Merge pull request #1550 from BRAINSia/addToSemtools

Added to semtools

Author: chrisgorgo

nipype/interfaces/semtools/brains/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import
 from .segmentation import SimilarityIndex, BRAINSTalairach, BRAINSTalairachMask
-from .utilities import HistogramMatchingFilter
+from .utilities import HistogramMatchingFilter, GenerateEdgeMapImage, GeneratePurePlugMask
 from .classify import BRAINSPosteriorToContinuousClass

nipype/interfaces/semtools/brains/utilities.py

@@ -46,3 +46,69 @@ class HistogramMatchingFilter(SEMLikeCommandLine):
     _cmd = " HistogramMatchingFilter "
     _outputs_filenames = {'outputVolume': 'outputVolume.nii'}
     _redirect_x = False
+
+class GenerateEdgeMapImageInputSpec(CommandLineInputSpec):
+    inputMRVolumes = InputMultiPath(File(exists=True), desc="List of input structural MR volumes to create the maximum edgemap", argstr="--inputMRVolumes %s...")
+    inputMask = File(desc="Input mask file name. If set, image histogram percentiles will be calculated within the mask", exists=True, argstr="--inputMask %s")
+    minimumOutputRange = traits.Int(desc="Map lower quantile and below to minimum output range. It should be a small number greater than zero. Default is 1", argstr="--minimumOutputRange %d")
+    maximumOutputRange = traits.Int(desc="Map upper quantile and above to maximum output range. Default is 255 that is the maximum range of unsigned char", argstr="--maximumOutputRange %d")
+    lowerPercentileMatching = traits.Float(desc="Map lower quantile and below to minOutputRange. It should be a value between zero and one", argstr="--lowerPercentileMatching %f")
+    upperPercentileMatching = traits.Float(desc="Map upper quantile and above to maxOutputRange. It should be a value between zero and one", argstr="--upperPercentileMatching %f")
+    outputEdgeMap = traits.Either(traits.Bool, File(), hash_files=False, desc="output edgemap file name", argstr="--outputEdgeMap %s")
+    outputMaximumGradientImage = traits.Either(traits.Bool, File(), hash_files=False, desc="output gradient image file name", argstr="--outputMaximumGradientImage %s")
+    numberOfThreads = traits.Int(desc="Explicitly specify the maximum number of threads to use.", argstr="--numberOfThreads %d")
+
+
+class GenerateEdgeMapImageOutputSpec(TraitedSpec):
+    outputEdgeMap = File(desc="(required) output file name", exists=True)
+    outputMaximumGradientImage = File(desc="output gradient image file name", exists=True)
+
+class GenerateEdgeMapImage(SEMLikeCommandLine):
+
+    """title: GenerateEdgeMapImage
+
+category: BRAINS.Utilities
+
+description: Automatic edgemap generation for edge-guided super-resolution reconstruction
+
+version: 1.0
+
+contributor: Ali Ghayoor
+
+"""
+
+    input_spec = GenerateEdgeMapImageInputSpec
+    output_spec = GenerateEdgeMapImageOutputSpec
+    _cmd = " GenerateEdgeMapImage "
+    _outputs_filenames = {'outputEdgeMap': 'outputEdgeMap', 'outputMaximumGradientImage': 'outputMaximumGradientImage'}
+    _redirect_x = False
+
+class GeneratePurePlugMaskInputSpec(CommandLineInputSpec):
+    inputImageModalities = InputMultiPath(File(exists=True), desc="List of input image file names to create pure plugs mask", argstr="--inputImageModalities %s...")
+    threshold = traits.Float(desc="threshold value to define class membership", argstr="--threshold %f")
+    numberOfSubSamples = InputMultiPath(traits.Int, desc="Number of continous index samples taken at each direction of lattice space for each plug volume", sep=",", argstr="--numberOfSubSamples %s")
+    outputMaskFile = traits.Either(traits.Bool, File(), hash_files=False, desc="Output binary mask file name", argstr="--outputMaskFile %s")
+
+
+class GeneratePurePlugMaskOutputSpec(TraitedSpec):
+    outputMaskFile = File(desc="(required) Output binary mask file name", exists=True)
+
+class GeneratePurePlugMask(SEMLikeCommandLine):
+
+    """title: GeneratePurePlugMask
+
+category: BRAINS.Utilities
+
+description: This program gets several modality image files and returns a binary mask that defines the pure plugs
+
+version: 1.0
+
+contributor: Ali Ghayoor
+
+"""
+
+    input_spec = GeneratePurePlugMaskInputSpec
+    output_spec = GeneratePurePlugMaskOutputSpec
+    _cmd = " GeneratePurePlugMask "
+    _outputs_filenames = {'outputMaskFile': 'outputMaskFile'}
+    _redirect_x = False