def RunVectorFieldAnalysis(self, inputWLIO):
import os, sys, vtk
loadablePath = os.path.join(
slicer.modules.plastimatch_slicer_bspline.path, ".." + os.sep + ".." + os.sep + "qt-loadable-modules"
)
if loadablePath not in sys.path:
sys.path.append(loadablePath)
import vtkSlicerPlastimatchPyModuleLogicPython
reg = vtkSlicerPlastimatchPyModuleLogicPython.vtkSlicerPlastimatchPyModuleLogic()
reg.SetMRMLScene(slicer.mrmlScene)
print "running RunVectorFieldAnalysis"
# Set input/output images
reg.SetOutputVolumeID(inputWLIO.outputJacobianNode.GetID())
reg.SetFixedImageID(inputWLIO.fixedImageNode.GetID())
reg.SetVFImageID(inputWLIO.vfImageNode.GetID())
print inputWLIO.vfImageNode.GetID()
print inputWLIO.outputJacobianNode.GetID()
print inputWLIO.fixedImageNode.GetID()
# Run Vector Field statistics
print "starting RunJacobian"
reg.RunJacobian()
print "control went past RunJacobian"
# return min/max values to caller
outputWLIO = PlmVectorFieldAnalysisWidgetLogicIO()
outputWLIO.SetMinJacobian(reg.GetJacobianMinString())
outputWLIO.SetMaxJacobian(reg.GetJacobianMaxString())
# Done
# outputVolume.SetAndObserveImageData(jacobian.GetOutput())
# make the output volume appear in all the slice views
# selectionNode = slicer.app.applicationLogic().GetSelectionNode()
# selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
# slicer.app.applicationLogic().PropagateVolumeSelection(0)
# return True
return outputWLIO
def RunVectorFieldAnalysis(self, inputWLIO):
import os, sys, vtk
loadablePath = os.path.join(
slicer.modules.plastimatch_slicer_bspline.path,
'..' + os.sep + '..' + os.sep + 'qt-loadable-modules')
if loadablePath not in sys.path:
sys.path.append(loadablePath)
import vtkSlicerPlastimatchPyModuleLogicPython
reg = vtkSlicerPlastimatchPyModuleLogicPython.vtkSlicerPlastimatchPyModuleLogic(
)
reg.SetMRMLScene(slicer.mrmlScene)
print "running RunVectorFieldAnalysis"
#Set input/output images
reg.SetOutputVolumeID(inputWLIO.outputJacobianNode.GetID())
reg.SetFixedImageID(inputWLIO.fixedImageNode.GetID())
reg.SetVFImageID(inputWLIO.vfImageNode.GetID())
print inputWLIO.vfImageNode.GetID()
print inputWLIO.outputJacobianNode.GetID()
print inputWLIO.fixedImageNode.GetID()
# Run Vector Field statistics
print "starting RunJacobian"
reg.RunJacobian()
print "control went past RunJacobian"
# return min/max values to caller
outputWLIO = PlmVectorFieldAnalysisWidgetLogicIO()
outputWLIO.SetMinJacobian(reg.GetJacobianMinString())
outputWLIO.SetMaxJacobian(reg.GetJacobianMaxString())
# Done
#outputVolume.SetAndObserveImageData(jacobian.GetOutput())
# make the output volume appear in all the slice views
#selectionNode = slicer.app.applicationLogic().GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
#slicer.app.applicationLogic().PropagateVolumeSelection(0)
#return True
return outputWLIO
def RunMismatchError(self, WLIO):
import os, sys, vtk, math
loadablePath = os.path.join(
slicer.modules.plastimatch_slicer_bspline.path,
'..' + os.sep + '..' + os.sep + 'qt-loadable-modules')
if loadablePath not in sys.path:
sys.path.append(loadablePath)
import vtkSlicerPlastimatchPyModuleLogicPython
reg = vtkSlicerPlastimatchPyModuleLogicPython.vtkSlicerPlastimatchPyModuleLogic(
)
reg.SetMRMLScene(slicer.mrmlScene)
print "running RunMismatchError"
# Set landmarks from Slicer
print "trying to SetFixed/MovingLandmarks"
fixpoints = vtk.vtkPoints()
movpoints = vtk.vtkPoints()
point = [
0,
] * 3
fixFidNode = WLIO.FixedFiducialsNode # it is a vtkMRMLMarkupsFiducialNode
nfix = fixFidNode.GetNumberOfFiducials()
print("found %s fiducials in fixed" % str(nfix))
for n in range(nfix):
fixFidNode.GetNthFiducialPosition(n, point)
fixpoints.InsertNextPoint(point)
#print("fix %s:" % str(point))
movFidNode = WLIO.MovingFiducialsNode # it is a vtkMRMLMarkupsFiducialNode
nmov = movFidNode.GetNumberOfFiducials()
print("found %s fiducials in moving" % str(nmov))
for n in range(nmov):
movFidNode.GetNthFiducialPosition(n, point)
movpoints.InsertNextPoint(point)
#print("mov %s:" % str(point))
WidgetLogicIO = PlmMismatchErrorWidgetLogicIO(
) # this is for output to GUI widget
p1 = [
0,
] * 3
p2 = [
0,
] * 3
counter = 0
d1sum = 0
d2sum = 0
d3sum = 0
for n in range(nfix):
fixpoints.GetPoint(n, p1)
movpoints.GetPoint(n, p2)
d2 = (p1[0] - p2[0]) * (p1[0] - p2[0]) + (p1[1] - p2[1]) * (
p1[1] - p2[1]) + (p1[2] - p2[2]) * (p1[2] - p2[2])
d1 = math.sqrt(d2)
d1sum += d1
d2sum += d2
counter += 1
WidgetLogicIO.landm_distance.append(d1)
#print (n, d1, d2, d1sum, d2sum)
average = d1sum / counter
for n in range(nfix):
fixpoints.GetPoint(n, p1)
movpoints.GetPoint(n, p2)
d2 = (p1[0] - p2[0]) * (p1[0] - p2[0]) + (p1[1] - p2[1]) * (
p1[1] - p2[1]) + (p1[2] - p2[2]) * (p1[2] - p2[2])
d1 = math.sqrt(d2)
d3 = (d1 - average) * (d1 - average)
d3sum += d3
counter += 1
variance = d3sum / counter
stdev = math.sqrt(variance)
#reg.SetFixedLandmarks( fixpoints)
#reg.SetMovingLandmarks(movpoints)
#print "Done SetFixed/MovingLandmarks"
# Run Mismatch Error
#print "starting RunMismatchError"
#reg.RunMismatchError()
#print "control went past RunMismatchError"
# Done
# return error values to caller
WidgetLogicIO.SetAverage(average)
WidgetLogicIO.SetVariance(variance)
WidgetLogicIO.SetStdev(stdev)
#WidgetLogicIO.SetSeparation(reg.GetSeparationString())
return WidgetLogicIO
def RunMismatchError(self, WLIO):
import os, sys, vtk, math
loadablePath = os.path.join(slicer.modules.plastimatch_slicer_bspline.path,'..'+os.sep+'..'+os.sep+'qt-loadable-modules')
if loadablePath not in sys.path:
sys.path.append(loadablePath)
import vtkSlicerPlastimatchPyModuleLogicPython
reg = vtkSlicerPlastimatchPyModuleLogicPython.vtkSlicerPlastimatchPyModuleLogic()
reg.SetMRMLScene(slicer.mrmlScene)
print "running RunMismatchError"
# Set landmarks from Slicer
print "trying to SetFixed/MovingLandmarks"
fixpoints = vtk.vtkPoints()
movpoints = vtk.vtkPoints()
point = [0,]*3
fixFidNode = WLIO.FixedFiducialsNode # it is a vtkMRMLMarkupsFiducialNode
nfix = fixFidNode.GetNumberOfFiducials()
print( "found %s fiducials in fixed" % str(nfix) )
for n in range(nfix):
fixFidNode.GetNthFiducialPosition(n, point)
fixpoints.InsertNextPoint(point)
#print("fix %s:" % str(point))
movFidNode = WLIO.MovingFiducialsNode # it is a vtkMRMLMarkupsFiducialNode
nmov = movFidNode.GetNumberOfFiducials()
print( "found %s fiducials in moving" % str(nmov) )
for n in range(nmov):
movFidNode.GetNthFiducialPosition(n, point)
movpoints.InsertNextPoint(point)
#print("mov %s:" % str(point))
WidgetLogicIO = PlmMismatchErrorWidgetLogicIO() # this is for output to GUI widget
p1 = [0,]*3
p2 = [0,]*3
counter = 0
d1sum = 0
d2sum = 0
d3sum = 0
for n in range(nfix):
fixpoints.GetPoint(n, p1)
movpoints.GetPoint(n, p2)
d2 = (p1[0]-p2[0])*(p1[0]-p2[0]) + (p1[1]-p2[1])*(p1[1]-p2[1]) + (p1[2]-p2[2])*(p1[2]-p2[2])
d1 = math.sqrt(d2)
d1sum += d1
d2sum += d2
counter += 1
WidgetLogicIO.landm_distance.append(d1)
#print (n, d1, d2, d1sum, d2sum)
average = d1sum/counter
for n in range(nfix):
fixpoints.GetPoint(n, p1)
movpoints.GetPoint(n, p2)
d2 = (p1[0]-p2[0])*(p1[0]-p2[0]) + (p1[1]-p2[1])*(p1[1]-p2[1]) + (p1[2]-p2[2])*(p1[2]-p2[2])
d1 = math.sqrt(d2)
d3 = (d1 - average)*(d1 - average)
d3sum += d3
counter += 1
variance = d3sum/counter
stdev = math.sqrt(variance)
#reg.SetFixedLandmarks( fixpoints)
#reg.SetMovingLandmarks(movpoints)
#print "Done SetFixed/MovingLandmarks"
# Run Mismatch Error
#print "starting RunMismatchError"
#reg.RunMismatchError()
#print "control went past RunMismatchError"
# Done
# return error values to caller
WidgetLogicIO.SetAverage(average)
WidgetLogicIO.SetVariance(variance)
WidgetLogicIO.SetStdev(stdev)
#WidgetLogicIO.SetSeparation(reg.GetSeparationString())
return WidgetLogicIO
