def test_vessel_tree_lar(self):
import lisa.gt_lar
tvg = TreeGenerator(lisa.gt_lar.GTLar)
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.voxelsize_mm = [1, 1, 1]
tvg.shape = [100, 100, 100]
output = tvg.generateTree() # noqa
if self.interactiveTests:
tvg.show()
def test_synthetic_data_vessel_tree_evaluation(self):
"""
Generovani umeleho stromu do 3D a jeho evaluace.
V testu dochazi ke kontrole predpokladaneho objemu a deky cev
"""
# import segmentation
# import misc
# generate 3d data from yaml for testing
tvg = TreeGenerator()
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.voxelsize_mm = [1, 1, 1]
tvg.shape = [100, 100, 100]
data3d = tvg.generateTree()
# init histology Analyser
metadata = {'voxelsize_mm': tvg.voxelsize_mm}
data3d = data3d * 10
threshold = 2.5
ha = HistologyAnalyser(data3d, metadata, threshold)
# segmented data
ha.data_to_binar()
ha.data_to_skeleton()
# get statistics
ha.data_to_statistics()
yaml_new = os.path.join(path_to_script, "hist_stats_new.yaml")
ha.writeStatsToYAML(filename=yaml_new)
# get histology reports
hr = HistologyReport()
hr.importFromYaml(yaml_path)
hr.generateStats()
stats_orig = hr.stats['Report']
hr = HistologyReport()
hr.importFromYaml(yaml_new)
hr.generateStats()
stats_new = hr.stats['Report']
ha.writeStatsToCSV(filename=yaml_new)
# compare
self.assertGreater(stats_orig['Other']['Total length mm'],stats_new['Other']['Total length mm']*0.9) # noqa
self.assertLess(stats_orig['Other']['Total length mm'],stats_new['Other']['Total length mm']*1.1) # noqa
self.assertGreater(stats_orig['Other']['Avg length mm'],stats_new['Other']['Avg length mm']*0.9) # noqa
self.assertLess(stats_orig['Other']['Avg length mm'],stats_new['Other']['Avg length mm']*1.1) # noqa
self.assertGreater(stats_orig['Other']['Avg radius mm'],stats_new['Other']['Avg radius mm']*0.9) # noqa
self.assertLess(stats_orig['Other']['Avg radius mm'],stats_new['Other']['Avg radius mm']*1.1) # noqa
def test_surface_measurement_find_edge(self):
import lisa.surface_measurement as sm
tvg = TreeGenerator()
yaml_path = os.path.join(path_to_script, "./hist_stats_test.yaml")
tvg.importFromYaml(yaml_path)
tvg.voxelsize_mm = [1, 1, 1]
tvg.shape = [100, 100, 100]
data3d = tvg.generateTree()
# init histology Analyser
# metadata = {'voxelsize_mm': tvg.voxelsize_mm}
# data3d = data3d * 10
# threshold = 2.5
im_edg = sm.find_edge(data3d, 0)
# in this area should be positive edge
self.assertGreater(
np.sum(im_edg[25:30, 25:30, 30]),
3
)