[ENH] Added new fsl.WarpPointsFromStd interface

Author: oesteban

nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py

@@ -30,10 +30,12 @@ def test_MRIsConvert_inputs():
     ),
     origname=dict(argstr='-o %s',
     ),
-    out_datatype=dict(xor=['out_file'],
+    out_datatype=dict(mandatory=True,
+    xor=['out_file'],
     ),
     out_file=dict(argstr='%s',
     genfile=True,
+    mandatory=True,
     position=-1,
     xor=['out_datatype'],
     ),

nipype/interfaces/fsl/__init__.py

@@ -17,7 +17,8 @@
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,
                     Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints,
-                    WarpPointsToStd, RobustFOV, CopyGeom, MotionOutliers)
+                    WarpPointsToStd, WarpPointsFromStd,
+                    RobustFOV, CopyGeom, MotionOutliers)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect, EpiReg)

nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py

@@ -0,0 +1,60 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..utils import WarpPointsFromStd
+
+
+def test_WarpPointsFromStd_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    coord_mm=dict(argstr='-mm',
+    xor=['coord_vox'],
+    ),
+    coord_vox=dict(argstr='-vox',
+    xor=['coord_mm'],
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    img_file=dict(argstr='-img %s',
+    mandatory=True,
+    ),
+    in_coords=dict(argstr='%s',
+    mandatory=True,
+    position=-1,
+    ),
+    out_file=dict(name_source='in_coords',
+    name_template='%s_warped',
+    output_name='out_file',
+    ),
+    std_file=dict(argstr='-std %s',
+    mandatory=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    transform=dict(argstr='-xfm %s',
+    ),
+    warp_file=dict(argstr='-warp %s',
+    xor=['xfm_file'],
+    ),
+    xfm_file=dict(argstr='-xfm %s',
+    xor=['warp_file'],
+    ),
+    )
+    inputs = WarpPointsFromStd.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_WarpPointsFromStd_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = WarpPointsFromStd.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/fsl/utils.py

@@ -2017,6 +2017,47 @@ class WarpPointsToStd(WarpPoints):
     _cmd = 'img2stdcoord'
 
 
+class WarpPointsFromStdInputSpec(WarpPointsBaseInputSpec):
+    img_file = File(exists=True, argstr='-img %s', mandatory=True,
+                    desc='filename of a destination image')
+    std_file = File(exists=True, argstr='-std %s', mandatory=True,
+                    desc='filename of the image in standard space')
+    transform = File(exists=True, argstr='-xfm %s',
+                     desc='filename of pre-warp affine transform '
+                          '(e.g. example_func2highres.mat)')
+
+
+class WarpPointsFromStd(WarpPoints):
+    """
+    Use FSL `std2imgcoord <http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/flirt/overview.html>`_
+    to transform point sets to standard space coordinates. Accepts plain text files and
+    vtk files.
+
+    .. Note:: transformation of TrackVis trk files is not yet implemented
+
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.fsl import WarpPointsFromStd
+    >>> warppoints = WarpPointsFromStd()
+    >>> warppoints.inputs.in_coords = 'surf.txt'
+    >>> warppoints.inputs.img_file = 'T1.nii'
+    >>> warppoints.inputs.std_file = 'mni.nii'
+    >>> warppoints.inputs.warp_file = 'warpfield.nii'
+    >>> warppoints.inputs.coord_mm = True
+    >>> warppoints.cmdline # doctest: +ELLIPSIS
+    'std2imgcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt'
+    >>> res = warppoints.run() # doctest: +SKIP
+
+
+    """
+
+    input_spec = WarpPointsFromStdInputSpec
+    output_spec = WarpPointsOutputSpec
+    _cmd = 'std2imgcoord'
+
+
 class MotionOutliersInputSpec(FSLCommandInputSpec):
     in_file = File(
         exists=True, mandatory=True, desc="unfiltered 4D image", argstr="-i %s")