Merge pull request #55 from neuro-ml/dev

Add fast EDT

.github/workflows/release.yml

@@ -35,7 +35,7 @@ jobs:
     needs: [ check_version ]
     strategy:
       matrix:
-        os: [ ubuntu-20.04, windows-2019, macOS-11 ]
+        os: [ ubuntu-22.04, windows-2019, macOS-11 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -59,13 +59,13 @@ jobs:
           gcc --version
           g++ --version
       - name: Install g++-11 for ubuntu
-        if: matrix.os == 'ubuntu-20.04'
+        if: matrix.os == 'ubuntu-22.04'
         id: install_cc
         uses: rlalik/setup-cpp-compiler@master
         with:
           compiler: g++-11
       - name: Check compilers for ubuntu
-        if: matrix.os == 'ubuntu-20.04'
+        if: matrix.os == 'ubuntu-22.04'
         run: |
           ls /usr/bin/gcc*
           ls /usr/bin/g++*
@@ -80,7 +80,7 @@ jobs:
         env:
           CIBW_ENVIRONMENT_MACOS: >
             PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*
+          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<2.0.0" --config-settings=setup-args="-Dallow-noblas=true"; fi'
       - uses: actions/upload-artifact@v3
         with:

.github/workflows/test_build.yml

@@ -9,7 +9,7 @@ jobs:
   build_wheels:
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macOS-11 ]
+        os: [ubuntu-22.04, windows-2019, macOS-11 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -33,13 +33,13 @@ jobs:
           gcc --version
           g++ --version
       - name: Install g++-11 for ubuntu
-        if: matrix.os == 'ubuntu-20.04'
+        if: matrix.os == 'ubuntu-22.04'
         id: install_cc
         uses: rlalik/setup-cpp-compiler@master
         with:
           compiler: g++-11
       - name: Check compilers for ubuntu
-        if: matrix.os == 'ubuntu-20.04'
+        if: matrix.os == 'ubuntu-22.04'
         run: |
           ls /usr/bin/gcc*
           ls /usr/bin/g++*
@@ -54,6 +54,6 @@ jobs:
         env:
           CIBW_ENVIRONMENT_MACOS: >
             PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
-          CIBW_BUILD: cp39-* cp36-* cp312-*
+          CIBW_BUILD: cp39-* cp312-*
           CIBW_SKIP: "*musllinux* *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<2.0.0" --config-settings=setup-args="-Dallow-noblas=true"; fi'

.github/workflows/tests.yml

@@ -7,10 +7,10 @@ env:
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: [ '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
@@ -50,7 +50,6 @@ jobs:
           isort --check .
           black --check .
       - name: Check Cython code style
-        if: matrix.python-version != '3.6'
         run: |
           pip install cython-lint
           cython-lint imops/src

README.md

@@ -156,4 +156,4 @@ Available backends:
 
 Some parts of our code for radon/inverse radon transform as well as the code for linear interpolation are inspired by
 the implementations from [`scikit-image`](https://github.com/scikit-image/scikit-image) and [`scipy`](https://github.com/scipy/scipy).
-Also we used [`fastremap`](https://github.com/seung-lab/fastremap) and [`cc3d`](https://github.com/seung-lab/connected-components-3d) out of the box.
+Also we used [`fastremap`](https://github.com/seung-lab/fastremap), [`edt`](https://github.com/seung-lab/euclidean-distance-transform-3d) and [`cc3d`](https://github.com/seung-lab/connected-components-3d) out of the box.

_build_utils.py

@@ -63,34 +63,16 @@ def get_ext_modules():
         '/O3' if on_windows else '-O3',
     ]  # FIXME: account for higher gcc versions
 
-    # 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
     modules = ['backprojection', 'measure', 'morphology', 'numeric', 'radon', 'zoom']
     modules_to_link_against_numpy_core_math_lib = ['numeric']
 
     src_dir = Path(__file__).parent / name / '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
         shutil.copyfile(src_dir / f'_{module}.pyx', src_dir / f'_fast_{module}.pyx')
 
-    return [
-        Extension(
-            f'{name}.src._{prefix}{module}',
-            [f'{name}/src/_{prefix}{module}.pyx'],
-            include_dirs=[LazyImport('numpy')],
-            library_dirs=[NumpyLibImport()] if module in modules_to_link_against_numpy_core_math_lib else [],
-            libraries=['npymath'] + ['m'] * (not on_windows)
-            if module in modules_to_link_against_numpy_core_math_lib
-            else [],
-            extra_compile_args=args + additional_args,
-            extra_link_args=args + additional_args,
-            define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
-        )
-        for module in modules
-        # FIXME: import of `ffast-math` compiled modules changes global FPU state, so now `fast=True` will just
-        # fallback to standard `-O2` compiled versions until https://github.com/neuro-ml/imops/issues/37 is resolved
-        # for prefix, additional_args in zip(['', 'fast_'], [[], ['-ffast-math']])
-        for prefix, additional_args in zip(['', 'fast_'], [[], []])
-    ] + [
+    extensions = [
         Extension(
             f'{name}.cpp.cpp_modules',
             [f'{name}/cpp/main.cpp'],
@@ -100,3 +82,32 @@ def get_ext_modules():
             language='c++',
         )
     ]
+    for module in modules:
+        libraries = []
+        library_dirs = []
+        include_dirs = [LazyImport('numpy')]
+
+        if module in modules_to_link_against_numpy_core_math_lib:
+            library_dirs.append(NumpyLibImport())
+            libraries.append('npymath')
+            if not on_windows:
+                libraries.append('m')
+
+        # FIXME: import of `ffast-math` compiled modules changes global FPU state, so now `fast=True` will just
+        # fallback to standard `-O2` compiled versions until https://github.com/neuro-ml/imops/issues/37 is resolved
+        # for prefix, additional_args in zip(['', 'fast_'], [[], ['-ffast-math']])
+        for prefix, additional_args in zip(['', 'fast_'], [[], []]):
+            extensions.append(
+                Extension(
+                    f'{name}.src._{prefix}{module}',
+                    [f'{name}/src/_{prefix}{module}.pyx'],
+                    include_dirs=include_dirs,
+                    library_dirs=library_dirs,
+                    libraries=libraries,
+                    extra_compile_args=args + additional_args,
+                    extra_link_args=args + additional_args,
+                    define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
+                )
+            )
+
+    return extensions

benchmarks/benchmark_morphology.py

@@ -14,7 +14,7 @@
         *[Cython(fast) for fast in [False, True]],
     ]
 
-from imops.morphology import binary_closing, binary_dilation, binary_erosion, binary_opening
+from imops.morphology import binary_closing, binary_dilation, binary_erosion, binary_opening, distance_transform_edt
 
 from .common import IMAGE_TYPE_BENCHMARK, IMAGE_TYPES_BENCHMARK, NUMS_THREADS_TO_BENCHMARK, discard_arg, load_npy_gz
 
@@ -104,3 +104,41 @@ def peakmem_closing(self, backend, num_threads, image_type, boxed):
             binary_closing(im, num_threads=num_threads, backend=backend, boxed=boxed)
         except TypeError:
             binary_closing(im, num_threads=num_threads, backend=backend)
+
+
+class EDTSuite:
+    params = [morphology_configs, ('bool', 'int32', 'int64'), NUMS_THREADS_TO_BENCHMARK, [False, True], [False, True]]
+    param_names = ['backend', 'dtype', 'num_threads', 'return_distances', 'return_indices']
+
+    @discard_arg(1)
+    @discard_arg(-1)
+    @discard_arg(-1)
+    @discard_arg(-1)
+    def setup(self, dtype):
+        self.image = np.random.randint(0, 5 if 'int' in dtype else 2, (512, 512, 512)).astype(dtype, copy=False)
+
+    @discard_arg(2)
+    def time_edt(self, backend, num_threads, return_distances, return_indices):
+        if not return_distances and not return_indices:
+            return
+
+        distance_transform_edt(
+            self.image,
+            return_distances=return_distances,
+            return_indices=return_indices,
+            backend=backend,
+            num_threads=num_threads,
+        )
+
+    @discard_arg(2)
+    def peakmem_edt(self, backend, num_threads, return_distances, return_indices):
+        if not return_distances and not return_indices:
+            return
+
+        distance_transform_edt(
+            self.image,
+            return_distances=return_distances,
+            return_indices=return_indices,
+            backend=backend,
+            num_threads=num_threads,
+        )

docs/index.md

@@ -46,6 +46,8 @@ pip install imops[numba]  # additionally install Numba backend
 
 ::: imops.morphology.binary_closing
 
+::: imops.morphology.distance_transform_edt
+
 ::: imops.measure.label
 
 ::: imops.measure.center_of_mass

imops/__version__.py

@@ -1 +1 @@
-__version__ = '0.8.7'
+__version__ = '0.8.8'