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FIX: Patch ApplyTransforms spec to permit identity in a chain #554

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Merged
merged 2 commits into from
Aug 14, 2020
Merged

FIX: Patch ApplyTransforms spec to permit identity in a chain #554

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7665fae
FIX: Patch ApplyTransforms spec to permit identity in a chain
effigies Aug 13, 2020
93eb5ee
ENH: Handle "identity" values when arranging xfms
effigies Aug 13, 2020
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14 changes: 12 additions & 2 deletions niworkflows/interfaces/fixes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,9 @@

import nibabel as nb

from nipype.interfaces.base import traits
from nipype.interfaces.base import traits, InputMultiObject, File
from nipype.utils.filemanip import fname_presuffix
from nipype.interfaces.ants.resampling import ApplyTransforms
from nipype.interfaces.ants.resampling import ApplyTransforms, ApplyTransformsInputSpec
from nipype.interfaces.ants.registration import Registration
from nipype.interfaces.ants.segmentation import (
N4BiasFieldCorrection as VanillaN4,
Expand All @@ -17,12 +17,22 @@
from .utils import _copyxform


class FixTraitApplyTransformsInputSpec(ApplyTransformsInputSpec):
transforms = InputMultiObject(
traits.Either(File(exists=True), 'identity'),
argstr="%s",
mandatory=True,
desc="transform files: will be applied in reverse order. For "
"example, the last specified transform will be applied first.",
)

class FixHeaderApplyTransforms(ApplyTransforms):
"""
A replacement for nipype.interfaces.ants.resampling.ApplyTransforms that
fixes the resampled image header to match the xform of the reference
image
"""
input_spec = FixTraitApplyTransformsInputSpec

def _run_interface(self, runtime, correct_return_codes=(0,)):
# Run normally
Expand Down
18 changes: 11 additions & 7 deletions niworkflows/interfaces/itk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,17 +12,17 @@
TraitedSpec,
BaseInterfaceInputSpec,
File,
InputMultiPath,
OutputMultiPath,
InputMultiObject,
OutputMultiObject,
SimpleInterface,
)
from nipype.interfaces.ants.resampling import ApplyTransformsInputSpec
from niworkflows.interfaces.fixes import FixTraitApplyTransformsInputSpec

LOGGER = logging.getLogger("nipype.interface")


class _MCFLIRT2ITKInputSpec(BaseInterfaceInputSpec):
in_files = InputMultiPath(
in_files = InputMultiObject(
File(exists=True), mandatory=True, desc="list of MAT files from MCFLIRT"
)
in_reference = File(
Expand Down Expand Up @@ -96,8 +96,8 @@ def _run_interface(self, runtime):
return runtime


class _MultiApplyTransformsInputSpec(ApplyTransformsInputSpec):
input_image = InputMultiPath(
class _MultiApplyTransformsInputSpec(FixTraitApplyTransformsInputSpec):
input_image = InputMultiObject(
File(exists=True),
mandatory=True,
desc="input time-series as a list of volumes after splitting"
Expand All @@ -115,7 +115,7 @@ class _MultiApplyTransformsInputSpec(ApplyTransformsInputSpec):


class _MultiApplyTransformsOutputSpec(TraitedSpec):
out_files = OutputMultiPath(File(), desc="the output ITKTransform file")
out_files = OutputMultiObject(File(), desc="the output ITKTransform file")
log_cmdline = File(desc="a list of command lines used to apply transforms")


Expand Down Expand Up @@ -254,6 +254,10 @@ def _arrange_xfms(transforms, num_files, tmp_folder):
# Initialize the transforms matrix
xfms_T = []
for i, tf_file in enumerate(transforms):
if tf_file == "identity":
xfms_T.append([tf_file] * num_files)
continue

# If it is a deformation field, copy to the tfs_matrix directly
if guess_type(tf_file)[0] != "text/plain":
xfms_T.append([tf_file] * num_files)
Expand Down