Slicer CPPYY example

guide.py

# Copyright Steve Pieper
# https://github.com/Slicer/Slicer/blob/master/License.txt
# Demo video: https://youtu.be/xcQKj4yp2nw

"""

exec(open('/Users/pieper/slicer/latest/SlicerTMSGuide/guide.py', 'r').read())

"""

import cppyy
import numpy
import os
import time

def arrayFromModelPointDataModified(modelNode, arrayName):
  """Indicate that modification of a numpy array returned by :py:meth:`arrayFromModelPoints` has been completed."""
  arrayVtk = modelNode.GetPolyData().GetPointData().GetArray(arrayName)
  arrayVtk.Modified()

slicer.util.arrayFromModelPointDataModified =  arrayFromModelPointDataModified

slicer.mrmlScene.Clear(0)

path = '/Users/pieper/slicer/latest/SlicerTMSGuide'
pialPath = os.path.join(path, 'data/lh.pial')
thicknessPath = os.path.join(path, 'data/lh.thickness')

pial = slicer.util.loadModel(pialPath)
slicer.util.loadScalarOverlay(thicknessPath, pial.GetID())

pial.GetDisplayNode().SetScalarRangeFlag(0)
pial.GetDisplayNode().SetScalarRange(0,50)
pial.GetDisplayNode().SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileCividis.txt')

ras = [-65, 10, 26]
markupsLogic = slicer.vtkSlicerMarkupsLogic()
markupsLogic.SetMRMLScene(slicer.mrmlScene)
markupsLogic.AddFiducial(*ras)
markupsLogic.JumpSlicesToLocation(*ras, False)
markupFiducials = slicer.util.getNode('F')
markupFiducials.GetDisplayNode().SetTextScale(0)
markupFiducials.GetDisplayNode().SetGlyphScale(10)
markupFiducials.GetDisplayNode().SetSelectedColor([1,1,0])
markupFiducials.GetDisplayNode().SetSnapMode(slicer.vtkMRMLMarkupsDisplayNode.SnapModeUnconstrained)

def updateOverlay(caller, event):
    pointsArray = slicer.util.arrayFromModelPoints(pial)
    scalarArray = slicer.util.arrayFromModelPointData(pial, 'lh.thickness')
    pointArray = slicer.util.arrayFromMarkupsControlPoints(markupFiducials)
    func1d = lambda p: numpy.linalg.norm(pointArray - p)
    scalarArray[:] = numpy.apply_along_axis(func1d, 1, pointsArray)
    slicer.util.arrayFromModelPointDataModified(pial, 'lh.thickness')

def compileAndImportCPP(cppSource):
    namespaceTag = "cppyy_"+str(time.time()).replace(".", "_")
    cppSource = "namespace " + namespaceTag + " {" + cppSource + " }"
    cppyy.cppdef(cppSource)
    exec("from cppyy.gbl import " + namespaceTag)
    namespace = eval("cppyy.gbl." + namespaceTag)
    return namespace

cppyy.include("math.h")
fillWithDistancesSource = """
    void fillWithDistances(void *pointsArrayData, void *pointData, void *scalarArrayData, unsigned int size) {
        float *pointsArray = (float *)pointsArrayData;
        double *point = (double *)pointData;
        float *scalarArray = (float *)scalarArrayData;
        unsigned int offset;
        for (offset = 0; offset < size; offset++) {
            scalarArray[offset] = sqrt ( 
              (pointsArray[offset*3 + 0] - point[0]) * (pointsArray[offset*3 + 0] - point[0]) +
              (pointsArray[offset*3 + 1] - point[1]) * (pointsArray[offset*3 + 1] - point[1]) +
              (pointsArray[offset*3 + 2] - point[2]) * (pointsArray[offset*3 + 2] - point[2]) );
        }
    }
"""
fillWithDistances = compileAndImportCPP(fillWithDistancesSource).fillWithDistances

def updateOverlayCpp(caller, event):
    pointsArray = slicer.util.arrayFromModelPoints(pial)
    scalarArray = slicer.util.arrayFromModelPointData(pial, 'lh.thickness')
    pointArray = slicer.util.arrayFromMarkupsControlPoints(markupFiducials)
    fillWithDistances(pointsArray.data, pointArray.data, scalarArray.data, scalarArray.size)
    slicer.util.arrayFromModelPointDataModified(pial, 'lh.thickness')

pointsArray = slicer.util.arrayFromModelPoints(pial)
scalarArray = slicer.util.arrayFromModelPointData(pial, 'lh.thickness')
pointArray = slicer.util.arrayFromMarkupsControlPoints(markupFiducials)
updateOverlayCpp(markupFiducials, slicer.vtkMRMLMarkupsNode.PointModifiedEvent)

ras = [50, 0, -70]
labelFiducial = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode")
markupsLogic.SetActiveListID(labelFiducial)
markupsLogic.AddFiducial(*ras)
markupsLogic.JumpSlicesToLocation(*ras, False)
labelFiducial.GetDisplayNode().SetTextScale(10)
labelFiducial.GetDisplayNode().SetGlyphScale(0)
labelFiducial.GetDisplayNode().SetSelectedColor([1,1,0])
labelFiducial.GetDisplayNode().SetSnapMode(slicer.vtkMRMLMarkupsDisplayNode.SnapModeUnconstrained)

#mode = "python"
mode = "cppyy"
if mode == "python":
    labelFiducial.SetNthControlPointLabel(0, "Python")
    markupFiducials.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, updateOverlay)
else:
    labelFiducial.SetNthControlPointLabel(0, "Python + CPPYY")
    markupFiducials.AddObserver(slicer.vtkMRMLMarkupsNode.PointModifiedEvent, updateOverlayCpp)

Installing on a mac build currently requires setting this variable so that the pip install succeeds in building the prereqs: SDKROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk ./Slicer-build/Slicer