ENH: Add SnapShotWriter Python Wrapper Outline

AutoWorkup/BRAINSTools/BRAINSSnapShotWriter.py

@@ -0,0 +1,41 @@
+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+from nipype.interfaces.slicer.base import SlicerCommandLine
+
+
+class BRAINSSnapShotWriterInputSpec(CommandLineInputSpec):
+    inputVolumes = File(desc="Images to be captured", exists=True, argstr="--inputVolumes %s")  ## check how to set multiple input
+    inputBinaryVolumes = File(desc="Binary images to be overlapped on top of inputVolumes", exists=False, argstr="--inputBinaryVolumes %s")  ## check how to set multiple input
+    inputPlaneDirection = InputMultiPath(traits.Int, desc="Plane to display. In general, 0=saggital, 1=coronal, and 2=axial plane. (default: 0,1,2)", argstr="inputPlaneDirection %s")
+    inputSliceToExtractInPercent = InputMultiPath(traits.Int, desc="2D slice number of input images. Percentage input from 0%-100%. (default: 50,50,50)", argstr="inputSliceToExtractInPercent %s")
+    inputSliceToExtractInIndex = InputMultiPath(traits.Int, desc="2D slice number of input images. For autoWorkUp output, which AC-PC aligned, 0,0,0 will be the center.", argstr="inputSliceToExtractInIndex %s")
+    inputSliceToExtractInPhysicalPoint = = InputMultiPath(traits.Float, desc="Input mask (binary) volume list to be extracted as 2D image. Multiple input is possible.", argstr="inputSliceToExtractInPhysicalPoint %s")
+
+class BRAINSSnapShotWriterOutputSpec(TraitedSpec):
+    outputFilename = File(desc="Resulting screen shots (*png)", exists=True)
+
+
+class BRAINSSnapShotWriter(SlicerCommandLine):
+    """title: Snap Shot Writer (BRAINS)
+
+category: Utilities 
+
+description:
+
+
+version: 1.0.0
+
+documentation-url: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSSnapShotWriter
+
+license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+
+contributor: This tool was developed by Eun Young (Regina) Kim
+
+acknowledgements: The development of this tool was supported by funding from grants NS050568 and NS40068 from the National Institute of Neurological Disorders and Stroke and grants MH31593, MH40856, from the National Institute of Mental Health.
+
+"""
+
+    input_spec = BRAINSSnapShotWriterInputSpec
+    output_spec = BRAINSSnapShotWriterOutputSpec
+    _cmd = " BRAINSSnapShotWriter "
+    _outputs_filenames = {'outputImage':'outputImage.png'}

AutoWorkup/WorkupT1T2.py

@@ -754,6 +754,36 @@ def WorkupT1T2(subjectid,mountPrefix,ExperimentBaseDirectoryCache, ExperimentBas
                     baw200.connect(myLocalSegWF[sessionid], 'outputspec.outputBinaryRightGlobus',SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightGlobus')
                     baw200.connect(myLocalSegWF[sessionid], 'outputspec.outputLabelImageName', SEGMENTATION_DataSink[sessionid],'Segmentations.@outputLabelImageName')
                     baw200.connect(myLocalSegWF[sessionid], 'outputspec.outputCSVFileName', SEGMENTATION_DataSink[sessionid],'Segmentations.@outputCSVFileName')
+
+                    ## SnapShotWriter for Segmented result checking:
+                    SnapShotWriter=pe.Node( interface=BRAINSSnapShotWriter(), name="SnapShotWriter")
+
+                    ## output specification
+                    SnapShotWriter.inputs.outputFilename = 'snapShot.png'
+
+                    ## neccessary parameters (FIXED)
+                    SnapShotWriter.inputs.inputPlaneDirection = "2,1,1,1,1,0,0"
+                    SnapShotWriter.inputs.inputSliceToExtractInPhysicalPoint = "-3,-7,-3,5,7,22,-22"
+
+                    ## connect SnapShotWriter to the baw200 
+                    baw200.connect( PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t1_average', SnapShotWriter, 'inputVolumes')
+                    baw200.connect( PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t2_average', SnapShotWriter, 'inputVolumes')
+
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftAccumben', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftCaudate', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftPutamen', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftGlobus', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftThalamus', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftHippocampus', SnapShotWriter, 'inputBinaryVolumes')
+
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightAccumben', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightCaudate', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightPutamen', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightGlobus', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightThalamus', SnapShotWriter, 'inputBinaryVolumes')
+                    baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightHippocampus', SnapShotWriter, 'inputBinaryVolumes')
+
+
                 else:
                     print("SKIPPING SEGMENTATION PHASE FOR {0} {1} {2}, lenT2s {3}".format(projectid, subjectid, sessionid, len(global_AllT2s) ))