def test_vessel_particles():
try:
# 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 to VesselParticles
input_ct = this_dir + '/../../../Testing/Data/Input/vesselgauss.nrrd'
input_mask = \
this_dir + '/../../../Testing/Data/Input/vessel_vesselSeedsMask.nrrd'
#tmp_dir = this_dir + '/../../../Testing/tmp/'
tmp_dir = tempfile.mkdtemp()
output_particles = os.path.join(tmp_dir, 'vessel_particles.vtk')
print tmp_dir
max_scale = 6.0
live_th = -100
seed_th = -80
scale_samples = 10
down_sample_rate = 1.0
min_intensity = -800
max_intensity = 400
# Generate the airway particles
vp = VesselParticles(input_ct, output_particles, tmp_dir, input_mask,
max_scale, live_th, seed_th, scale_samples,
down_sample_rate, min_intensity, max_intensity)
vp.execute()
# Read in the reference data set for comparison
ref_reader = vtk.vtkPolyDataReader()
ref_reader.SetFileName(this_dir + \
'/../../../Testing/Data/Input/vessel_particles.vtk')
ref_reader.Update()
# Now read in the output data set
test_reader = vtk.vtkPolyDataReader()
test_reader.SetFileName(output_particles)
test_reader.Update()
pm = ParticleMetrics(ref_reader.GetOutput(), test_reader.GetOutput(),
'vessel')
assert pm.get_particles_dice() > 0.97, \
"Vessel particle Dice score lower than expected"
finally:
#Clear particles cache
vp._clean_tmp_dir = True
vp.clean_tmp_dir()
shutil.rmtree(tmp_dir)
def execute(self):
header=nrrd.read_header(open(self._ct_file_name))
max_z=header['sizes'][2]
spacing=[header['space directions'][kk][kk] for kk in xrange(3)]
if len(crop) < 2:
crop_flag = False
else:
if crop[0]<0:
crop[0]=0
elif crop[1]>max_z:
crop_flag = False
crop_flag = True
ct_file_name = self._ct_file_name
pl_file_name = self._pl_file_name
#Data preprocessing (cropping and/or resampling) before region based analysis
if self._justparticles == False:
#Crop volume if flag is set
ct_file_name_crop = os.path.join(self._tmp_dir,self._case_id + "_crop.nhdr")
pl_file_name_crop = os.path.join(self._tmp_dir,self._case_id + "_croppartialLungLabelMap.nhdr")
if crop_flag == True:
if self._rate == 1:
ratestr = "="
else:
ratestr = 'x%f' % rate
tmpCommand = "unu crop -min 0 0 %(z1)d -max M M %(z2)d -i %(in)s | unu resample -k %(kernel)s -s = = %(ratestr)s -o %(out)s"
tmpCommandCT = tmpCommand % {'z1':crop[0],'z2':crop[1],'in':ct_file_name,'out':ct_file_name_crop,'ratestr':ratestr,'kernel':"cubic:1,0"}
tmpCommandPL = tmpCommand % {'z1':crop[0],'z2':crop[1],'in':pl_file_name,'out':pl_file_name_crop,'ratestr':ratestr,'kernel':"cheap"}
print tmpCommandCT
print tmpCommandPL
subprocess.call(tmpCommandCT,shell=True)
subprocess.call(tmpCommandPL,shell=True)
ct_file_name = ct_file_name_crop
pl_file_name = pl_file_name_crop
#Do resampling to isotropic voxel size to compute accurate scale measurements
ct_file_name_resample = os.path.join(self._tmp_dir,self._case_id + "_resample.nhdr")
pl_file_name_resample = os.path.join(self._tmp_dir,self._case_id + "_resamplepartialLungLabelMap.nhdr")
if self._voxel_size>0:
tmpCommand = "unu resample -k %(kernel)s -s x%(f1)f x%(f2)f x%(f3)f -i %(in)s -o %(out)s"
tmpCommandCT = tmpCommand % {'in':ct_file_name,'out':ct_file_name_resample,'kernel':"tent",'f1':spacing[0]/self._voxel_size,'f2':spacing[1]/self._voxel_size,'f3':spacing[2]/self._voxel_size}
tmpCommandPL = tmpCommand % {'in':pl_file_name,'out':pl_file_name_resample,'kernel':"cheap",'f1':spacing[0]/self._voxel_size,'f2':spacing[1]/self._voxel_size,'f3':spacing[2]/self._voxel_size}
print tmpCommandCT
print tmpCommandPL
subprocess.call(tmpCommandCT,shell=True)
subprocess.call(tmpCommandPL,shell=True)
ct_file_name = ct_file_name_resample
pl_file_name = pl_file_name_resample
for ii in self._regions:
rtag = ii.lower()
tmpDir = os.path.join(self._tmp_dir,rtag)
if os.path.exists(tmpDir) == False:
os.mkdir(tmpDir)
# Define FileNames that will be used
pl_file_nameRegion= os.path.join(tmpDir,self._case_id + "_" + rtag + "_partialLungLabelMap.nhdr")
ct_file_nameRegion= os.path.join(tmpDir,self._case_id + "_" + rtag + ".nhdr")
featureMapFileNameRegion = os.path.join(tmpDir,self._case_id + "_" + rtag + "_featureMap.nhdr")
maskFileNameRegion = os.path.join(tmpDir,self._case_id + "_" + rtag + "_mask.nhdr")
particlesFileNameRegion = os.path.join(self._output_prefix+ "_" + rtag + "VesselParticles.vtk")
if self._justparticles == False:
#Create SubVolume Region
tmpCommand ="CropLung -r %(region)s -m 0 -v -1000 -i %(ct-in)s --plf %(lm-in)s -o %(ct-out)s --opl %(lm-out)s"
tmpCommand = tmpCommand % {'region':ii,'ct-in':ct_file_name,'lm-in':pl_file_name,'ct-out':ct_file_nameRegion,'lm-out':pl_file_nameRegion}
tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
print tmpCommand
subprocess.call( tmpCommand, shell=True )
#Extract Lung Region + Distance map to peel lung
tmpCommand ="ExtractChestLabelMap -r %(region)s -i %(lm-in)s -o %(lm-out)s"
tmpCommand = tmpCommand % {'region':ii,'lm-in':pl_file_nameRegion,'lm-out':pl_file_nameRegion}
tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
print tmpCommand
subprocess.call( tmpCommand, shell=True )
tmpCommand ="unu 2op gt %(lm-in)s 0.5 -o %(lm-out)s"
tmpCommand = tmpCommand % {'lm-in':pl_file_nameRegion,'lm-out':pl_file_nameRegion}
print tmpCommand
subprocess.call( tmpCommand, shell=True )
#tmpCommand ="ComputeDistanceMap -l %(lm-in)s -d %(distance-map)s -s 2"
#tmpCommand = tmpCommand % {'lm-in':self._pl_file_nameRegion,'distance-map':self._pl_file_nameRegion}
#tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
#print tmpCommand
#subprocess.call( tmpCommand, shell=True )
tmpCommand ="pxdistancetransform -in %(lm-in)s -out %(distance-map)s"
tmpCommand = tmpCommand % {'lm-in':pl_file_nameRegion,'distance-map':pl_file_nameRegion}
tmpCommand = os.path.join(path['ITKTOOLS_PATH'],tmpCommand)
print tmpCommand
subprocess.call( tmpCommand, shell=True )
tmpCommand ="unu 2op lt %(distance-map)s %(distance)f -t short -o %(lm-out)s"
tmpCommand = tmpCommand % {'distance-map':pl_file_nameRegion,'distance':self._distance_from_wall,'lm-out':pl_file_nameRegion}
print tmpCommand
subprocess.call( tmpCommand, shell=True )
# Compute Frangi
if self._init_method == 'Frangi':
tmpCommand = "ComputeFeatureStrength -i %(in)s -m Frangi -f RidgeLine --std %(minscale)f,4,%(maxscale)f --ssm 1 --alpha 0.5 --beta 0.5 --C 250 -o %(out)s"
tmpCommand = tmpCommand % {'in':ct_file_nameRegion,'out':featureMapFileNameRegion,'minscale':self._min_scale,'maxscale':self._max_scale}
tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
print tmpCommand
#subprocess.call( tmpCommand, shell=True )
#Hist equalization, threshold Feature strength and masking
tmpCommand = "unu 2op x %(feat)s %(mask)s -t float | unu heq -b 10000 -a 0.5 -s 2 | unu 2op gt - %(vesselness_th)f | unu convert -t short -o %(out)s"
tmpCommand = tmpCommand % {'feat':featureMapFileNameRegion,'mask':pl_file_nameRegion,'vesselness_th':self._vesselness_th,'out':maskFileNameRegion}
print tmpCommand
subprocess.call( tmpCommand , shell=True)
elif self._init_method == 'StrainEnergy':
tmpCommand = "ComputeFeatureStrength -i %(in)s -m StrainEnergy -f RidgeLine --std %(minscale)f,4,%(maxscale)f --ssm 1 --alpha 0.2 --beta 0.1 --kappa 0.5 --nu 0.1 -o %(out)s"
tmpCommand = tmpCommand % {'in':ct_file_nameRegion,'out':featureMapFileNameRegion,'minscale':self._min_scale,'maxscale':self._max_scale}
tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
print tmpCommand
subprocess.call( tmpCommand, shell=True )
#Hist equalization, threshold Feature strength and masking
tmpCommand = "unu 2op x %(feat)s %(mask)s -t float | unu heq -b 10000 -a 0.5 -s 2 | unu 2op gt - %(vesselness_th)f | unu convert -t short -o %(out)s"
tmpCommand = tmpCommand % {'feat':featureMapFileNameRegion,'mask':pl_file_nameRegion,'vesselness_th':self._vesselness_th,'out':maskFileNameRegion}
print tmpCommand
subprocess.call( tmpCommand , shell=True)
elif self._init_method == 'Threshold':
tmpCommand = "unu 2op gt %(in)s %(intensity_th)f | unu 2op x - %(mask)s -o %(out)s"
tmpCommand = tmpCommand % {'in':ct_file_nameRegion,'mask':pl_file_nameRegion,'intensity_th':self._intensity_th,'out':maskFileNameRegion}
print tmpCommand
subprocess.call( tmpCommand , shell=True)
#Binary Thinning
tmpCommand = "GenerateBinaryThinning3D -i %(in)s -o %(out)s"
tmpCommand = tmpCommand % {'in':maskFileNameRegion,'out':maskFileNameRegion}
tmpCommand = os.path.join(path['CIP_PATH'],tmpCommand)
print tmpCommand
subprocess.call( tmpCommand, shell=True)
# Vessel Particles For the Region
if self._multires==False:
particlesGenerator = VesselParticles(ct_file_nameRegion,particlesFileNameRegion,tmpDir,maskFileNameRegion,live_thresh=self._lth,seed_thresh=self._sth,min_intensity=-950,max_intensity=100)
particlesGenerator._clean_tmp_dir=self._clean_cache
particlesGenerator._interations_phase3 = 70
particlesGenerator._irad_phase3 = 0.9
particlesGenerator._srad_phase3 = 4
particlesGenerator._verbose = 0
particlesGenerator.execute()
else:
particlesGenerator = MultiResVesselParticles(ct_file_nameRegion,particlesFileNameRegion,tmpDir,maskFileNameRegion,live_thresh=-600,seed_thresh=-600)
particlesGenerator._clean_tmp_dir=self._clean_cache
particlesGenerator.execute()
