def backUp(inputDirs, backUpTo, DataBaseAddress, spreadsheet):
subjectClassList = []
for newDirectory in inputDirs:
subjClass = subj.subject(newDirectory, backUpTo)
checkFileNumbers(subjClass)
subjectClassList.append(subjClass)
executeCopy(subjClass)
subjDf = saveLog(subjClass)
dbDf = processDB(DataBaseAddress)
newDf = pd.concat([dbDf, subjDf]).reset_index()
newDf = newDf[[
u'koreanName', u'subjectName', u'subjectInitial', u'group', u'sex',
u'age', u'DOB', u'scanDate', u'timeline', u'studyname',
u'patientNumber', u'T1', u'T2', u'REST_LR', u'REST_LR_SBRef',
u'REST_BLIP_LR', u'REST_BLIP_RL', u'DTI_LR_1000', u'DTI_LR_2000',
u'DTI_LR_3000', u'DTI_BLIP_LR', u'DTI_BLIP_RL', u'dx',
u'folderName', u'backUpBy', u'note'
]]
#please confirm here
newDf['koreanName'] = newDf['koreanName'].str.decode('utf-8')
newDf['note'] = newDf['note'].str.decode('utf-8')
newDf.to_excel(DataBaseAddress, 'Sheet1')
# os.chmod(DataBaseAddress, 0o2770)
updateSpreadSheet.main(False, DataBaseAddress, spreadsheet) #False
print('Completed\n')
def backUp(inputDirs, backUpTo,
DataBaseAddress, spreadsheet):
subjectClassList = []
for newDirectory in inputDirs:
subjClass = subj.subject(newDirectory, backUpTo)
checkFileNumbers(subj.correct_modality_re_dict, subjClass)
subjectClassList.append(subjClass)
executeCopy(subjClass)
subjDf = saveLog(subjClass)
print(subjDf)
dbDf = processDB(DataBaseAddress)
newDf = pd.concat([dbDf, subjDf]).reset_index()
# ordering
newDf = newDf[[ u'koreanName',
u'subjectName',
u'subjectInitial',
u'group',
u'sex',
u'age',
u'DOB',
u'scanDate',
u'timeline',
u'studyname',
u'patientNumber'] + \
[subj.correct_modality_re_dict] + \
[u'dx',
u'folderName',
u'backUpBy',
u'note']]
#please confirm here
newDf['koreanName'] = newDf['koreanName'].str.decode('utf-8')
newDf['note'] = newDf['note'].str.decode('utf-8')
newDf.to_excel(DataBaseAddress, 'Sheet1', encode='utf-8')
# os.chmod(DataBaseAddress, 0o2770)
updateSpreadSheet.main(False, DataBaseAddress, spreadsheet)#False
print('Completed\n')
def backUp(inputDirs, backUpFrom, USBlogFile, backUpTo, DataBaseAddress, spreadsheet, freesurferOn, motionOn, copyExecuteOn, nasBackupOn):
# External HDD log
if USBlogFile:
logFileInUSB = USBlogFile
elif inputDirs:
logFileInUSB = os.path.join(os.getcwd(),"log.xlsx")
else:
logFileInUSB = os.path.join(backUpFrom,"log.xlsx")
logDf = copiedDirectoryCheck(backUpFrom,logFileInUSB)
newDirectoryList,logDf = newDirectoryGrep(inputDirs, backUpFrom,logDf)
logDf.to_excel(logFileInUSB,'Sheet1')
if newDirectoryList==[]:
sys.exit('Everything have been backed up !')
subjectClassList = []
for newDirectory in newDirectoryList:
subjClass = subj.subject(newDirectory, backUpTo)
checkFileNumbers(subjClass)
subjectClassList.append(subjClass)
if copyExecuteOn:
executeCopy(subjClass)
subjDf = saveLog(subjClass)
dbDf = processDB(DataBaseAddress)
newDf = pd.concat([dbDf, subjDf]).reset_index()
newDf = newDf[[ u'koreanName', u'subjectName', u'subjectInitial',
u'group', u'sex', u'age',
u'DOB', u'scanDate', u'timeline',
u'studyname', u'patientNumber', u'T1Number',
u'DTINumber', u'DKINumber', u'RESTNumber',
u'REST2Number', u'folderName', u'backUpBy',
u'note']]
newDf['koreanName'] = newDf['koreanName'].str.decode('utf-8')
newDf['note'] = newDf['note'].str.decode('utf-8')
newDf.to_excel(DataBaseAddress, 'Sheet1')
#os.chmod(DataBaseAddress, 0o2770)
updateSpreadSheet.main(False, DataBaseAddress, spreadsheet)
if motionOn:
print 'Now, running motion_extraction'
for subjectClass in subjectClassList:
motion_extraction.main(subjectClass.targetDir, True, True, False)
if nasBackupOn:
server = '147.47.228.192'
for subjectClass in subjectClassList:
copiedDir=os.path.dirname(subjectClass.targetDir)
server_connect(server, copiedDir)
if freesurferOn:
for subjectClass in subjectClassList:
freesurfer.main(subjectClass.targetDir,
os.path.join(subjectClass.targetDir, 'FREESURFER'))
freesurfer_summary.main(copiedDir, None, "ctx_lh_G_cuneus", True, True, True, True)
print 'Completed\n'
def backUp(inputDirs, backUpFrom, USBlogFile, backUpTo,
DataBaseAddress, spreadsheet,
freesurfer, motion, copyExecute, nasBackup):
# External HDD log
if USBlogFile:
logFileInUSB = USBlogFile
elif inputDirs:
logFileInUSB = os.path.join(os.getcwd(),"log.xlsx")
else:
logFileInUSB = os.path.join(backUpFrom,"log.xlsx")
logDf = copiedDirectoryCheck(backUpFrom, logFileInUSB)
newDirectoryList,logDf = newDirectoryGrep(inputDirs, backUpFrom, logDf)
logDf.to_excel(logFileInUSB,'Sheet1')
if newDirectoryList == []:
sys.exit('Everything have been backed up !')
subjectClassList = []
for newDirectory in newDirectoryList:
subjClass = subj.subject(newDirectory, backUpTo)
checkFileNumbers(subjClass)
subjectClassList.append(subjClass)
if copyExecute:
executeCopy(subjClass)
subjDf = saveLog(subjClass)
dbDf = processDB(DataBaseAddress)
newDf = pd.concat([dbDf, subjDf]).reset_index()
newDf = newDf[[ u'koreanName', u'subjectName', u'subjectInitial',
u'group', u'sex', u'age',
u'DOB', u'scanDate', u'timeline',
u'studyname', u'patientNumber', u'T1Number',
u'DTINumber', u'DKINumber', u'RESTNumber',
u'REST2Number', u'folderName', u'backUpBy',
u'note']]
newDf['koreanName'] = newDf['koreanName'].str.decode('utf-8')
newDf['note'] = newDf['note'].str.decode('utf-8')
newDf.to_excel(DataBaseAddress, 'Sheet1')
# os.chmod(DataBaseAddress, 0o2770)
updateSpreadSheet.main(False, DataBaseAddress, spreadsheet)#False
if motion:
print 'Now, running motion_extraction'
for subjectClass in subjectClassList:
motionExtraction.main(subjectClass.targetDir, True, True, False)
bien.dtiFit(os.path.join(subjectClass.targetDir,'DTI'))
if nasBackup:
server = '147.47.228.192'
for subjectClass in subjectClassList:
copiedDir = os.path.dirname(subjectClass.targetDir)
server_connect(server, copiedDir)
if freesurfer:
for subjectClass in subjectClassList:
easyFreesurfer.main(subjectClass.targetDir,
os.path.join(subjectClass.targetDir,'FREESURFER'))
freesurfer_Summary.main(copiedDir, None, #bienseo: only use freesurfer.
"ctx_lh_G_cuneus", True, True, True, True)
print 'Completed\n'
def main():
#--------------------------------------------------------------------------------
# Load previously copied directories
#--------------------------------------------------------------------------------
# logDf : log saved in external hard drive
# newDirectoryList : recently added directory to the external hard drive
#
# If user wants a directory not to be called again,
# logDf is updated with the directory
#
# If there is no new directory --> sys.exit
#================================================================================
try:
logDf=copiedDirectoryCheck(backUpFrom,logFileInUSB)
newDirectoryList,logDf=newDirectoryGrep(backUpFrom,logDf)
logDf.to_excel(logFileInUSB,'Sheet1')
if newDirectoryList==[]:
sys.exit()
except:
sys.exit('Please insert USB external drive')
#================================================================================
#--------------------------------------------------------------------------------
# check the number of images in the new directories
#--------------------------------------------------------------------------------
# foundDict : {newDirName:{modalityName:modalitySource,fileNumber}}
#
# allInfo : {newDirName:[group,followUp,birthday,note,target,
# subjInitial,fullname,subjNum,targetDirectory,sex,
# allModalityWithLocation,maxNum,backUpTo,backUpFrom,
# koreanName]
#
# df : pandas dataframe made with the function 'log'
# including information about the new subjects
#================================================================================
foundDict=findDtiDkiT1restRest2(newDirectoryList)
allInfo,df,newDfList=verifyNumbersAndLog(foundDict,backUpTo,backUpFrom)
#================================================================================
#--------------------------------------------------------------------------------
# check the number of images in the new directories
#================================================================================
executeCopy(allInfo,df,newDfList)
#individualLog(allInfo,df)
#================================================================================
#--------------------------------------------------------------------------------
# Update the database excel and log in the external hard-drive
#================================================================================
#df = changeencode(df,['koreanName','note'])
#writer = pd.ExcelWriter(DataBaseAddress)
#df.to_excel(DataBaseAddress,sheet_name='rearrangeWithId',engine='xlsxwriter')
#writer.save()
#df.to_excel(DataBaseAddress,sheet_name='rearrangeWithId',engine='xlsxwriter')
df.to_excel(DataBaseAddress,sheet_name='rearrangeWithId')
for dirName,value in allInfo.iteritems():
logDf = noCall(logDf,backUpFrom,dirName)
logDf.to_excel(logFileInUSB,'Sheet1')
#================================================================================
#--------------------------------------------------------------------------------
# Update the database excel for CCNC
#================================================================================
updateSpreadSheet.main('noInput')
print '-----------------'
print 'Completed\n'
