def get_cmds(self, assessor, jobdir):
"""Method to generate the spider command for cluster job.
:param assessor: pyxnat assessor object
:param jobdir: jobdir where the job's output will be generated
:return: command to execute the spider in the job script
"""
proj_label = assessor.parent().parent().parent().label()
subj_label = assessor.parent().parent().label()
sess_label = assessor.parent().label()
nb_acq = 1
csess = XnatUtils.CachedImageSession(assessor._intf, proj_label,
subj_label, sess_label)
reg_verdict = ''
for cassr in csess.assessors():
if XnatUtils.is_cassessor_good_type(cassr, [self.proctype]):
reg_verdict = cassr
if XnatUtils.has_resource(reg_verdict, 'ACQ2'):
nb_acq = 2
cmd = SPIDER_FORMAT.format(spider=self.spider_path,
proj=proj_label,
subj=subj_label,
sess=sess_label,
dir=jobdir,
nb_acq=nb_acq,
proctype=self.proctype,
mc=self.mc,
camino=self.camino,
scheme=self.scheme_file,
suffix_proc=self.suffix_proc)
return [cmd]
def has_inputs(self, csess):
"""Method overridden from base class.
By definition:
status = 0 -> NEED_INPUTS,
status = 1 -> NEED_TO_RUN
status = -1 -> NO_DATA
qcstatus needs a value only when -1 or 0.
You need to set qcstatus to a short string that explain
why it's no ready to run. e.g: No NIFTI
:param csess: object csess define in dax.XnatUtils
(see XnatUtils in dax for information)
:return: status, qcstatus
"""
verdict_cscans = XnatUtils.get_good_cscans(csess, self.modalities)
if not verdict_cscans:
LOGGER.debug('Processor_Registration_Verdict: \
cannot run at all, no VERDICT image found')
return -1, 'VERDICT not found'
verdict_cassrs = list()
for cassr in csess.assessors():
if XnatUtils.is_cassessor_good_type(cassr, [self.proctype]):
verdict_cassrs.append(cassr)
if not verdict_cassrs:
LOGGER.debug('Processor_Compute_ADC_Verdict: \
cannot run, no good QA Registration VERDICT found')
return 0, 'Registration missing'
cassr = verdict_cassrs[0]
LOGGER.debug('Processor_Compute_ADC_Verdict: \
good registration assessor found: %s', cassr.info()['label'])
if not XnatUtils.has_resource(cassr, 'ACQ1'):
LOGGER.debug('Processor_Compute_ADC_Verdict: \
cannot run, no ACQ resource found for %s assessor',
cassr.info()['label'])
return 0, "Missing ACQ#"
return 1, None
