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gnodar01gnodar01
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Refactor to newer CP5 API
- update provider adding via new add_provider method - activate readers manually
1 parent b928c0b commit 9483a68

3 files changed

Lines changed: 27 additions & 19 deletions

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‎tests/conftest.py‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Something in CellProfiler is importing wx before we can set
2-
# headless mode. Setting headless here efore importing anything
2+
# headless mode. Setting headless here before importing anything
33
# else from CellProfiler.
44
import cellprofiler_core.preferences
55

@@ -10,6 +10,7 @@
1010
import cellprofiler_core.object
1111
import cellprofiler_core.pipeline
1212
import cellprofiler_core.workspace
13+
import cellprofiler_core.reader
1314
import numpy
1415
import skimage.data
1516
import skimage.color
@@ -18,6 +19,9 @@
1819
import pytest
1920

2021

22+
def pytest_sessionstart(session):
23+
cellprofiler_core.reader.fill_readers(check_config=True)
24+
2125
@pytest.fixture(
2226
scope="module",
2327
params=[

‎unmaintained_plugins/CellProfiler3/tests/conftest.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@
1010
import cellprofiler.object
1111
import cellprofiler.pipeline
1212
import cellprofiler.workspace
13+
import cellprofiler_core.reader
1314
import numpy
1415
import skimage.data
1516
import skimage.color
@@ -18,6 +19,9 @@
1819
import pytest
1920

2021

22+
def pytest_sessionstart(session):
23+
cellprofiler_core.reader.fill_readers(check_config=True)
24+
2125
@pytest.fixture(
2226
scope="module",
2327
params=[

‎unmaintained_tests/test_identifyyeastcells.py‎

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,7 @@ def test_01_00_test_zero_objects(self):
102102
image = cpi.Image(img, file_name="test_01_00_test_zero_objects")
103103
image_set_list = cpi.ImageSetList()
104104
image_set = image_set_list.get_image_set(0)
105-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
105+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
106106
object_set = cpo.ObjectSet()
107107
measurements = cpmeas.Measurements()
108108
pipeline = cellprofiler.pipeline.Pipeline()
@@ -137,7 +137,7 @@ def test_01_01_test_one_object(self):
137137
image = cpi.Image(img, file_name="test_01_01_test_one_object")
138138
image_set_list = cpi.ImageSetList()
139139
image_set = image_set_list.get_image_set(0)
140-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
140+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
141141
object_set = cpo.ObjectSet()
142142
measurements = cpmeas.Measurements()
143143
pipeline = cellprofiler.pipeline.Pipeline()
@@ -182,7 +182,7 @@ def test_01_02_test_two_bright_objects(self):
182182
image = cpi.Image(img, file_name="test_01_02_test_two_bright_objects")
183183
image_set_list = cpi.ImageSetList()
184184
image_set = image_set_list.get_image_set(0)
185-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
185+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
186186
object_set = cpo.ObjectSet()
187187
measurements = cpmeas.Measurements()
188188
pipeline = cellprofiler.pipeline.Pipeline()
@@ -218,7 +218,7 @@ def test_01_03_test_two_dark_objects(self):
218218
image = cpi.Image(img, file_name="test_01_03_test_two_dark_objects")
219219
image_set_list = cpi.ImageSetList()
220220
image_set = image_set_list.get_image_set(0)
221-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
221+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
222222
object_set = cpo.ObjectSet()
223223
measurements = cpmeas.Measurements()
224224
pipeline = cellprofiler.pipeline.Pipeline()
@@ -256,7 +256,7 @@ def test_01_04_test_two_flu_bright_objects(self):
256256
image = cpi.Image(img, file_name="test_01_04_test_two_flu_bright_objects")
257257
image_set_list = cpi.ImageSetList()
258258
image_set = image_set_list.get_image_set(0)
259-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
259+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
260260
object_set = cpo.ObjectSet()
261261
measurements = cpmeas.Measurements()
262262
pipeline = cellprofiler.pipeline.Pipeline()
@@ -294,7 +294,7 @@ def test_01_05_test_two_flu_dark_objects(self):
294294
image = cpi.Image(img, file_name="test_01_05_test_two_flu_dark_objects")
295295
image_set_list = cpi.ImageSetList()
296296
image_set = image_set_list.get_image_set(0)
297-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
297+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
298298
object_set = cpo.ObjectSet()
299299
measurements = cpmeas.Measurements()
300300
pipeline = cellprofiler.pipeline.Pipeline()
@@ -336,7 +336,7 @@ def test_01_06_fill_holes(self):
336336
image = cpi.Image(img, file_name="test_01_06_fill_holes")
337337
image_set_list = cpi.ImageSetList()
338338
image_set = image_set_list.get_image_set(0)
339-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
339+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
340340
object_set = cpo.ObjectSet()
341341
measurements = cpmeas.Measurements()
342342
pipeline = cellprofiler.pipeline.Pipeline()
@@ -359,7 +359,7 @@ def test_01_07_extreme_params(self):
359359
image = cpi.Image(img, file_name="test_01_07_extreme_params")
360360
image_set_list = cpi.ImageSetList()
361361
image_set = image_set_list.get_image_set(0)
362-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
362+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
363363
object_set = cpo.ObjectSet()
364364
measurements = cpmeas.Measurements()
365365
pipeline = cellprofiler.pipeline.Pipeline()
@@ -387,7 +387,7 @@ def test_02_01_discard_large(self):
387387
image = cpi.Image(img, file_name="test_02_01_discard_large")
388388
image_set_list = cpi.ImageSetList()
389389
image_set = image_set_list.get_image_set(0)
390-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
390+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
391391
object_set = cpo.ObjectSet()
392392
measurements = cpmeas.Measurements()
393393
pipeline = cellprofiler.pipeline.Pipeline()
@@ -418,7 +418,7 @@ def test_02_02_discard_small(self):
418418
image = cpi.Image(img, file_name="test_02_02_discard_small")
419419
image_set_list = cpi.ImageSetList()
420420
image_set = image_set_list.get_image_set(0)
421-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
421+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
422422
object_set = cpo.ObjectSet()
423423
measurements = cpmeas.Measurements()
424424
pipeline = cellprofiler.pipeline.Pipeline()
@@ -454,8 +454,8 @@ def test_02_03_use_background_image(self):
454454

455455
image_set_list = cpi.ImageSetList()
456456
image_set = image_set_list.get_image_set(0)
457-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
458-
image_set.providers.append(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
457+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
458+
image_set.add_provider(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
459459
object_set = cpo.ObjectSet()
460460
measurements = cpmeas.Measurements()
461461
pipeline = cellprofiler.pipeline.Pipeline()
@@ -487,8 +487,8 @@ def test_02_04_mask_input_image(self):
487487
mask = cpi.Image(msk)
488488
image_set_list = cpi.ImageSetList()
489489
image_set = image_set_list.get_image_set(0)
490-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
491-
image_set.providers.append(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
490+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
491+
image_set.add_provider(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
492492

493493
# first try without masking
494494
object_set = cpo.ObjectSet()
@@ -548,7 +548,7 @@ def test_03_01_simple_fitting(self):
548548
image = cpi.Image(img, file_name="test_03_01_simple_fitting")
549549
image_set_list = cpi.ImageSetList()
550550
image_set = image_set_list.get_image_set(0)
551-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
551+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
552552

553553
old_params = ast.literal_eval(x.autoadapted_params.value)
554554
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):
629629

630630
image_set_list = cpi.ImageSetList()
631631
image_set = image_set_list.get_image_set(0)
632-
image_set.providers.append(cpi.VanillaImageProvider(IMAGE_NAME, image))
633-
image_set.providers.append(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
634-
image_set.providers.append(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
632+
image_set.add_provider(cpi.VanillaImageProvider(IMAGE_NAME, image))
633+
image_set.add_provider(cpi.VanillaImageProvider(MASK_IMAGE_NAME, mask))
634+
image_set.add_provider(cpi.VanillaImageProvider(BACKGROUND_IMAGE_NAME, background))
635635

636636
old_params = ast.literal_eval(x.autoadapted_params.value)
637637
input_processed, background_processed, ignore_mask_processed = x.preprocess_images(img, background_mask, ignore_mask)

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