for reader in settings['Readers']:
segFiles = glob.glob(segmentationsPath+'/'+reader+'-'+structure+'*')
if not len(segFiles):
continue
segFiles.sort()
canonicalType = getCanonicalType(data,c,s)
print 'Canonical type:',canonicalType,seriesAttributes['CanonicalType']
# consider only the most recent seg file for the given reader
segmentationFile = segFiles[-1]
imageFile = os.path.join(studyDir,s,'Reconstructions',s+'.nrrd')
measurements = mpReviewUtil.computeMeasurements(imageFile,segmentationFile,settings['MeasurementTypes'])
measurementsDir = os.path.join(studyDir,s,'Measurements')
try:
os.mkdir(measurementsDir)
except:
import shutil
oldDir = os.path.join(studyDir,s,'Measurements-old')
if not os.path.exists(oldDir):
shutil.move(measurementsDir, oldDir)
os.mkdir(measurementsDir)
measurementsFile = os.path.join(measurementsDir,s+'-'+structure+'-'+reader+'.json')
f = open(measurementsFile,'w')
print measurements
f.write(json.dumps(measurements))
f.close()
#print 'Would save PK mask to',ktransThreshFileName
sitk.WriteImage(ktransThreshImage,str(ktransThreshFileName))
map2mask[m] = ktransThreshFileName
#print maps
measurements = {}
measurementsDir = os.path.join(studyDir,s,'Measurements')
measurementsFile = os.path.join(measurementsDir,s+'-'+structure+'-'+reader+'.json')
if os.path.exists(measurementsFile):
# will need to append to the file
measurements = json.loads(open(measurementsFile,'r').read())
for m in maps:
if m.endswith('.nrrd'):
imageFile = m
measurements = mpReviewUtil.computeMeasurements(imageFile,map2mask[imageFile],settings['MeasurementTypes'])
measurements['ValidVoxelsPercentage'] = map2validVoxels[m]
pkMasksDir = os.path.split(map2mask[imageFile])[0]+'/PKmasks'
if len(os.path.split(map2mask[imageFile])[1].split('-'))>3:
#print map2mask[imageFile]
#print pkMasksDir
try:
os.mkdir(pkMasksDir)
except:
pass
try:
shutil.move(map2mask[imageFile],pkMasksDir)
except:
os.remove(pkMasksDir+'/'+os.path.split(map2mask[imageFile])[1])
shutil.move(map2mask[imageFile],pkMasksDir)
