def main(InputNii,Fs,itl):
tr=1./Fs
RootDir,FileName=os.path.split(InputNii)
trash='.exe'
FileBase=FileName
while trash:
FileBase,trash=os.path.splitext(FileBase)
OutputFile=os.path.join(RootDir,'{}_FSL.nii.gz'.format(FileBase))
n=1
while os.path.exists(OutputFile):
OutputFile=os.path.join(RootDir,'{}_FSL{}.nii.gz'.format(FileBase,n))
n=n+1
WrkDir=os.path.join(RootDir,'{}_Work'.format(FileBase))
FSLFiles=os.path.join(WrkDir,'WorkFiles','FSL')
ClusterJobDir=os.path.join(WrkDir,'ShFiles','FSL')
ErrorOutput=os.path.join(WrkDir,'ClusterError','FSL')
ClusterOutput=os.path.join(WrkDir,'ClusterOutput','FSL')
BaseDir,fname=os.path.split(InputNii)
while not fname.find('.')==-1:
fname,trash=os.path.splitext(fname)
if not os.path.exists(WrkDir):
os.makedirs(WrkDir)
if not os.path.exists(ClusterJobDir):
os.makedirs(ClusterJobDir)
if not os.path.exists(FSLFiles):
os.makedirs(FSLFiles)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
JobName=os.path.join(ClusterJobDir,'{}_FSL.sh'.format(FileBase))
SliceTiming=MaketFile(InputNii,itl,tr)
STfile=os.path.join(FSLFiles,'SliceTiming.txt')
np.savetxt(STfile,SliceTiming)
FSLsh.main(InputNii,OutputFile,JobName,ErrorOutput,ClusterOutput,STfile)
SubmitFiles=glob.glob(ClusterJobDir+'/*.sh')
for fl in SubmitFiles:
base,sh=os.path.split(fl)
cmd='cd {};./{}'.format(base,sh)
pr=sp.Popen(cmd,shell=True)
pr.wait()
#print SubmitCmd
#os.system(SubmitCmd)
Min=0
while (not os.path.exists(OutputFile)) and Min<60*10:
time.sleep(60)
Min=Min+1
if (not os.path.exists(OutputFile)) and Min==60:
print ('Timeout Error For {}'.format(OutputFile))
time.sleep(30)
def main(InputNii,Fs,itl):
tr=1./Fs
RootDir,FileName=os.path.split(InputNii)
trash='.exe'
FileBase=FileName
while trash:
FileBase,trash=os.path.splitext(FileBase)
OutputFile=os.path.join(RootDir,'{}_FSL.nii.gz'.format(FileBase))
n=1
while os.path.exists(OutputFile):
OutputFile=os.path.join(RootDir,'{}_FSL{}.nii.gz'.format(FileBase,n))
n=n+1
WrkDir=os.path.join(RootDir,'{}_Work'.format(FileBase))
FSLFiles=os.path.join(WrkDir,'WorkFiles','FSL')
ClusterJobDir=os.path.join(WrkDir,'ShFiles','FSL')
ErrorOutput=os.path.join(WrkDir,'ClusterError','FSL')
ClusterOutput=os.path.join(WrkDir,'ClusterOutput','FSL')
BaseDir,fname=os.path.split(InputNii)
while not fname.find('.')==-1:
fname,trash=os.path.splitext(fname)
if not os.path.exists(WrkDir):
os.makedirs(WrkDir)
if not os.path.exists(ClusterJobDir):
os.makedirs(ClusterJobDir)
if not os.path.exists(FSLFiles):
os.makedirs(FSLFiles)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
JobName=os.path.join(ClusterJobDir,'{}_FSL.sh'.format(FileBase))
SliceTiming=MaketFile(InputNii,itl,tr)
STfile=os.path.join(FSLFiles,'SliceTiming.txt')
np.savetxt(STfile,SliceTiming)
FSLsh.main(InputNii,OutputFile,JobName,ErrorOutput,ClusterOutput,STfile)
SubmitCmd='for Dir in `/bin/ls '+ClusterJobDir+'/*.sh`; do echo "Running FSL Slice Timing on ${Dir}.";qsub -cwd $Dir;sleep 2; done'
print SubmitCmd
os.system(SubmitCmd)
Min=0
while (not os.path.exists(OutputFile)) and Min<60*10:
time.sleep(60)
Min=Min+1
if (not os.path.exists(OutputFile)) and Min==60:
print ('Timeout Error For {}'.format(OutputFile))
time.sleep(30)
