20x fast convex_hull_image for 2D

.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'

_build_utils.py

@@ -63,7 +63,7 @@ def get_ext_modules():
         '/O3' if on_windows else '-O3',
     ]  # FIXME: account for higher gcc versions
 
-    modules = ['backprojection', 'measure', 'morphology', 'numeric', 'radon', 'zoom']
+    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'

docs/index.md

@@ -48,6 +48,8 @@ pip install imops[numba]  # additionally install Numba backend
 
 ::: imops.morphology.distance_transform_edt
 
+::: imops.morphology.convex_hull_image
+
 ::: imops.measure.label
 
 ::: imops.measure.center_of_mass

imops/__version__.py

@@ -1 +1 @@
-__version__ = '0.9.0'
+__version__ = '0.9.1'

imops/morphology.py

@@ -5,18 +5,28 @@
 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,
     binary_erosion as scipy_binary_erosion,
     binary_opening as scipy_binary_opening,
 )
+from skimage.util import unique_rows
 
 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 .crop import crop_to_box
 from .pad import restore_crop
+from .src._convex_hull import _grid_points_in_poly, _left_right_bounds, _offset_unique
 from .src._fast_morphology import (
     _binary_dilation as cython_fast_binary_dilation,
     _binary_erosion as cython_fast_binary_erosion,
@@ -517,3 +527,77 @@ def distance_transform_edt(
         return result[0]
 
     return None
+
+
+def convex_hull_image(image, offset_coordinates=True):
+    """
+    Fast convex hull of an image. Similar to skimage.morphology.convex_hull_image with include_borders=True
+
+    Parameters
+    ----------
+    image: np.ndarray
+        input image, must be 2D
+    offset_coordinates: bool
+        If True, a pixel at coordinate, e.g., (4, 7) will be represented by coordinates
+        (3.5, 7), (4.5, 7), (4, 6.5), and (4, 7.5).
+        This adds some “extent” to a pixel when computing the hull.
+
+    Returns
+    -------
+    output: np.ndarray
+        resulting convex hull of the input image
+
+    Examples
+    --------
+    ```python
+    chull = convex_hull_image(x)
+    ```
+    """
+
+    ndim = image.ndim
+    if ndim != 2:
+        raise RuntimeError(f'convex_hull_image is currently implemented only for 2D arrays, got {ndim}D array')
+
+    if np.count_nonzero(image) == 0:
+        warn(
+            'Input image is entirely zero, no valid convex hull. ' 'Returning empty image',
+            UserWarning,
+        )
+        return np.zeros(image.shape, dtype=bool)
+
+    # In 2D, we do an optimisation by choosing only pixels that are
+    # the starting or ending pixel of a row or column.  This vastly
+    # limits the number of coordinates to examine for the virtual hull.
+    image = np.ascontiguousarray(image, dtype=np.uint8)
+
+    coords = _left_right_bounds(image)
+
+    if offset_coordinates:
+        coords = _offset_unique(coords)
+    else:
+        coords = unique_rows(coords)
+
+    # Find the convex hull
+    try:
+        hull = ConvexHull(coords)
+    except QhullError as err:
+        warn(f'Failed to get convex hull image. ' f'Returning empty image, see error message below: \n' f'{err}')
+        return np.zeros(image.shape, dtype=bool)
+
+    vertices = hull.points[hull.vertices]
+
+    # return vertices
+
+    # If 2D, use fast Cython function to locate convex hull pixels
+    labels = _grid_points_in_poly(
+        np.ascontiguousarray(vertices[:, 0], dtype=np.float32),
+        np.ascontiguousarray(vertices[:, 1], dtype=np.float32),
+        image.shape[0],
+        image.shape[1],
+        len(vertices),
+    )
+
+    # edge points and vertices are included
+    mask = labels.view(bool)
+
+    return mask