def f_stage2callback(**kwargs):
str_cwd = os.getcwd()
lst_subj = []
for key, val in kwargs.iteritems():
if key == 'subj': lst_subj = val
if key == 'obj': stage = val
for subj in lst_subj:
# find the relevant input files in each <subj> dir
os.chdir(subj)
l_B0 = misc.find(_str_b0)
l_ASL = misc.find(_str_asl)
if not l_B0: error.fatal(pipe_hypothermia, 'noB0')
if not l_ASL: error.fatal(pipe_hypothermia, 'noASL')
_str_B0File = l_B0[0]
_str_ASLFile = l_ASL[0]
_str_outDir = 'outDir'
_str_outFile = 'asl2b0.nii'
misc.mkdir(_str_outDir)
log = stage.log()
log('Scheduling masconorm for "%s: ASL"..\n' % (subj))
str_cmd = 'masconorm.py --input %s/asl2b0.nii.gz --mask %s/b0Brain_mask.nii.gz --outStem %s/asl' % (
_str_outDir,
_str_outDir,
_str_outDir)
#cluster = crun.crun_mosix()
cluster = crun.crun()
cluster.echo(False)
cluster.echoStdOut(False)
cluster.detach(False)
cluster(str_cmd, waitForChild=True, stdoutflush=True, stderrflush=True)
if cluster.exitCode():
error.fatal(pipe_hypothermia, 'stageExec', cluster.stderr())
os.chdir(str_cwd)
return True
def f_stage3callback(**kwargs):
str_cwd = os.getcwd()
lst_subj = []
for key, val in kwargs.iteritems():
if key == 'subj': lst_subj = val
if key == 'obj': stage = val
for subj in lst_subj:
# find the relevant input files in each <subj> dir
os.chdir(subj)
l_ADC = misc.find(_str_adc)
if not l_ADC: error.fatal(pipe_hypothermia, 'noADC')
_str_ADCFile = l_ADC[0]
_str_outDir = 'outDir'
misc.mkdir(_str_outDir)
log = stage.log()
log('Scheduling masconorm for "%s: ADC"..\n' % (subj))
str_cmd = 'masconorm.py --input %s --mask %s/b0Brain_mask.nii.gz --outStem %s/adc' % (
_str_ADCFile,
_str_outDir,
_str_outDir)
cluster = crun.crun()
cluster.echo(False)
cluster.echoStdOut(False)
cluster.detach(False)
cluster(str_cmd, waitForChild=True, stdoutflush=True, stderrflush=True)
os.chdir(str_cwd)
return True
def f_stage0callback(**kwargs):
str_cwd = os.getcwd()
lst_subj = []
for key, val in kwargs.iteritems():
if key == 'subj': lst_subj = val
if key == 'obj': stage = val
for subj in lst_subj:
# find the relevant input files in each <subj> dir
os.chdir(subj)
l_B0 = misc.find(_str_b0)
if not l_B0: error.fatal(pipe_hypothermia, 'noB0')
_str_B0File = l_B0[0]
_str_outDir = '%s/outDir' % os.getcwd()
_str_outFile = 'b0Brain.nii'
misc.mkdir(_str_outDir)
str_prefixCmd = '( cd %s ; ' % (os.getcwd())
log = stage.log()
log('Scheduling brain extraction for "%s"...\n' % (subj))
str_cmd = 'bet.py --input %s --output %s/%s' % (_str_B0File,
_str_outDir, _str_outFile)
#cluster = crun.crun_mosix(cmdPrefix=str_prefixCmd)
#cluster = crun.crun_mosix()
cluster = crun.crun()
#str_ccmd = cluster.echo(True)
#log(str_ccmd)
cluster.echo(False)
cluster.echoStdOut(False)
cluster.detach(False)
cluster(str_cmd, waitForChild=True, stdoutflush=True, stderrflush=True)
if cluster.exitCode():
error.fatal(pipe_hypothermia, 'stageExec', cluster.stderr())
os.chdir(str_cwd)
return True