next release v2.3.0

.github/workflows/test.yml

@@ -2,7 +2,7 @@ name: Test
 on: [push, pull_request]
 jobs:
   check:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
     runs-on: ubuntu-latest
     name: Check
     steps:
@@ -19,7 +19,7 @@ jobs:
         pip install -U pre-commit
         sudo apt-get install -yqq clang-format
     - uses: reviewdog/action-setup@v1
-    - if: github.event_name != 'schedule'
+    - if: github.event_name == 'push' || github.event_name == 'pull_request'
       name: comment
       run: |
         if [[ $EVENT == pull_request ]]; then
@@ -34,12 +34,12 @@ jobs:
         EVENT: ${{ github.event_name }}
     - run: pre-commit run -a --show-diff-on-failure
   test:
-    if: github.event_name != 'pull_request' || github.head_ref != 'devel'
+    if: github.event_name != 'pull_request' || github.repository_owner != 'NiftyPET'
+    name: Test py${{ matrix.python }}
     runs-on: [self-hosted, cuda, python]
     strategy:
       matrix:
-        python: [3.6, 3.9]
-    name: Test py${{ matrix.python }}
+        python: [3.7, 3.9]
     steps:
     - uses: actions/checkout@v2
       with:
@@ -48,7 +48,7 @@ jobs:
       run: setup-python -p${{ matrix.python }}
     - run: pip install -U -e .[dev]
     - run: pytest
-    - run: codecov
+    - uses: codecov/codecov-action@v1
     - name: Post Run setup-python
       run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1
+  rev: v4.1.0
   hooks:
   - id: check-added-large-files
   - id: check-case-conflict
@@ -31,21 +31,24 @@ repos:
   - id: flake8
     args: [-j8]
     additional_dependencies:
+    - flake8-broken-line
     - flake8-bugbear
     - flake8-comprehensions
     - flake8-debugger
+    - flake8-isort
     - flake8-string-format
 - repo: https://github.com/google/yapf
-  rev: 6db9374
+  rev: v0.32.0
   hooks:
   - id: yapf
     args: [-i]
+    additional_dependencies: [toml]
 - repo: https://github.com/PyCQA/isort
-  rev: 5.9.3
+  rev: 5.10.1
   hooks:
   - id: isort
 - repo: https://github.com/doublify/pre-commit-clang-format
-  rev: master
+  rev: '6230247'
   hooks:
   - id: clang-format
     files: \.(cc?|cuh?|cxx|cpp|h|hpp|hxx|java|js)$

niftypet/nimpa/__init__.py

@@ -19,18 +19,25 @@
     'LOG_FORMAT', 'LogHandler',
     # config
     'path_resources', 'resources', 'cmake_prefix',
+    # numcu
+    'add', 'div', 'mul',
+    # improc
+    'conv_separable', 'isub', 'nlm',
     # core
     'create_disk', 'imdiff', 'imscroll', 'profile_points', 'imtrimup',
-    'affine_fsl', 'affine_niftyreg', 'array2nii', 'bias_field_correction',
-    'centre_mass_img', 'coreg_spm', 'coreg_vinci', 'create_dir', 'create_mask',
-    'ct2mu', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort',
-    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getnii', 'getnii_descr',
-    'im_cut', 'imfill', 'imsmooth', 'iyang', 'motion_reg', 'nii_gzip',
-    'nii_modify', 'nii_ugzip', 'niisort', 'orientnii', 'pet2pet_rigid',
-    'pick_t1w', 'psf_gaussian', 'psf_measured', 'pvc_iyang', 'realign_mltp_spm',
-    'resample_fsl', 'resample_mltp_spm', 'resample_niftyreg', 'resample_spm',
-    'resample_vinci', 'time_stamp'] # yapf: disable
+    'affine_fsl', 'affine_dipy', 'affine_niftyreg',
+    'array2nii', 'bias_field_correction',
+    'centre_mass_img', 'centre_mass_corr', 'coreg_spm', 'coreg_vinci',
+    'create_dir', 'create_mask', 'ct2mu',
+    'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort',
+    'dice_coeff', 'dice_coeff_multiclass', 'fwhm2sig', 'getnii',
+    'getnii_descr', 'im_cut', 'imfill', 'imsmooth', 'iyang', 'motion_reg', 'nii_gzip',
+    'nii_modify', 'nii_ugzip', 'niisort', 'orientnii', 'pet2pet_rigid', 'pick_t1w',
+    'psf_gaussian', 'psf_measured', 'pvc_iyang', 'realign_mltp_spm', 'resample_fsl',
+    'resample_mltp_spm', 'resample_niftyreg', 'resample_spm', 'resample_vinci', 'resample_dipy',
+    'time_stamp'] # yapf: disable
 
+from numcu import add, div, mul
 from pkg_resources import resource_filename
 
 from niftypet.ninst import cudasetup as cs
@@ -40,11 +47,14 @@
 from .img import create_disk, imdiff, imscroll, profile_points
 from .prc import imtrimup  # for backward compatibility
 from .prc import (
+    affine_dipy,
     affine_fsl,
     affine_niftyreg,
     array2nii,
     bias_field_correction,
+    centre_mass_corr,
     centre_mass_img,
+    conv_separable,
     coreg_spm,
     coreg_vinci,
     create_dir,
@@ -63,19 +73,22 @@
     im_cut,
     imfill,
     imsmooth,
+    isub,
     iyang,
     motion_reg,
     nii_gzip,
     nii_modify,
     nii_ugzip,
     niisort,
+    nlm,
     orientnii,
     pet2pet_rigid,
     pick_t1w,
     psf_gaussian,
     psf_measured,
     pvc_iyang,
     realign_mltp_spm,
+    resample_dipy,
     resample_fsl,
     resample_mltp_spm,
     resample_niftyreg,

niftypet/nimpa/img/gen.py

@@ -4,6 +4,7 @@
 """
 import logging
 import math
+import pathlib
 
 import numpy as np
 import scipy.ndimage as ndi
@@ -80,9 +81,9 @@ def profile_points(im, p0, p1, steps=100):
 def imdiff(imref, imnew, verbose=False, plot=False, cmap='bwr'):
     """
     Compare the new image (imnew) to the reference image (imref),
-    returning (and optionallt plotting) the difference.
+    returning (and optional plotting) the difference.
     """
-    if isinstance(imref, str):
+    if isinstance(imref, (str, pathlib.Path)):
         imref = imio.getnii(imref)
         log.info('using NIfTI files as image input for the reference')
     elif isinstance(imref, (np.ndarray, np.generic)):

niftypet/nimpa/include/isub.h

@@ -0,0 +1,7 @@
+#ifndef _NIMPA_ISUB_H_
+#define _NIMPA_ISUB_H_
+
+/// 2D
+void d_isub(float *dst, const float *src, const int *idxs, int J, int X, bool _sync = true);
+
+#endif // _NIMPA_ISUB_H_

niftypet/nimpa/include/nlm.h

@@ -3,6 +3,6 @@
 
 /// main NLM function
 void d_nlm3d(float *dst, const float *src, const float *ref, float sigma, int Z, int Y, int X,
-             int HALF_WIDTH, bool _sync);
+             int HALF_WIDTH, bool _sync = true);
 
 #endif // _NIMPA_NLM_H_

niftypet/nimpa/prc/__init__.py

@@ -1,18 +1,21 @@
 # initialise the module folder
 __all__ = [
     # imio
-    'array2nii', 'create_dir', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo',
-    'dcmsort', 'fwhm2sig', 'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip',
-    'niisort', 'orientnii', 'pick_t1w', 'time_stamp',
+    'array2nii', 'create_dir', 'dcm2im', 'dcm2nii', 'dcmanonym', 'dcminfo', 'dcmsort', 'fwhm2sig',
+    'getnii', 'getnii_descr', 'nii_gzip', 'nii_ugzip', 'niisort', 'orientnii', 'pick_t1w',
+    'time_stamp',
     # prc
-    'bias_field_correction', 'centre_mass_img', 'ct2mu', 'im_cut', 'imsmooth',
-    'imtrimup', 'iyang', 'nii_modify', 'pet2pet_rigid', 'psf_gaussian',
-    'psf_measured', 'pvc_iyang',
+    'bias_field_correction', 'centre_mass_img', 'centre_mass_corr', 'ct2mu', 'im_cut',
+    'imsmooth', 'imtrimup',
+    'iyang', 'nii_modify', 'pet2pet_rigid', 'psf_gaussian', 'psf_measured', 'pvc_iyang',
+    # num
+    'conv_separable', 'isub', 'nlm',
     # regseg
-    'affine_fsl', 'affine_niftyreg', 'coreg_spm', 'coreg_vinci', 'create_mask',
-    'dice_coeff', 'dice_coeff_multiclass', 'imfill', 'motion_reg',
-    'realign_mltp_spm', 'resample_fsl', 'resample_mltp_spm',
-    'resample_niftyreg', 'resample_spm', 'resample_vinci'] # yapf: disable
+    'affine_dipy', 'affine_fsl', 'affine_niftyreg',
+    'coreg_spm', 'coreg_vinci', 'create_mask', 'dice_coeff', 'dice_coeff_multiclass',
+    'imfill', 'motion_reg', 'realign_mltp_spm', 'resample_fsl', 'resample_dipy',
+    'resample_mltp_spm', 'resample_niftyreg', 'resample_spm',
+    'resample_vinci'] # yapf: disable
 
 from .imio import (
     array2nii,
@@ -32,10 +35,12 @@
     pick_t1w,
     time_stamp,
 )
+from .num import conv_separable, isub, nlm
 
 # will be deprecated
 from .prc import (
     bias_field_correction,
+    centre_mass_corr,
     centre_mass_img,
     ct2mu,
     im_cut,
@@ -49,6 +54,7 @@
     pvc_iyang,
 )
 from .regseg import (
+    affine_dipy,
     affine_fsl,
     affine_niftyreg,
     coreg_spm,
@@ -59,6 +65,7 @@
     imfill,
     motion_reg,
     realign_mltp_spm,
+    resample_dipy,
     resample_fsl,
     resample_mltp_spm,
     resample_niftyreg,