Merge pull request #20 from DavidStirling/compart-4-2-8-ai-test

Update to 4.2.8 & migrate internal bio-formats
glencoesoftware · Oct 24, 2024 · 2af1ec7 · 2af1ec7
2 parents 8a252f0 + 17781ed
commit 2af1ec7
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -4,7 +4,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ macos-12, windows-2019 ]
+        os: [ macos-13, windows-2019 ]
         python-version: [ "3.8" ]
       fail-fast: false
     steps:
@@ -21,7 +21,7 @@ jobs:
         name: Install Java
         with:
           distribution: "temurin"
-          java-version: "11" # The JDK version to make available on the path.
+          java-version: "11.0.20+8" # The JDK version to make available on the path.
           java-package: jdk
           architecture: x64
 
@@ -47,28 +47,24 @@ jobs:
           brew install [email protected]
           brew link [email protected]
           pip install mysqlclient==2.0.3
-          pip install centrosome==1.2.2 --no-cache-dir --no-build-isolation
-          git clone https://github.com/glencoesoftware/core.git
-          cd core
-          git checkout compat-4-2
-          pip install --editable . --upgrade --no-use-pep517
-          cd ..
-          pip install --editable . --no-use-pep517
+          pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
+          pip install .
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - env:
           JDK_HOME: ${{ env.JAVA_HOME }}
+          CPPFLAGS: -I/usr/local/opt/[email protected]/include
+          LDFLAGS: "-L/usr/local/opt/[email protected]/lib -L/usr/local/opt/openssl/lib"
         if: startsWith(matrix.os, 'windows')
         name: Windows dependency install
         run: |
           python -m pip install --upgrade pip setuptools wheel
           pip install mysqlclient==2.0.3
-          pip install centrosome==1.2.2 --no-cache-dir --no-build-isolation
-          git clone https://github.com/glencoesoftware/core.git
-          cd core
-          git checkout compat-4-2
-          pip install --editable . --upgrade --no-use-pep517
-          cd ..
-          pip install --editable . --no-use-pep517
+          pip install https://github.com/glencoesoftware/core/releases/download/v4.2.80001/cellprofiler_core-4.2.8-py3-none-any.whl
+          pip install .
           pip install wxpython==4.1.1
+          pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation
+          pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl
       - name: Install plugins
         run: |
           pip install torch==2.2.1
@@ -85,29 +81,26 @@ jobs:
         run: |
           pyinstaller distribution/windows/cellprofiler.spec
           rm ./dist/CellProfiler/jvm.dll
-          iscc /dMyAppVersion="4.2.60001-ai" "distribution/windows/cellprofiler.iss"
+          iscc /dMyAppVersion="4.2.80001-ai" "distribution/windows/cellprofiler.iss"
       - if: startsWith(matrix.os, 'macos')
         name: MacOS pyinstaller build and package
         run: |
           pyinstaller -y ./distribution/macos/CellProfiler.spec
       - if: startsWith(matrix.os, 'macos')
-        name: MacOS dmg package
-        continue-on-error: true
-        run: |
-          cd dist
-          echo Creating DMG
-          create-dmg 'CellProfiler+AI.app' --dmg-title "CellProfiler+AI.dmg"
+        name: MacOS tar package
+        run: tar -cvf CellProfiler+AI.tar CellProfiler+AI.app
+        working-directory: ./dist
       - if: startsWith(matrix.os, 'macos')
         uses: actions/upload-artifact@v4
-        name: MacOS dmg upload
+        name: MacOS tar upload
         with:
-          name: CellProfiler-macOS-4.2.60001-ai.dmg
-          path: ./dist/*.dmg
+          name: CellProfiler-macOS-4.2.80001-ai.tar
+          path: ./dist/*.tar
       - if: startsWith(matrix.os, 'windows')
         uses: actions/upload-artifact@v4
         name: Windows artifact upload
         with:
-          name: CellProfiler-Windows-4.2.60001-ai.exe
+          name: CellProfiler-Windows-4.2.80001-ai.exe
           path: ./distribution/windows/Output/*.exe
   upload:
     name: upload

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 ![CellProfiler](cellprofiler/data/images/splash.png)
 
-[![Version](https://img.shields.io/badge/version-4.2.6-green.svg)](https://cellprofiler.org/releases)
-[![Docs](https://img.shields.io/badge/documentation-4.2.6-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.6/index.html)
+[![Version](https://img.shields.io/badge/version-4.2.8-green.svg)](https://cellprofiler.org/releases)
+[![Docs](https://img.shields.io/badge/documentation-4.2.8-brightgreen.svg)](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.8/index.html)
 [![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftag%2Fcellprofiler.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/cellprofiler)
 
 **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. More information can be found in the [CellProfiler Wiki](https://github.com/CellProfiler/CellProfiler/wiki).

diff --git a/cellprofiler/__init__.py b/cellprofiler/__init__.py
@@ -1,3 +1,3 @@
 __test__ = False
 
-__version__ = "4.2.60001"
+__version__ = "4.2.80001"
diff --git a/cellprofiler/gui/checkupdate.py b/cellprofiler/gui/checkupdate.py
@@ -7,10 +7,10 @@
 
 
 def check_update(parent, force=False):
-    if not force and not check_date():
+    if not force:
         return
     try:
-        response = requests.get("https://api.github.com/repos/cellprofiler/cellprofiler/releases/latest", timeout=0.25)
+        response = requests.get("https://api.github.com/repos/glencoesoftware/cellprofiler/releases/latest", timeout=0.25)
     except:
         response = False
         message = "CellProfiler was unable to connect to GitHub to check for updates"
@@ -19,6 +19,8 @@ def check_update(parent, force=False):
         response = response.json()
         if status == 200 and 'name' in response:
             latest_version = response['name'][1:]
+            if '-' in latest_version:
+                latest_version = latest_version.split('-')[0]
             if current_version < latest_version or len(current_version) != len(latest_version):
                 body_text = response['body']
                 if len(body_text) > 1000:

diff --git a/cellprofiler/modules/classifyobjects.py b/cellprofiler/modules/classifyobjects.py
@@ -1080,7 +1080,7 @@ def run_two_measurements(self, workspace):
 
         if self.show_window:
             workspace.display_data.in_high_class = in_high_class
-            workspace.display_data.labels = (objects.segmented,)
+            workspace.display_data.labels = objects.segmented
             workspace.display_data.saved_values = saved_values
 
     def display_two_measurements(self, workspace, figure):

diff --git a/cellprofiler/modules/flagimage.py b/cellprofiler/modules/flagimage.py
@@ -716,6 +716,10 @@ def load_classifier(self, measurement_group):
                 d[path_] = joblib.load(path_)
         return d[path_]
 
+    def get_dictionary_for_worker(self):
+        # Sklearn models can't be serialized, so workers will need to read them from disk.
+        return {}
+
     def get_classifier(self, measurement_group):
         return self.load_classifier(measurement_group)[0]
 

diff --git a/cellprofiler/modules/measureimageoverlap.py b/cellprofiler/modules/measureimageoverlap.py
@@ -310,6 +310,9 @@ def run(self, workspace):
 
         # In volumetric case the 3D image stack gets converted to a long 2D image and gets analyzed
         if ground_truth_image.volumetric:
+
+            orig_shape = ground_truth_pixels.shape
+
             ground_truth_pixels = ground_truth_pixels.reshape(
                 -1, ground_truth_pixels.shape[-1]
             )
@@ -451,6 +454,15 @@ def run(self, workspace):
             )
 
         if self.show_window:
+
+            workspace.display_data.dimensions = test_image.dimensions
+
+            if ground_truth_image.volumetric:
+                true_positives = true_positives.reshape(orig_shape)
+                true_negatives = true_negatives.reshape(orig_shape)
+                false_positives = false_positives.reshape(orig_shape)
+                false_negatives = false_negatives.reshape(orig_shape)
+
             workspace.display_data.true_positives = true_positives
 
             workspace.display_data.true_negatives = true_negatives
@@ -741,7 +753,7 @@ def get_weights(self, i, j, labels_mask):
 
     def display(self, workspace, figure):
         """Display the image confusion matrix & statistics"""
-        figure.set_subplots((3, 2))
+        figure.set_subplots((3, 2),dimensions=workspace.display_data.dimensions)
 
         for x, y, image, label in (
             (0, 0, workspace.display_data.true_positives, "True positives"),

diff --git a/cellprofiler/modules/measureimagequality.py b/cellprofiler/modules/measureimagequality.py
@@ -1036,7 +1036,7 @@ def get_measurement_scales(
                         if image_names in self.images_to_process(
                             image_group, None, pipeline
                         ):
-                            result += [scale_group.scale]
+                            result += [scale_group.scale.value]
                 return result
             if measurement.startswith(F_THRESHOLD):
                 result = []

diff --git a/cellprofiler/modules/measureimageskeleton.py b/cellprofiler/modules/measureimageskeleton.py
@@ -199,8 +199,8 @@ def get_measurements(self, pipeline, object_name, category):
 
         if object_name == "Image" and category == "Skeleton":
             return [
-                "Skeleton_Branches_{}".format(name),
-                "Skeleton_Endpoints_{}".format(name),
+                "Branches",
+                "Endpoints"
             ]
 
         return []

diff --git a/cellprofiler/modules/measureobjectneighbors.py b/cellprofiler/modules/measureobjectneighbors.py
@@ -323,9 +323,9 @@ def run(self, workspace):
             neighbor_has_pixels = has_pixels
         else:
             _, neighbor_numbers = neighbor_objects.relate_labels(
-                neighbor_labels, neighbor_objects.small_removed_segmented
+                neighbor_labels, neighbor_kept_labels
             )
-            neighbor_has_pixels = numpy.bincount(neighbor_labels.ravel())[1:] > 0
+            neighbor_has_pixels = numpy.bincount(neighbor_kept_labels.ravel())[1:] > 0
         neighbor_count = numpy.zeros((nobjects,))
         pixel_count = numpy.zeros((nobjects,))
         first_object_number = numpy.zeros((nobjects,), int)
@@ -703,6 +703,7 @@ def run(self, workspace):
             )
 
         labels = kept_labels
+        neighbor_labels = neighbor_kept_labels
 
         neighbor_count_image = numpy.zeros(labels.shape, int)
         object_mask = objects.segmented != 0

diff --git a/cellprofiler/modules/runimagejmacro.py b/cellprofiler/modules/runimagejmacro.py
@@ -292,7 +292,7 @@ def run(self, workspace):
 
             cmd += [self.stringify_metadata(tempdir)]
 
-            result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True)
+            result = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True, errors='backslashreplace')
             for image_group in self.image_groups_out:
                 if not os.path.exists(os.path.join(tempdir, image_group.input_filename.value)):
                     # Cleanup the error logs for display, we want to remove less-useful lines to keep it succinct.

diff --git a/cellprofiler/modules/threshold.py b/cellprofiler/modules/threshold.py
@@ -932,6 +932,10 @@ def get_local_threshold(self, image, mask, volumetric):
         elif numpy.all(image_data == image_data[0]):
             local_threshold = numpy.full_like(image_data, image_data[0])
 
+        elif numpy.all((image_data == 0) | numpy.isnan(image_data)):
+            #test if all values are a mixture of 0 or nan
+            local_threshold = numpy.zeros_like(image_data)
+
         elif self.threshold_operation == TM_LI:
             local_threshold = self._run_local_threshold(
                 image_data,

diff --git a/distribution/macos/CellProfiler.spec b/distribution/macos/CellProfiler.spec
@@ -50,6 +50,7 @@ hiddenimports += PyInstaller.utils.hooks.collect_submodules("wx")
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.gui')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.modules')
+hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core.modules')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('skimage.io._plugins')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules("skimage.feature")

diff --git a/distribution/windows/CellProfiler.spec b/distribution/windows/CellProfiler.spec
@@ -27,6 +27,7 @@ hiddenimports = []
 
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('centrosome')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.modules')
+hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler_core.modules')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules('cellprofiler.utilities')
 hiddenimports += PyInstaller.utils.hooks.collect_submodules("scipy")

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -67,7 +67,7 @@
 # The short X.Y version.
 version = "4.2"
 # The full version, including alpha/beta/rc tags.
-release = "4.2.6"
+release = "4.2.8"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,17 +1,3 @@
-[tool.black]
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | build
-    | dist
-  )/
-)
-'''
-target_version = ['py38']
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
diff --git a/setup.py b/setup.py
@@ -51,20 +51,21 @@ def package_data():
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Image Recognition",
         "Topic :: Scientific/Engineering",
     ],
     entry_points={"console_scripts": ["cellprofiler=cellprofiler.__main__:main"]},
     extras_require={
-        "build": ["black", "pre-commit", "pyinstaller", "twine"],
-        "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0"],
-        "test": ["pytest>=3.3.2,<4"],
+        "build": ["pyinstaller", "twine"],
+        "docs": ["Sphinx>=3.1.1", "sphinx-rtd-theme>=0.5.0", "markupsafe<2.0.1"],
+        "test": ["pytest~=7.4.1"],
     },
     install_requires=[
-        "boto3==1.14.23",
-        "cellprofiler-core",
-        "centrosome==1.2.2",
+        "boto3>=1.12.28",
+        "cellprofiler-core==4.2.8",
+        "centrosome~=1.2.3",
         "docutils==0.15.2",
         "h5py==3.6.0",
         "imageio==2.34.0",
@@ -79,17 +80,17 @@ def package_data():
         "opencv-python-headless==4.5.3.56",
         "Pillow==8.3.2",
         "prokaryote==2.4.4",
-        "python-bioformats==4.0.7",
-        "python-javabridge==4.0.3",
+        "python-bioformats~=4.1.0",
+        "python-javabridge==4.0.4",
         "pyzmq==22.3.0",
         "sentry-sdk==0.18.0",
         "requests==2.22",
         "scikit-image==0.18.3",
         "scikit-learn==0.24.1",
         "scipy==1.9.0",
         "six",
-        "tifffile==2023.2.3",
-        "wxPython==4.2.1",
+        "tifffile<2022.4.22",
+        "wxPython>=4.1.0,<5",
     ],
     license="BSD",
     name="CellProfiler",

diff --git a/tests/modules/test_measureimageskeleton.py b/tests/modules/test_measureimageskeleton.py
@@ -87,7 +87,7 @@ def test_get_measurement_columns(module, pipeline):
 def test_get_measurements_image_skeleton(module, pipeline):
     module.skeleton_name.value = "example"
 
-    expected_measurements = ["Skeleton_Branches_example", "Skeleton_Endpoints_example"]
+    expected_measurements = ["Branches", "Endpoints"]
 
     measurements = module.get_measurements(
         pipeline, "Image", "Skeleton"
@@ -127,7 +127,7 @@ def test_get_measurement_images(module, pipeline):
         pipeline,
         "Image",
         "Skeleton",
-        "Skeleton_Branches_example",
+        "Branches",
     )
 
     assert images == expected_images