def test_t2_star_map(self):
ys, _, _, _ = self._generate_mock_data()
scan = Cones(ys)
# No mask
tissue = FemoralCartilage()
map1 = scan.generate_t2_star_map(tissue,
num_workers=util.num_workers())
assert map1 is not None, "map should not be None"
mask = MedicalVolume(np.ones(ys[0].shape), np.eye(4))
# Use a mask
tissue.set_mask(mask)
map2 = scan.generate_t2_star_map(tissue,
num_workers=util.num_workers())
assert map2 is not None, "map should not be None"
assert map1.volumetric_map.is_identical(map2.volumetric_map)
# Use a mask as a path
tissue = FemoralCartilage()
mask_path = os.path.join(self.data_dirpath,
"test_t2_star_map_mask.nii.gz")
NiftiWriter().save(mask, mask_path)
map2 = scan.generate_t2_star_map(tissue,
num_workers=util.num_workers(),
mask_path=mask_path)
assert map2 is not None, "map should not be None"
assert map1.volumetric_map.is_identical(map2.volumetric_map)
def test_t2_star_map(self):
scan = self.SCAN_TYPE(dicom_path=self.dicom_dirpath)
scan.interregister(target_path=QDESS_ECHO1_PATH, target_mask_path=TARGET_MASK_PATH)
# run analysis with femoral cartilage, without mask in tissue, but mask as additional input.
tissue = FemoralCartilage()
map1 = scan.generate_t2_star_map(tissue, TARGET_MASK_PATH)
assert map1 is not None, "map should not be None"
# add mask to femoral cartilage and run
nr = NiftiReader()
tissue.set_mask(nr.load(TARGET_MASK_PATH))
map2 = scan.generate_t2_star_map(tissue)
assert map2 is not None, "map should not be None"
# map1 and map2 should be identical
assert (map1.volumetric_map.is_identical(map2.volumetric_map))
def test_generate_t2_map(self):
ys, _, _, _, _ = self._generate_mock_data()
scan = Mapss(ys)
mask = MedicalVolume(np.ones(ys[0].shape), np.eye(4))
mask_path = os.path.join(self.data_dirpath, "test_t2_mask.nii.gz")
NiftiWriter().save(mask, mask_path)
tissue = FemoralCartilage()
map1 = scan.generate_t2_map(tissue)
assert map1 is not None
tissue.set_mask(mask)
map2 = scan.generate_t2_map(tissue, num_workers=util.num_workers())
assert map2 is not None
assert map1.volumetric_map.is_identical(map2.volumetric_map)
map2 = scan.generate_t2_map(tissue, mask_path=mask, num_workers=util.num_workers())
assert map2 is not None
assert map1.volumetric_map.is_identical(map2.volumetric_map)
def test_quant_val_fitting(self):
"""Test quantitative fitting (T1-rho, T2)"""
scan = self.SCAN_TYPE(dicom_path=self.dicom_dirpath)
actions = [scan.generate_t1_rho_map, scan.generate_t2_map]
for action in actions:
tissue = FemoralCartilage()
map1 = action(tissue, MANUAL_SEGMENTATION_MASK_PATH)
assert map1 is not None, "%s: map1 should not be None" % str(
action)
nr = NiftiReader()
tissue.set_mask(nr.load(MANUAL_SEGMENTATION_MASK_PATH))
map2 = action(tissue)
assert map2 is not None, "%s: map2 should not be None" % str(
action)
# map1 and map2 should be identical
assert map1.volumetric_map.is_identical(
map2.volumetric_map
), "%s: map1 and map2 should be identical" % str(action)