cellprofiler-library-nightly 5.0.0.dev65__tar.gz

cellprofiler_library_nightly-5.0.0.dev65/LICENSE

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+The BSD 3-Clause License
+
+Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    1.  Redistributions of source code must retain the above copyright notice,
+        this list of conditions and the following disclaimer.
+
+    2.  Redistributions in binary form must reproduce the above copyright
+        notice, this list of conditions and the following disclaimer in the
+        documentation and/or other materials provided with the distribution.
+
+    3.  Neither the name of the Broad Institute, Inc. nor the names of its
+        contributors may be used to endorse or promote products derived from
+        this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED “AS IS.”  BROAD MAKES NO EXPRESS OR IMPLIED
+REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND
+COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION,
+NON-INFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT
+DISCOVERABLE. IN NO EVENT SHALL BROAD, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN
+FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE.
+
+If, by operation of law or otherwise, any of the aforementioned warranty
+disclaimers are determined inapplicable, your sole remedy, regardless of the
+form of action, including, but not limited to, negligence and strict
+liability, shall be replacement of the software with an updated version if one
+exists.
+
+Development of CellProfiler has been funded in whole or in part with federal
+funds from the National Institutes of Health, the National Science Foundation,
+and the Human Frontier Science Program.

cellprofiler_library_nightly-5.0.0.dev65/PKG-INFO

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+Metadata-Version: 2.1
+Name: cellprofiler-library-nightly
+Version: 5.0.0.dev65
+Summary: cellprofiler-lirary implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
+Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
+Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>
+Maintainer-email: Beth Cimini <bcimini@broadinstitute.org>, Nodar Gogoberidze <ngogober@broadinstitute.org>
+License: The BSD 3-Clause License
+        
+        Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+            1.  Redistributions of source code must retain the above copyright notice,
+                this list of conditions and the following disclaimer.
+        
+            2.  Redistributions in binary form must reproduce the above copyright
+                notice, this list of conditions and the following disclaimer in the
+                documentation and/or other materials provided with the distribution.
+        
+            3.  Neither the name of the Broad Institute, Inc. nor the names of its
+                contributors may be used to endorse or promote products derived from
+                this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED “AS IS.”  BROAD MAKES NO EXPRESS OR IMPLIED
+        REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND
+        COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION,
+        NON-INFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT
+        DISCOVERABLE. IN NO EVENT SHALL BROAD, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS
+        BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+        CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE
+        GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+        HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+        LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+        OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN
+        FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+        If, by operation of law or otherwise, any of the aforementioned warranty
+        disclaimers are determined inapplicable, your sole remedy, regardless of the
+        form of action, including, but not limited to, negligence and strict
+        liability, shall be replacement of the software with an updated version if one
+        exists.
+        
+        Development of CellProfiler has been funded in whole or in part with federal
+        funds from the National Institutes of Health, the National Science Foundation,
+        and the Human Frontier Science Program.
+        
+Project-URL: Homepage, https://cellprofiler.org/
+Project-URL: Documentation, https://cellprofiler.org/manuals
+Project-URL: Wiki, https://github.com/CellProfiler/CellProfiler/wiki
+Project-URL: Repository, https://github.com/CellProfiler/CellProfiler
+Project-URL: Issues, https://github.com/CellProfiler/CellProfiler/issues
+Project-URL: Changelog, https://github.com/CellProfiler/CellProfiler/releases
+Keywords: computer vision,image analysis,biology,cell,cellprofiler
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy~=1.24.4
+Requires-Dist: scikit-image~=0.20.0
+Requires-Dist: scipy<1.11,>=1.9.1
+Requires-Dist: mahotas~=1.4.13
+Requires-Dist: centrosome~=1.2.2
+Requires-Dist: matplotlib<4,>=3.1.3
+Requires-Dist: packaging>=20.0
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: pyinstaller; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest~=7.4.1; extra == "test"
+
+# library
+
+This subpackage contains the code to build the `cellprofiler-library` package. It contains the image processing modules required by the [CellProfiler](cellprofiler.org) software. Both the [core](../core/) subpackage, and the [frontend](../../frontend/) rely on this subpackage. This package can be used in isolation, separate from the `cellprofiler` and `cellprofiler-core` packages to access CellProfiler's image processing functionality as a Python package.
+
+It is currently a work under progress, and does not yet contain all or even most of CellProfiler's image processing capabilities.

cellprofiler_library_nightly-5.0.0.dev65/README.md

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+# library
+
+This subpackage contains the code to build the `cellprofiler-library` package. It contains the image processing modules required by the [CellProfiler](cellprofiler.org) software. Both the [core](../core/) subpackage, and the [frontend](../../frontend/) rely on this subpackage. This package can be used in isolation, separate from the `cellprofiler` and `cellprofiler-core` packages to access CellProfiler's image processing functionality as a Python package.
+
+It is currently a work under progress, and does not yet contain all or even most of CellProfiler's image processing capabilities.

cellprofiler_library_nightly-5.0.0.dev65/cellprofiler_library/_version.py

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+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '5.0.0.dev65'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev65')

cellprofiler_library_nightly-5.0.0.dev65/cellprofiler_library/functions/file_processing.py

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+import os
+
+import numpy
+import skimage
+
+def save_object_image_crops(
+    input_image,
+    input_objects,
+    save_dir,
+    file_format="tiff8",
+    nested_save=False,
+    save_names = {"input_filename": None, "input_objects_name": None},
+    volumetric=False
+    ):
+    """
+    For a given input_objects array, save crops for each 
+    object of the provided input_image.
+    """
+    # Build save paths
+    if nested_save:
+        if not save_names["input_filename"] and not save_names["input_objects_name"]:
+            raise ValueError("Must provide a save_names['input_filename'] or save_names['input_objects_name'] for nested save.")
+        save_path = os.path.join(
+            save_dir, 
+            save_names["input_filename"] if save_names["input_filename"] else save_names["input_objects_name"],
+            )
+    else:
+        save_path = save_dir
+
+    if not os.path.exists(save_path):
+        os.makedirs(save_path, exist_ok=True)
+
+    unique_labels = numpy.unique(input_objects)
+
+    if unique_labels[0] == 0:
+        unique_labels = unique_labels[1:]
+
+    labels = input_objects
+
+    if len(input_image.shape) == len(input_objects.shape) + 1 and not volumetric:
+        labels = numpy.repeat(
+            labels[:, :, numpy.newaxis], input_image.shape[-1], axis=2
+        )
+
+    # Construct filename
+    save_filename = f"{save_names['input_filename']+'_' if save_names['input_filename'] else ''}{save_names['input_objects_name']+'_' if save_names['input_objects_name'] else ''}"
+
+    save_filenames = []
+    
+    for label in unique_labels:
+        file_extension = "tiff" if "tiff" in file_format else "png"
+
+        label_save_filename = os.path.join(save_path, save_filename + f"{label}.{file_extension}")
+        save_filenames.append(label_save_filename)
+        mask_in = labels == label
+        properties = skimage.measure.regionprops(
+                mask_in.astype(int), intensity_image=input_image
+            )
+        mask = properties[0].intensity_image
+        
+        if file_format.casefold() == "png":
+                skimage.io.imsave(
+                    label_save_filename, 
+                    skimage.img_as_ubyte(mask), 
+                    check_contrast=False
+                )
+        elif file_format.casefold() == "tiff8":
+            skimage.io.imsave(
+                label_save_filename,
+                skimage.img_as_ubyte(mask),
+                compress=6,
+                check_contrast=False,
+            )
+        elif file_format.casefold() == "tiff16":
+            skimage.io.imsave(
+                label_save_filename,
+                skimage.img_as_uint(mask),
+                compress=6,
+                check_contrast=False,
+            )
+        else:
+            raise ValueError(f"{file_format} not in 'png', 'tiff8', or 'tiff16'")
+    
+    return save_filenames
+
+def save_object_masks(
+    input_objects,
+    save_dir,
+    file_format="tiff8",
+    nested_save=False,
+    save_names = {"input_filename": None, "input_objects_name": None},
+    ):
+    """
+    For a given object array, save objects as individual masks
+    """
+    # Build save paths
+    if nested_save:
+        if not save_names["input_filename"] and not save_names["input_objects_name"]:
+            raise ValueError("Must provide a save_names['input_filename'] or save_names['input_objects_name'] for nested save.")
+        save_path = os.path.join(
+            save_dir, 
+            save_names["input_filename"] if save_names["input_filename"] else save_names["input_objects_name"],
+            )
+    else:
+        save_path = save_dir
+
+    if not os.path.exists(save_path):
+        os.makedirs(save_path, exist_ok=True)
+
+    unique_labels = numpy.unique(input_objects)
+
+    if unique_labels[0] == 0:
+        unique_labels = unique_labels[1:]
+
+    labels = input_objects
+
+    # Construct filename
+    save_filename = f"{save_names['input_filename']+'_' if save_names['input_filename'] else ''}{save_names['input_objects_name']+'_' if save_names['input_objects_name'] else ''}"
+
+    filenames = []
+    
+    for label in unique_labels:
+        file_extension = "tiff" if "tiff" in file_format else "png"
+
+        label_save_filename = os.path.join(save_path, save_filename + f"{label}.{file_extension}")
+
+        filenames.append(label_save_filename)
+
+        mask = labels == label
+        
+        if file_format.casefold() == "png":
+                skimage.io.imsave(
+                    label_save_filename, 
+                    skimage.img_as_ubyte(mask), 
+                    check_contrast=False
+                )
+        elif file_format.casefold() == "tiff8":
+            skimage.io.imsave(
+                label_save_filename,
+                skimage.img_as_ubyte(mask),
+                compress=6,
+                check_contrast=False,
+            )
+        elif file_format.casefold() == "tiff16":
+            skimage.io.imsave(
+                label_save_filename,
+                skimage.img_as_uint(mask),
+                compress=6,
+                check_contrast=False,
+            )
+        else:
+            raise ValueError(f"{file_format} not in 'png', 'tiff8', or 'tiff16'")
+        
+    return filenames