Merge pull request #1152 from mick-d/FSLgeom

New interface for fslcpgeom

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
 * FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
        replaced by https://github.com/nipy/nipype/pull/1093)
 * ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings

nipype/interfaces/fsl/__init__.py

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

nipype/interfaces/fsl/tests/test_auto_CopyGeom.py

@@ -0,0 +1,44 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import CopyGeom
+
+def test_CopyGeom_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    dest_file=dict(argstr='%s',
+    copyfile=True,
+    mandatory=True,
+    position=1,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_dims=dict(argstr='-d',
+    position='-1',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=0,
+    ),
+    output_type=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = CopyGeom.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_CopyGeom_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = CopyGeom.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/utils.py

@@ -26,11 +26,36 @@
 from ..base import (traits, TraitedSpec, OutputMultiPath, File,
                     CommandLine, CommandLineInputSpec, isdefined)
 from ...utils.filemanip import (load_json, save_json, split_filename,
-                                fname_presuffix)
+                                fname_presuffix, copyfile)
 
 warn = warnings.warn
 warnings.filterwarnings('always', category=UserWarning)
 
+class CopyGeomInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True, mandatory=True, argstr="%s", position=0,
+                   desc="source image")
+    dest_file = File(exists=True, mandatory=True, argstr="%s", position=1,
+                     desc="destination image", copyfile=True, output_name='out_file',
+                     name_source='dest_file', name_template='%s')
+    ignore_dims = traits.Bool(desc=('Do not copy image dimensions'),
+                              argstr='-d', position="-1")
+
+class CopyGeomOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc="image with new geometry header")
+
+class CopyGeom(FSLCommand):
+    """Use fslcpgeom to copy the header geometry information to another image.
+    Copy certain parts of the header information (image dimensions, voxel dimensions,
+    voxel dimensions units string, image orientation/origin or qform/sform info)
+    from one image to another. Note that only copies from Analyze to Analyze
+    or Nifti to Nifti will work properly. Copying from different files will result
+    in loss of information or potentially incorrect settings.
+    """
+    _cmd = "fslcpgeom"
+    input_spec = CopyGeomInputSpec
+    output_spec = CopyGeomOutputSpec
+
+
 class RobustFOVInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True,
                    desc='input filename',