CellProfiler-nightly 5.0.0.dev83__tar.gz → 5.0.0.dev91__tar.gz

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CellProfiler-nightly
-Version: 5.0.0.dev83
+Version: 5.0.0.dev91
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 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>
@@ -90,7 +90,7 @@ Requires-Dist: scipy<1.11,>=1.9.1
 Requires-Dist: scyjava>=1.9.1
 Requires-Dist: six~=1.16.0
 Requires-Dist: tifffile<2022.4.22,>=2022.4.8
-Requires-Dist: wxPython==4.2.0
+Requires-Dist: wxPython~=4.2.0
 Requires-Dist: rapidfuzz~=3.0.0
 Requires-Dist: packaging>=20.0
 Provides-Extra: build

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/CellProfiler_nightly.egg-info/SOURCES.txt

@@ -378,6 +378,7 @@ cellprofiler/modules/watershed.py
 cellprofiler/modules/plugins/__init__.py
 cellprofiler/modules/plugins/imagetemplate.py
 cellprofiler/modules/plugins/measurementtemplate.py
+cellprofiler/modules/plugins/segmentationtemplatewithdependencies.py
 cellprofiler/utilities/__init__.py
 cellprofiler/utilities/morphology.py
 cellprofiler/utilities/rules.py

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/CellProfiler_nightly.egg-info/requires.txt

@@ -22,7 +22,7 @@ scipy<1.11,>=1.9.1
 scyjava>=1.9.1
 six~=1.16.0
 tifffile<2022.4.22,>=2022.4.8
-wxPython==4.2.0
+wxPython~=4.2.0
 rapidfuzz~=3.0.0
 packaging>=20.0
 

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CellProfiler-nightly
-Version: 5.0.0.dev83
+Version: 5.0.0.dev91
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 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>
@@ -90,7 +90,7 @@ Requires-Dist: scipy<1.11,>=1.9.1
 Requires-Dist: scyjava>=1.9.1
 Requires-Dist: six~=1.16.0
 Requires-Dist: tifffile<2022.4.22,>=2022.4.8
-Requires-Dist: wxPython==4.2.0
+Requires-Dist: wxPython~=4.2.0
 Requires-Dist: rapidfuzz~=3.0.0
 Requires-Dist: packaging>=20.0
 Provides-Extra: build

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/cellprofiler/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '5.0.0.dev83'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev83')
+__version__ = version = '5.0.0.dev91'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev91')

cellprofiler_nightly-5.0.0.dev91/cellprofiler/modules/plugins/segmentationtemplatewithdependencies.py

@@ -0,0 +1,243 @@
+#################################
+#
+# Imports from useful Python libraries
+#
+#################################
+
+import numpy
+import os
+import skimage
+import subprocess
+import uuid
+import shutil
+import logging
+import sys
+
+from your_dependency_with_a_long_and_improbable_name import somefunction
+
+#################################
+#
+# Imports from CellProfiler
+#
+##################################
+
+from cellprofiler_core.module.image_segmentation import ImageSegmentation
+from cellprofiler_core.object import Objects
+from cellprofiler_core.setting.choice import Choice
+from cellprofiler_core.preferences import get_default_output_directory
+from cellprofiler_core.setting.text import (
+    Integer
+)
+
+LOGGER = logging.getLogger(__name__)
+
+__doc__ = f"""\
+SegmentationTemplateWithDependencies
+====================================
+
+============ ============ ===============
+Supports 2D? Supports 3D? Respects masks?
+============ ============ ===============
+YES/NO       YES/NO       YES/NO
+============ ============ ===============
+
+This template class is intended to aid in adding segmentation models that
+introduce external dependencies (often, but not always, deep learning).
+
+In order to use a plugin that requires dependencies packaged with CellProfiler's build,
+the user will need to do one of two things - install CellProfiler with Python 
+or get that dependency from a software container like Docker. Here we assume you 
+want to support both possible options; if not, you can delete the docker_or_python settings 
+(and any settings that relate to that, or to the mode you don't want to support).
+
+If you're using deep learning and want to do GPU stuff, you may want to add things
+from that library that test for GPU access; we recommend checking RunCellpose for
+examples of doing this with PyTorch and RunStardist for exampels of doing this with 
+Tensorflow
+"""
+#
+# Constants
+#
+# It's good programming practice to replace things like strings with
+# constants if they will appear more than once in your program. That way,
+# if someone wants to change the text, that text will change everywhere.
+# Also, you can't misspell it by accident.
+#
+
+DOCKER_NAME = "cellprofiler/cellprofiler:v4.2.6"
+
+SOME_CHOICES = []
+
+
+class SegmentationTemplateWithDependencies(ImageSegmentation):
+    category = "Object Processing"
+
+    module_name = "SegmentationTemplateWithDependencies"
+
+    variable_revision_number = 1
+
+    doi = {
+        "Optional paper that one can ask the user to cite:": "https://doi.org/some_doi",
+    }
+
+    def create_settings(self):
+        super(SegmentationTemplateWithDependencies, self).create_settings()
+
+        self.docker_or_python = Choice(
+            text="Run this segmentation thing in docker or local python environment",
+            choices=["Docker", "Python"],
+            value="Docker",
+            doc="""\
+If Docker is selected, ensure that Docker Desktop is open and running on your
+computer. On first run of the X plugin, the Docker container will be
+downloaded, which may be slow . However, this slow downloading process will only have to happen
+once.
+
+If Python is selected, the Python environment in which CellProfiler is installed will be used.
+""",
+        )
+
+        self.docker_image = Choice(
+            text="Select your external docker image",
+            choices=[DOCKER_NAME],
+            value=DOCKER_NAME,
+            doc="""\
+Select which Docker image to use for running your plugin.
+"""
+        )
+
+        self.some_numerical_parameter = Integer(
+            text="Some configurable parameter",
+            value=30,
+            minval=0,
+            doc="""\
+""",
+        )
+
+        self.some_listy_parameter = Choice(
+            text="Parameter where the user picks from a list",
+            choices=SOME_CHOICES,
+            value=SOME_CHOICES[0],
+            doc="""
+""",
+        )
+
+
+    def settings(self):
+        return [
+            self.x_name,
+            self.docker_or_python,
+            self.docker_image,
+            self.some_listy_parameter,
+            self.some_numerical_parameter,
+            self.y_name,
+        ]
+
+    def visible_settings(self):
+        vis_settings = [self.docker_or_python]
+
+        if self.docker_or_python.value == "Docker":
+            vis_settings += [self.docker_image]
+
+        vis_settings += [
+            self.some_numerical_parameter,
+            self.some_listy_parameter,
+            self.y_name,
+        ]
+
+        return vis_settings
+
+
+    def run(self, workspace):
+        x_name = self.x_name.value
+        y_name = self.y_name.value
+        images = workspace.image_set
+        x = images.get_image(x_name)
+        x_data = x.pixel_data
+        dimensions = x.dimensions
+
+        if self.docker_or_python.value == "Python":
+
+            try:
+                y_data = somefunction(x_data, self.some_numerical_parameter.value,self.some_listy_parameter.value)
+        
+            except Exception as a:
+                        print(f"Unable to create masks. Check your module settings. {a}")
+        elif self.docker_or_python.value == "Docker":
+            # Define how to call docker
+            docker_path = "docker" if sys.platform.lower().startswith("win") else "/usr/local/bin/docker"
+            # Create a UUID for this run
+            unique_name = str(uuid.uuid4())
+            # Directory that will be used to pass images to the docker container
+            temp_dir = os.path.join(get_default_output_directory(), ".cellprofiler_temp", unique_name)
+            temp_img_dir = os.path.join(temp_dir, "img")
+            
+            os.makedirs(temp_dir, exist_ok=True)
+            os.makedirs(temp_img_dir, exist_ok=True)
+
+            temp_img_path = os.path.join(temp_img_dir, unique_name+".tiff")
+
+            # Save the image to the Docker mounted directory
+            skimage.io.imsave(temp_img_path, x_data)
+
+            # You will need of course to figure out exactly the right command in your docker container
+            cmd = [docker_path,"run","--rm","-v",f"{temp_dir}:/data",self.docker_image.value,
+                   "--some-numerical-flag", self.some_numerical_parameter.value,
+                   "--some-other-flag", self.some_listy_parameter.value]
+
+            try:
+                subprocess.run(cmd, text=True)
+                #here the external library made a numpy array, you might use skimage.io.imread if it's a tiff file, etc
+                y_data = numpy.load(os.path.join(temp_img_dir, "some_segmentation_file_name"), allow_pickle=True).item()
+
+            finally:      
+                # Delete the temporary files
+                try:
+                    shutil.rmtree(temp_dir)
+                except:
+                    LOGGER.error("Unable to delete temporary directory, files may be in use by another program.")
+                    LOGGER.error(f"Temp folder is subfolder {temp_dir} in your Default Output Folder.\nYou may need to remove it manually.")
+
+
+        y = Objects()
+        y.segmented = y_data
+        y.parent_image = x.parent_image
+        objects = workspace.object_set
+        objects.add_objects(y, y_name)
+
+
+        self.add_measurements(workspace)
+
+        if self.show_window:
+            if x.volumetric:
+                workspace.display_data.x_data = x.pixel_data
+            else:
+                workspace.display_data.x_data = x_data
+            workspace.display_data.y_data = y_data
+            workspace.display_data.dimensions = dimensions
+
+    def display(self, workspace, figure):
+
+        layout = (2, 1)
+
+        figure.set_subplots(
+            dimensions=workspace.display_data.dimensions, subplots=layout
+        )
+
+        figure.subplot_imshow(
+            colormap="gray",
+            image=workspace.display_data.x_data,
+            title="Input Image",
+            x=0,
+            y=0,
+        )
+
+        figure.subplot_imshow_labels(
+            image=workspace.display_data.y_data,
+            sharexy=figure.subplot(0, 0),
+            title=self.y_name.value,
+            x=1,
+            y=0,
+        )
+
+

{cellprofiler_nightly-5.0.0.dev83 → cellprofiler_nightly-5.0.0.dev91}/pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.md"
 requires-python = ">=3.9"
 keywords = [ "computer vision", "image analysis", "biology", "cell", "cellprofiler",]
 classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python :: 3.9", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Image Recognition", "Topic :: Scientific/Engineering :: Image Processing", "Topic :: Scientific/Engineering",]
-dependencies = [ "cellprofiler-library-nightly>=5.dev", "cellprofiler-core-nightly>=5.dev", "boto3~=1.28.41", "centrosome>=1.2.3", "docutils==0.15.2", "h5py~=3.6.0", "imageio~=2.31.3", "inflect~=7.0.0", "Jinja2~=3.1.2", "joblib~=1.3.2", "mahotas~=1.4.13", "matplotlib>=3.1.3,<4", "mysqlclient~=2.2.3", "numpy~=1.24.4", "Pillow~=10.0.0", "pyzmq~=22.3.0", "sentry-sdk>=0.18.0,<=1.31.0", "requests~=2.31.0", "scikit-image~=0.20.0", "scikit-learn~=1.3.0", "scipy>=1.9.1,<1.11", "scyjava>=1.9.1", "six~=1.16.0", "tifffile>=2022.4.8,<2022.4.22", "wxPython==4.2.0", "rapidfuzz~=3.0.0", "packaging>=20.0",]
+dependencies = [ "cellprofiler-library-nightly>=5.dev", "cellprofiler-core-nightly>=5.dev", "boto3~=1.28.41", "centrosome>=1.2.3", "docutils==0.15.2", "h5py~=3.6.0", "imageio~=2.31.3", "inflect~=7.0.0", "Jinja2~=3.1.2", "joblib~=1.3.2", "mahotas~=1.4.13", "matplotlib>=3.1.3,<4", "mysqlclient~=2.2.3", "numpy~=1.24.4", "Pillow~=10.0.0", "pyzmq~=22.3.0", "sentry-sdk>=0.18.0,<=1.31.0", "requests~=2.31.0", "scikit-image~=0.20.0", "scikit-learn~=1.3.0", "scipy>=1.9.1,<1.11", "scyjava>=1.9.1", "six~=1.16.0", "tifffile>=2022.4.8,<2022.4.22", "wxPython~=4.2.0", "rapidfuzz~=3.0.0", "packaging>=20.0",]
 dynamic = [ "version",]
 [[project.authors]]
 name = "Anne Carpenter"