Numpy2 (#134)

* try numpy 2.0 builds

* fix index print bug

.github/workflows/cibuildwheel.yml

@@ -13,7 +13,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- os: [ubuntu-latest, windows-latest, macos-latest, macos-14]
+ os: [ubuntu-latest, windows-latest, macos-12, macos-14]
 
  steps:
  - uses: actions/checkout@v4
@@ -24,23 +24,32 @@ jobs:
  python-version: '3.10'
 
  - name: Build wheels
- uses: pypa/cibuildwheel@v2.16.5
+ uses: pypa/cibuildwheel@v2.19.2
  env:
+ CIBW_BUILD_FRONTEND: "build"
  CIBW_ARCHS: "auto64"
- CIBW_SKIP: "pp* cp36-* cp37-* *musllinux* cp38-macosx_arm64"
+ CIBW_SKIP: "pp* *musllinux*"
+ CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
  CIBW_TEST_REQUIRES: pytest
- CIBW_TEST_COMMAND: pytest --pyargs nlsam --verbose
- CIBW_TEST_COMMAND_LINUX: >
+ CIBW_TEST_COMMAND_WINDOWS: pytest --pyargs nlsam --verbose
+ CIBW_TEST_COMMAND: >
  pytest --pyargs nlsam --verbose &&
  cd {package}/example &&
- chmod +x  {package}/nlsam/tests/test_scripts1.sh &&
+ chmod +x {package}/nlsam/tests/test_scripts1.sh &&
  bash {package}/nlsam/tests/test_scripts1.sh &&
- chmod +x  {package}/nlsam/tests/test_scripts2.sh &&
+ chmod +x {package}/nlsam/tests/test_scripts2.sh &&
  bash {package}/nlsam/tests/test_scripts2.sh
 
+ - name: Test against oldest supported numpy version
+ shell: bash
+ run: |
+ python -m pip install ./wheelhouse/*cp310*.whl
+ python -m pip install numpy==1.21.3 scipy==1.8 pytest
+ pytest --pyargs nlsam --verbose
+
  - uses: actions/upload-artifact@v4
  with:
- name: nlsam_${{ runner.os }}
+ name: cibw-nlsam_${{ matrix.os }}
  path: ./wheelhouse/*.whl
 
  build_sdist:
@@ -61,14 +70,15 @@ jobs:
 
  - uses: actions/upload-artifact@v4
  with:
+ name: cibw-sdist
  path: dist/*.tar.gz
 
  build_pyinstaller:
  name: Build pyinstaller on ${{ matrix.os }}
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- os: [ubuntu-20.04, windows-2019, macos-11]
+ os: [ubuntu-20.04, windows-2019, macos-12, macos-14]
  steps:
  - uses: actions/checkout@v4
 
@@ -92,7 +102,7 @@ jobs:
 
  - uses: actions/upload-artifact@v4
  with:
- name: nlsam_${{ env.version }}_${{ runner.os }}
+ name: nlsam_${{ env.version }}_${{ runner.os }}_${{ runner.arch }}
  path: |
  ./dist/nlsam_denoising*
  CHANGELOG.md

.github/workflows/release.yml

@@ -9,6 +9,10 @@ on:
 jobs:
  publish_artifacts:
  runs-on: ubuntu-latest
+ environment: release
+ permissions:
+ # IMPORTANT: this permission is mandatory for trusted publishing
+ id-token: write
  # upload to PyPI on every tag starting with 'v'
  # if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
  # alternatively, to publish when a GitHub Release is created, use the following rule:
@@ -17,23 +21,17 @@ jobs:
  - name: Download builds
  uses: actions/download-artifact@v4
  with:
- name: artifact
  path: dist
+ pattern: cibw-*
+ merge-multiple: true
 
  - name: upload to pypi
  uses: pypa/gh-action-pypi-publish@release/v1
- with:
- verbose: true
- print-hash: true
- user: ${{ secrets.PYPI_USERNAME }}
- password: ${{ secrets.PYPI_PASSWORD }}
- # password: ${{ secrets.testpypi_password }}
- # repository_url: https://test.pypi.org/legacy/
 
  - name: publish to github release
- uses: softprops/action-gh-release@v1
- # permissions:
- # contents: write
+ uses: softprops/action-gh-release@v2
+ permissions:
+ contents: write
  if: startsWith(github.ref, 'refs/tags/')
  with:
  files: dist/*

.gitignore

@@ -26,15 +26,18 @@ var/
 .ipynb_checkpoints
 .DS_Store
 pip-wheel-metadata/*
+*.whl
 
 # PyInstaller
 # Usually these files are written by a python script from a template
 # before PyInstaller builds the exe, so as to inject date/other infos into it.
 *.manifest
+*.spec
 
 # Installer logs
 pip-log.txt
 pip-delete-this-directory.txt
+log
 
 # Unit test / coverage reports
 htmlcov/
@@ -43,6 +46,7 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+*.html
 
 # Translations
 *.mo
@@ -61,3 +65,5 @@ target/
 
 nlsam.zip
 *.code-workspace
+*.nii.gz
+*.nii

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.7.2] - 2023-07-03
+
+- Support for numpy 2.0 and python 3.9 and up
+- Fixes for Cython 3 and newer Scipy
+
 ## [0.7.1] - 2023-07-03
 
 - Some speed improvements internally

docs/conf.py

@@ -59,9 +59,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.7.1'
+version = '0.7.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.7.1'
+release = '0.7.2'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

nlsam/bias_correction.py

@@ -85,14 +85,14 @@ def root_finder_sigma(data, sigma, N, mask=None, verbose=False, n_cores=-1):
  output, ndarray
  Corrected sigma value, where sigma_gaussian = sigma / sqrt(xi)
  """
- data = np.array(data)
- sigma = np.array(sigma)
- N = np.array(N)
+ data = np.asarray(data)
+ sigma = np.asarray(sigma)
+ N = np.asarray(N)
 
  if mask is None:
  mask = np.ones(data.shape[:-1], dtype=bool)
  else:
- mask = np.array(mask, dtype=bool)
+ mask = np.asarray(mask, dtype=bool)
 
  # Force 3D/4D broadcasting if needed
  if sigma.ndim == (data.ndim - 1):

nlsam/denoiser.py

@@ -90,8 +90,8 @@ def nlsam_denoise(data, sigma, bvals, bvecs, block_size,
  if not ((dtype == np.float32) or (dtype == np.float64)):
  raise ValueError(f'dtype should be either np.float32 or np.float64, but is {dtype}')
 
- b0_loc = np.where(bvals <= b0_threshold)[0]
- dwis = np.where(bvals > b0_threshold)[0]
+ b0_loc = np.flatnonzero(bvals <= b0_threshold)
+ dwis = np.flatnonzero(bvals > b0_threshold)
  num_b0s = len(b0_loc)
  variance = sigma**2
  angular_size = block_size[-1]
@@ -166,7 +166,7 @@ def nlsam_denoise(data, sigma, bvals, bvecs, block_size,
  to_denoise[..., 1:] = data[..., idx]
  divider[list(b0_loc + idx)] += 1
 
- logger.info(f'Now denoising volumes {b0_loc + idx} / block {i} out of {len(indexes)}.')
+ logger.info(f'Now denoising volumes {np.hstack((b0_loc, idx))} / block {i} out of {len(indexes)}.')
 
  data_denoised[..., b0_loc + idx] += local_denoise(to_denoise,
  b0_block_size,

nlsam/stabilizer.pyx

@@ -1,4 +1,5 @@
 # cython: wraparound=False, cdivision=True, boundscheck=False, language_level=3, embedsignature=True, infer_types=True
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
 
 import numpy as np
 cimport numpy as np
@@ -293,7 +294,7 @@ cdef inline double xi(double eta, double sigma, double N) noexcept nogil:
  # It starts to accumulate error around SNR ~ 1e4 though,
  # so we clip it to 1 (if needed) to stay on the safe side.
 
- if fabs(out) > 1:
+ if fabs(out) > 1.0:
  out = 1.0
 
  return out
@@ -349,7 +350,7 @@ def root_finder_loop(const floating[:] data, const floating1[:] sigma, const flo
  for idx in range(imax):
  theta = data[idx] / sigma[idx]
  gaussian_SNR = root_finder(theta, N[idx])
- corrected_sigma[idx] = sigma[idx] / sqrt(xi(gaussian_SNR, 1, N[idx]))
+ corrected_sigma[idx] = sigma[idx] / sqrt(xi(gaussian_SNR, 1.0, N[idx]))
 
  return corrected_sigma
 

nlsam/tests/test_bias_correction.py

@@ -22,14 +22,14 @@ def test_root_finder_sigma():
  assert_allclose(output, sigma, atol=1e-4)
 
  # magnitude SNR of 0.5 -> sigma = 50, eta = 25 for N = 1
- a = [np.sqrt((25 + np.random.randn(10000) * 50)**2 + (np.random.randn(10000) * 50)**2) for ii in range(250)]
+ a = [np.sqrt((25 + np.random.randn(10000) * 50)**2 + (np.random.randn(10000) * 50)**2) for ii in range(1250)]
  eta = np.mean(a, axis=1, keepdims=True, dtype=np.float64)
  sigma = np.std(a, axis=1, keepdims=True, dtype=np.float64)
  N = np.ones(sigma.shape, dtype=np.float32)
  output = root_finder_sigma(eta, sigma, N)
 
- # everything less than 10% error of real value?
- assert_allclose(output, 50, atol=5)
+ # everything less than 12% error of real value?
+ assert_allclose(output, 50, atol=6)
 
 
 # Taken from original example

nlsam/tests/test_scripts1.sh

@@ -14,10 +14,10 @@ python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz"
 python -c 'import nibabel as nib; import numpy as np; d = nib.load("mask.nii.gz").get_fdata(); nib.save(nib.Nifti1Image(np.random.rayleigh(10, d[40:50, 80:85].shape),np.eye(4)), "noise.nii.gz")'
 
 # Test on example dataset
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -f -N 1 --noise_est local_std --sh_order 0 --log log --cores 1 -m mask_crop.nii.gz
+nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -f -N 1 --noise_est local_std --sh_order 0 --cores 1 -m mask_crop.nii.gz -v
 check_return_code $?
 
-nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f -N 1 --noise_est local_std --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz
+nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f -N 1 --noise_est local_std --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz --log log.txt
 check_return_code $?
 
 nlsam_denoising dwi_crop.nii.gz dwi_nlsam.nii.gz bvals bvecs -m mask_crop.nii.gz -f --noise_est auto --sh_order 6 --iterations 5 --verbose --save_sigma sigma.nii.gz --save_N N.nii.gz

nlsam/utils.pyx

@@ -1,4 +1,5 @@
 # cython: wraparound=False, cdivision=True, boundscheck=False, language_level=3, embedsignature=True, infer_types=True
+# distutils: define_macros=NPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
 
 import numpy as np
 

pyproject.toml

@@ -1,25 +1,24 @@
 [build-system]
-requires = ["Cython>=0.29.33",
+requires = ["Cython>=3.0",
  "scipy>=1.5",
- "oldest-supported-numpy",
+ "numpy>=2.0",
  "setuptools",
  "wheel"]
 build-backend = "setuptools.build_meta"
 
 
 [project]
 name = "nlsam"
-version = '0.7.1'
+version = '0.7.2'
 authors = [{name = "Samuel St-Jean"}]
 description='Implementation of "Non Local Spatial and Angular Matching : Enabling higher spatial resolution diffusion MRI datasets through adaptive denoising"'
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.9"
 license = {text = "GPLv3"}
 
 dependencies = [
- 'numpy>=1.19',
+ 'numpy>=1.21.3',
  'scipy>=1.5',
- 'cython>=0.29.33',
  'nibabel>=2.0',
  'joblib>=0.14.1',
  'autodmri>=0.2.1',