Merge pull request #861 from oesteban/enh/AddInterfaceFSLWarpUtils

Interfaces for fnirtfileutils and convertwarp (FSL)

Author: oesteban

CHANGES

@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* ENH: Added new interfaces (fsl.utils.WarpUtils, ConvertWarp) to fnirtfileutils and convertwarp
 * API: Interfaces to external packages are no longer available in the top-level
        ``nipype`` namespace, and must be imported directly (e.g.
        ``from nipype.interfaces import fsl``).

nipype/interfaces/fsl/__init__.py

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

nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py

@@ -0,0 +1,74 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.utils import ConvertWarp
+
+def test_ConvertWarp_inputs():
+    input_map = dict(abswarp=dict(argstr='--abs',
+    xor=['relwarp'],
+    ),
+    args=dict(argstr='%s',
+    ),
+    cons_jacobian=dict(argstr='--constrainj',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    jacobian_max=dict(argstr='--jmax=%f',
+    ),
+    jacobian_min=dict(argstr='--jmin=%f',
+    ),
+    out_abswarp=dict(argstr='--absout',
+    xor=['out_relwarp'],
+    ),
+    out_file=dict(argstr='--out=%s',
+    name_source=['reference'],
+    name_template='%s_concatwarp',
+    output_name='out_file',
+    position=-1,
+    ),
+    out_relwarp=dict(argstr='--relout',
+    xor=['out_abswarp'],
+    ),
+    output_type=dict(),
+    postmat=dict(argstr='--postmat=%s',
+    ),
+    premat=dict(argstr='--premat=%s',
+    ),
+    reference=dict(argstr='--ref=%s',
+    mandatory=True,
+    position=1,
+    ),
+    relwarp=dict(argstr='--rel',
+    xor=['abswarp'],
+    ),
+    shift_direction=dict(argstr='--shiftdir=%s',
+    requires=['shift_in_file'],
+    ),
+    shift_in_file=dict(argstr='--shiftmap=%s',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    warp1=dict(argstr='--warp1=%s',
+    ),
+    warp2=dict(argstr='--warp2=%s',
+    ),
+    )
+    inputs = ConvertWarp.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_ConvertWarp_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = ConvertWarp.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_WarpUtils.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 WarpUtils
+
+def test_WarpUtils_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='--in=%s',
+    mandatory=True,
+    ),
+    knot_space=dict(argstr='--knotspace=%d,%d,%d',
+    ),
+    out_file=dict(argstr='--out=%s',
+    name_source=['in_file'],
+    output_name='out_file',
+    position=-1,
+    ),
+    out_format=dict(argstr='--outformat=%s',
+    ),
+    out_jacobian=dict(argstr='--jac=%s',
+    ),
+    output_type=dict(),
+    reference=dict(argstr='--ref=%s',
+    mandatory=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f',
+    ),
+    with_affine=dict(argstr='--withaff',
+    ),
+    write_jacobian=dict(mandatory=True,
+    usedefault=True,
+    ),
+    )
+    inputs = WarpUtils.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_WarpUtils_outputs():
+    output_map = dict(out_file=dict(),
+    out_jacobian=dict(),
+    )
+    outputs = WarpUtils.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+