imops 0.8.2__cp39-cp39-musllinux_1_1_i686.whl → 0.8.3__cp39-cp39-musllinux_1_1_i686.whl

imops/utils.py

@@ -1,39 +1,92 @@
 import os
+from contextlib import contextmanager
 from itertools import permutations
 from typing import Callable, Optional, Sequence, Tuple, Union
 from warnings import warn
 
 import numpy as np
 
-from .backend import BACKEND2NUM_THREADS_VAR_NAME, SINGLE_THREADED_BACKENDS, Backend
+from .backend import BACKEND_NAME2ENV_NUM_THREADS_VAR_NAME, SINGLE_THREADED_BACKENDS, Backend
 
 
 AxesLike = Union[int, Sequence[int]]
 AxesParams = Union[float, Sequence[float]]
 
 ZOOM_SRC_DIM = 4
+# TODO: define imops-specific environment variable like `OMP_NUM_THREADS`?
+IMOPS_NUM_THREADS = None
 
 
-def normalize_num_threads(num_threads: int, backend: Backend):
+def set_num_threads(num_threads: int) -> int:
+    assert isinstance(num_threads, int) or num_threads is None, 'Number of threads must be int value or None.'
+    global IMOPS_NUM_THREADS
+    current = IMOPS_NUM_THREADS
+    IMOPS_NUM_THREADS = num_threads
+    return current
+
+
+@contextmanager
+def imops_num_threads(num_threads: int):
+    previous = set_num_threads(num_threads)
+    try:
+        yield
+    finally:
+        set_num_threads(previous)
+
+
+def normalize_num_threads(num_threads: int, backend: Backend, warn_stacklevel: int = 1) -> int:
+    """Calculate the effective number of threads"""
+
+    global IMOPS_NUM_THREADS
     if backend.name in SINGLE_THREADED_BACKENDS:
         if num_threads != -1:
-            warn(f'"{backend.name}" backend is single-threaded. Setting `num_threads` has no effect.')
+            warn(
+                f'"{backend.name}" backend is single-threaded. Setting `num_threads` has no effect.',
+                stacklevel=warn_stacklevel,
+            )
         return 1
+
+    env_num_threads_var_name = BACKEND_NAME2ENV_NUM_THREADS_VAR_NAME[backend.name]
+    # here we also handle the case `env_num_threads_var_name`=" " gracefully
+    env_num_threads = os.environ.get(env_num_threads_var_name, '').strip()
+    env_num_threads = int(env_num_threads) if env_num_threads else None
+    # TODO: maybe let user set the absolute maximum number of threads?
+    num_available_cpus = len(os.sched_getaffinity(0))
+
+    max_num_threads = min(filter(bool, [IMOPS_NUM_THREADS, env_num_threads, num_available_cpus]))
+
     if num_threads >= 0:
         # FIXME
         if backend.name == 'Numba':
             warn(
                 'Setting `num_threads` has no effect with "Numba" backend. '
-                'Use `NUMBA_NUM_THREADS` environment variable.'
+                'Use `NUMBA_NUM_THREADS` environment variable.',
+                stacklevel=warn_stacklevel,
             )
-        return num_threads
-
-    num_threads_var_name = BACKEND2NUM_THREADS_VAR_NAME[backend.name]
-    # here we also handle the case `num_threads_var`=" " gracefully
-    env_num_threads = os.environ.get(num_threads_var_name, '').strip()
-    max_threads = int(env_num_threads) if env_num_threads else len(os.sched_getaffinity(0))
-
-    return max_threads + num_threads + 1
+            return num_threads
+
+        if num_threads > max_num_threads:
+            if max_num_threads == IMOPS_NUM_THREADS:
+                warn(
+                    f'Required number of threads ({num_threads}) is greater than `IMOPS_NUM_THREADS` '
+                    f'({IMOPS_NUM_THREADS}). Using {IMOPS_NUM_THREADS} threads.',
+                    stacklevel=warn_stacklevel,
+                )
+            elif max_num_threads == env_num_threads:
+                warn(
+                    f'Required number of threads ({num_threads}) is greater than `{env_num_threads_var_name}` '
+                    f'({env_num_threads}). Using {env_num_threads} threads.',
+                    stacklevel=warn_stacklevel,
+                )
+            else:
+                warn(
+                    f'Required number of threads ({num_threads}) is greater than number of available CPU-s '
+                    f'({num_available_cpus}). Using {num_available_cpus} threads.',
+                    stacklevel=warn_stacklevel,
+                )
+        return min(num_threads, max_num_threads)
+
+    return max_num_threads + num_threads + 1
 
 
 def get_c_contiguous_permutaion(array: np.ndarray) -> Optional[np.ndarray]:

imops/zoom.py

@@ -208,7 +208,7 @@ def _zoom(
 
     See `https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.zoom.html`
     """
-    backend = resolve_backend(backend)
+    backend = resolve_backend(backend, warn_stacklevel=4)
     if backend.name not in ('Scipy', 'Numba', 'Cython'):
         raise ValueError(f'Unsupported backend "{backend.name}".')
 
@@ -216,7 +216,7 @@ def _zoom(
     dtype = input.dtype
     cval = np.dtype(dtype).type(cval)
     zoom = fill_by_indices(np.ones(input.ndim, 'float64'), zoom, range(input.ndim))
-    num_threads = normalize_num_threads(num_threads, backend)
+    num_threads = normalize_num_threads(num_threads, backend, warn_stacklevel=4)
 
     if backend.name == 'Scipy':
         return scipy_zoom(

{imops-0.8.2.dist-info → imops-0.8.3.dist-info}/METADATA

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: imops
-Version: 0.8.2
+Version: 0.8.3
 Summary: Efficient parallelizable algorithms for multidimensional arrays to speed up your data pipelines
 Home-page: https://github.com/neuro-ml/imops
-Download-URL: https://github.com/neuro-ml/imops/archive/v0.8.2.tar.gz
+Download-URL: https://github.com/neuro-ml/imops/archive/v0.8.3.tar.gz
 Author: maxme1, vovaf709, talgat
 Author-email: maxme1 <maxs987@gmail.com>, vovaf709 <vovaf709@yandex.ru>, talgat <saparov2130@gmail.com>
 License: MIT License
@@ -45,6 +45,7 @@ Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: scipy <2.0.0,>=1.0
+Requires-Dist: scikit-image
 Requires-Dist: connected-components-3d
 Requires-Dist: fastremap
 Requires-Dist: dataclasses ; python_version < "3.7"

imops-0.8.3.dist-info/RECORD

@@ -0,0 +1,61 @@
+_build_utils.py,sha256=kAKNl7QL-PNT8k4py6PtQY5k_1SK3BU_tkphRehyKA4,3175
+imops-0.8.3.dist-info/METADATA,sha256=_HIocNc4bo0fcnhbDoCuvuEJyWeZrykHBvYA_gDLOk4,8849
+imops-0.8.3.dist-info/LICENSE,sha256=s4td51soCfOr_HP5fF2gTARksncu_DD1TgugcUGTBQ0,1064
+imops-0.8.3.dist-info/WHEEL,sha256=v-8vN2Z1wRfhJEi3opfRVfxTNuxBOvco3uYBajkO8Zw,109
+imops-0.8.3.dist-info/RECORD,,
+imops-0.8.3.dist-info/top_level.txt,sha256=jd2uO-zsYvKeqkZbjEjtkGqCca0IEXEiEuoyr3nsHB0,19
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+imops/morphology.py,sha256=rIzE7HXyBE91NWMR9rR1di4s0QccRnPMxivA3PnlM1M,12376
+imops/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+imops/backend.py,sha256=9kJtdd4-66SOP7MEXF-o9-aFImLtvpaqTKe1ttNb0hk,2503
+imops/__version__.py,sha256=LokQdkRCwhhLh0zOp7jizhyDgbtAU-IWRIObrz2zLjA,22
+imops/radon.py,sha256=bygHhDe_SD7sjubcGBsXtTa3z4-z1JiOXpkIRSt8xpw,8968
+imops/crop.py,sha256=PSOOlJUb_R8Hj3P18aRicwFXil19Q6a1QrwLmZZfZkQ,3945
+imops/utils.py,sha256=X6dYRExW4nnpgO1z5-DcHhmReIvzaOBdBNKd5TeUbjg,6684
+imops/measure.py,sha256=ehJ1F4DJK6FTS0XsuKzzxQnFX78Fo4eShinYYrbItu8,8433
+imops/pad.py,sha256=AjgLCQVgGOwVNxYY7xMMyX7YO82uObxEroApuQxZE34,9069
+imops/_configs.py,sha256=PoPlwnmmCz-Z8GmKYIqR8xsqcWHPKiYSGWldbQX9GU0,705
+imops/zoom.py,sha256=cHKuXrKY5GmBDLMat1_ElIBuZGd8Mk5MXHtVD5WtEQk,9664
+imops/__init__.py,sha256=FUVB4d2PQlM4PJUSIjyz9oRlWaqU6RSskyyrX56-RrY,504
+imops/numeric.py,sha256=OUu-aXg2ZsULvBxwxFd3pbeFzIhlTlt5fO2Koje7wPo,13274
+imops/box.py,sha256=3WrOdpUigoGKNnWhLLgX5NX_D9WzgwDKIWf75baTK-Y,1794
+imops/interp1d.py,sha256=FUVvEIldoIf4_-RbRcZHrbNZ6UoW9cpRfW4flWCxdyI,8195
+imops/testing.py,sha256=JgUWoD7fzshdaVrrgmf9y9jpl3EHgmoYYmHHGCFI4Ws,1650
+imops/src/_numeric.pyx,sha256=05GbyyFzdill8M_L9KYA9hfYP7ULiAnvMpWyBATl7vQ,7979
+imops/src/_radon.pyx,sha256=ztXVnOfUjsRY5R22-7LbodG_FAbUoBemTnaIDZsPeI4,2896
+imops/src/_fast_backprojection.c,sha256=j9QpYhes4hotdrf2Fypt6dY2OMldgUUokVbSktiQb7Q,1035216
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+imops/src/_fast_numeric.cpython-39-i386-linux-gnu.so,sha256=qaLAsgVWh_RPdrg-KzuMOT_KsqrIEed0KtTfSmniats,2905728
+imops/src/_fast_radon.pyx,sha256=ztXVnOfUjsRY5R22-7LbodG_FAbUoBemTnaIDZsPeI4,2896
+imops/src/_fast_zoom.cpython-39-i386-linux-gnu.so,sha256=sMNc7dWBvudS7zwr0JHwDlOV-XEm8bns572vXHHyKzU,2943564
+imops/src/_zoom.c,sha256=yAbBBqLFgRvb-5kCehNdQbjpgPn5UIgwPn9pVr1PcY8,2124853
+imops/src/_fast_measure.pyx,sha256=pKFBt8ITxy1QsO5wFkRrhdYMfT2ENCA7yPZ-ZJRCh44,2650
+imops/src/_fast_morphology.pyx,sha256=X96ad1iadGPelOipNjXNd9s77x95LCVFBTAs0gr4iXE,9209
+imops/src/_numeric.cpython-39-i386-linux-gnu.so,sha256=Qj-yRfnWI7H7N4w1wsOzntU7980TXpBRM0d2IXBDBP8,2901620
+imops/src/_fast_radon.c,sha256=6l7vPKYgPdcvUxZr6kO3sWwvTHYNQfpX0rouiLiHxmA,1189207
+imops/src/_morphology.pyx,sha256=X96ad1iadGPelOipNjXNd9s77x95LCVFBTAs0gr4iXE,9209
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+imops/src/_radon.c,sha256=d7yPZPwHhL4m1p71yyC0XCv-_y4_0rXLp5mHtdtn8lo,1177318
+imops/src/_fast_morphology.c,sha256=PumLSSj2JY9OFBUIYaY9TL7ngpIpAHj9PJm5fqrosxA,970737
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+imops/src/_fast_numeric.c,sha256=zqF1r0ElLWNDhBOw6i_1Ba3OJUSTeN-gCQ3UDXETqG0,2106273
+imops/src/_fast_zoom.c,sha256=NvOfZAi9WnR35Xo2KEw9LxP-vMdR7dtyH5VCmoaKEhg,2144201
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+imops/src/_measure.pyx,sha256=pKFBt8ITxy1QsO5wFkRrhdYMfT2ENCA7yPZ-ZJRCh44,2650
+imops/src/_numeric.c,sha256=pZIN7HdJm-fTLk7CL4BEiOO-qvFT6jebNdiYCk2jrDU,2090063
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+imops/src/_backprojection.pyx,sha256=RMB_GS2mbOS8mQWeo640p9FdeHHFjmjW3qrlEGGoL0s,2645
+imops/src/_fast_numeric.pyx,sha256=05GbyyFzdill8M_L9KYA9hfYP7ULiAnvMpWyBATl7vQ,7979
+imops/src/_morphology.c,sha256=N2TyGuWEKCrxMttf1mz3GidHnzyUZxU4M6AWGb0hrCo,959244
+imops/src/_backprojection.cpython-39-i386-linux-gnu.so,sha256=p7ntY89INTCI0vmjdSlUSXZe9mPrXgMpCF1Vd3K7Cx0,1264212
+imops/src/_fast_measure.c,sha256=ZAjXPsjaMTjkD2_RKX-LBkBYSJBdFwi5To8PCkyzV-4,1335494
+imops/src/_measure.c,sha256=hMojG43NjBtHFDRMjkMY537lDIv9dX20NZDNE7t_GTY,1323252
+imops/src/_fast_morphology.cpython-39-i386-linux-gnu.so,sha256=8F52XMvxLMbHuJXtaEt2Vz90kjWJwJEJ22OBDg9pCP4,1079312
+imops/src/_fast_zoom.pyx,sha256=_7cPgowHRuFuc7WFuqSnbr_gVzsQi2Bu1nhwoi_yDmw,22566
+imops/src/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+imops/src/_measure.cpython-39-i386-linux-gnu.so,sha256=GP6FUPodHVwrbFnzeNj5kdxKMOW5j59s7MiszJI6p9I,1702620
+imops/src/_zoom.cpython-39-i386-linux-gnu.so,sha256=MdVg-XtsXOWKSRqSUGmeB9wqP9qtLT89DlpB6hIeQMA,2943552
+imops/src/_morphology.cpython-39-i386-linux-gnu.so,sha256=ymwqob7dwCAZxZ8Oyt-QY2OtgMRSxjGWNR4fSoy3HqA,1079304
+imops/src/_backprojection.c,sha256=XADOHzBEuXVXw4PLSuYtzZZmh0ZtfQZGfzTDYjgJ3_M,1024265
+imops/src/_fast_backprojection.pyx,sha256=RMB_GS2mbOS8mQWeo640p9FdeHHFjmjW3qrlEGGoL0s,2645
+imops/src/_zoom.pyx,sha256=_7cPgowHRuFuc7WFuqSnbr_gVzsQi2Bu1nhwoi_yDmw,22566

{imops-0.8.2.dist-info → imops-0.8.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.1)
+Generator: bdist_wheel (0.41.2)
 Root-Is-Purelib: false
 Tag: cp39-cp39-musllinux_1_1_i686
 

imops-0.8.3.dist-info/top_level.txt

@@ -0,0 +1,2 @@
+_build_utils
+imops

_pyproject_build.py

@@ -1,61 +0,0 @@
-import shutil
-from pathlib import Path
-
-from setuptools import Extension
-from setuptools.command.build_py import build_py
-
-
-class NumpyImport(dict):
-    """Hacky way to return Numpy's include path with lazy import."""
-
-    # Must be json-serializable due to
-    # https://github.com/cython/cython/blob/6ad6ca0e9e7d030354b7fe7d7b56c3f6e6a4bc23/Cython/Compiler/ModuleNode.py#L773
-    def __init__(self):
-        return super().__init__(self, description=self.__doc__)
-
-    # Must be hashable due to
-    # https://github.com/cython/cython/blob/6ad6ca0e9e7d030354b7fe7d7b56c3f6e6a4bc23/Cython/Compiler/Main.py#L307
-    def __hash__(self):
-        return id(self)
-
-    def __repr__(self):
-        import numpy as np
-
-        return np.get_include()
-
-    __fspath__ = __repr__
-
-
-class PyprojectBuild(build_py):
-    def run(self):
-        self.run_command('build_ext')
-        return super().run()
-
-    def initialize_options(self):
-        super().initialize_options()
-
-        name = 'imops'
-        args = ['-fopenmp']
-
-        if self.distribution.ext_modules is None:
-            self.distribution.ext_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
-        modules = ['backprojection', 'measure', 'morphology', 'numeric', 'radon', 'zoom']
-        for module in modules:
-            src_dir = Path(__file__).parent / name / 'src'
-            shutil.copyfile(src_dir / f'_{module}.pyx', src_dir / f'_fast_{module}.pyx')
-
-        for module in modules:
-            for prefix, additional_args in zip(['', 'fast_'], [[], ['-ffast-math']]):
-                self.distribution.ext_modules.append(
-                    Extension(
-                        f'{name}.src._{prefix}{module}',
-                        [f'{name}/src/_{prefix}{module}.pyx'],
-                        include_dirs=[NumpyImport()],
-                        extra_compile_args=args + additional_args,
-                        extra_link_args=args + additional_args,
-                        define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
-                    )
-                )

imops/_numeric.py

@@ -1,124 +0,0 @@
-from warnings import warn
-
-import numpy as np
-
-from .backend import BackendLike, resolve_backend
-from .src._fast_numeric import (
-    _parallel_pointwise_mul as cython_fast_parallel_pointwise_mul,
-    _parallel_sum as cython_fast_parallel_sum,
-)
-from .src._numeric import _parallel_pointwise_mul as cython_parallel_pointwise_mul, _parallel_sum as cython_parallel_sum
-from .utils import normalize_num_threads
-
-
-def _sum(nums: np.ndarray, num_threads: int = -1, backend: BackendLike = None) -> float:
-    """
-    Parallel sum of flat numpy array
-
-    Parameters
-    ----------
-    nums: np.ndarray
-        1-dimensional array
-    num_threads: int
-        the number of threads to use for computation. Default = the cpu count. If negative value passed
-        cpu count + num_threads + 1 threads will be used
-    backend: BackendLike
-        which backend to use. `cython` and `scipy` (primarly for benchmarking) are available,
-        `cython` is used by default
-
-    Returns
-    -------
-    sum: float
-
-    Examples
-    --------
-    >>> s = _sum(x, num_threads=1)
-    >>> s = _sum(x, num_threads=8, backend=Cython(fast=True))  # ffast-math compiled version
-    """
-    ndim = nums.ndim
-
-    if ndim != 1:
-        raise ValueError(f'Input must be 1-dimensional instead of {ndim}-dimensional.')
-
-    backend = resolve_backend(backend)
-    if backend.name not in ('Cython', 'Scipy'):
-        raise ValueError(f'Unsupported backend "{backend.name}"')
-
-    num_threads = normalize_num_threads(num_threads, backend)
-
-    if backend.name == 'Scipy':
-        return nums.sum()
-
-    if backend.name == 'Cython':
-        src_parallel_sum = cython_fast_parallel_sum if backend.fast else cython_parallel_sum
-
-    return src_parallel_sum(nums, num_threads)
-
-
-def _mul(nums1: np.ndarray, nums2: np.ndarray, num_threads: int = -1, backend: BackendLike = None) -> np.ndarray:
-    """
-    Parallel pointwise multiplication of 2 numpy arrays (aka x * y). Works faster only for ndim <= 3.
-
-    Parameters
-    ----------
-    nums1: np.ndarray
-    nums2: np.ndarray
-    num_threads: int
-        the number of threads to use for computation. Default = the cpu count. If negative value passed
-        cpu count + num_threads + 1 threads will be used
-    backend: BackendLike
-        which backend to use. `cython` and `scipy` (primarly for benchmarking) are available,
-        `cython` is used by default
-
-    Returns
-    -------
-    multiplied: np.ndarray
-        result of nums1 * nums2
-
-    Examples
-    --------
-    >>> mul = _mul(nums1, nums2, num_threads=8)
-    >>> mul = _mul(np.ones((2, 3)), np.ones((1, 3)))  # broadcasting, mul.shape == (2, 3)
-    >>> mul = _mul(nums1, nums2, backend=Cython(fast=True))  # ffast-math compiled version
-    """
-    if not nums1.size and not nums2.size:
-        return np.array([], dtype=nums1.dtype)
-    if bool(nums1.size) ^ bool(nums2.size):
-        raise ValueError('One of the arrays is empty, hence pointwise multiplication cannot be performed.')
-    if len(nums1.shape) != len(nums2.shape):
-        raise ValueError('Both arrays must have the same number of dimensions for pointwise multiplication.')
-    for dim1, dim2 in zip(nums1.shape, nums2.shape):
-        if dim1 != dim2 and dim1 != 1 and dim2 != 1:
-            raise ValueError(f'Arrays of shapes {nums1.shape} and {nums2.shape} are not broadcastable.')
-
-    if nums1.ndim > 3:
-        warn('Parallel pointwise multiplication is only supported for ndim<=3. Falling back to naive x * y.')
-
-        return nums1 * nums2
-
-    backend = resolve_backend(backend)
-    if backend.name not in ('Cython', 'Scipy'):
-        raise ValueError(f'Unsupported backend "{backend.name}"')
-
-    num_threads = normalize_num_threads(num_threads, backend)
-
-    if backend.name == 'Scipy':
-        return nums1 * nums2
-
-    if backend.name == 'Cython':
-        src_parallel_pointwise_mul = (
-            cython_fast_parallel_pointwise_mul if backend.fast else cython_parallel_pointwise_mul
-        )
-
-    n_dummy = 3 - nums1.ndim
-
-    if n_dummy:
-        nums1 = nums1[(None,) * n_dummy]
-        nums2 = nums2[(None,) * n_dummy]
-
-    out = src_parallel_pointwise_mul(nums1, nums2, np.maximum(nums1.shape, nums2.shape), num_threads)
-
-    if n_dummy:
-        out = out[(0,) * n_dummy]
-
-    return out

imops-0.8.2.dist-info/RECORD

@@ -1,61 +0,0 @@
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imops-0.8.2.dist-info/top_level.txt

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