Refactor to newer CP5 API

- update provider adding via new add_provider method - activate readers manually
CellProfiler · Mar 20, 2024 · 9483a68 · 9483a68
1 parent b928c0b
commit 9483a68
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Showing 3 changed files with 27 additions and 19 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,5 +1,5 @@
 # Something in CellProfiler is importing wx before we can set
-# headless mode. Setting headless here efore importing anything
+# headless mode. Setting headless here before importing anything
 # else from CellProfiler.
 import cellprofiler_core.preferences
 
@@ -10,6 +10,7 @@
 import cellprofiler_core.object
 import cellprofiler_core.pipeline
 import cellprofiler_core.workspace
+import cellprofiler_core.reader
 import numpy
 import skimage.data
 import skimage.color
@@ -18,6 +19,9 @@
 import pytest
 
 
+def pytest_sessionstart(session):
+    cellprofiler_core.reader.fill_readers(check_config=True)
+
 @pytest.fixture(
     scope="module",
     params=[

diff --git a/unmaintained_plugins/CellProfiler3/tests/conftest.py b/unmaintained_plugins/CellProfiler3/tests/conftest.py
@@ -10,6 +10,7 @@
 import cellprofiler.object
 import cellprofiler.pipeline
 import cellprofiler.workspace
+import cellprofiler_core.reader
 import numpy
 import skimage.data
 import skimage.color
@@ -18,6 +19,9 @@
 import pytest
 
 
+def pytest_sessionstart(session):
+    cellprofiler_core.reader.fill_readers(check_config=True)
+
 @pytest.fixture(
     scope="module",
     params=[

diff --git a/unmaintained_tests/test_identifyyeastcells.py b/unmaintained_tests/test_identifyyeastcells.py
@@ -102,7 +102,7 @@ def test_01_00_test_zero_objects(self):
         image = cpi.Image(img, file_name="test_01_00_test_zero_objects")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -137,7 +137,7 @@ def test_01_01_test_one_object(self):
         image = cpi.Image(img, file_name="test_01_01_test_one_object")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -182,7 +182,7 @@ def test_01_02_test_two_bright_objects(self):
         image = cpi.Image(img, file_name="test_01_02_test_two_bright_objects")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -218,7 +218,7 @@ def test_01_03_test_two_dark_objects(self):
         image = cpi.Image(img, file_name="test_01_03_test_two_dark_objects")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -256,7 +256,7 @@ def test_01_04_test_two_flu_bright_objects(self):
         image = cpi.Image(img, file_name="test_01_04_test_two_flu_bright_objects")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -294,7 +294,7 @@ def test_01_05_test_two_flu_dark_objects(self):
         image = cpi.Image(img, file_name="test_01_05_test_two_flu_dark_objects")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -336,7 +336,7 @@ def test_01_06_fill_holes(self):
         image = cpi.Image(img, file_name="test_01_06_fill_holes")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -359,7 +359,7 @@ def test_01_07_extreme_params(self):
         image = cpi.Image(img, file_name="test_01_07_extreme_params")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -387,7 +387,7 @@ def test_02_01_discard_large(self):
         image = cpi.Image(img, file_name="test_02_01_discard_large")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -418,7 +418,7 @@ def test_02_02_discard_small(self):
         image = cpi.Image(img, file_name="test_02_02_discard_small")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -454,8 +454,8 @@ def test_02_03_use_background_image(self):
 
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
-        image_set.providers.append(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
         object_set = cpo.ObjectSet()
         measurements = cpmeas.Measurements()
         pipeline = cellprofiler.pipeline.Pipeline()
@@ -487,8 +487,8 @@ def test_02_04_mask_input_image(self):
         mask = cpi.Image(msk)
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
-        image_set.providers.append(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
 
         # first try without masking
         object_set = cpo.ObjectSet()
@@ -548,7 +548,7 @@ def test_03_01_simple_fitting(self):
         image = cpi.Image(img, file_name="test_03_01_simple_fitting")
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
 
         old_params = ast.literal_eval(x.autoadapted_params.value)
         input_processed, background_processed, ignore_mask_processed = x.preprocess_images(img, None, None)
@@ -629,9 +629,9 @@ def test_03_02_fitting_background_masked(self):
 
         image_set_list = cpi.ImageSetList()
         image_set = image_set_list.get_image_set(0)
-        image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
-        image_set.providers.append(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
-        image_set.providers.append(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
+        image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
+        image_set.add_provider(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
+        image_set.add_provider(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
 
         old_params = ast.literal_eval(x.autoadapted_params.value)
         input_processed, background_processed, ignore_mask_processed = x.preprocess_images(img, background_mask, ignore_mask)