def getSubjectSessions(self):
global getHCP
# self.sessionsComboBox.clear()
getHCP.Subject = str(self.subjectsListWidget.currentItem().text())
# getHCP.Subject = str(self.subjectsComboBox.currentText())
Sessions = getHCP.getSubjectSessions()
SessionsList = list(set(Sessions.get('Sessions')))
# self.sessionsTextEdit.setText('\n'.join(Sessions.get('Sessions')))
# self.sessionsComboBox.addItems(SessionsList)
self.sessionsListWidget.clear()
for i in xrange(0, len(SessionsList)):
self.sessionsListWidget.addItem(SessionsList[i])
def getSubjectSessions(self):
global getHCP
# self.sessionsComboBox.clear()
getHCP.Subject = str(self.subjectsListWidget.currentItem().text())
# getHCP.Subject = str(self.subjectsComboBox.currentText())
Sessions = getHCP.getSubjectSessions()
SessionsList = list(set(Sessions.get('Sessions')))
# self.sessionsTextEdit.setText('\n'.join(Sessions.get('Sessions')))
# self.sessionsComboBox.addItems(SessionsList)
self.sessionsListWidget.clear()
for i in xrange(0, len(SessionsList)):
self.sessionsListWidget.addItem(SessionsList[i])
#===============================================================================
# grab output files...
# NOTES: need to deal with xtr QC...
#===============================================================================
for i in xrange(0, len(inputSubjectsList)):
getHCP.Subject = inputSubjectsList[i]
print i, getHCP.Subject
getHCP.Session = getHCP.Subject + '_strc'
getHCP.SessionType = 'Structural'
# getHCP.AssessorDataType = 'qcAssessmentData'
AssessorIDs = getHCP.getAssessorIDs( )
currSessions, currSessionType = getHCP.getSubjectSessions()
StrcIdx = [k for k, element in enumerate(currSessionType) if element == 'strc']
for j in xrange(0, len(StrcIdx)):
writeScanQuality = list()
writeScanSeries = list()
writeAssessorFileURIList = list()
getHCP.Session = currSessions[StrcIdx[j]]
# get quality and scan type to match up with QC output...
Quality, ScanId, Series, Sessions, ScanType = getHCP.getSessionQuality()
#===============================================================================
# make a list of quality and series for printing...
ScanTypeIdx = [k for k, element in enumerate(ScanType) if (element == 'T1w') or (element == 'T2w')]
for k in xrange(0, len(ScanTypeIdx)):
if (Pipeline == 'FunctionalHCP'): PipelineSubString = ['fnc', 'task', 'rest']
elif (Pipeline == 'StructuralHCP'): PipelineSubString = ['strc']
elif (Pipeline == 'DiffusionHCP'): PipelineSubString = ['diff']
elif (Pipeline == 'FIX_HCP'): PipelineSubString = ['fnc', 'rest']
elif (Pipeline == 'TaskfMRIHCP'): PipelineSubString = ['fnc']
else: PipelineSubString = None
UsableList = ['good', 'excellent', 'usable', 'undetermined']
linIdx = 0
for h in xrange(0, len(SubjectsList)):
getHCP.Subject = SubjectsList[h]
SubjectSessions = getHCP.getSubjectSessions()
SubjectMetaData = getHCP.getSubjectMeta()
# find correct session...
for i in xrange(0, len(SubjectSessions.get('Sessions'))):
getHCP.Session = SubjectSessions.get('Sessions')[i]
sessionMeta = getHCP.getSessionMeta()
if (FunctSeries != None) and (FunctSeries in sessionMeta.get('Series')):
break
else:
try:
getHCP.Session = SubjectSessions.get('Sessions')[SubjectSessions.get('Types').index(PipelineSubString[0])]
except:
break
sessionMeta = getHCP.getSessionMeta()
T1wList.append('T1wDividedByT2w.nii.gz')
T1wList.append('T1wDividedByT2w_ribbon.nii.gz')
T1wList.append('brainmask_fs.nii.gz')
T1wList.append('wmparc.nii.gz')
T1wList.append('BiasField_acpc_dc.nii.gz')
#
# SourceDir = '/MNINonLinear/xfms'
xfmsList = list()
xfmsList.append('acpc_dc2standard.nii.gz')
xfmsList.append('NonlinearRegJacobians.nii.gz')
xfmsList.append('standard2acpc_dc.nii.gz')
#===============================================================================
getHCP.DestinationDir = DestDir
getHCP.Project = Project
getHCP.Subject = Subject
SubjectSessions, SubjectSessionsType = getHCP.getSubjectSessions()
SubjectResources = getHCP.getSubjectResources()
SubjectSessionsUniq = set(SubjectResources.get('FileSessions'))
print 'Length of unique File Names, URIs, Sessions, and Labels: %s %s %s %s' % (
len(set(SubjectResources.get('FileNames'))),
len(set(SubjectResources.get('FileURIs'))),
len(set(SubjectResources.get('FileSessions'))),
len(set(SubjectResources.get('FileLabels'))))
Keywords = [
'MNINonLinear', 'MNINonLinear/Native', 'MNINonLinear/fsaverage_LR32k',
'T1w/Native'
]
FileURIs = SubjectResources.get('FileURIs')
FileSessions = SubjectResources.get('FileSessions')
#===============================================================================
# grab output files...
# NOTES: need to deal with xtr QC...
#===============================================================================
for i in xrange(0, len(inputSubjectsList)):
getHCP.Subject = inputSubjectsList[i]
print i, getHCP.Subject
getHCP.Session = getHCP.Subject + '_strc'
getHCP.SessionType = 'Structural'
# getHCP.AssessorDataType = 'qcAssessmentData'
AssessorIDs = getHCP.getAssessorIDs()
currSessions, currSessionType = getHCP.getSubjectSessions()
StrcIdx = [
k for k, element in enumerate(currSessionType) if element == 'strc'
]
for j in xrange(0, len(StrcIdx)):
writeScanQuality = list()
writeScanSeries = list()
writeAssessorFileURIList = list()
getHCP.Session = currSessions[StrcIdx[j]]
# get quality and scan type to match up with QC output...
Quality, ScanId, Series, Sessions, ScanType = getHCP.getSessionQuality(
)
#===============================================================================
# getScanParms
# getServer
# getSessionId
# getSessionMeta
# getSessionQuality
# getSubjectResourceMeta
# getSubjectResourcesMeta
# getSubjects
# getSubjectSessions
# getSubjectsSessions
# getURLString
#==============================================================================
Projects = getHCP.getProjects()
getHCP.Subject = getHCP.Subjects[0]
getHCP.SubjectSessions = getHCP.getSubjectSessions()
getHCP.Session = getHCP.SubjectSessions.get('Sessions')[0]
getHCP.SessionMeta = getHCP.getSessionMeta()
ScanParms = getHCP.getScanParms()
ScanMeta = getHCP.getScanMeta()
print ScanMeta.get('URIs')[ScanMeta.get('Collections').index('NIFTI')]
writeHCP.writeFileFromURL(getHCP, ScanMeta.get('URIs')[ScanMeta.get('Collections').index('NIFTI')])
if (getHCP.Server.find('intradb') != -1):
AssessorIDs = getHCP.getAssessorIDs( )
AssessorFileURIList = getHCP.getAssessorOutputFile( AssessorIDs )
# getScanParms
# getServer
# getSessionId
# getSessionMeta
# getSessionQuality
# getSubjectResourceMeta
# getSubjectResourcesMeta
# getSubjects
# getSubjectSessions
# getSubjectsSessions
# getURLString
# ==============================================================================
Projects = getHCP.getProjects()
getHCP.Subject = getHCP.Subjects[0]
getHCP.SubjectSessions = getHCP.getSubjectSessions()
getHCP.Session = getHCP.SubjectSessions.get("Sessions")[0]
getHCP.SessionMeta = getHCP.getSessionMeta()
ScanParms = getHCP.getScanParms()
ScanMeta = getHCP.getScanMeta()
print ScanMeta.get("URIs")[ScanMeta.get("Collections").index("NIFTI")]
writeHCP.writeFileFromURL(getHCP, ScanMeta.get("URIs")[ScanMeta.get("Collections").index("NIFTI")])
if getHCP.Server.find("intradb") != -1:
AssessorIDs = getHCP.getAssessorIDs()
AssessorFileURIList = getHCP.getAssessorOutputFile(AssessorIDs)
print getHCP.getProjects()
print getHCP.SessionId, getHCP.getSessionId()
else:
BuildArray = numpy.tile(BuildList, 1)
if (Pipeline == 'FunctionalHCP'): PipelineSubString = ['fnc', 'task', 'rest']
elif (Pipeline == 'StructuralHCP'): PipelineSubString = ['strc']
elif (Pipeline == 'DiffusionHCP'): PipelineSubString = ['diff']
elif (Pipeline == 'FIX_HCP'): PipelineSubString = ['fnc', 'rest']
elif (Pipeline == 'TaskfMRIHCP'): PipelineSubString = ['fnc']
else: PipelineSubString = None
UsableList = ['good', 'excellent', 'usable', 'undetermined']
linIdx = 0
for h in xrange(0, len(SubjectsList)):
getHCP.Subject = SubjectsList[h]
SubjectSessions = getHCP.getSubjectSessions()
SubjectMetaData = getHCP.getSubjectMeta()
# find correct session...
for i in xrange(0, len(SubjectSessions.get('Sessions'))):
getHCP.Session = SubjectSessions.get('Sessions')[i]
sessionMeta = getHCP.getSessionMeta()
if (FunctSeries != None) and (FunctSeries
in sessionMeta.get('Series')):
break
else:
try:
getHCP.Session = SubjectSessions.get('Sessions')[
SubjectSessions.get('Types').index(PipelineSubString[0])]
except:
break