♻️ Replace CopyImageHeaderInformation with PrintHeader + `SetDire…

…ctionByMatrix`

ref https://github.com/ANTsX/ANTs/wiki/Inputs-do-not-occupy-the-same-physical-space#fixing-precision-errors

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+per-file-ignores =
+  CPAC/func_preproc/func_preproc.py:E402

CPAC/func_preproc/func_preproc.py

@@ -1,25 +1,19 @@
+# pylint: disable=ungrouped-imports,wrong-import-order,wrong-import-position
 from nipype import logging
-from nipype.interfaces import ants
-
+from nipype.interfaces import afni, ants, fsl, utility as util
 logger = logging.getLogger('nipype.workflow')
-
 from CPAC.pipeline import nipype_pipeline_engine as pe
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.utility as util
-from nipype.interfaces import afni
 from nipype.interfaces.afni import preprocess
 from nipype.interfaces.afni import utils as afni_utils
+
 from CPAC.func_preproc.utils import add_afni_prefix, nullify, chunk_ts, \
     split_ts_chunks, oned_text_concat, notch_filter_motion
-from CPAC.utils.interfaces.function import Function
 from CPAC.generate_motion_statistics import motion_power_statistics
-
+from CPAC.utils.interfaces.ants import AI  # niworkflows
+from CPAC.utils.interfaces.ants import PrintHeader, SetDirectionByMatrix
+from CPAC.utils.interfaces.function import Function
 from CPAC.utils.utils import check_prov_for_motion_tool
 
-# niworkflows
-from ..utils.interfaces.ants import AI, \
-    CopyImageHeaderInformation  # noqa: E402
-
 
 def collect_arguments(*args):
     command_args = []
@@ -1667,8 +1661,10 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
 
     # Fix precision errors
     # https://github.com/ANTsX/ANTs/wiki/Inputs-do-not-occupy-the-same-physical-space#fixing-precision-errors
-    restore_header = pe.Node(CopyImageHeaderInformation(),
-                             name=f'restore_header_{pipe_num}')
+    print_header = pe.Node(PrintHeader(what_information=4),
+                           name=f'print_header_{pipe_num}')
+    set_direction = pe.Node(SetDirectionByMatrix(),
+                            name=f'set_direction_{pipe_num}')
 
     # Run N4 normally, force num_threads=1 for stability (images are
     # small, no need for >1)
@@ -1714,7 +1710,6 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
     wf.connect([(node, init_aff, [(out, "moving_image")]),
                 (node, map_brainmask, [(out, "reference_image")]),
                 (node, norm, [(out, "moving_image")]),
-                (node, restore_header, [(out, "refimage")]),
                 (init_aff, norm, [
                     ("output_transform", "initial_moving_transform")]),
                 (norm, map_brainmask, [
@@ -1723,9 +1718,10 @@ def bold_mask_fsl_afni(wf, cfg, strat_pool, pipe_num, opt=None):
                 ]),
                 (map_brainmask, binarize_mask, [("output_image", "in_file")]),
                 (binarize_mask, pre_dilate, [("out_file", "in_file")]),
-                (pre_dilate, restore_header, [
-                    ("out_file", "imagetocopyrefimageinfoto")]),
-                (restore_header, n4_correct, [("imageout", "mask_image")]),
+                (pre_dilate, print_header, [("out_file", "image")]),
+                (print_header, set_direction, [("header", "direction")]),
+                (node, set_direction, [(out, "infile"), (out, "outfile")]),
+                (set_direction, n4_correct, [("outfile", "mask_image")]),
                 (node, n4_correct, [(out, "input_image")]),
                 (n4_correct, skullstrip_first_pass,
                  [('output_image', 'in_file')]),

CPAC/utils/interfaces/ants.py

@@ -11,81 +11,12 @@
 # https://fmriprep.readthedocs.io/
 # https://poldracklab.stanford.edu/
 # We are temporarily maintaining our own copy for more granular control.
-
 import os
-from glob import glob
 from nipype.interfaces import base
 from nipype.interfaces.ants.base import ANTSCommandInputSpec, ANTSCommand
 from nipype.interfaces.base import traits, isdefined
 
 
-class CopyImageHeaderInformationInputSpec(ANTSCommandInputSpec):
-    """InputSpec for ``CopyImageHeaderInformation``.
-
-    ``imagetocopyrefimageinfoto`` is also used for ``imageout`` if
-    ``imageout`` is not specified.
-    """
-    def __setattr__(self, name, value):
-        super(ANTSCommandInputSpec, self).__setattr__(name, value)
-        if name == 'imagetocopyrefimageinfoto':
-            self._infer_imageout()
-
-    def _infer_imageout(self):
-        if (self.imageout == base.Undefined):
-            self.trait_set(imageout=self.imagetocopyrefimageinfoto)
-
-    refimage = base.File(position=1, argstr='%s', name_source=['refimage'],
-                         desc='reference image (with header to copy from)',
-                         exists=True, mandatory=True)
-
-    imagetocopyrefimageinfoto = base.File(position=2, argstr='%s',
-                                          name_source=[
-                                              'imagetocopyrefimageinfoto'
-                                          ], desc='image to copy header to',
-                                          exists=True, mandatory=True)
-
-    imageout = base.File(position=3, argstr='%s', name_sources=[
-                            'imagetocopyrefimageinfoto',
-                            'imageout'
-                         ],
-                         desc='output image file', usedefault=True)
-
-    boolcopydirection = traits.Bool(True, argstr='%d', position=4,
-                                    desc='copy direction?', usedefault=True)
-
-    boolcopyorigin = traits.Bool(True, argstr='%d', position=5,
-                                 desc='copy origin?', usedefault=True)
-
-    boolcopyspacing = traits.Bool(True, argstr='%d', position=6,
-                                  desc='copy spacing?', usedefault=True)
-
-
-class CopyImageHeaderInformationOutputSpec(base.TraitedSpec):
-    """OutputSpec for CopyImageHeaderInformation"""
-    imageout = base.File(exists=True, desc='output image file')
-
-
-class CopyImageHeaderInformation(ANTSCommand):
-    """Copy image header information from one file to another,
-    optionally as a copy.
-
-    Examples
-    --------
-    >>> CopyImageHeaderInformation(
-    ...     refimage='/cpac_templates/MacaqueYerkes19_T1w_2mm_brain.nii.gz',
-    ...     imagetocopyrefimageinfoto='/cpac_templates/MacaqueYerkes19_'
-    ...                               'T1w_2mm_brain_mask.nii.gz'
-    ... ).cmdline
-    'CopyImageHeaderInformation /cpac_templates/MacaqueYerkes19_T1w_2mm_brain.nii.gz /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz /cpac_templates/MacaqueYerkes19_T1w_2mm_brain_mask.nii.gz 1 1 1'
-    """  # noqa: E501
-    _cmd = 'CopyImageHeaderInformation'
-    input_spec = CopyImageHeaderInformationInputSpec
-    output_spec = CopyImageHeaderInformationOutputSpec
-
-    def _list_outputs(self):
-        return {'imageout': self.inputs.imageout}
-
-
 class ImageMathInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(3, usedefault=True, position=1, argstr='%d',
                            desc='dimension of output image')
@@ -112,12 +43,49 @@ class ImageMath(ANTSCommand):
     --------
 
     """
-
     _cmd = 'ImageMath'
     input_spec = ImageMathInputSpec
     output_spec = ImageMathOuputSpec
 
 
+class PrintHeaderInputSpec(ANTSCommandInputSpec):
+    """InputSpec for ``PrintHeader``.
+
+    See `PrintHeader: DESCRIPTION <https://manpages.debian.org/testing/ants/PrintHeader.1.en.html#DESCRIPTION>`_ for ``what_information`` values.
+    """  # noqa: E501  # pylint: disable=line-too-long
+    image = base.File(position=2, argstr='%s', name_source=['image'],
+                      desc='image to read header from', exists=True,
+                      mandatory=True)
+
+    what_information = traits.Int(position=3, argstr='%i',
+                                  name='what_information',
+                                  desc='read what from header')
+
+
+class PrintHeaderOutputSpec(base.TraitedSpec):
+    """OutputSpec for ``PrintHeader``."""
+    header = traits.String(name='header')
+
+
+class PrintHeader(ANTSCommand):
+    """Print image header information."""
+    _cmd = 'PrintHeader'
+    # pylint: disable=protected-access
+    _gen_filename = base.StdOutCommandLine._gen_filename
+    input_spec = PrintHeaderInputSpec
+    output_spec = PrintHeaderOutputSpec
+    _terminal_output = 'stream'
+
+    def aggregate_outputs(self, runtime=None, needed_outputs=None):
+        outputs = super().aggregate_outputs(runtime, needed_outputs)
+        outputs.trait_set(header=runtime.stdout)
+        self.output_spec().trait_set(header=runtime.stdout)
+        return outputs
+
+    def _list_outputs(self):
+        return self._outputs().get()
+
+
 class ResampleImageBySpacingInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(3, usedefault=True, position=1, argstr='%d',
                            desc='dimension of output image')
@@ -189,6 +157,40 @@ def _format_arg(self, name, trait_spec, value):
             name, trait_spec, value)
 
 
+class SetDirectionByMatrixInputSpec(ANTSCommandInputSpec):
+    """InputSpec for ``SetDirectionByMatrix``."""
+    infile = base.File(position=2, argstr='%s', name_source=['infile'],
+                       desc='image to copy header to', exists=True,
+                       mandatory=True)
+    outfile = base.File(position=3, argstr='%s',
+                        name_sources=['infile', 'outfile'],
+                        desc='output image file', usedefault=True)
+    direction = traits.String(argstr='%s', position=4,
+                              desc='dimensions, x-delimited')
+
+
+class SetDirectionByMatrixOutputSpec(base.TraitedSpec):
+    """OutputSpec for ``SetDirectionByMatrix``"""
+    outfile = base.File(exists=True, desc='output image file')
+
+
+class SetDirectionByMatrix(ANTSCommand):
+    """Set image header information from a matrix of dimensions."""
+    _cmd = 'SetDirectionByMatrix'
+    # pylint: disable=protected-access
+    _gen_filename = base.StdOutCommandLine._gen_filename
+    input_spec = SetDirectionByMatrixInputSpec
+    output_spec = SetDirectionByMatrixOutputSpec
+
+    def _format_arg(self, name, trait_spec, value):
+        if name == 'direction':
+            return value.replace('x', ' ')
+        return super()._format_arg(name, trait_spec, value)
+
+    def _list_outputs(self):
+        return {'outfile': self.inputs.outfile}
+
+
 class ThresholdImageInputSpec(ANTSCommandInputSpec):
     dimension = traits.Int(3, usedefault=True, position=1, argstr='%d',
                            desc='dimension of output image')