cellprofiler-core-nightly 5.0.0.dev65__tar.gz

cellprofiler_core_nightly-5.0.0.dev65/LICENSE

@@ -0,0 +1,41 @@
+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_core_nightly-5.0.0.dev65/PKG-INFO

@@ -0,0 +1,101 @@
+Metadata-Version: 2.1
+Name: cellprofiler-core-nightly
+Version: 5.0.0.dev65
+Summary: cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
+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: cellprofiler-library-nightly>=5.dev
+Requires-Dist: boto3>=1.12.28
+Requires-Dist: centrosome~=1.2.2
+Requires-Dist: docutils==0.15.2
+Requires-Dist: future>=0.18.2
+Requires-Dist: fsspec>=2021.11.0
+Requires-Dist: h5py~=3.6.0
+Requires-Dist: lxml>=4.6.4
+Requires-Dist: matplotlib<4,>=3.1.3
+Requires-Dist: numpy~=1.24.4
+Requires-Dist: psutil>=5.9.5
+Requires-Dist: pyzmq~=22.3.0
+Requires-Dist: scikit-image~=0.20.0
+Requires-Dist: scipy<1.11,>=1.9.1
+Requires-Dist: scyjava>=1.9.1
+Requires-Dist: zarr~=2.16.1
+Requires-Dist: google-cloud-storage~=2.10.0
+Requires-Dist: packaging>=20.0
+Provides-Extra: build
+Requires-Dist: build; extra == "build"
+Requires-Dist: pyinstaller; extra == "build"
+Requires-Dist: twine; extra == "build"
+Requires-Dist: sphinx>=3.1.1; extra == "build"
+Requires-Dist: click>=7.1.2; extra == "build"
+Provides-Extra: test
+Requires-Dist: pytest~=7.4.1; extra == "test"
+Requires-Dist: pytest-timeout~=2.1.0; extra == "test"
+Provides-Extra: wx
+Requires-Dist: wxPython==4.2.0; extra == "wx"
+
+# core
+
+This subpackage contains the code to build the `cellprofiler-core` package. It contains the critical classes and components required by the [CellProfiler](cellprofiler.org) software, whereas the [frontend](../../frontend/) contains non-essential modules and the GUI interface. This package can be used in isolation, separate from the frontend, to access CellProfiler's functionality as a Python package, see [this page](https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-as-a-Python-package) for more details.

cellprofiler_core_nightly-5.0.0.dev65/README.md

@@ -0,0 +1,3 @@
+# core
+
+This subpackage contains the code to build the `cellprofiler-core` package. It contains the critical classes and components required by the [CellProfiler](cellprofiler.org) software, whereas the [frontend](../../frontend/) contains non-essential modules and the GUI interface. This package can be used in isolation, separate from the frontend, to access CellProfiler's functionality as a Python package, see [this page](https://github.com/CellProfiler/CellProfiler/wiki/CellProfiler-as-a-Python-package) for more details.

cellprofiler_core_nightly-5.0.0.dev65/cellprofiler_core/__init__.py

@@ -0,0 +1 @@
+from cellprofiler_core._version import __version__

cellprofiler_core_nightly-5.0.0.dev65/cellprofiler_core/__main__.py

@@ -0,0 +1,55 @@
+import os
+import pathlib
+
+import click
+
+import cellprofiler_core.commands
+
+CONTEXT_SETTINGS = dict(auto_envvar_prefix="COMPLEX")
+
+
+class Command(click.MultiCommand):
+    def get_command(self, context, name):
+        try:
+            name = f"cellprofiler_core.commands._{name}_command"
+
+            imported_module = __import__(name, None, None, ["command"])
+        except ImportError:
+            return
+
+        return imported_module.command
+
+    def list_commands(self, context):
+        command_names = []
+
+        commands_pathname = cellprofiler_core.commands.__file__
+
+        commands_directory = pathlib.Path(commands_pathname).parent
+
+        for filename in os.listdir(commands_directory):
+            if filename.endswith("_command.py") and filename.startswith("_"):
+                command_name = filename[1:-11]
+
+                command_names += [command_name]
+
+        command_names.sort()
+
+        return command_names
+
+
+class Environment:
+    def __init__(self):
+        pass
+
+
+pass_environment = click.make_pass_decorator(Environment, ensure=True)
+
+
+@click.command(cls=Command, context_settings=CONTEXT_SETTINGS)
+@pass_environment
+def main(context):
+    pass
+
+
+if __name__ == "__main__":
+    main({})

cellprofiler_core_nightly-5.0.0.dev65/cellprofiler_core/_version.py

@@ -0,0 +1,16 @@
+# 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_core_nightly-5.0.0.dev65/cellprofiler_core/analysis/__init__.py

@@ -0,0 +1,32 @@
+"""
+Run pipelines on imagesets to produce measurements.
+"""
+
+import sys
+
+
+use_analysis = True
+
+DEBUG = "DEBUG"
+ANNOUNCE_DONE = "DONE"
+
+
+###############################
+# Request, Replies, Events
+###############################
+
+
+if sys.platform == "darwin":
+    pass
+
+if __name__ == "__main__":
+    # This is an ugly hack, but it's necesary to unify the Request/Reply
+    # classes above, so that regardless of whether this is the current module,
+    # or a separately imported one, they see the same classes.
+    import cellprofiler_core.analysis
+    from ._runner import Runner
+
+    globals().update(cellprofiler_core.analysis.__dict__)
+
+    Runner.start_workers(2)
+    Runner.stop_workers()

cellprofiler_core_nightly-5.0.0.dev65/cellprofiler_core/analysis/_analysis.py

@@ -0,0 +1,109 @@
+import gc
+import threading
+import uuid
+
+from ._runner import Runner
+from ..measurement import Measurements
+
+
+class Analysis:
+    """An Analysis is the application of a particular pipeline of modules to a
+    set of images to produce measurements.
+
+    Multiprocessing for analyses is handled by multiple layers of threads and
+    processes, to keep the GUI responsive and simplify the code.  Threads and
+    processes are organized as below.  Display/Interaction requests and
+    Exceptions are sent directly to the pipeline listener.
+
+    +------------------------------------------------+
+    |           CellProfiler GUI/WX thread           |
+    |                                                |
+    +- Analysis() methods down,  Events/Requests up -+
+    |                                                |
+    |       AnalysisRunner.interface() thread        |
+    |                                                |
+    +----------------  Queues  ----------------------+
+    |                                                |
+    |  AnalysisRunner.jobserver()/announce() threads |
+    |                                                |
+    +----------------------------------------------- +
+    |              zmqrequest.Boundary()             |
+    +---------------+----------------+---------------+
+    |     Worker    |     Worker     |   Worker      |
+    +---------------+----------------+---------------+
+
+    Workers are managed by class variables in the AnalysisRunner.
+    """
+
+    def __init__(self, pipeline, initial_measurements=None):
+        """create an Analysis applying pipeline to a set of images, writing out
+        to measurements_filename, optionally starting with previous
+        measurements."""
+        self.pipeline = pipeline
+        initial_measurements = Measurements(copy=initial_measurements)
+        self.initial_measurements_buf = initial_measurements.file_contents()
+        initial_measurements.close()
+        self.debug_mode = False
+        self.analysis_in_progress = False
+        self.runner = None
+
+        self.runner_lock = threading.Lock()  # defensive coding purposes
+
+    def start(self, analysis_event_callback, num_workers=None, overwrite=True):
+        """Start the analysis runner
+
+        analysis_event_callback - callback from runner to UI thread for
+                                  event progress and UI handlers
+
+        num_workers - # of worker processes to instantiate, default is # of cores
+
+        overwrite - True (default) to process all image sets, False to only
+                    process incomplete ones (or incomplete groups if grouping)
+        """
+        with self.runner_lock:
+            assert not self.analysis_in_progress
+            self.analysis_in_progress = uuid.uuid1().hex
+
+            self.runner = Runner(
+                self.analysis_in_progress,
+                self.pipeline,
+                self.initial_measurements_buf,
+                analysis_event_callback,
+            )
+            self.runner.start(num_workers=num_workers, overwrite=overwrite)
+            return self.analysis_in_progress
+
+    def pause(self):
+        with self.runner_lock:
+            assert self.analysis_in_progress
+            self.runner.pause()
+
+    def resume(self):
+        with self.runner_lock:
+            assert self.analysis_in_progress
+            self.runner.resume()
+
+    def cancel(self):
+        with self.runner_lock:
+            if not self.analysis_in_progress:
+                return
+            self.analysis_in_progress = False
+            self.runner.cancel()
+            self.runner = None
+            """
+            Explicitly call GC here so that the old runner's threads and 
+            queues get deleted before any new analysis can be started.
+            On rare occasions CP can hang when threads get GC'd during a run
+            """
+            gc.collect()
+
+    def check_running(self):
+        """Verify that an analysis is running, allowing the GUI to recover even
+        if the AnalysisRunner fails in some way.
+
+        Returns True if analysis is still running (threads are still alive).
+        """
+        with self.runner_lock:
+            if self.analysis_in_progress:
+                return self.runner.check()
+            return False