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ENH: Add AI result SR support #260

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ENH: Add AI result SR support #260

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120 changes: 91 additions & 29 deletions DICOMPlugins/DICOMTID1500Plugin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ class DICOMTID1500PluginClass(DICOMPluginBase, ModuleLogicMixin):

UID_EnhancedSRStorage = "1.2.840.10008.5.1.4.1.1.88.22"
UID_ComprehensiveSRStorage = "1.2.840.10008.5.1.4.1.1.88.33"
UID_Comprehensive3DSRStorage = "1.2.840.10008.5.1.4.1.1.88.34"
UID_SegmentationStorage = "1.2.840.10008.5.1.4.1.1.66.4"
UID_RealWorldValueMappingStorage = "1.2.840.10008.5.1.4.1.1.67"

Expand All @@ -36,6 +37,8 @@ def __init__(self):
"trackingUniqueIdentifier": { "scheme": "DCM", "value": "112040" },
"findingSite": { "scheme": "SRT", "value": "G-C0E3" },
"length": { "scheme": "SRT", "value": "G-D7FE" },
"score": { "scheme": "SCT", "value": "246262008" },
"imageRegion": { "scheme": "DCM", "value": "111030" },
}


Expand Down Expand Up @@ -74,7 +77,8 @@ def isDICOMTID1500(self, dataset):
try:
isDicomTID1500 = self.getDICOMValue(dataset, "Modality") == 'SR' and \
(self.getDICOMValue(dataset, "SOPClassUID") == self.UID_EnhancedSRStorage or
self.getDICOMValue(dataset, "SOPClassUID") == self.UID_ComprehensiveSRStorage) and \
self.getDICOMValue(dataset, "SOPClassUID") == self.UID_ComprehensiveSRStorage or \
self.getDICOMValue(dataset, "SOPClassUID") == self.UID_Comprehensive3DSRStorage) and \
self.getDICOMValue(dataset, "ContentTemplateSequence")[0].TemplateIdentifier == '1500'
except (AttributeError, IndexError):
isDicomTID1500 = False
Expand Down Expand Up @@ -409,41 +413,99 @@ def loadAdditionalMeasurements(self, srUID, loadable):
for lengthItem in measurementItem.ContentSequence:
measurement['polyline'] = lengthItem.GraphicData
for selectionItem in lengthItem.ContentSequence:
if selectionItem.RelationshipType == "SELECTED FROM":
if selectionItem.RelationshipType in ("SELECTED FROM", "INFERRED FROM"):
for reference in selectionItem.ReferencedSOPSequence:
measurement['referencedSOPInstanceUID'] = reference.ReferencedSOPInstanceUID
if hasattr(reference, "ReferencedFrameNumber") and reference.ReferencedFrameNumber != "1":
print('Error - only single frame references supported')
if self.isConcept(measurementItem, "score"):
slicer.modules.measurementItem = measurementItem
for scoreItem in measurementItem.ContentSequence:
if scoreItem.RelationshipType in ("SELECTED FROM", "INFERRED FROM"):
for reference in scoreItem.ReferencedSOPSequence:
measurement['referencedSOPInstanceUID'] = reference.ReferencedSOPInstanceUID
if hasattr(reference, "ReferencedFrameNumber") and reference.ReferencedFrameNumber != "1":
print('Error - only single frame references supported')
if self.isConcept(measurementItem, "imageRegion"):
measurement['polygon'] = measurementItem.GraphicData
if hasattr(measurementItem, "MeasuredValueSequence"):
measurement['score'] = measurementItem.MeasuredValueSequence[0].FloatingPointValue
measurements.append(measurement)

appendPolyData = None
scores = []
for measurement in contents['measurements']:
markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsLineNode")
markupsNode.SetName(str(contents['personObserver']))
self.addSeriesInSubjectHierarchy(loadable, markupsNode)

referenceFilePath = slicer.dicomDatabase.fileForInstance(measurement['referencedSOPInstanceUID'])
reference = pydicom.read_file(referenceFilePath)
origin = numpy.array(reference.ImagePositionPatient)
alongColumnVector = numpy.array(reference.ImageOrientationPatient[:3])
alongRowVector = numpy.array(reference.ImageOrientationPatient[3:])
alongColumnVector *= reference.PixelSpacing[1]
alongRowVector *= reference.PixelSpacing[0]
col1,row1,col2,row2 = measurement['polyline']
lpsToRAS = numpy.array([-1,-1,1])
p1 = (origin + col1 * alongColumnVector + row1 * alongRowVector) * lpsToRAS
p2 = (origin + col2 * alongColumnVector + row2 * alongRowVector) * lpsToRAS
markupsNode.AddControlPoint(vtk.vtkVector3d(p1))
markupsNode.AddControlPoint(vtk.vtkVector3d(p2))

# Instead of calling markupsNode.SetLocked(True), lock each control point.
# This allows interacting with the points but not change their position.
slicer.modules.markups.logic().SetAllMarkupsLocked(markupsNode, True)

colorIndex = 1 + slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLMarkupsLineNode')
colorNode = slicer.mrmlScene.GetNodeByID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
color = numpy.zeros(4)
colorNode.GetColor(colorIndex, color)
markupsNode.GetDisplayNode().SetSelectedColor(*color[:3])
if not hasattr(contents, 'personObserver'):
contents['personObserver'] = "Unspecified Person Observer"
if hasattr(measurement, 'polyline'):
markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsLineNode")
markupsNode.SetName(str(contents['personObserver']))
self.addSeriesInSubjectHierarchy(loadable, markupsNode)

print(measurement)
referenceFilePath = slicer.dicomDatabase.fileForInstance(measurement['referencedSOPInstanceUID'])
reference = pydicom.read_file(referenceFilePath)
origin = numpy.array(reference.ImagePositionPatient)
alongColumnVector = numpy.array(reference.ImageOrientationPatient[:3])
alongRowVector = numpy.array(reference.ImageOrientationPatient[3:])
alongColumnVector *= reference.PixelSpacing[1]
alongRowVector *= reference.PixelSpacing[0]
col1,row1,col2,row2 = measurement['polyline']
lpsToRAS = numpy.array([-1,-1,1])
p1 = (origin + col1 * alongColumnVector + row1 * alongRowVector) * lpsToRAS
p2 = (origin + col2 * alongColumnVector + row2 * alongRowVector) * lpsToRAS
markupsNode.AddControlPoint(vtk.vtkVector3d(p1))
markupsNode.AddControlPoint(vtk.vtkVector3d(p2))

# Instead of calling markupsNode.SetLocked(True), lock each control point.
# This allows interacting with the points but not change their position.
slicer.modules.markups.logic().SetAllMarkupsLocked(markupsNode, True)

colorIndex = 1 + slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLMarkupsLineNode')
colorNode = slicer.mrmlScene.GetNodeByID("vtkMRMLColorTableNodeFileGenericAnatomyColors.txt")
color = numpy.zeros(4)
colorNode.GetColor(colorIndex, color)
markupsNode.GetDisplayNode().SetSelectedColor(*color[:3])

if 'polygon' in measurement:
if appendPolyData is None:
appendPolyData = vtk.vtkAppendPolyData()
points = numpy.array(measurement['polygon']).reshape(5,3)
polyLineSource = vtk.vtkPolyLineSource()
polyLineSource.SetNumberOfPoints(5)
for pointIndex in range(5):
point = points[pointIndex]
polyLineSource.SetPoint(pointIndex, -point[0], -point[1], point[2])
appendPolyData.AddInputConnection(polyLineSource.GetOutputPort())
if 'score' in measurement:
scores.append(measurement['score'])
else:
scores.append(0)

if appendPolyData is not None:
appendPolyData.Update()
srNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLModelNode())
srNode.SetName(str(contents['personObserver']))
srNode.SetAndObservePolyData(appendPolyData.GetOutputDataObject(0))
srNode.CreateDefaultDisplayNodes()

scoreArray = vtk.vtkFloatArray()
boxCount = appendPolyData.GetNumberOfInputConnections(0)
scoreArray.SetNumberOfTuples(5 * boxCount)
scoreArray.SetName("Score")
pointData = srNode.GetPolyData().GetPointData()
pointData.AddArray(scoreArray)
scoreNumpy = slicer.util.arrayFromModelPointData(srNode, "Score")
byBox = scoreNumpy.reshape(boxCount,5)
for boxIndex in range(boxCount):
byBox[boxIndex] = scores[boxIndex]
slicer.util.arrayFromModelPointDataModified(srNode, "Score")
displayNode = srNode.GetDisplayNode()
displayNode.SetOpacity(0.7)
displayNode.SetLineWidth(4)
displayNode.SetActiveScalarName("Score")
displayNode.SetScalarVisibility(True)

class DICOMLongitudinalTID1500PluginClass(DICOMTID1500PluginClass):

def __init__(self):
Expand Down