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ENH: add bidimensional measurement support #269

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92 changes: 56 additions & 36 deletions DICOMPlugins/DICOMTID1500Plugin.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,9 @@ def __init__(self):
"trackingUniqueIdentifier": { "scheme": "DCM", "value": "112040" },
"findingSite": { "scheme": "SRT", "value": "G-C0E3" },
"length": { "scheme": "SRT", "value": "G-D7FE" },
"longAxis": { "scheme": "SRT", "value": "G-A185" },
"shortAxis": { "scheme": "SRT", "value": "G-A186" },
"cornerstoneFreeText": { "scheme": "CST4", "value": "CORNERSTONEFREETEXT" },
}


Expand Down Expand Up @@ -372,9 +375,16 @@ def enumerateDuplicateNames(self, items):
items[idx]["name"] = item
return items

def isConcept(self, item, coding):
def isConcept(self, item, codings):
""" accepts single coding string or list of codings """
codings = [codings] if isinstance(codings, str) else codings
code = item.ConceptNameCodeSequence[0]
return code.CodingSchemeDesignator == self.codings[coding]["scheme"] and code.CodeValue == self.codings[coding]["value"]
conceptMatch = False
for coding in codings:
schemeMatch = code.CodingSchemeDesignator == self.codings[coding]["scheme"]
valueMatch = code.CodeValue == self.codings[coding]["value"]
conceptMatch = conceptMatch or (schemeMatch and valueMatch)
return conceptMatch

def loadAdditionalMeasurements(self, srUID, loadable):
"""
Expand Down Expand Up @@ -405,52 +415,62 @@ def loadAdditionalMeasurements(self, srUID, loadable):
measurement['trackingUniqueIdentifier'] = measurementItem.UID
if self.isConcept(measurementItem, "findingSite"):
measurement['findingSite'] = measurementItem.ConceptCodeSequence[0].CodeMeaning
if self.isConcept(measurementItem, "length"):
if self.isConcept(measurementItem, "cornerstoneFreeText"):
measurement['caption'] = measurementItem.ConceptCodeSequence[0].CodeMeaning
if self.isConcept(measurementItem, ["length", "longAxis", "shortAxis"]):
for lengthItem in measurementItem.ContentSequence:
measurement['polyline'] = lengthItem.GraphicData
if 'polylines' not in measurement:
measurement['polylines'] = []
measurement['polylines'].append(lengthItem.GraphicData)
for selectionItem in lengthItem.ContentSequence:
if selectionItem.RelationshipType == "SELECTED 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')
logging.error('Error - only single frame references supported')
measurements.append(measurement)

for measurement in contents['measurements']:
if not 'polyline' in measurement:
if not 'polylines' in measurement:
# only polyline measurements are loaded as nodes
logging.debug('Measurement with no polyline is being skipped')
continue

markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsLineNode")
markupsNode.SetName(str(contents['personObserver']))
self.addSeriesInSubjectHierarchy(loadable, markupsNode)

# 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])

referenceFilePath = slicer.dicomDatabase.fileForInstance(measurement['referencedSOPInstanceUID'])
if not referenceFilePath:
raise Exception(f"Referenced image is not found in the database (referencedSOPInstanceUID={measurement['referencedSOPInstanceUID']}). Polyline point positions cannot be determined in 3D.")

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))
for polyline in measurement['polylines']:
markupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsLineNode")
if 'caption' in measurement:
name = measurement['caption']
else:
name = contents['personObserver']
markupsNode.SetName(str(name))
self.addSeriesInSubjectHierarchy(loadable, markupsNode)

# 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().SetAllControlPointsLocked(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])

referenceFilePath = slicer.dicomDatabase.fileForInstance(measurement['referencedSOPInstanceUID'])
if not referenceFilePath:
raise Exception(f"Referenced image is not found in the database (referencedSOPInstanceUID={measurement['referencedSOPInstanceUID']}). Polyline point positions cannot be determined in 3D.")

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 = 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))

class DICOMLongitudinalTID1500PluginClass(DICOMTID1500PluginClass):

Expand Down