Python XnatUtils.get_good_cscans方法代码示例

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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
        """
        assessor_label = assessor.label()
        proj_label = assessor.parent().parent().parent().label()
        subj_label = assessor.parent().parent().label()
        sess_label = assessor.parent().label()

        csess = XnatUtils.CachedImageSession(assessor._intf, proj_label,
                                             subj_label, sess_label)

        gad_cscans = XnatUtils.get_good_cscans(csess, self.gad_type)
        gad = self.get_file_path(gad_cscans[0], SCAN_RESOURCE)

        vessels_cscans = XnatUtils.get_good_cscans(csess, self.vessels_type)
        vessels = self.get_file_path(vessels_cscans, SCAN_RESOURCE)
        vessel_ids = [ves.info()['ID'] for ves in vessels_cscans]

        cmd = SPIDER_FORMAT.format(spider=self.spider_path,
                                   assr=assessor_label,
                                   dir=jobdir,
                                   exe=self.exe,
                                   gad=','.join(gad),
                                   vessels=','.join(vessels),
                                   vesselsids=','.join(vessel_ids),
                                   number_core=self.ppn,
                                   working_dir=self.working_dir)

        return [cmd]

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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
        """
        gad_cscans = XnatUtils.get_good_cscans(csess, self.gad_type)
        if not gad_cscans:
            LOGGER.debug('Vessel Registration: No GAD scan found.')
            return -1, 'No GAD found'
        elif len(gad_cscans) > 1:
            LOGGER.debug('Vessel Registration: Too many GAD scans found.')
            return 0, 'Too many GAD found'

        vessels_cscans = XnatUtils.get_good_cscans(csess, self.vessels_type)
        if not vessels_cscans:
            LOGGER.debug('Vessel Registration: No Vessels scans found.')
            return -1, 'No Vessels found'

        return 1, None

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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()

        csess = XnatUtils.CachedImageSession(assessor._intf, proj_label,
                                             subj_label, sess_label)
        target_cscans = XnatUtils.get_good_cscans(csess, self.target_type)
        target_id = target_cscans[0].info()['ID']
        source_cscans = XnatUtils.get_good_cscans(csess, self.sources_type)
        sources_id = ','.join([sc.info()['ID'] for sc in source_cscans])

        cmd = SPIDER_FORMAT.format(spider=self.spider_path,
                                   proj=proj_label,
                                   subj=subj_label,
                                   sess=sess_label,
                                   dir=jobdir,
                                   target=target_id,
                                   sources=sources_id,
                                   regaladin=self.regaladin,
                                   number_core=self.ppn,
                                   suffix_proc=self.suffix_proc)

        return [cmd]

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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()
        assr_label = assessor.label()

        csess = XnatUtils.CachedImageSession(assessor._intf, proj_label,
                                             subj_label, sess_label)
        dti_cscans = XnatUtils.get_good_cscans(csess, self.dtitypes)
        dtis = ','.join([cscan.info()['ID'] for cscan in dti_cscans])
        gif_cassrs = XnatUtils.get_good_cassr(csess, self.giftypes)
        working_dir = os.path.join(self.working_dir, assr_label)

        cmd = SPIDER_FORMAT.format(spider=self.spider_path,
                                   proj=proj_label,
                                   subj=subj_label,
                                   sess=sess_label,
                                   dir=jobdir,
                                   suffix_proc=self.suffix_proc,
                                   dti=dtis,
                                   gif=gif_cassrs[0].info()['label'],
                                   exe=self.exe,
                                   gif_path=self.exe_args,
                                   number_core=self.ppn,
                                   working_dir=working_dir)

        return [cmd]

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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
        """
        # Check that there is only one scan usable with the reference type and
        # that the reference file as a NIFTI
        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'
        for cscan in verdict_cscans:
            if not XnatUtils.has_resource(cscan, 'NIFTI'):
                LOGGER.debug('Processor_Registration_Verdict: \
        cannot run, no NIFTI found for %s scan', cscan.info()['ID'])
                return 0, "Missing NIFTI"

        return 1, None

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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
        """
        # DTI:
        dti_cscans = XnatUtils.get_good_cscans(csess, self.dtitypes)
        if not dti_cscans:
            LOGGER.debug('Processor_Diffusion_Model_Fitting: \
cannot run at all, no DTI images found')
            return -1, 'DTI not found'
        for dti_cscan in dti_cscans:
            if not XnatUtils.has_resource(dti_cscan, 'NIFTI'):
                LOGGER.debug('Processor_Diffusion_Model_Fitting: cannot run, \
no NIFTI found for DTI image %s' % dti_cscan.info()['ID'])
                return 0, "no NIFTI for %s" % dti_cscan.info()['ID']
        # T1:
        t1_cscans = XnatUtils.get_good_cscans(csess, self.t1types)
        if not t1_cscans:
            LOGGER.debug('Processor_Diffusion_Model_Fitting: \
cannot run at all, no T1 images found')
            return -1, 'T1 not found'
        # GIF:
        gif_cassrs = XnatUtils.get_good_cassr(csess, self.giftypes)
        if not gif_cassrs:
            LOGGER.debug('Processor_Diffusion_Model_Fitting: \
cannot run, no good GIF Parcellation found')
            return 0, 'good GIF not found'
        if len(gif_cassrs) > 1:
            LOGGER.debug('Processor_Diffusion_Model_Fitting: \
cannot run, no good GIF Parcellation found')
            return 0, 'too many good GIF'

        return 1, None

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
def get_usable_cscans(csess, stype):
    """
    Get only the usable cscans for a csess.
    """
    usable_cscans = list()
    cscans = XnatUtils.get_good_cscans(csess, stype)
    for cscan in cscans:
        if cscan.info()['quality'] == 'usable':
            usable_cscans.append(cscan)
    return usable_cscans

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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
        """
        # Check that there is only one scan usable with the reference type and
        # that the reference file as a NIFTI
        target_cscans = XnatUtils.get_good_cscans(csess, self.target)
        if not target_cscans:
            LOGGER.debug('Processor_Registration2Ref: \
cannot run at all, no T2 image found')
            return -1, 'T2 not found'
        if len(target_cscans) > 1:
            LOGGER.debug('Processor_Registration2Ref: \
cannot run at all, too many T2 images found')
            return 0, 'Too many T2 scans'
        if not XnatUtils.has_resource(target_cscans[0], 'NIFTI'):
            LOGGER.debug('Processor_Registration2Ref: \
cannot run, no NIFTI for T2 image')
            return 0, "no T2's NIFTI"

        source_cscans = XnatUtils.get_good_cscans(csess, self.sources)
        if not source_cscans:
            LOGGER.debug('Processor_Registration2Ref: \
cannot run at all, no ADC/DCE image found')
            return -1, 'ADC/DCE not found'
        for cscan in source_cscans:
            if not XnatUtils.has_resource(cscan, 'NIFTI'):
                LOGGER.debug('Processor_Registration2Ref: \
cannot run, no NIFTI found for %s scan', cscan.info()['ID'])
                return 0, "Missing NIFTI"

        return 1, None

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_good_cscans [as 别名]
    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