def main(InputNii,con,Regressor,meth,TR,itl,Fs,WrkDir=''):
txt=np.loadtxt(Regressor)
if not all([i==0 for i in txt]):
RootDir,FileName=os.path.split(InputNii)
trash='.exe'
FileBase=FileName
while trash:
FileBase,trash=os.path.splitext(FileBase)
OutputPath=os.path.join(RootDir,'tPython',meth,con)
if not WrkDir:
WrkDir=os.path.join(RootDir,'{}_Work'.format(FileBase))
GLMFiles=os.path.join(WrkDir,'WorkFiles','GLM',meth,con)
ClusterJobDir=os.path.join(WrkDir,'ShFiles','GLM',meth,con)
ErrorOutput=os.path.join(WrkDir,'ClusterError','GLM',meth,con)
ClusterOutput=os.path.join(WrkDir,'ClusterOutput','GLM',meth,con)
ReportFile=os.path.join(GLMFiles,'Report.txt')
if os.path.exists(ReportFile):
cmd='rm {}'.format(ReportFile)
print cmd
os.system(cmd)
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)
else:
cmd='rm {}/*.sh'.format(ClusterJobDir)
Report(ReportFile,cmd)
os.system(cmd)
if not os.path.exists(GLMFiles):
os.makedirs(GLMFiles)
else:
cmd='rm {}/*'.format(GLMFiles)
Report(ReportFile,cmd)
os.system(cmd)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
else:
cmd='rm {}/*'.format(ErrorOutput)
Report(ReportFile,cmd)
os.system(cmd)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
else:
cmd='rm {}/*'.format(ClusterOutput)
Report(ReportFile,cmd)
os.system(cmd)
if not os.path.exists(OutputPath):
os.makedirs(OutputPath)
print InputNii
img=nb.load(InputNii)
nslice=img.get_shape()[2]
nb.loadsave.save(img,'{}/FullNii.nii.gz'.format(GLMFiles))
# cmd='cp {} {}/FullNii.nii'.format(InputNii,GLMFiles)
# print cmd
# process=sp.Popen(cmd,shell=True)
# process.wait()
cmd='fslsplit {0}/FullNii.nii {0}/RefVol -t'.format(GLMFiles)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
RVs=glob.glob(os.path.join(GLMFiles,'RefVol*'))
for r in RVs[1:]:
cmd='rm {}'.format(r)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
RV=RVs[0]
cmd='fslsplit {} {}/RefZ -z'.format(RV,GLMFiles)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
RefVol=RV
RVs=glob.glob(os.path.join(GLMFiles,'RefZ*'))
for r in RVs[1:]:
cmd='rm {}'.format(r)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
RV=RVs[0]
cmd='fslsplit {0}/FullNii.nii {0}/vol -z'.format(GLMFiles)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
vols=sorted(glob.glob(os.path.join(GLMFiles,'vol*.nii.gz')))
nVols=len(vols)
SlicesOrder,SliceTiming=MakeT(itl,0,nslice,TR)
Regressor=np.loadtxt(Regressor)
if not len(Regressor) >= img.shape[-1]*np.round(Fs*TR):
print 'Interpolating'
t1=np.array(range(len(Regressor)))*2
t20=np.arange(t1[0],t1[-1],1./Fs)
f=tpl.interp1d(t1,Regressor,kind='cubic')
Regressor=f(t20)
for k in xrange(img.shape[2]):
RegressorDownsampled=np.zeros((img.shape[-1]))
if len(Regressor[np.round(SliceTiming[k]*Fs)::(np.round(Fs*TR))])<img.shape[3]:
RegressorDownsampled = list(Regressor[np.round(SliceTiming[k]*Fs)::np.round(Fs*TR)]).append(0)
else:
RegressorDownsampled = Regressor[np.round((SliceTiming[k])*Fs)::np.round(Fs*TR)]
print 'slice {} starting at {}*{}={}::{}'.format(k,SliceTiming[k],Fs,np.round(SliceTiming[k]*Fs),np.round(Fs*TR))
print len(RegressorDownsampled)
np.savetxt(os.path.join(GLMFiles,'SliceReg{0:04d}.txt'.format(int(k))),RegressorDownsampled,fmt='%1.16f')
regs=sorted(glob.glob(os.path.join(GLMFiles,'SliceReg*.txt')))
nRegs=len(regs)
if not nRegs==nVols:
print ('Number of slices does not equal number of regs')
return
Report(ReportFile,'Number of Vols: {}'.format(nVols))
for v,r in zip(vols,regs):
trash,volID=os.path.split(v)
volID,trash=os.path.splitext(volID)
while trash:
volID,trash=os.path.splitext(volID)
rpt='Making SH for Volume {}'.format(volID)
Report(ReportFile,rpt)
shPath=os.path.join(ClusterJobDir,volID+'.sh')
GLMsh.main(v,r,RV,shPath,ErrorOutput,ClusterOutput)
SubmitCmd='for Dir in `/bin/ls '+ClusterJobDir+'/*.sh`; do echo "Running GLM on ${Dir}.";qsub -cwd $Dir;sleep 2; done'
Report(ReportFile,cmd)
os.system(SubmitCmd)
Min=0
Nvols=len(glob.glob(os.path.join(GLMFiles,'vol*')))
NBetas=len(glob.glob(os.path.join(GLMFiles,'Beta*')))
while not Nvols==NBetas and Min<120:
time.sleep(60)
Min=Min+1
Nvols=len(glob.glob(os.path.join(GLMFiles,'vol*')))
NBetas=len(glob.glob(os.path.join(GLMFiles,'Beta*')))
if Min==120:
print ('Timeout Error For {}'.format(InputNii))
Report(ReportFile,'Timeout Error For {}'.format(InputNii))
print 'waiting'
Betas=sorted(glob.glob(os.path.join(GLMFiles,'Beta*')))
#Report(ReportFile,cmd)
files=''
for b in Betas:
files=files+b+' '
cmd='fslmerge -z {} {}'.format(os.path.join(OutputPath,'Beta'),files)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
cmd='fslcpgeom {} {}'.format(RefVol,os.path.join(OutputPath,'Beta'))
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
Betas=sorted(glob.glob(os.path.join(GLMFiles,'tStat*')))
#print Betas
files=''
for b in Betas:
files=files+b+' '
cmd='fslmerge -z {} {}'.format(os.path.join(OutputPath,'tStat'),files)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
cmd='fslcpgeom {} {}'.format(RefVol,os.path.join(OutputPath,'tStat'))
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
Betas=sorted(glob.glob(os.path.join(GLMFiles,'pVal*')))
#print Betas
files=''
for b in Betas:
files=files+b+' '
cmd='fslmerge -z {} {}'.format(os.path.join(OutputPath,'pVal'),files)
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
cmd='fslcpgeom {} {}'.format(RefVol,os.path.join(OutputPath,'pVal'))
Report(ReportFile,cmd)
process=sp.Popen(cmd,shell=True)
process.wait()
else:
print ('All Zero Regressor. Skipping.')
def main(InputNii, con, Regressor, meth, WrkDir="", OutputDir=""):
txt = np.loadtxt(Regressor)
if not all([i == 0 for i in txt]):
RootDir, FileName = os.path.split(InputNii)
trash = ".exe"
FileBase = FileName
while trash:
FileBase, trash = os.path.splitext(FileBase)
OutputPath = os.path.join(RootDir, "tPython", meth, con)
if not WrkDir:
WrkDir = os.path.join(RootDir, "{}_Work".format(FileBase))
GLMFiles = os.path.join(WrkDir, "WorkFiles", "GLM", meth, con)
ClusterJobDir = os.path.join(WrkDir, "ShFiles", "GLM", meth, con)
ErrorOutput = os.path.join(WrkDir, "ClusterError", "GLM", meth, con)
ClusterOutput = os.path.join(WrkDir, "ClusterOutput", "GLM", meth, con)
ReportFile = os.path.join(GLMFiles, "Report.txt")
if os.path.exists(ReportFile):
cmd = "rm {}".format(ReportFile)
print cmd
os.system(cmd)
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)
else:
cmd = "rm {}/*.sh".format(ClusterJobDir)
Report(ReportFile, cmd)
os.system(cmd)
if not os.path.exists(GLMFiles):
os.makedirs(GLMFiles)
else:
cmd = "rm {}/*".format(GLMFiles)
Report(ReportFile, cmd)
os.system(cmd)
if not os.path.exists(ErrorOutput):
os.makedirs(ErrorOutput)
else:
cmd = "rm {}/*".format(ErrorOutput)
Report(ReportFile, cmd)
os.system(cmd)
if not os.path.exists(ClusterOutput):
os.makedirs(ClusterOutput)
else:
cmd = "rm {}/*".format(ClusterOutput)
Report(ReportFile, cmd)
os.system(cmd)
if not os.path.exists(OutputPath):
os.makedirs(OutputPath)
print InputNii
img = nb.load(InputNii)
nb.loadsave.save(img, "{}/FullNii.nii.gz".format(GLMFiles))
# cmd='cp {} {}/FullNii.nii'.format(InputNii,GLMFiles)
# print cmd
# process=sp.Popen(cmd,shell=True)
# process.wait()
cmd = "fslsplit {0}/FullNii.nii {0}/RefVol -t".format(GLMFiles)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
RVs = glob.glob(os.path.join(GLMFiles, "RefVol*"))
for r in RVs[1:]:
cmd = "rm {}".format(r)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
RV = RVs[0]
cmd = "fslsplit {} {}/RefZ -z".format(RV, GLMFiles)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
RefVol = RV
RVs = glob.glob(os.path.join(GLMFiles, "RefZ*"))
for r in RVs[1:]:
cmd = "rm {}".format(r)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
RV = RVs[0]
cmd = "fslsplit {0}/FullNii.nii {0}/vol -z".format(GLMFiles)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
vols = glob.glob(os.path.join(GLMFiles, "vol*.nii.gz"))
nVols = len(vols)
Report(ReportFile, "Number of Vols: {}".format(nVols))
for v in vols:
trash, volID = os.path.split(v)
volID, trash = os.path.splitext(volID)
while trash:
volID, trash = os.path.splitext(volID)
rpt = "Making SH for Volume {}".format(volID)
Report(ReportFile, rpt)
shPath = os.path.join(ClusterJobDir, volID + ".sh")
GLMsh.main(v, Regressor, RV, shPath, ErrorOutput, ClusterOutput)
SubmitCmd = (
"for Dir in `/bin/ls "
+ ClusterJobDir
+ '/*.sh`; do echo "Running GLM on ${Dir}.";qsub -cwd $Dir;sleep 2; done'
)
Report(ReportFile, cmd)
os.system(SubmitCmd)
Min = 0
Nvols = len(glob.glob(os.path.join(GLMFiles, "vol*")))
NBetas = len(glob.glob(os.path.join(GLMFiles, "Beta*")))
while not Nvols == NBetas and Min < 120 * 2:
time.sleep(60)
Min = Min + 1
Nvols = len(glob.glob(os.path.join(GLMFiles, "vol*")))
NBetas = len(glob.glob(os.path.join(GLMFiles, "Beta*")))
if Min == 120 * 2:
print ("Timeout Error For {}".format(InputNii))
Report(ReportFile, "Timeout Error For {}".format(InputNii))
print "waiting"
if Min < 120 * 2:
Betas = sorted(glob.glob(os.path.join(GLMFiles, "Beta*")))
# Report(ReportFile,cmd)
files = ""
for b in Betas:
files = files + b + " "
cmd = "fslmerge -z {} {}".format(os.path.join(OutputPath, "Beta"), files)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
cmd = "fslcpgeom {} {}".format(RefVol, os.path.join(OutputPath, "Beta"))
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
Betas = sorted(glob.glob(os.path.join(GLMFiles, "tStat*")))
# print Betas
files = ""
for b in Betas:
files = files + b + " "
cmd = "fslmerge -z {} {}".format(os.path.join(OutputPath, "tStat"), files)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
cmd = "fslcpgeom {} {}".format(RefVol, os.path.join(OutputPath, "tStat"))
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
Betas = sorted(glob.glob(os.path.join(GLMFiles, "pVal*")))
# print Betas
files = ""
for b in Betas:
files = files + b + " "
cmd = "fslmerge -z {} {}".format(os.path.join(OutputPath, "pVal"), files)
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
cmd = "fslcpgeom {} {}".format(RefVol, os.path.join(OutputPath, "pVal"))
Report(ReportFile, cmd)
process = sp.Popen(cmd, shell=True)
process.wait()
else:
print ("All Zero Regressor. Skipping.")
