Merge pull request #888 from oesteban/enh/FSLimg2coords

FSL new interfaces: img2imgcoords and img2stdcoords

Author: oesteban

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.
 * ENH: New Freesurfer interface: MRIPretess
 * ENH: New miscelaneous interface: AddCSVRow
 * ENH: FUGUE interface has been refactored to use the name_template system, 3 examples 

nipype/interfaces/fsl/__init__.py

@@ -16,7 +16,7 @@
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,
-                    Complex, InvWarp, WarpUtils, ConvertWarp)
+                    Complex, InvWarp, WarpUtils, ConvertWarp, WarpPoints, WarpPointsToStd)
 
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect)

nipype/interfaces/fsl/tests/test_auto_WarpPoints.py

@@ -0,0 +1,58 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import WarpPoints
+
+def test_WarpPoints_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    coord_mm=dict(argstr='-mm',
+    xor=['coord_vox'],
+    ),
+    coord_vox=dict(argstr='-vox',
+    xor=['coord_mm'],
+    ),
+    dest_file=dict(argstr='-dest %s',
+    mandatory=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=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',
+    ),
+    src_file=dict(argstr='-src %s',
+    mandatory=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    warp_file=dict(argstr='-warp %s',
+    xor=['xfm_file'],
+    ),
+    xfm_file=dict(argstr='-xfm %s',
+    xor=['warp_file'],
+    ),
+    )
+    inputs = WarpPoints.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_WarpPoints_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = WarpPoints.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py

@@ -0,0 +1,60 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import WarpPointsToStd
+
+def test_WarpPointsToStd_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',
+    ),
+    premat_file=dict(argstr='-premat %s',
+    ),
+    std_file=dict(argstr='-std %s',
+    mandatory=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    warp_file=dict(argstr='-warp %s',
+    xor=['xfm_file'],
+    ),
+    xfm_file=dict(argstr='-xfm %s',
+    xor=['warp_file'],
+    ),
+    )
+    inputs = WarpPointsToStd.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_WarpPointsToStd_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = WarpPointsToStd.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+