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"
#print "------------- iteration {0} -------------".format(i)
#print params
# 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)
