def test_compute_dice_coefficient():
ref = np.zeros([3, 3, 3])
test = np.zeros([3, 3, 3])
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 1.0, "Unexpected Dice coefficient"
test += 1
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 0.0, "Unexpected Dice coefficient"
ref += 1
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 1.0, "Unexpected Dice coefficient"
ref[1, 1, 1] = 0
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 26*2/(27+26.), "Unexpected Dice coefficient"
ref[1, 1, 1] = 2
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 26*2/(27+27.), "Unexpected Dice coefficient"
def test_compute_dice_coefficient():
ref = np.zeros([3, 3, 3])
test = np.zeros([3, 3, 3])
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 1.0, "Unexpected Dice coefficient"
test += 1
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 0.0, "Unexpected Dice coefficient"
ref += 1
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 1.0, "Unexpected Dice coefficient"
ref[1, 1, 1] = 0
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 26 * 2 / (27 + 26.), "Unexpected Dice coefficient"
ref[1, 1, 1] = 2
dice = compute_dice_coefficient(ref, test, 1)
assert dice == 26 * 2 / (27 + 27.), "Unexpected Dice coefficient"
def test_vessel_particles_mask_workflow():
# Get the path to the this test so that we can reference the test data
this_dir = os.path.dirname(os.path.realpath(__file__))
# Set up the inputs and run the workflow
ct_file_name = this_dir + '/../../../../Testing/Data/Input/vessel.nrrd'
label_map_file_name = \
this_dir + '/../../../../Testing/Data/Input/vessel_volumeMask.nrrd'
seeds_mask_file_name = \
this_dir + '/../../../../Testing/Data/Input/vessel_vesselSeedsMask.nrrd'
tmp_dir = tempfile.mkdtemp()
vessel_seeds_mask_file_name = os.path.join(tmp_dir, 'vesselSeedsMask.nrrd')
wf = VesselParticlesMaskWorkflow(ct_file_name, label_map_file_name,
tmp_dir, vessel_seeds_mask_file_name)
wf.run()
ref, ref_header = nrrd.read(seeds_mask_file_name)
test, test_header = nrrd.read(vessel_seeds_mask_file_name)
dice = compute_dice_coefficient(ref, test, 1)
shutil.rmtree(tmp_dir)
assert dice > 0.995, "Dice coefficient lower than expected"
# Get the path to the this test so that we can reference the test data
this_dir = os.path.dirname(os.path.realpath(__file__))
# Set up the inputs and run the workflow
ct_file_name = '/Users/jinho/Github/ChestImagingPlatform/Testing/Data/Input/vessel.nrrd'
label_map_file_name = '/Users/jinho/Github/ChestImagingPlatform/Testing/Data/Input/vessel_volumeMask.nrrd'
seeds_mask_file_name = '/Users/jinho/Github/ChestImagingPlatform/Testing/Data/Input/vessel_vesselSeedsMask.nrrd'
tmp_dir = tempfile.mkdtemp()
vessel_seeds_mask_file_name = os.path.join(tmp_dir, 'vesselSeedsMask.nrrd')
gaussianStd = [0.7, 4.0, params['num_steps']]
wf = VesselParticlesMaskWorkflow(ct_file_name, label_map_file_name,
tmp_dir, vessel_seeds_mask_file_name)
wf.get_node('compute_feature_strength').inputs.alpha = params['alpha']
wf.get_node('compute_feature_strength').inputs.beta = params['beta']
wf.get_node('compute_feature_strength').inputs.C = params['C']
wf.get_node('compute_feature_strength').inputs.std = gaussianStd
wf.get_node('unu_heq').inputs.amount = params['amount']
wf.get_node('unu_heq').inputs.smart = params['smart']
wf.run()
ref, ref_header = nrrd.read(seeds_mask_file_name)
test, test_header = nrrd.read(vessel_seeds_mask_file_name)
score = compute_dice_coefficient(ref, test, 1)
#print vessel_seeds_mask_file_name
scientist.update(params, score)
shutil.rmtree(tmp_dir)