Merge pull request #46 from neuro-ml/dev

Dev

.flake8

@@ -4,7 +4,8 @@
 # F401: unused imports in __init__.py-s
 # I251: allow absolute imports in upper files
 # B028: !r is not supported for python<3.8
-ignore = W503,E203,B028
+# W604: backticks in str-s are ok
+ignore = W503,E203,B028,W604
 per-file-ignores =
     __init__.py:F401
     tests/*:I251

.github/workflows/docs.yml

@@ -11,10 +11,10 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: fregante/setup-git-user@v1
+      - uses: actions/checkout@v4
+      - uses: fregante/setup-git-user@v2
       - run: git fetch origin gh-pages --depth=1
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
       - name: Install

.github/workflows/release.yml

@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
@@ -41,10 +41,10 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.10.0
+        run: python -m pip install cibuildwheel==2.17.0
       - name: Install gcc for mac
         if: matrix.os == 'macOS-11'
         run: |
@@ -78,7 +78,7 @@ 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-*
+          CIBW_BUILD: cp36-* 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:
@@ -88,11 +88,13 @@ jobs:
     needs: [ check_version ]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
       - name: Build
-        run: python setup.py sdist
+        run: |
+          pip install build
+          python -m build --sdist
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.tar.gz

.github/workflows/test_build.yml

@@ -15,10 +15,12 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.9' 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.10.0
+        run: python -m pip install cibuildwheel==2.17.0
       - name: Install gcc for mac
         if: matrix.os == 'macOS-11'
         run: |
@@ -52,6 +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-*
+          CIBW_BUILD: cp39-* cp36-* 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

@@ -10,12 +10,12 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+        python-version: [ '3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -28,7 +28,8 @@ jobs:
           if [ "$GITHUB_BASE_REF" = "master" ] && [ "$MATCH" != "" ]; then exit 1; fi
       - name: Build the package
         run: |
-          python setup.py sdist
+          pip install build
+          python -m build --sdist
 
       - name: Install
         run: |
@@ -73,7 +74,9 @@ jobs:
         if: ${{ always() }}
 
       - name: Upload coverage results
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           fail_ci_if_error: true
           files: reports/coverage-${{ matrix.python-version }}.xml

README.md

@@ -53,7 +53,7 @@ y = zoom(x, 2, axis=[0, 1])
 # without the need to compute the scale factor
 z = zoom_to_shape(x, (4, 120, 67))
 ```
-Works faster only for `ndim<=4, dtype=float32 or float64 (and bool-int16-32-64 if order == 0), output=None, order=0 or 1, mode='constant', grid_mode=False`
+Works faster only for `ndim<=4, dtype=float32 or float64 (and bool-int16-32-64-uint8-16-32 if order == 0), output=None, order=0 or 1, mode='constant', grid_mode=False`
 ### Fast 1d linear interpolation
 
 ```python

imops/__version__.py

@@ -1 +1 @@
-__version__ = '0.8.6'
+__version__ = '0.8.7'

imops/crop.py

@@ -3,7 +3,7 @@
 from .backend import BackendLike
 from .numeric import _NUMERIC_DEFAULT_NUM_THREADS
 from .pad import pad
-from .utils import AxesLike, AxesParams, broadcast_axis, fill_by_indices
+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:
@@ -35,6 +35,9 @@ def crop_to_shape(x: np.ndarray, shape: AxesLike, axis: AxesLike = None, ratio:
     >>> cropped = crop_to_shape(x, [3, 4, 5])  # fail due to bigger resulting shape
     """
     x = np.asarray(x)
+    shape = np.asarray(shape)
+    assert_subdtype(shape.dtype, np.integer, 'shape')
+
     axis, shape, ratio = broadcast_axis(axis, x.ndim, shape, ratio)
 
     old_shape, new_shape = np.array(x.shape), np.array(fill_by_indices(x.shape, shape, axis))
@@ -89,6 +92,9 @@ def crop_to_box(
     >>> cropped = crop_to_box(x, np.array([[0], [5]]), axis=0, padding_values=0)  # pad with 0-s to shape [5, 3, 4]
     """
     x = np.asarray(x)
+    box = np.asarray(box)
+    assert_subdtype(box.dtype, np.integer, 'box')
+
     start, stop = box
     axis, start, stop = broadcast_axis(axis, x.ndim, start, stop)
 

imops/morphology.py

@@ -80,13 +80,13 @@ def wrapped(
             raise ValueError('Input image and footprint number of dimensions must be the same.')
 
         if not image.any():
-            warn(f'{op_name} is applied to the fully False mask (mask.any() == False).', stacklevel=3)
+            warn(f'{op_name} is applied to the fully False mask (mask.any() == False).', stacklevel=3)  # noqa
             output.fill(False)
 
             return output
 
         if image.all():
-            warn(f'{op_name} is applied to the fully True mask (mask.all() == True).', stacklevel=3)
+            warn(f'{op_name} is applied to the fully True mask (mask.all() == True).', stacklevel=3)  # noqa
             output.fill(True)
 
             return output

imops/src/_zoom.pyx

@@ -18,6 +18,8 @@ from libc.math cimport floor, sqrt
 ctypedef cython.floating FLOAT
 ctypedef fused NUM:
     np.uint8_t
+    np.uint16_t
+    np.uint32_t
     short
     int
     long long

imops/utils.py

@@ -196,3 +196,8 @@ def check_len(*args) -> None:
     lengths = list(map(len, args))
     if any(length != lengths[0] for length in lengths):
         raise ValueError(f'Arguments of equal length are required: {", ".join(map(str, lengths))}')
+
+
+def assert_subdtype(dtype, ref_dtype, name):
+    if not np.issubdtype(dtype, ref_dtype):
+        raise ValueError(f'`{name}` must be of {ref_dtype.__name__} dtype, got {dtype}')

imops/zoom.py

@@ -81,7 +81,7 @@ def zoom(
     """
     Rescale `x` according to `scale_factor` along the `axis`.
 
-    Uses a fast parallelizable implementation for fp32 / fp64 (and bool-int16-32-64 if order == 0) inputs,
+    Uses a fast parallelizable implementation for fp32-fp64 and bool-int16-32-64-uint8-16-32 if order == 0 inputs,
     ndim <= 4 and order = 0 or 1.
 
     Parameters
@@ -136,7 +136,7 @@ def zoom_to_shape(
     """
     Rescale `x` to match `shape` along the `axis`.
 
-    Uses a fast parallelizable implementation for fp32 / fp64 (and bool-int16-32-64 if order == 0) inputs,
+    Uses a fast parallelizable implementation for fp32-fp64 and bool-int16-32-64-uint8-16-32 if order == 0 inputs,
     ndim <= 4 and order = 0 or 1.
 
     Parameters
@@ -198,7 +198,7 @@ def _zoom(
     backend: BackendLike = None,
 ) -> np.ndarray:
     """
-    Faster parallelizable version of `scipy.ndimage.zoom` for fp32 / fp64 (and bool-int16-32-64 if order == 0) inputs.
+    Faster parallelizable version of `scipy.ndimage.zoom` for fp32-fp64 and bool-int16-32-64-uint8-16-32 if order == 0
 
     Works faster only for ndim <= 4. Shares interface with `scipy.ndimage.zoom`
     except for
@@ -228,16 +228,17 @@ def _zoom(
         or (
             dtype not in (np.float32, np.float64)
             if order == 1
-            else dtype not in (bool, np.float32, np.float64, np.int16, np.int32, np.int64)
+            else dtype
+            not in (bool, np.float32, np.float64, np.int16, np.int32, np.int64, np.uint8, np.uint16, np.uint32)
         )
         or ndim > 4
         or output is not None
         or mode != 'constant'
         or grid_mode
     ):
         warn(
-            'Fast zoom is only supported for ndim<=4, dtype=fp32 or fp64 (and bool-int16-32-64 if order == 0), '
-            "output=None, order=0 or 1, mode='constant', grid_mode=False. Falling back to scipy's implementation.",
+            'Fast zoom is only supported for ndim<=4, dtype=fp32-fp64 and bool-int16-32-64-uint8-16-32 if order == 0, '
+            "output=None, order=0 or 1 , mode='constant', grid_mode=False. Falling back to scipy's implementation.",
             stacklevel=3,
         )
         return scipy_zoom(

pyproject.toml

@@ -25,6 +25,7 @@ classifiers = [
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
 ]
 
 [options]

setup.py

@@ -15,6 +15,7 @@
     'Programming Language :: Python :: 3.9',
     'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
 ]
 
 with open(root / 'requirements.txt', encoding='utf-8') as file:

tests/test_crop.py

@@ -52,7 +52,21 @@ def test_raises():
 @seeded_by(SEED)
 def test_crop_to_shape():
     x = np.random.rand(3, 10, 10)
-    shape = 3, 4, 8
+    shape = (3, 4, 8)
     assert crop_to_shape(x, shape).shape == shape
     with pytest.raises(ValueError):
         crop_to_shape(x, (3, 15, 10))
+
+
+def test_crop_to_float_shape():
+    x = np.random.rand(3, 10, 10)
+    float_shape = (1.337, 3.1415, 2.7182)
+    with pytest.raises(ValueError):
+        crop_to_shape(x, float_shape)
+
+
+def test_crop_to_float_box():
+    x = np.random.rand(3, 10, 10)
+    float_box = [[0, 1], [4, 4.5], [3.1, 9]]
+    with pytest.raises(ValueError):
+        crop_to_box(x, float_box)

tests/test_pad.py

@@ -140,6 +140,9 @@ def test_restore_crop_invalid_box():
     with pytest.raises(ValueError):
         restore_crop(x, np.array([[0, 0, 0], [1, 1, 1]]), [4, 4, 4])
 
+    with pytest.raises(ValueError):
+        restore_crop(x, np.array([[0.5, 0.5, 0.5], [1.5, 1.5, 1.5]]), [4.5, 4.5, 4.5])
+
 
 def test_pad_to_divisible():
     x = np.zeros((4, 8, 12))

tests/test_zoom.py

@@ -39,7 +39,7 @@ def order(request):
     return request.param
 
 
-@pytest.fixture(params=[np.float32, np.float64, bool, np.int16, np.int32, np.int64])
+@pytest.fixture(params=[np.float32, np.float64, bool, np.int16, np.int32, np.int64, np.uint8, np.uint16, np.uint32])
 def dtype(request):
     return request.param