def addAppliedToolToSegment(self, segment, toolName, toolType=None):
self.updatingSegmentTags = True
# append list of applied tools
tools = vtk.mutable('')
tools = str(tools).split(';') if segment.GetTag(
'QuantitativeReporting.AppliedTools', tools) else []
if not toolName in tools:
tools.append(toolName)
segment.SetTag('QuantitativeReporting.AppliedTools',
";".join(tools))
segmentWasImported = tools[0] != 'Add'
# determine algorithm type (if not specified by user)
if not toolType:
if toolName in self.manualTools:
toolType = 'MANUAL'
elif toolName in self.automaticTools:
toolType = 'AUTOMATIC'
else: # default tool type
toolType = 'SEMIAUTOMATIC'
# update DICOM algorithm type
oldAlgorithmType = vtk.mutable('')
segment.GetTag('DICOM.SegmentAlgorithmType', oldAlgorithmType)
updatedAlgorithmType = oldAlgorithmType
if oldAlgorithmType == '': # no other editor effect was applied before
if segmentWasImported:
updatedAlgorithmType = 'SEMIAUTOMATIC'
else:
updatedAlgorithmType = toolType
elif oldAlgorithmType == 'MANUAL' and toolType != 'MANUAL':
updatedAlgorithmType = 'SEMIAUTOMATIC'
elif oldAlgorithmType == 'AUTOMATIC':
updatedAlgorithmType = 'SEMIAUTOMATIC'
if oldAlgorithmType != updatedAlgorithmType:
segment.SetTag('DICOM.SegmentAlgorithmType', updatedAlgorithmType)
# update DICOM algorithm name
GenericSlicerAlgorithmName = slicer.app.applicationName + ' ' + slicer.app.applicationVersion
GenericSegmentEditorAlgorithmName = GenericSlicerAlgorithmName + ' Segment Editor'
ToolSegmentEditorAlgorithmName = GenericSlicerAlgorithmName + ' ' + toolName + ' Effect'
oldAlgorithmName = vtk.mutable('')
segment.GetTag('DICOM.SegmentAlgorithmName', oldAlgorithmName)
updatedAlgorithmName = oldAlgorithmName
if oldAlgorithmName == '': # no other editor tool was applied before
if segmentWasImported:
updatedAlgorithmName = GenericSlicerAlgorithmName
else:
updatedAlgorithmName = ToolSegmentEditorAlgorithmName
elif oldAlgorithmName != ToolSegmentEditorAlgorithmName:
if oldAlgorithmName.startswith(GenericSegmentEditorAlgorithmName):
updatedAlgorithmName = GenericSegmentEditorAlgorithmName
else:
updatedAlgorithmName = GenericSlicerAlgorithmName
if oldAlgorithmName != updatedAlgorithmName:
segment.SetTag('DICOM.SegmentAlgorithmName', updatedAlgorithmName)
self.updatingSegmentTags = False
def main():
# Create a square in the x-y plane.
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 1.0, 0.0)
points.InsertNextPoint(0.0, 1.0, 0.0)
# Create the polygon
polygon = vtk.vtkPolygon()
polygon.GetPoints().DeepCopy(points)
polygon.GetPointIds().SetNumberOfIds(4) # The 4 corners of the square
for i in range(4):
polygon.GetPointIds().SetId(i, i)
# Inputs
p1 = [0.1, 0, -1.0]
p2 = [0.1, 0, 1.0]
tolerance = 0.001
# Outputs
t = vtk.mutable(
0
) # Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
iD = polygon.IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId)
print('intersected? ', 'Yes' if iD == 1 else 'No')
print('intersection: ', x)
def get_external_surface(_mesh, external=True):
_center = np.zeros(3)
_bounds = np.zeros(6)
_ray_start = np.zeros(3)
cell_id = vtk.mutable(-1)
xyz = np.zeros(3)
pcoords = np.zeros(3)
t = vtk.mutable(0)
sub_id = vtk.mutable(0)
if external:
surf = 1.1
else:
surf = -1.1
_mesh.GetOutput().GetCenter(_center)
_mesh.GetOutput().GetPoints().GetBounds(_bounds)
for j in range(3):
_ray_start[j] = _bounds[2 * j + 1] * surf
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(_mesh.GetOutput())
cell_locator.BuildLocator()
cell_locator.IntersectWithLine(_ray_start, _center, 0.0001, t, xyz,
pcoords, sub_id, cell_id)
print('ID of the cell on the outer surface: {}'.format(cell_id))
connectivity_filter = vtk.vtkConnectivityFilter()
connectivity_filter.SetInputConnection(_mesh.GetOutputPort())
connectivity_filter.SetExtractionModeToCellSeededRegions()
connectivity_filter.InitializeSeedList()
connectivity_filter.AddSeed(cell_id)
connectivity_filter.Update()
return connectivity_filter
def onAddButton(self):
print " -- Adding Keyframe at t =", self.Time
camera = slicer.mrmlScene.CreateNodeByClass('vtkMRMLCameraNode')
slicer.mrmlScene.AddNode(camera)
x = vtk.mutable(0)
y = vtk.mutable(0)
z = vtk.mutable(0)
value = [x, y, z]
self.defaultCam.GetPosition(value)
camera.SetPosition(value)
self.defaultCam.GetFocalPoint(value)
camera.SetFocalPoint(value)
self.defaultCam.GetViewUp(value)
camera.SetViewUp(value)
cameraName = 'Camera T = ' + str(self.Time)
print cameraName
camera.SetName(cameraName)
self.cameraPath.AddKeyFrame(self.Time, camera)
self.Time += 100
self.CameraList.append(camera)
self.FlyButton.setEnabled(False)
def _createSegmentData(self, segmentID):
segmentData = dict()
segmentData["labelID"] = 1
segment = self.segmentationNode.GetSegmentation().GetSegment(segmentID)
terminologyEntry = self.getDeserializedTerminologyEntry(segment)
category = terminologyEntry.GetCategoryObject()
segmentData["SegmentDescription"] = category.GetCodeMeaning()
algorithmType = vtk.mutable('')
if not segment.GetTag("DICOM.SegmentAlgorithmType", algorithmType):
algorithmType = "MANUAL"
if not algorithmType in ["MANUAL","SEMIAUTOMATIC","AUTOMATIC"]:
raise ValueError("Segment {} has invalid attribute for SegmentAlgorithmType."\
+"Should be one of (MANUAL,SEMIAUTOMATIC,AUTOMATIC).".format(segment.GetName()))
algorithmName = vtk.mutable('')
if not segment.GetTag("DICOM.SegmentAlgorithmName", algorithmName):
algorithmName = None
if algorithmType!="MANUAL" and not algorithmName:
raise ValueError("Segment {} has has missing SegmentAlgorithmName, which"\
+"should be specified for non-manual segmentations.".format(segment.GetName()))
segmentData["SegmentAlgorithmType"] = str(algorithmType)
if algorithmName:
segmentData["SegmentAlgorithmName"] = str(algorithmName)
rgb = segment.GetColor()
segmentData["recommendedDisplayRGBValue"] = [rgb[0] * 255, rgb[1] * 255, rgb[2] * 255]
segmentData.update(self.createJSONFromTerminologyContext(terminologyEntry))
segmentData.update(self.createJSONFromAnatomicContext(terminologyEntry))
return segmentData
def findZofXYOnPolydata(points,vtkPolydata):
# Make the cell locator
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(vtkPolydata)
cellLocator.BuildLocator()
# Find the min/max of the polydata.
lbot, ltop = np.array(vtkPolydata.GetBounds())[4::]
# Loop over all the locations.
intersectList = []
try:
for nr, loc in enumerate(points):
# Make line
p1 = np.hstack((loc[0:2],ltop))
p2 = np.hstack((loc[0:2],lbot))
# Pre define variables as in C++
t = vtk.mutable(0)
pIntSect = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
sub_id = vtk.mutable(0)
cellLocator.IntersectWithLine(p1,p2,1e-6,t,pIntSect,pcoords,sub_id)
intersectList.append(pIntSect)
except KeyboardInterrupt as k:
print 'Stopped at iteration {:d} in the for loop.'.format(nr)
raise k
# Return the intersects
return np.array(intersectList)
def get_tpc_intersection(point, direction, box=None):
""" Abstract class to calculate the TPC crossings """
if box is None:
tpc_box = [
TPC.x_min, TPC.x_max, TPC.y_min, TPC.y_max, TPC.z_min, TPC.z_max
]
else:
tpc_box = box
t1 = vtk.mutable(0)
t2 = vtk.mutable(0)
plane1 = vtk.mutable(0)
plane2 = vtk.mutable(0)
entry = [-1., -1., -1.]
exit = [-1., -1., -1.]
l = 5000
ray = [l * direction[0], l * direction[1], l * direction[2]]
end_point = np.add(point, ray).tolist()
vtk.vtkBox().IntersectWithLine(tpc_box, point, end_point, t1, t2, entry,
exit, plane1, plane2)
return [entry, exit]
def get_external_surface(self):
print('getting external surface')
_center = np.zeros(3)
_bounds = np.zeros(6)
_ray_start = np.zeros(3)
cell_id = vtk.mutable(-1)
xyz = np.zeros(3)
pcoords = np.zeros(3)
t = vtk.mutable(0)
sub_id = vtk.mutable(0)
_surf = 1.1
self.mesh.GetOutput().GetCenter(_center)
self.mesh.GetOutput().GetPoints().GetBounds(_bounds)
for j in range(3):
_ray_start[j] = _bounds[2 * j + 1] * _surf
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(self.mesh.GetOutput())
cell_locator.BuildLocator()
cell_locator.IntersectWithLine(_ray_start, _center, 0.0001, t, xyz,
pcoords, sub_id, cell_id)
connectivity_filter = vtk.vtkConnectivityFilter()
connectivity_filter.SetInputConnection(self.mesh.GetOutputPort())
connectivity_filter.SetExtractionModeToCellSeededRegions()
connectivity_filter.InitializeSeedList()
connectivity_filter.AddSeed(cell_id)
connectivity_filter.Update()
self.mesh = connectivity_filter # UnstructuredGrid
def addMappingFromPointsToCells(ugrid_points, ugrid_cells, verbose=True):
if (verbose): print '*** addMappingFromPointsToCells ***'
nb_points = ugrid_points.GetNumberOfPoints()
nb_cells = ugrid_cells.GetNumberOfCells()
print "nb_points = " + str(nb_points)
print "nb_cells = " + str(nb_cells)
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(ugrid_cells)
cell_locator.Update()
closest_point = [0.] * 3
generic_cell = vtk.vtkGenericCell()
num_cell = vtk.mutable(0)
subId = vtk.mutable(0)
dist = vtk.mutable(0.)
iarray_num_cell = createIntArray("num_cell", 1, nb_points)
for num_point in range(nb_points):
point = ugrid_points.GetPoint(num_point)
cell_locator.FindClosestPoint(point, closest_point, generic_cell,
num_cell, subId, dist)
#num_cell = cell_locator.FindCell(point)
iarray_num_cell.InsertTuple(num_point, [num_cell])
#print "num_point = " + str(num_point)
#print "num_cell = " + str(num_cell)
ugrid_points.GetPointData().AddArray(iarray_num_cell)
def intersection(surfaces, ray):
# Surfaces is as VTKmodifiedBSPtree object
# Ray contains the coordinates of 2 points defining the line
# Mainly based on "https://lorensen.github.io/VTKExamples/site/Python/GeometricObjects/PolygonIntersection/"
# tutorial, adapted because ModifiedBSPTree is used instead of a set of polygons.
p1 = ray[0] # The coordinates of the light source of the kinect
p2 = ray[
1] # The coordinates of the intersection between the ground and the ray
tolerance = 0.001
bestT = 2 # the best t parameter for the intersection, 1 is the worst possible value, 0 is the best one
bestID = -300000
bestX = [-100, -100, -100]
atLeastOne = False
t = vtk.mutable(
0
) # Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
x = [
-100, -100, -100
] # Setting an impossible value for the intersection (just to check problematic case)
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
iD = surfaces.IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId)
# This part was initially there because "surfaces" parameter was a list of polygons (so a ray can intersect
# with several polygons and we need to find the nearest intersection with the light source)
# TODO refactor the code so it benefits more of the specification of modifiedBSPtree (see comment above)
if iD == 1:
atLeastOne = True
if t < bestT:
# bestID = i
bestT = t
bestX = x
return bestID, bestT, bestX, atLeastOne
def surface2surfacedistance(ref, target, arrayname):
"""Compute distance between two surfaces. Output is added as point array."""
# adapted from vtkvmtkSurfaceDistance
# initialise
locator = vtk.vtkCellLocator()
genericcell = vtk.vtkGenericCell()
cellid = vtk.mutable(0)
point = [0., 0., 0.]
closestpoint = [0., 0., 0.]
subid = vtk.mutable(0)
distance2 = vtk.mutable(0)
# create array
distarray = vtk.vtkDoubleArray()
distarray.SetName(arrayname)
distarray.SetNumberOfTuples(target.GetNumberOfPoints())
target.GetPointData().AddArray(distarray)
# build locator
locator.SetDataSet(ref)
locator.BuildLocator()
# compute distance
for i in range(target.GetNumberOfPoints()):
point = target.GetPoint(i)
locator.FindClosestPoint(point, closestpoint, genericcell, cellid,
subid, distance2)
distance = math.sqrt(distance2)
# add value to array
distarray.SetValue(i, distance)
target.Update()
return target
def _createSegmentData(self, segmentID):
segmentData = dict()
segmentData["labelID"] = 1
segment = self.segmentationNode.GetSegmentation().GetSegment(segmentID)
terminologyEntry = self.getDeserializedTerminologyEntry(segment)
category = terminologyEntry.GetCategoryObject()
segmentData["SegmentLabel"] = segment.GetName()
segmentData["SegmentDescription"] = category.GetCodeMeaning()
algorithmType = vtk.mutable('')
if not segment.GetTag("DICOM.SegmentAlgorithmType", algorithmType):
algorithmType = "MANUAL"
if not algorithmType in ["MANUAL", "SEMIAUTOMATIC", "AUTOMATIC"]:
raise ValueError("Segment {} has invalid attribute for SegmentAlgorithmType."\
+"Should be one of (MANUAL,SEMIAUTOMATIC,AUTOMATIC).".format(segment.GetName()))
algorithmName = vtk.mutable('')
if not segment.GetTag("DICOM.SegmentAlgorithmName", algorithmName):
algorithmName = None
if algorithmType != "MANUAL" and not algorithmName:
raise ValueError("Segment {} has has missing SegmentAlgorithmName, which"\
+"should be specified for non-manual segmentations.".format(segment.GetName()))
segmentData["SegmentAlgorithmType"] = str(algorithmType)
if algorithmName:
segmentData["SegmentAlgorithmName"] = str(algorithmName)
rgb = segment.GetColor()
segmentData["recommendedDisplayRGBValue"] = [
rgb[0] * 255, rgb[1] * 255, rgb[2] * 255
]
segmentData.update(
self.createJSONFromTerminologyContext(terminologyEntry))
segmentData.update(
self.createJSONFromAnatomicContext(terminologyEntry))
return segmentData
def testTangent2():
# segment is tangent to cell
tBeg, tEnd = vtk.mutable(-1.0), vtk.mutable(-1.0)
piHalf = numpy.pi / 2.
# cell
lam0, the0 = 0.025 * piHalf, 0.05 * piHalf
lam1, the1 = 0.050 * piHalf, 0.05 * piHalf
lam2, the2 = 0.050 * piHalf, 0.1 * piHalf
lam3, the3 = 0.025 * piHalf, 0.1 * piHalf
lamA, theA = 0.02 * piHalf, 0.05 * piHalf
lamB, theB = 0.07 * piHalf, 0.05 * piHalf
cli = CellLineIntersector()
cli.setCartesianCell(lam0, the0, lam1, the1, lam2, the2, lam3, the3)
cli.setCartesianLine(lamA, theA, lamB, theB)
xiBeg = numpy.zeros((2, ), numpy.float64)
xiEnd = numpy.zeros((2, ), numpy.float64)
found = cli.findIntersection(tBeg, tEnd, xiBeg, xiEnd)
print('testTangent2: tBeg = {} tEnd = {} xiBeg = {} xiEnd = {}'.format(
tBeg.get(), tEnd.get(), xiBeg, xiEnd))
assert abs(tBeg.get() - 0.1) < 1.e-3
assert abs(tEnd.get() - 0.6) < 1.e-3
def testFloatMutable(self):
m = vtk.mutable(3.0)
n = vtk.mutable(4.0)
m *= 2
self.assertEqual(m, 6.0)
self.assertEqual(str(m), str(m.get()))
o = n + m
self.assertEqual(o, 10.0)
def testFloatMutable(self):
m = vtk.mutable(3.0)
n = vtk.mutable(4.0)
m *= 2
self.assertEqual(m, 6.0)
self.assertEqual(str(m), str(m.get()))
o = n + m
self.assertEqual(o, 10.0)
def testGetRangeTwoDoubleStarArg(self):
cmap = vtk.vtkColorTransferFunction()
localMin = vtk.mutable(-1)
localMax = vtk.mutable(-1)
cmap.GetRange(localMin, localMax)
self.assertEqual(localMin, 0.0)
self.assertEqual(localMax, 0.0)
def addAppliedToolToSegment(self, segment, toolName, toolType=None):
self.updatingSegmentTags = True
# append list of applied tools
tools = vtk.mutable('')
tools = str(tools).split(';') if segment.GetTag('QuantitativeReporting.AppliedTools', tools) else []
if not toolName in tools:
tools.append(toolName)
segment.SetTag('QuantitativeReporting.AppliedTools',";".join(tools))
segmentWasImported = tools[0]!='Add'
# determine algorithm type (if not specified by user)
if not toolType:
if toolName in self.manualTools:
toolType = 'MANUAL'
elif toolName in self.automaticTools:
toolType = 'AUTOMATIC'
else: # default tool type
toolType = 'SEMIAUTOMATIC'
# update DICOM algorithm type
oldAlgorithmType = vtk.mutable('')
segment.GetTag('DICOM.SegmentAlgorithmType', oldAlgorithmType)
updatedAlgorithmType = oldAlgorithmType
if oldAlgorithmType=='': # no other editor effect was applied before
if segmentWasImported:
updatedAlgorithmType = 'SEMIAUTOMATIC'
else:
updatedAlgorithmType = toolType
elif oldAlgorithmType=='MANUAL' and toolType!='MANUAL':
updatedAlgorithmType = 'SEMIAUTOMATIC'
elif oldAlgorithmType=='AUTOMATIC':
updatedAlgorithmType = 'SEMIAUTOMATIC'
if oldAlgorithmType!=updatedAlgorithmType:
segment.SetTag('DICOM.SegmentAlgorithmType' ,updatedAlgorithmType)
# update DICOM algorithm name
GenericSlicerAlgorithmName = slicer.app.applicationName+' '+slicer.app.applicationVersion
GenericSegmentEditorAlgorithmName = GenericSlicerAlgorithmName+' Segment Editor'
ToolSegmentEditorAlgorithmName = GenericSlicerAlgorithmName+' '+toolName+' Effect'
oldAlgorithmName = vtk.mutable('')
segment.GetTag('DICOM.SegmentAlgorithmName', oldAlgorithmName)
updatedAlgorithmName = oldAlgorithmName
if oldAlgorithmName=='': # no other editor tool was applied before
if segmentWasImported:
updatedAlgorithmName = GenericSlicerAlgorithmName
else:
updatedAlgorithmName = ToolSegmentEditorAlgorithmName
elif oldAlgorithmName!=ToolSegmentEditorAlgorithmName:
if oldAlgorithmName.startswith(GenericSegmentEditorAlgorithmName):
updatedAlgorithmName = GenericSegmentEditorAlgorithmName
else:
updatedAlgorithmName = GenericSlicerAlgorithmName
if oldAlgorithmName!=updatedAlgorithmName:
segment.SetTag('DICOM.SegmentAlgorithmName', updatedAlgorithmName)
self.updatingSegmentTags = False
def findClosestPoint(self, p):
# TODO: compute the closest point, compute the triangle coordinates of the intersection point in that triangle, and
subId = vtk.mutable(0)
meshPoint = np.zeros(3)
cellId = vtk.mutable(0)
dist2 = vtk.mutable(0.)
self.locator.FindClosestPoint(p, meshPoint, cellId, subId, dist2)
meshPoint
cellId
np.linalg.solve(self.points[self.triangles[cellId]], meshPoint)
def __init__(self, vtk_mesh):
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(vtk_mesh)
cell_locator.BuildLocator()
self.cell_locator = cell_locator
# prepare some private properties that will be filled in for us by VTK
self._c_point = [0., 0., 0.]
self._cell_id = vtk.mutable(0)
self._sub_id = vtk.mutable(0)
self._distance = vtk.mutable(0.0)
def convertRasToViewport(self, viewNode, positionRas):
"""Computes normalized view coordinates from RAS coordinates for a particular view
Normalized view coordinates origin is in bottom-left corner, range is [-1,+1]
"""
x = vtk.mutable(positionRas[0])
y = vtk.mutable(positionRas[1])
z = vtk.mutable(positionRas[2])
view = slicer.app.layoutManager().threeDWidget(
self.getThreeDWidgetIndex(viewNode)).threeDView()
renderer = view.renderWindow().GetRenderers().GetItemAsObject(0)
renderer.WorldToView(x, y, z)
return [x.get(), y.get(), z.get()]
def __init__(self): self.source = None self.locator = vtk.vtkCellLocator() self.mapper = vtk.vtkPolyDataMapper() self.actor = vtk.vtkActor() self.density = 1.0 self.transform = vtk.vtkTransform() self.transformFilter=vtk.vtkTransformPolyDataFilter() self.transformFilter.SetTransform(self.transform) self.tolerance = 0.00001 self.tmut = vtk.mutable(0) self.subId = vtk.mutable(0)
def toUVSpace(self, p):
""" This function converts a 3D world space to 2D texture coordinates.
Args:
p (iterable of type float): 2D texture coordinate in (x,y) format
with x and y values between 0 and 1 representing a relative
position on the image texure.
Returns:
worldPoint(iterable of type float): 3D euclidian coordinate of the
point corresponding to the 2D texture coordinate 'p' in the VTK
polyData object's frame.
normalVector(iterable of type float): 3D vector (x,y,z) representing
the normal vector on the current face.
TODO:
* Return color data
"""
# Add dimensions if necessary
points3D = np.atleast_2d(p)
if points3D.ndim != 2 or points3D.shape[1] != 3:
raise TypeError('toWorldSpace: input point must be 3xN')
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
dist = vtk.mutable(0)
closest = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
tCoords = [0.0, 0.0, 0.0]
weights = [0.0, 0.0, 0.0]
points2D = np.empty(points2D.shape)
for idx, point3D in enumerate(points3D):
self.pointLocator.FindClosestPoint(point3D, closest, self._cell,
cellId, subId, dist)
self._cell.EvaluatePosition(point3D, closest, subId, pcoords, dist,
weights)
if type(pcoords) == str:
raise TypeError(
'VTK function EvaluatePosition returned a null pointer. please use either '
+
'a newer version of VTK or build the dvrk_vision package with vtkCell.h'
)
self.polyData2D.GetCell(cellId).EvaluateLocation(
subId, pcoords, tCoords, weights)
points2D[idx, :] = tCoords
# If only queried one point, only return one point, no need for 2D array
if len(points2D) == 1:
return points2D[0]
return points2D
def get_spline_actor(surface_data, chassis_cg_path, surface_bounds):
# Iterate over chassis CG points and create a spline which marks the driving path.
# Return the spline as a vtkActor for being added later to the renderer.
# Update the pipeline so that vtkCellLocator finds cells
surface_data.Update()
# Define a cellLocator to be able to compute intersections between lines
# and the surface
locator = vtkCellLocator()
locator.SetDataSet(surface_data.GetOutput())
locator.BuildLocator()
tolerance = 0.01 # Set intersection searching tolerance
# Make a list of points. Each point is the intersection of a vertical line
# defined by p1 and p2 and the surface.
points = vtkPoints()
for chassis_cg in chassis_cg_path:
p1 = [chassis_cg[0], chassis_cg[1], surface_bounds[4]]
p2 = [chassis_cg[0], chassis_cg[1], surface_bounds[5]]
t = mutable(0)
pos = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = mutable(0)
locator.IntersectWithLine(p1, p2, tolerance, t, pos, pcoords, subId)
# Add a slight offset in z
pos[2] += 0.05
# Add the x, y, z position of the intersection
points.InsertNextPoint(pos)
# Create a spline and add the pointsoi
spline = vtkParametricSpline()
spline.SetPoints(points)
spline_function = vtkParametricFunctionSource()
spline_function.SetUResolution(len(chassis_cg_path))
spline_function.SetParametricFunction(spline)
# Map the spline
spline_mapper = vtkPolyDataMapper()
spline_mapper.SetInputConnection(spline_function.GetOutputPort())
# Define the line actor
spline_actor = vtkActor()
spline_actor.SetMapper(spline_mapper)
spline_actor.GetProperty().SetColor([0, 0.7, 0])
spline_actor.GetProperty().SetLineWidth(10)
return spline_actor
def toWorldSpace(self, p):
""" This function converts a 2D texture coordinate to 3D object space.
Args:
p (iterable of type float): 2D texture coordinate in (x,y) format
with x and y values between 0 and 1 representing a relative
position on the image texure.
Returns:
worldPoint(iterable of type float): 3D euclidian coordinate of the
point corresponding to the 2D texture coordinate 'p' in the VTK
polyData object's frame.
normalVector(iterable of type float): 3D vector (x,y,z) representing
the normal vector on the current face.
TODO:
* Return color data
"""
# Add dimensions if necessary
points2D = np.atleast_2d(p)
if points2D.shape[-1] == 2:
points2D = np.hstack((points2D, np.zeros((1, len(points2D)))))
if points2D.ndim != 2 or points2D.shape[1] != 3:
raise TypeError('toWorldSpace: input point must be 2xN or 3xN')
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
dist = vtk.mutable(0)
closest = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
tCoords = [0.0, 0.0, 0.0]
weights = [0.0, 0.0, 0.0]
points3D = np.empty(points2D.shape)
normals = np.zeros(points2D.shape)
for idx, point2D in enumerate(points2D):
self.pointLocator2D.FindClosestPoint(point2D, closest, self._cell,
cellId, subId, dist)
self._cell.EvaluatePosition(point2D, closest, subId, pcoords, dist,
weights)
self.polyData.GetCell(cellId).EvaluateLocation(
subId, pcoords, tCoords, weights)
points3D[idx, :] = tCoords
pointIds = self.polyData.GetCell(cellId).GetPointIds()
normals[idx, :] = np.array(
self.polyData.GetCellData().GetNormals().GetTuple(cellId))
# If only queried one point, only return one point, no need for 2D array
if len(points3D) == 1:
return points3D[0], normals[0]
return points3D, normals
def closestPoint(actor, pt, N=1, radius=None, returnIds=False):
"""
Find the closest point on a polydata given an other point.
The appropriate locator is built on the fly and cached for speed.
If N>1, return a list of N ordered closest points.
If radius is given, get all points within.
"""
poly = polydata(actor, True)
if N > 1 or radius:
plocexists = hasattr(actor, 'point_locator')
if not plocexists or (plocexists and actor.point_locator is None):
point_locator = vtk.vtkPointLocator()
point_locator.SetDataSet(poly)
point_locator.BuildLocator()
setattr(actor, 'point_locator', point_locator)
vtklist = vtk.vtkIdList()
if N > 1:
actor.point_locator.FindClosestNPoints(N, pt, vtklist)
else:
actor.point_locator.FindPointsWithinRadius(radius, pt, vtklist)
if returnIds:
return [
int(vtklist.GetId(k)) for k in range(vtklist.GetNumberOfIds())
]
else:
trgp = []
for i in range(vtklist.GetNumberOfIds()):
trgp_ = [0, 0, 0]
vi = vtklist.GetId(i)
poly.GetPoints().GetPoint(vi, trgp_)
trgp.append(trgp_)
return np.array(trgp)
clocexists = hasattr(actor, 'cell_locator')
if not clocexists or (clocexists and actor.cell_locator is None):
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(poly)
cell_locator.BuildLocator()
setattr(actor, 'cell_locator', cell_locator)
trgp = [0, 0, 0]
cid = vtk.mutable(0)
dist2 = vtk.mutable(0)
subid = vtk.mutable(0)
actor.cell_locator.FindClosestPoint(pt, trgp, cid, subid, dist2)
if returnIds:
return int(cid)
else:
return np.array(trgp)
def distanceField(surfaceMesh, targetGrid, targetArrayName: str, signed=False):
"""Create a distance field between a vtkStructuredGrid and a surface.
:param surfaceMesh: Outer polygonal surface
:param targetGrid: Grid array of points
:type targetGrid: vtk.vtkStructuredGrid
:param targetArrayName: The distance field values will be stored in the \
target grid, with this array name.
:type targetArrayName: str
:param signed: Signed/unsigned distance field, defaults to False (unsigned)
:type signed: bool, optional
"""
# Initialize distance field:
df = vtk.vtkDoubleArray()
df.SetNumberOfTuples(targetGrid.GetNumberOfPoints())
df.SetName(targetArrayName)
# Data structure to quickly find cells:
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(surfaceMesh)
cellLocator.BuildLocator()
for i in range(0, targetGrid.GetNumberOfPoints()):
# Take a point from the target...
testPoint = [0] * 3
targetGrid.GetPoint(i, testPoint)
# ... find the point in the surface closest to it
cID, subID, dist2 = vtk.mutable(0), vtk.mutable(0), vtk.mutable(0.0)
closestPoint = [0] * 3
cellLocator.FindClosestPoint(
testPoint, closestPoint, cID, subID, dist2)
dist = math.sqrt(dist2)
df.SetTuple1(i, dist)
if signed:
pts = vtk.vtkPolyData()
pts.SetPoints(targetGrid.GetPoints())
enclosedPointSelector = vtk.vtkSelectEnclosedPoints()
enclosedPointSelector.CheckSurfaceOn()
enclosedPointSelector.SetInputData(pts)
enclosedPointSelector.SetSurfaceData(surfaceMesh)
enclosedPointSelector.SetTolerance(1e-9)
enclosedPointSelector.Update()
enclosedPoints = enclosedPointSelector.GetOutput()
for i in range(0, targetGrid.GetNumberOfPoints()):
if enclosedPointSelector.IsInside(i):
df.SetTuple1(i, -df.GetTuple1(i)) # invert sign
targetGrid.GetPointData().AddArray(df)
def getPointOnOtherMesh( a, a_locator, b, p ):
'''Given two vtkPolyData's with matching topology and a vtkCellLocator for the first, carry point p from one to the other.'''
cell_id = vtk.mutable(0)
sub_id = vtk.mutable(0)
d2 = vtk.mutable(0.0)
cell = vtk.vtkGenericCell()
p2 = p
found = a_locator.FindClosestPoint( p, p2, cell, cell_id, sub_id, d2 )
p3 = p2
pcoords = [0,0,0]
weights = []
cell.EvaluatePosition( p2, p3, sub_id, pcoords, d2, weights )
p4 = p3
b.GetCell( cell_id ).EvaluateLocation( sub_id, pcoords, p4, weights )
return p4
def getCellLocator(mesh, verbose=0):
myVTK.myPrint(verbose, "*** getCellLocator ***")
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(mesh)
cell_locator.Update()
closest_point = [0.] * 3
generic_cell = vtk.vtkGenericCell()
k_cell = vtk.mutable(0)
subId = vtk.mutable(0)
dist = vtk.mutable(0.)
return (cell_locator, closest_point, generic_cell, k_cell, subId, dist)
def getPointOnOtherMesh(a, a_locator, b, p):
'''Given two vtkPolyData's with matching topology and a vtkCellLocator for the first, carry point p from one to the other.'''
cell_id = vtk.mutable(0)
sub_id = vtk.mutable(0)
d2 = vtk.mutable(0.0)
cell = vtk.vtkGenericCell()
p2 = p
found = a_locator.FindClosestPoint(p, p2, cell, cell_id, sub_id, d2)
p3 = p2
pcoords = [0, 0, 0]
weights = []
cell.EvaluatePosition(p2, p3, sub_id, pcoords, d2, weights)
p4 = p3
b.GetCell(cell_id).EvaluateLocation(sub_id, pcoords, p4, weights)
return p4
def updateSelector(self, selector, model_types, param, filtered, defaultIndex=0):
wasSelectorBlocked = selector.blockSignals(True)
selector.clear()
currentSegment = self.currentSegment()
currentSegmentName = currentSegment.GetName().lower() if currentSegment else ""
for model_name, model in self.models.items():
if model['type'] in model_types:
if filtered and not (currentSegmentName in model_name.lower()):
continue
selector.addItem(model_name)
selector.setItemData(selector.count - 1, model['description'], qt.Qt.ToolTipRole)
model = self.scriptedEffect.parameter(param) if self.scriptedEffect.parameterDefined(param) else ""
if not model and currentSegment:
model = vtk.mutable("")
currentSegment.GetTag(param, model)
modelIndex = selector.findText(model)
modelIndex = defaultIndex if modelIndex < 0 < selector.count else modelIndex
selector.setCurrentIndex(modelIndex)
try:
modelInfo = self.models[model]
selector.setToolTip(modelInfo["description"])
except:
selector.setToolTip("")
selector.blockSignals(wasSelectorBlocked)
def onClickEditPoints(self):
segment = self.currentSegment()
segmentId = self.currentSegmentID()
self.segmentMarkupNode.RemoveAllMarkups()
if segmentId:
v = self.scriptedEffect.parameterSetNode().GetMasterVolumeNode()
IjkToRasMatrix = vtk.vtkMatrix4x4()
v.GetIJKToRASMatrix(IjkToRasMatrix)
fPosStr = vtk.mutable("")
segment.GetTag("AIAA.DExtr3DExtremePoints", fPosStr)
pointset = str(fPosStr)
logging.debug('{} => {} Extreme points are: {}'.format(
segmentId, segment.GetName(), pointset))
if fPosStr is not None and len(pointset) > 0:
points = json.loads(pointset)
for p in points:
p_Ijk = [p[0], p[1], p[2], 1.0]
p_Ras = IjkToRasMatrix.MultiplyDoublePoint(p_Ijk)
logging.debug('Add Fiducial: {} => {}'.format(
p_Ijk, p_Ras))
self.segmentMarkupNode.AddFiducialFromArray(p_Ras[0:3])
self.updateGUIFromMRML()
def getDeserializedTerminologyEntry(vtkSegment):
terminologyEntry = slicer.vtkSlicerTerminologyEntry()
tag = vtk.mutable("")
vtkSegment.GetTag(vtkSegment.GetTerminologyEntryTagName(), tag)
terminologyLogic = slicer.modules.terminologies.logic()
terminologyLogic.DeserializeTerminologyEntry(tag, terminologyEntry)
return terminologyEntry
def getDeserializedTerminologyEntry(vtkSegment):
terminologyEntry = slicer.vtkSlicerTerminologyEntry()
tag = vtk.mutable("")
vtkSegment.GetTag(vtkSegment.GetTerminologyEntryTagName(), tag)
terminologyLogic = slicer.modules.terminologies.logic()
terminologyLogic.DeserializeTerminologyEntry(tag, terminologyEntry)
return terminologyEntry
def testPassByReference(self):
t = vtk.mutable(0.0)
p0 = (0.5, 0.0, 0.0)
n = (1.0, 0.0, 0.0)
p1 = (0.0, 0.0, 0.0)
p2 = (1.0, 1.0, 1.0)
x = [0.0, 0.0, 0.0]
vtk.vtkPlane.IntersectWithLine(p1, p2, n, p0, t, x)
self.assertEqual(round(t, 6), 0.5)
self.assertEqual(round(x[0], 6), 0.5)
self.assertEqual(round(x[1], 6), 0.5)
self.assertEqual(round(x[2], 6), 0.5)
vtk.vtkPlane().IntersectWithLine(p1, p2, n, p0, t, x)
self.assertEqual(round(t, 6), 0.5)
self.assertEqual(round(x[0], 6), 0.5)
self.assertEqual(round(x[1], 6), 0.5)
self.assertEqual(round(x[2], 6), 0.5)
t.set(0)
p = vtk.vtkPlane()
p.SetOrigin(0.5, 0.0, 0.0)
p.SetNormal(1.0, 0.0, 0.0)
p.IntersectWithLine(p1, p2, t, x)
self.assertEqual(round(t, 6), 0.5)
self.assertEqual(round(x[0], 6), 0.5)
self.assertEqual(round(x[1], 6), 0.5)
self.assertEqual(round(x[2], 6), 0.5)
vtk.vtkPlane.IntersectWithLine(p, p1, p2, t, x)
self.assertEqual(round(t, 6), 0.5)
self.assertEqual(round(x[0], 6), 0.5)
self.assertEqual(round(x[1], 6), 0.5)
self.assertEqual(round(x[2], 6), 0.5)
def testPassByReference(self):
t = vtk.mutable(0.0)
p0 = (0.5, 0.0, 0.0)
n = (1.0, 0.0, 0.0)
p1 = (0.0, 0.0, 0.0)
p2 = (1.0, 1.0, 1.0)
x = [0.0, 0.0, 0.0]
vtk.vtkPlane.IntersectWithLine(p1, p2, n, p0, t, x)
self.assertEqual(round(t,6), 0.5)
self.assertEqual(round(x[0],6), 0.5)
self.assertEqual(round(x[1],6), 0.5)
self.assertEqual(round(x[2],6), 0.5)
vtk.vtkPlane().IntersectWithLine(p1, p2, n, p0, t, x)
self.assertEqual(round(t,6), 0.5)
self.assertEqual(round(x[0],6), 0.5)
self.assertEqual(round(x[1],6), 0.5)
self.assertEqual(round(x[2],6), 0.5)
t.set(0)
p = vtk.vtkPlane()
p.SetOrigin(0.5, 0.0, 0.0)
p.SetNormal(1.0, 0.0, 0.0)
p.IntersectWithLine(p1, p2, t, x)
self.assertEqual(round(t,6), 0.5)
self.assertEqual(round(x[0],6), 0.5)
self.assertEqual(round(x[1],6), 0.5)
self.assertEqual(round(x[2],6), 0.5)
vtk.vtkPlane.IntersectWithLine(p, p1, p2, t, x)
self.assertEqual(round(t,6), 0.5)
self.assertEqual(round(x[0],6), 0.5)
self.assertEqual(round(x[1],6), 0.5)
self.assertEqual(round(x[2],6), 0.5)
def onClickEditPoints(self):
segmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
label = segment.GetName()
self.segmentMarkupNode.RemoveAllMarkups()
v = self.scriptedEffect.parameterSetNode().GetMasterVolumeNode()
IjkToRasMatrix = vtk.vtkMatrix4x4()
v.GetIJKToRASMatrix(IjkToRasMatrix)
fPosStr = vtk.mutable("")
segment.GetTag("DExtr3DExtremePoints", fPosStr)
logging.info('{} => {} Extreme points are: '.format(
segmentID, label, fPosStr))
if fPosStr is not None and len(fPosStr) > 0:
points = json.loads(str(fPosStr))
for p in points:
p_Ijk = [p[0], p[1], p[2], 1.0]
p_Ras = IjkToRasMatrix.MultiplyDoublePoint(p_Ijk)
logging.info('Add Fiducial: {} => {}'.format(p_Ijk, p_Ras))
self.segmentMarkupNode.AddFiducialFromArray(p_Ras[0:3])
else:
qt.QMessageBox.information(
slicer.util.mainWindow(), 'NVIDIA AIAA',
'There are no pre-existing extreme points available for (' +
segment.GetName() + ')' + '\t')
self.updateGUIFromMRML()
def onEdit(self):
# Create empty model node
if self.segmentModel is None:
self.segmentModel = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(self.segmentModel)
segmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
fPosStr = vtk.mutable("")
segment.GetTag("DrawTubeEffectMarkupPositions", fPosStr)
# convert from space-separated list o fnumbers to 1D array
import numpy
fPos = numpy.fromstring(str(fPosStr), sep=' ')
# convert from 1D array (N*3) to 2D array (N,3)
fPosNum = int(len(fPos) / 3)
fPos = fPos.reshape((fPosNum, 3))
for i in xrange(fPosNum):
self.segmentMarkupNode.AddFiducialFromArray(fPos[i])
self.editButton.setEnabled(False)
self.updateModelFromSegmentMarkupNode()
def updateScalarBarRange(sliceLogic, volumeNode, scalarBar, selectedLayer):
vdn = volumeNode.GetDisplayNode()
if vdn:
vcn = vdn.GetColorNode()
if vcn is None:
return
lut = vcn.GetLookupTable()
lut2 = vtk.vtkLookupTable()
lut2.DeepCopy(lut)
width = vtk.mutable(0)
level = vtk.mutable(0)
rangeLow = vtk.mutable(0)
rangeHigh = vtk.mutable(0)
if selectedLayer == 'background':
sliceLogic.GetBackgroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
else:
sliceLogic.GetForegroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
lut2.SetRange(level-width/2,level+width/2)
scalarBar.SetLookupTable(lut2)
def getCellLocator(
mesh,
verbose=0):
myVTK.myPrint(verbose, "*** getCellLocator ***")
cell_locator = vtk.vtkCellLocator()
cell_locator.SetDataSet(mesh)
cell_locator.Update()
closest_point = [0.]*3
generic_cell = vtk.vtkGenericCell()
k_cell = vtk.mutable(0)
subId = vtk.mutable(0)
dist = vtk.mutable(0.)
return (cell_locator,
closest_point,
generic_cell,
k_cell,
subId,
dist)
def AddTimestamp( self, time, matrix, point, role ):
if ( self.targetNode == None or self.bspTree == None ):
return
# To speed things up, if the structure has already been scanned, then skip
if ( self.structureScanned ):
return
# Assume the matrix is ImageToRAS
# For each scan line
# Assume the x-axis is equivalent to the marked-unmarked axis
for i in range( self.imageMinX, self.imageMaxX ):
# Find end points of the current scan line in the Image coordinate system
startPoint_Image = [ i, self.imageMinY, 0, 1 ]
endPoint_Image = [ i, self.imageMaxY, 0, 1 ]
# Transform the end points into the RAS coordinate system
startPoint_RAS = [ 0, 0, 0, 1 ]
endPoint_RAS = [ 0, 0, 0, 1 ]
matrix.MultiplyPoint( startPoint_Image, startPoint_RAS )
matrix.MultiplyPoint( endPoint_Image, endPoint_RAS )
startPoint_RAS = [ startPoint_RAS[ 0 ], startPoint_RAS[ 1 ], startPoint_RAS[ 2 ] ]
endPoint_RAS = [ endPoint_RAS[ 0 ], endPoint_RAS[ 1 ], endPoint_RAS[ 2 ] ]
# Check for intersection with the model
# These parameters
INTERSECTION_POINT = [ 0, 0, 0 ]
INTERSECTION_TOLERANCE = 0.001
P_COORDS = [ 0, 0, 0 ]
T = vtk.mutable( 0 )
SUB_ID = vtk.mutable( 0 )
scanlineIntersection = self.bspTree.IntersectWithLine( startPoint_RAS, endPoint_RAS, INTERSECTION_TOLERANCE, T, INTERSECTION_POINT, P_COORDS, SUB_ID )
if ( scanlineIntersection == 1 ):
self.structureScanned = True
return
def find_cell(self, locator, point=None):
""" Use vtk rountines to find cell/element containing the point."""
if point is None:
point = self.pos
cell_index = vtk.mutable(0)
locator.FindClosestPoint(point, ARGV, cell_index, ARGI, ARGR)
# locator.FindCell(point)
if cell_index==-1:
cell_index = None
return cell_index
def CatTransformedCautious(self, pdb_ext, trans, pointlocator, cutoff=1.2):
"""Transforms pdb_ext and concatenates it to self. checks if the new molecule is not within the
distance of cutoff from all the points in pointlocator.dataset .
pointlocator : vtkPointLocator()
"""
pdb_aux = pdb_ext.MakeCopy()
pdb_aux.ApplyTransform(trans)
pointlocator.Update()
dataset = pointlocator.GetDataSet()
points = dataset.GetPoints()
distance = vtk.mutable(0.0) # FindClosestPointWithinRadius writes on distance and its useless here.
if not points:
points = vtk.vtkPoints()
dataset.SetPoints(points)
if not self.empty: # do not check if empty
for atom_itr in pdb_aux:
pointid = pointlocator.FindClosestPointWithinRadius(cutoff, atom_itr.pos, distance)
if pointid != -1: # There have been an atom within "cutoff" distance.
return False
## There have been no atom within the cutoff distance.
self.Concatenate(pdb_aux)
self.empty = False # not empty anymore.
## add the newly added atom's position and its repeats to the pointlocator.
pos = [0, 0, 0]
for atom_itr in pdb_aux:
points.InsertNextPoint(atom_itr.pos)
pointlocator.InsertNextPoint(atom_itr.pos)
coords = [[], [], []]
for coord in [0, 1, 2]:
if atom_itr.pos[coord] > self.unit_cell_size:
coords[coord].append(atom_itr.pos[coord])
coords[coord].append(atom_itr.pos[coord] - self.unit_cell_size)
elif atom_itr.pos[coord] < cutoff:
coords[coord].append(atom_itr.pos[coord])
coords[coord].append(atom_itr.pos[coord] + self.unit_cell_size)
else:
coords[coord].append(atom_itr.pos[coord])
for xcoord in coords[0]:
for ycoord in coords[1]:
for zcoord in coords[2]:
pos[0] = xcoord
pos[1] = ycoord
pos[2] = zcoord
points.InsertNextPoint(pos)
pointlocator.InsertNextPoint(pos)
return True
def closest_point(mesh, vector, radius = None):
locator = vtk.vtkPointLocator()
ugrid = read_ugrid(mesh)
locator.SetDataSet(ugrid)
vector = map(float, vector)
assert len(vector) == 3
if radius is None:
index = locator.FindClosestPoint(vector)
else:
a = vtk.mutable(0.0)
index = locator.FindClosestPointWithinRadius(radius, vector, a)
point = ugrid.GetPoint(index)
distance = math.sqrt(sum(starmap(lambda a, b: (b-a)**2, zip(vector, point))))
return {'index': index, 'point': point, 'dist': distance}
def normalHistogram(opts,argv):
poly = nv.readVTK(argv[0])
normfilt = vtk.vtkPolyDataNormals()
normfilt.ConsistencyOn()
normfilt.AutoOrientNormalsOn()
normfilt.ComputeCellNormalsOn()
normfilt.SetInput(poly)
normfilt.SetFeatureAngle(90)
normfilt.Update()
poly = normfilt.GetOutput()
nv.writeVTK("nrom.vtk", poly)
normals = poly.GetCellData().GetArray("Normals", vtk.mutable(0))
normMap = vtk.vtkUnstructuredGrid()
normMap.SetPoints(vtk.vtkPoints())
normPts = normMap.GetPoints()
for i in range(0, normals.GetNumberOfTuples()):
norm = [0,0,0]
normals.GetTuple(i, norm)
normPts.InsertNextPoint(norm)
nv.writeVTK(argv[1], normMap)
def testMethods(self):
"""Test overloaded methods"""
# single-argument method vtkTransform::SetMatrix()
t = vtk.vtkTransform()
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 2)
t.SetMatrix(m)
self.assertEqual(t.GetMatrix().GetElement(0, 0), 2)
t.SetMatrix([0,1,0,0, 1,0,0,0, 0,0,-1,0, 0,0,0,1])
self.assertEqual(t.GetMatrix().GetElement(0, 0), 0)
# mixed number of arguments
fd = vtk.vtkFieldData()
fa = vtk.vtkFloatArray()
fa.SetName("Real")
ia = vtk.vtkIntArray()
ia.SetName("Integer")
fd.AddArray(fa)
fd.AddArray(ia)
a = fd.GetArray("Real")
self.assertEqual(id(a), id(fa))
i = vtk.mutable(0)
a = fd.GetArray("Integer", i)
self.assertEqual(id(a), id(ia))
self.assertEqual(i, 1)
def collide(self, k, delta_t, vel=None, force=None, pa=None, level=0):
"""Collision detection routine.
Args:
k (float): Displacement
dt (float): Timestep
v (float, optional): velocity
f (float, optional): forcing
pa (float, optional): starting position in subcycle
level (int) count to control maximum depth
"""
if pa is None:
pa = self.pos
if level == 10:
return k * delta_t, None, vel - self.vel, None
pos = pa+delta_t*k
s = vtk.mutable(-1.0)
x = [0.0, 0.0, 0.0]
cell_index = vtk.mutable(0)
bndl = self.system.boundary.bndl
intersect = bndl.IntersectWithLine(pa, pos,
1.0e-8, s,
x, ARGV, ARGI, cell_index)
if intersect:
if self.system.boundary.bnd.GetCellData().HasArray('SurfaceIds'):
if self.system.boundary.bnd.GetCellData().GetScalars('SurfaceIds').GetValue(cell_index) in self.system.boundary.outlet_ids:
return pos - pa, None, vel + delta_t * force - self.vel, None
data, _, names = self.system.temporal_cache(self.time)
# assert IO.test_in_cell(IO.get_linear_block(data[0][2]).GetCell(self.find_cell(data[0][3], pa)), pa) or sum((pa-x)**2)<1.0-10
print 'collision', intersect, cell_index, s, x, pos, pa
x = numpy.array(x)
old_pos = pos
cell = self.system.boundary.bnd.GetCell(cell_index)
normal = numpy.zeros(3)
vec1 = (numpy.array(cell.GetPoints().GetPoint(1))
-numpy.array(cell.GetPoints().GetPoint(0)))
if cell.GetCellType() == vtk.VTK_TRIANGLE:
vec2 = (numpy.array(cell.GetPoints().GetPoint(2))
-numpy.array(cell.GetPoints().GetPoint(0)))
else:
vec2 = numpy.array(((pos-pa)[1]*vec1[2]-(pos-pa)[2]*vec1[1],
(pos-pa)[2]*vec1[0]-(pos-pa)[0]*vec1[2],
(pos-pa)[0]*vec1[1]-(pos-pa)[1]*vec1[0]))
normal[0] = vec1[1]*vec2[2]-vec1[2]*vec2[1]
normal[1] = vec1[2]*vec2[0]-vec1[0]*vec2[2]
normal[2] = vec1[0]*vec2[1]-vec1[1]*vec2[0]
if sum(normal**2) > 1.0e-32:
normal = normal / numpy.sqrt(sum(normal**2))
else:
print normal
print vec1, vec2
raise Collision.CollisionException
normal = normal * numpy.sign(numpy.dot(normal, (pos-pa)))
coeff = self.system.coefficient_of_restitution(self, cell)
pos = x + delta_t * (k - (1.0 + coeff) * normal * (numpy.dot(normal, k)))
theta = abs(numpy.arcsin(numpy.dot(normal, (x-pa))
/ numpy.sqrt(numpy.dot(x - pa, x - pa))))
coldat = []
if any(vel):
vels = vel + s * delta_t * force
else:
vels = self.vel + s * delta_t * force
par_col = copy.copy(self)
if self.system.boundary.dist:
par_col.pos = IO.get_real_x(cell, ARGV)
else:
par_col.pos = x
par_col.vel = vels
par_col.time = self.time + s * delta_t
coldat.append(Collision.CollisionInfo(par_col, cell_index,
theta, normal))
vels += -(1.0 + coeff)* normal * numpy.dot(normal, vels)
px, col, velo, dummy_vel = self.collide(vels, (1 - s) * delta_t,
vel=vels, force=force,
pa=x + 1.0e-9 * vels,
level=level + 1)
pos = px + x + 1.0e-9 * vels
if col:
coldat += col
return pos - pa, coldat, velo, vels
return pos - pa, None, vel + delta_t * force - self.vel, None
maxloop = 1000
dist = 20.0/maxloop
tolerance = 0.001
# Make a list of points. Each point is the intersection of a vertical line
# defined by p1 and p2 and the surface.
points = vtk.vtkPoints()
for i in range(maxloop):
p1 = [2+i*dist, 16, -1]
p2 = [2+i*dist, 16, 6]
# Outputs (we need only pos which is the x, y, z position
# of the intersection)
t = vtk.mutable(0)
pos = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
locator.IntersectWithLine(p1, p2, tolerance, t, pos, pcoords, subId)
# Add a slight offset in z
pos[2] += 0.01
# Add the x, y, z position of the intersection
points.InsertNextPoint(pos)
# Create a spline and add the points
spline = vtk.vtkParametricSpline()
spline.SetPoints(points)
functionSource = vtk.vtkParametricFunctionSource()
functionSource.SetUResolution(maxloop)
# Create a square in the x-y plane.
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 1.0, 0.0)
points.InsertNextPoint(0.0, 1.0, 0.0)
# Create the polygon
polygon = vtk.vtkPolygon()
polygon.GetPoints().DeepCopy(points)
polygon.GetPointIds().SetNumberOfIds(4) # The 4 corners of the square
for i in range(4):
polygon.GetPointIds().SetId(i, i)
# Inputs
p1 = [0.1, 0, -1.0]
p2 = [0.1, 0, 1.0]
tolerance = 0.001;
# Outputs
t = vtk.mutable(0) # Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
iD = polygon.IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId);
print "intersected? ", iD
print "intersection: ", x
from particle_model import IO
from particle_model import DragModels
from particle_model import Collision
from particle_model import System
from particle_model import Options
from particle_model import ParticleBase
from particle_model import Parallel
import numpy
import vtk
import scipy.linalg as la
import itertools
import copy
ARGV = [0.0, 0.0, 0.0]
ARGI = vtk.mutable(0)
ARGR = vtk.mutable(0.0)
def invert(mat):
""" Hard coded 2D matrix inverse."""
if mat.shape == (2, 2):
return (numpy.array(((mat[1, 1], -mat[0, 1]),
(-mat[1, 0], mat[0, 0])))
/(mat[0, 0]*mat[1, 1]-mat[0, 1]*mat[1, 0]))
else:
return la.inv(mat)
class Particle(ParticleBase.ParticleBase):
"""Class representing a single Lagrangian particle with mass"""
def __init__(self, data,
def smoothMultipleSegments(self):
import vtkSegmentationCorePython as vtkSegmentationCore
# Generate merged labelmap of all visible segments
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
visibleSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(visibleSegmentIds)
if visibleSegmentIds.GetNumberOfValues() == 0:
logging.info("Smoothing operation skipped: there are no visible segments")
return
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
if not segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS_PADDED,
None, visibleSegmentIds):
logging.error('Failed to apply smoothing: cannot get list of visible segments')
return
segmentColorIndices = [] # list of [segmentId, colorIndex]
for i in range(visibleSegmentIds.GetNumberOfValues()):
segmentId = visibleSegmentIds.GetValue(i)
segment = segmentationNode.GetSegmentation().GetSegment(segmentId)
colorIndexStr = vtk.mutable("")
if not segment.GetTag(slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(), colorIndexStr):
logging.error("Joint smoothing: failed to get color index for segment " + segmentId)
segmentColorIndices.append([segmentId, int(colorIndexStr)])
# Perform smoothing in voxel space
ici = vtk.vtkImageChangeInformation()
ici.SetInputData(mergedImage)
ici.SetOutputSpacing(1, 1, 1)
ici.SetOutputOrigin(0, 0, 0)
# Convert labelmap to combined polydata
convertToPolyData = vtk.vtkDiscreteMarchingCubes()
convertToPolyData.SetInputConnection(ici.GetOutputPort())
convertToPolyData.SetNumberOfContours(len(segmentColorIndices))
contourIndex = 0
for segmentId, colorIndex in segmentColorIndices:
convertToPolyData.SetValue(contourIndex, colorIndex)
contourIndex += 1
# Low-pass filtering using Taubin's method
smoothingFactor = self.scriptedEffect.doubleParameter("JointTaubinSmoothingFactor")
smoothingIterations = 100 # according to VTK documentation 10-20 iterations could be enough but we use a higher value to reduce chance of shrinking
passBand = pow(10.0, -4.0*smoothingFactor) # gives a nice range of 1-0.0001 from a user input of 0-1
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputConnection(convertToPolyData.GetOutputPort())
smoother.SetNumberOfIterations(smoothingIterations)
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(90.0)
smoother.SetPassBand(passBand)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
# Extract a label
threshold = vtk.vtkThreshold()
threshold.SetInputConnection(smoother.GetOutputPort())
# Convert to polydata
geometryFilter = vtk.vtkGeometryFilter()
geometryFilter.SetInputConnection(threshold.GetOutputPort())
# Convert polydata to stencil
polyDataToImageStencil = vtk.vtkPolyDataToImageStencil()
polyDataToImageStencil.SetInputConnection(geometryFilter.GetOutputPort())
polyDataToImageStencil.SetOutputSpacing(1,1,1)
polyDataToImageStencil.SetOutputOrigin(0,0,0)
polyDataToImageStencil.SetOutputWholeExtent(mergedImage.GetExtent())
# Convert stencil to image
stencil = vtk.vtkImageStencil()
emptyBinaryLabelMap = vtk.vtkImageData()
emptyBinaryLabelMap.SetExtent(mergedImage.GetExtent())
emptyBinaryLabelMap.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
vtkSegmentationCore.vtkOrientedImageDataResample.FillImage(emptyBinaryLabelMap, 0)
stencil.SetInputData(emptyBinaryLabelMap)
stencil.SetStencilConnection(polyDataToImageStencil.GetOutputPort())
stencil.ReverseStencilOn()
stencil.SetBackgroundValue(1) # General foreground value is 1 (background value because of reverse stencil)
imageToWorldMatrix = vtk.vtkMatrix4x4()
mergedImage.GetImageToWorldMatrix(imageToWorldMatrix)
for segmentId, colorIndex in segmentColorIndices:
threshold.ThresholdBetween(colorIndex, colorIndex)
stencil.Update()
smoothedBinaryLabelMap = vtkSegmentationCore.vtkOrientedImageData()
smoothedBinaryLabelMap.ShallowCopy(stencil.GetOutput())
smoothedBinaryLabelMap.SetImageToWorldMatrix(imageToWorldMatrix)
# Write results to segments directly, bypassing masking
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(smoothedBinaryLabelMap,
segmentationNode, segmentId, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, smoothedBinaryLabelMap.GetExtent())
def register(self, fixedData, movingData, index = -1, discard = False, delta = 0, fov = 9999999.0,
down_fix = 1, down_mov = 1, occ = 9999999.0, op = False, useMask = False, isTime = False, MaxRate = 0.2,
aug = False, distance_fix = 0.3, distance_mov = 0.1, w_wrong = 1.5, truth_mov = None):
time1 = time.time()
if index == -1:
index = self.gui.getDataIndex({'Contour': 0, 'Centerline': 1}, 'Select the object')
if index is None:
return None, None, None
if index == 0:
fixed_points = fixedData.getPointSet('Contour').copy()
moving_points = movingData.getPointSet('Contour').copy()
else:
fixed_points = fixedData.getPointSet('Centerline').copy()
moving_points = movingData.getPointSet('Centerline').copy()
if truth_mov is None:
truth_mov = moving_points.copy()
fixed_bif = db.getBifurcation(fixed_points)
moving_bif = db.getBifurcation(moving_points)
if useMask:
mask_points = movingData.getPointSet('Mask')
for point in mask_points:
moving_points = npy.delete(moving_points, npy.where((npy.abs(moving_points[:, 2] - point[2]) < 0.0001) & (npy.round(moving_points[:, -1]) == point[3])), axis = 0)
fixed_res = fixedData.getResolution().tolist()
moving_res = movingData.getResolution().tolist()
fixed_points = fixed_points[npy.where(fixed_points[:, 0] >= 0)]
moving_points = moving_points[npy.where(moving_points[:, 0] >= 0)]
# Use the bifurcation as the initial position
if (fixed_bif < 0) or (moving_bif < 0):
fixed_min = 0
# Augmentation of pointset
fixed = fixed_points.copy()
moving = moving_points.copy()
if index == 1 and aug:
fixed = util.augmentCenterline(fixed, 1, 10)
moving = util.augmentCenterline(moving, 1, 10)
fix_dis = util.getAxisSin(fixed, 3 / fixed_res[2]) * distance_fix
mov_dis = util.getAxisSin(moving, 3 / moving_res[2]) * distance_mov
fixed = util.resampleCenterline(fixed, fix_dis / fixed_res[2])
moving = util.resampleCenterline(moving, mov_dis / moving_res[2])
fixed = fixed[npy.cast[npy.int32](npy.abs(fixed[:, 2] - fixed_bif)) % down_fix == 0]
moving = moving[npy.cast[npy.int32](npy.abs(moving[:, 2] - moving_bif)) % down_mov == 0]
fixed[:, :3] *= fixed_res[:3]
moving[:, :3] *= moving_res[:3]
new_trans_points = truth_mov
result_center_points = movingData.getPointSet('Centerline').copy()
new_trans_points = new_trans_points[new_trans_points[:, 3] >= 0]
result_center_points = result_center_points[result_center_points[:, 3] >= 0]
new_trans_points[:, :3] *= moving_res[:3]
result_center_points[:, :3] *= moving_res[:3]
if (fixed_bif >= 0) and (moving_bif >= 0):
fixed[:, 2] -= (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
# Prepare for ICP
MaxIterNum = 50
#MaxNum = 600
MaxNum = int(MaxRate * moving.shape[0] + 0.5)
targetPoints = [vtk.vtkPoints(), vtk.vtkPoints(), vtk.vtkPoints()]
targetVertices = [vtk.vtkCellArray(), vtk.vtkCellArray(), vtk.vtkCellArray()]
target = [vtk.vtkPolyData(), vtk.vtkPolyData(), vtk.vtkPolyData()]
Locator = [vtk.vtkCellLocator(), vtk.vtkCellLocator(), vtk.vtkCellLocator()]
for i in range(3):
for x in fixed[npy.round(fixed[:, 3]) == i]:
id = targetPoints[i].InsertNextPoint(x[0], x[1], x[2])
targetVertices[i].InsertNextCell(1)
targetVertices[i].InsertCellPoint(id)
target[i].SetPoints(targetPoints[i])
target[i].SetVerts(targetVertices[i])
Locator[i].SetDataSet(target[i])
Locator[i].SetNumberOfCellsPerBucket(1)
Locator[i].BuildLocator()
step = 1
if moving.shape[0] > MaxNum:
ind = moving[:, 2].argsort()
moving = moving[ind, :]
step = moving.shape[0] / MaxNum
nb_points = moving.shape[0] / step
points1 = vtk.vtkPoints()
points1.SetNumberOfPoints(nb_points)
label = npy.zeros([MaxNum * 2], dtype = npy.int8)
j = 0
for i in range(nb_points):
points1.SetPoint(i, moving[j][0], moving[j][1], moving[j][2])
label[i] = moving[j][3]
j += step
closestp = vtk.vtkPoints()
closestp.SetNumberOfPoints(nb_points)
points2 = vtk.vtkPoints()
points2.SetNumberOfPoints(nb_points)
id1 = id2 = vtk.mutable(0)
dist = vtk.mutable(0.0)
outPoint = [0.0, 0.0, 0.0]
p1 = [0.0, 0.0, 0.0]
p2 = [0.0, 0.0, 0.0]
iternum = 0
a = points1
b = points2
if (op and index == 0) or (not op and index == 1):
w_mat = [[1, w_wrong, w_wrong], [w_wrong, 1, 99999999], [w_wrong, 99999999, 1]]
else:
w_mat = [[1, 1, 1], [1, 1, 1], [1, 1, 1]]
accumulate = vtk.vtkTransform()
accumulate.PostMultiply()
LandmarkTransform = vtk.vtkLandmarkTransform()
LandmarkTransform.SetModeToRigidBody()
while True:
for i in range(nb_points):
min_dist = 99999999
min_outPoint = [0.0, 0.0, 0.0]
for j in range(3):
Locator[j].FindClosestPoint(a.GetPoint(i), outPoint, id1, id2, dist)
dis = npy.sqrt(npy.sum((npy.array(outPoint) - a.GetPoint(i)) ** 2))
if dis * w_mat[label[i]][j] < min_dist:
min_dist = dis * w_mat[label[i]][j]
min_outPoint = copy.deepcopy(outPoint)
closestp.SetPoint(i, min_outPoint)
LandmarkTransform.SetSourceLandmarks(a)
LandmarkTransform.SetTargetLandmarks(closestp)
LandmarkTransform.Update()
accumulate.Concatenate(LandmarkTransform.GetMatrix())
iternum += 1
for i in range(nb_points):
a.GetPoint(i, p1)
LandmarkTransform.InternalTransformPoint(p1, p2)
b.SetPoint(i, p2)
b, a = a, b
if iternum >= MaxIterNum:
break
matrix = accumulate.GetMatrix()
T = ml.mat([matrix.GetElement(0, 3), matrix.GetElement(1, 3), matrix.GetElement(2, 3)]).T
R = ml.mat([[matrix.GetElement(0, 0), matrix.GetElement(0, 1), matrix.GetElement(0, 2)],
[matrix.GetElement(1, 0), matrix.GetElement(1, 1), matrix.GetElement(1, 2)],
[matrix.GetElement(2, 0), matrix.GetElement(2, 1), matrix.GetElement(2, 2)]]).I
result_center_points[:, :3] = util.applyTransformForPoints(result_center_points[:, :3], npy.array([1.0, 1, 1]), npy.array([1.0, 1, 1]), R, T, ml.zeros([3, 1], dtype = npy.float32))
new_trans_points[:, :3] = util.applyTransformForPoints(new_trans_points[:, :3], npy.array([1.0, 1, 1]), npy.array([1.0, 1, 1]), R, T, ml.zeros([3, 1], dtype = npy.float32))
LandmarkTransform = vtk.vtkThinPlateSplineTransform()
LandmarkTransform.SetBasisToR()
iternum = 0
# Non-rigid
while True:
for i in range(nb_points):
min_dist = 99999999
min_outPoint = [0.0, 0.0, 0.0]
for j in range(3):
Locator[j].FindClosestPoint(a.GetPoint(i), outPoint, id1, id2, dist)
dis = npy.sqrt(npy.sum((npy.array(outPoint) - a.GetPoint(i)) ** 2))
if dis * w_mat[label[i]][j] < min_dist:
min_dist = dis * w_mat[label[i]][j]
min_outPoint = copy.deepcopy(outPoint)
closestp.SetPoint(i, min_outPoint)
LandmarkTransform.SetSourceLandmarks(a)
LandmarkTransform.SetTargetLandmarks(closestp)
LandmarkTransform.Update()
'''
for i in range(result_center_points.shape[0]):
LandmarkTransform.InternalTransformPoint([result_center_points[i, 0], result_center_points[i, 1], result_center_points[i, 2]], p2)
result_center_points[i, :3] = p2
'''
for i in range(new_trans_points.shape[0]):
LandmarkTransform.InternalTransformPoint([new_trans_points[i, 0], new_trans_points[i, 1], new_trans_points[i, 2]], p2)
new_trans_points[i, :3] = p2
iternum += 1
if iternum >= 1:
break
for i in range(nb_points):
a.GetPoint(i, p1)
LandmarkTransform.InternalTransformPoint(p1, p2)
b.SetPoint(i, p2)
b, a = a, b
time2 = time.time()
if (fixed_bif >= 0) and (moving_bif >= 0):
new_trans_points[:, 2] += (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
result_center_points[:, 2] += (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
new_trans_points[:, :3] /= fixed_res[:3]
result_center_points[:, :3] /= fixed_res[:3]
resultImage = movingData.getData().copy()
sa = SurfaceErrorAnalysis(None)
dataset = db.BasicData(npy.array([[[0]]]), fixedData.getInfo(), {'Contour': new_trans_points, 'Centerline': result_center_points})
mean_dis, mean_whole, max_dis, max_whole = sa.analysis(dataset, point_data_fix = fixedData.getPointSet('Contour').copy(), useResult = True)
del dataset
print mean_dis
print mean_whole
if isTime:
return resultImage, {'Contour': new_trans_points, 'Centerline': result_center_points}, [mean_dis, mean_whole], time2 - time1
return resultImage, {'Contour': new_trans_points, 'Centerline': result_center_points}, [mean_dis, mean_whole]
def testStringMutable(self):
m = vtk.mutable("%s %s!")
m %= ("hello", "world")
self.assertEqual(m, "hello world!")
def testIntMutable(self):
m = vtk.mutable(3)
n = vtk.mutable(4)
m |= n
self.assertEqual(m, 7.0)
self.assertEqual(str(m), str(m.get()))
# Clip data to spit out unstructured tets clipper = vtk.vtkClipDataSet() clipper.SetInputConnection(mandel.GetOutputPort()) clipper.SetClipFunction(sphere) clipper.InsideOutOn() clipper.Update() output = clipper.GetOutput() numCells = output.GetNumberOfCells() bounds = output.GetBounds() #print bounds # Support subsequent method calls genCell = vtk.vtkGenericCell() t = vtk.mutable(0.0) x = [0,0,0] pc = [0,0,0] subId = vtk.mutable(0) cellId = vtk.mutable(0) # Build the locator locator = vtk.vtkStaticCellLocator() #locator = vtk.vtkCellLocator() locator.SetDataSet(output) locator.AutomaticOn() locator.SetNumberOfCellsPerNode(20) locator.CacheCellBoundsOn() locator.BuildLocator() # Now visualize the locator
def analysis(self, data, point_data_fix = None, point_data_mov = None, point_data_mask = None, spacing_mov = None, useResult = False):
if point_data_fix is None:
point_data_fix = self.gui.dataModel[data.getFixedIndex()].getPointSet('Contour').copy()
point_data_mov = self.gui.dataModel[data.getMovingIndex()].getPointSet('Contour').copy()
point_data_mask = self.gui.dataModel[data.getMovingIndex()].getPointSet('Mask').copy()
spacing_mov = self.gui.dataModel[data.getMovingIndex()].getResolution().tolist()
self.spacing = data.getResolution().tolist()
point_data_fix = point_data_fix[point_data_fix[:, 0] >= 0]
bif = db.getBifurcation(point_data_fix)
point_data_fix = util.augmentPointset(point_data_fix, 3, -1, bif, nn = 20)
point_data_fix[:, :3] *= self.spacing[:3]
if point_data_mov is not None:
point_data_mov = point_data_mov[point_data_mov[:, 0] >= 0]
if not useResult:
para = npy.array(data.info.getData('transform')).flatten()
point_data_result = point_data_mov.copy()
for point in point_data_mask:
point_data_result = npy.delete(point_data_result, npy.where((npy.abs(point_data_result[:, 2] - point[2]) < 0.0001) & (npy.round(point_data_result[:, -1]) == point[3])), axis = 0)
point_data_result[:, :3] *= spacing_mov[:3]
R = ml.mat(para[:9]).reshape(3, 3)
T = ml.mat(para[9:12]).T
if para.shape[0] > 12:
C = ml.mat(para[12:]).T
else:
C = ml.zeros([3, 1], dtype = npy.float32)
T = R.I * T
T = -T
point_data_result[:, :3] = util.applyTransformForPoints(point_data_result[:, :3], npy.array([1.0, 1, 1]), npy.array([1.0, 1, 1]), R, T, C)
else:
point_data_result = data.getPointSet('Contour').copy()
point_data_result = point_data_result[point_data_result[:, -1] >= 0]
point_data_result[:, :3] *= self.spacing[:3]
targetPoints = [vtk.vtkPoints(), vtk.vtkPoints(), vtk.vtkPoints()]
targetVertices = [vtk.vtkCellArray(), vtk.vtkCellArray(), vtk.vtkCellArray()]
target = [vtk.vtkPolyData(), vtk.vtkPolyData(), vtk.vtkPolyData()]
Locator = [vtk.vtkCellLocator(), vtk.vtkCellLocator(), vtk.vtkCellLocator()]
label_dis = [3, 2, 1]
for i in range(3):
for x in point_data_fix[npy.round(point_data_fix[:, 3]) != label_dis[i]]:
id = targetPoints[i].InsertNextPoint(x[0], x[1], x[2])
targetVertices[i].InsertNextCell(1)
targetVertices[i].InsertCellPoint(id)
target[i].SetPoints(targetPoints[i])
target[i].SetVerts(targetVertices[i])
Locator[i].SetDataSet(target[i])
Locator[i].SetNumberOfCellsPerBucket(1)
Locator[i].BuildLocator()
'''
Locator = vtk.vtkCellLocator()
targetPoints = vtk.vtkPoints()
targetVertices = vtk.vtkCellArray()
target = vtk.vtkPolyData()
for x in point_data_fix:
id = targetPoints.InsertNextPoint(x[0], x[1], x[2])
targetVertices.InsertNextCell(1)
targetVertices.InsertCellPoint(id)
target.SetPoints(targetPoints)
target.SetVerts(targetVertices)
Locator.SetDataSet(target)
Locator.SetNumberOfCellsPerBucket(1)
Locator.BuildLocator()
'''
id1 = id2 = vtk.mutable(0)
dist = vtk.mutable(0.0)
outPoint = [0.0, 0.0, 0.0]
cnt_num = npy.array([0, 0, 0])
mean_dis = npy.array([0.0, 0.0, 0.0])
max_dis = npy.array([0.0, 0.0, 0.0])
for pt in point_data_result:
cnt = int(pt[-1] + 0.5)
Locator[cnt].FindClosestPoint(pt[:3].tolist(), outPoint, id1, id2, dist)
dis = npy.sqrt(npy.sum((npy.array(outPoint) - pt[:3]) ** 2))
mean_dis[cnt] += dis
max_dis[cnt] = npy.max([max_dis[cnt], dis])
cnt_num[cnt] += 1
cnt_total = npy.sum(cnt_num)
mean_whole = npy.sum(mean_dis) / cnt_total
mean_dis /= cnt_num
mean_dis[mean_dis != mean_dis] = 0 # Replace the NAN in the mean distance
max_whole = npy.max(max_dis)
if self.gui is not None:
message = "Error on Vessel 0: %0.2fmm (Total %d slices)\nError on Vessel 1: %0.2fmm (Total %d slices)\nError on Vessel 2: %0.2fmm (Total %d slices)\nWhole Error: %0.2fmm (Total %d slices)\n" \
% (mean_dis[0], cnt_num[0], mean_dis[1], cnt_num[1], mean_dis[2], cnt_num[2], mean_whole, cnt_total) + \
"-----------------------------------------------------------------------------\n" + \
"Max Error on Vessel 0: %0.2fmm\nMax Error on Vessel 1: %0.2fmm\nMax Error on Vessel 2: %0.2fmm\nTotal Max Error: %0.2fmm" \
% (max_dis[0], max_dis[1], max_dis[2], npy.max(max_dis));
self.gui.showErrorMessage("Centerline Registration Error", message)
return mean_dis, mean_whole, max_dis, max_whole
def growCut(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.DeepCopy(imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(masterImageData) # Copy geometry
masterImageData = masterImageDataShort
# Generate merged labelmap as input to GrowCut
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage, vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS, masterImageData)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType( vtk.VTK_SHORT )
thresh.SetInputData( mergedImage )
thresh.SetOutput( outputLabelmap )
thresh.Update()
outputLabelmap.DeepCopy( mergedImage ) #TODO: It was thresholded just above, why deep copy now?
# Perform grow cut
import vtkITK
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
growCutFilter.SetInputData( 0, masterImageData )
growCutFilter.SetInputData( 1, mergedImage )
#TODO: This call sets an empty image for the optional "previous segmentation", and
# is apparently needed for the first segmentation too. Why?
growCutFilter.SetInputConnection( 2, thresh.GetOutputPort() )
#TODO: These are magic numbers inherited from EditorLib/GrowCut.py
objectSize = 5.
contrastNoiseRatio = 0.8
priorStrength = 0.003
segmented = 2
conversion = 1000
spacing = mergedImage.GetSpacing()
voxelVolume = reduce(lambda x,y: x*y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1./3.
oSize = int(round(pow(voxelNumber,cubeRoot)))
growCutFilter.SetObjectSize( oSize )
growCutFilter.SetContrastNoiseRatio( contrastNoiseRatio )
growCutFilter.SetPriorSegmentConfidence( priorStrength )
growCutFilter.Update()
outputLabelmap.DeepCopy( growCutFilter.GetOutput() )
# Write output segmentation results in segments
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
for index in xrange(segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Get label corresponding to segment in merged labelmap (and so GrowCut output)
colorIndexStr = vtk.mutable("")
tagFound = segment.GetTag(slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(), colorIndexStr);
if not tagFound:
logging.error('Failed to apply GrowCut result on segment ' + segmentID)
continue
colorIndex = int(colorIndexStr.get())
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.ThresholdBetween(colorIndex, colorIndex);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, segmentationNode, segmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, newSegmentLabelmap.GetExtent())
def register(self, fixedData, movingData, index = -1, discard = False, delta = 0, fov = 9999999.0,
down_fix = 1, down_mov = 1, occ = 9999999.0, op = False, useMask = False, isTime = False, MaxRate = 0.2,
aug = False, distance_fix = 0.3, distance_mov = 0.1):
time1 = time.time()
if index == -1:
index = self.gui.getDataIndex({'Contour': 0, 'Centerline': 1}, 'Select the object')
if index is None:
return None, None, None
if index == 0:
fixed_points = fixedData.getPointSet('Contour').copy()
moving_points = movingData.getPointSet('Contour').copy()
else:
fixed_points = fixedData.getPointSet('Centerline').copy()
moving_points = movingData.getPointSet('Centerline').copy()
fixed_bif = db.getBifurcation(fixed_points)
moving_bif = db.getBifurcation(moving_points)
if useMask:
mask_points = movingData.getPointSet('Mask')
for point in mask_points:
moving_points = npy.delete(moving_points, npy.where((npy.abs(moving_points[:, 2] - point[2]) < 0.0001) & (npy.round(moving_points[:, -1]) == point[3])), axis = 0)
fixed_res = fixedData.getResolution().tolist()
moving_res = movingData.getResolution().tolist()
fixed_points = fixed_points[npy.where(fixed_points[:, 0] >= 0)]
moving_points = moving_points[npy.where(moving_points[:, 0] >= 0)]
# Use the bifurcation as the initial position
if (fixed_bif < 0) or (moving_bif < 0):
fixed_min = 0
# Augmentation of pointset
fixed = fixed_points.copy()
moving = moving_points.copy()
if index == 1 and aug:
fixed = util.augmentCenterline(fixed, 1, 10)
moving = util.augmentCenterline(moving, 1, 10)
fix_dis = util.getAxisSin(fixed, 3 / fixed_res[2]) * distance_fix
mov_dis = util.getAxisSin(moving, 3 / moving_res[2]) * distance_mov
fixed = util.resampleCenterline(fixed, fix_dis / fixed_res[2])
moving = util.resampleCenterline(moving, mov_dis / moving_res[2])
fixed = fixed[npy.cast[npy.int32](npy.abs(fixed[:, 2] - fixed_bif)) % down_fix == 0]
moving = moving[npy.cast[npy.int32](npy.abs(moving[:, 2] - moving_bif)) % down_mov == 0]
fixed[:, :3] *= fixed_res[:3]
moving[:, :3] *= moving_res[:3]
if (fixed_bif >= 0) and (moving_bif >= 0):
fixed[:, 2] -= (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
# Prepare for ICP
LandmarkTransform = vtk.vtkLandmarkTransform()
LandmarkTransform.SetModeToRigidBody()
MaxIterNum = 50
#MaxNum = 600
MaxNum = int(MaxRate * moving.shape[0] + 0.5)
targetPoints = [vtk.vtkPoints(), vtk.vtkPoints(), vtk.vtkPoints()]
targetVertices = [vtk.vtkCellArray(), vtk.vtkCellArray(), vtk.vtkCellArray()]
target = [vtk.vtkPolyData(), vtk.vtkPolyData(), vtk.vtkPolyData()]
Locator = [vtk.vtkCellLocator(), vtk.vtkCellLocator(), vtk.vtkCellLocator()]
if index == 0:
if not op:
label_dis = [3, 3, 3]
else:
label_dis = [3, 2, 1]
else:
if op:
label_dis = [3, 3, 3]
else:
label_dis = [3, 2, 1]
for i in range(3):
for x in fixed[npy.round(fixed[:, 3]) != label_dis[i]]:
id = targetPoints[i].InsertNextPoint(x[0], x[1], x[2])
targetVertices[i].InsertNextCell(1)
targetVertices[i].InsertCellPoint(id)
target[i].SetPoints(targetPoints[i])
target[i].SetVerts(targetVertices[i])
Locator[i].SetDataSet(target[i])
Locator[i].SetNumberOfCellsPerBucket(1)
Locator[i].BuildLocator()
step = 1
if moving.shape[0] > MaxNum:
ind = moving[:, 2].argsort()
moving = moving[ind, :]
step = moving.shape[0] / MaxNum
nb_points = moving.shape[0] / step
accumulate = vtk.vtkTransform()
accumulate.PostMultiply()
points1 = vtk.vtkPoints()
points1.SetNumberOfPoints(nb_points)
label = npy.zeros([MaxNum * 2], dtype = npy.int8)
j = 0
for i in range(nb_points):
points1.SetPoint(i, moving[j][0], moving[j][1], moving[j][2])
label[i] = moving[j][3]
j += step
closestp = vtk.vtkPoints()
closestp.SetNumberOfPoints(nb_points)
points2 = vtk.vtkPoints()
points2.SetNumberOfPoints(nb_points)
id1 = id2 = vtk.mutable(0)
dist = vtk.mutable(0.0)
outPoint = [0.0, 0.0, 0.0]
p1 = [0.0, 0.0, 0.0]
p2 = [0.0, 0.0, 0.0]
iternum = 0
a = points1
b = points2
'''
path = sys.argv[0]
if os.path.isfile(path):
path = os.path.dirname(path)
path += '/Data/Transform'
wfile = open("%s/transform.txt" % path, 'w')
matrix = accumulate.GetMatrix()
T = ml.mat([matrix.GetElement(0, 3), matrix.GetElement(1, 3), matrix.GetElement(2, 3)]).T;
R = ml.mat([[matrix.GetElement(0, 0), matrix.GetElement(0, 1), matrix.GetElement(0, 2)],
[matrix.GetElement(1, 0), matrix.GetElement(1, 1), matrix.GetElement(1, 2)],
[matrix.GetElement(2, 0), matrix.GetElement(2, 1), matrix.GetElement(2, 2)]]).I
if (fixed_bif >= 0) and (moving_bif >= 0):
T[2] += (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
saveTransform(wfile, T, R)
'''
while True:
for i in range(nb_points):
Locator[label[i]].FindClosestPoint(a.GetPoint(i), outPoint, id1, id2, dist)
closestp.SetPoint(i, outPoint)
LandmarkTransform.SetSourceLandmarks(a)
LandmarkTransform.SetTargetLandmarks(closestp)
LandmarkTransform.Update()
accumulate.Concatenate(LandmarkTransform.GetMatrix())
iternum += 1
if iternum >= MaxIterNum:
break
dist_err = 0
for i in range(nb_points):
a.GetPoint(i, p1)
LandmarkTransform.InternalTransformPoint(p1, p2)
b.SetPoint(i, p2)
dist_err += npy.sqrt((p1[0] - p2[0]) ** 2 + (p1[1] - p2[1]) ** 2 + (p1[2] - p2[2]) ** 2)
dist_err /= nb_points
print "iter = %d: %f" % (iternum, dist_err)
'''
matrix = accumulate.GetMatrix()
T = ml.mat([matrix.GetElement(0, 3), matrix.GetElement(1, 3), matrix.GetElement(2, 3)]).T;
R = ml.mat([[matrix.GetElement(0, 0), matrix.GetElement(0, 1), matrix.GetElement(0, 2)],
[matrix.GetElement(1, 0), matrix.GetElement(1, 1), matrix.GetElement(1, 2)],
[matrix.GetElement(2, 0), matrix.GetElement(2, 1), matrix.GetElement(2, 2)]]).I;
if (fixed_bif >= 0) and (moving_bif >= 0):
T[2] += (fixed_bif * fixed_res[2] - moving_bif * moving_res[2])
saveTransform(wfile, T, R)
'''
b, a = a, b
time2 = time.time()
#wfile.close()
# Get the result transformation parameters
matrix = accumulate.GetMatrix()
T = ml.mat([matrix.GetElement(0, 3), matrix.GetElement(1, 3), matrix.GetElement(2, 3)]).T
R = ml.mat([[matrix.GetElement(0, 0), matrix.GetElement(0, 1), matrix.GetElement(0, 2)],
[matrix.GetElement(1, 0), matrix.GetElement(1, 1), matrix.GetElement(1, 2)],
[matrix.GetElement(2, 0), matrix.GetElement(2, 1), matrix.GetElement(2, 2)]]).I
#T = ml.mat([0, 0, 0]).T
#R = ml.mat([[1, 0, 0], [0, 1, 0], [0, 0, 1]]).T
if (fixed_bif >= 0) and (moving_bif >= 0):
T[2] += (fixed_bif * fixed_res[2] - moving_bif * moving_res[2] + delta)
# Resample the moving contour
moving_points = movingData.getPointSet('Contour').copy()
moving_center = movingData.getPointSet('Centerline').copy()
#new_trans_points, result_center_points = util.resliceTheResultPoints(moving_points, moving_center, 20, moving_res, fixed_res, discard, R, T)
new_trans_points, result_center_points = moving_points, moving_center
result_center_points[:, :3] = util.applyTransformForPoints(result_center_points[:, :3], moving_res, fixed_res, R, T, ml.zeros([3, 1], dtype = npy.float32))
new_trans_points[:, :3] = util.applyTransformForPoints(new_trans_points[:, :3], moving_res, fixed_res, R, T, ml.zeros([3, 1], dtype = npy.float32))
T = -T
T = R * T
transform = sitk.Transform(3, sitk.sitkAffine)
para = R.reshape(1, -1).tolist()[0] + T.T.tolist()[0]
transform.SetParameters(para)
movingImage = movingData.getSimpleITKImage()
fixedImage = fixedData.getSimpleITKImage()
resultImage = sitk.Resample(movingImage, fixedImage, transform, sitk.sitkLinear, 0, sitk.sitkFloat32)
if isTime:
return sitk.GetArrayFromImage(resultImage), {'Contour': new_trans_points, 'Centerline': result_center_points}, para + [0, 0, 0], time2 - time1
return sitk.GetArrayFromImage(resultImage), {'Contour': new_trans_points, 'Centerline': result_center_points}, para + [0, 0, 0]