ENH: Added pipeline for BRAINSTools to BRAINSTools

AutoWorkup/BRAINSTools/ANTSWrapper.py

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+#! /usr/bin/env python
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+
+Program:       PINC/nipype/Wrappers/ants.py
+Date:          Tue Jan  3 10:47:45 2012
+Author:        David Welch, [email protected]                                                #
+Purpose:       Wrap a Bash script to interface ANTS with Nipype
+
+Requirements:  <<< Interface specifications >>>
+
+$ ANTS_wrapper.sh <FixedT1Image> <FixedT2Image> <MovingT1Image> <MovingT2Image> <OutputPrefix>
+
+               where the script implicitly generates three output files:
+               <OutputPrefix>Affine.txt
+               <OutputPrefix>Warp.nii.gz
+               <OutputPrefix>InverseWarp.nii.gz
+
+
+"""
+from nipype.interfaces.base import ( File, TraitedSpec, Interface, CommandLineInputSpec, CommandLine, traits )
+
+### Node Interface
+class ANTSWrapperInputSpec( TraitedSpec ):
+    fixed_T1_image = File( desc = "T1 Fixed Volume", exists = True, mandatory = True)
+    fixed_T2_image = File( desc = "T2 Fixed Volume", exists = True, mandatory = True)
+    moving_T1_image = File( desc = "T1 Moving Volume", exists = True, mandatory = True)
+    moving_T2_image = File( desc = "T2 Moving Volume", exists = True, mandatory = True)
+    prefix_desc = "Output volume prefix for Affine.txt, Warp.nii.gz, and InverseWarp.nii.gz"
+    output_prefix = traits.Str( desc = prefix_desc, exists = True, mandatory = False,
+                                default_value = "./ANTS_")
+
+class ANTSWrapperOutputSpec(TraitedSpec):
+    output_affine = File( desc = "Affine Transform Text File")
+    output_warp = File( desc = "Warped Output Volume")
+    output_invwarp = File( desc = "Inverse Warp Output Volume")
+
+class ANTSWrapper(Interface):
+    input_spec = ANTSWrapperInputSpec
+    output_spec = ANTSWrapperOutputSpec
+
+    def _list_outputs(self):
+        """
+        The ANTS package implicitly outputs three files based on the prefix given at the commandline:
+        {prefix}Affine.txt, {prefix}Warp.nii.gz, and {prefix}InverseWarp.nii.gz.  This function exposes
+        them for subsequent nodes.
+        """
+        from os.path import abspath
+        outputs = self.output_spec().get()
+        outputs['output_affine'] = abspath( self.inputs.output_prefix + 'Affine.txt')
+        outputs['output_warp'] = abspath( self.inputs.output_prefix + 'Warp.nii.gz')
+        outputs['output_invwarp'] = abspath( self.inputs.output_prefix + 'InverseWarp.nii.gz')
+        return outputs
+
+### CommandLine
+class ANTSWrapperCLInputSpec(CommandLineInputSpec):
+    fixed_T1_image = File(desc="T1 Fixed Volume", exists=True, mandatory=True, position=0, argstr="%s" )
+    fixed_T2_image = File(desc="T2 Fixed Volume", exists=True, mandatory=True, position=1, argstr="%s" )
+    moving_T1_image = File(desc="T1 Moving Volume", exists=True, mandatory=True, position=2, argstr="%s" )
+    moving_T2_image = File(desc="T2 Moving Volume", exists=True, mandatory=True, position=3, argstr="%s" )
+    prefix_desc = "Output volume prefix for Affine.txt, Warp.nii.gz, and InverseWarp.nii.gz"
+    output_prefix = traits.Str(desc=prefix_desc, exists=True, mandatory=False, position=4, argstr="%s",
+                               default_value="./ANTS_" )
+
+class ANTSWrapperCLOutputSpec(CommandLineInputSpec):
+    output_affine = File( desc = "Affine Transform Text File", exists = True, mandatory = False)
+    output_warp = File( desc = "Warped Output Volume", exists = True, mandatory = True )
+    output_invwarp = File( desc = "Inverse Warp Output Volume", exists = True, mandatory = False)
+
+class ANTSWrapper(CommandLine):
+    _cmd = 'ANTS_wrapper.sh'
+    input_spec = ANTSWrapperCLInputSpec
+    output_spec = ANTSWrapperCLOutputSpec
+
+    def _list_outputs(self):
+        """
+        The ANTS package implicitly outputs three files based on the prefix given at the commandline:
+        {prefix}Affine.txt, {prefix}Warp.nii.gz, and {prefix}InverseWarp.nii.gz.  This function exposes
+        them for subsequent nodes.
+        """
+        from os.path import abspath
+        outputs = self.output_spec().get()
+        outputs['output_affine'] = abspath( self.inputs.output_prefix + 'Affine.txt')
+        outputs['output_warp'] = abspath( self.inputs.output_prefix + 'Warp.nii.gz')
+        outputs['output_invwarp'] = abspath( self.inputs.output_prefix + 'InverseWarp.nii.gz')
+        return outputs
+
+if __name__ == '__main__':
+    ants = ANTSWrapper(sys.argv)
+    ants.run()

AutoWorkup/BRAINSTools/BRAINSABC.py

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+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+class BRAINSABCInputSpec(CommandLineInputSpec):
+    inputVolumes = InputMultiPath(File(exists=True), argstr = "--inputVolumes %s...")
+    atlasDefinition = File( exists = True,argstr = "--atlasDefinition %s")
+    inputVolumeTypes = InputMultiPath(traits.Str, sep = ",",argstr = "--inputVolumeTypes %s")
+    outputDir = traits.Either(traits.Bool, Directory(), hash_files = False,argstr = "--outputDir %s")
+    atlasToSubjectTransformType = traits.Enum("ID","Rigid","Affine","BSpline", argstr = "--atlasToSubjectTransformType %s")
+    atlasToSubjectTransform = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--atlasToSubjectTransform %s")
+    atlasToSubjectInitialTransform = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--atlasToSubjectInitialTransform %s")
+    subjectIntermodeTransformType = traits.Enum("ID","Rigid","Affine","BSpline", argstr = "--subjectIntermodeTransformType %s")
+    outputVolumes = traits.Either(traits.Bool, InputMultiPath(File(),), hash_files = False,argstr = "--outputVolumes %s...")
+    outputLabels = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--outputLabels %s")
+    outputDirtyLabels = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--outputDirtyLabels %s")
+    posteriorTemplate = traits.Str( argstr = "--posteriorTemplate %s")
+    outputFormat = traits.Enum("NIFTI","Meta","Nrrd", argstr = "--outputFormat %s")
+    resamplerInterpolatorType = traits.Enum("BSpline","NearestNeighbor","WindowedSinc","Linear","ResampleInPlace","Hamming","Cosine","Welch","Lanczos","Blackman", argstr = "--interpolationMode %s")
+    maxIterations = traits.Int( argstr = "--maxIterations %d")
+    medianFilterSize = InputMultiPath(traits.Int, sep = ",",argstr = "--medianFilterSize %s")
+    filterIteration = traits.Int( argstr = "--filterIteration %d")
+    filterTimeStep = traits.Float( argstr = "--filterTimeStep %f")
+    filterMethod = traits.Enum("None","CurvatureFlow","GradientAnisotropicDiffusion","Median", argstr = "--filterMethod %s")
+    maxBiasDegree = traits.Int( argstr = "--maxBiasDegree %d")
+    atlasWarpingOff = traits.Bool( argstr = "--atlasWarpingOff ")
+    gridSize = InputMultiPath(traits.Int, sep = ",",argstr = "--gridSize %s")
+    defaultSuffix = traits.Str( argstr = "--defaultSuffix %s")
+    implicitOutputs = traits.Either(traits.Bool, InputMultiPath(File(),), hash_files = False,argstr = "--implicitOutputs %s...")
+    debuglevel = traits.Int( argstr = "--debuglevel %d")
+    writeLess = traits.Bool( argstr = "--writeLess ")
+    numberOfThreads = traits.Int( argstr = "--numberOfThreads %d")
+
+
+class BRAINSABCOutputSpec(TraitedSpec):
+    outputDir = Directory( exists = True)
+    atlasToSubjectTransform = File( exists = True)
+    atlasToSubjectInitialTransform = File( exists = True)
+    outputVolumes = OutputMultiPath(File(exists=True), exists = True)
+    outputLabels = File( exists = True)
+    outputDirtyLabels = File( exists = True)
+    implicitOutputs = OutputMultiPath(File(exists=True), exists = True)
+
+
+class BRAINSABC(CommandLine):
+
+    input_spec = BRAINSABCInputSpec
+    output_spec = BRAINSABCOutputSpec
+    _cmd = " BRAINSABC "
+    _outputs_filenames = {'outputLabels':'outputLabels.nii.gz','atlasToSubjectTransform':'atlasToSubjectTransform.mat','atlasToSubjectInitialTransform':'atlasToSubjectInitialTransform.mat','outputDirtyLabels':'outputDirtyLabels.nii.gz','outputVolumes':'outputVolumes.nii.gz','outputDir':'outputDir','implicitOutputs':'implicitOutputs.nii.gz'}
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        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(BRAINSABC, self)._format_arg(name, spec, value)
+

AutoWorkup/BRAINSTools/BRAINSAlignMSP.py

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+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+class BRAINSAlignMSPInputSpec(CommandLineInputSpec):
+    inputVolume = File( exists = True,argstr = "--inputVolume %s")
+    resampleMSP = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--OutputresampleMSP %s")
+    verbose = traits.Bool( argstr = "--verbose ")
+    resultsDir = traits.Either(traits.Bool, Directory(), hash_files = False,argstr = "--resultsDir %s")
+    writedebuggingImagesLevel = traits.Int( argstr = "--writedebuggingImagesLevel %d")
+    mspQualityLevel = traits.Int( argstr = "--mspQualityLevel %d")
+    rescaleIntensities = traits.Bool( argstr = "--rescaleIntensities ")
+    trimRescaledIntensities = traits.Float( argstr = "--trimRescaledIntensities %f")
+    rescaleIntensitiesOutputRange = InputMultiPath(traits.Int, sep = ",",argstr = "--rescaleIntensitiesOutputRange %s")
+    backgroundFillValueString = traits.Str( argstr = "--BackgroundFillValue %s")
+    interpolationMode = traits.Enum("NearestNeighbor","Linear","ResampleInPlace","BSpline","WindowedSinc","Hamming","Cosine","Welch","Lanczos","Blackman", argstr = "--interpolationMode %s")
+    numberOfThreads = traits.Int( argstr = "--numberOfThreads %d")
+
+
+class BRAINSAlignMSPOutputSpec(TraitedSpec):
+    resampleMSP = File( exists = True)
+    resultsDir = Directory( exists = True)
+
+
+class BRAINSAlignMSP(CommandLine):
+
+    input_spec = BRAINSAlignMSPInputSpec
+    output_spec = BRAINSAlignMSPOutputSpec
+    _cmd = " BRAINSAlignMSP "
+    _outputs_filenames = {'resampleMSP':'resampleMSP.nii','resultsDir':'resultsDir'}
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        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(BRAINSAlignMSP, self)._format_arg(name, spec, value)
+

AutoWorkup/BRAINSTools/BRAINSClipInferior.py

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+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+class BRAINSClipInferiorInputSpec(CommandLineInputSpec):
+    inputVolume = File( exists = True,argstr = "--inputVolume %s")
+    outputVolume = traits.Either(traits.Bool, File(), hash_files = False,argstr = "--outputVolume %s")
+    acLowerBound = traits.Float( argstr = "--acLowerBound %f")
+    backgroundFillValueString = traits.Str( argstr = "--BackgroundFillValue %s")
+    numberOfThreads = traits.Int( argstr = "--numberOfThreads %d")
+
+
+class BRAINSClipInferiorOutputSpec(TraitedSpec):
+    outputVolume = File( exists = True)
+
+
+class BRAINSClipInferior(CommandLine):
+
+    input_spec = BRAINSClipInferiorInputSpec
+    output_spec = BRAINSClipInferiorOutputSpec
+    _cmd = " BRAINSClipInferior "
+    _outputs_filenames = {'outputVolume':'outputVolume.nii'}
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        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(BRAINSClipInferior, self)._format_arg(name, spec, value)
+