Merge pull request #59 from neuro-ml/dev

Dev

.flake8

@@ -1,15 +1,17 @@
 [flake8]
 # W503: line break before binary operator is actually considered best-practice
 # E203: spaces around complex variables in slices are pep-right
-# F401: unused imports in __init__.py-s
+# F401: unused imports in __init__.py-s and compat.py
 # I251: allow absolute imports in upper files
 # B028: !r is not supported for python<3.8
 # W604: backticks in str-s are ok
-ignore = W503,E203,B028,W604
+# S101: asserts are ok for now
+# S102: exec in build scripts is ok
+ignore = W503,E203,B028,W604,S101
 per-file-ignores =
-    __init__.py:F401
-    tests/*:I251
-    benchmarks/*:I251
+    setup.py,_build_utils.py:S102
+    __init__.py,compat.py:F401
+    tests/*,benchmarks/*:I251
 max-line-length = 120
 banned-modules =
     imops.* = Use relative imports

.github/workflows/release.yml

@@ -35,7 +35,7 @@ jobs:
     needs: [ check_version ]
     strategy:
       matrix:
-        os: [ ubuntu-22.04, windows-2019, macOS-11 ]
+        os: [ ubuntu-22.04, windows-2019, macOS-12 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -48,7 +48,7 @@ jobs:
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.17.0
       - name: Install gcc for mac
-        if: matrix.os == 'macOS-11'
+        if: matrix.os == 'macOS-12'
         run: |
           brew install llvm libomp
           echo $PATH
@@ -81,7 +81,7 @@ jobs:
           CIBW_ENVIRONMENT_MACOS: >
             PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
           CIBW_BUILD: 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'
+          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
         with:
           path: ./wheelhouse/*.whl

.github/workflows/test_build.yml

@@ -9,7 +9,7 @@ jobs:
   build_wheels:
     strategy:
       matrix:
-        os: [ubuntu-22.04, windows-2019, macOS-11 ]
+        os: [ubuntu-22.04, windows-2019, macOS-12 ]
 
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
@@ -22,7 +22,7 @@ jobs:
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.17.0
       - name: Install gcc for mac
-        if: matrix.os == 'macOS-11'
+        if: matrix.os == 'macOS-12'
         run: |
           brew install llvm libomp
           echo $PATH
@@ -56,4 +56,4 @@ jobs:
             PATH="/usr/local/opt/llvm/bin:$PATH" LDFLAGS="-L/usr/local/opt/llvm/lib" CPPFLAGS="-I/usr/local/opt/llvm/include"
           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'
+          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'

.gitignore

@@ -1,6 +1,7 @@
 __pycache__/
 .pytest_cache/
 build/
+imops/src/*.cpp
 imops/src/*.c
 imops/src/*.so
 imops/src/_fast*.pyx

_build_utils.py

@@ -80,7 +80,16 @@ def get_ext_modules():
             extra_compile_args=args + cpp_args,
             extra_link_args=args + cpp_args,
             language='c++',
-        )
+        ),
+        Extension(
+            f'{name}.src._utils',
+            [f'{name}/src/_utils.pyx'],
+            language='c++',
+            include_dirs=[LazyImport('numpy')],
+            extra_compile_args=args + cpp_args,
+            extra_link_args=args + cpp_args,
+            define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
+        ),
     ]
     for module in modules:
         libraries = []
@@ -93,6 +102,7 @@ def get_ext_modules():
             if not on_windows:
                 libraries.append('m')
 
+        # TODO: mb throw `ffast-math` away?
         # 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']])
@@ -101,6 +111,7 @@ def get_ext_modules():
                 Extension(
                     f'{name}.src._{prefix}{module}',
                     [f'{name}/src/_{prefix}{module}.pyx'],
+                    language='c',
                     include_dirs=include_dirs,
                     library_dirs=library_dirs,
                     libraries=libraries,

asv.conf.json

@@ -3,16 +3,16 @@
     "project": "imops",
     "project_url": "https://github.com/neuro-ml/imops",
     "repo": ".",
-    "branches": ["master", "dev"],
+    "branches": ["dev"],
     "dvcs": "git",
     "environment_type": "conda",
     "show_commit_url": "https://github.com/neuro-ml/imops/commit",
-    "pythons": ["3.10"],
+    "pythons": ["3.12.3"],
     "conda_channels": ["defaults", "conda-forge"],
     "matrix": {
         "req": {
             "numpy": [],
-            "Cython": ["0.29.36"],
+            "Cython": ["3.0.10"],
             "scipy": [],
             "scikit-image": [],
             "numba": [],

docs/index.md

@@ -63,3 +63,5 @@ pip install imops[numba]  # additionally install Numba backend
 ::: imops.radon.radon
 
 ::: imops.radon.inverse_radon
+
+::: imops.utils.isin

imops/__version__.py

@@ -1 +1 @@
-__version__ = '0.8.8'
+__version__ = '0.9.0'

imops/compat.py

@@ -0,0 +1,14 @@
+try:
+    from numpy.lib.array_utils import normalize_axis_tuple
+except ModuleNotFoundError:
+    from numpy.core.numeric import normalize_axis_tuple
+
+try:
+    from numpy.exceptions import VisibleDeprecationWarning
+except ModuleNotFoundError:
+    from numpy import VisibleDeprecationWarning
+
+try:
+    from scipy.ndimage._morphology import _ni_support
+except ImportError:
+    from scipy.ndimage.morphology import _ni_support

imops/measure.py

@@ -29,6 +29,7 @@
 }
 
 
+# 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,
@@ -213,8 +214,8 @@ def center_of_mass(
 
         src_center_of_mass = _fast_labeled_center_of_mass if backend.fast else _labeled_center_of_mass
 
-    if array.dtype != 'float64':
-        array = array.astype(float)
+    if array.dtype not in ('float32', 'float64'):
+        array = array.astype(np.float32)
 
     n_dummy = 3 - ndim
     if n_dummy:

imops/morphology.py

@@ -5,13 +5,6 @@
 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
-
-
-try:
-    from scipy.ndimage._morphology import _ni_support
-except ImportError:
-    from scipy.ndimage.morphology import _ni_support
-
 from skimage.morphology import (
     binary_closing as scipy_binary_closing,
     binary_dilation as scipy_binary_dilation,
@@ -21,6 +14,7 @@
 
 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 .crop import crop_to_box
 from .pad import restore_crop
 from .src._fast_morphology import (

imops/radon.py

@@ -4,6 +4,7 @@
 from scipy.fftpack import fft, ifft
 
 from .backend import BackendLike, resolve_backend
+from .compat import normalize_axis_tuple
 from .numeric import copy
 from .src._backprojection import backprojection3d
 from .src._fast_backprojection import backprojection3d as fast_backprojection3d
@@ -208,7 +209,7 @@ def normalize_axes(x: np.ndarray, axes):
             raise ValueError('For arrays of higher dimensionality the `axis` arguments is required')
         axes = [0, 1]
 
-    axes = np.core.numeric.normalize_axis_tuple(axes, x.ndim, 'axes')
+    axes = normalize_axis_tuple(axes, x.ndim, 'axes')
     x = np.moveaxis(x, axes, (-2, -1))
     extra = x.shape[:-2]
     x = x.reshape(-1, *x.shape[-2:])

imops/src/_backprojection.pyx

@@ -19,7 +19,7 @@ ctypedef np.uint8_t uint8
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cdef inline FLOAT interpolate(FLOAT x, FLOAT* ys, FLOAT radius, FLOAT right_limit) nogil:
+cdef inline FLOAT interpolate(FLOAT x, const FLOAT* ys, FLOAT radius, FLOAT right_limit) noexcept nogil:
     cdef Py_ssize_t idx
     cdef FLOAT val, value
 
@@ -40,8 +40,8 @@ cdef inline FLOAT interpolate(FLOAT x, FLOAT* ys, FLOAT radius, FLOAT right_limi
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cdef FLOAT accumulate(FLOAT x, FLOAT y, FLOAT* sinuses, FLOAT* cosinuses, FLOAT* ys,
-                      Py_ssize_t size, Py_ssize_t image_size, FLOAT radius, FLOAT right_limit) nogil:
+cdef FLOAT accumulate(FLOAT x, FLOAT y, const FLOAT* sinuses, const FLOAT* cosinuses, const FLOAT* ys,
+                      Py_ssize_t size, Py_ssize_t image_size, FLOAT radius, FLOAT right_limit) noexcept nogil:
     cdef FLOAT accumulator = 0
     cdef Py_ssize_t k
 
@@ -52,9 +52,9 @@ cdef FLOAT accumulate(FLOAT x, FLOAT y, FLOAT* sinuses, FLOAT* cosinuses, FLOAT*
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
-cpdef FLOAT[:, :, :] backprojection3d(FLOAT[:, :, :] sinogram, FLOAT[:] theta, FLOAT[:] xs,
-                                      uint8[:, :] inside_circle, FLOAT fill_value, int image_size, int output_size,
-                                      Py_ssize_t num_threads):
+cpdef FLOAT[:, :, :] backprojection3d(const FLOAT[:, :, :] sinogram, const FLOAT[:] theta, const FLOAT[:] xs,
+                                      const uint8[:, :] inside_circle, FLOAT fill_value, int image_size,
+                                      int output_size, Py_ssize_t num_threads):
     cdef FLOAT[:, :, :] result = np.zeros_like(sinogram, shape=(len(sinogram), output_size, output_size))
     cdef Py_ssize_t slc, i, j, n_angles = len(theta), n_slices = len(sinogram)
     cdef FLOAT min_val = image_size // 2, right_lim = image_size - 1

imops/src/_measure.pyx

@@ -7,11 +7,14 @@
 
 import numpy as np
 
+cimport cython
 cimport numpy as np
 
 from cython.parallel import prange
 
 
+ctypedef cython.floating FLOAT
+
 ctypedef fused LABEL:
     signed char
     short
@@ -23,7 +26,7 @@ ctypedef fused LABEL:
     unsigned long long
 
 
-cdef inline Py_ssize_t _find(LABEL num, LABEL[:] nums) nogil:
+cdef inline Py_ssize_t _find(LABEL num, const LABEL[:] nums) noexcept nogil:
     cdef Py_ssize_t i
 
     for i in range(len(nums)):
@@ -33,15 +36,16 @@ cdef inline Py_ssize_t _find(LABEL num, LABEL[:] nums) nogil:
     return -1
 
 
-def _labeled_center_of_mass(double[:, :, :] nums, LABEL[:, :, :] labels, LABEL[:] index) -> np.ndarray:
-    cdef double[:, :, ::1] contiguous_nums = np.ascontiguousarray(nums)
-    cdef LABEL[:, :, ::1] contiguous_labels = np.ascontiguousarray(labels)
-    cdef LABEL[:] contiguous_index = np.ascontiguousarray(index)
+def _labeled_center_of_mass(const FLOAT[:, :, :] nums, const LABEL[:, :, :] labels,
+                            const LABEL[:] index) -> np.ndarray:
+    cdef const FLOAT[:, :, ::1] contiguous_nums = np.ascontiguousarray(nums)
+    cdef const LABEL[:, :, ::1] contiguous_labels = np.ascontiguousarray(labels)
+    cdef const LABEL[:] contiguous_index = np.ascontiguousarray(index)
 
     cdef Py_ssize_t index_len = len(index)
 
-    cdef double[:, ::1] output = np.zeros((index_len, 3))
-    cdef double[:] normalizers = np.zeros(index_len)
+    cdef FLOAT[:, ::1] output = np.zeros_like(nums, shape=(index_len, 3))
+    cdef FLOAT[:] normalizers = np.zeros_like(nums, shape=(index_len,))
 
     cdef Py_ssize_t rows = nums.shape[0], cols = nums.shape[1], dims = nums.shape[2]
     cdef Py_ssize_t i, j, k, pos
@@ -66,11 +70,11 @@ def _labeled_center_of_mass(double[:, :, :] nums, LABEL[:, :, :] labels, LABEL[:
     return np.asarray(output)
 
 
-def _center_of_mass(double[:, :, :] nums, Py_ssize_t num_threads) -> np.ndarray:
-    cdef double[:, :, ::1] contiguous_nums = np.ascontiguousarray(nums)
+def _center_of_mass(const FLOAT[:, :, :] nums, Py_ssize_t num_threads) -> np.ndarray:
+    cdef const FLOAT[:, :, ::1] contiguous_nums = np.ascontiguousarray(nums)
 
-    cdef double output_x = 0, output_y = 0, output_z = 0
-    cdef double normalizer = 0
+    cdef FLOAT output_x = 0, output_y = 0, output_z = 0
+    cdef FLOAT normalizer = 0
 
     cdef Py_ssize_t rows = nums.shape[0], cols = nums.shape[1], dims = nums.shape[2]
     cdef Py_ssize_t i, j, k