def test_polygon_merger_tiled_masks(self, girderClient): # noqa
"""Test Polygon_merger.run()."""
# read GTCodes dataframe
gtcodePath = getTestFilePath('sample_GTcodes.csv')
GTCodes_df = read_csv(gtcodePath)
GTCodes_df.index = GTCodes_df.loc[:, 'group']
# This is where masks for adjacent rois are saved
mask_loadpath = getTestFilePath(
os.path.join('annotations_and_masks', 'polygon_merger_roi_masks'))
maskpaths = [
os.path.join(mask_loadpath, j) for j in os.listdir(mask_loadpath)
if j.endswith('.png')
]
# init and run polygon merger on masks grid
pm = Polygon_merger(maskpaths=maskpaths,
GTCodes_df=GTCodes_df,
discard_nonenclosed_background=True,
verbose=1)
contours_df = pm.run()
# make sure it is what we expect
assert contours_df.shape == (13, 13)
assert set(contours_df.loc[:, 'group']) == {
'roi', 'mostly_tumor', 'mostly_stroma',
'mostly_lymphocytic_infiltrate'
}
# deleting existing annotations in target slide (if any)
sampleSlideItem = girderClient.resourceLookup(
'/user/admin/Public/TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39.svs'
) # noqa
sampleSlideId = str(sampleSlideItem['_id'])
delete_annotations_in_slide(girderClient, sampleSlideId)
# get list of annotation documents
annotation_docs = get_annotation_documents_from_contours(
contours_df.copy(),
separate_docs_by_group=True,
docnamePrefix='test',
verbose=False,
monitorPrefix=sampleSlideId + ": annotation docs")
# post annotations to slide -- make sure it posts without errors
for annotation_doc in annotation_docs:
resp = girderClient.post("/annotation?itemId=" + sampleSlideId,
json=annotation_doc)
assert 'annotation' in resp.keys()
def test_get_annotation_documents_from_contours(self,
girderClient): # noqa
"""Test get_contours_from_bin_mask()."""
self._setup()
sampleSlideItem = girderClient.resourceLookup(
'/user/admin/Public/TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39.svs'
) # noqa
sampleSlideId = str(sampleSlideItem['_id'])
# get list of annotation documents
annprops = {
'X_OFFSET': self.X_OFFSET,
'Y_OFFSET': self.Y_OFFSET,
'opacity': 0.2,
'lineWidth': 4.0,
}
annotation_docs = get_annotation_documents_from_contours(
self.CONTOURS_DF.copy(),
separate_docs_by_group=True,
annots_per_doc=10,
docnamePrefix='test',
annprops=annprops,
verbose=False,
monitorPrefix=self.MASKNAME[:12] + ": annotation docs")
# make sure its what we expect
assert len(annotation_docs) == 8
assert {j['name']
for j in annotation_docs} == {
'test_blood_vessel-0', 'test_exclude-0',
'test_mostly_lymphocytic_infiltrate-0',
'test_mostly_stroma-0', 'test_mostly_tumor-0',
'test_mostly_tumor-1', 'test_normal_acinus_or_duct-0',
'test_roi-0'
}
# deleting existing annotations in target slide (if any)
delete_annotations_in_slide(girderClient, sampleSlideId)
# post annotations to slide -- make sure it posts without errors
resp = girderClient.post("/annotation?itemId=" + sampleSlideId,
json=annotation_docs[0])
assert 'annotation' in resp.keys()