def __convertDicomToNrrd(self, dicomDir, convertedFileNameWithPath, seriesNumber):
nrrdList = glob.glob(os.path.dirname(convertedFileNameWithPath) + "/*_" + seriesNumber + ".nrrd")
if os.path.exists(convertedFileNameWithPath) or len(nrrdList) > 0:
self.logger.info(convertedFileNameWithPath + " already exists, no conversion needed.")
numVols = re.search("DWI-(\d+)", convertedFileNameWithPath).group(1)
return numVols
# commandList = ["/scratch/msscully/development/DicomToNrrd/StandAloneDicomToNrrdConverter-build/bin/DicomToNrrdConverter"]
commandList = [self.dicomToNrrdPath]
commandList.append("--inputDicomDirectory")
commandList.append(dicomDir)
commandList.append("--outputVolume")
commandList.append(convertedFileNameWithPath)
# Will only affect Seimens data
commandList.append("--useBMatrixGradientDirections")
self.logger.info(" ".join(commandList))
self.logger.info("Converting " + dicomDir + " to " + convertedFileNameWithPath)
my_env = os.environ
my_env["FREESURFER_HOME"] = "/opt/freesurfer"
# output = phdUtils.check_output(commandList,stderr=sys.stdout,env=my_env)
output = phdUtils.check_output(commandList, env=my_env)
self.logger.info(output)
searchMatch = re.search("Number of usable volumes\: (\d+)", output)
if searchMatch:
numberVolumes = searchMatch.group(1)
return numberVolumes
else:
# TODO Decide if this is really an error and handle it more gracefully
self.logger.warn("Couldn't find number of volumes. Error?")
exit(1)
def __convertNiftiToMGZ(self, niftiGZFileNameWithPath, newMGZFileNameWithPath, tempDir):
if os.path.exists(newMGZFileNameWithPath):
self.logger.info(newMGZFileNameWithPath + " already exists, no conversion needed.")
return
# Need to unzip the .nii.gz version
commandList = ["gunzip", "-f", niftiGZFileNameWithPath]
self.logger.info(phdUtils.check_output(commandList, stderr=sys.stdout))
niftiFileName = niftiGZFileNameWithPath.rstrip(".gz")
dicomFiles = os.listdir(tempDir)
data = dicom.read_file(os.path.join(tempDir, dicomFiles[0]))
te = data.EchoTime
tr = data.RepetitionTime
flip = data.FlipAngle
# Pass all the above to mri_convert
commandList = ["/opt/freesurfer/bin/mri_convert"]
commandList.append("-te")
commandList.append(str(te))
commandList.append("-tr")
commandList.append(str(tr))
if "InversionTime" in data:
commandList.append("-TI")
commandList.append(str(data.InversionTime))
commandList.append("-flip_angle")
commandList.append(str(flip))
commandList.append("-it")
commandList.append("nii")
commandList.append(niftiFileName)
commandList.append(newMGZFileNameWithPath)
self.logger.info("Converting " + niftiGZFileNameWithPath + " to " + newMGZFileNameWithPath)
# print " ".join(commandList)
self.logger.info(phdUtils.check_output(commandList, stderr=sys.stdout))
# Re-zip the .nii file
commandList = ["gzip", niftiFileName]
self.logger.info(phdUtils.check_output(commandList, stderr=sys.stdout))
def __convertDicomToNifti(self, dicomDir, convertedFileNameWithPath):
if os.path.exists(convertedFileNameWithPath):
self.logger.info(convertedFileNameWithPath + " already exists, no conversion needed.")
return
# commandList = ["/opt/brains2/bin/ConvertBetweenFileFormats"]
commandList = [self.convertBetweenFormatsPath]
commandList.append(dicomDir)
commandList.append(convertedFileNameWithPath)
self.logger.info(" ".join(commandList))
self.logger.info("Converting " + dicomDir + " to " + convertedFileNameWithPath)
try:
self.logger.info(phdUtils.check_output(commandList, stderr=sys.stdout))
except subprocess.CalledProcessError as e:
self.logger.error("ConvertBetweenFileFormats threw an exception.")
self.logger.error(e)
def __convertDicomToMGZ(self, dicomDir, convertedFileNameWithPath):
if os.path.exists(convertedFileNameWithPath):
self.logger.info(convertedFileNameWithPath + " already exists, no conversion needed.")
return
# commandList = ["/opt/freesurfer/bin/mri_convert"]
commandList = [self.mriConvertPath]
commandList.append("-it")
commandList.append("dicom")
commandList.append(dicomDir)
commandList.append(convertedFileNameWithPath)
self.logger.info("Converting " + dicomDir + " to " + convertedFileNameWithPath)
self.logger.info(" ".join(commandList))
my_env = os.environ
my_env["FREESURFER_HOME"] = "/opt/freesurfer"
try:
self.logger.info(phdUtils.check_output(commandList, stderr=sys.stdout, env=my_env))
except subprocess.CalledProcessError as e:
self.logger.warn("mri_convert threw an exception." + str(e), exc_info=True)
def __uploadScanToPredict(self,dicomDirs,newScanID,predictProjectName,rpacsSubjectLabel):
" upload images to predict xnat"
self.logger.info("Starting upload of {0} to predict project {1}".format(
newScanID, predictProjectName))
dicomRemap = self.predictDicomRemap
baseAnon = self.predictBaseAnon
dicomScp = self.predictDicomScp
tempAnonDir = tempfile.mkdtemp()
anonScript = tempAnonDir+"/anon-"+predictProjectName+"_"+rpacsSubjectLabel+"_"+str(newScanID)+".das"
shutil.copy(baseAnon,anonScript)
anonOut = open(anonScript,'a')
anonOut.write("// TODO: fix this later\n")
anonOut.write("//(0008,103e) := $ { SERIES_DESCRIPTION }\n")
anonOut.write('\n')
anonOut.write("// Note: this part isn't suitable for DicomRemap, which doesn't\n")
anonOut.write("// yet handle user-assigned variables.\n")
anonOut.write("(0020,0010) := \"{0}\"\n".format('site-024'))
anonOut.write("(0008,0050) := \"{0}\"\n".format(predictProjectName))
anonOut.write("(0008,1030) := \"{0}\"\n".format(predictProjectName))
anonOut.write("(0010,0010) := \"{0}\"\n".format(rpacsSubjectLabel))
anonOut.write("(0010,0020) := \"{0}\"\n".format(newScanID))
## http://www.xnat.org/DicomServer has notes regarding the exact formatting of this field
anonOut.write("(0010,4000) := \"Project: {0}; Subject: {1}; Session: {2}; AA:true\"\n".format(predictProjectName,rpacsSubjectLabel,newScanID))
anonOut.close()
## # All the directories to anonimize
dicomDirs = " ".join(dicomDirs)
remapCommand=dicomRemap+" -d "+anonScript+" -o "+dicomScp+" "+ dicomDirs
self.logger.debug(remapCommand)
command_list=[dicomRemap, '-d '+anonScript, '-o '+dicomScp, dicomDirs]
try:
tmpOutput = phdUtils.check_output(command_list,stderr=subprocess.STDOUT)
if re.search('Exception',tmpOutput):
self.logger.critical("An exception occurred while running the dicom remap command. Output follows.\n"+tmpOutput)
self.logger.debug(tmpOutput)
except Exception as e:
self.logger.critical("An Exception occurred when running the dicom remap command! " + e)
exit(1)
