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)
self._anat_file = self.inputs.realigned_file
self._mask_file = high_variance_masks
self._seg_files = [high_variance_masks]
self._masked = False
NIWORKFLOWS_LOG.info(
'Generating report for tCompCor. file "%s", mask "%s"',
self.inputs.realigned_file,
self.aggregate_outputs(runtime=runtime).high_variance_masks,
)
return super(TCompCorRPT, self)._post_run_hook(runtime)
class _SimpleShowMaskInputSpec(nrc._SVGReportCapableInputSpec):
background_file = File(exists=True, mandatory=True, desc="file before")
mask_file = File(exists=True, mandatory=True, desc="file before")
class SimpleShowMaskRPT(nrc.SegmentationRC, nrc.ReportingInterface):
input_spec = _SimpleShowMaskInputSpec
def _post_run_hook(self, runtime):
self._anat_file = self.inputs.background_file
self._mask_file = self.inputs.mask_file
self._seg_files = [self.inputs.mask_file]
self._masked = True
return super(SimpleShowMaskRPT, self)._post_run_hook(runtime)
def _post_run_hook(self, runtime):
self._fixed_image = self.inputs.reference
self._moving_image = self.aggregate_outputs(runtime=runtime).out_file
self._contour = self.inputs.wm_seg if isdefined(self.inputs.wm_seg) else None
NIWORKFLOWS_LOG.info(
"Report - setting fixed (%s) and moving (%s) images",
self._fixed_image,
self._moving_image,
)
return super(FLIRTRPT, self)._post_run_hook(runtime)
class _ApplyXFMInputSpecRPT(
nrc._SVGReportCapableInputSpec, fsl.preprocess.ApplyXFMInputSpec
):
pass
class ApplyXFMRPT(FLIRTRPT, fsl.ApplyXFM):
input_spec = _ApplyXFMInputSpecRPT
output_spec = _FLIRTOutputSpecRPT
if LooseVersion("0.0.0") < fs.Info.looseversion() < LooseVersion("6.0.0"):
_BBRegisterInputSpec = fs.preprocess.BBRegisterInputSpec
else:
_BBRegisterInputSpec = fs.preprocess.BBRegisterInputSpec6
class _BBRegisterInputSpecRPT(nrc._SVGReportCapableInputSpec, _BBRegisterInputSpec):
def _post_run_hook(self, runtime):
self._fixed_image_label = "after"
self._moving_image_label = "before"
self._fixed_image = self.aggregate_outputs(runtime=runtime).unwarped_file
self._moving_image = self.inputs.in_file
self._contour = self.inputs.wm_seg if isdefined(self.inputs.wm_seg) else None
NIWORKFLOWS_LOG.info(
"Report - setting corrected (%s) and warped (%s) images",
self._fixed_image,
self._moving_image,
)
return super(FUGUERPT, self)._post_run_hook(runtime)
class _FLIRTInputSpecRPT(nrc._SVGReportCapableInputSpec, fsl.preprocess.FLIRTInputSpec):
pass
class _FLIRTOutputSpecRPT(
reporting.ReportCapableOutputSpec, fsl.preprocess.FLIRTOutputSpec
):
pass
class FLIRTRPT(nrc.RegistrationRC, fsl.FLIRT):
input_spec = _FLIRTInputSpecRPT
output_spec = _FLIRTOutputSpecRPT
def _post_run_hook(self, runtime):
self._fixed_image = self.inputs.reference
self._moving_image = self.aggregate_outputs(runtime=runtime).out_file
output_spec = _ANTSApplyTransformsOutputSpecRPT
def _post_run_hook(self, runtime):
self._fixed_image = self.inputs.reference_image
self._moving_image = self.aggregate_outputs(runtime=runtime).output_image
NIWORKFLOWS_LOG.info(
"Report - setting fixed (%s) and moving (%s) images",
self._fixed_image,
self._moving_image,
)
return super(ANTSApplyTransformsRPT, self)._post_run_hook(runtime)
class _ApplyTOPUPInputSpecRPT(
nrc._SVGReportCapableInputSpec, fsl.epi.ApplyTOPUPInputSpec
):
wm_seg = File(argstr="-wmseg %s", desc="reference white matter segmentation mask")
class _ApplyTOPUPOutputSpecRPT(
reporting.ReportCapableOutputSpec, fsl.epi.ApplyTOPUPOutputSpec
):
pass
class ApplyTOPUPRPT(nrc.RegistrationRC, fsl.ApplyTOPUP):
input_spec = _ApplyTOPUPInputSpecRPT
output_spec = _ApplyTOPUPOutputSpecRPT
def _post_run_hook(self, runtime):
self._fixed_image_label = "after"
self._anat_file = os.path.join(
outputs.subjects_dir, outputs.subject_id, "mri", "brain.mgz"
)
self._contour = os.path.join(
outputs.subjects_dir, outputs.subject_id, "mri", "ribbon.mgz"
)
self._masked = False
NIWORKFLOWS_LOG.info(
"Generating report for ReconAll (subject %s)", outputs.subject_id
)
return super(ReconAllRPT, self)._post_run_hook(runtime)
class _MELODICInputSpecRPT(nrc._SVGReportCapableInputSpec, fsl.model.MELODICInputSpec):
out_report = File(
"melodic_reportlet.svg",
usedefault=True,
desc="Filename for the visual" " report generated " "by Nipype.",
)
report_mask = File(
desc="Mask used to draw the outline on the reportlet. "
"If not set the mask will be derived from the data."
)
class _MELODICOutputSpecRPT(
reporting.ReportCapableOutputSpec, fsl.model.MELODICOutputSpec
):
pass
self._anat_file = self.inputs.in_file
self._mask_file = self.aggregate_outputs(runtime=runtime).mask_file
self._seg_files = [self._mask_file]
self._masked = self.inputs.mask
NIWORKFLOWS_LOG.info(
'Generating report for BET. file "%s", and mask file "%s"',
self._anat_file,
self._mask_file,
)
return super(BETRPT, self)._post_run_hook(runtime)
class _BrainExtractionInputSpecRPT(
nrc._SVGReportCapableInputSpec, ants.segmentation.BrainExtractionInputSpec
):
pass
class _BrainExtractionOutputSpecRPT(
reporting.ReportCapableOutputSpec, ants.segmentation.BrainExtractionOutputSpec
):
pass
class BrainExtractionRPT(nrc.SegmentationRC, ants.segmentation.BrainExtraction):
input_spec = _BrainExtractionInputSpecRPT
output_spec = _BrainExtractionOutputSpecRPT
def _post_run_hook(self, runtime):
""" generates a report showing slices from each axis """
from nipype.interfaces.base import (
File,
BaseInterfaceInputSpec,
traits,
isdefined,
InputMultiPath,
Str,
)
from nipype.interfaces.mixins import reporting
from nipype.algorithms import confounds
from seaborn import color_palette
from .. import NIWORKFLOWS_LOG
from . import report_base as nrc
class _BETInputSpecRPT(nrc._SVGReportCapableInputSpec, fsl.preprocess.BETInputSpec):
pass
class _BETOutputSpecRPT(
reporting.ReportCapableOutputSpec, fsl.preprocess.BETOutputSpec
):
pass
class BETRPT(nrc.SegmentationRC, fsl.BET):
input_spec = _BETInputSpecRPT
output_spec = _BETOutputSpecRPT
def _run_interface(self, runtime):
if self.generate_report:
self.inputs.mask = True
res = mri_vol2vol.run()
self._fixed_image = target_file
self._moving_image = res.outputs.transformed_file
self._contour = os.path.join(mri_dir, "ribbon.mgz")
NIWORKFLOWS_LOG.info(
"Report - setting fixed (%s) and moving (%s) images",
self._fixed_image,
self._moving_image,
)
return super(BBRegisterRPT, self)._post_run_hook(runtime)
class _MRICoregInputSpecRPT(
nrc._SVGReportCapableInputSpec, fs.registration.MRICoregInputSpec
):
pass
class _MRICoregOutputSpecRPT(
reporting.ReportCapableOutputSpec, fs.registration.MRICoregOutputSpec
):
pass
class MRICoregRPT(nrc.RegistrationRC, fs.MRICoreg):
input_spec = _MRICoregInputSpecRPT
output_spec = _MRICoregOutputSpecRPT
def _post_run_hook(self, runtime):
outputs = self.aggregate_outputs(runtime=runtime)