MAINT #42: get tumor center coordinates using transform matrix instea…

…d of markups node

LumpNav2/LumpNav2.py

@@ -2430,6 +2430,10 @@ def setRASMarkups(self, observer, eventid):
       centerOfMassFilter.SetUseScalarsAsWeights(False)
       centerOfMassFilter.Update()
       center = centerOfMassFilter.GetCenter()
+      needleToReference = parameterNode.GetNodeReference(self.NEEDLE_TO_REFERENCE)
+      needleToRASMatrix = vtk.vtkMatrix4x4()
+      needleToReference.GetMatrixTransformToWorld(needleToRASMatrix)
+      centerWorld = needleToRASMatrix.MultiplyFloatPoint(np.append(center, 1))
 
       # Calculate how far from center to put markups
       bounds = [0, 0, 0, 0, 0, 0]
@@ -2440,9 +2444,6 @@ def setRASMarkups(self, observer, eventid):
       # Update RAS markup points
       RASMarkups = parameterNode.GetNodeReference(self.RAS_MARKUPS)
       RASMarkups.RemoveAllMarkups()
-      RASMarkups.AddControlPoint(center, "")
-      centerWorld = RASMarkups.GetNthControlPointPositionWorld(0)
-      RASMarkups.RemoveAllMarkups()
       RASMarkups.AddControlPointWorld(centerWorld[0] + distanceFromCenter, centerWorld[1], centerWorld[2], "R")
       RASMarkups.AddControlPointWorld(centerWorld[0], centerWorld[1] + distanceFromCenter, centerWorld[2], "A")
       RASMarkups.AddControlPointWorld(centerWorld[0], centerWorld[1], centerWorld[2] + distanceFromCenter, "S")