def main(InputNii, Fs, itl):
tr = 1.0 / Fs
RootDir, FileName = os.path.split(InputNii)
trash = ".exe"
FileBase = FileName
while trash:
FileBase, trash = os.path.splitext(FileBase)
cmd = "cp {0} {1}/SPM{2}.nii.gz;gunzip -f {1}/SPM{2}.nii.gz;mv {1}/SPM{2}.nii {1}/{2}.nii;".format(
InputNii, RootDir, FileBase
)
print cmd
pr = sp.Popen(cmd, shell=True)
pr.wait()
trash = ".exe"
FileBase = FileName
while trash:
FileBase, trash = os.path.splitext(FileBase)
OutputFile = os.path.join(RootDir, "{}_SPM.nii.gz".format(FileBase))
n = 1
while os.path.exists(OutputFile):
OutputFile = os.path.join(RootDir, "{}_SPM{}.nii.gz".format(FileBase, n))
n = n + 1
WrkDir = os.path.join(RootDir, "{}_Work".format(FileBase))
SPMFiles = os.path.join(WrkDir, "WorkFiles", "SPM")
ClusterJobDir = os.path.join(WrkDir, "ShFiles", "SPM")
ErrorOutput = os.path.join(WrkDir, "ClusterError", "SPM")
ClusterOutput = os.path.join(WrkDir, "ClusterOutput", "SPM")
BaseDir, fname = os.path.split(InputNii)
while not fname.find(".") == -1:
fname, trash = os.path.splitext(fname)
targetNii = os.path.join(BaseDir, "{}.nii".format(fname))
if not os.path.exists(WrkDir):
os.makedirs(WrkDir)
if not os.path.exists(ClusterJobDir):
os.makedirs(ClusterJobDir)
if not os.path.exists(SPMFiles):
os.makedirs(SPMFiles)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
JobName = "{}_SPM".format(FileBase)
MakeSliceTimingJobs(os.path.join(RootDir, "{}.nii".format(FileBase)), Fs, itl, SPMFiles)
# (Nii,Fs,itl,OutDir)
SPMsh.main(targetNii, ClusterJobDir, ErrorOutput, ClusterOutput, SPMFiles)
SubmitCmd = (
"for Dir in `/bin/ls "
+ ClusterJobDir
+ '/*.sh`; do echo "Running SPM Slice Timing on ${Dir}.";qsub -cwd $Dir;sleep 2; done'
)
print SubmitCmd
pr = sp.Popen(SubmitCmd, shell=True)
pr.wait()
CheckPath = os.path.join(RootDir, "{}_SPM.nii".format(FileBase))
print CheckPath
Min = 0
while (not os.path.exists(CheckPath)) and Min < 60 * 10:
time.sleep(60)
Min = Min + 1
print "Waiting"
time.sleep(20)
if Min == 60 and not os.path.exists(CheckPath):
print ("File {} TImeout".format(FileBase))
CheckPath = os.path.join(RootDir, "a{}.mat".format(FileBase))
if os.path.exists(CheckPath):
cmd = "mv {} {}/a{}.mat".format(CheckPath, SPMFiles, FileBase)
# print cmd
pr = sp.Popen(cmd, shell=True)
pr.wait()
CheckPath = os.path.join(RootDir, "{}_SPM.nii".format(FileBase))
print CheckPath
if os.path.exists(CheckPath):
cmd = "gzip -f {}".format(CheckPath)
# print cmd
pr = sp.Popen(cmd, shell=True)
pr.wait()
cmd = "rm {}/{}.nii".format(RootDir, FileBase)
pr = sp.Popen(cmd, shell=True)
pr.wait()
time.sleep(60)
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)
cmd='cp {0} {1}/SPM{2}.nii.gz;gunzip -f {1}/SPM{2}.nii.gz;mv {1}/SPM{2}.nii {1}/{2}.nii;'.format(InputNii,RootDir,FileBase)
print cmd
pr=sp.Popen(cmd,shell=True)
pr.wait()
trash='.exe'
FileBase=FileName
while trash:
FileBase,trash=os.path.splitext(FileBase)
OutputFile=os.path.join(RootDir,'{}_SPM.nii.gz'.format(FileBase))
n=1
while os.path.exists(OutputFile):
OutputFile=os.path.join(RootDir,'{}_SPM{}.nii.gz'.format(FileBase,n))
n=n+1
WrkDir=os.path.join(RootDir,'{}_Work'.format(FileBase))
SPMFiles=os.path.join(WrkDir,'WorkFiles','SPM')
ClusterJobDir=os.path.join(WrkDir,'ShFiles','SPM')
ErrorOutput=os.path.join(WrkDir,'ClusterError','SPM')
ClusterOutput=os.path.join(WrkDir,'ClusterOutput','SPM')
BaseDir,fname=os.path.split(InputNii)
while not fname.find('.')==-1:
fname,trash=os.path.splitext(fname)
targetNii=os.path.join(BaseDir,'{}.nii'.format(fname))
if not os.path.exists(WrkDir):
os.makedirs(WrkDir)
if not os.path.exists(ClusterJobDir):
os.makedirs(ClusterJobDir)
if not os.path.exists(SPMFiles):
os.makedirs(SPMFiles)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
JobName='{}_SPM'.format(FileBase)
MakeSliceTimingJobs(os.path.join(RootDir,'{}.nii'.format(FileBase)),Fs,itl,SPMFiles)
#(Nii,Fs,itl,OutDir)
SPMsh.main(targetNii,ClusterJobDir,ErrorOutput,ClusterOutput,SPMFiles)
