target = []
for j in range(0, len(M.StructureSetROISequence)):
target.append(M.StructureSetROISequence[j].ROIName)
print target
for k in range(0, len(target)):
try:
print i, k
Image, Mask = PyrexReader.Img_Bimask(
Img_path[i], RT_path[i],
target[k]) #create image array and binary mask
featureVector = PyrexWithParams.CalculationRun(
Image, Mask, paramsFile) #compute radiomics
featureVector.update({
'patient': PatientID[i],
'contour': target[k]
}) #add patient ID and contour
if export_format == 'csv' and i == 0 and k == 0:
with open(os.path.join(exportDir, export_name),
'wb') as mydata:
w = csv.DictWriter(mydata, featureVector.keys())
w.writeheader()
w.writerow(featureVector)
else:
PyrexOutput.RadiomicsStore(
featureVector, exportDir, PatientID[i], target[k],
export_format, export_name
) #store radiomics locally with a specific format
except:
# logging.debug('Error: Could not find %s' % target[k])
print 'Error: Could not find', target[k]
def executeORAWbatch_roi(myWorkingDirectory, roi, myStructUID, exportDir,
export_format, export_name):
outPath = r''
#read Params file of Pyradiomics
progress_filename = os.path.join(outPath, 'pyrexbatch_log.txt')
# Configure logging
rLogger = logging.getLogger('radiomics')
# Set logging level
# rLogger.setLevel(logging.INFO) # Not needed, default log level of logger is INFO
handler = logging.FileHandler(
filename=progress_filename,
mode='w') # Create handler for writing to log file
handler.setFormatter(
logging.Formatter('%(levelname)s:%(name)s: %(message)s'))
rLogger.addHandler(handler)
logger = rLogger.getChild(
'batch') # Initialize logging for batch log messages
# Set verbosity level for output to stderr (default level = WARNING)
#radiomics.setVerbosity(logging.INFO)
logger.info('pyradiomics version: %s', radiomics.__version__)
logger.info('Reading Params file for pyradiomics')
# Reading Params file for pyradiomics
try:
paramsFile = os.path.join(os.getcwd(), 'ParamsSettings',
'Pyradiomics_Params.yaml')
except Exception:
logger.error('Could not find params file of Pyradiomics!',
exc_info=True)
exit(-1)
# logger.info('Reading Params file of Pyrex')
patient = os.listdir(myWorkingDirectory)
# logger.info('Parsing DICOM files and RTSTRUCT in working directory')
#xnat_collection(myWorkingDirectory,collectionURL,myProjectID)
Img_path, RT_path = ParseStructure(
myWorkingDirectory) #detect the path of Image and RTstruct
logger.info('DICOM and RTSTRUCT Parsing Done')
flists = pandas.DataFrame(data={
'patient': patient
}).T # create a pandas data frame for data
logger.info('Starting Pyrex')
# define export output format
if export_format == 'csv':
RESULT = pandas.DataFrame()
else:
RESULT = Graph()
for entry in flists:
results = pandas.DataFrame()
# logger.info('processing patient: %s', patient[entry])
mask_vol = PyrexReader.Read_RTSTRUCT(RT_path[entry])
logger.info('Loading RTSTRUCT: %s', RT_path[entry])
M = mask_vol[0]
target = []
for j in range(0, len(M.StructureSetROISequence)):
target.append(M.StructureSetROISequence[j].ROIName)
logger.info('ROI: %s', target)
if roi in target:
try:
featureVector = flists[entry]
#featureVector['patient'] = featureVector['patient'] + 'Pyrex_' + target[k]
Image, Mask = PyrexReader.Img_Bimask(Img_path[entry],
RT_path[entry], roi)
logger.info('Processing Radiomics on %s of Patient (%s)', roi,
patient[entry])
if export_format == 'csv': # sava results in csv
try:
result = pandas.Series(
PyrexWithParams.CalculationRun(
Image, Mask, paramsFile))
contour = pandas.Series({'contour': roi})
structUID = pandas.Series({'structUID': myStructUID})
featureVector = featureVector.append(contour)
featureVector = featureVector.append(structUID)
featureVector = featureVector.append(result)
featureVector.name = 1
results = results.join(featureVector, how='outer')
Image = []
Mask = []
result = []
RESULT = pandas.concat([RESULT, results], axis=1)
except Exception:
logger.error(
'FEATURE EXTRACTION FAILED for CSV output:',
exc_info=True)
else: # save results in triple stroe
try:
featureVector = PyrexWithParams.CalculationRun(
Image, Mask, paramsFile) #compute radiomics
featureVector.update({
'patient': patient[entry],
'contour': target[k],
'RTid': myStructUID
}) #add patient ID and contour
graph_roi = PyrexOutput.RadiomicsRDF(
featureVector, exportDir, patient[entry],
myStructUID, target[k], export_format, export_name
) #store radiomics locally with a specific format
RESULT = RESULT + graph_roi
logger.info('Extraction complete, writing rdf')
except Exception:
logger.error(
'FEATURE EXTRACTION FAILED for RDF output:',
exc_info=True)
except Exception:
logger.info('FEATURE EXTRACTION FAILED:')
logger.info('-------------------------------------------')
print(patient[entry], roi)
else:
print('%s is not exist in RTSTRUCTURE', roi)