Merge pull request #472 from chrisfilo/enh/c3c

added C3dAffineTool for converting FSL to ITK affines

Author: chrisgorgo

CHANGES

@@ -2,7 +2,7 @@ Next release
 ============
 
 * ENH: Add basic support for LSF plugin.
-* ENH: New interfaces: ICC, Meshfix, ants.Register
+* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool
 * ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
 * ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate), 
 	  how to set SGE specific options (smri_ants_build_template_new)

nipype/interfaces/base.py

@@ -1256,6 +1256,39 @@ def _gen_filename(self, name):
     def _gen_outfilename(self):
         raise NotImplementedError
 
+class SEMLikeCommandLine(CommandLine):
+    """By default in SEM derived interface all outputs have corresponding inputs.
+    However, some SEM commands create outputs that are not defined in the XML.
+    In those cases one has to create a subclass of the autogenerated one and
+    overload the _list_outputs method. _outputs_from_inputs should still be
+    used but only for the reduced (by excluding those that do not have
+    corresponding inputs list of outputs.
+    """
+    def _list_outputs(self):
+	outputs = self.output_spec().get()
+	return self._outputs_from_inputs(outputs)
+
+    def _outputs_from_inputs(self, outputs):
+	for name in outputs.keys():
+	    coresponding_input = getattr(self.inputs, name)
+	    if isdefined(coresponding_input):
+		if isinstance(coresponding_input, bool) and coresponding_input == True:
+		    outputs[name] = os.path.abspath(self._outputs_filenames[name])
+		else:
+		    if isinstance(coresponding_input, list):
+			outputs[name] = [os.path.abspath(inp) for inp in coresponding_input]
+		    else:
+			outputs[name] = os.path.abspath(coresponding_input)
+	return outputs
+
+    def _format_arg(self, name, spec, value):
+	if name in self._outputs_filenames.keys():
+	    if isinstance(value, bool):
+		if value == True:
+		    value = os.path.abspath(self._outputs_filenames[name])
+		else:
+		    return ""
+	return super(SEMLikeCommandLine, self)._format_arg(name, spec, value)
 
 class MultiPath(traits.List):
     """ Abstract class - shared functionality of input and output MultiPath

nipype/interfaces/c3.py

@@ -0,0 +1,43 @@
+"""The ants module provides basic functions for interfacing with ants functions.
+
+   Change directory to provide relative paths for doctests
+   >>> import os
+   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+   >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+   >>> os.chdir(datadir)
+"""
+from nipype.interfaces.base import (CommandLineInputSpec, traits, TraitedSpec,
+				    File, SEMLikeCommandLine)
+
+
+class C3dAffineToolInputSpec(CommandLineInputSpec):
+    reference_file = File(exists=True, argstr="-ref %s", position=1)
+    source_file = File(exists=True, argstr='-src %s', position=2)
+    transform_file = File(exists=True, argstr='%s', position=3)
+    itk_transform = traits.Either(traits.Bool, File(), hash_files=False,
+				  desc="Export ITK transform.",
+				  argstr="-oitk %s", position=5)
+    fsl2ras = traits.Bool(argstr='-fsl2ras', position=4)
+
+
+class C3dAffineToolOutputSpec(TraitedSpec):
+    itk_transform = File(exists=True)
+
+
+class C3dAffineTool(SEMLikeCommandLine):
+    """Converts fsl-style Affine registration into ANTS compatible itk format
+
+    Example
+    >>> from nipype.interfaces.c3 import C3dAffineTool
+    >>> c3 = C3dAffineTool()
+    >>> c3.inputs.source_file = 'cmatrix.mat'
+    >>> c3.inputs.itk_transform = 'affine.txt'
+    >>> c3.inputs.fsl2ras = True
+    >>> c3.cmdline
+    'c3d_affine_tool -src cmatrix.mat -fsl2ras -oitk affine.txt'
+    """
+    input_spec = C3dAffineToolInputSpec
+    output_spec = C3dAffineToolOutputSpec
+
+    _cmd = 'c3d_affine_tool'
+    _outputs_filenames = {'itk_transform': 'affine.txt'}

nipype/interfaces/slicer/base.py

@@ -1,37 +1,4 @@
-from nipype.interfaces.base import CommandLine, isdefined
-import os
+from ..base import SEMLikeCommandLine
 
-
-class SlicerCommandLine(CommandLine):
-    """By default in SEM derived interface all outputs have corresponding inputs.
-    However, some SEM commands create outputs that are not defined in the XML.
-    In those cases one has to create a subclass of the autogenerated one and
-    overload the _list_outputs method. _outputs_from_inputs should still be
-    used but only for the reduced (by excluding those that do not have
-    corresponding inputs list of outputs.
-    """
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        return self._outputs_from_inputs(outputs)
-
-    def _outputs_from_inputs(self, outputs):
-        for name in outputs.keys():
-            coresponding_input = getattr(self.inputs, name)
-            if isdefined(coresponding_input):
-                if isinstance(coresponding_input, bool) and coresponding_input == True:
-                    outputs[name] = os.path.abspath(self._outputs_filenames[name])
-                else:
-                    if isinstance(coresponding_input, list):
-                        outputs[name] = [os.path.abspath(inp) for inp in coresponding_input]
-                    else:
-                        outputs[name] = os.path.abspath(coresponding_input)
-        return outputs
-
-    def _format_arg(self, name, spec, value):
-        if name in self._outputs_filenames.keys():
-            if isinstance(value, bool):
-                if value == True:
-                    value = os.path.abspath(self._outputs_filenames[name])
-                else:
-                    return ""
-        return super(SlicerCommandLine, self)._format_arg(name, spec, value)
+class SlicerCommandLine(SEMLikeCommandLine):
+    pass

nipype/interfaces/slicer/converters.py

@@ -1,16 +1,17 @@
+# -*- coding: utf8 -*- 
 """Autogenerated file - DO NOT EDIT
 If you spot a bug, please report it on the mailing list and/or change the generator."""
 
-from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
 import os
-from nipype.interfaces.slicer.base import SlicerCommandLine
 
 
 class DicomToNrrdConverterInputSpec(CommandLineInputSpec):
+    inputDicomDirectory = Directory(desc="Directory holding Dicom series", exists=True, argstr="--inputDicomDirectory %s")
     outputDirectory = traits.Either(traits.Bool, Directory(), hash_files=False, desc="Directory holding the output NRRD format", argstr="--outputDirectory %s")
     outputVolume = traits.Str(desc="Output filename (.nhdr or .nrrd)", argstr="--outputVolume %s")
     smallGradientThreshold = traits.Float(desc="If a gradient magnitude is greater than 0 and less than smallGradientThreshold, then DicomToNrrdConverter will display an error message and quit, unless the useBMatrixGradientDirections option is set.", argstr="--smallGradientThreshold %f")
-    writeProtocolGradientsFile = traits.Bool(desc="Write the protocol gradients to a file suffixed by \".txt\" as they were specified in the procol by multiplying each diffusion gradient direction by the measurement frame.  This file is for debugging purposes only, the format is not fixed, and will likely change as debugging of new dicom formats is necessary.", argstr="--writeProtocolGradientsFile ")
+    writeProtocolGradientsFile = traits.Bool(desc="Write the protocol gradients to a file suffixed by \'.txt\' as they were specified in the procol by multiplying each diffusion gradient direction by the measurement frame.  This file is for debugging purposes only, the format is not fixed, and will likely change as debugging of new dicom formats is necessary.", argstr="--writeProtocolGradientsFile ")
     useIdentityMeaseurementFrame = traits.Bool(desc="Adjust all the gradients so that the measurement frame is an identity matrix.", argstr="--useIdentityMeaseurementFrame ")
     useBMatrixGradientDirections = traits.Bool(desc="Fill the nhdr header with the gradient directions and bvalues computed out of the BMatrix. Only changes behavior for Siemens data.", argstr="--useBMatrixGradientDirections ")
 
@@ -19,7 +20,7 @@ class DicomToNrrdConverterOutputSpec(TraitedSpec):
     outputDirectory = Directory(desc="Directory holding the output NRRD format", exists=True)
 
 
-class DicomToNrrdConverter(SlicerCommandLine):
+class DicomToNrrdConverter(SEMLikeCommandLine):
     """title: DICOM to NRRD Converter
 
 category: Converters
@@ -45,6 +46,7 @@ class DicomToNrrdConverter(SlicerCommandLine):
 
 
 class OrientScalarVolumeInputSpec(CommandLineInputSpec):
+    inputVolume1 = File(position=-2, desc="Input volume 1", exists=True, argstr="%s")
     outputVolume = traits.Either(traits.Bool, File(), position=-1, hash_files=False, desc="The oriented volume", argstr="%s")
     orientation = traits.Enum("Axial", "Coronal", "Sagittal", "RIP", "LIP", "RSP", "LSP", "RIA", "LIA", "RSA", "LSA", "IRP", "ILP", "SRP", "SLP", "IRA", "ILA", "SRA", "SLA", "RPI", "LPI", "RAI", "LAI", "RPS", "LPS", "RAS", "LAS", "PRI", "PLI", "ARI", "ALI", "PRS", "PLS", "ARS", "ALS", "IPR", "SPR", "IAR", "SAR", "IPL", "SPL", "IAL", "SAL", "PIR", "PSR", "AIR", "ASR", "PIL", "PSL", "AIL", "ASL", desc="Orientation choices", argstr="--orientation %s")
 
@@ -53,7 +55,7 @@ class OrientScalarVolumeOutputSpec(TraitedSpec):
     outputVolume = File(position=-1, desc="The oriented volume", exists=True)
 
 
-class OrientScalarVolume(SlicerCommandLine):
+class OrientScalarVolume(SEMLikeCommandLine):
     """title: Orient Scalar Volume
 
 category: Converters