress.maximum = len(tiltAngles) * num_scalars + 1
+
+        for array_idx, array_name in enumerate(scalars_names):
+            tiltSeries = dataset.scalars(array_name)
+            tiltSeries = np.double(tiltSeries)
+            (Nx, Ny, Nproj) = tiltSeries.shape
+            Npad = Ny * 2
+
+            tiltAngles = np.double(tiltAngles)
+            pad_pre = int(np.ceil((Npad - Ny) / 2.0))
+            pad_post = int(np.floor((Npad - Ny) / 2.0))
+
+            # Initialization
+            self.progress.message = f'{array_name}: Initialization'
+            Nz = Ny
+            w = np.zeros((Nx, Ny, Nz // 2 + 1)) #store weighting factors
+            v = pyfftw.zeros_aligned(
+                (Nx, Ny, Nz // 2 + 1), dtype='complex64', n=16)
+
+            p = pyfftw.empty_aligned((Nx, Npad), dtype='float32', n=16)
+            pF = pyfftw.empty_aligned(
+                (Nx, Npad // 2 + 1), dtype='complex64', n=16)
+            p_fftw_object = pyfftw.FFTW(p, pF, axes=(0, 1))
+
+            dk = np.double(Ny) / np.double(Npad)
+
+            step = 0
+
+            t0 = time.time()
+            etcMessage = 'Estimated time to complete: n/a'
+            counter = 1
+            for a in range(Nproj):
+                if self.canceled:
+                    return
+                self.progress.message = f'{array_name}: Tilt image No.%d/%d. ' % (
+                    a + 1, Nproj) + etcMessage
+
+                ang = tiltAngles[a] * np.pi / 180
+                projection = tiltSeries[:, :, a] #2D projection image
+                p = np.pad(projection, ((0, 0), (pad_pre, pad_post)),
                            'constant', constant_values=(0, 0)) #pad zeros
-            p = np.float32(np.fft.ifftshift(p))
-            p_fftw_object.update_arrays(p, pF)
-            p_fftw_object()
-            p = None #Garbage collector (gc)
-
-            if ang < 0:
-                pF = np.conj(pF)
-                pF[1:, :] = np.flipud(pF[1:, :])
-                ang = np.pi + ang
-
-            # Bilinear extrapolation
-            for i in range(0, np.int(np.ceil(Npad / 2)) + 1):
-                ky = i * dk
-                #kz = 0
-                ky_new = np.cos(ang) * ky #new coord. after rotation
-                kz_new = np.sin(ang) * ky
-                sy = abs(np.floor(ky_new) - ky_new) #calculate weights
-                sz = abs(np.floor(kz_new) - kz_new)
-                for b in range(1, 5): #bilinear extrapolation
-                    pz, py, weight = bilinear(kz_new, ky_new, sz, sy, Ny, b)
-                    if 0 <= py < Ny and 0 <= pz < np.floor(Nz / 2 + 1):
-                        w[:, py, pz] = w[:, py, pz] + weight
-                        v[:, py, pz] = v[:, py, pz] + \
-                            weight * pF[:, i]
+                p = np.ascontiguousarray(np.fft.ifftshift(p).astype(np.float32))
+                p_fftw_object.update_arrays(p, pF)
+                p_fftw_object()
+                p = None #Garbage collector (gc)
+
+                if ang < 0:
+                    pF = np.conj(pF)
+                    pF[1:, :] = np.flipud(pF[1:, :])
+                    ang = np.pi + ang
+
+                # Bilinear extrapolation
+                for i in range(0, np.int64(np.ceil(Npad / 2)) + 1):
+                    ky = i * dk
+                    #kz = 0
+                    ky_new = np.cos(ang) * ky #new coord. after rotation
+                    kz_new = np.sin(ang) * ky
+                    sy = abs(np.floor(ky_new) - ky_new) #calculate weights
+                    sz = abs(np.floor(kz_new) - kz_new)
+                    for b in range(1, 5): #bilinear extrapolation
+                        pz, py, weight = bilinear(kz_new, ky_new, sz, sy, Ny, b)
+                        if 0 <= py < Ny and 0 <= pz < np.floor(Nz / 2 + 1):
+                            w[:, py, pz] = w[:, py, pz] + weight
+                            v[:, py, pz] = v[:, py, pz] + \
+                                weight * pF[:, i]
+
+                step += 1
+                self.progress.value = step + array_idx * Nproj
+                timeLeft = (time.time() - t0) / counter * (Nproj - counter)
+                counter += 1
+                timeLeftMin, timeLeftSec = divmod(timeLeft, 60)
+                timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)
+                etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (
+                    timeLeftHour, timeLeftMin, timeLeftSec)
+
+            p = pF = None #gc
+
+            self.progress.message = f'{array_name}: Inverse Fourier transform'
+            v_temp = v.copy()
+            recon = pyfftw.empty_aligned(
+                (Nx, Ny, Nz), dtype='float32', order='F', n=16)
+            recon_fftw_object = pyfftw.FFTW(
+                v_temp, recon, direction='FFTW_BACKWARD', axes=(0, 1, 2))
+            v[w != 0] = v[w != 0] / w[w != 0]
+            recon_fftw_object.update_arrays(v, recon)
+            v = v_temp = []    #gc
+            recon_fftw_object()
+            recon[:] = np.fft.fftshift(recon)
+
             step += 1
             self.progress.value = step
-            timeLeft = (time.time() - t0) / counter * (Nproj - counter)
-            counter += 1
-            timeLeftMin, timeLeftSec = divmod(timeLeft, 60)
-            timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)
-            etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (
-                timeLeftHour, timeLeftMin, timeLeftSec)
-
-        p = pF = None #gc
-
-        self.progress.message = 'Inverse Fourier transform'
-        v_temp = v.copy()
-        recon = pyfftw.empty_aligned(
-            (Nx, Ny, Nz), dtype='float32', order='F', n=16)
-        recon_fftw_object = pyfftw.FFTW(
-            v_temp, recon, direction='FFTW_BACKWARD', axes=(0, 1, 2))
-        v[w != 0] = v[w != 0] / w[w != 0]
-        recon_fftw_object.update_arrays(v, recon)
-        v = v_temp = []    #gc
-        recon_fftw_object()
-        recon[:] = np.fft.fftshift(recon)
-
-        step += 1
-        self.progress.value = step
 
-        self.progress.message = 'Passing data to Tomviz'
+            if child_dataset is None:
+                child_dataset = dataset.create_child_dataset()
 
-        child = dataset.create_child_dataset()
-        child.active_scalars = recon
+            child_dataset.set_scalars(array_name, recon)
+
+        self.progress.message = 'Passing data to Tomviz'
 
         returnValues = {}
-        returnValues["reconstruction"] = child
+        returnValues["reconstruction"] = child_dataset
         return returnValues
 
 
diff --git a/tomviz/python/Recon_DFT_constraint.json b/tomviz/python/Recon_DFT_constraint.json
index fddc39011..27c1a57e3 100644
--- a/tomviz/python/Recon_DFT_constraint.json
+++ b/tomviz/python/Recon_DFT_constraint.json
@@ -45,6 +45,15 @@
       "minimum" : 0,
       "maximum" : 100,
       "step" : 5
+    },
+    {
+      "name" : "seed",
+      "label" : "Random Number Generator Seed",
+      "description" : "Seed for the random number generator used to create the initial guess. The seed is kept here so that when the pipeline is re-ran, the results are reproducible",
+      "type" : "int",
+      "default" : 0,
+      "minimum" : 0,
+      "maximum" : 10000000000000
     }
   ]
 }
diff --git a/tomviz/python/Recon_DFT_constraint.py b/tomviz/python/Recon_DFT_constraint.py
index 5b4d18691..6386c2ed5 100644
--- a/tomviz/python/Recon_DFT_constraint.py
+++ b/tomviz/python/Recon_DFT_constraint.py
@@ -7,142 +7,152 @@
 class ReconConstrintedDFMOperator(tomviz.operators.CancelableOperator):
 
     def transform(self, dataset, Niter=None, Niter_update_support=None,
-                  supportSigma=None, supportThreshold=None):
+                  supportSigma=None, supportThreshold=None,
+                  seed=0):
         """
         3D Reconstruct from a tilt series using constraint-based Direct Fourier
         Method
         """
         self.progress.maximum = 1
 
-        import numpy as np
+        rng = np.random.default_rng(seed=seed)
 
         supportThreshold = supportThreshold / 100.0
 
         nonnegativeVoxels = True
         tiltAngles = dataset.tilt_angles #Get Tilt angles
 
-        tiltSeries = dataset.active_scalars
-        if tiltSeries is None:
+        if dataset.active_scalars is None:
             raise RuntimeError("No scalars found!")
 
-        self.progress.message = 'Initialization'
-
-        #Direct Fourier recon without constraints
-        (recon, recon_F) \
-            = dfm3(tiltSeries, tiltAngles, np.size(tiltSeries, 1) * 2)
-
-        kr_cutoffs = np.linspace(0.05, 0.5, 10)
-        #average Fourier magnitude of tilt series as a function of kr
-        I_data = radial_average(tiltSeries, kr_cutoffs)
-
-        (Nx, Ny, Nz) = recon_F.shape
-        #Note: Nz = np.int(Ny/2+1)
-        Ntot = Nx * Ny * Ny
-        f = pyfftw.n_byte_align_empty((Nx, Ny, Nz), 16, dtype=np.complex64)
-        r = pyfftw.n_byte_align_empty((Nx, Ny, Ny), 16, dtype=np.float32)
-        fft_forward = pyfftw.FFTW(r, f, axes=(0, 1, 2))
-        fft_inverse = pyfftw.FFTW(
-            f, r, direction='FFTW_BACKWARD', axes=(0, 1, 2))
-
-        kx = np.fft.fftfreq(Nx)
-        ky = np.fft.fftfreq(Ny)
-        kz = ky[0:Nz]
-
-        kX, kY, kZ = np.meshgrid(ky, kx, kz)
-        kR = np.sqrt(kY**2 + kX**2 + kZ**2)
-
-        sigma = 0.5 * supportSigma
-        G = np.exp(-kR**2 / (2 * sigma**2))
-
-        #create initial support using sw
-        f = (recon_F * G).astype(np.complex64)
-        fft_inverse.update_arrays(f, r)
-        fft_inverse.execute()
-        cutoff = np.amax(r) * supportThreshold
-        support = r >= cutoff
-
-        recon_F[kR > kr_cutoffs[-1]] = 0
-
-        x = np.random.rand(Nx, Ny, Ny).astype(np.float32) #initial solution
-
-        self.progress.maximum = Niter
-        step = 0
-
-        t0 = time.time()
-        counter = 1
-        etcMessage = 'Estimated time to complete: n/a'
-
-        for i in range(Niter):
-            if self.canceled:
-                return
-            self.progress.message = 'Iteration No.%d/%d. ' % (
-                i + 1, Niter) + etcMessage
-
-            #image space projection
-            y1 = x.copy()
-
-            if nonnegativeVoxels:
-                y1[y1 < 0] = 0  #non-negative constraint
-
-            y1[np.logical_not(support)] = 0 #support constraint
-
-            #Fourier space projection
-            y2 = 2 * y1 - x
-            r = y2.copy().astype(np.float32)
-            fft_forward.update_arrays(r, f)
-            fft_forward.execute()
-
-            f[kR > kr_cutoffs[-1]] = 0 #apply low pass filter
-            f[recon_F != 0] = recon_F[recon_F != 0] #data constraint
-
-            #Fourier magnitude constraint
-            #leave the inner shell unchanged
-            for j in range(1, kr_cutoffs.size):
-                shell = np.logical_and(
-                    kR > kr_cutoffs[j - 1], kR <= kr_cutoffs[j])
-                shell[recon_F != 0] = False
-                I = np.sum(np.absolute(f[shell]))
-                if I != 0:
-                    I = I / np.sum(shell)
-                    # lower magnitude for high frequency information to reduce
-                    # artifacts
-                    f[shell] = f[shell] / I * I_data[j] * 0.5
+        num_scalars = dataset.num_scalars
+        scalars_names = dataset.scalars_names
+        child_dataset = None
 
+        self.progress.maximum = Niter * num_scalars
+
+        for array_idx, array_name in enumerate(scalars_names):
+            self.progress.message = f'{array_name}: Initialization'
+
+            tiltSeries = dataset.scalars(array_name)
+
+            #Direct Fourier recon without constraints
+            (recon, recon_F) \
+                = dfm3(tiltSeries, tiltAngles, np.size(tiltSeries, 1) * 2)
+
+            kr_cutoffs = np.linspace(0.05, 0.5, 10)
+            #average Fourier magnitude of tilt series as a function of kr
+            I_data = radial_average(tiltSeries, kr_cutoffs)
+
+            (Nx, Ny, Nz) = recon_F.shape
+            #Note: Nz = np.int64(Ny/2+1)
+            Ntot = Nx * Ny * Ny
+            f = pyfftw.n_byte_align_empty((Nx, Ny, Nz), 16, dtype=np.complex64)
+            r = pyfftw.n_byte_align_empty((Nx, Ny, Ny), 16, dtype=np.float32)
+            fft_forward = pyfftw.FFTW(r, f, axes=(0, 1, 2))
+            fft_inverse = pyfftw.FFTW(
+                f, r, direction='FFTW_BACKWARD', axes=(0, 1, 2))
+
+            kx = np.fft.fftfreq(Nx)
+            ky = np.fft.fftfreq(Ny)
+            kz = ky[0:Nz]
+
+            kX, kY, kZ = np.meshgrid(ky, kx, kz)
+            kR = np.sqrt(kY**2 + kX**2 + kZ**2)
+
+            sigma = 0.5 * supportSigma
+            G = np.exp(-kR**2 / (2 * sigma**2))
+
+            #create initial support using sw
+            f = (recon_F * G).astype(np.complex64)
             fft_inverse.update_arrays(f, r)
             fft_inverse.execute()
-            y2 = r.copy() / Ntot
+            cutoff = np.amax(r) * supportThreshold
+            support = r >= cutoff
 
-            #update
-            x = x + y2 - y1
+            recon_F[kR > kr_cutoffs[-1]] = 0
 
-            #update support
-            if (i < Niter and np.mod(i, Niter_update_support) == 0):
-                recon[:] = (y2 + y1) / 2
-                r = recon.copy()
+            x = rng.random((Nx, Ny, Ny)).astype(np.float32) #initial solution
+
+            step = 0
+
+            t0 = time.time()
+            counter = 1
+            etcMessage = 'Estimated time to complete: n/a'
+
+            for i in range(Niter):
+                if self.canceled:
+                    return
+                self.progress.message = f'{array_name}: Iteration No.%d/%d. ' % (
+                    i + 1, Niter) + etcMessage
+
+                #image space projection
+                y1 = x.copy()
+
+                if nonnegativeVoxels:
+                    y1[y1 < 0] = 0  #non-negative constraint
+
+                y1[np.logical_not(support)] = 0 #support constraint
+
+                #Fourier space projection
+                y2 = 2 * y1 - x
+                r = y2.copy().astype(np.float32)
                 fft_forward.update_arrays(r, f)
                 fft_forward.execute()
-                f = (f * G).astype(np.complex64)
+
+                f[kR > kr_cutoffs[-1]] = 0 #apply low pass filter
+                f[recon_F != 0] = recon_F[recon_F != 0] #data constraint
+
+                #Fourier magnitude constraint
+                #leave the inner shell unchanged
+                for j in range(1, kr_cutoffs.size):
+                    shell = np.logical_and(
+                        kR > kr_cutoffs[j - 1], kR <= kr_cutoffs[j])
+                    shell[recon_F != 0] = False
+                    I = np.sum(np.absolute(f[shell]))
+                    if I != 0:
+                        I = I / np.sum(shell)
+                        # lower magnitude for high frequency information to reduce
+                        # artifacts
+                        f[shell] = f[shell] / I * I_data[j] * 0.5
+
                 fft_inverse.update_arrays(f, r)
                 fft_inverse.execute()
-                cutoff = np.amax(r) * supportThreshold
-                support = r >= cutoff
-            step += 1
-            self.progress.value = step
-            timeLeft = (time.time() - t0) / counter * (Niter - counter)
-            counter += 1
-            timeLeftMin, timeLeftSec = divmod(timeLeft, 60)
-            timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)
-            etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (
-                timeLeftHour, timeLeftMin, timeLeftSec)
-
-        recon[:] = (y2 + y1) / 2
-        recon[:] = np.fft.fftshift(recon)
-
-        child = dataset.create_child_dataset()
-        child.active_scalars = recon
+                y2 = r.copy() / Ntot
+
+                #update
+                x = x + y2 - y1
+
+                #update support
+                if (i < Niter and np.mod(i, Niter_update_support) == 0):
+                    recon[:] = (y2 + y1) / 2
+                    r = recon.copy()
+                    fft_forward.update_arrays(r, f)
+                    fft_forward.execute()
+                    f = (f * G).astype(np.complex64)
+                    fft_inverse.update_arrays(f, r)
+                    fft_inverse.execute()
+                    cutoff = np.amax(r) * supportThreshold
+                    support = r >= cutoff
+                step += 1
+                self.progress.value = step + array_idx * Niter
+                timeLeft = (time.time() - t0) / counter * (Niter - counter)
+                counter += 1
+                timeLeftMin, timeLeftSec = divmod(timeLeft, 60)
+                timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)
+                etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (
+                    timeLeftHour, timeLeftMin, timeLeftSec)
+
+            recon[:] = (y2 + y1) / 2
+            recon[:] = np.fft.fftshift(recon)
+
+            if child_dataset is None:
+                child_dataset = dataset.create_child_dataset()
+
+            child_dataset.set_scalars(array_name, recon)
 
         returnValues = {}
-        returnValues["reconstruction"] = child
+        returnValues["reconstruction"] = child_dataset
         return returnValues
 
 
@@ -173,9 +183,9 @@ def dfm3(input, angles, Npad):
     for a in range(0, Nproj):
         ang = angles[a] * np.pi / 180
         projection = input[:, :, a].astype(np.float32) #2D projection image
-        p = np.lib.pad(projection, ((0, 0), (pad_pre, pad_post)),
-                       'constant', constant_values=(0, 0)) #pad zeros
-        p = np.fft.ifftshift(p)
+        p = np.pad(projection, ((0, 0), (pad_pre, pad_post)),
+                   'constant', constant_values=(0, 0)) #pad zeros
+        p = np.ascontiguousarray(np.fft.ifftshift(p))
         p_fftw_object.update_arrays(p, pF)
         p_fftw_object()
 
@@ -186,7 +196,7 @@ def dfm3(input, angles, Npad):
             ang = np.pi + ang
 
         # Bilinear extrapolation
-        for i in range(0, np.int(np.ceil(Npad / 2)) + 1):
+        for i in range(0, np.int64(np.ceil(Npad / 2)) + 1):
             ky = i * dk
             #kz = 0
             ky_new = np.cos(ang) * ky #new coord. after rotation
diff --git a/tomviz/python/Recon_SIRT.py b/tomviz/python/Recon_SIRT.py
index ac2fe746e..91f7a47d7 100644
--- a/tomviz/python/Recon_SIRT.py
+++ b/tomviz/python/Recon_SIRT.py
@@ -1,11 +1,13 @@
 import numpy as np
 import scipy.sparse as ss
 import tomviz.operators
+from tomviz.utils import apply_to_each_array
 import time
 
 
 class ReconSirtOperator(tomviz.operators.CompletableOperator):
 
+    @apply_to_each_array
     def transform(self, dataset, Niter=10, stepSize=0.0001,
                   updateMethodIndex=0, Nupdates=0):
         """
diff --git a/tomviz/python/Recon_TV_minimization.py b/tomviz/python/Recon_TV_minimization.py
index afcb52f4a..a987b3d10 100644
--- a/tomviz/python/Recon_TV_minimization.py
+++ b/tomviz/python/Recon_TV_minimization.py
@@ -139,7 +139,7 @@ def transform(self, dataset, Niter=10, Nupdates=0):  # noqa: C901
 
 
 def tv_derivative(recon):
-    r = np.lib.pad(recon, ((1, 1), (1, 1), (1, 1)), 'edge')
+    r = np.pad(recon, ((1, 1), (1, 1), (1, 1)), 'edge')
     v1n = 3 * r - np.roll(r, 1, axis=0) - \
                           np.roll(r, 1, axis=1) - np.roll(r, 1, axis=2) # noqa TODO reformat this
     v1d = np.sqrt(1e-8 + (r - np.roll(r, 1, axis=0))**2 + (r -
@@ -169,7 +169,7 @@ def tv_derivative(recon):
 
 
 def tv(recon):
-    r = np.lib.pad(recon, ((1, 1), (1, 1), (1, 1)), 'edge')
+    r = np.pad(recon, ((1, 1), (1, 1), (1, 1)), 'edge')
     tv = np.sqrt(1e-8 + (r - np.roll(r, -1, axis=0))**2 +
                  (r - np.roll(r, -1, axis=1))**2 +
                  (r - np.roll(r, -1, axis=2))**2)
diff --git a/tomviz/python/Recon_WBP.py b/tomviz/python/Recon_WBP.py
index 95006f6bf..f9b259a8f 100644
--- a/tomviz/python/Recon_WBP.py
+++ b/tomviz/python/Recon_WBP.py
@@ -85,8 +85,8 @@ def wbp2(sinogram, angles, N=None, filter="ramp", interp="linear"):
     # Create Fourier filter
     F = makeFilter(Nray, filter)
     # Pad sinogram for filtering
-    s = np.lib.pad(sinogram, ((0, F.size - Nray), (0, 0)),
-                   'constant', constant_values=(0, 0))
+    s = np.pad(sinogram, ((0, F.size - Nray), (0, 0)),
+               'constant', constant_values=(0, 0))
     # Apply Fourier filter
     s = np.fft.fft(s, axis=0) * F
     s = np.real(np.fft.ifft(s, axis=0))
diff --git a/tomviz/python/Recon_tomopy_gridrec.py b/tomviz/python/Recon_tomopy_gridrec.py
index 644ecad9f..f09c36837 100644
--- a/tomviz/python/Recon_tomopy_gridrec.py
+++ b/tomviz/python/Recon_tomopy_gridrec.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, rot_center=0, tune_rot_center=True):
     """Reconstruct sinograms using the tomopy gridrec algorithm
 
diff --git a/tomviz/python/RemoveBadPixelsTiltSeries.py b/tomviz/python/RemoveBadPixelsTiltSeries.py
index 165f9a327..2e15cb47d 100644
--- a/tomviz/python/RemoveBadPixelsTiltSeries.py
+++ b/tomviz/python/RemoveBadPixelsTiltSeries.py
@@ -8,7 +8,7 @@ def transform(dataset, threshold=None):
 
     for i in range(tiltSeries.shape[2]):
         I = tiltSeries[:, :, i]
-        I_pad = np.lib.pad(I, (1, 1), 'edge')
+        I_pad = np.pad(I, (1, 1), 'edge')
 
         # calculate standard deviation in a 3 x 3 window
         averageI2 = scipy.ndimage.filters.uniform_filter(I_pad ** 2)
diff --git a/tomviz/python/Resample.py b/tomviz/python/Resample.py
index 615ddf604..0dff1de59 100644
--- a/tomviz/python/Resample.py
+++ b/tomviz/python/Resample.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, resampling_factor=[1, 1, 1]):
     """Resample dataset"""
 
diff --git a/tomviz/python/Rotate3D.py b/tomviz/python/Rotate3D.py
index 97e66b0af..9317c93da 100644
--- a/tomviz/python/Rotate3D.py
+++ b/tomviz/python/Rotate3D.py
@@ -1,11 +1,9 @@
-# Rotate a 3D dataset using SciPy Interpolation libraries.
-#
-# Developed as part of the tomviz project (www.tomviz.com).
+from tomviz import utils
 
 
+@utils.apply_to_each_array
 def transform(dataset, rotation_angle=90.0, rotation_axis=0):
 
-    from tomviz import utils
     import numpy as np
     from scipy import ndimage
 
diff --git a/tomviz/python/Shift3D.py b/tomviz/python/Shift3D.py
index a16bd863b..39b2443ff 100644
--- a/tomviz/python/Shift3D.py
+++ b/tomviz/python/Shift3D.py
@@ -1,8 +1,10 @@
 # Shift a 3D dataset using SciPy Interpolation libraries.
 #
 # Developed as part of the tomviz project (www.tomviz.com).
+from tomviz.utils import apply_to_each_array
 
 
+@apply_to_each_array
 def transform(dataset, SHIFT=None):
 
     from scipy import ndimage
diff --git a/tomviz/python/Shift_Stack_Uniformly.py b/tomviz/python/Shift_Stack_Uniformly.py
index 273cc1072..5087fbfe0 100644
--- a/tomviz/python/Shift_Stack_Uniformly.py
+++ b/tomviz/python/Shift_Stack_Uniformly.py
@@ -2,7 +2,10 @@
 #
 # Developed as part of the tomviz project (www.tomviz.com).
 
+from tomviz.utils import apply_to_each_array
 
+
+@apply_to_each_array
 def transform(dataset, shift=[0, 0, 0]):
     import numpy as np
 
diff --git a/tomviz/python/SwapAxes.py b/tomviz/python/SwapAxes.py
index 370fb5ac6..6ee15acb8 100644
--- a/tomviz/python/SwapAxes.py
+++ b/tomviz/python/SwapAxes.py
@@ -1,3 +1,7 @@
+from tomviz.utils import apply_to_each_array
+
+
+@apply_to_each_array
 def transform(dataset, axis1, axis2):
     """Swap two axes in a dataset"""
 
diff --git a/tomviz/python/tomviz/__init__.py b/tomviz/python/tomviz/__init__.py
index 69e3be50d..9413ba279 100644
--- a/tomviz/python/tomviz/__init__.py
+++ b/tomviz/python/tomviz/__init__.py
@@ -1 +1,15 @@
-__path__ = __import__('pkgutil').extend_path(__path__, __name__)
+from pathlib import Path
+import os
+import sys
+
+from .fix_pdb import fix_pdb
+
+fix_pdb()
+
+
+# Override sys.executable to contain an actual Python executable, if available
+if not Path(sys.executable).exists():
+    if 'CONDA_PREFIX' in os.environ:
+        try_path = Path(os.environ['CONDA_PREFIX']) / 'bin/python'
+        if try_path.exists():
+            sys.executable = str(try_path)
diff --git a/tomviz/python/tomviz/_realtime/wbp.py b/tomviz/python/tomviz/_realtime/wbp.py
index 8d12edc0c..a1a1cc436 100644
--- a/tomviz/python/tomviz/_realtime/wbp.py
+++ b/tomviz/python/tomviz/_realtime/wbp.py
@@ -31,8 +31,8 @@ def wbp2(self, sinogram, filter="ramp", interp="linear"):
         # Create Fourier filter
         F = self.makeFilter(filter)
         # Pad sinogram for filtering
-        s = np.lib.pad(sinogram, ((0, F.size - self.Nray), (0, 0)),
-                       'constant', constant_values=(0, 0))
+        s = np.pad(sinogram, ((0, F.size - self.Nray), (0, 0)),
+                   'constant', constant_values=(0, 0))
         # Apply Fourier filter
         s = np.fft.fft(s, axis=0) * F
         s = np.real(np.fft.ifft(s, axis=0))
diff --git a/tomviz/python/tomviz/executor.py b/tomviz/python/tomviz/executor.py
index 01a3b00c3..0536dde37 100644
--- a/tomviz/python/tomviz/executor.py
+++ b/tomviz/python/tomviz/executor.py
@@ -1,18 +1,18 @@
+import abc
 import collections
 import copy
-import h5py
+import errno
 import importlib
-import os
-import numpy as np
+import json
 import logging
-import tempfile
+import os
+from pathlib import Path
 import socket
-import abc
 import stat
-import json
-import six
-import errno
+import tempfile
 
+import h5py
+import numpy as np
 from tqdm import tqdm
 
 from tomviz._internal import find_transform_function
@@ -336,6 +336,7 @@ def _progress(progress_method, progress_path):
 
 class OperatorWrapper(object):
     canceled = False
+    completed = False
 
 
 def _load_operator_module(label, script):
@@ -432,7 +433,10 @@ def is_hard_link(name):
 
         # If this is a tilt series, swap the X and Z axes
         tilt_axis = None
-        if dims[0].name == b'angles' or dims[0].units in ANGLE_UNITS:
+        if (
+            dims[0].name in ('angles', b'angles') or
+            dims[0].units in ANGLE_UNITS
+        ):
             arrays = [(name, np.transpose(data, [2, 1, 0])) for (name, data)
                       in arrays]
 
@@ -450,7 +454,7 @@ def is_hard_link(name):
             'metadata': {},
         }
 
-        if dims is not None and dims[-1].name == b'angles':
+        if dims is not None and dims[-1].name in ('angles', b'angles'):
             output['tilt_angles'] = dims[-1].values[:].astype(np.float64)
 
         return output
@@ -523,7 +527,7 @@ def _get_dims_for_writing(dataset, data, default_dims=None):
     else:
         # In case the input was a tilt series, make the first dim x,
         # and the units [n_m]
-        if dims[0].name == 'angles':
+        if dims[0].name in ('angles', b'angles'):
             dims[0].name = 'x'
             dims[0].units = '[n_m]'
 
@@ -562,7 +566,7 @@ def _write_emd(path, dataset, dims=None):
         tomviz_scalars[active_name] = h5py.SoftLink('/data/tomography/data')
 
 
-def _read_data_exchange(path, options=None):
+def _read_data_exchange(path: Path, options: dict | None = None):
     with h5py.File(path, 'r') as f:
         g = f['/exchange']
 
@@ -592,14 +596,15 @@ def _read_data_exchange(path, options=None):
                 # Swap x and z axes
                 swap_keys = ['data', 'data_dark', 'data_white']
                 for key in swap_keys:
-                    datasets[key] = np.transpose(datasets[key], [2, 1, 0])
+                    if key in datasets:
+                        datasets[key] = np.transpose(datasets[key], [2, 1, 0])
 
         tilt_axis = None
         if 'theta' in datasets:
             tilt_axis = 2 if to_fortran else 0
 
         output = {
-            'arrays': [('data', datasets.get('data'))],
+            'arrays': [(path.stem, datasets.get('data'))],
             'data_dark': datasets.get('data_dark'),
             'data_white': datasets.get('data_white'),
             'tilt_angles': datasets.get('theta'),
@@ -695,7 +700,7 @@ def _load_transform_functions(operators):
 
 
 def _write_child_data(result, operator_index, output_file_path, dims):
-    for (label, dataobject) in six.iteritems(result):
+    for label, dataobject in result.items():
         # Only need write out data if the operator made updates.
         output_path = '.'
         if output_file_path is not None:
@@ -721,6 +726,7 @@ def _write_child_data(result, operator_index, output_file_path, dims):
 
 
 def load_dataset(data_file_path, read_options=None):
+    data_file_path = Path(data_file_path)
     if _is_data_exchange(data_file_path):
         output = _read_data_exchange(data_file_path, read_options)
     else:
diff --git a/tomviz/python/tomviz/external_dataset.py b/tomviz/python/tomviz/external_dataset.py
index ab6a6a1ac..20e3ed6d0 100644
--- a/tomviz/python/tomviz/external_dataset.py
+++ b/tomviz/python/tomviz/external_dataset.py
@@ -14,10 +14,10 @@ def __init__(self, arrays, active=None):
         self.tilt_axis = None
         # The currently active scalar
         self.active_name = active
-        # If we weren't given the active array and we only have one array, set
-        # it as the active array.
+        # If we weren't given the active array, set the first as the active
+        # array.
         if active is None and len(arrays.keys()):
-            (self.active_name,) = arrays.keys()
+            self.active_name = next(iter(arrays.keys()))
 
         self._spacing = None
 
@@ -31,11 +31,15 @@ def __init__(self, arrays, active=None):
 
     @property
     def active_scalars(self):
-        return self.arrays[self.active_name]
+        return self.scalars(self.active_name)
 
     @active_scalars.setter
     def active_scalars(self, array):
-        self.arrays[self.active_name] = array
+        self.set_scalars(self.active_name, array)
+
+    @property
+    def num_scalars(self):
+        return len(self.arrays)
 
     @property
     def scalars_names(self):
@@ -46,6 +50,9 @@ def scalars(self, name=None):
             name = self.active_name
         return self.arrays[name]
 
+    def set_scalars(self, name, array):
+        self.arrays[name] = array
+
     @property
     def spacing(self):
         return self._spacing
@@ -69,3 +76,6 @@ def create_child_dataset(self):
             s = self.spacing
             child.spacing = [s[0], s[1], s[0]]
         return child
+
+    def rename_active(self, new_name: str):
+        self.arrays[new_name] = self.arrays.pop(self.active_name)
diff --git a/tomviz/python/tomviz/fix_pdb.py b/tomviz/python/tomviz/fix_pdb.py
new file mode 100644
index 000000000..947075d02
--- /dev/null
+++ b/tomviz/python/tomviz/fix_pdb.py
@@ -0,0 +1,37 @@
+import pdb
+import sys
+
+
+class FixedPdb(pdb.Pdb):
+    """
+    Since we re-direct stdin, stdout, and stderr in other parts of
+    the application, pdb can't interpret things like arrow keys
+    and auto-complete correctly.
+    This class fixes the issue by getting pdb to always use
+    the default stdout and stderr.
+    """
+    def set_trace(self, *args, **kwargs):
+        self._use_default_pipes()
+        return super().set_trace(*args, **kwargs)
+
+    def do_continue(self, *args, **kwargs):
+        self._restore_pipes()
+        return super().do_continue(*args, **kwargs)
+
+    def _use_default_pipes(self):
+        self._prev_stdout = sys.stdout
+        self._prev_stderr = sys.stderr
+        self._prev_stdin = sys.stdin
+        sys.stdout = sys.__stdout__
+        sys.stderr = sys.__stderr__
+        sys.stdin = sys.__stdin__
+
+    def _restore_pipes(self):
+        sys.stdout = self._prev_stdout
+        sys.stderr = self._prev_stderr
+        sys.stdin = self._prev_stdin
+
+
+def fix_pdb():
+    if not isinstance(pdb.Pdb, FixedPdb):
+        pdb.Pdb = FixedPdb
diff --git a/tomviz/python/tomviz/internal_dataset.py b/tomviz/python/tomviz/internal_dataset.py
index 7150346de..ffc85b7cf 100644
--- a/tomviz/python/tomviz/internal_dataset.py
+++ b/tomviz/python/tomviz/internal_dataset.py
@@ -16,6 +16,14 @@ def active_scalars(self):
     def active_scalars(self, v):
         utils.set_array(self._data_object, v)
 
+    @property
+    def active_name(self):
+        return utils.get_active_scalars_name(self._data_object)
+
+    @property
+    def num_scalars(self):
+        return len(self.scalars_names)
+
     @property
     def scalars_names(self):
         return utils.array_names(self._data_object)
@@ -23,6 +31,9 @@ def scalars_names(self):
     def scalars(self, name=None):
         return utils.get_array(self._data_object, name)
 
+    def set_scalars(self, name, array):
+        utils.set_array(self._data_object, array, name=name)
+
     @property
     def spacing(self):
         return utils.get_spacing(self._data_object)
@@ -71,6 +82,10 @@ def create_child_dataset(self):
         new_data = utils.make_child_dataset(self._data_object)
         return Dataset(new_data, self._data_source)
 
+    def rename_active(self, new_name: str):
+        scalars = self._data_object.GetPointData().GetScalars()
+        scalars.SetName(new_name)
+
 
 def create_dataset(data_object, data_source):
     return Dataset(data_object, data_source)
diff --git a/tomviz/python/tomviz/operators.py b/tomviz/python/tomviz/operators.py
index 2b3c3d7f9..6619bffca 100644
--- a/tomviz/python/tomviz/operators.py
+++ b/tomviz/python/tomviz/operators.py
@@ -60,10 +60,13 @@ def message(self, msg):
         self._operator._operator_wrapper.progress_message = msg
 
     def _data(self, value):
-        # Make sure this is a vtkDataObject before setting
-        from tomviz._internal import convert_to_vtk_data_object
-        data = convert_to_vtk_data_object(value)
-        self._operator._operator_wrapper.progress_data = data
+        from tomviz._internal import in_application
+        if in_application():
+            # Make sure this is a vtkDataObject before setting
+            from tomviz._internal import convert_to_vtk_data_object
+            value = convert_to_vtk_data_object(value)
+
+        self._operator._operator_wrapper.progress_data = value
 
     # Write-only property to update child data
     data = property(fset=_data)
diff --git a/tomviz/python/tomviz/ptycho/__init__.py b/tomviz/python/tomviz/ptycho/__init__.py
new file mode 100644
index 000000000..11c7258a4
--- /dev/null
+++ b/tomviz/python/tomviz/ptycho/__init__.py
@@ -0,0 +1,30 @@
+import os
+
+try:
+    from .ptycho import (
+        gather_ptycho_info,
+        get_use_and_versions_from_csv,
+        filter_sid_list,
+        load_stack_ptycho,
+    )
+    requirements_installed = True
+except ImportError:
+    requirements_installed = False
+
+    import traceback
+    import_error_exc = traceback.format_exc()
+
+    if 'TOMVIZ_REQUIRE_PTYCHO' in os.environ:
+        # Raise an exception so we can be notified if Ptycho import fails
+        raise
+
+
+def installed():
+    return requirements_installed
+
+
+def import_error():
+    if requirements_installed:
+        return ''
+    else:
+        return import_error_exc
diff --git a/tomviz/python/tomviz/ptycho/ptycho.py b/tomviz/python/tomviz/ptycho/ptycho.py
new file mode 100644
index 000000000..5b2cf2b03
--- /dev/null
+++ b/tomviz/python/tomviz/ptycho/ptycho.py
@@ -0,0 +1,432 @@
+import math
+from pathlib import Path
+import sys
+
+import numpy as np
+from scipy.ndimage.interpolation import rotate
+from scipy.optimize import leastsq
+from tqdm import tqdm
+
+from tomviz.executor import _write_emd
+from tomviz.external_dataset import Dataset
+
+PathLike = Path | str
+
+
+def gather_ptycho_info(ptycho_dir: PathLike) -> dict:
+    ptycho_dir = Path(ptycho_dir)
+
+    sid_list = sorted([int(x.name[1:]) for x in ptycho_dir.iterdir()
+                      if x.is_dir() and x.name.startswith('S')])
+
+    sid_dirs = [ptycho_dir / f'S{sid}' for sid in sid_list]
+
+    version_dict = {}
+    for sid, d in zip(sid_list, sid_dirs):
+        versions = []
+        for subdir in d.iterdir():
+            if subdir.is_dir():
+                versions.append(subdir.name)
+
+        if not versions:
+            # There will be an error, but at least put in 't1'
+            versions.append('t1')
+
+        version_dict[sid] = sorted(versions)
+
+    # Create angles and error lists for each SID and version
+    angle_dict = {}
+    error_dict = {}
+    for sid in sid_list:
+        these_angles = []
+        these_errors = []
+        for version in version_dict[sid]:
+            these_angles.append(load_angle_from_sid(sid, version,
+                                                    ptycho_dir))
+            these_errors.append(validate_sid(sid, version, ptycho_dir))
+
+        angle_dict[sid] = these_angles
+        error_dict[sid] = these_errors
+
+    version_list = [version_dict[sid] for sid in sid_list]
+    angle_list = [angle_dict[sid] for sid in sid_list]
+    error_list = [error_dict[sid] for sid in sid_list]
+    return {
+        'sid_list': sid_list,
+        'version_list': version_list,
+        'angle_list': angle_list,
+        'error_list': error_list,
+    }
+
+
+def validate_sid(sid: int, version: str, ptycho_dir: PathLike) -> str:
+    # Validate the sid and version, that it contains the data and angles.
+    # If it is valid, the returned string will be empty. Otherwise, the
+    # returned string will contain the error message as to what is not
+    # valid.
+    ptycho_dir = Path(ptycho_dir)
+    dir_path = ptycho_dir / f'S{sid}/{version}/recon_data'
+    f_path = dir_path / f'recon_{sid}_{version}_object_ave.npy'
+    g_path = dir_path / f'recon_{sid}_{version}_probe_ave.npy'
+    if not f_path.exists():
+        return 'Ptycho data missing'
+
+    if not g_path.exists():
+        return 'Probe data missing'
+
+    angle = load_angle_from_sid(sid, version, ptycho_dir)
+    if np.isnan(angle):
+        return 'Angle not found'
+
+    return ''
+
+
+def load_angle_from_sid(sid: int, version: str,
+                        ptycho_dir: PathLike) -> float:
+    path = locate_ptycho_hyan_file(sid, version, ptycho_dir)
+    if path is None:
+        return math.nan
+
+    return fetch_angle_from_ptycho_hyan_file(path)
+
+
+def locate_ptycho_hyan_file(sid: int, version: str,
+                            ptycho_dir: PathLike) -> str | None:
+    recon_data_dir = Path(ptycho_dir) / f'S{sid}' / version / 'recon_data'
+    matches = list(recon_data_dir.glob(f'{sid}_{version}*'))
+
+    for match in matches:
+        try:
+            with open(match.resolve(), 'r') as rf:
+                if 'angle =' in rf.read():
+                    return match.resolve()
+        except Exception:
+            # Move on to the next one
+            continue
+
+    return None
+
+
+def get_use_and_versions_from_csv(csv_path: str) -> dict:
+    data = np.genfromtxt(csv_path, delimiter=',', names=True, dtype=None)
+
+    sids = []
+    try:
+        sids = data['Scan_ID'].tolist()
+    except Exception:
+        print('"Scan_ID" column not found in CSV file', file=sys.stderr)
+
+    use = []
+    try:
+        use = data['Use'].tolist()
+        # Convert to boolean
+        use = [x in (1, '1', 'x') for x in use]
+    except Exception:
+        print('"Use" column not found in CSV file', file=sys.stderr)
+
+    versions = []
+    try:
+        versions = data['Version'].tolist()
+    except Exception:
+        print('"Version" column not found in CSV file', file=sys.stderr)
+
+    return {
+        'sids': sids,
+        'use': use,
+        'versions': versions,
+    }
+
+
+def filter_sid_list(sid_list: list[int], filter_string: str) -> list[int]:
+    if not filter_string.strip():
+        # All SIDs are valid
+        return list(sid_list)
+
+    # Either a comma-delimited list or numpy slicing
+    sid_strings = filter_string.split(',')
+    valid_sids = []
+    for this_str in sid_strings:
+        if ':' in this_str:
+            this_slice = slice(
+                *(int(s) if s else None for s in this_str.split(':'))
+            )
+            # If there was no stop specified, go to the end of the sid_list
+            if this_slice.stop is None:
+                this_slice = slice(this_slice.start, max(sid_list) + 1,
+                                   this_slice.step)
+
+            valid_sids += np.r_[this_slice].tolist()
+        else:
+            valid_sids.append(int(this_str))
+
+    return [sid for sid in sid_list if sid in valid_sids]
+
+
+# Load all Ptycho data, stack with padded size for max
+# Returns a path pointing to the output file that was created.
+def load_stack_ptycho(version_list: list[str],
+                      sid_list: list[int],
+                      angle_list: list[float],
+                      ptycho_dir: PathLike,
+                      output_dir: PathLike,
+                      rotate_datasets: bool = True) -> PathLike:
+
+    filespty_obj = []
+    filespty_prb = []
+    currentsidlist = []
+
+    if len(version_list) == 1:
+        version_list = np.repeat(version_list, len(sid_list))
+
+    ptycho_dir = Path(ptycho_dir)
+
+    pixel_size_x = None
+    pixel_size_y = None
+    for i, sid in tqdm(enumerate(sid_list[0: len(version_list)]),
+                       desc="Loading Ptycho"):
+        sid = int(sid)
+        version = version_list[i]
+        dir_path = ptycho_dir / f'S{sid}/{version}/recon_data'
+        f_path = dir_path / f'recon_{sid}_{version}_object_ave.npy'
+        g_path = dir_path / f'recon_{sid}_{version}_probe_ave.npy'
+        if f_path.exists():
+            filespty_obj.append(f_path)
+            currentsidlist.append((i, sid, angle_list[i], version))
+            filespty_prb.append(g_path)
+            if i == 0:
+                print('Attempting to read pixel sizes from the '
+                      f'first scan ID: {sid}')
+                result = attempt_to_read_pixel_sizes(sid, version, ptycho_dir)
+                if result is not None:
+                    pixel_size_x, pixel_size_y = result
+        else:
+            print(f"didn't find: {sid}")
+
+    has_pixel_sizes = pixel_size_x is not None
+    print(f"found: {len(filespty_obj)}")
+
+    tempPtyobj = []
+    tempPtyprb = []
+    tempPtyamp = []
+    for i in tqdm(range(len(filespty_obj)), desc="processing ptycho"):
+        obj = np.load(filespty_obj[i])
+        prb = np.load(filespty_prb[i])
+
+        if obj.ndim == 3:
+            # Get the 0th order result
+            obj = obj[0]
+
+        if prb.ndim == 3:
+            # Get the 0th order result
+            prb = prb[0]
+
+        space = 15
+        obj = np.fliplr(np.rot90(obj))
+        prb = np.fliplr(np.rot90(prb))
+        prb_sz = np.shape(prb)
+        # prb_sz_list.append(prb_sz)
+        obj_sz = np.shape(obj)
+        # obj_sz_list.append(obj_sz)
+        obj_c = obj[
+            int(prb_sz[0] / 2) + space: obj_sz[0] - int(prb_sz[0] / 2) - space,
+            int(prb_sz[1] / 2) + space: obj_sz[1] - int(prb_sz[1] / 2) - space,
+        ]
+        # obj_c_sz_list.append(obj_c.shape)
+        obj_c_arg = np.angle(obj_c)
+        obj_c_amp = np.abs(obj_c)
+        if True:
+            obj_c_arg = remove_background(obj_c_arg)
+        objectoutput = obj_c_amp * np.exp((0 + 1j) * obj_c_arg)
+        obj_c_arg = np.angle(objectoutput)
+        obj_c_amp = np.abs(obj_c)
+        tempPtyamp.append(obj_c_amp)
+        tempPtyobj.append(obj_c_arg * -1)
+        tempPtyprb.append(prb)
+
+    # imt = tf.imread(filelist[0][0])
+    # load fluor1 and get shape of first array
+    probes = np.asarray(tempPtyprb)
+    probes_phase = np.angle(probes)
+    probes_amp = np.abs(probes)
+    # imt = ptfluor[0]
+    # l, w = imt.shape
+    # factor= 2
+    shapeslist = [i.shape for i in tempPtyobj]
+    shapeslist = np.asarray(shapeslist)
+    lmax = shapeslist[:, 0].max()
+    wmax = shapeslist[:, 1].max()
+    ptychodatanew = np.zeros((len(tempPtyobj), int(lmax), int(wmax)))
+    ampdatanew = np.zeros((len(tempPtyobj), int(lmax), int(wmax)))
+    # Loop checking size, find largest, #try for if its larger, crop step
+    for n, i in tqdm(enumerate(tempPtyobj), desc="correcting shape"):
+        lerr = np.abs(i.shape[0] - lmax)
+        werr = np.abs(i.shape[1] - wmax)
+        ti = np.pad(i, ((lerr // 2, lerr // 2), (werr // 2, werr // 2)))
+        ta = np.pad(
+            tempPtyamp[n], ((lerr // 2, lerr // 2), (werr // 2, werr // 2)),
+        )
+        ptychodatanew[n, :, :] = ti
+        ampdatanew[n, :, :] = ta
+
+    arrays = {
+        'Phase': ptychodatanew,
+        'Amplitude': ampdatanew,
+        'Probes Phase': probes_phase,
+        'Probes Amplitude': probes_amp,
+    }
+
+    # Do all necessary processing of the output arrays.
+    for key, array in arrays.items():
+        if rotate_datasets:
+            array = rotate(array, -90.0, axes=(1, 2))
+
+        array = array.swapaxes(0, 2)
+        arrays[key] = array
+
+    # Make sure the output directory exists
+    Path(output_dir).mkdir(parents=True, exist_ok=True)
+
+    # Now write out the datasets in EMD format
+    output_files = []
+    datasets = {
+        # Ptycho and Amp have the same shape, so we write them together
+        'ptycho_object.emd': ['Phase', 'Amplitude'],
+        # Probe has a different shape
+        'ptycho_probe.emd': ['Probes Phase', 'Probes Amplitude'],
+    }
+    for filename, array_names in datasets.items():
+        dataset = Dataset({key: arrays[key] for key in array_names})
+        dataset.tilt_angles = np.array([x[2] for x in currentsidlist])
+        dataset.tilt_axis = 2
+        if filename == 'ptycho_object.emd' and has_pixel_sizes:
+            # Also set the pixel sizes if they are available
+            dataset.spacing = (pixel_size_x, pixel_size_y, 1)
+        output_path = Path(output_dir) / filename
+        _write_emd(output_path, dataset)
+        output_files.append(str(output_path))
+
+    # Now write out the text file containing info about what was used
+    # FIXME: also add reconstruction pixel sizes
+    currentsidlist_str = []
+    for row in currentsidlist:
+        this_row = []
+        for entry in row:
+            if isinstance(entry, float):
+                s = f'{entry:.3f}'
+            else:
+                s = entry
+            this_row.append(s)
+
+        currentsidlist_str.append(this_row)
+
+    col_delim = ' '
+    headers = ['Angle', 'SID', 'Version']
+    index_order = [2, 1, 3]
+    col_width = 10
+    with open(Path(output_dir) / 'stacked_ptycho_info.txt', 'w') as wf:
+        header_str = col_delim.join([f'{x:>{col_width}}' for x in headers])
+        # Replace first character with '#'
+        header_str = '#' + header_str[1:]
+        wf.write(header_str + '\n')
+        for row in currentsidlist_str:
+            row_str = col_delim.join([
+                f'{row[idx]:>{col_width}}' for idx in index_order
+            ])
+            wf.write(row_str + '\n')
+
+    return output_files
+
+
+def remove_background(im: np.ndarray) -> np.ndarray:
+    params = [0, 0, 0]
+
+    def err_func(p):
+        return np.ravel(fit_func(*p)(*np.indices(im.shape)) - im)
+
+    p, success = leastsq(err_func, params)
+    return im - fit_func(*p)(*np.indices(im.shape))
+
+
+def fit_func(
+    p0,
+    px1,
+    py1,
+):
+    return lambda x, y: p0 + x * px1 + py1 * y
+
+
+def attempt_to_read_pixel_sizes(sid, version, ptycho_dir) -> tuple[float, float] | None:
+    path = locate_ptycho_hyan_file(sid, version, ptycho_dir)
+    if path is None:
+        print(
+            f'Failed to locate config file for {sid} {version}\n'
+            f'Pixel sizes will not be read',
+            file=sys.stderr,
+        )
+        return None
+
+
+    result = fetch_pixel_sizes_from_ptycho_hyan_file(path)
+    if result is None:
+        print(
+            'Failed to obtain pixel sizes. Pixel sizes '
+            'will not be applied to datasets.',
+            file=sys.stderr,
+        )
+        return None
+
+    print('Pixel sizes identified as:', result[0], result[1])
+    return result[0], result[1]
+
+
+def fetch_angle_from_ptycho_hyan_file(filepath: PathLike) -> float | None:
+    with open(filepath, 'r') as rf:
+        for line in rf:
+            line = line.lstrip()
+            if line.startswith('angle = '):
+                angle = float(line.split('=')[1].strip())
+                return angle
+
+    # Angle was not found
+    return math.nan
+
+
+def fetch_pixel_sizes_from_ptycho_hyan_file(
+    filepath: PathLike,
+) -> tuple[float, float] | None:
+    print(f'Obtaining pixel sizes from config file: {filepath})')
+    vars_required = [
+        'lambda_nm', 'z_m', 'x_arr_size', 'y_arr_size', 'ccd_pixel_um'
+    ]
+    results = {}
+    try:
+        with open(filepath, 'r') as rf:
+            for line in rf:
+                if '=' not in line:
+                    continue
+
+                lhs = line.split('=')[0].strip()
+                if lhs in vars_required:
+                    value = float(line.split('=')[1].strip())
+                    results[lhs] = value
+    except Exception as e:
+        print('Failed to fetch pixel sizes with error:', e, file=sys.stderr)
+        return None
+
+    missing = [x for x in vars_required if x not in results]
+    if missing:
+        print(
+            'Failed to fetch pixel sizes. Some required variables '
+            f'were not found: {missing}'
+        )
+        return None
+
+    # Now compute them. They can both use the same numerator
+    numerator = (
+        results['lambda_nm'] * results['z_m'] * 1e6 / results['ccd_pixel_um']
+    )
+
+    x_pixel_size = numerator / results['x_arr_size']
+    y_pixel_size = numerator / results['y_arr_size']
+
+    return x_pixel_size, y_pixel_size
diff --git a/tomviz/python/tomviz/pyxrf/__init__.py b/tomviz/python/tomviz/pyxrf/__init__.py
index 65d20e532..8334e0f3a 100644
--- a/tomviz/python/tomviz/pyxrf/__init__.py
+++ b/tomviz/python/tomviz/pyxrf/__init__.py
@@ -1,7 +1,9 @@
+import os
+
 try:
     from .load_output import list_elements, extract_elements  # noqa
-    from .make_hdf5 import make_hdf5  # noqa
-    from .process_projections import fix_python_paths, ic_names, process_projections  # noqa
+    from .ic_names import ic_names  # noqa
+    from .sids import filter_sids
     requirements_installed = True
 except ImportError:
     requirements_installed = False
@@ -9,6 +11,10 @@
     import traceback
     import_error_exc = traceback.format_exc()
 
+    if 'TOMVIZ_REQUIRE_PYXRF' in os.environ:
+        # Raise an exception so we can be notified if PyXRF import fails
+        raise
+
 
 def installed():
     return requirements_installed
diff --git a/tomviz/python/tomviz/pyxrf/ic_names.py b/tomviz/python/tomviz/pyxrf/ic_names.py
new file mode 100644
index 000000000..207e9b114
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/ic_names.py
@@ -0,0 +1,16 @@
+from pathlib import Path
+
+import h5py
+
+def ic_names(working_directory):
+    # Find any HDF5 file in the working directory and grab the ic names
+    files = [x for x in Path(working_directory).iterdir() if x.suffix == '.h5']
+    if not files:
+        raise Exception(f'No .h5 files found in "{working_directory}"')
+
+    first_file = files[0]
+
+    with h5py.File(first_file, 'r') as rf:
+        names = rf["xrfmap"]["scalers"]["name"]
+        names = [x.decode() for x in names]
+        return names
diff --git a/tomviz/python/tomviz/pyxrf/load_output.py b/tomviz/python/tomviz/pyxrf/load_output.py
index 64c8df9e4..b579fbc6e 100644
--- a/tomviz/python/tomviz/pyxrf/load_output.py
+++ b/tomviz/python/tomviz/pyxrf/load_output.py
@@ -1,6 +1,11 @@
 import h5py
 from pathlib import Path
 
+from scipy.ndimage.interpolation import rotate
+
+from tomviz.executor import _write_emd
+from tomviz.external_dataset import Dataset
+
 
 def list_elements(filename):
     with h5py.File(filename, 'r') as f:
@@ -9,24 +14,36 @@ def list_elements(filename):
     return [x.decode() for x in elements]
 
 
-def extract_elements(filename, elements, output_path):
+def extract_elements(filename, elements, output_path, rotate_datasets,
+                     pixel_size_x, pixel_size_y):
     output_path = Path(output_path)
     output_path.mkdir(parents=True, exist_ok=True)
 
     all_elements = list_elements(filename)
     keep_indices = [all_elements.index(x) for x in elements]
 
+    has_pixel_sizes = pixel_size_x > 0 and pixel_size_y > 0
+
     with h5py.File(filename, 'r') as f:
         angles = f['/exchange/theta'][()]
         recon = f['/reconstruction/fitting/data'][:, keep_indices]
 
     ret = []
     for i, element in enumerate(elements):
-        file_path = f'{output_path / element}.h5'
-        with h5py.File(file_path, 'w') as wf:
-            wf['/exchange/theta'] = angles
-            wf['/exchange/data'] = recon[:, i]
-
+        this_recon = recon[:, i]
+        if rotate_datasets:
+            this_recon = rotate(this_recon, -90.0, axes=(1, 2))
+
+        dataset = Dataset({element: this_recon.swapaxes(0, 2)})
+        dataset.active_name = element
+        dataset.tilt_angles = angles
+        dataset.tilt_axis = 2
+        if has_pixel_sizes:
+            # Also set the pixel sizes if they are available
+            dataset.spacing = (pixel_size_x, pixel_size_y, 1)
+
+        file_path = f'{output_path / element}.emd'
+        _write_emd(file_path, dataset)
         ret.append(file_path)
 
     return ret
diff --git a/tomviz/python/tomviz/pyxrf/make_hdf5.py b/tomviz/python/tomviz/pyxrf/make_hdf5.py
deleted file mode 100644
index aa43ba298..000000000
--- a/tomviz/python/tomviz/pyxrf/make_hdf5.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from pyxrf.api_dev import make_hdf
-
-from xrf_tomo import create_log_file
-
-
-def make_hdf5(start_scan, stop_scan, working_directory, successful_scans_only,
-              log_file_name):
-
-    kwargs = {
-        'start': start_scan,
-        'end': stop_scan,
-        'wd': working_directory,
-        'successful_scans_only': successful_scans_only,
-    }
-    make_hdf(**kwargs)
-
-    kwargs = {
-        'fn_log': log_file_name,
-        'wd': working_directory,
-    }
-    create_log_file(**kwargs)
diff --git a/tomviz/python/tomviz/pyxrf/process_projections.py b/tomviz/python/tomviz/pyxrf/process_projections.py
deleted file mode 100644
index c3203f1f3..000000000
--- a/tomviz/python/tomviz/pyxrf/process_projections.py
+++ /dev/null
@@ -1,126 +0,0 @@
-import os
-import multiprocessing
-from pathlib import Path
-import shutil
-
-import h5py
-from xrf_tomo import process_proj, make_single_hdf
-
-# sys.stderr has been replaced by vtkPythonStdStreamCaptureHelper
-# As such, it does not have an "isatty()" function. Therefore, turn off
-# the tty check in the progress library.
-try:
-    import progress
-    progress.Infinite.check_tty = False
-except Exception:
-    # Maybe a new version of pyxrf removed dependency on progress...
-    # Or maybe progress refactored. Either way, let it go...
-    pass
-
-
-def ic_names(working_directory):
-    # Find any HDF5 file in the working directory and grab the ic names
-    files = [x for x in Path(working_directory).iterdir() if x.suffix == '.h5']
-    if not files:
-        raise Exception(f'No .h5 files found in "{working_directory}"')
-
-    first_file = files[0]
-
-    with h5py.File(first_file, 'r') as rf:
-        names = rf["xrfmap"]["scalers"]["name"]
-        names = [x.decode() for x in names]
-        return names
-
-
-def process_projections(working_directory, parameters_file_name, log_file_name,
-                        ic_name, skip_processed, output_directory):
-    # FIXME: this shouldn't be necessary. When we get time, figure out why
-    # we have to specify these paths. Currently, if we do not, then the
-    # multiprocessing will encounter errors about missing standard python
-    # libraries.
-    fix_python_paths()
-
-    # Because we are running an embedded tomviz, multiprocessing can't
-    # find the python executable. Therefore, we need to try to find it
-    # automatically and tell multiprocessing where it is.
-    python_exec = find_python_executable()
-    multiprocessing.set_executable(python_exec)
-
-    kwargs = {
-        'wd': working_directory,
-        'fn_param': parameters_file_name,
-        'fn_log': log_file_name,
-        'ic_name': ic_name,
-        'skip_processed': skip_processed,
-    }
-    process_proj(**kwargs)
-
-    kwargs = {
-        'fn': 'tomo.h5',
-        'fn_log': log_file_name,
-        'wd_src': working_directory,
-        'wd_dest': output_directory,
-        'ic_name': ic_name,
-    }
-    make_single_hdf(**kwargs)
-
-    # Copy the csv file into the output directory
-    log_file_path = Path(log_file_name)
-    if not log_file_path.is_absolute():
-        log_file_path = Path(working_directory).resolve() / log_file_path
-
-    output_file_path = Path(output_directory).resolve() / log_file_path.name
-    if log_file_path != output_file_path:
-        # Copy the csv file into the output directory
-        shutil.copyfile(log_file_path, output_file_path)
-
-
-def fix_python_paths():
-    # FIXME: this shouldn't be necessary, but otherwise, we get errors
-    # indicating that python standard libraries couldn't be found.
-    # It seems the embedded python in our conda package doesn't set up
-    # its sys.path correctly.
-    python_path_var = os.environ.get('PYTHONPATH', '')
-    python_paths = python_path_var.split(':') if python_path_var else []
-
-    conda_path = Path(os.environ.get('CONDA_PREFIX', ''))
-    need_to_add = [
-        conda_path / 'lib/python3.7/site-packages',
-        conda_path / 'lib/python3.7/lib-dynload',
-    ]
-
-    for path in need_to_add:
-        if str(path) not in python_paths:
-            python_paths.append(str(path))
-
-    os.environ['PYTHONPATH'] = ':'.join(python_paths)
-
-
-def find_python_executable():
-    # Since we are in tomviz, sys.executable does not work
-    failure_msg = (
-        'Could not find python executable for multiprocessing. '
-        'Please set it to the environment variable "TOMVIZ_PYTHON_EXECUTABLE" '
-        'and restart tomviz.'
-    )
-
-    # First, check if the user set it via an environment variable
-    path = os.environ.get('TOMVIZ_PYTHON_EXECUTABLE')
-    if path and Path(path).exists():
-        return path
-
-    # Next, try to find it via the conda prefix
-    conda_path = os.environ.get('CONDA_PREFIX')
-    if conda_path is None:
-        raise Exception(failure_msg)
-
-    try_list = [
-        Path(conda_path) / 'bin' / 'python',
-        Path(conda_path) / 'bin' / 'python3',
-        Path(conda_path) / 'bin' / 'python.exe',
-    ]
-    for path in try_list:
-        if path.exists():
-            return str(path)
-
-    raise Exception(failure_msg)
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/README.md b/tomviz/python/tomviz/pyxrf/pyxrf-utils/README.md
new file mode 100644
index 000000000..67f9731ad
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/README.md
@@ -0,0 +1,21 @@
+# PyXRF Utilities
+
+Simple utility functions for interacting with PyXRF.
+
+For example, make a set of PyXRF HDF5 files in a directory:
+
+```bash
+pyxrf-utils make-hdf5 -s 157391 -e 157637 -b -l log.csv /path/to/output/directory
+```
+
+Make a CSV log file from the HDF5 files:
+
+```bash
+pyxrf-utils make-csv -w /path/to/working/directory -s "157391:157637" log.csv
+```
+
+Process projections using a PyXRF params.json file:
+
+```bash
+pyxrf-utils process-projections -p params.json -l log.csv -i sclr1_ch4 -s -o /output /input/dir
+```
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pixi.toml b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pixi.toml
new file mode 100644
index 000000000..20a48b726
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pixi.toml
@@ -0,0 +1,42 @@
+[workspace]
+name = "pyxrf-utils"
+version = "1.0.0"
+description = "PyXRF Utilities"
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+
+[dependencies]
+python = ">=3.10,<3.14"
+numpy = "*"
+h5py = "*"
+pandas = "*"
+xraylib = "*"
+tomopy = "*"
+
+[pypi-dependencies]
+bluesky-tiled-plugins = ">=2.0.0rc1"
+pyxrf = "*"
+hxntools = "*"
+xrf-tomo = "*"
+scikit-beam = "*"
+tiled = { version = ">=0.2.0", extras = ["client"] }
+
+[tasks]
+# Install the package in development mode
+install = "pip install -e ."
+
+# Run the CLI tool
+pyxrf-utils = "python -m pyxrf_utils.cli"
+
+[environments]
+default = { solve-group = "default" }
+dev     = { features = ["dev"], solve-group = "default" }
+
+[feature.dev.dependencies]
+pytest = "*"
+ruff = "*"
+ipython = "*"
+matplotlib-base = "*"
+
+[feature.dev.tasks]
+lint = "ruff check"
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyproject.toml b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyproject.toml
new file mode 100644
index 000000000..731a87599
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyproject.toml
@@ -0,0 +1,52 @@
+[build-system]
+requires = ["hatchling", "setuptools"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyxrf-utils"
+version = "1.0.0"
+description = "PyXRF Utilities"
+readme = "README.md"
+requires-python = ">=3.8"
+license = {text = "BSD-3-Clause"}
+keywords = ["xrf", "data-processing", "hdf5", "tomography"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering",
+]
+
+# Dependencies managed by pixi, but listed here for pip compatibility
+dependencies = [
+    "numpy",
+    "h5py",
+    "pandas",
+    "h5py",
+    "xraylib",
+    "tomopy",
+    "bluesky-tiled-plugins",
+    "pyxrf",
+    "hxntools",
+    "xrf-tomo",
+    "scikit-beam",
+    "tiled",
+]
+
+[project.scripts]
+pyxrf-utils = "pyxrf_utils.cli:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["pyxrf_utils"]
+
+[tool.ruff]
+line-length = 100
+target-version = "py38"
+select = ["E", "F", "W", "I"]
+ignore = []
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/__init__.py b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/cli.py b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/cli.py
new file mode 100644
index 000000000..aff7083b4
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/cli.py
@@ -0,0 +1,221 @@
+#!/usr/bin/env python3
+"""
+PyXRF Utilities
+
+This script provides utilities for working with PyXRF data including
+downloading the data and writing to PyXRF HDF5 files,
+CSV log file creation, and projection processing.
+"""
+import argparse
+import sys
+
+from pyxrf_utils.create_log_file import create_log_file
+from pyxrf_utils.make_hdf5 import make_hdf5
+from pyxrf_utils.process_projections import process_projections
+
+
+def make_csv_cmd(args):
+    """
+    Read PyXRF HDF5 files and write a CSV log file.
+
+    Args:
+        args: Parsed arguments from argparse
+    """
+    create_log_file(
+        log_file_name=args.output_csv,
+        working_directory=args.working_directory,
+        sid_selection=args.sid_selection,
+        hdf5_glob_pattern=args.hdf5_glob_pattern,
+        skip_invalid=args.skip_invalid,
+    )
+
+
+def make_hdf5_cmd(args):
+    """
+    Download and save scan data in PyXRF HDF5 format.
+
+    Args:
+        args: Parsed arguments from argparse
+    """
+    make_hdf5(
+        start_scan=args.start_scan,
+        stop_scan=args.end_scan,
+        working_directory=args.output_directory,
+        successful_scans_only=args.successful_scans_only,
+        log_file_name=args.log_file,
+    )
+
+
+def process_projections_cmd(args):
+    """
+    Process XRF projection data using PyXRF.
+
+    Args:
+        args: Parsed arguments from argparse
+    """
+    process_projections(
+        working_directory=args.working_directory,
+        parameters_file_name=args.parameters_file,
+        log_file_name=args.log_file,
+        ic_name=args.ic_name,
+        skip_processed=args.skip_processed,
+        output_directory=args.output_directory,
+    )
+
+
+def main():
+    """Main entry point for the pyxrf-utils command-line tool."""
+
+    # Create the top-level parser
+    parser = argparse.ArgumentParser(
+        prog='pyxrf-utils',
+        description='PyXRF Utilities - Tools for XRF data processing',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  pyxrf-utils make-hdf5 -s 157391 -e 157637 -b -l log.csv /path/to/output/directory
+  pyxrf-utils make-csv -w /path/to/working/directory -s "157391:157637" log.csv
+  pyxrf-utils process-projections -p params.json -l log.csv -i sclr1_ch4 -s -o /output /working
+        """  # noqa
+    )
+
+    # Add version argument
+    parser.add_argument(
+        '--version',
+        action='version',
+        version='%(prog)s 1.0.0'
+    )
+
+    # Create subparsers
+    subparsers = parser.add_subparsers(
+        title='subcommands',
+        description='Available commands',
+        dest='command',
+        help='Use "pyxrf-utils <command> --help" for more information',
+        required=True
+    )
+
+    # ========== make-csv subcommand ==========
+    parser_csv = subparsers.add_parser(
+        'make-csv',
+        help='Create log CSV file',
+        description='Create log CSV file from PyXRF HDF5 files'
+    )
+    parser_csv.add_argument(
+        'output_csv',
+        help='Output CSV file path (e.g., log.csv)'
+    )
+    parser_csv.add_argument(
+        '-w', '--working-directory',
+        required=True,
+        help='Path to working directory containing input data'
+    )
+    parser_csv.add_argument(
+        '-s', '--sid-selection',
+        required=False,
+        default=None,
+        help='SID selection string (comma-separated scan IDs or pattern)'
+    )
+    parser_csv.add_argument(
+        '-p', '--hdf5-glob-pattern',
+        required=False,
+        default='scan2D_*.h5',
+        help='Glob pattern for identifying which HDF5 files to read.',
+    )
+    parser_csv.add_argument(
+        '-i', '--skip-invalid',
+        action='store_true',
+        required=False,
+        default=False,
+        help='Skip invalid scans whose properties could not be read.',
+    )
+    parser_csv.set_defaults(func=make_csv_cmd)
+
+    # ========== make-hdf5 subcommand ==========
+    parser_hdf5 = subparsers.add_parser(
+        'make-hdf5',
+        help='Download and save scans in PyXRF HDF5 format',
+        description='Download and save scans in PyXRF HDF5 format'
+    )
+    parser_hdf5.add_argument(
+        'output_directory',
+        help='Path to output directory where HDF5 files will be saved'
+    )
+    parser_hdf5.add_argument(
+        '-s', '--start-scan',
+        type=int,
+        required=True,
+        help='Starting scan number'
+    )
+    parser_hdf5.add_argument(
+        '-e', '--end-scan',
+        type=int,
+        required=True,
+        help='Ending scan number'
+    )
+    parser_hdf5.add_argument(
+        '-b', '--successful-scans-only',
+        action='store_true',
+        required=False,
+        default=False,
+        help='Process only successful scans'
+    )
+    parser_hdf5.add_argument(
+        '-l', '--log-file',
+        required=True,
+        help='Log file name for recording conversion process'
+    )
+    parser_hdf5.set_defaults(func=make_hdf5_cmd)
+
+    # ========== process-projections subcommand ==========
+    parser_proj = subparsers.add_parser(
+        'process-projections',
+        help='Process XRF projection data',
+        description='Process XRF projection data using PyXRF'
+    )
+    parser_proj.add_argument(
+        'working_directory',
+        help='Path to working directory containing projection data'
+    )
+    parser_proj.add_argument(
+        '-p', '--parameters-file',
+        required=True,
+        help='Path to parameters file (e.g., JSON or config file)'
+    )
+    parser_proj.add_argument(
+        '-l', '--log-file',
+        required=True,
+        help='Path to log file for recording processing steps'
+    )
+    parser_proj.add_argument(
+        '-i', '--ic-name',
+        required=True,
+        help='Ion chamber name for normalization'
+    )
+    parser_proj.add_argument(
+        '-s', '--skip-processed',
+        required=False,
+        default=False,
+        action='store_true',
+        help='Skip already processed data'
+    )
+    parser_proj.add_argument(
+        '-o', '--output-directory',
+        required=True,
+        help='Path to output directory for reconstructed data'
+    )
+    parser_proj.set_defaults(func=process_projections_cmd)
+
+    # Parse arguments
+    args = parser.parse_args()
+
+    # Call the appropriate function
+    try:
+        args.func(args)
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/create_log_file.py b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/create_log_file.py
new file mode 100644
index 000000000..d292c8a95
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/create_log_file.py
@@ -0,0 +1,142 @@
+from pathlib import Path
+import glob
+import os
+import sys
+
+import h5py
+import numpy as np
+import pandas as pd
+import time
+
+from pyxrf.core.utils import convert_time_from_nexus_string
+
+
+def create_log_file(log_file_name: str, working_directory: str,
+                    sid_selection: str | None = None,
+                    hdf5_glob_pattern: str = "scan2D_*.h5",
+                    skip_invalid: bool = True):
+    """
+    Create log file ``fn`` based on the files contained in ``wd``. If ``fn``
+    is a relative path, it is assumed that the root is in ``wd``.
+    """
+    wd = Path(working_directory).resolve()
+    fn_log = Path(log_file_name)
+    if not fn_log.is_absolute():
+        fn_log = wd / fn_log
+
+    selected_sids = []
+    if sid_selection is not None:
+        sid_strings = sid_selection.split(',')
+        for this_str in sid_strings:
+            if ':' in this_str:
+                this_slice = slice(
+                    *(int(s) if s else None for s in this_str.split(':'))
+                )
+                selected_sids += np.r_[this_slice].tolist()
+            else:
+                selected_sids.append(int(this_str))
+
+    # Create the list of HDF5 files
+    hdf5_list = glob.glob(os.path.join(wd, hdf5_glob_pattern))
+
+    mdata_keys = [
+        "scan_time_start",
+        "scan_id",
+        "param_theta",
+        "param_theta_units",
+        "param_input",
+        "scan_uid",
+        "scan_exit_status",
+    ]
+    hdf5_mdata = {}
+
+    for hdf5_fn in hdf5_list:
+        try:
+            mdata, mdata_selected = {}, {}
+            with h5py.File(hdf5_fn, "r") as f:
+                # Retrieve metadata if it exists
+                metadata = f["xrfmap/scan_metadata"]
+                for key, value in metadata.attrs.items():
+                    # Convert ndarrays to lists
+                    # (they were lists before they were saved)
+                    if isinstance(value, np.ndarray):
+                        value = list(value)
+                    mdata[key] = value
+            mdata_available_keys = set(mdata.keys())
+            mdata_missing_keys = set(mdata_keys) - mdata_available_keys
+            if mdata_missing_keys:
+                raise IndexError(
+                    "The following metadata keys are missing in file "
+                    f"'{hdf5_fn}': {mdata_missing_keys}. "
+                    "Log file can not be created. Make sure that the files "
+                    "are created using recent version of PyXRF"
+                )
+
+            if sid_selection is not None:
+                sid = int(mdata['scan_id'])
+                if sid not in selected_sids:
+                    # Skip over ones that were not selected.
+                    continue
+
+            mdata_selected = {_: mdata[_] for _ in mdata_keys}
+            if mdata_selected["param_theta_units"] == "mdeg":
+                mdata_selected["param_theta"] /= 1000
+                mdata_selected["param_theta_units"] = "deg"
+
+            hdf5_mdata[os.path.basename(hdf5_fn)] = mdata_selected
+
+        except Exception as ex:
+            msg = f"Failed to load metadata from '{hdf5_fn}': {ex}"
+            if not skip_invalid:
+                raise IOError(msg) from ex
+
+            print(msg, file=sys.stderr)
+            print(f"Skipping '{hdf5_fn}'", file=sys.stderr)
+
+    # List of file names sorted by the angle 'theta'
+    hdf5_names_sorted = sorted(
+        hdf5_mdata,
+        key=lambda _: hdf5_mdata[_]["param_theta"],
+    )
+
+    column_labels = [
+        "Start Time",
+        "Scan ID",
+        "Theta",
+        "Use",
+        "Filename",
+        "X Start",
+        "X Stop",
+        "Num X",
+        "Y Start",
+        "Y Stop",
+        "Num Y",
+        "Dwell",
+        "UID",
+        "Status",
+        "Version",
+    ]
+    hdf5_mdata_sorted = []
+    for hdf5_fn in hdf5_names_sorted:
+        md = hdf5_mdata[hdf5_fn]
+        hdf5_mdata_sorted.append(
+            [
+                time.strftime(
+                    "%a %b %d %H:%M:%S %Y",
+                    convert_time_from_nexus_string(md["scan_time_start"]),
+                ),
+                md["scan_id"],
+                np.round(md["param_theta"], 3),
+                "1",
+                hdf5_fn,
+                *[np.round(_, 3) for _ in md["param_input"][0:7]],
+                md["scan_uid"],
+                md["scan_exit_status"],
+                "t1",
+            ]
+        )
+    df = pd.DataFrame(data=hdf5_mdata_sorted, columns=column_labels)
+
+    os.makedirs(os.path.dirname(fn_log), exist_ok=True)
+    df.to_csv(fn_log, sep=",", index=False)
+    print(f"Log file '{fn_log}' was successfully created.")
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/make_hdf5.py b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/make_hdf5.py
new file mode 100644
index 000000000..2b92cc0e5
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/make_hdf5.py
@@ -0,0 +1,35 @@
+from pathlib import Path
+
+from pyxrf.api_dev import make_hdf
+import pyxrf.model.load_data_from_db
+
+from .create_log_file import create_log_file
+
+if pyxrf.model.load_data_from_db.db is None:
+    # Manually force the database to be HXN if it was not identified correctly
+    pyxrf.model.load_data_from_db.catalog_info.set_name('HXN')
+
+    from hxntools.CompositeBroker import db
+    pyxrf.model.load_data_from_db.db = db
+
+
+def make_hdf5(
+    start_scan: int,
+    stop_scan: int,
+    working_directory: Path,
+    successful_scans_only: bool,
+    log_file_name: Path,
+):
+    kwargs = {
+        'start': start_scan,
+        'end': stop_scan,
+        'wd': working_directory,
+        'successful_scans_only': successful_scans_only,
+    }
+    make_hdf(**kwargs)
+
+    kwargs = {
+        'log_file_name': log_file_name,
+        'working_directory': working_directory,
+    }
+    create_log_file(**kwargs)
diff --git a/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/process_projections.py b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/process_projections.py
new file mode 100644
index 000000000..7634a30fe
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/pyxrf-utils/pyxrf_utils/process_projections.py
@@ -0,0 +1,43 @@
+from pathlib import Path
+import shutil
+
+from xrf_tomo import process_proj, make_single_hdf
+
+
+def process_projections(
+    working_directory: str,
+    parameters_file_name: str,
+    log_file_name: str,
+    ic_name: str,
+    skip_processed: bool,
+    output_directory: str,
+):
+    kwargs = {
+        'wd': working_directory,
+        'fn_param': parameters_file_name,
+        'fn_log': log_file_name,
+        'ic_name': ic_name,
+        'skip_processed': skip_processed,
+    }
+    process_proj(**kwargs)
+
+    # Ensure the output directory exists
+    Path(output_directory).mkdir(parents=True, exist_ok=True)
+    kwargs = {
+        'fn': 'tomo.h5',
+        'fn_log': log_file_name,
+        'wd_src': working_directory,
+        'wd_dest': output_directory,
+        'ic_name': ic_name,
+    }
+    make_single_hdf(**kwargs)
+
+    # Copy the csv file into the output directory
+    log_file_path = Path(log_file_name)
+    if not log_file_path.is_absolute():
+        log_file_path = Path(working_directory).resolve() / log_file_path
+
+    output_file_path = Path(output_directory).resolve() / log_file_path.name
+    if log_file_path != output_file_path:
+        # Copy the csv file into the output directory
+        shutil.copyfile(log_file_path, output_file_path)
diff --git a/tomviz/python/tomviz/pyxrf/sids.py b/tomviz/python/tomviz/pyxrf/sids.py
new file mode 100644
index 000000000..3180c7827
--- /dev/null
+++ b/tomviz/python/tomviz/pyxrf/sids.py
@@ -0,0 +1,27 @@
+import numpy as np
+
+
+def filter_sids(all_sids: list[str], filter_string: str) -> list[str]:
+    # The sids are taken as strings instead of ints to make it easier
+    # for the C++ side to call this and process the output.
+    all_sid_ints = [int(s) for s in all_sids]
+    max_sid = max(all_sid_ints)
+
+    sid_strings = filter_string.split(',')
+    valid_sids = []
+    for this_str in sid_strings:
+        if ':' in this_str:
+            this_slice = slice(
+                *(int(s) if s else None for s in this_str.split(':'))
+            )
+            # If there was no stop specified, go to the end of the sid_list
+            if this_slice.stop is None:
+                this_slice = slice(this_slice.start, max_sid + 1,
+                                   this_slice.step)
+
+            valid_sids += np.r_[this_slice].tolist()
+        else:
+            valid_sids.append(int(this_str))
+
+    # Sort and return
+    return [str(sid) for sid in sorted(all_sid_ints) if sid in valid_sids]
diff --git a/tomviz/python/tomviz/state/_schemata.py b/tomviz/python/tomviz/state/_schemata.py
index eb8c8e69a..50859c9c8 100644
--- a/tomviz/python/tomviz/state/_schemata.py
+++ b/tomviz/python/tomviz/state/_schemata.py
@@ -77,6 +77,11 @@ def _deserialize(self, value, attr, data, **kwargs):
 
         return op
 
+    @property
+    def context(self):
+        # Fall back to an empty dictionary if no context exists on the root
+        return getattr(self.root, 'context', {})
+
 
 class OperatorSchema(Schema):
     operator = OperatorField()
@@ -130,6 +135,11 @@ def _deserialize(self, value, attr, data, **kwargs):
 
         return mod
 
+    @property
+    def context(self):
+        # Fall back to an empty dictionary if no context exists on the root
+        return getattr(self.root, 'context', {})
+
 
 class ModuleSchema(Schema):
     module = ModuleField()
@@ -232,7 +242,7 @@ def make_datasource(self, data, **kwargs):
         ds = DataSource(**data)
         # Has this data source been removed, if so recurrent it,
         # rather than creating a new one.
-        removed_cache = self.context.get('dataSources', {})
+        removed_cache = getattr(self, 'context', {}).get('dataSources', {})
         if ds.id in removed_cache:
             update(ds, removed_cache.pop(ds.id))
 
diff --git a/tomviz/python/tomviz/state/_utils.py b/tomviz/python/tomviz/state/_utils.py
index a5ee2db66..e23c3deef 100644
--- a/tomviz/python/tomviz/state/_utils.py
+++ b/tomviz/python/tomviz/state/_utils.py
@@ -1,11 +1,11 @@
-import collections
+from collections.abc import Mapping
 from types import SimpleNamespace
 
 
 def iter_paths(tree, parent_path=()):
     for path, node in tree.items():
         current_path = parent_path + (path,)
-        if isinstance(node, collections.Mapping):
+        if isinstance(node, Mapping):
             for inner_path in iter_paths(node, current_path):
                 yield inner_path
         else:
diff --git a/tomviz/python/tomviz/utils.py b/tomviz/python/tomviz/utils.py
index 60ef1434d..f744784d9 100644
--- a/tomviz/python/tomviz/utils.py
+++ b/tomviz/python/tomviz/utils.py
@@ -4,7 +4,10 @@
 # This source file is part of the Tomviz project, https://tomviz.org/.
 # It is released under the 3-Clause BSD License, see "LICENSE".
 ###############################################################################
+import copy
+import functools
 import math
+
 import numpy as np
 from tomviz._internal import in_application
 from tomviz._internal import require_internal_mode
@@ -14,6 +17,9 @@
 if in_application():
     import vtk.numpy_interface.dataset_adapter as dsa
     import vtk.util.numpy_support as np_s
+    from tomviz.internal_dataset import Dataset
+else:
+    from tomviz.external_dataset import Dataset
 
 
 @with_vtk_dataobject
@@ -28,6 +34,11 @@ def get_scalars(dataobject, name=None):
     return vtkarray
 
 
+@with_vtk_dataobject
+def get_active_scalars_name(dataobject):
+    return dataobject.GetPointData().GetScalars().GetName()
+
+
 def is_numpy_vtk_type(newscalars):
     # Indicate whether the type is known/supported by VTK to NumPy routines.
     require_internal_mode()
@@ -91,7 +102,7 @@ def arrays(dataobject):
 
 
 @with_vtk_dataobject
-def set_array(dataobject, newarray, minextent=None, isFortran=True):
+def set_array(dataobject, newarray, minextent=None, isFortran=True, name=None):
     # Set the extent if needed, i.e. if the minextent is not the same as
     # the data object starting index, or if the newarray shape is not the same
     # as the size of the dataobject.
@@ -109,12 +120,11 @@ def set_array(dataobject, newarray, minextent=None, isFortran=True):
         arr = newarray.reshape(-1, order='F')
         vtkshape = newarray.shape
     else:
-        print('Warning, array does not have Fortran order, making deep copy '
-              'and fixing...')
+        # This used to print a warning, but we shouldn't worry about
+        # it...
         vtkshape = newarray.shape
         tmp = np.asfortranarray(newarray)
         arr = tmp.reshape(-1, order='F')
-        print('...done.')
 
     if not is_numpy_vtk_type(arr):
         arr = arr.astype(np.float32)
@@ -134,13 +144,19 @@ def set_array(dataobject, newarray, minextent=None, isFortran=True):
     vtkarray = np_s.numpy_to_vtk(arr)
     vtkarray.Association = dsa.ArrayAssociation.POINT
     do = dsa.WrapDataObject(dataobject)
-    oldscalars = do.PointData.GetScalars()
-    arrayname = "Scalars"
-    if oldscalars is not None:
-        arrayname = oldscalars.GetName()
-    del oldscalars
+
+    if name is None:
+        oldscalars = do.PointData.GetScalars()
+        arrayname = "Scalars"
+        if oldscalars is not None:
+            arrayname = oldscalars.GetName()
+    else:
+        arrayname = name
+
     do.PointData.append(arr, arrayname)
-    do.PointData.SetActiveScalars(arrayname)
+
+    if do.PointData.GetNumberOfArrays() == 1:
+        do.PointData.SetActiveScalars(arrayname)
 
 
 @with_vtk_dataobject
@@ -594,3 +610,146 @@ def get_center(dataobject):
         "Center array requires 3 components"
 
     return np.array(center_array.GetTuple(0))
+
+
+def apply_to_each_array(func):
+
+    is_method = (
+        func.__name__ != func.__qualname__ and
+        '.<locals>.' not in func.__qualname__
+    )
+    dataset_idx = 1 if is_method else 0
+
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        dataset = args[dataset_idx]
+        if dataset.num_scalars == 1:
+            # Just run the function like we normally would...
+            return func(*args, **kwargs)
+
+        num_arrays = dataset.num_scalars
+        array_names = dataset.scalars_names
+        active_name = dataset.active_name
+
+        is_internal = in_application()
+
+        if is_internal:
+            # Run the function multiple times. Each time with a single, different
+            # array on the shallow-copied data object
+            from vtk import vtkImageData
+            orig_do = dataset._data_object
+            pd = orig_do.GetPointData()
+            all_arrays = [pd.GetAbstractArray(i) for i in range(num_arrays)]
+
+            # Remove all arrays
+            while pd.GetNumberOfArrays() > 0:
+                pd.RemoveArray(0)
+        else:
+            all_arrays = [dataset.arrays[name] for name in array_names]
+            dataset.arrays.clear()
+            orig_dataset = dataset
+
+        output_arrays = []
+        results = []
+        for i, name in enumerate(array_names):
+            if is_internal:
+                if i == num_arrays - 1:
+                    # Use the original data object
+                    image_data = orig_do
+                else:
+                    image_data = vtkImageData()
+                    image_data.ShallowCopy(orig_do)
+
+                this_pd = image_data.GetPointData()
+                this_pd.AddArray(all_arrays[i])
+                this_pd.SetActiveScalars(name)
+                dataset._data_object = image_data
+            else:
+                if i == num_arrays - 1:
+                    # Use the original dataset for the final one
+                    dataset = orig_dataset
+                else:
+                    dataset = copy.deepcopy(orig_dataset)
+
+                dataset.arrays[name] = all_arrays[i]
+                dataset.active_name = name
+
+            # Put the dataset where it belongs in the argument list
+            new_args = (
+                list(args[:dataset_idx]) +
+                [dataset] +
+                list(args[dataset_idx + 1:])
+            )
+            print('Transforming array:', name)
+            result = func(*new_args, **kwargs)
+            results.append(result)
+
+            if is_internal:
+                output_arrays.append(this_pd.GetAbstractArray(0))
+            else:
+                output_arrays.append(dataset.arrays[name])
+
+        if is_internal:
+            # Now add back in the arrays in the same order
+            this_pd.RemoveArray(0)
+            for array in output_arrays:
+                this_pd.AddArray(array)
+
+            # Set the active one
+            this_pd.SetActiveScalars(active_name)
+        else:
+            # The metadata should have been modified on this dataset
+            # object from the last call to the function
+            dataset.arrays.clear()
+            for name, array in zip(array_names, output_arrays):
+                dataset.arrays[name] = array
+
+            dataset.active_name = active_name
+
+        # For any data sources in the result, add all the scalars to it
+        if isinstance(result, dict):
+            for k, v in result.items():
+                if isinstance(v, Dataset):
+                    # Rename the active array
+                    v.rename_active(array_names[-1])
+                    # Go back through the other results and set scalars on this
+                    # one
+                    for i, other_result in enumerate(results[:-1]):
+                        if (
+                            isinstance(other_result, dict) and
+                            isinstance(other_result.get(k), Dataset)
+                        ):
+                            other_dataset = other_result[k]
+                            other_dataset.rename_active(array_names[i])
+                            v.set_scalars(other_dataset.active_name,
+                                          other_dataset.active_scalars)
+
+        # Return the final result
+        return result
+
+    return wrapper
+
+
+def pad_array(array, padding, tilt_axis):
+    # Add padding to an array. Ignore the tilt axis.
+    if padding <= 0:
+        return array
+
+    pad_list = []
+    for i in range(3):
+        pad_list.append([0, 0] if i == tilt_axis else [padding, padding])
+
+    return np.pad(array, pad_list)
+
+
+def depad_array(array, padding, tilt_axis):
+    # Remove padding from an array. Ignore the tilt axis.
+    if padding <= 0:
+        return array
+
+    slice_list = []
+    for i in range(3):
+        start = padding if i != tilt_axis else 0
+        end = padding * -1 if i != tilt_axis else array.shape[i]
+        slice_list.append(slice(start, end))
+    return array[tuple(slice_list)]
diff --git a/tomviz/templates/Back_Projection_Reconstruction.tvsm b/tomviz/templates/Back_Projection_Reconstruction.tvsm
index fc2a0ff37..d6a5a4f56 100644
--- a/tomviz/templates/Back_Projection_Reconstruction.tvsm
+++ b/tomviz/templates/Back_Projection_Reconstruction.tvsm
@@ -10,7 +10,7 @@
             "description": "",
             "id": "0x56251acc7eb0",
             "label": "Remove Bad Pixels",
-            "script": "def transform(dataset, threshold=None):\n    \"\"\"Remove bad pixels in tilt series.\"\"\"\n\n    import scipy.ndimage\n    import numpy as np\n\n    tiltSeries = dataset.active_scalars.astype(np.float32)\n\n    for i in range(tiltSeries.shape[2]):\n        I = tiltSeries[:, :, i]\n        I_pad = np.lib.pad(I, (1, 1), 'edge')\n\n        # calculate standard deviation in a 3 x 3 window\n        averageI2 = scipy.ndimage.filters.uniform_filter(I_pad ** 2)\n        averageI = scipy.ndimage.filters.uniform_filter(I_pad)\n        std = np.sqrt(abs(averageI2 - averageI**2))[1:-1, 1:-1]\n\n        medianI = scipy.ndimage.filters.median_filter(I_pad, 2)[1:-1, 1:-1]\n\n        #identify bad pixels\n        badPixelsMask = abs(I - medianI) > std * threshold\n\n        I[badPixelsMask] = medianI[badPixelsMask]\n        tiltSeries[:, :, i] = I\n\n    # Set the result as the new scalars.\n    dataset.active_scalars = tiltSeries\n",
+            "script": "def transform(dataset, threshold=None):\n    \"\"\"Remove bad pixels in tilt series.\"\"\"\n\n    import scipy.ndimage\n    import numpy as np\n\n    tiltSeries = dataset.active_scalars.astype(np.float32)\n\n    for i in range(tiltSeries.shape[2]):\n        I = tiltSeries[:, :, i]\n        I_pad = np.pad(I, (1, 1), 'edge')\n\n        # calculate standard deviation in a 3 x 3 window\n        averageI2 = scipy.ndimage.filters.uniform_filter(I_pad ** 2)\n        averageI = scipy.ndimage.filters.uniform_filter(I_pad)\n        std = np.sqrt(abs(averageI2 - averageI**2))[1:-1, 1:-1]\n\n        medianI = scipy.ndimage.filters.median_filter(I_pad, 2)[1:-1, 1:-1]\n\n        #identify bad pixels\n        badPixelsMask = abs(I - medianI) > std * threshold\n\n        I[badPixelsMask] = medianI[badPixelsMask]\n        tiltSeries[:, :, i] = I\n\n    # Set the result as the new scalars.\n    dataset.active_scalars = tiltSeries\n",
             "type": "Python"
         },
         {
@@ -240,7 +240,7 @@
             },
             "id": "0x56251c442b20",
             "label": "Reconstruct (Back Projection)",
-            "script": "import numpy as np\nfrom scipy.interpolate import interp1d\nimport tomviz.operators\nimport time\n\n\nclass ReconWBPOperator(tomviz.operators.CancelableOperator):\n\n    def transform(self, dataset, Nrecon=None, filter=None, interp=None,\n                  Nupdates=None):\n        \"\"\"\n        3D Reconstruct from a tilt series using Weighted Back-projection Method\n        \"\"\"\n        self.progress.maximum = 1\n\n        interpolation_methods = ('linear', 'nearest', 'spline', 'cubic')\n        filter_methods = ('none', 'ramp', 'shepp-logan',\n                          'cosine', 'hamming', 'hann')\n\n        # Get Tilt angles\n        tilt_angles = dataset.tilt_angles\n        tiltSeries = dataset.active_scalars\n        if tiltSeries is None:\n            raise RuntimeError(\"No scalars found!\")\n\n        Nslice = tiltSeries.shape[0]\n\n        self.progress.maximum = Nslice\n        step = 0\n\n        recon = np.empty([Nslice, Nrecon, Nrecon], dtype=np.float32, order='F')\n        t0 = time.time()\n        counter = 1\n        etcMessage = 'Estimated time to complete: n/a'\n\n        child = dataset.create_child_dataset() #create child for recon\n\n        for i in range(Nslice):\n            if self.canceled:\n                return\n            self.progress.message = 'Slice No.%d/%d. ' % (\n                i + 1, Nslice) + etcMessage\n\n            recon[i, :, :] = wbp2(tiltSeries[i, :, :], tilt_angles, Nrecon,\n                                  filter_methods[filter],\n                                  interpolation_methods[interp])\n            step += 1\n            self.progress.value = step\n            timeLeft = (time.time() - t0) / counter * (Nslice - counter)\n            counter += 1\n            timeLeftMin, timeLeftSec = divmod(timeLeft, 60)\n            timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)\n            etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (\n                timeLeftHour, timeLeftMin, timeLeftSec)\n\n            # Update only once every so many steps\n            if Nupdates != 0 and (i + 1) % (Nslice//Nupdates) == 0:\n                child.active_scalars = recon #add recon to child\n                # This copies data to the main thread\n                self.progress.data = child\n\n        # One last update of the child data.\n        child.active_scalars = recon #add recon to child\n        self.progress.data = child\n\n        returnValues = {}\n        returnValues[\"reconstruction\"] = child\n        return returnValues\n\n\ndef wbp2(sinogram, angles, N=None, filter=\"ramp\", interp=\"linear\"):\n    if sinogram.ndim != 2:\n        raise ValueError('Sinogram must be 2D')\n    (Nray, Nproj) = sinogram.shape\n    if Nproj != angles.size:\n        raise ValueError('Sinogram does not match angles!')\n\n    interpolation_methods = ('linear', 'nearest', 'spline', 'cubic')\n    if interp not in interpolation_methods:\n        raise ValueError(\"Unknown interpolation: %s\" % interp)\n    if not N:  # if output size is not given\n        N = int(np.floor(np.sqrt(Nray**2 / 2.0)))\n\n    ang = np.double(angles) * np.pi / 180.0\n    # Create Fourier filter\n    F = makeFilter(Nray, filter)\n    # Pad sinogram for filtering\n    s = np.lib.pad(sinogram, ((0, F.size - Nray), (0, 0)),\n                   'constant', constant_values=(0, 0))\n    # Apply Fourier filter\n    s = np.fft.fft(s, axis=0) * F\n    s = np.real(np.fft.ifft(s, axis=0))\n    # Change back to original\n    s = s[:Nray, :]\n\n    # Back projection\n    recon = np.zeros((N, N), np.float32)\n    center_proj = Nray // 2  # Index of center of projection\n    [X, Y] = np.mgrid[0:N, 0:N]\n    xpr = X - int(N) // 2\n    ypr = Y - int(N) // 2\n\n    for j in range(Nproj):\n        t = ypr * np.cos(ang[j]) - xpr * np.sin(ang[j])\n        x = np.arange(Nray) - center_proj\n        if interp == 'linear':\n            bp = np.interp(t, x, s[:, j], left=0, right=0)\n        elif interp == 'spline':\n            interpolant = interp1d(\n                x, s[:, j], kind='slinear', bounds_error=False, fill_value=0)\n            bp = interpolant(t)\n        else:\n            interpolant = interp1d(\n                x, s[:, j], kind=interp, bounds_error=False, fill_value=0)\n            bp = interpolant(t)\n        recon = recon + bp\n\n    # Normalize\n    recon = recon * np.pi / 2 / Nproj\n    return recon\n\n# Filter (1D) projections.\n\n\ndef makeFilter(Nray, filterMethod=\"ramp\"):\n    # Calculate next power of 2\n    N2 = 2**np.ceil(np.log2(Nray))\n    # Make a ramp filter.\n    freq = np.fft.fftfreq(int(N2)).reshape(-1, 1)\n    omega = 2 * np.pi * freq\n    filter = 2 * np.abs(freq)\n\n    if filterMethod == \"ramp\":\n        pass\n    elif filterMethod == \"shepp-logan\":\n        filter[1:] = filter[1:] * np.sin(omega[1:]) / omega[1:]\n    elif filterMethod == \"cosine\":\n        filter[1:] = filter[1:] * np.cos(filter[1:])\n    elif filterMethod == \"hamming\":\n        filter[1:] = filter[1:] * (0.54 + 0.46 * np.cos(omega[1:] / 2))\n    elif filterMethod == \"hann\":\n        filter[1:] = filter[1:] * (1 + np.cos(omega[1:] / 2)) / 2\n    elif filterMethod == \"none\":\n        filter[:] = 1\n    else:\n        raise ValueError(\"Unknown filter: %s\" % filterMethod)\n\n    return filter\n",
+            "script": "import numpy as np\nfrom scipy.interpolate import interp1d\nimport tomviz.operators\nimport time\n\n\nclass ReconWBPOperator(tomviz.operators.CancelableOperator):\n\n    def transform(self, dataset, Nrecon=None, filter=None, interp=None,\n                  Nupdates=None):\n        \"\"\"\n        3D Reconstruct from a tilt series using Weighted Back-projection Method\n        \"\"\"\n        self.progress.maximum = 1\n\n        interpolation_methods = ('linear', 'nearest', 'spline', 'cubic')\n        filter_methods = ('none', 'ramp', 'shepp-logan',\n                          'cosine', 'hamming', 'hann')\n\n        # Get Tilt angles\n        tilt_angles = dataset.tilt_angles\n        tiltSeries = dataset.active_scalars\n        if tiltSeries is None:\n            raise RuntimeError(\"No scalars found!\")\n\n        Nslice = tiltSeries.shape[0]\n\n        self.progress.maximum = Nslice\n        step = 0\n\n        recon = np.empty([Nslice, Nrecon, Nrecon], dtype=np.float32, order='F')\n        t0 = time.time()\n        counter = 1\n        etcMessage = 'Estimated time to complete: n/a'\n\n        child = dataset.create_child_dataset() #create child for recon\n\n        for i in range(Nslice):\n            if self.canceled:\n                return\n            self.progress.message = 'Slice No.%d/%d. ' % (\n                i + 1, Nslice) + etcMessage\n\n            recon[i, :, :] = wbp2(tiltSeries[i, :, :], tilt_angles, Nrecon,\n                                  filter_methods[filter],\n                                  interpolation_methods[interp])\n            step += 1\n            self.progress.value = step\n            timeLeft = (time.time() - t0) / counter * (Nslice - counter)\n            counter += 1\n            timeLeftMin, timeLeftSec = divmod(timeLeft, 60)\n            timeLeftHour, timeLeftMin = divmod(timeLeftMin, 60)\n            etcMessage = 'Estimated time to complete: %02d:%02d:%02d' % (\n                timeLeftHour, timeLeftMin, timeLeftSec)\n\n            # Update only once every so many steps\n            if Nupdates != 0 and (i + 1) % (Nslice//Nupdates) == 0:\n                child.active_scalars = recon #add recon to child\n                # This copies data to the main thread\n                self.progress.data = child\n\n        # One last update of the child data.\n        child.active_scalars = recon #add recon to child\n        self.progress.data = child\n\n        returnValues = {}\n        returnValues[\"reconstruction\"] = child\n        return returnValues\n\n\ndef wbp2(sinogram, angles, N=None, filter=\"ramp\", interp=\"linear\"):\n    if sinogram.ndim != 2:\n        raise ValueError('Sinogram must be 2D')\n    (Nray, Nproj) = sinogram.shape\n    if Nproj != angles.size:\n        raise ValueError('Sinogram does not match angles!')\n\n    interpolation_methods = ('linear', 'nearest', 'spline', 'cubic')\n    if interp not in interpolation_methods:\n        raise ValueError(\"Unknown interpolation: %s\" % interp)\n    if not N:  # if output size is not given\n        N = int(np.floor(np.sqrt(Nray**2 / 2.0)))\n\n    ang = np.double(angles) * np.pi / 180.0\n    # Create Fourier filter\n    F = makeFilter(Nray, filter)\n    # Pad sinogram for filtering\n    s = np.pad(sinogram, ((0, F.size - Nray), (0, 0)),\n                   'constant', constant_values=(0, 0))\n    # Apply Fourier filter\n    s = np.fft.fft(s, axis=0) * F\n    s = np.real(np.fft.ifft(s, axis=0))\n    # Change back to original\n    s = s[:Nray, :]\n\n    # Back projection\n    recon = np.zeros((N, N), np.float32)\n    center_proj = Nray // 2  # Index of center of projection\n    [X, Y] = np.mgrid[0:N, 0:N]\n    xpr = X - int(N) // 2\n    ypr = Y - int(N) // 2\n\n    for j in range(Nproj):\n        t = ypr * np.cos(ang[j]) - xpr * np.sin(ang[j])\n        x = np.arange(Nray) - center_proj\n        if interp == 'linear':\n            bp = np.interp(t, x, s[:, j], left=0, right=0)\n        elif interp == 'spline':\n            interpolant = interp1d(\n                x, s[:, j], kind='slinear', bounds_error=False, fill_value=0)\n            bp = interpolant(t)\n        else:\n            interpolant = interp1d(\n                x, s[:, j], kind=interp, bounds_error=False, fill_value=0)\n            bp = interpolant(t)\n        recon = recon + bp\n\n    # Normalize\n    recon = recon * np.pi / 2 / Nproj\n    return recon\n\n# Filter (1D) projections.\n\n\ndef makeFilter(Nray, filterMethod=\"ramp\"):\n    # Calculate next power of 2\n    N2 = 2**np.ceil(np.log2(Nray))\n    # Make a ramp filter.\n    freq = np.fft.fftfreq(int(N2)).reshape(-1, 1)\n    omega = 2 * np.pi * freq\n    filter = 2 * np.abs(freq)\n\n    if filterMethod == \"ramp\":\n        pass\n    elif filterMethod == \"shepp-logan\":\n        filter[1:] = filter[1:] * np.sin(omega[1:]) / omega[1:]\n    elif filterMethod == \"cosine\":\n        filter[1:] = filter[1:] * np.cos(filter[1:])\n    elif filterMethod == \"hamming\":\n        filter[1:] = filter[1:] * (0.54 + 0.46 * np.cos(omega[1:] / 2))\n    elif filterMethod == \"hann\":\n        filter[1:] = filter[1:] * (1 + np.cos(omega[1:] / 2)) / 2\n    elif filterMethod == \"none\":\n        filter[:] = 1\n    else:\n        raise ValueError(\"Unknown filter: %s\" % filterMethod)\n\n    return filter\n",
             "type": "Python"
         }
     ]
diff --git a/tomviz/vtkVolumeScaleRepresentation.cxx b/tomviz/vtkVolumeScaleRepresentation.cxx
deleted file mode 100644
index 9b93d1b48..000000000
--- a/tomviz/vtkVolumeScaleRepresentation.cxx
+++ /dev/null
@@ -1,172 +0,0 @@
-/* This source file is part of the Tomviz project, https://tomviz.org/.
-   It is released under the 3-Clause BSD License, see "LICENSE". */
-
-#include "vtkVolumeScaleRepresentation.h"
-#include "vtkAxisActor2D.h"
-#include "vtkMath.h"
-#include "vtkObjectFactory.h"
-#include "vtkPointHandleRepresentation2D.h"
-#include "vtkProperty2D.h"
-#include "vtkRenderer.h"
-#include "vtkTextActor.h"
-#include "vtkTextProperty.h"
-#include "vtkWindow.h"
-
-#include "Utilities.h"
-
-#include <sstream>
-
-vtkStandardNewMacro(vtkVolumeScaleRepresentation)
-
-//----------------------------------------------------------------------
-vtkVolumeScaleRepresentation::vtkVolumeScaleRepresentation()
-{
-  double p[3] = { 0., 0., 0. };
-  this->SetWorldPosition(p);
-
-  // Disable the vtkBillboardTextActor3D, and replace it with our own
-  // vtkTextActor.
-  this->SetLabelVisibility(0);
-
-  this->Label = vtkTextActor::New();
-  this->Label->SetVisibility(true);
-  this->Label->GetTextProperty()->SetColor(tomviz::offWhite);
-  this->Label->SetPosition(0, 0);
-  this->Label->GetTextProperty()->SetFontSize(40);
-  this->Label->GetTextProperty()->SetJustificationToCentered();
-
-  this->Update2DLabel();
-}
-
-//----------------------------------------------------------------------
-vtkVolumeScaleRepresentation::~vtkVolumeScaleRepresentation()
-{
-  this->Label->Delete();
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::BuildRepresentation()
-{
-  this->Superclass::BuildRepresentation();
-
-  if (this->Label &&
-      (this->Label->GetMTime() > this->BuildTime ||
-       (this->Renderer && this->Renderer->GetVTKWindow() &&
-        this->Renderer->GetVTKWindow()->GetMTime() > this->BuildTime))) {
-    this->Update2DLabel();
-
-    this->BuildTime.Modified();
-  }
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::GetActors2D(vtkPropCollection* pc)
-{
-  this->Label->GetActors(pc);
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::Update2DLabel()
-{
-  {
-    std::stringstream s;
-    s << this->SideLength << " " << std::string(this->LengthUnit);
-    this->Label->SetInput(s.str().c_str());
-  }
-
-  double labelPosition[3] = { 0., 0., 0. };
-  if (this->Renderer) {
-    this->GetWorldPosition(labelPosition);
-
-    this->Renderer->SetWorldPoint(labelPosition);
-    this->Renderer->WorldToDisplay();
-    this->Renderer->GetDisplayPoint(labelPosition);
-
-    double bbox[4];
-    this->Label->GetBoundingBox(this->Renderer, bbox);
-    labelPosition[1] -= 2. * (bbox[3] - bbox[2]);
-  }
-
-  this->Label->SetDisplayPosition(labelPosition[0], labelPosition[1]);
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::SetRepresentationVisibility(bool choice)
-{
-  this->Superclass::SetHandleVisibility(choice);
-  this->Label->SetVisibility(choice);
-  this->Modified();
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::ReleaseGraphicsResources(vtkWindow* win)
-{
-  this->Superclass::ReleaseGraphicsResources(win);
-  this->Label->ReleaseGraphicsResources(win);
-}
-
-//----------------------------------------------------------------------
-int vtkVolumeScaleRepresentation::RenderOverlay(vtkViewport* v)
-{
-  int count = 0;
-  vtkRenderer* renderer = vtkRenderer::SafeDownCast(v);
-  if (renderer) {
-    this->SetRenderer(renderer);
-    this->ScaleIfNecessary(v);
-    this->Update2DLabel();
-  }
-  count += this->Superclass::RenderOverlay(v);
-  this->Label->SetPropertyKeys(this->GetPropertyKeys());
-
-  count += this->Label->RenderOverlay(v);
-  return count;
-}
-
-//----------------------------------------------------------------------
-int vtkVolumeScaleRepresentation::RenderOpaqueGeometry(vtkViewport* v)
-{
-  int count = 0;
-  vtkRenderer* renderer = vtkRenderer::SafeDownCast(v);
-  if (renderer) {
-    this->SetRenderer(renderer);
-    this->ScaleIfNecessary(v);
-    this->Update2DLabel();
-  }
-  count += this->Superclass::RenderOpaqueGeometry(v);
-  this->Label->SetPropertyKeys(this->GetPropertyKeys());
-  count += this->Label->RenderOpaqueGeometry(v);
-  return count;
-}
-
-//-----------------------------------------------------------------------------
-int vtkVolumeScaleRepresentation::RenderTranslucentPolygonalGeometry(
-  vtkViewport* v)
-{
-  int count = 0;
-  vtkRenderer* renderer = vtkRenderer::SafeDownCast(v);
-  if (renderer) {
-    this->SetRenderer(renderer);
-    this->ScaleIfNecessary(v);
-    this->Update2DLabel();
-  }
-  count += this->Superclass::RenderTranslucentPolygonalGeometry(v);
-  this->Label->SetPropertyKeys(this->GetPropertyKeys());
-  count += this->Label->RenderTranslucentPolygonalGeometry(v);
-  return count;
-}
-
-//-----------------------------------------------------------------------------
-int vtkVolumeScaleRepresentation::HasTranslucentPolygonalGeometry()
-{
-  int result = 0;
-  result |= this->Superclass::HasTranslucentPolygonalGeometry();
-  result |= this->Label->HasTranslucentPolygonalGeometry();
-  return result;
-}
-
-//----------------------------------------------------------------------
-void vtkVolumeScaleRepresentation::PrintSelf(ostream& os, vtkIndent indent)
-{
-  // Superclass typedef defined in vtkTypeMacro() found in vtkSetGet.h
-  this->Superclass::PrintSelf(os, indent);
-}
diff --git a/tomviz/vtkVolumeScaleRepresentation.h b/tomviz/vtkVolumeScaleRepresentation.h
deleted file mode 100644
index dbecccf24..000000000
--- a/tomviz/vtkVolumeScaleRepresentation.h
+++ /dev/null
@@ -1,88 +0,0 @@
-/* This source file is part of the Tomviz project, https://tomviz.org/.
-   It is released under the 3-Clause BSD License, see "LICENSE". */
-
-/**
- * @class   vtkVolumeScaleRepresentation
- * @brief   represent the vtkDistanceWidget
- *
- * The vtkVolumeScaleRepresentation is a representation for the
- * vtkHandleWidget. This representation consists of a measuring cube. The size
- * of the cube adapts to fit within a minimum and maximum fraction of the
- * viewing area.
- *
- * @sa
- * vtkMeasurementCubeHandleRepresentation3D
-*/
-
-#ifndef vtkVolumeScaleRepresentation_h
-#define vtkVolumeScaleRepresentation_h
-
-#include "vtkMeasurementCubeHandleRepresentation3D.h"
-
-class vtkTextActor;
-
-class vtkVolumeScaleRepresentation
-  : public vtkMeasurementCubeHandleRepresentation3D
-{
-public:
-  /**
-   * Instantiate class.
-   */
-  static vtkVolumeScaleRepresentation* New();
-
-  /**
-   * Method to satisfy superclasses' API.
-   */
-  void BuildRepresentation() override;
-
-  //@{
-  /**
-   * Standard VTK methods.
-   */
-  vtkTypeMacro(
-    vtkVolumeScaleRepresentation,
-    vtkMeasurementCubeHandleRepresentation3D) void PrintSelf(ostream& os,
-                                                             vtkIndent indent)
-    override;
-  //@}
-
-  //@{
-  /**
-   * Get the label actor
-   */
-  vtkGetObjectMacro(Label, vtkTextActor);
-  //@}
-
-  //@{
-  /**
-   * Set the visibility of both the cube and the label
-   */
-  void SetRepresentationVisibility(bool choice);
-  //@}
-
-  //@{
-  /**
-   * Methods to make this class properly act like a vtkWidgetRepresentation.
-   */
-  void GetActors2D(vtkPropCollection*) override;
-  void ReleaseGraphicsResources(vtkWindow*) override;
-  int RenderOverlay(vtkViewport*) override;
-  int RenderOpaqueGeometry(vtkViewport*) override;
-  int RenderTranslucentPolygonalGeometry(vtkViewport*) override;
-  int HasTranslucentPolygonalGeometry() override;
-  //@}
-
-protected:
-  vtkVolumeScaleRepresentation();
-  ~vtkVolumeScaleRepresentation() override;
-
-  void Update2DLabel();
-
-  vtkTextActor* Label;
-
-private:
-  vtkVolumeScaleRepresentation(const vtkVolumeScaleRepresentation&) = delete;
-  void operator=(const vtkVolumeScaleRepresentation&) = delete;
-};
-
-#endif