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ENH: Add SnapShotWriter to nipype
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@hjmjohnson
hjmjohnson committed Nov 14, 2012
1 parent dea4dc6 commit 54995e8
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Showing 2 changed files with 41 additions and 744 deletions.
66 changes: 41 additions & 25 deletions AutoWorkup/WorkupT1T2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def MergeByExtendListElements(t1_averageList,t2_averageList,pd_averageList,fl_av
'T2':DefaultContinuousInterpolationType,
'PD':DefaultContinuousInterpolationType,
'FL':DefaultContinuousInterpolationType,
'BRAINMASK':'NearestNeighbor'
'BRAINMASK':'MultiLabel'
}
## NOTE: ALl input lists MUST have the same number of elements (even if they are null)
for list_index in range(0,len(t1_averageList)):
Expand Down Expand Up @@ -655,6 +655,10 @@ def WorkupT1T2(subjectid,mountPrefix,ExperimentBaseDirectoryCache, ExperimentBas
FSPREP_DataSink=dict()
FS_DS=dict()

MergeStage2AverageImages=dict()
MergeStage2BinaryVolumes=dict()
SnapShotWriter=dict()

if 'SEGMENTATION' in WORKFLOW_COMPONENTS: ## Run the ANTS Registration from Atlas to Subject for BCut spatial priors propagation.
import PipeLineFunctionHelpers

Expand Down Expand Up @@ -717,7 +721,7 @@ def WorkupT1T2(subjectid,mountPrefix,ExperimentBaseDirectoryCache, ExperimentBas
if ( len(global_AllT2s) > 0 ): # Currently only works with multi-modal_data
print("HACK len(global_AllT2s) > 0 : {0}".format(len(global_AllT2s) ))
print("HACK")
if ( 'SEGMENTATION' in WORKFLOW_COMPONENTS ) and ( len(global_AllT2s) > 0 ): # Currently only works with multi-modal_data
if ( False ) and ( 'SEGMENTATION' in WORKFLOW_COMPONENTS ) and ( len(global_AllT2s) > 0 ): # Currently only works with multi-modal_data
from WorkupT1T2BRAINSCut import CreateBRAINSCutWorkflow
myLocalSegWF[sessionid] = CreateBRAINSCutWorkflow(projectid, subjectid, sessionid,'Segmentation',
CLUSTER_QUEUE,BAtlas[subjectid]) ##Note: Passing in the entire BAtlas Object here!
Expand Down Expand Up @@ -754,34 +758,46 @@ def WorkupT1T2(subjectid,mountPrefix,ExperimentBaseDirectoryCache, ExperimentBas
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")
MergeStage2BinaryVolumesName="99_MergeStage2BinaryVolumes_"+str(sessionid)
MergeStage2BinaryVolumes[sessionid] = pe.Node(interface=Merge(12),
run_without_submitting=True,
name=MergeStage2BinaryVolumesName)
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftAccumben', MergeStage2BinaryVolumes[sessionid], 'in1')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftCaudate', MergeStage2BinaryVolumes[sessionid], 'in2')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftPutamen', MergeStage2BinaryVolumes[sessionid], 'in3')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftGlobus', MergeStage2BinaryVolumes[sessionid], 'in4')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftThalamus', MergeStage2BinaryVolumes[sessionid], 'in5')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryLeftHippocampus', MergeStage2BinaryVolumes[sessionid], 'in6')

baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightAccumben', MergeStage2BinaryVolumes[sessionid], 'in7')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightCaudate', MergeStage2BinaryVolumes[sessionid], 'in8')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightPutamen', MergeStage2BinaryVolumes[sessionid], 'in9')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightGlobus', MergeStage2BinaryVolumes[sessionid], 'in10')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightThalamus', MergeStage2BinaryVolumes[sessionid], 'in11')
baw200.connect(SEGMENTATION_DataSink[sessionid], 'Segmentations.@outputBinaryRightHippocampus', MergeStage2BinaryVolumes[sessionid], 'in12')

MergeStage2AverageImagesName="99_mergeAvergeStage2Images_"+str(sessionid)
MergeStage2AverageImages[sessionid] = pe.Node(interface=Merge(2),
run_without_submitting=True,
name=MergeStage2AverageImagesName)
baw200.connect( PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t1_average', MergeStage2AverageImages[sessionid], 'in1')
baw200.connect( PHASE_2_oneSubjWorkflow[sessionid], 'outputspec.t2_average', MergeStage2AverageImages[sessionid], 'in2')


## SnapShotWriter[sessionid] for Segmented result checking:
SnapShotWriterNodeName="99_SnapShotWriter_"+str(sessionid)
SnapShotWriter[sessionid]=pe.Node( interface=BRAINSSnapShotWriter(), name=SnapShotWriterNodeName)

## output specification
SnapShotWriter.inputs.outputFilename = 'snapShot.png'
SnapShotWriter[sessionid].inputs.outputFilename = 'snapShot'+str(sessionid)+'.png'

## neccessary parameters (FIXED)
SnapShotWriter.inputs.inputPlaneDirection = "2,1,1,1,1,0,0"
SnapShotWriter.inputs.inputSliceToExtractInPhysicalPoint = "-3,-7,-3,5,7,22,-22"
SnapShotWriter[sessionid].inputs.inputPlaneDirection = [2,1,1,1,1,0,0]
SnapShotWriter[sessionid].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')

## connect SnapShotWriter[sessionid] to the baw200
baw200.connect( MergeStage2AverageImages[sessionid], 'out', SnapShotWriter[sessionid], 'inputVolumes')
baw200.connect( MergeStage2BinaryVolumes[sessionid], 'out', SnapShotWriter[sessionid], 'inputBinaryVolumes')

else:
print("SKIPPING SEGMENTATION PHASE FOR {0} {1} {2}, lenT2s {3}".format(projectid, subjectid, sessionid, len(global_AllT2s) ))
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