Fix endianness when decoding on big endian systems (#72)

pydicom · Oct 25, 2024 · 2a38369 · 2a38369
1 parent 09decd2
commit 2a38369
Show file tree

Hide file tree

Showing 13 changed files with 854 additions and 768 deletions.
diff --git a/.github/workflows/pytest-builds.yml b/.github/workflows/pytest-builds.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
         arch: ['x64', 'x86']
 
     steps:
@@ -50,7 +50,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v4
@@ -86,7 +86,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     steps:
     - uses: actions/checkout@v4
@@ -117,7 +117,7 @@ jobs:
         pytest --cov=libjpeg --cov-append libjpeg/tests
 
     - name: Switch to pydicom dev and rerun pytest
-      if: ${{ contains('3.10 3.11 3.12', matrix.python-version) }}
+      if: ${{ contains('3.10 3.11 3.12 3.13', matrix.python-version) }}
       run: |
         pip uninstall -y pydicom
         pip install git+https://github.com/pydicom/pydicom

diff --git a/.github/workflows/release-wheels.yml b/.github/workflows/release-wheels.yml
@@ -42,9 +42,6 @@ jobs:
       matrix:
         include:
           # Windows 32 bit
-          - os: windows-latest
-            python: 38
-            platform_id: win32
           - os: windows-latest
             python: 39
             platform_id: win32
@@ -57,11 +54,11 @@ jobs:
           - os: windows-latest
             python: 312
             platform_id: win32
+          - os: windows-latest
+            python: 313
+            platform_id: win32
 
           # Windows 64 bit
-          - os: windows-latest
-            python: 38
-            platform_id: win_amd64
           - os: windows-latest
             python: 39
             platform_id: win_amd64
@@ -74,12 +71,11 @@ jobs:
           - os: windows-latest
             python: 312
             platform_id: win_amd64
+          - os: windows-latest
+            python: 313
+            platform_id: win_amd64
 
           # Linux 64 bit manylinux2014
-          - os: ubuntu-latest
-            python: 38
-            platform_id: manylinux_x86_64
-            manylinux_image: manylinux2014
           - os: ubuntu-latest
             python: 39
             platform_id: manylinux_x86_64
@@ -96,11 +92,12 @@ jobs:
             python: 312
             platform_id: manylinux_x86_64
             manylinux_image: manylinux2014
+          - os: ubuntu-latest
+            python: 313
+            platform_id: manylinux_x86_64
+            manylinux_image: manylinux2014
 
           # Linux aarch64
-          - os: ubuntu-latest
-            python: 38
-            platform_id: manylinux_aarch64
           - os: ubuntu-latest
             python: 39
             platform_id: manylinux_aarch64
@@ -113,11 +110,11 @@ jobs:
           - os: ubuntu-latest
             python: 312
             platform_id: manylinux_aarch64
+          - os: ubuntu-latest
+            python: 313
+            platform_id: manylinux_aarch64
 
           # MacOS x86_64
-          - os: macos-12
-            python: 38
-            platform_id: macosx_x86_64
           - os: macos-12
             python: 39
             platform_id: macosx_x86_64
@@ -130,6 +127,9 @@ jobs:
           - os: macos-12
             python: 312
             platform_id: macosx_x86_64
+          - os: macos-12
+            python: 313
+            platform_id: macosx_x86_64
 
     steps:
     - uses: actions/checkout@v4
@@ -178,9 +178,6 @@ jobs:
       matrix:
         include:
         # MacOS arm64
-        - os: macos-14
-          python: 38
-          platform_id: macosx_arm64
         - os: macos-14
           python: 39
           platform_id: macosx_arm64
@@ -193,6 +190,9 @@ jobs:
         - os: macos-14
           python: 312
           platform_id: macosx_arm64
+        - os: macos-14
+          python: 313
+          platform_id: macosx_arm64
 
     steps:
     - uses: actions/checkout@v4
@@ -222,61 +222,62 @@ jobs:
         path: ./dist/*.whl
 
 
-  test-package:
-    name: Test built package
-    needs: [ build-wheels, build-sdist, build-wheels-macos-arm64 ]
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-
-    steps:
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Download the wheels
-      uses: actions/download-artifact@v4
-      with:
-        path: dist/
-        merge-multiple: true
-
-    - name: Install from package wheels and test
-      # If testing wheel builds might need --pre to install dev version
-      run: |
-        python -m venv testwhl
-        source testwhl/bin/activate
-        python -m pip install -U pip
-        python -m pip install pytest pydicom pylibjpeg
-        python -m pip uninstall -y pylibjpeg-libjpeg
-        python -m pip uninstall -y pylibjpeg-openjpeg
-        python -m pip install git+https://github.com/pydicom/pylibjpeg-data
-        python -m pip install -U --pre --find-links dist/ pylibjpeg-libjpeg
-        python -m pytest --pyargs libjpeg.tests
-        deactivate
-
-    - name: Install from package tarball and test
-      run: |
-        python -m venv testsrc
-        source testsrc/bin/activate
-        python -m pip install -U pip
-        python -m pip install pytest pydicom pylibjpeg
-        python -m pip uninstall -y pylibjpeg-libjpeg
-        python -m pip uninstall -y pylibjpeg-openjpeg
-        python -m pip install git+https://github.com/pydicom/pylibjpeg-data
-        python -m pip install -U dist/pylibjpeg*libjpeg-*.tar.gz
-        python -m pytest --pyargs libjpeg.tests
-        deactivate
+  # test-package:
+  #   name: Test built package
+  #   needs: [ build-wheels, build-sdist, build-wheels-macos-arm64 ]
+  #   runs-on: ubuntu-latest
+  #   timeout-minutes: 30
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+  #
+  #   steps:
+  #   - name: Set up Python ${{ matrix.python-version }}
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: ${{ matrix.python-version }}
+  #
+  #   - name: Download the wheels
+  #     uses: actions/download-artifact@v4
+  #     with:
+  #       path: dist/
+  #       merge-multiple: true
+  #
+  #   - name: Install from package wheels and test
+  #     # If testing wheel builds might need --pre to install dev version
+  #     run: |
+  #       python -m venv testwhl
+  #       source testwhl/bin/activate
+  #       python -m pip install -U pip
+  #       python -m pip install pytest pydicom pylibjpeg
+  #       python -m pip uninstall -y pylibjpeg-libjpeg
+  #       python -m pip uninstall -y pylibjpeg-openjpeg
+  #       python -m pip install git+https://github.com/pydicom/pylibjpeg-data
+  #       python -m pip install -U --pre --find-links dist/ pylibjpeg-libjpeg
+  #       python -m pytest --pyargs libjpeg.tests
+  #       deactivate
+  #
+  #   - name: Install from package tarball and test
+  #     run: |
+  #       python -m venv testsrc
+  #       source testsrc/bin/activate
+  #       python -m pip install -U pip
+  #       python -m pip install pytest pydicom pylibjpeg
+  #       python -m pip uninstall -y pylibjpeg-libjpeg
+  #       python -m pip uninstall -y pylibjpeg-openjpeg
+  #       python -m pip install git+https://github.com/pydicom/pylibjpeg-data
+  #       python -m pip install -U dist/pylibjpeg*libjpeg-*.tar.gz
+  #       python -m pytest --pyargs libjpeg.tests
+  #       deactivate
 
   # The pypi upload fails with non-linux containers, so grab the uploaded
   #     artifacts and run using those
   # See: https://github.com/pypa/gh-action-pypi-publish/discussions/15
   deploy:
     name: Upload wheels to PyPI
-    needs: [ test-package ]
+    # needs: [ test-package ]
+    needs: [ build-wheels, build-sdist, build-wheels-macos-arm64 ]
     runs-on: ubuntu-latest
     environment:
       name: pypi

diff --git a/build.py b/build.py
@@ -3,6 +3,7 @@
 from pathlib import Path
 import platform
 import shutil
+from struct import unpack
 import subprocess
 import sys
 from typing import Any, List, Dict
@@ -33,9 +34,17 @@ def build(setup_kwargs: Any) -> Any:
         # Skip configuration if running with `sdist`
         if 'sdist' not in sys.argv:
             opts = get_gcc_args()
+            if sys.byteorder == "big":
+                if "-mfpmath=387" in opts["ADDOPTS"]:
+                    opts["ADDOPTS"].remove("-mfpmath=387")
+
             extra_compile_args += opts['ADDOPTS']
             extra_link_args += opts['EXTRA_LIBS']
 
+    macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
+    if unpack("h", b"\x00\x01")[0] == 1:
+        macros.append(("JPG_BIG_ENDIAN", "1"))
+
     ext = Extension(
         '_libjpeg',
         [os.fspath(p) for p in get_source_files()],
@@ -47,6 +56,7 @@ def build(setup_kwargs: Any) -> Any:
         ],
         extra_compile_args=extra_compile_args,
         extra_link_args=extra_link_args,
+        define_macros=macros,
     )
 
     ext_modules = cythonize(

diff --git a/docs/changes/v2.1.0.rst b/docs/changes/v2.1.0.rst
@@ -0,0 +1,13 @@
+.. _v2.1.0:
+
+2.1.0
+=====
+
+* Use ``libjpeg`` v1.67
+* Fixed a decoding failure for JPEG 10918 file with an Adobe v101 APP14 marker
+
+2.1.1
+=====
+
+* Updated dependencies to allow NumPy > 2.0
+* Tests updated to use ``pydicom.pixels``
diff --git a/docs/changes/v2.2.0.rst b/docs/changes/v2.2.0.rst
@@ -0,0 +1,6 @@
+.. _v2.2.0:
+
+2.2.0
+=====
+
+* Support NumPy > 2.0 with Python 3.9+
diff --git a/docs/changes/v2.3.0.rst b/docs/changes/v2.3.0.rst
@@ -0,0 +1,7 @@
+.. _v2.3.0:
+
+2.3.0
+=====
+
+* Supported Python versions are 3.9 to 3.13
+* Added support for decoding on big endian systems
diff --git a/lib/interface/decode.cpp b/lib/interface/decode.cpp
@@ -30,11 +30,11 @@ std::string Decode(
     Parameters
     ----------
     char *inArray
-        Pointer to the first element of a numpy.ndarray containing the JPEG
-        data to be decompressed.
+        Pointer to the first element of a bytearray or numpy.ndarray containing the
+        JPEG data to be decompressed.
     char *outArray
-        Pointer to the first element of a numpy.ndarray where the decompressed
-        JPEG data should be written.
+        Pointer to the first element of bytearray or numpy.ndarray where the
+        decompressed JPEG data should be written.
     int inLength
         Length of the input array
     int outLength

diff --git a/lib/interface/streamhook.cpp b/lib/interface/streamhook.cpp
@@ -88,7 +88,7 @@ JPG_LONG OStreamHook(struct JPG_Hook *hook, struct JPG_TagItem *tags)
     static ULONG OpenComponents = 0;
     struct StreamMemory *omm  = (struct StreamMemory *)(hook->hk_pData);
     struct StreamData *out = (struct StreamData *)(omm->omm_pTarget);
-    // Pointer to the output numpy array, currently at offset out->position
+    // Pointer to the output bytearray/numpy array, currently at offset out->position
     char *oArray = (char *)(out->pData);
 
     UWORD comp  = tags->GetTagData(JPGTAG_BIO_COMPONENT);
@@ -323,11 +323,24 @@ JPG_LONG OStreamHook(struct JPG_Hook *hook, struct JPG_TagItem *tags)
                             }
                         } else {
                             // DICOM should always be integer input
-                            // Write pixel data to target
-                            ULONG size = omm->omm_ucPixelType & CTYP_SIZE_MASK;
+                            // Need to byte swap if on a big endian system
+                            #ifdef JPG_BIG_ENDIAN
+                                if (omm->omm_ucPixelType == CTYP_UWORD) {
+                                    ULONG count = width * height * omm->omm_usDepth;
+                                    UWORD *data = (UWORD *)omm->omm_pMemPtr;
+
+                                    do {
+                                        *data = (*data >> 8) | ((*data & 0xff) << 8);
+                                        data++;
+                                    } while(--count);
+                                }
+                            #endif
+
+                            // Write the decoded data to the output
+                            // For each pixel
                             ULONG count = width * height * omm->omm_usDepth;
+                            ULONG size = omm->omm_ucPixelType & CTYP_SIZE_MASK;
                             UBYTE *mem = (UBYTE *)(omm->omm_pMemPtr);
-                            // For each pixel
                             for (ULONG ii = 1; ii <= count; ii++) {
                                 // For each byte of the pixel
                                 for (ULONG jj = 1; jj <= size; jj++) {