Merge branch 'enh/FSLstd2imgcoords' into fix/1407

Integrate the code from that branch that was stale waiting for `terminal_output` to be revised. Close #1398.

Author: oesteban

CHANGES

@@ -1,6 +1,9 @@
 Upcoming release
 ================
 
+* ENH: Improve terminal_output feature (https://github.com/nipy/nipype/pull/2209)
+* ENH: Simple interface to FSL std2imgcoords (https://github.com/nipy/nipype/pull/2209, prev #1398)
+
 
 0.13.1 (May 20, 2017)
 =====================
@@ -21,6 +24,7 @@ Upcoming release
 0.13.0 (May 11, 2017)
 =====================
 
+<<<<<<< HEAD
 * ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991)
 * FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000)
 * ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910)

nipype/interfaces/fsl/__init__.py

@@ -18,7 +18,9 @@
                     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)
 from .dti import (BEDPOSTX, XFibres, DTIFit,

nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py

@@ -0,0 +1,54 @@
+# 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=[u'coord_vox'],
+    ),
+    coord_vox=dict(argstr='-vox',
+    xor=[u'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=-2,
+    ),
+    std_file=dict(argstr='-std %s',
+    mandatory=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    warp_file=dict(argstr='-warp %s',
+    xor=[u'xfm_file'],
+    ),
+    xfm_file=dict(argstr='-xfm %s',
+    xor=[u'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

@@ -17,7 +17,7 @@
     os.chdir(datadir)
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import map, range
+from builtins import map, range, open
 
 import os
 import os.path as op
@@ -2110,6 +2110,59 @@ class WarpPointsToStd(WarpPoints):
     input_spec = WarpPointsToStdInputSpec
     output_spec = WarpPointsOutputSpec
     _cmd = 'img2stdcoord'
+    _terminal_output = 'file_split'
+
+
+class WarpPointsFromStdInputSpec(CommandLineInputSpec):
+    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')
+    in_coords = File(exists=True, position=-2, argstr='%s', mandatory=True,
+                     desc='filename of file containing coordinates')
+    xfm_file = File(exists=True, argstr='-xfm %s', xor=['warp_file'],
+                    desc='filename of affine transform (e.g. source2dest.mat)')
+    warp_file = File(exists=True, argstr='-warp %s', xor=['xfm_file'],
+                     desc='filename of warpfield (e.g. '
+                          'intermediate2dest_warp.nii.gz)')
+    coord_vox = traits.Bool(True, argstr='-vox', xor=['coord_mm'],
+                            desc='all coordinates in voxels - default')
+    coord_mm = traits.Bool(False, argstr='-mm', xor=['coord_vox'],
+                           desc='all coordinates in mm')
+
+
+class WarpPointsFromStd(CommandLine):
+    """
+    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 coordinates
+    files.
+
+
+    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 +IGNORE_UNICODE
+    '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'
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath('stdout.nipype')
+        return outputs
 
 
 class MotionOutliersInputSpec(FSLCommandInputSpec):