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 _setup(self):
# read GTCodes dataframe
gtcodePath = getTestFilePath('sample_GTcodes.csv')
self.GTCodes_df = read_csv(gtcodePath)
self.GTCodes_df.index = self.GTCodes_df.loc[:, 'group']
# read sample contours_df dataframe to test against
contoursDfPath = getTestFilePath(
os.path.join('annotations_and_masks', 'sample_contours_df.tsv'))
self.CONTOURS_DF = read_csv(contoursDfPath, sep='\t', index_col=0)
# read mask
self.X_OFFSET = 59206
self.Y_OFFSET = 33505
self.MASKNAME = (
'TCGA-A2-A0YE-01Z-00-DX1.8A2E3094-5755-42BC-969D-7F0A2ECA0F39_'
'left-%d_top-%d_mag-BASE.png' % (self.X_OFFSET, self.Y_OFFSET))
MASKPATH = getTestFilePath(
os.path.join('annotations_and_masks', self.MASKNAME))
self.MASK = imread(MASKPATH)
def test_prep(girderClient): # noqa
cfg.gc = girderClient
cfg.URL = cfg.gc.urlBase.replace('api/v1/', '')
# GT codes dict for parsing into label mask
gtcodePath = getTestFilePath('sample_GTcodes.csv')
cfg.GTCodes_dict = read_csv(gtcodePath)
cfg.GTCodes_dict.index = cfg.GTCodes_dict.loc[:, 'group']
cfg.GTCodes_dict = cfg.GTCodes_dict.to_dict(orient='index')
# just a temp directory to save masks
cfg.BASE_SAVEPATH = tempfile.mkdtemp()
cfg.SAVEPATHS = {
'contours': os.path.join(cfg.BASE_SAVEPATH, 'contours'),
'rgb': os.path.join(cfg.BASE_SAVEPATH, 'rgbs'),
'visualization': os.path.join(cfg.BASE_SAVEPATH, 'vis'),
}
for _, savepath in cfg.SAVEPATHS.items():
os.mkdir(savepath)
# where to save gallery
cfg.combinedvis_savepath = os.path.join(cfg.BASE_SAVEPATH, 'combinedvis')
os.mkdir(cfg.combinedvis_savepath)
# get original item
iteminfo = cfg.gc.get('/item',
parameters={'text': "TCGA-A2-A0YE-01Z-00-DX1"})[0]
# create the folder to parse its contents into galleries
folderinfo = cfg.gc.post('/folder',
data={
'parentId': iteminfo['folderId'],
'name': 'test'
})
cfg.folderid = folderinfo['_id']
# create girder folder to post resultant galleries
post_folderinfo = cfg.gc.post('/folder',
data={
'parentId': iteminfo['folderId'],
'name': 'test-post'
})
cfg.post_folderid = post_folderinfo['_id']
# copy the item multiple times to create dummy database
for i in range(2):
_ = cfg.gc.post("/item/%s/copy" % iteminfo['_id'],
data={
'name': 'testSlide%dForRevGal' % i,
'copyAnnotations': True,
'folderId': cfg.folderid,
})