Merge branch 'convex_hull_2d' of https://github.com/neuro-ml/imops in…

…to convex_hull_2d

.github/workflows/lint.yml

@@ -0,0 +1,27 @@
+name: Lint
+
+on: [ pull_request ]
+
+env:
+  MODULE_NAME: imops
+
+jobs:
+  lint:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Check python code style
+        run: |
+          pip install -r requirements-linters.txt
+          flake8 .
+          isort --check .
+          black --check .
+      - name: Check Cython code style
+        run: |
+          pip install cython-lint
+          cython-lint imops/src

.github/workflows/release.yml

@@ -35,7 +35,7 @@ jobs:
     needs: [ check_version ]
     strategy:
       matrix:
-        os: [ ubuntu-22.04, windows-2019, macOS-12 ]
+        os: [ ubuntu-22.04, windows-2019, macOS-13 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -47,17 +47,10 @@ jobs:
           python-version: '3.9'
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.17.0
-      - name: Install gcc for mac
-        if: matrix.os == 'macOS-12'
+      - name: Install llvm for mac
+        if: matrix.os == 'macOS-13'
         run: |
-          brew install llvm libomp
-          echo $PATH
-          ln -sf /usr/local/bin/gcc-11 /usr/local/bin/gcc
-          ln -sf /usr/local/bin/g++-11 /usr/local/bin/g++
-          ls /usr/local/bin/gcc*
-          ls /usr/local/bin/g++*
-          gcc --version
-          g++ --version
+          brew install llvm
       - name: Install g++-11 for ubuntu
         if: matrix.os == 'ubuntu-22.04'
         id: install_cc
@@ -79,7 +72,7 @@ jobs:
           python -m cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ENVIRONMENT_MACOS: >
-            PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
+            CC="$(brew --prefix llvm)/bin/clang" CXX="$(brew --prefix llvm)/bin/clang++"
           CIBW_BUILD: cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
           CIBW_BEFORE_BUILD_LINUX: 'if [ $(python -c "import sys; print(sys.version_info[1])") -ge 9 ]; then python -m pip install "numpy<3.0.0" --config-settings=setup-args="-Dallow-noblas=true"; fi'
       - uses: actions/upload-artifact@v3

.github/workflows/test_build.yml

@@ -9,7 +9,7 @@ jobs:
   build_wheels:
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-2019, macOS-12 ]
+        os: [ubuntu-22.04, windows-2019, macOS-13 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -21,17 +21,10 @@ jobs:
           python-version: '3.9' 
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.17.0
-      - name: Install gcc for mac
-        if: matrix.os == 'macOS-12'
+      - name: Install llvm for mac
+        if: matrix.os == 'macOS-13'
         run: |
-          brew install llvm libomp
-          echo $PATH
-          ln -sf /usr/local/bin/gcc-11 /usr/local/bin/gcc
-          ln -sf /usr/local/bin/g++-11 /usr/local/bin/g++
-          ls /usr/local/bin/gcc*
-          ls /usr/local/bin/g++*
-          gcc --version
-          g++ --version
+          brew install llvm
       - name: Install g++-11 for ubuntu
         if: matrix.os == 'ubuntu-22.04'
         id: install_cc
@@ -53,7 +46,7 @@ jobs:
           python -m cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ENVIRONMENT_MACOS: >
-            PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
+            CC="$(brew --prefix llvm)/bin/clang" CXX="$(brew --prefix llvm)/bin/clang++"
           CIBW_BUILD: cp37-* cp39-* cp312-*
           CIBW_SKIP: "*manylinux_x86_64"
           CIBW_BEFORE_BUILD_LINUX: 'if [ $(python -c "import sys; print(sys.version_info[1])") -ge 9 ]; then python -m pip install "numpy<3.0.0" --config-settings=setup-args="-Dallow-noblas=true"; fi'

.github/workflows/tests.yml

@@ -43,17 +43,6 @@ jobs:
           echo $MODULE_PARENT
           echo "MODULE_PARENT=$(echo $MODULE_PARENT)" >> $GITHUB_ENV
 
-      - name: Check python code style
-        run: |
-          pip install -r requirements-linters.txt
-          flake8 .
-          isort --check .
-          black --check .
-      - name: Check Cython code style
-        run: |
-          pip install cython-lint
-          cython-lint imops/src
-
       - name: Test with pytest
         run: |
           pytest tests -m "not nonumba" --junitxml=reports/junit-${{ matrix.python-version }}.xml --cov="$MODULE_PARENT/$MODULE_NAME" --cov-report=xml --cov-branch

.gitignore

@@ -10,3 +10,4 @@ imops/src/_fast*.pyx
 dist/
 *.so
 .vscode/
+.idea/

MANIFEST.in

@@ -1,6 +1,6 @@
 include *.md
 include requirements.txt
 include pyproject.toml
-include _build_utils.py
 recursive-include imops *.py
 recursive-include imops/cpp *.h *.hpp *.cpp
+exclude tests/*

_build_utils.py → imops/_build_utils.py

@@ -66,7 +66,7 @@ def get_ext_modules():
     modules = ['backprojection', 'measure', 'morphology', 'numeric', 'radon', 'zoom', 'convex_hull']
     modules_to_link_against_numpy_core_math_lib = ['numeric']
 
-    src_dir = Path(__file__).parent / name / 'src'
+    src_dir = Path(__file__).parent / 'src'
     for module in modules:
         # Cython extension and .pyx source file names must be the same to compile
         # https://stackoverflow.com/questions/8024805/cython-compiled-c-extension-importerror-dynamic-module-does-not-define-init-fu

imops/compat.py

@@ -12,3 +12,13 @@
     from scipy.ndimage._morphology import _ni_support
 except ImportError:
     from scipy.ndimage.morphology import _ni_support
+
+try:
+    from scipy.spatial import QhullError
+except ImportError:
+    from scipy.spatial.qhull import QhullError
+
+from scipy.ndimage._nd_image import euclidean_feature_transform  # noqa
+
+
+normalize_sequence = _ni_support._normalize_sequence  # noqa

imops/crop.py

@@ -1,3 +1,5 @@
+from typing import Optional
+
 import numpy as np
 
 from .backend import BackendLike
@@ -6,7 +8,9 @@
 from .utils import AxesLike, AxesParams, assert_subdtype, broadcast_axis, fill_by_indices
 
 
-def crop_to_shape(x: np.ndarray, shape: AxesLike, axis: AxesLike = None, ratio: AxesParams = 0.5) -> np.ndarray:
+def crop_to_shape(
+    x: np.ndarray, shape: AxesLike, axis: Optional[AxesLike] = None, ratio: AxesParams = 0.5
+) -> np.ndarray:
     """
     Crop `x` to match `shape` along `axis`.
 
@@ -57,8 +61,8 @@ def crop_to_shape(x: np.ndarray, shape: AxesLike, axis: AxesLike = None, ratio:
 def crop_to_box(
     x: np.ndarray,
     box: np.ndarray,
-    axis: AxesLike = None,
-    padding_values: AxesParams = None,
+    axis: Optional[AxesLike] = None,
+    padding_values: Optional[AxesParams] = None,
     num_threads: int = _NUMERIC_DEFAULT_NUM_THREADS,
     backend: BackendLike = None,
 ) -> np.ndarray:

imops/interp1d.py

@@ -1,4 +1,4 @@
-from typing import Union
+from typing import Optional, Union
 from warnings import warn
 
 import numpy as np
@@ -71,7 +71,7 @@ def __init__(
         kind: Union[int, str] = 'linear',
         axis: int = -1,
         copy: bool = True,
-        bounds_error: bool = None,
+        bounds_error: Optional[bool] = None,
         fill_value: Union[float, str] = np.nan,
         assume_sorted: bool = False,
         num_threads: int = -1,

imops/interp2d.py

@@ -1,4 +1,5 @@
 from platform import python_version
+from typing import Optional
 
 import numpy as np
 from scipy.spatial import KDTree
@@ -47,9 +48,9 @@ class Linear2DInterpolator(Linear2DInterpolatorCpp):
     def __init__(
         self,
         points: np.ndarray,
-        values: np.ndarray = None,
+        values: Optional[np.ndarray] = None,
         num_threads: int = 1,
-        triangles: np.ndarray = None,
+        triangles: Optional[np.ndarray] = None,
         **kwargs,
     ):
         if triangles is not None:
@@ -77,7 +78,7 @@ def __init__(
         # FIXME: add backend dispatch
         self.num_threads = normalize_num_threads(num_threads, Cython(), warn_stacklevel=3)
 
-    def __call__(self, points: np.ndarray, values: np.ndarray = None, fill_value: float = 0.0) -> np.ndarray:
+    def __call__(self, points: np.ndarray, values: Optional[np.ndarray] = None, fill_value: float = 0.0) -> np.ndarray:
         """
         Evaluate the interpolant
 

imops/measure.py

@@ -1,6 +1,6 @@
 from collections import namedtuple
 from platform import python_version
-from typing import List, NamedTuple, Sequence, Tuple, Union
+from typing import List, NamedTuple, Optional, Sequence, Tuple, Union
 from warnings import warn
 
 import numpy as np
@@ -32,12 +32,12 @@
 # TODO: Make it work and test on immutable arrays as soon as `cc3d` package is fixed
 def label(
     label_image: np.ndarray,
-    background: int = None,
-    connectivity: int = None,
+    background: Optional[int] = None,
+    connectivity: Optional[int] = None,
     return_num: bool = False,
     return_labels: bool = False,
     return_sizes: bool = False,
-    dtype: type = None,
+    dtype: Optional[type] = None,
 ) -> Union[np.ndarray, NamedTuple]:
     """
     Fast version of `skimage.measure.label` which optionally returns number of connected components, labels and sizes.
@@ -139,8 +139,8 @@ def label(
 
 def center_of_mass(
     array: np.ndarray,
-    labels: np.ndarray = None,
-    index: Union[int, Sequence[int]] = None,
+    labels: Union[np.ndarray, None] = None,
+    index: Union[int, Sequence[int], None] = None,
     num_threads: int = -1,
     backend: BackendLike = None,
 ) -> Union[Tuple[float, ...], List[Tuple[float, ...]]]:

imops/morphology.py

@@ -1,18 +1,10 @@
-from typing import Callable, Tuple, Union
+from typing import Callable, Optional, Tuple, Union
 from warnings import warn
 
 import numpy as np
 from edt import edt
 from scipy.ndimage import distance_transform_edt as scipy_distance_transform_edt, generate_binary_structure
-from scipy.ndimage._nd_image import euclidean_feature_transform
 from scipy.spatial import ConvexHull
-
-
-try:
-    from scipy.spatial import QhullError
-except ImportError:
-    from scipy.spatial.qhull import QhullError  # Old scipy has another structure
-
 from skimage.morphology import (
     binary_closing as scipy_binary_closing,
     binary_dilation as scipy_binary_dilation,
@@ -23,7 +15,7 @@
 
 from .backend import BackendLike, Cython, Scipy, resolve_backend
 from .box import add_margin, box_to_shape, mask_to_box, shape_to_box
-from .compat import _ni_support
+from .compat import QhullError, euclidean_feature_transform, normalize_sequence
 from .crop import crop_to_box
 from .pad import restore_crop
 from .src._convex_hull import _grid_points_in_poly, _left_right_bounds, _offset_unique
@@ -40,8 +32,8 @@ def morphology_op_wrapper(
 ) -> Callable:
     def wrapped(
         image: np.ndarray,
-        footprint: np.ndarray = None,
-        output: np.ndarray = None,
+        footprint: Optional[np.ndarray] = None,
+        output: Optional[np.ndarray] = None,
         boxed: bool = False,
         num_threads: int = -1,
         backend: BackendLike = None,
@@ -171,8 +163,8 @@ def wrapped(
 
 def binary_dilation(
     image: np.ndarray,
-    footprint: np.ndarray = None,
-    output: np.ndarray = None,
+    footprint: Optional[np.ndarray] = None,
+    output: Optional[np.ndarray] = None,
     boxed: bool = False,
     num_threads: int = -1,
     backend: BackendLike = None,
@@ -225,8 +217,8 @@ def binary_dilation(
 
 def binary_erosion(
     image: np.ndarray,
-    footprint: np.ndarray = None,
-    output: np.ndarray = None,
+    footprint: Optional[np.ndarray] = None,
+    output: Optional[np.ndarray] = None,
     boxed: bool = False,
     num_threads: int = -1,
     backend: BackendLike = None,
@@ -279,8 +271,8 @@ def binary_erosion(
 
 def binary_closing(
     image: np.ndarray,
-    footprint: np.ndarray = None,
-    output: np.ndarray = None,
+    footprint: Optional[np.ndarray] = None,
+    output: Optional[np.ndarray] = None,
     boxed: bool = False,
     num_threads: int = -1,
     backend: BackendLike = None,
@@ -334,8 +326,8 @@ def binary_closing(
 
 def binary_opening(
     image: np.ndarray,
-    footprint: np.ndarray = None,
-    output: np.ndarray = None,
+    footprint: Optional[np.ndarray] = None,
+    output: Optional[np.ndarray] = None,
     boxed: bool = False,
     num_threads: int = -1,
     backend: BackendLike = None,
@@ -379,7 +371,7 @@ def binary_opening(
 
 def distance_transform_edt(
     image: np.ndarray,
-    sampling: Tuple[float] = None,
+    sampling: Optional[Tuple[float]] = None,
     return_distances: bool = True,
     return_indices: bool = False,
     num_threads: int = -1,
@@ -499,7 +491,7 @@ def distance_transform_edt(
     if image.dtype != bool:
         image = np.atleast_1d(np.where(image, 1, 0))
     if sampling is not None:
-        sampling = _ni_support._normalize_sequence(sampling, image.ndim)
+        sampling = normalize_sequence(sampling, image.ndim)
         sampling = np.asarray(sampling, dtype=np.float64)
         if not sampling.flags.contiguous:
             sampling = sampling.copy()
@@ -529,7 +521,7 @@ def distance_transform_edt(
     return None
 
 
-def convex_hull_image(image, offset_coordinates=True):
+def convex_hull_image(image: np.ndarray, offset_coordinates: bool = True) -> np.ndarray:
     """
     Fast convex hull of an image. Similar to skimage.morphology.convex_hull_image with include_borders=True
 
@@ -560,7 +552,7 @@ def convex_hull_image(image, offset_coordinates=True):
 
     if np.count_nonzero(image) == 0:
         warn(
-            'Input image is entirely zero, no valid convex hull. ' 'Returning empty image',
+            'Input image is entirely zero, no valid convex hull. Returning empty image',
             UserWarning,
         )
         return np.zeros(image.shape, dtype=bool)