def __init__(self):
self.DBClient = DbUtils()
self.MatchDBClient = DbUtils(database=pc.ADNI_dataMatchDBName)
self.PETHelper = PETHelper()
def __init__(self):
self.DBClient = DbUtils()
self.MatchDBClient = DbUtils(database=pc.ADNI_dataMatchDBName)
self.PETHelper = PETHelper()
class ADNI_V2_AV45:
def __init__(self):
self.DBClient = DbUtils()
self.MatchDBClient = DbUtils(database=pc.ADNI_dataMatchDBName)
self.PETHelper = PETHelper()
def process(self, processingItem):
processingItemObj = ProcessingItemObj(processingItem)
matching_t1 = ADNI_T1_Helper().getMatchingT1(processingItemObj)
if not matching_t1:
PipelineLogger.log('root', 'error', 'PET cannot be processed no matching T1 found. - {0} - {1} - {2}.'.format(processingItemObj.subject_rid, processingItemObj.modality, processingItemObj.scan_date))
return 0
processed = ADNI_T1_Helper().checkProcessed(matching_t1)
if not processed:
PipelineLogger.log('root', 'error', 'PET cannot be processed due to matching T1 not being processed - {0}'.format(matching_t1))
return 0
else:
PipelineLogger.log('root', 'INFO', '+++++++++ PET ready to be processed. Will check for initial xfm. - {0} - {1}'.format(processingItemObj.subject_rid, processingItemObj.scan_date))
if processingItemObj.manual_xfm == 'Req_man_reg':
coregDone = self.PETHelper.checkIfAlreadyDone(processingItemObj, matching_t1)
if coregDone:
manualXFM = coregDone
setPPTableSQL = "UPDATE {0}_{1}_Pipeline SET MANUAL_XFM = '{2}' WHERE RECORD_ID = {3}".format(processingItemObj.study, processingItemObj.modality, manualXFM, processingItemObj.table_id)
self.DBClient.executeNoResult(setPPTableSQL)
self.processPET(processingItemObj, processed)
else:
self.PETHelper.requestCoreg(processingItemObj, matching_t1)
PipelineLogger.log('root', 'INFO', 'Manual XFM was not found. Request to create one may have added. - {0} - {1}'.format(processingItemObj.subject_rid, processingItemObj.scan_date))
return 0
else:
self.processPET(processingItemObj, processed)
def getScanType(self, processingItemObj):
r = self.DBClient.executeAllResults("SELECT SCAN_TYPE FROM Conversion WHERE STUDY = '{0}' AND RID = '{1}' "
"AND SCAN_DATE = '{2}' AND S_IDENTIFIER = '{3}' "
"AND I_IDENTIFIER = '{4}'".format(processingItemObj.study,
processingItemObj.subject_rid,
processingItemObj.scan_date,
processingItemObj.s_identifier,
processingItemObj.i_identifier))
return r[0][0]
def processPET(self, processingItemObj, matchT1Path):
petFileName = '{0}/{1}_{2}{3}{4}{5}_{6}.mnc'.format(processingItemObj.converted_folder, processingItemObj.study,
processingItemObj.subject_rid, processingItemObj.scan_date.replace('-', ''),
processingItemObj.s_identifier, processingItemObj.i_identifier,
self.getScanType(processingItemObj))
processedFolder = '{0}/processed'.format(processingItemObj.root_folder)
logDir = '{0}/logs'.format(processingItemObj.root_folder)
PipelineLogger.log('manager', 'info', 'PET processing starting for {0}'.format(petFileName))
try:
distutils.dir_util.mkpath(logDir)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in creating log folder \n {0}'.format(e))
return 0
id = '{0}{1}{2}{3}'.format(processingItemObj.subject_rid, processingItemObj.scan_date.replace('-', ''), processingItemObj.s_identifier, processingItemObj.i_identifier)
paramStrd = ast.literal_eval(processingItemObj.parameters)
paramStrt = ' '.join(['[\"{0}\"]=\"{1}\"'.format(k, v) for k,v in paramStrd.items()])
paramStr = '({0})'.format(paramStrt)
petCMD = "source /opt/minc-toolkit/minc-toolkit-config.sh; Pipelines/ADNI_AV45/ADNI_V2_AV45_Process {0} {1} {2} {3} {4} {5} '{6}' {7} {8}".format(id, petFileName, processedFolder, matchT1Path, 'auto' if processingItemObj.manual_xfm == '' else processingItemObj.manual_xfm, logDir, paramStr,socket.gethostname(), 50500)
try:
processedFolder_del = '{0}/processed_del'.format(processingItemObj.root_folder)
os.rename(processedFolder, processedFolder_del)
shutil.rmtree(processedFolder_del)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in deleting old processing folder. \n {0}'.format(e))
try:
distutils.dir_util.mkpath(processedFolder)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in creating processing folder. \n {0}'.format(e))
return 0
PipelineLogger.log('manager', 'debug', 'Command : {0}'.format(petCMD))
p = subprocess.Popen(petCMD, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, executable='/bin/bash')
out, err = p.communicate()
PipelineLogger.log('manager', 'debug', 'Process Log Output : \n{0}'.format(out))
PipelineLogger.log('manager', 'debug', 'Process Log Err : \n{0}'.format(err))
QSubJobHandler.submittedJobs[id] = QSubJob(id, '02:00:00', processingItemObj, 'av45')
return 1
class ADNI_V1_AV1451:
def __init__(self):
self.DBClient = DbUtils()
self.MatchDBClient = DbUtils(database=pc.ADNI_dataMatchDBName)
self.PETHelper = PETHelper()
def process(self, processingItem):
processingItemObj = ProcessingItemObj(processingItem)
matching_t1 = ADNI_T1_Helper().getMatchingT1(processingItemObj)
if not matching_t1:
PipelineLogger.log('root', 'error', 'PET cannot be processed no matching T1 found. - {0} - {1} - {2}.'.format(processingItemObj.subject_rid, processingItemObj.modality, processingItemObj.scan_date))
return 0
processed = ADNI_T1_Helper().checkProcessed(matching_t1)
if not processed:
PipelineLogger.log('root', 'error', 'PET cannot be processed due to matching T1 not being processed - {0}'.format(matching_t1))
return 0
else:
PipelineLogger.log('root', 'INFO', '+++++++++ PET ready to be processed. Will check for xfm. - {0} - {1}'.format(processingItemObj.subject_rid, processingItemObj.scan_date))
if processingItemObj.manual_xfm == '':
manualXFM = self.PETHelper.getManualXFM(processingItemObj, matching_t1)
processingItemObj.manual_xfm = manualXFM
elif processingItemObj.manual_xfm == 'Req_man_reg':
coregDone = self.PETHelper.checkIfAlreadyDone(processingItemObj, matching_t1)
if coregDone:
manualXFM = coregDone
setPPTableSQL = "UPDATE {0}_{1}_Pipeline SET MANUAL_XFM = '{2}' WHERE RECORD_ID = {3}".format(processingItemObj.study, processingItemObj.modality, manualXFM, processingItemObj.table_id)
self.DBClient.executeNoResult(setPPTableSQL)
else:
self.PETHelper.requestCoreg(processingItemObj, matching_t1)
PipelineLogger.log('root', 'INFO', 'Manual XFM was not found. Request to create one may have added. - {0} - {1}'.format(processingItemObj.subject_rid, processingItemObj.scan_date))
return 0
else:
manualXFM = processingItemObj.manual_xfm
if manualXFM:
self.processPET(processingItemObj, processed)
else:
PipelineLogger.log('root', 'INFO', 'Manual XFM was not found. Request to create one may have added. - {0} - {1}'.format(processingItemObj.subject_rid, processingItemObj.scan_date))
return 0
def getScanType(self, processingItemObj):
r = self.DBClient.executeAllResults("SELECT SCAN_TYPE FROM Conversion WHERE STUDY = '{0}' AND RID = '{1}' "
"AND SCAN_DATE = '{2}' AND S_IDENTIFIER = '{3}' "
"AND I_IDENTIFIER = '{4}'".format(processingItemObj.study,
processingItemObj.subject_rid,
processingItemObj.scan_date,
processingItemObj.s_identifier,
processingItemObj.i_identifier))
return r[0][0]
def processPET(self, processingItemObj, matchT1Path):
petFileName = '{0}/{1}_{2}{3}{4}{5}_{6}.mnc'.format(processingItemObj.converted_folder, processingItemObj.study,
processingItemObj.subject_rid, processingItemObj.scan_date.replace('-', ''),
processingItemObj.s_identifier, processingItemObj.i_identifier,
self.getScanType(processingItemObj))
processedFolder = '{0}/processed'.format(processingItemObj.root_folder)
logDir = '{0}/logs'.format(processingItemObj.root_folder)
PipelineLogger.log('manager', 'info', 'PET processing starting for {0}'.format(petFileName))
try:
distutils.dir_util.mkpath(logDir)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in creating log folder \n {0}'.format(e))
return 0
id = '{0}{1}{2}{3}'.format(processingItemObj.subject_rid, processingItemObj.scan_date.replace('-', ''), processingItemObj.s_identifier, processingItemObj.i_identifier)
paramStrd = ast.literal_eval(processingItemObj.parameters)
paramStrt = ' '.join(['[\"{0}\"]=\"{1}\"'.format(k, v) for k,v in paramStrd.items()])
paramStr = '({0})'.format(paramStrt)
petCMD = "source /opt/minc-1.9.15/minc-toolkit-config.sh; Pipelines/ADNI_AV1451/ADNI_V1_AV1451_Process {0} {1} {2} {3} {4} {5} '{6}' {7} {8}".format(id, petFileName, processedFolder, matchT1Path, processingItemObj.manual_xfm, logDir, paramStr,socket.gethostname(), 50500)
try:
processedFolder_del = '{0}/processed_del'.format(processingItemObj.root_folder)
os.rename(processedFolder, processedFolder_del)
shutil.rmtree(processedFolder_del)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in deleting old processing folder. \n {0}'.format(e))
try:
distutils.dir_util.mkpath(processedFolder)
except Exception as e:
PipelineLogger.log('manager', 'error', 'Error in creating processing folder. \n {0}'.format(e))
return 0
### This section is new for ADNI Pre processing - Per scanner type blurring. Only required if
### the images are aquired from different scanners and need to get to same PSF.
blur_x, blur_y, blur_z = self.PETHelper.getBlurringParams(processingItemObj)
### End pre processing.
PipelineLogger.log('manager', 'debug', 'Command : {0}'.format(petCMD))
p = subprocess.Popen(petCMD, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, executable='/bin/bash')
out, err = p.communicate()
PipelineLogger.log('manager', 'debug', 'Process Log Output : \n{0}'.format(out))
PipelineLogger.log('manager', 'debug', 'Process Log Err : \n{0}'.format(err))
QSubJobHandler.submittedJobs[id] = QSubJob(id, '02:00:00', processingItemObj, 'av1451')
return 1