Merge pull request #1119 from nipy/AddSEMTools

ENH: A set of autogenerated interfaces

Author: satra

nipype/interfaces/semtools/__init__.py

@@ -0,0 +1,10 @@
+from diffusion import *
+from featurecreator import GenerateCsfClippedFromClassifiedImage
+from segmentation import *
+from filtering import *
+from brains import *
+from testing import *
+from utilities import *
+from legacy import *
+from registration import *
+from converters import DWISimpleCompare, DWICompare

nipype/interfaces/semtools/brains/__init__.py

@@ -0,0 +1,3 @@
+from segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask
+from utilities import HistogramMatchingFilter
+from classify import BRAINSPosteriorToContinuousClass

nipype/interfaces/semtools/brains/classify.py

@@ -0,0 +1,48 @@
+# -*- 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, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+
+class BRAINSPosteriorToContinuousClassInputSpec(CommandLineInputSpec):
+    inputWhiteVolume = File(desc="White Matter Posterior Volume", exists=True, argstr="--inputWhiteVolume %s")
+    inputBasalGmVolume = File(desc="Basal Grey Matter Posterior Volume", exists=True, argstr="--inputBasalGmVolume %s")
+    inputSurfaceGmVolume = File(desc="Surface Grey Matter Posterior Volume", exists=True, argstr="--inputSurfaceGmVolume %s")
+    inputCsfVolume = File(desc="CSF Posterior Volume", exists=True, argstr="--inputCsfVolume %s")
+    inputVbVolume = File(desc="Venous Blood Posterior Volume", exists=True, argstr="--inputVbVolume %s")
+    inputCrblGmVolume = File(desc="Cerebellum Grey Matter Posterior Volume", exists=True, argstr="--inputCrblGmVolume %s")
+    inputCrblWmVolume = File(desc="Cerebellum White Matter Posterior Volume", exists=True, argstr="--inputCrblWmVolume %s")
+    outputVolume = traits.Either(traits.Bool, File(), hash_files=False, desc="Output Continuous Tissue Classified Image", argstr="--outputVolume %s")
+
+
+class BRAINSPosteriorToContinuousClassOutputSpec(TraitedSpec):
+    outputVolume = File(desc="Output Continuous Tissue Classified Image", exists=True)
+
+
+class BRAINSPosteriorToContinuousClass(SEMLikeCommandLine):
+
+    """title: Tissue Classification
+
+category: BRAINS.Classify
+
+description: This program will generate an 8-bit continuous tissue classified image based on BRAINSABC posterior images.
+
+version: 3.0
+
+documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Vincent A. Magnotta
+
+acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568
+
+"""
+
+    input_spec = BRAINSPosteriorToContinuousClassInputSpec
+    output_spec = BRAINSPosteriorToContinuousClassOutputSpec
+    _cmd = " BRAINSPosteriorToContinuousClass "
+    _outputs_filenames = {'outputVolume': 'outputVolume'}
+    _redirect_x = False

nipype/interfaces/semtools/brains/segmentation.py

@@ -0,0 +1,126 @@
+# -*- 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, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+
+class SimilarityIndexInputSpec(CommandLineInputSpec):
+    outputCSVFilename = File(desc="output CSV Filename", exists=True, argstr="--outputCSVFilename %s")
+    ANNContinuousVolume = File(desc="ANN Continuous volume to be compared to the manual volume", exists=True, argstr="--ANNContinuousVolume %s")
+    inputManualVolume = File(desc="input manual(reference) volume", exists=True, argstr="--inputManualVolume %s")
+    thresholdInterval = traits.Float(desc="Threshold interval to compute similarity index between zero and one", argstr="--thresholdInterval %f")
+
+
+class SimilarityIndexOutputSpec(TraitedSpec):
+    pass
+
+
+class SimilarityIndex(SEMLikeCommandLine):
+
+    """title: BRAINSCut:SimilarityIndexComputation
+
+category: BRAINS.Segmentation
+
+description: Automatic analysis of BRAINSCut Output
+
+version: 1.0
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Eunyoung Regin Kim
+
+"""
+
+    input_spec = SimilarityIndexInputSpec
+    output_spec = SimilarityIndexOutputSpec
+    _cmd = " SimilarityIndex "
+    _outputs_filenames = {}
+    _redirect_x = False
+
+
+class BRAINSTalairachInputSpec(CommandLineInputSpec):
+    AC = InputMultiPath(traits.Float, desc="Location of AC Point ", sep=",", argstr="--AC %s")
+    ACisIndex = traits.Bool(desc="AC Point is Index", argstr="--ACisIndex ")
+    PC = InputMultiPath(traits.Float, desc="Location of PC Point ", sep=",", argstr="--PC %s")
+    PCisIndex = traits.Bool(desc="PC Point is Index", argstr="--PCisIndex ")
+    SLA = InputMultiPath(traits.Float, desc="Location of SLA Point ", sep=",", argstr="--SLA %s")
+    SLAisIndex = traits.Bool(desc="SLA Point is Index", argstr="--SLAisIndex ")
+    IRP = InputMultiPath(traits.Float, desc="Location of IRP Point ", sep=",", argstr="--IRP %s")
+    IRPisIndex = traits.Bool(desc="IRP Point is Index", argstr="--IRPisIndex ")
+    inputVolume = File(desc="Input image used to define physical space of images", exists=True, argstr="--inputVolume %s")
+    outputBox = traits.Either(traits.Bool, File(), hash_files=False, desc="Name of the resulting Talairach Bounding Box file", argstr="--outputBox %s")
+    outputGrid = traits.Either(traits.Bool, File(), hash_files=False, desc="Name of the resulting Talairach Grid file", argstr="--outputGrid %s")
+
+
+class BRAINSTalairachOutputSpec(TraitedSpec):
+    outputBox = File(desc="Name of the resulting Talairach Bounding Box file", exists=True)
+    outputGrid = File(desc="Name of the resulting Talairach Grid file", exists=True)
+
+
+class BRAINSTalairach(SEMLikeCommandLine):
+
+    """title: BRAINS Talairach
+
+category: BRAINS.Segmentation
+
+description: This program creates a VTK structured grid defining the Talairach coordinate system based on four points: AC, PC, IRP, and SLA. The resulting structred grid can be written as either a classic VTK file or the new VTK XML file format. Two representations of the resulting grid can be written. The first is a bounding box representation that also contains the location of the AC and PC points. The second representation is the full Talairach grid representation that includes the additional rows of boxes added to the inferior allowing full coverage of the cerebellum.
+
+version: 0.1
+
+documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairach
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Steven Dunn and Vincent Magnotta
+
+acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568
+
+"""
+
+    input_spec = BRAINSTalairachInputSpec
+    output_spec = BRAINSTalairachOutputSpec
+    _cmd = " BRAINSTalairach "
+    _outputs_filenames = {'outputGrid': 'outputGrid', 'outputBox': 'outputBox'}
+    _redirect_x = False
+
+
+class BRAINSTalairachMaskInputSpec(CommandLineInputSpec):
+    inputVolume = File(desc="Input image used to define physical space of resulting mask", exists=True, argstr="--inputVolume %s")
+    talairachParameters = File(desc="Name of the Talairach parameter file.", exists=True, argstr="--talairachParameters %s")
+    talairachBox = File(desc="Name of the Talairach box file.", exists=True, argstr="--talairachBox %s")
+    hemisphereMode = traits.Enum("left", "right", "both", desc="Mode for box creation: left, right, both", argstr="--hemisphereMode %s")
+    expand = traits.Bool(desc="Expand exterior box to include surface CSF", argstr="--expand ")
+    outputVolume = traits.Either(traits.Bool, File(), hash_files=False, desc="Output filename for the resulting binary image", argstr="--outputVolume %s")
+
+
+class BRAINSTalairachMaskOutputSpec(TraitedSpec):
+    outputVolume = File(desc="Output filename for the resulting binary image", exists=True)
+
+
+class BRAINSTalairachMask(SEMLikeCommandLine):
+
+    """title: Talairach Mask
+
+category: BRAINS.Segmentation
+
+description: This program creates a binary image representing the specified Talairach region. The input is an example image to define the physical space for the resulting image, the Talairach grid representation in VTK format, and the file containing the Talairach box definitions to be generated. These can be combined in BRAINS to create a label map using the procedure Brains::WorkupUtils::CreateLabelMapFromBinaryImages.
+
+version: 0.1
+
+documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairachMask
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Steven Dunn and Vincent Magnotta
+
+acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568
+
+"""
+
+    input_spec = BRAINSTalairachMaskInputSpec
+    output_spec = BRAINSTalairachMaskOutputSpec
+    _cmd = " BRAINSTalairachMask "
+    _outputs_filenames = {'outputVolume': 'outputVolume.nii'}
+    _redirect_x = False

nipype/interfaces/semtools/brains/utilities.py

@@ -0,0 +1,44 @@
+# -*- 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, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+
+class HistogramMatchingFilterInputSpec(CommandLineInputSpec):
+    inputVolume = File(desc="The Input image to be computed for statistics", exists=True, argstr="--inputVolume %s")
+    referenceVolume = File(desc="The Input image to be computed for statistics", exists=True, argstr="--referenceVolume %s")
+    outputVolume = traits.Either(traits.Bool, File(), hash_files=False, desc="Output Image File Name", argstr="--outputVolume %s")
+    referenceBinaryVolume = File(desc="referenceBinaryVolume", exists=True, argstr="--referenceBinaryVolume %s")
+    inputBinaryVolume = File(desc="inputBinaryVolume", exists=True, argstr="--inputBinaryVolume %s")
+    numberOfMatchPoints = traits.Int(desc=" number of histogram matching points", argstr="--numberOfMatchPoints %d")
+    numberOfHistogramBins = traits.Int(desc=" number of histogram bin", argstr="--numberOfHistogramBins %d")
+    writeHistogram = traits.Str(desc=" decide if histogram data would be written with prefixe of the file name", argstr="--writeHistogram %s")
+    histogramAlgorithm = traits.Enum("OtsuHistogramMatching", desc=" histogram algrithm selection", argstr="--histogramAlgorithm %s")
+    verbose = traits.Bool(desc=" verbose mode running for debbuging", argstr="--verbose ")
+
+
+class HistogramMatchingFilterOutputSpec(TraitedSpec):
+    outputVolume = File(desc="Output Image File Name", exists=True)
+
+
+class HistogramMatchingFilter(SEMLikeCommandLine):
+
+    """title: Write Out Image Intensities
+
+category: BRAINS.Utilities
+
+description: For Analysis
+
+version: 0.1
+
+contributor: University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu
+
+"""
+
+    input_spec = HistogramMatchingFilterInputSpec
+    output_spec = HistogramMatchingFilterOutputSpec
+    _cmd = " HistogramMatchingFilter "
+    _outputs_filenames = {'outputVolume': 'outputVolume.nii'}
+    _redirect_x = False

nipype/interfaces/semtools/converters.py

@@ -0,0 +1,79 @@
+# -*- 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, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+
+class DWISimpleCompareInputSpec(CommandLineInputSpec):
+    inputVolume1 = File(desc="First input volume (.nhdr or .nrrd)", exists=True, argstr="--inputVolume1 %s")
+    inputVolume2 = File(desc="Second input volume (.nhdr or .nrrd)", exists=True, argstr="--inputVolume2 %s")
+    checkDWIData = traits.Bool(desc="check for existence of DWI data, and if present, compare it", argstr="--checkDWIData ")
+
+
+class DWISimpleCompareOutputSpec(TraitedSpec):
+    pass
+
+
+class DWISimpleCompare(SEMLikeCommandLine):
+
+    """title: Nrrd DWI comparison
+
+category: Converters
+
+description: Compares two nrrd format DWI images and verifies that gradient magnitudes, gradient directions, measurement frame, and max B0 value are identicle.  Used for testing DWIConvert.
+
+version: 0.1.0.$Revision: 916 $(alpha)
+
+documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DWIConvert
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Mark Scully (UIowa)
+
+acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.  Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.
+
+"""
+
+    input_spec = DWISimpleCompareInputSpec
+    output_spec = DWISimpleCompareOutputSpec
+    _cmd = " DWISimpleCompare "
+    _outputs_filenames = {}
+    _redirect_x = False
+
+
+class DWICompareInputSpec(CommandLineInputSpec):
+    inputVolume1 = File(desc="First input volume (.nhdr or .nrrd)", exists=True, argstr="--inputVolume1 %s")
+    inputVolume2 = File(desc="Second input volume (.nhdr or .nrrd)", exists=True, argstr="--inputVolume2 %s")
+
+
+class DWICompareOutputSpec(TraitedSpec):
+    pass
+
+
+class DWICompare(SEMLikeCommandLine):
+
+    """title: Nrrd DWI comparison
+
+category: Converters
+
+description: Compares two nrrd format DWI images and verifies that gradient magnitudes, gradient directions, measurement frame, and max B0 value are identicle.  Used for testing DWIConvert.
+
+version: 0.1.0.$Revision: 916 $(alpha)
+
+documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DWIConvert
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: Mark Scully (UIowa)
+
+acknowledgements: This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.  Additional support for DTI data produced on Philips scanners was contributed by Vincent Magnotta and Hans Johnson at the University of Iowa.
+
+"""
+
+    input_spec = DWICompareInputSpec
+    output_spec = DWICompareOutputSpec
+    _cmd = " DWICompare "
+    _outputs_filenames = {}
+    _redirect_x = False

nipype/interfaces/semtools/diffusion/__init__.py

@@ -0,0 +1,4 @@
+from diffusion import dtiaverage, dtiestim, dtiprocess, DWIConvert
+from tractography import *
+from gtract import gtractTransformToDisplacementField, gtractInvertBSplineTransform, gtractConcatDwi, gtractAverageBvalues, gtractCoregBvalues, gtractResampleAnisotropy, gtractResampleCodeImage, gtractCopyImageOrientation, gtractCreateGuideFiber, gtractAnisotropyMap, gtractClipAnisotropy, gtractResampleB0, gtractInvertRigidTransform, gtractImageConformity, compareTractInclusion, gtractFastMarchingTracking, gtractInvertDisplacementField, gtractCoRegAnatomy, gtractResampleDWIInPlace, gtractCostFastMarching, gtractFiberTracking, extractNrrdVectorIndex, gtractResampleFibers, gtractTensor
+from maxcurvature import maxcurvature