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Slicer CPPYY example
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# 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
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Thanks!
Yes, good points - a caveat here is that cppyy is still experimental and only works on a developer build for now since the install step requires compilation. So this is not really ready to promote to the whole community, but it's close.
We are working an updated neuroimaging dataset but I don't have it released in sampledata yet. Of course this demo could work with any model.
Maybe the best thing is just to strip down the scalar array part to a small example and put it in the script repository for reference.