def BlenderToPolyData(me, uvlayer=None): pcoords = vtk.vtkFloatArray() pcoords.SetNumberOfComponents(3) pcoords.SetNumberOfTuples(len(me.verts)) for i in range(len(me.verts)): p0 = me.verts[i].co[0] p1 = me.verts[i].co[1] p2 = me.verts[i].co[2] pcoords.SetTuple3(i, p0, p1, p2) points = vtk.vtkPoints() points.SetData(pcoords) polys = vtk.vtkCellArray() lines = vtk.vtkCellArray() for face in me.faces: if len(face.v) == 4: polys.InsertNextCell(4) polys.InsertCellPoint(face.v[0].index) polys.InsertCellPoint(face.v[1].index) polys.InsertCellPoint(face.v[2].index) polys.InsertCellPoint(face.v[3].index) elif len(face.v) == 3: polys.InsertNextCell(3) polys.InsertCellPoint(face.v[0].index) polys.InsertCellPoint(face.v[1].index) polys.InsertCellPoint(face.v[2].index) elif len(face.v) == 2: lines.InsertNextCell(2) lines.InsertCellPoint(face.v[0].index) lines.InsertCellPoint(face.v[1].index) for edge in me.edges: lines.InsertNextCell(2) lines.InsertCellPoint(edge.v1.index) lines.InsertCellPoint(edge.v2.index) pdata =vtk.vtkPolyData() pdata.SetPoints(points) pdata.SetPolys(polys) pdata.SetLines(lines) if me.faceUV: if uvlayer: uvnames = me.getUVLayerNames() if uvlayer in uvnames: me.activeUVLayer = uvlayer tcoords = vtk.vtkFloatArray() tcoords.SetNumberOfComponents(2) tcoords.SetNumberOfTuples(len(me.verts)) for face in me.faces: for i in range(len(face.verts)): uv = face.uv[i] tcoords.SetTuple2(face.v[i].index, uv[0], uv[1]) pdata.GetPointData().SetTCoords(tcoords); pdata.Update() return pdata
def generatePolyData(orientation,fillWith,factor):
"""
Generate poly-data and point-scalars
"""
poly = vtk.vtkPolyData()
pts = vtk.vtkPoints()
coords=[ (0,0,0),(1,0,0),(1,1,0),(0,1,0)]
for coord in coords:
pts.InsertNextPoint(coord[0],coord[1],coord[2])
poly.SetPoints(pts)
# Vertices at all corners
# two 1-point vertices and 1 2-point poly-vertex
vertices = [[0],[1],[2,3]]
verts = vtk.vtkCellArray()
for vertex in vertices:
InsertCell(verts,vertex,orientation)
poly.SetVerts(verts)
# Lines at all sides of the quad
# two 2-point lines and 1 3-point line
edges = [ (0,1),(1,2),(2,3,0) ]
lines = vtk.vtkCellArray()
for edge in edges:
InsertCell(lines,edge,orientation)
poly.SetLines(lines)
# Fill with one quad, two triangles or a triangle-strip
if fillWith=='quad':
quad = (0,1,2,3)
polys = vtk.vtkCellArray()
InsertCell(polys,quad,orientation)
poly.SetPolys(polys)
elif fillWith=='triangles':
triangles=[(0,1,3),(3,1,2)]
strips = vtk.vtkCellArray()
for triangle in triangles:
InsertCell(strips,triangle,orientation)
poly.SetStrips(strips)
elif fillWith=='strip':
strip=(0,1,3,2)
strips = vtk.vtkCellArray()
InsertCell(strips,strip,orientation)
poly.SetStrips(strips)
# Scalars for contouring
values = [ 0.0, 0.5, 1.5, 1.0 ]
array=vtk.vtkDoubleArray()
for v in values:
array.InsertNextValue(factor*v)
poly.GetPointData().SetScalars(array)
return poly
def draw_lines(nodes, color):
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
cnt = 0
noderange = 100
mod = 1
edges = nodes[0].getedges()
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
nodecnt = 0
while cnt < len(nodes):
node = nodes[cnt]
cnt += 1
edges = node.getedges()
for edge in edges:
x0,y0,z0 = edge[0]
x1,y1,z1 = edge[1]
points.InsertNextPoint(edge[0])
points.InsertNextPoint(edge[1])
line = vtk.vtkLine()
line.GetPointIds().SetId(0,nodecnt)
line.GetPointIds().SetId(1,nodecnt+1)
lines.InsertNextCell(line)
nodecnt += 2
colors.InsertNextTupleValue(color)
if cnt % mod == 0:
print "noderange", noderange, "cnt", cnt, "mod",mod
# Create a polydata to store everything in
linesPolyData = vtk.vtkPolyData()
# Add the points to the dataset
linesPolyData.SetPoints(points)
# Add the lines to the dataset
linesPolyData.SetLines(lines)
linesPolyData.GetCellData().SetScalars(colors)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(linesPolyData)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer.AddActor(actor)
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
nodecnt = 0
renderWindow.Render()
camera = renderer.GetActiveCamera()
camera.Azimuth(0.1)
print "done!"
def BlenderToPolyData(me): pcoords = vtk.vtkFloatArray() pcoords.SetNumberOfComponents(3) pcoords.SetNumberOfTuples(len(me.verts)) for i in range(len(me.verts)): p0 = me.verts[i][0] p1 = me.verts[i][1] p2 = me.verts[i][2] pcoords.SetTuple3(i, p0, p1, p2) points = vtk.vtkPoints() points.SetData(pcoords) polys = vtk.vtkCellArray() lines = vtk.vtkCellArray() for face in me.faces: if len(face.v) == 4: polys.InsertNextCell(4) polys.InsertCellPoint(face.v[0].index) polys.InsertCellPoint(face.v[1].index) polys.InsertCellPoint(face.v[2].index) polys.InsertCellPoint(face.v[3].index) elif len(face.v) == 3: polys.InsertNextCell(3) polys.InsertCellPoint(face.v[0].index) polys.InsertCellPoint(face.v[1].index) polys.InsertCellPoint(face.v[2].index) elif len(face.v) == 2: lines.InsertNextCell(2) lines.InsertCellPoint(face.v[0].index) lines.InsertCellPoint(face.v[1].index) pdata =vtk.vtkPolyData() pdata.SetPoints(points) pdata.SetPolys(polys) pdata.SetLines(lines) #------------------------------------------------------------------ # CODIGO INTRODUCIDO PARA PERMITIR LA INCLUSION DE LA # # INFORMACION DE LA TEXTURA EN EL POLYDATA GENERADO # if me.hasFaceUV(): pdata.GetPointData().SetTCoords(calc_coords(me)) # Se insertan las coordenadas en el polydata #------------------------------------------------------------------ pdata.Update() return pdata
def add_lines(self, points, lines, colors=(255, 0, 0)):
line_collection = vtk.vtkCellArray()
line_collection.Allocate(len(lines))
for line in lines:
line_collection.InsertNextCell(len(line), line)
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(self._convert_points_array(points))
poly_data.SetLines(line_collection)
actor = self._actor_from_poly_data(poly_data)
colors = np.asarray(colors)
if colors.size == 3: # only one color given
colors = colors.ravel()
actor.GetProperty().SetColor(colors[0], colors[1], colors[2])
elif colors.shape[0] == len(lines): # array of line colors
colors = np.ascontiguousarray(
colors.astype(np.uint8, subok=True, copy=False))
colors_array = numpy_to_vtk(colors)
colors_array.SetName("Colors")
# to avoid the colors array going out of scope
setattr(colors_array, '_np_color_array', colors)
poly_data.GetCellData().SetScalars(colors_array)
else: # array of vertex colors
self._add_color_to_actor(actor, colors)
return self._add_mesh_actor(actor)
def createPolyData(faces, vtList, verts, tcoords):
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
points.SetNumberOfPoints(len(vtList))
tcoordArray = vtk.vtkDoubleArray()
tcoordArray.SetName('tcoords')
tcoordArray.SetNumberOfComponents(2)
tcoordArray.SetNumberOfTuples(len(vtList))
for i, vt in enumerate(vtList):
vi, ti = vt
xyz = verts[vi]
uv = tcoords[ti]
points.SetPoint(i, xyz)
tcoordArray.SetTuple2(i, uv[0], uv[1])
cells = vtk.vtkCellArray()
for i, face in enumerate(faces):
tri = vtk.vtkTriangle()
tri.GetPointIds().SetId(0, face[0])
tri.GetPointIds().SetId(1, face[1])
tri.GetPointIds().SetId(2, face[2])
cells.InsertNextCell(tri)
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
polyData.SetPolys(cells)
polyData.GetPointData().SetTCoords(tcoordArray)
return polyData
def vertices(indices):
"""
Maps a numpy ndarray of shape (n,) to an vtkCellArray of vertex indices
Args:
indices (numpy.ndarray<int>): A numpy.ndarray of shape (n,) of indices that defines the n vertices
Returns:
vtk_vertices (vtk.vtkCellArray): VTK representation of the vertices
"""
if not isinstance(indices, numpy.ndarray):
raise Numpy2VtkFormatException(
'vertices needs numpy array as input'
)
if len(indices.shape) != 1:
raise Numpy2VtkFormatException(
'vertices needs a one dimensional array as input, was {}-dimensional'.format(len(indices.shape))
)
if indices.dtype != numpy.int:
raise Numpy2VtkFormatException(
'vertices need to be numpy array of type numpy.int'
)
vtk_vertices = vtk.vtkCellArray()
for v in indices:
vtk_vertices.InsertNextCell(1)
vtk_vertices.InsertCellPoint(v)
return vtk_vertices
def make_cylinderActor (r, x0, x1, rgb, opacity):
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
lines.InsertNextCell(2)
# point 0
points.InsertNextPoint(x0[0], x0[1], x0[2])
lines.InsertCellPoint(0)
# point 1
points.InsertNextPoint(x1[0], x1[1], x1[2])
lines.InsertCellPoint(1)
cData = vtk.vtkPolyData()
cData.SetPoints(points)
cData.SetLines(lines)
c = vtk.vtkTubeFilter()
c.SetNumberOfSides(8)
c.SetInput(cData)
c.SetRadius(r)
cMapper = vtk.vtkPolyDataMapper()
cMapper.SetInput(c.GetOutput())
cActor = vtk.vtkActor()
cActor.SetMapper(cMapper)
cActor.GetProperty().SetColor(rgb[0], rgb[1], rgb[2])
cActor.GetProperty().SetOpacity(opacity)
return cActor
def copyFirstNLines(self, sourcePolyData, lineCount):
"""make a polydata with only the first N polylines"""
polyData = vtk.vtkPolyData()
points = vtk.vtkPoints()
polyData.SetPoints(points)
lines = vtk.vtkCellArray()
polyData.SetLines(lines)
sourcePoints = sourcePolyData.GetPoints()
sourceLines = sourcePolyData.GetLines()
sourceIdList = vtk.vtkIdList()
sourceLines.InitTraversal()
while sourceLines.GetNextCell(sourceIdList):
pointCount = sourceIdList.GetNumberOfIds()
idList = vtk.vtkIdList()
for idIndex in range(pointCount):
sourceId = sourceIdList.GetId(idIndex)
point = sourcePoints.GetPoint(sourceId)
id = points.InsertNextPoint(point)
idList.InsertNextId(id)
lines.InsertNextCell(idList)
if lines.GetNumberOfCells() > lineCount:
break
return polyData
def _update_vtk_objects(self):
"""When n is changed the thus the number of coordinates this function is needed
to update the vtk objects with the new number of points."""
# self._vtk_points.SetNumberOfPoints(len(self._points))
# for i, c in enumerate(self._points):
# self._vtk_points.InsertPoint(i, c[0], c[1], c[2])
self._vtk_points = _vtk.vtkPoints()
for coordinates in self._points:
self._vtk_points.InsertNextPoint(coordinates[0], coordinates[1], coordinates[2])
self._vtk_polygons = _vtk.vtkCellArray()
for polygon in self._polygons:
vtk_polygon = _vtk.vtkPolygon()
vtk_polygon.GetPointIds().SetNumberOfIds(3)
for local_index, global_index in enumerate(polygon):
vtk_polygon.GetPointIds().SetId(local_index, global_index)
self._vtk_polygons.InsertNextCell(vtk_polygon)
self._vtk_poly_data.SetPoints(self._vtk_points)
self._vtk_poly_data.SetPolys(self._vtk_polygons)
self._vtk_scalars = _vtk.vtkFloatArray()
self._vtk_scalars.SetNumberOfValues(self._vtk_poly_data.GetPoints().GetNumberOfPoints())
for i in range(self._vtk_scalars.GetNumberOfTuples()):
self._vtk_scalars.SetValue(i, 0.)
self._vtk_poly_data.GetPointData().SetScalars(self._vtk_scalars)
self._vtk_poly_data.Modified()
def createCurtain( self, **args ):
trajectory_points = self.getTrajectoryPoints( **args )
extent = self.input().GetExtent()
spacing = self.input().GetSpacing()
nStrips = extent[5] - extent[4]
zmax = spacing[2] * nStrips
z_inc = zmax / nStrips
polydata = vtk.vtkPolyData()
stripArray = vtk.vtkCellArray()
stripData = [ vtk.vtkIdList() for ix in range(nStrips) ]
points = vtk.vtkPoints()
for iPt in range( trajectory_points.GetNumberOfPoints() ):
pt_coords = trajectory_points.GetPoint( iPt )
z = 0.0
for iLevel in range( nStrips ):
vtkId = points.InsertNextPoint( pt_coords[0], pt_coords[1], z )
sd = stripData[ iLevel ]
sd.InsertNextId( vtkId )
sd.InsertNextId( vtkId+1 )
z = z + z_inc
points.InsertNextPoint( pt_coords[0], pt_coords[1], z )
for strip in stripData:
stripArray.InsertNextCell(strip)
polydata.SetPoints( points )
polydata.SetStrips( stripArray )
return polydata
def draw_lines(nodes, color):
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
nodecnt = 0
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
for node in nodes:
edges = node.getedges()
for edge in edges:
x0,y0,z0 = edge[0]
x1,y1,z1 = edge[1]
points.InsertNextPoint(edge[0])
points.InsertNextPoint(edge[1])
line = vtk.vtkLine()
line.GetPointIds().SetId(0,nodecnt)
line.GetPointIds().SetId(1,nodecnt+1)
lines.InsertNextCell(line)
nodecnt += 2
colors.InsertNextTupleValue(color)
# Create a polydata to store everything in
linesPolyData = vtk.vtkPolyData()
# Add the points to the dataset
linesPolyData.SetPoints(points)
# Add the lines to the dataset
linesPolyData.SetLines(lines)
linesPolyData.GetCellData().SetScalars(colors)
return linesPolyData
def latitude_create(
arg_lat,
arg_projection):
if arg_projection == 'linear' :
n_polypoints=2
polygonpoints=vtk.vtkPoints()
polygonpoints.SetNumberOfPoints(n_polypoints)
polygonpoints.InsertPoint(0,-180,arg_lat,0)
polygonpoints.InsertPoint(1,540,arg_lat,0)
else:
n_polypoints=360
polygonpoints=vtk.vtkPoints()
polygonpoints.SetNumberOfPoints(n_polypoints)
deg2rad=numpy.pi/180.
for n in range(n_polypoints) :
theta=2*numpy.pi*n/(n_polypoints-1)
x=numpy.cos(arg_lat*deg2rad)*numpy.cos(theta)
y=numpy.cos(arg_lat*deg2rad)*numpy.sin(theta)
z=numpy.sin(arg_lat*deg2rad)
polygonpoints.InsertPoint(n,x,y,z)
polygonlines=vtk.vtkCellArray()
polygonlines.InsertNextCell(n_polypoints)
for n in range(n_polypoints) :
polygonlines.InsertCellPoint(n)
latpolydata=vtk.vtkPolyData()
latpolydata.SetPoints(polygonpoints)
latpolydata.SetLines(polygonlines)
return latpolydata
def setEdgesPolydata(self, vd):
self.edges = []
self.edges = vd.getEdgesGenerators()
self.epts = vtk.vtkPoints()
nid = 0
lines=vtk.vtkCellArray()
for e in self.edges:
p1 = self.scale*e[0]
p2 = self.scale*e[1]
self.epts.InsertNextPoint( p1.x, p1.y, p1.z)
self.epts.InsertNextPoint( p2.x, p2.y, p2.z)
line = vtk.vtkLine()
line.GetPointIds().SetId(0,nid)
line.GetPointIds().SetId(1,nid+1)
nid = nid+2
lines.InsertNextCell(line)
linePolyData = vtk.vtkPolyData()
linePolyData.SetPoints(self.epts)
linePolyData.SetLines(lines)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(linePolyData)
self.edge_actor = vtk.vtkActor()
self.edge_actor.SetMapper(mapper)
self.edge_actor.GetProperty().SetColor( camvtk.cyan )
myscreen.addActor( self.edge_actor )
myscreen.render()
def CreatePolyData( pts, faces ):
"""
Creates vtkPolyData from vertices and faces
pts numpy.array: Nx3 array of vertices
faces numpy.array: Mx3 array of faces
Return vtkPolyData
"""
(nv,mv) = pts.shape
(nf,mf) = faces.shape
cells = vtk.vtkCellArray()
for j in range(nf):
cell = vtk.vtkTriangle()
cell.GetPointIds().SetNumberOfIds(3)
cell.GetPointIds().SetId( 0, faces[j,0] )
cell.GetPointIds().SetId( 1, faces[j,1] )
cell.GetPointIds().SetId( 2, faces[j,2] )
cells.InsertNextCell( cell )
points = vtk.vtkPoints()
points.SetNumberOfPoints(nv)
for j in range(nv):
points.SetPoint( j, pts[j,0], pts[j,1], pts[j,2] )
new_mesh = vtk.vtkPolyData()
new_mesh.SetPoints( points )
new_mesh.SetPolys( cells )
new_mesh.BuildCells()
return new_mesh
def VTKPoints2PolyData( pts ):
"""
Transforms numpy point array into vtkPolyData
pts numpy.array: Nx3 array of vertices
Return vtkPolyData
"""
(nv,mv) = pts.shape
vertices = vtk.vtkCellArray()
points = vtk.vtkPoints()
points.SetNumberOfPoints(nv)
for j in range(nv):
points.SetPoint( j, pts[j,0], pts[j,1], pts[j,2] )
vertices.InsertNextCell(1)
vertices.InsertCellPoint(j)
# Create a polydata object
mesh = vtk.vtkPolyData()
# Set the points and vertices we created as the geometry and topology of the polydata
mesh.SetPoints(points)
mesh.SetVerts(vertices)
mesh.BuildCells()
return mesh
def __init__(self, pointlist=[]):
points = vtk.vtkPoints()
cellArr = vtk.vtkCellArray()
Colors = vtk.vtkUnsignedCharArray()
Colors.SetNumberOfComponents(3)
Colors.SetName("Colors")
n=0
for p in pointlist:
vert = vtk.vtkVertex()
points.InsertNextPoint(p.x, p.y, p.z)
vert.GetPointIds().SetId(0,n)
cellArr.InsertNextCell( vert )
col = clColor(p.cc())
Colors.InsertNextTuple3( float(255)*col[0], float(255)*col[1], float(255)*col[2] )
n=n+1
polydata= vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetVerts( cellArr )
polydata.GetPointData().SetScalars(Colors)
polydata.Modified()
polydata.Update()
self.src=polydata
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInput(self.src)
self.SetMapper(self.mapper)
def get_cell(self, name):
try:
return getattr(self, 'cell_'+name)
except AttributeError:
cellarray = vtk.vtkCellArray()
setattr(self, 'cell_'+name, cellarray)
return cellarray
def asVtkUnstructuredGrid(self):
'''
Return object as a vtk.vtkUnstructuredMesh instance.
.. note:: This method uses the compiled vtk module (which is a wrapper atop the c++ VTK library) -- in contrast to :obj:`UnstructuredMesh.getVTKRepresentation`, which uses the pyvtk module (python-only implementation of VTK i/o supporting only VTK File Format version 2).
'''
import vtk
# vertices
pts=vtk.vtkPoints()
for ip in range(self.getNumberOfVertices()): pts.InsertNextPoint(self.getVertex(ip).getCoordinates())
# cells
cells,cellTypes=vtk.vtkCellArray(),[]
for ic in range(self.getNumberOfCells()):
c=self.getCell(ic)
cgt=c.getGeometryType()
cellGeomTypeMap={
CellGeometryType.CGT_TRIANGLE_1: (vtk.vtkTriangle,vtk.VTK_TRIANGLE),
CellGeometryType.CGT_QUAD: (vtk.vtkQuad,vtk.VTK_QUAD),
CellGeometryType.CGT_TETRA: (vtk.vtkTetra,vtk.VTK_TETRA),
CellGeometryType.CGT_HEXAHEDRON: (vtk.vtkHexahedron,vtk.VTK_HEXAHEDRON),
CellGeometryType.CGT_TRIANGLE_2: (vtk.vtkQuadraticTriangle,vtk.VTK_QUADRATIC_TRIANGLE)
}
c2klass,c2type=cellGeomTypeMap[cgt] # instantiate the VTK cell with the correct type
c2=c2klass()
verts=c.getVertices() # those should be all instances of Vertex...? Hopefully so.
for i,v in enumerate(verts): c2.GetPointIds().SetId(i,v.getNumber())
cells.InsertNextCell(c2)
cellTypes.append(c2type)
ret=vtk.vtkUnstructuredGrid()
ret.SetPoints(pts)
ret.SetCells(cellTypes,cells)
return ret
def __init__(self,center=(0,0,0) , radius=1, color=(0,1,1), resolution=50 ):
""" create circle """
lines =vtk.vtkCellArray()
id = 0
points = vtk.vtkPoints()
for n in xrange(0,resolution):
line = vtk.vtkLine()
angle1 = (float(n)/(float(resolution)))*2*math.pi
angle2 = (float(n+1)/(float(resolution)))*2*math.pi
p1 = (center[0]+radius*math.cos(angle1), center[1]+radius*math.sin(angle1), center[2])
p2 = (center[0]+radius*math.cos(angle2), center[1]+radius*math.sin(angle2), center[2])
points.InsertNextPoint(p1)
points.InsertNextPoint(p2)
line.GetPointIds().SetId(0,id)
id=id+1
line.GetPointIds().SetId(1,id)
id=id+1
lines.InsertNextCell(line)
self.pdata = vtk.vtkPolyData()
self.pdata.SetPoints(points)
self.pdata.SetLines(lines)
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInput(self.pdata)
self.SetMapper(self.mapper)
self.SetColor(color)
def skippoints(polydata,nskippoints):
"""Generate a single cell line from points in idlist."""
# derive number of nodes
numberofnodes = polydata.GetNumberOfPoints() - nskippoints
# define points and line
points = vtk.vtkPoints()
polyline = vtk.vtkPolyLine()
polyline.GetPointIds().SetNumberOfIds(numberofnodes)
# assign id and x,y,z coordinates
for i in range(nskippoints,polydata.GetNumberOfPoints()):
pointid = i - nskippoints
polyline.GetPointIds().SetId(pointid,pointid)
point = polydata.GetPoint(i)
points.InsertNextPoint(point)
# define cell
cells = vtk.vtkCellArray()
cells.InsertNextCell(polyline)
# add to polydata
polyout = vtk.vtkPolyData()
polyout.SetPoints(points)
polyout.SetLines(cells)
return polyout
def __init__(self, parent = None):
super(VTKFrame, self).__init__(parent)
self.vtkWidget = QVTKRenderWindowInteractor(self)
vl = QtGui.QVBoxLayout(self)
vl.addWidget(self.vtkWidget)
vl.setContentsMargins(0, 0, 0, 0)
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(0.1, 0.2, 0.4)
self.vtkWidget.GetRenderWindow().AddRenderer(self.ren)
self.iren = self.vtkWidget.GetRenderWindow().GetInteractor()
# Create source
# Create five points.
origin = [0.0, 0.0, 0.0]
p0 = [1.0, 0.0, 0.0]
p1 = [0.0, 1.0, 0.0]
p2 = [0.0, 1.0, 2.0]
p3 = [1.0, 2.0, 3.0]
p4 = [1.0, 2.0, 8.0]
# Create a vtkPoints object and store the points in it
points = vtk.vtkPoints()
points.InsertNextPoint(origin)
points.InsertNextPoint(p0)
points.InsertNextPoint(p1)
points.InsertNextPoint(p2)
points.InsertNextPoint(p3)
points.InsertNextPoint(p4)
# Create a cell array to store the lines in and add the lines to it
lines = vtk.vtkCellArray()
for i in range(4):
line = vtk.vtkLine()
line.GetPointIds().SetId(0,i)
line.GetPointIds().SetId(1,i+1)
lines.InsertNextCell(line)
# Create a polydata to store everything in
linesPolyData = vtk.vtkPolyData()
# Add the points to the dataset
linesPolyData.SetPoints(points)
# Add the lines to the dataset
linesPolyData.SetLines(lines)
# Setup actor and mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(linesPolyData)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
def __init__(self, dataShape, interactor):
self.dataShape = dataShape
self.planes = []
self.coordinate = [0,0,0]
self.lastChangedAxis = -1
for i in range(3):
p = vtkImplicitPlaneRepresentation()
p.SetPlaceFactor(1.0)
p.OutsideBoundsOn()
p.ScaleEnabledOff()
p.SetOrigin(0.25,0.25,0.25)
p.PlaceWidget([0.1,dataShape[0],0.1,dataShape[1],0.1,dataShape[2]])
args = [0, 0, 0]
args[i] = 1
p.SetNormal(*args)
p.GetSelectedPlaneProperty().SetColor(*args)
p.GetEdgesProperty().SetColor(*args) #bug in VTK
p.GetPlaneProperty().SetOpacity(0.001)
#do not draw outline
p.GetOutlineProperty().SetColor(0,0,0)
p.GetOutlineProperty().SetOpacity(0.0)
#do not draw normal
p.GetSelectedNormalProperty().SetOpacity(0.0)
p.GetNormalProperty().SetOpacity(0.0)
p.OutlineTranslationOff()
p.TubingOff()
self.cross = vtkPolyData()
points = vtkPoints()
polys = vtkCellArray()
points.SetNumberOfPoints(6)
for i in range(3):
polys.InsertNextCell(2)
polys.InsertCellPoint(2*i); polys.InsertCellPoint(2*i+1)
self.cross.SetPoints(points)
self.cross.SetLines(polys)
pw = vtkImplicitPlaneWidget2()
pw.SetRepresentation(p)
pw.SetInteractor(interactor)
pw.AddObserver("InteractionEvent", self.__PlanePositionCallback)
self.planes.append(pw)
tubes = vtkTubeFilter()
tubes.SetNumberOfSides(16)
tubes.SetInput(self.cross)
tubes.SetRadius(1.0)
crossMapper = vtkPolyDataMapper()
crossMapper.SetInput(self.cross)
crossActor = vtkActor()
crossActor.SetMapper(crossMapper)
crossActor.GetProperty().SetColor(0,0,0)
self.AddPart(crossActor)
#initially invoke the event!
self.InvokeEvent("CoordinatesEvent")
def ExtractSingleLine(centerlines,id):
cell = vtk.vtkGenericCell()
centerlines.GetCell(id,cell)
line = vtk.vtkPolyData()
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
cellArray.InsertNextCell(cell.GetNumberOfPoints())
radiusArray = vtk.vtkDoubleArray()
radiusArray.SetName(radiusArrayName)
radiusArray.SetNumberOfComponents(1)
radiusArray.SetNumberOfTuples(cell.GetNumberOfPoints())
radiusArray.FillComponent(0,0.0)
for i in range(cell.GetNumberOfPoints()):
point = [0.0,0.0,0.0]
point = cell.GetPoints().GetPoint(i)
points.InsertNextPoint(point)
cellArray.InsertCellPoint(i)
radius = centerlines.GetPointData().GetArray(radiusArrayName).GetTuple1(cell.GetPointId(i))
radiusArray.SetTuple1(i,radius)
line.SetPoints(points)
line.SetLines(cellArray)
line.GetPointData().AddArray(radiusArray)
return line
def makeEdgeVTKObject(mesh,model):
"""
Make and return a edge based VTK object for a simpeg mesh and model.
Input:
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param model, dictionary of numpy.array - Name('s) and array('s).
Property array must be order hstack(Ex,Ey,Ez)
Output:
:rtype: vtkUnstructuredGrid object
:return: vtkObj
"""
## Convert simpeg mesh to VTK properties
# Convert mesh nodes to vtkPoints
vtkPts = vtk.vtkPoints()
vtkPts.SetData(npsup.numpy_to_vtk(mesh.gridN,deep=1))
# Define the face "cells"
# Using VTK_QUAD cell for faces (see VTK file format)
nodeMat = mesh.r(np.arange(mesh.nN,dtype='int64'),'N','N','M')
def edgeR(mat,length):
return mat.T.reshape((length,1))
# First direction
nTEx = np.prod(mesh.nEx)
ExCellBlock = np.hstack([ 2*np.ones((nTEx,1),dtype='int64'),edgeR(nodeMat[:-1,:,:],nTEx),edgeR(nodeMat[1:,:,:],nTEx)])
# Second direction
if mesh.dim >= 2:
nTEy = np.prod(mesh.nEy)
EyCellBlock = np.hstack([ 2*np.ones((nTEy,1),dtype='int64'),edgeR(nodeMat[:,:-1,:],nTEy),edgeR(nodeMat[:,1:,:],nTEy)])
# Third direction
if mesh.dim == 3:
nTEz = np.prod(mesh.nEz)
EzCellBlock = np.hstack([ 2*np.ones((nTEz,1),dtype='int64'),edgeR(nodeMat[:,:,:-1],nTEz),edgeR(nodeMat[:,:,1:],nTEz)])
# Cells -cell array
ECellArr = vtk.vtkCellArray()
ECellArr.SetNumberOfCells(mesh.nE)
ECellArr.SetCells(mesh.nE,npsup.numpy_to_vtkIdTypeArray(np.vstack([ExCellBlock,EyCellBlock,EzCellBlock]),deep=1))
# Cell type
ECellType = npsup.numpy_to_vtk(vtk.VTK_LINE*np.ones(mesh.nE,dtype='uint8'),deep=1)
# Cell location
ECellLoc = npsup.numpy_to_vtkIdTypeArray(np.arange(0,mesh.nE*3,3,dtype='int64'),deep=1)
## Make the object
vtkObj = vtk.vtkUnstructuredGrid()
# Set the objects properties
vtkObj.SetPoints(vtkPts)
vtkObj.SetCells(ECellType,ECellLoc,ECellArr)
# Assign the model('s) to the object
for item in model.iteritems():
# Convert numpy array
vtkDoubleArr = npsup.numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
vtkObj.Update()
return vtkObj
def polygons(indices):
"""
Maps a numpy ndarray to an vtkCellArray of vtkPolygons
Args:
indices (numpy.ndarray<int>): A numpy.ndarray of shape (n,m) of indices that define n polygons with m points each
Returns:
vtk_polygons (vtk.vtkCellArray): VTK representation of the polygons
"""
if not isinstance(indices, numpy.ndarray):
raise Numpy2VtkFormatException(
'polygons needs numpy array as input'
)
if len(indices.shape) != 2:
raise Numpy2VtkFormatException(
'polygons needs a nxm ndarray as input'
)
if indices.dtype != numpy.int:
raise Numpy2VtkFormatException(
'polygons needs to be numpy array of type numpy.int'
)
number_of_polygons = indices.shape[0]
poly_shape = indices.shape[1]
vtk_polygons = vtk.vtkCellArray()
for j in range(0, number_of_polygons):
polygon = vtk.vtkPolygon()
polygon.GetPointIds().SetNumberOfIds(poly_shape)
for i in range(0, poly_shape):
polygon.GetPointIds().SetId(i, indices[j, i])
vtk_polygons.InsertNextCell(polygon)
return vtk_polygons
def SaveParentArtery(centerlines):
numberOfCells = centerlines.GetNumberOfCells()
cell0 = centerlines.GetCell(0)
numberOfArteryPoints = centerlines.GetNumberOfPoints()-cell0.GetNumberOfPoints()
artery = vtk.vtkPolyData()
arteryPoints = vtk.vtkPoints()
arteryCellArray = vtk.vtkCellArray()
radiusArray = vtk.vtkDoubleArray()
radiusArray.SetName(radiusArrayName)
radiusArray.SetNumberOfComponents(1)
radiusArray.SetNumberOfTuples(numberOfArteryPoints)
radiusArray.FillComponent(0,0.0)
count = 0
for i in range(1,numberOfCells): # cell0 is the one that goes to the aneurysm dome
cell = vtk.vtkGenericCell()
centerlines.GetCell(i,cell)
arteryCellArray.InsertNextCell(cell.GetNumberOfPoints())
for j in range(cell.GetNumberOfPoints()):
arteryPoints.InsertNextPoint(cell.GetPoints().GetPoint(j))
radiusArray.SetTuple1(count,centerlines.GetPointData().GetArray(radiusArrayName).GetTuple1(cell.GetPointId(j)))
arteryCellArray.InsertCellPoint(count)
count+=1
artery.SetPoints(arteryPoints)
artery.SetLines(arteryCellArray)
artery.GetPointData().AddArray(radiusArray)
return artery
def displayClickPoints(clickPoints): points = vtk.vtkPoints() lines = vtk.vtkCellArray() polygon = vtk.vtkPolyData() polygonMapper = vtk.vtkPolyDataMapper() polygonActor = vtk.vtkActor() points.SetNumberOfPoints(4) points.SetPoint(0, 0.0, -1.0, 0.0) points.SetPoint(1, -0.7, -0.5, 0.0) points.SetPoint(2, 0.7, 0.5, 0.0) points.SetPoint(3, 0.0, -1.0, 0.0) lines.InsertNextCell(4) lines.InsertCellPoint(0) lines.InsertCellPoint(1) lines.InsertCellPoint(2) lines.InsertCellPoint(3) polygon.SetPoints(points) polygon.SetLines(lines) polygonMapper.SetInputConnection(polygon.GetProducerPort()) polygonActor.SetMapper(polygonMapper) mpv_renderer[1].ResetCamera() mpv_renderer[1].AddActor(polygonActor) rw.Render()
def edges(indices):
"""
Maps a numpy ndarray to an vtkCellArray of vtkLines
Args:
indices (numpy.ndarray<int>): A numpy.ndarray of shape (n,2) of indices that define n edges
Returns:
vtk_lines (vtk.vtkCellArray): VTK representation of the edges
"""
if not isinstance(indices, numpy.ndarray):
raise Numpy2VtkFormatException(
'lines needs numpy array as input'
)
if len(indices.shape) != 2 or indices.shape[1] != 2:
raise Numpy2VtkFormatException(
'lines needs a nx2 ndarray as input'
)
if indices.dtype != numpy.int:
raise Numpy2VtkFormatException(
'lines needs to be numpy array of type numpy.int'
)
vtk_lines = vtk.vtkCellArray()
for e in indices:
line = vtk.vtkLine()
line.GetPointIds().SetId(0, e[0])
line.GetPointIds().SetId(1, e[1])
vtk_lines.InsertNextCell(line)
return vtk_lines
def findPointsInCell(points,
cell,
verbose=1):
ugrid_cell = vtk.vtkUnstructuredGrid()
ugrid_cell.SetPoints(cell.GetPoints())
cell = vtk.vtkHexahedron()
for k_point in xrange(8): cell.GetPointIds().SetId(k_point, k_point)
cell_array_cell = vtk.vtkCellArray()
cell_array_cell.InsertNextCell(cell)
ugrid_cell.SetCells(vtk.VTK_HEXAHEDRON, cell_array_cell)
geometry_filter = vtk.vtkGeometryFilter()
geometry_filter.SetInputData(ugrid_cell)
geometry_filter.Update()
cell_boundary = geometry_filter.GetOutput()
pdata_points = vtk.vtkPolyData()
pdata_points.SetPoints(points)
enclosed_points_filter = vtk.vtkSelectEnclosedPoints()
enclosed_points_filter.SetSurfaceData(cell_boundary)
enclosed_points_filter.SetInputData(pdata_points)
enclosed_points_filter.Update()
points_in_cell = [k_point for k_point in xrange(points.GetNumberOfPoints()) if enclosed_points_filter.GetOutput().GetPointData().GetArray('SelectedPoints').GetTuple(k_point)[0]]
return points_in_cell
def CreateOutline9076(color = (255, 99, 71), depth = 80.0, resolution=10):
"""
Create outline for the 9076 probe. The outline is contained in the XZ-plane
"""
# Avoid multiple generations
if CreateOutline9076.output is not None and CreateOutline9076.depth == depth:
print("reused outline")
return CreateOutline9076.output
nElements = 144
pitch = 0.2101
roc = 50.006
height = 5.0
azR = roc
azArcLength = pitch * (nElements - 1.0)
azSegment = azArcLength / azR
dAz = azSegment / (nElements - 1.0)
az = dAz * (np.r_[0:nElements] - 0.5*(nElements - 1.0))
az0 = az[0] - 0.5*dAz
azN = az[nElements-1] + 0.5*dAz
# Create first arc
arc0 = vtk.vtkArcSource()
arc0.SetCenter(0, 0, -azR)
arc0.SetPoint1(azR*np.sin(az0), 0, azR*np.cos(az0) - azR)
arc0.SetPoint2(azR*np.sin(azN), 0, azR*np.cos(azN) - azR)
arc0.SetResolution( resolution )
arc0.Update()
arcData0 = arc0.GetOutput()
# Create second arc
arc1 = vtk.vtkArcSource()
arc1.SetCenter(0, 0, -azR)
arc1.SetPoint1((azR+depth)*np.sin(azN), 0, (azR+depth)*np.cos(azN) - azR)
arc1.SetPoint2((azR+depth)*np.sin(az0), 0, (azR+depth)*np.cos(az0) - azR)
arc1.SetResolution( resolution )
arc1.Update()
arcData1 = arc1.GetOutput()
# Resulting poly data
linesPolyData = vtk.vtkPolyData()
lines = vtk.vtkCellArray()
points = vtk.vtkPoints()
# Iterate through points and and create new lines
arcData0.GetLines().InitTraversal()
idList = vtk.vtkIdList()
while arcData0.GetLines().GetNextCell(idList):
pointId = idList.GetId(0)
points.InsertNextPoint(arcData0.GetPoint(pointId))
for i in range(1, idList.GetNumberOfIds()):
pointId = idList.GetId(i)
points.InsertNextPoint(arcData0.GetPoint(pointId))
line = vtk.vtkLine()
line.GetPointIds().SetId(0,i-1)
line.GetPointIds().SetId(1,i) # last i value is 10=resolution
lines.InsertNextCell(line)
# i = resolution
arcData1.GetLines().InitTraversal()
idList = vtk.vtkIdList()
while arcData1.GetLines().GetNextCell(idList):
pointId = idList.GetId(0)
points.InsertNextPoint(arcData1.GetPoint(pointId))
# Line from 1st arc to second arc
line = vtk.vtkLine()
line.GetPointIds().SetId(0,i)
j = 0
line.GetPointIds().SetId(1, i+1+j)
lines.InsertNextCell(line)
for j in range(1, idList.GetNumberOfIds()):
pointId = idList.GetId(j)
points.InsertNextPoint(arcData1.GetPoint(pointId))
line = vtk.vtkLine()
line.GetPointIds().SetId(0,i+j-1+1)
line.GetPointIds().SetId(1,i+j+1)
lines.InsertNextCell(line)
# Insert one extra line joining the two arcs
line = vtk.vtkLine()
line.GetPointIds().SetId(0,i+j)
line.GetPointIds().SetId(1,0)
lines.InsertNextCell(line)
linesPolyData.SetPoints(points)
linesPolyData.SetLines(lines)
# Create polyline(s) from line segments. There will be
# two due to the the ordering
cutStrips = vtk.vtkStripper()
cutStrips.SetInputData(linesPolyData)
cutStrips.Update()
# Transform points forward such arcs have center in (0,0,0)
transform = vtk.vtkTransform()
transform.Translate(0.0, 0.0, roc)
transform.Update()
transformPolyDataFilter = vtk.vtkTransformPolyDataFilter()
transformPolyDataFilter.SetInputConnection(cutStrips.GetOutputPort())
transformPolyDataFilter.SetTransform(transform)
transformPolyDataFilter.Update()
outline = transformPolyDataFilter.GetOutput()
# Color the lines
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
for i in range(outline.GetNumberOfCells()):
colors.InsertNextTypedTuple(color)
outline.GetCellData().SetScalars(colors)
CreateOutline9076.depth = depth
CreateOutline9076.output = outline
return CreateOutline9076.output
def _read_rays(self, hplfile):
'''
ASSUMPTION - _read_header() has been called and the file handle is pointing
to the correct spot in the file.
Read the sequences of LiDAR beam data. These always start after the header on
line 18.
There are 'No. of rays in file' sections.
These have 1 initial line with:
<time> <azimuth> <elevation> <pitch> <roll>
Followed by 'Number of gates' lines of
<gate ID> <doppler> <intensity> <beta>
'''
# a first pass would be to just grab the <azimuth> <elevation> and calculate
# an x,y,z triple with
# r = gate_ID * 'Range gate length (m)'
# x = r*sin(elevation)*cos(azimuth)
# y = r*sin(elevation)*sin(azimuth)
# z = r*cos(elevation)
gate_length = self.header['Range gate length (m)']
num_gates = self.header['Number of gates']
# these are locals because they get added to self.scan
pts = vtk.vtkPoints()
vts = vtk.vtkCellArray()
dopplerScalars = vtk.vtkFloatArray()
dopplerScalars.SetName('doppler')
dopplerScalars.SetNumberOfComponents(1)
intensityScalars = vtk.vtkFloatArray()
intensityScalars.SetName('intensity')
intensityScalars.SetNumberOfComponents(1)
betaScalars = vtk.vtkFloatArray()
betaScalars.SetName('beta')
betaScalars.SetNumberOfComponents(1)
gateIDScalars = vtk.vtkIntArray()
gateIDScalars.SetName('gateID')
gateIDScalars.SetNumberOfComponents(1)
beamIDScalars = vtk.vtkIntArray()
beamIDScalars.SetName('beamID')
beamIDScalars.SetNumberOfComponents(1)
azimuthScalars = vtk.vtkFloatArray()
azimuthScalars.SetName('azimuth')
azimuthScalars.SetNumberOfComponents(1)
elevationScalars = vtk.vtkFloatArray()
elevationScalars.SetName('elevation')
elevationScalars.SetNumberOfComponents(1)
if self.pitchAndRoll:
pitchScalars = vtk.vtkFloatArray()
pitchScalars.SetName('pitch')
pitchScalars.SetNumberOfComponents(1)
rollScalars = vtk.vtkFloatArray()
rollScalars.SetName('roll')
rollScalars.SetNumberOfComponents(1)
beamID = 0
# outer while is each beam
while True:
beam = hplfile.readline().strip()
if not beam: break
# beam header line
time, azimuth, elevation, pitch, roll = [
float(x) for x in beam.split()
]
razimuth, relevation = radians(azimuth), radians(elevation)
rpitch, rroll = radians(pitch), radians(roll)
# convert elevation to inclination
inclination = pi / 2 - relevation
# gates along ray
for g in range(num_gates):
gate_ID, doppler, intensity, beta = hplfile.readline().strip(
).split()
gateIDScalars.InsertNextValue(int(gate_ID))
dopplerScalars.InsertNextValue(float(doppler))
intensityScalars.InsertNextValue(float(intensity))
betaScalars.InsertNextValue(float(beta))
beamIDScalars.InsertNextValue(beamID)
azimuthScalars.InsertNextValue(azimuth)
elevationScalars.InsertNextValue(elevation)
if self.pitchAndRoll:
pitchScalars.InsertNextValue(pitch)
rollScalars.InsertNextValue(roll)
# this behaves as:
# azimuth 0 is N and increases CW
# elevation 0 is vertically straight up and increases towards ground
# but what I want is
# elevation 0 is horizontally and increases to 90 being straight up.
# IIUC wikipedia says this is the "horizontal" or "topocentric" coordinate
# system in the family of celestial coordiantes.
r = (int(gate_ID) + 1) * gate_length
y = r * sin(inclination) * cos(razimuth)
x = r * sin(inclination) * sin(razimuth)
z = r * cos(inclination)
if self.pitchAndRoll:
# blech, hand-transforms
pitchedy = y * cos(rpitch) - z * sin(rpitch)
pitchedz = y * sin(rpitch) + z * cos(rpitch)
y = pitchedy
z = pitchedz
rolledx = x * cos(rroll) + z * sin(rroll)
rolledz = -x * sin(rroll) + z * cos(rroll)
x = rolledx
z = rolledz
pts.InsertNextPoint([x, y, z])
beamID += 1
# could apply pitch and roll here, since they are beam-wise.
# pitch is absolute pitch around East-West axis (X)
# > 0 means N tilted above S, so azimuth (-90,90) tilt up
# and azimuth(90, -90) tilt down
# roll is absolute pitch around N-S axis (Y)
# >0 means west tilted above E, so azimuth (180,0) tilt up
# and azimuth (0,180) tilt down.
# for the life of me, not sure how to do this through VTK
# VTK transforms are meant to act as pipeline filters, but
# this is in the modeling stage...
# hand distributing the matrix multiplication gives
self.scan.SetPoints(pts)
self.scan.GetPointData().AddArray(gateIDScalars)
self.scan.GetPointData().AddArray(dopplerScalars)
self.scan.GetPointData().AddArray(intensityScalars)
self.scan.GetPointData().AddArray(betaScalars)
self.scan.GetPointData().AddArray(beamIDScalars)
self.scan.GetPointData().AddArray(azimuthScalars)
self.scan.GetPointData().AddArray(elevationScalars)
if self.pitchAndRoll:
self.scan.GetPointData().AddArray(pitchScalars)
self.scan.GetPointData().AddArray(rollScalars)
# This creates separate vertex cells
print("MVM: {}".format(pts.GetNumberOfPoints()))
vts.InsertNextCell(pts.GetNumberOfPoints())
for i in range(pts.GetNumberOfPoints()):
vts.InsertCellPoint(i)
if self.geomType == 'sweep':
if self.scanType == 'RHI' or self.scanType == 'VAD':
self.scan.SetDimensions([
self.header['Number of gates'],
self.header['No. of rays in file'], 1
])
elif self.scanType == 'User1':
self.scan.SetDimensions(
[self.header['Number of gates'], beamID, 1])
else:
self.scan.SetDimensions(
[self.header['Number of gates'], beamID, 1])
if self.geomType == 'gates':
self.scan.SetVerts(vts)
elif self.geomType == 'rays':
# when I do it this way, I get one cell of multiple lines
# I'd rather have multiple cells, I think
# which means... either inserting after
self.scan.SetLines(vts)
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]
# create planes # Create the RenderWindow, Renderer # ren = vtk.vtkRenderer() renWin = vtk.vtkRenderWindow() renWin.AddRenderer(ren) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(renWin) # Custom polydata to test intersections. Loop are ordered in # reverse directions. polysData = vtk.vtkPolyData() polysPts = vtk.vtkPoints() polysPolys = vtk.vtkCellArray() polysData.SetPoints(polysPts) polysData.SetPolys(polysPolys) polysPts.SetNumberOfPoints(8) polysPts.SetPoint(0, 0.0, 0.0, 0.0) polysPts.SetPoint(1, 2.0, 0.0, 0.0) polysPts.SetPoint(2, 2.0, 2.0, 0.0) polysPts.SetPoint(3, 0.0, 2.0, 0.0) polysPts.SetPoint(4, -2.0, -2.0, 0.0) polysPts.SetPoint(5, 0.0, -2.0, 0.0) polysPts.SetPoint(6, 0.0, 0.0, 0.0) polysPts.SetPoint(7, -2.0, 0.0, 0.0) polysPolys.InsertNextCell(4) polysPolys.InsertCellPoint(0)
# Add the actors to the renderer, set the background and size ren.AddActor(ia) ren.SetBackground(0.1, 0.2, 0.4) renWin.SetSize(400, 400) renWin.Render() cam1 = ren.GetActiveCamera() ren.ResetCameraClippingRange() renWin.Render() ### Supporting data for callbacks pts = vtk.vtkPoints() pts.SetNumberOfPoints(4) lines = vtk.vtkCellArray() lines.InsertNextCell(5) lines.InsertCellPoint(0) lines.InsertCellPoint(1) lines.InsertCellPoint(2) lines.InsertCellPoint(3) lines.InsertCellPoint(0) pd = vtk.vtkPolyData() pd.SetPoints(pts) pd.SetLines(lines) bboxMapper = vtk.vtkPolyDataMapper2D() bboxMapper.SetInputData(pd) bboxActor = vtk.vtkActor2D() bboxActor.SetMapper(bboxMapper) bboxActor.GetProperty().SetColor(1, 0, 0) ren.AddViewProp(bboxActor)
def drawOffsets2(myscreen, ofs):
# draw loops
nloop = 0
lineColor = ovdvtk.lgreen
arcColor = ovdvtk.green # grass
ofs_points = []
for lop in ofs:
points = []
n = 0
N = len(lop)
first_point = []
previous = []
for p in lop:
# p[0] is the Point
# p[1] is -1 for lines, and r for arcs
if n == 0: # don't draw anything on the first iteration
previous = p[0]
# first_point = p[0]
else:
cw = p[3] # cw/ccw flag
cen = p[2] # center
r = p[1] # radius
p = p[0] # target point
if r == -1: # r=-1 means line-segment
points.extend([previous, p]) # drawLine(myscreen, previous, p, lineColor)
else: # otherwise we have an arc
points.extend(arc_pts(previous, p, r, cen, cw))
previous = p
n = n + 1
ofs_points.append(points)
# print "rendered loop ",nloop, " with ", len(lop), " points"
nloop = nloop + 1
# now draw each loop with polydata
oPoints = vtk.vtkPoints()
lineCells = vtk.vtkCellArray()
# self.colorLUT = vtk.vtkLookupTable()
print "offset2vtk.drawOffsets2(): ", len(ofs_points), " loops to render:"
idx = 0
last_idx = 0
for of in ofs_points:
epts = of
segs = []
first = 1
print " loop with ", len(epts), " points"
for p in epts:
oPoints.InsertNextPoint(p.x, p.y, 0)
if first == 0:
seg = [last_idx, idx]
segs.append(seg)
first = 0
last_idx = idx
idx = idx + 1
# create line and cells
for seg in segs:
line = vtk.vtkLine()
line.GetPointIds().SetId(0, seg[0])
line.GetPointIds().SetId(1, seg[1])
# print " indexes: ", seg[0]," to ",seg[1]
lineCells.InsertNextCell(line)
linePolyData = vtk.vtkPolyData()
linePolyData.SetPoints(oPoints)
linePolyData.SetLines(lineCells)
linePolyData.Modified()
# linePolyData.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(linePolyData)
edge_actor = vtk.vtkActor()
edge_actor.SetMapper(mapper)
edge_actor.GetProperty().SetColor(ovdvtk.lgreen)
myscreen.addActor(edge_actor)
def __init__(self):
self.points = vtk.vtkPoints()
self.vertices = vtk.vtkCellArray()
return node_num_order
node_ordered = nodeReorder(node_list)
#VTK insert points
points = vtk.vtkPoints()
print("adding nodes now.")
for node in node_list:
points.InsertNextPoint(node.X, node.Y, node.Z)
#vtk generate mesh
mesh = vtk.vtkUnstructuredGrid()
tetra = vtk.vtkTetra()
cellarray = vtk.vtkCellArray()
for tet in tet4_list:
tetra.GetPointIds().SetId(0, node_ordered[tet.node1])
tetra.GetPointIds().SetId(1, node_ordered[tet.node2])
tetra.GetPointIds().SetId(2, node_ordered[tet.node3])
tetra.GetPointIds().SetId(3, node_ordered[tet.node4])
cellarray.InsertNextCell(tetra)
mesh.SetPoints(points)
mesh.SetCells(vtk.VTK_TETRA, cellarray)
#extract surface
surface_filter = vtk.vtkDataSetSurfaceFilter()
surface_filter.SetInputData(mesh)
surface_filter.Update()
polydata = vtk.vtkPolyData()
# Outline around the entire dataset outline = vtk.vtkOutlineFilter() outline.SetInputConnection(mandel.GetOutputPort()) outlineMapper = vtk.vtkPolyDataMapper() outlineMapper.SetInputConnection(outline.GetOutputPort()) outlineActor = vtk.vtkActor() outlineActor.SetMapper(outlineMapper) # Intersect the clipped output with a ray ray = vtk.vtkPolyData() rayPts = vtk.vtkPoints() rayPts.InsertPoint(0, -7.5, -5, -5) rayPts.InsertPoint(1, 2.5, 2, 2.5) rayLine = vtk.vtkCellArray() rayLine.InsertNextCell(2) rayLine.InsertCellPoint(0) rayLine.InsertCellPoint(1) ray.SetPoints(rayPts) ray.SetLines(rayLine) rayMapper = vtk.vtkPolyDataMapper() rayMapper.SetInputData(ray) rayActor = vtk.vtkActor() rayActor.SetMapper(rayMapper) rayActor.GetProperty().SetColor(0, 1, 0) # Produce intersection point hit = locator.IntersectWithLine(rayPts.GetPoint(0), rayPts.GetPoint(1), 0.001,
for iface in faces:
print("face=", iface)
proj = projector[iface]
#project faces
for i in range(N):
for j in range(N):
ipix = coord2pix(iface, i, j)
#print("pix",(iface,i,j),ipix)
p = array(proj(x[i, j], y[i, j]))
if doNorm:
p = normalize(p)
pts.InsertPoint(ipix, p)
#cells
polys = vtk.vtkCellArray()
colors = vtk.vtkFloatArray()
for iface in faces:
for i in range(N - 1):
for j in range(N - 1):
cid = polys.InsertNextCell(4)
ip = coord2pix(iface, i, j)
polys.InsertCellPoint(ip)
ip1 = coord2pix(iface, i + 1, j)
polys.InsertCellPoint(ip1)
ip2 = coord2pix(iface, i + 1, j + 1)
polys.InsertCellPoint(ip2)
def CreateOutline9076(color=(255, 99, 71), depth=80.0):
"""
Create outline for the 9076 probe. The outline is contained in the XZ-plane
"""
# Default color for the outline is "Tomato"
nElements = 144
pitch = 0.2101
roc = 50.006
height = 5.0
azR = roc
azArcLength = pitch * (nElements - 1.0)
azSegment = azArcLength / azR
dAz = azSegment / (nElements - 1.0)
az = dAz * (np.r_[0:nElements] - 0.5 * (nElements - 1.0))
az0 = az[0] - 0.5 * dAz
azN = az[nElements - 1] + 0.5 * dAz
appendFilter = vtk.vtkAppendPolyData()
# Create first arc
arc0 = vtk.vtkArcSource()
arc0.SetCenter(0, 0, -azR)
arc0.SetPoint1(azR * np.sin(az0), 0, azR * np.cos(az0) - azR)
arc0.SetPoint2(azR * np.sin(azN), 0, azR * np.cos(azN) - azR)
arc0.SetResolution(10)
arc0.Update()
appendFilter.AddInputData(arc0.GetOutput())
appendFilter.Update()
arc1 = vtk.vtkArcSource()
arc1.SetCenter(0, 0, -azR)
arc1.SetPoint1((azR + depth) * np.sin(az0), 0,
(azR + depth) * np.cos(az0) - azR)
arc1.SetPoint2((azR + depth) * np.sin(azN), 0,
(azR + depth) * np.cos(azN) - azR)
arc1.SetResolution(10)
arc1.Update()
appendFilter.AddInputData(arc1.GetOutput())
appendFilter.Update()
# Create lines
linesPolyData = vtk.vtkPolyData()
pts = vtk.vtkPoints()
pts.InsertNextPoint((azR * np.sin(az0), 0, azR * np.cos(az0) - azR))
pts.InsertNextPoint(
((azR + depth) * np.sin(az0), 0, (azR + depth) * np.cos(az0) - azR))
pts.InsertNextPoint((azR * np.sin(azN), 0, azR * np.cos(azN) - azR))
pts.InsertNextPoint(
((azR + depth) * np.sin(azN), 0, (azR + depth) * np.cos(azN) - azR))
linesPolyData.SetPoints(pts)
line0 = vtk.vtkLine()
line0.GetPointIds().SetId(0, 0)
line0.GetPointIds().SetId(1, 1)
line1 = vtk.vtkLine()
line1.GetPointIds().SetId(0, 2)
line1.GetPointIds().SetId(1, 3)
# Create a vtkCellArray container and store the lines in it
lines = vtk.vtkCellArray()
lines.InsertNextCell(line0)
lines.InsertNextCell(line1)
linesPolyData.SetLines(lines)
appendFilter.AddInputData(linesPolyData)
appendFilter.Update()
outline = appendFilter.GetOutput()
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
for i in range(outline.GetNumberOfCells()):
colors.InsertNextTypedTuple(color)
outline.GetCellData().SetScalars(colors)
return outline
def DrawTrajectory():
nbrPoints = 1000
w0 = array([0.0, 1.0, 0.0])
time = linspace(0.0, 40.0, nbrPoints)
trajectory = integrate.odeint(Lorenz, w0, time,args=())
# Total number of points.
numberOfInputPoints = nbrPoints
# One spline for each direction.
aSplineX = vtk.vtkCardinalSpline()
aSplineY = vtk.vtkCardinalSpline()
aSplineZ = vtk.vtkCardinalSpline()
inputPoints = vtk.vtkPoints()
for i in range(0, numberOfInputPoints):
x = trajectory[i,0]
y = trajectory[i,1]
z = trajectory[i,2]
aSplineX.AddPoint(i, trajectory[i,0])
aSplineY.AddPoint(i, trajectory[i,1])
aSplineZ.AddPoint(i, trajectory[i,2])
inputPoints.InsertPoint(i, x, y, z)
# The following section will create glyphs for the pivot points
# in order to make the effect of the spline more clear.
# Create a polydata to be glyphed.
inputData = vtk.vtkPolyData()
inputData.SetPoints(inputPoints)
# Use sphere as glyph source.
balls = vtk.vtkSphereSource()
balls.SetRadius(.01)
balls.SetPhiResolution(10)
balls.SetThetaResolution(10)
glyphPoints = vtk.vtkGlyph3D()
glyphPoints.SetInputData(inputData)
glyphPoints.SetSourceConnection(balls.GetOutputPort())
glyphMapper = vtk.vtkPolyDataMapper()
glyphMapper.SetInputConnection(glyphPoints.GetOutputPort())
glyph = vtk.vtkActor()
glyph.SetMapper(glyphMapper)
glyph.GetProperty().SetDiffuseColor(tomato)
glyph.GetProperty().SetSpecular(.3)
glyph.GetProperty().SetSpecularPower(30)
# Generate the polyline for the spline.
points = vtk.vtkPoints()
profileData = vtk.vtkPolyData()
# Number of points on the spline
numberOfOutputPoints = nbrPoints*10
# Interpolate x, y and z by using the three spline filters and
# create new points
for i in range(0, numberOfOutputPoints):
t = (numberOfInputPoints-1.0)/(numberOfOutputPoints-1.0)*i
points.InsertPoint(i, aSplineX.Evaluate(t), aSplineY.Evaluate(t),
aSplineZ.Evaluate(t))
# Create the polyline.
lines = vtk.vtkCellArray()
lines.InsertNextCell(numberOfOutputPoints)
for i in range(0, numberOfOutputPoints):
lines.InsertCellPoint(i)
profileData.SetPoints(points)
profileData.SetLines(lines)
# Add thickness to the resulting line.
profileTubes = vtk.vtkTubeFilter()
profileTubes.SetNumberOfSides(8)
profileTubes.SetInputData(profileData)
profileTubes.SetRadius(.05)
profileMapper = vtk.vtkPolyDataMapper()
profileMapper.SetInputConnection(profileTubes.GetOutputPort())
profile = vtk.vtkActor()
profile.SetMapper(profileMapper)
profile.GetProperty().SetDiffuseColor(gold)
profile.GetProperty().SetSpecular(.3)
profile.GetProperty().SetSpecularPower(30)
return glyph, profile
def ReadTecplotMeshFile(self):
self.PrintLog('Reading Tecplot surface file.')
if self.InputFileName[-3:] == '.gz':
import gzip
f = gzip.open(self.InputFileName, 'r')
else:
f = open(self.InputFileName, 'r')
line = f.readline()
if line.split()[0] == 'TITLE':
line = f.readline()
if (line.split()[0] == 'VARIABLES') | (line.split('=')[0]
== 'VARIABLES'):
arrayNames = line.split('=')[1].strip().split(',')
arrayNames[0:3] = []
self.PrintLog("ArrayNames" + str(arrayNames))
line = f.readline()
if line.split()[0] == 'ZONE':
lineNid = line.find('N=')
lineN = line[lineNid:lineNid +
line[lineNid:].find(',')].split('=')[1]
numberOfNodes = int(lineN)
lineEid = line.find('E=')
lineE = line[lineEid:lineEid +
line[lineEid:].find(',')].split('=')[1]
numberOfElements = int(lineE)
self.PrintLog("Reading " + str(numberOfNodes) + " nodes.")
points = vtk.vtkPoints()
cells = vtk.vtkCellArray()
points.SetNumberOfPoints(numberOfNodes)
self.Mesh = vtk.vtkUnstructuredGrid()
self.Mesh.SetPoints(points)
for arrayName in arrayNames:
array = vtk.vtkDoubleArray()
array.SetName(arrayName)
array.SetNumberOfTuples(numberOfNodes)
self.Mesh.GetPointData().AddArray(array)
data = f.read().split()
dataCounter = 0
for i in range(numberOfNodes):
point = [
float(data[dataCounter]),
float(data[dataCounter + 1]),
float(data[dataCounter + 2])
]
dataCounter += 3
points.SetPoint(i, point)
for j in range(len(arrayNames)):
self.Mesh.GetPointData().GetArray(arrayNames[j]).SetComponent(
i, 0, float(data[dataCounter]))
dataCounter += 1
self.PrintLog("Reading " + str(numberOfElements) + " elements.")
cellIds = vtk.vtkIdList()
for i in range(numberOfElements):
cellIds.Initialize()
cellIds.InsertNextId(int(data[dataCounter]) - 1)
dataCounter += 1
cellIds.InsertNextId(int(data[dataCounter]) - 1)
dataCounter += 1
cellIds.InsertNextId(int(data[dataCounter]) - 1)
dataCounter += 1
cellIds.InsertNextId(int(data[dataCounter]) - 1)
dataCounter += 1
legal = 1
for j in range(cellIds.GetNumberOfIds()):
if cellIds.GetId(j) < 0:
legal = 0
break
if not legal:
continue
cells.InsertNextCell(cellIds)
self.Mesh.SetCells(10, cells)
self.Mesh.Update()
from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # create two boxes and interpolate between them # pts = vtk.vtkPoints() pts.InsertNextPoint(-1, -1, -1) pts.InsertNextPoint(1, -1, -1) pts.InsertNextPoint(1, 1, -1) pts.InsertNextPoint(-1, 1, -1) pts.InsertNextPoint(-1, -1, 1) pts.InsertNextPoint(1, -1, 1) pts.InsertNextPoint(1, 1, 1) pts.InsertNextPoint(-1, 1, 1) faces = vtk.vtkCellArray() faces.InsertNextCell(4) faces.InsertCellPoint(0) faces.InsertCellPoint(3) faces.InsertCellPoint(2) faces.InsertCellPoint(1) faces.InsertNextCell(4) faces.InsertCellPoint(4) faces.InsertCellPoint(5) faces.InsertCellPoint(6) faces.InsertCellPoint(7) faces.InsertNextCell(4) faces.InsertCellPoint(0) faces.InsertCellPoint(1) faces.InsertCellPoint(5) faces.InsertCellPoint(4)
for t in range( nLineTimePt ): time_pt = ( t1 - t0 ) * t / nLineTimePt + t0 v_t = manifolds.sphere_tVec( nDimManifold ) v_t.SetTangentVector( [ ( gamma0_tilde.tVector[ 0 ] + gamma1_tilde.tVector[ 0 ] * c_pt ) * time_pt, ( gamma0_tilde.tVector[ 1 ] + gamma1_tilde.tVector[ 1 ] * c_pt ) * time_pt, ( gamma0_tilde.tVector[ 2 ] + gamma1_tilde.tVector[ 2 ] * c_pt ) * time_pt ] ) p_t = p0_c.ExponentialMap( v_t ) group_geodesic_pt_list.append( p_t ) group_geodesic_vtk = vtk.vtkPolyData() group_geodesic_pts = vtk.vtkPoints() for t in range( len( group_geodesic_pt_list ) ): group_geodesic_pts.InsertNextPoint( group_geodesic_pt_list[ t ].pt[ 0 ], group_geodesic_pt_list[ t ].pt[ 1 ], group_geodesic_pt_list[ t ].pt[ 2 ] ) group_geodesic_line = vtk.vtkCellArray() for t in range( len( group_geodesic_pt_list ) - 1 ): line_i = vtk.vtkLine() line_i.GetPointIds().SetId( 0, t ) line_i.GetPointIds().SetId( 1, t + 1 ) group_geodesic_line.InsertNextCell( line_i ) group_geodesic_vtk.SetPoints( group_geodesic_pts ) group_geodesic_vtk.SetLines( group_geodesic_line ) group_vtk_list_s1.append( group_geodesic_vtk ) # Point List with Covariates pt_list = [] t_list = []
def make__uGrid(self):
# ------------------------------------------------- #
# --- [1] element IDs & offset = define cells --- #
# ------------------------------------------------- #
# -- [1-1] offset & elemIDs -- #
nVertArray = np.sum(np.ones_like(self.elems), axis=1)
offset = np.cumsum(np.insert(nVertArray, 0, 0.0))
offset = npv.numpy_to_vtkIdTypeArray(
(offset[:-1]).astype(self.ID_TYPE))
# -- [1-2] cell type -- #
if (self.elementType is not None):
cellType = np.full((self.nElem, ), self.elementType)
if (self.nVert == 4):
cellType = np.full((self.nElem, ), vtk.VTK_TETRA)
if (self.nVert == 8):
cellType = np.full((self.nElem, ), vtk.VTK_HEXAHEDRON)
cellType = cellType.astype(np.uint8)
cellType = npv.numpy_to_vtk(cellType)
# -- [1-3] cell array -- #
elemIDs = np.concatenate( [ np.reshape( nVertArray, ( self.nElem,1) ), \
self.elems ], axis=1 )
elemIDs = npv.numpy_to_vtkIdTypeArray(np.ravel(elemIDs))
cellArray = vtk.vtkCellArray()
cellArray.SetCells(self.nElem, elemIDs)
# -- elemID Data Structure -- #
# [ [ N, e1, e2, e3, ...., eN ], [ N, e1, e2, e3, ...., eN ], .... ]
# --
# ------------------------------------------------- #
# --- [2] node definition --- #
# ------------------------------------------------- #
vtkPoints = vtk.vtkPoints()
vtkPoints.SetData(npv.numpy_to_vtk(self.nodes))
# ------------------------------------------------- #
# --- [3] Define unstructured Grid --- #
# ------------------------------------------------- #
self.ugrid = vtk.vtkUnstructuredGrid()
self.ugrid.SetPoints(vtkPoints)
self.ugrid.SetCells(cellType, offset, cellArray)
# ------------------------------------------------- #
# --- [4] cellData & pointData --- #
# ------------------------------------------------- #
# -- [4-1] cellData -- #
if (self.cellData is not None):
self.cellDataDict = { key: npv.numpy_to_vtk( self.cellData[:,ik], deep=True ) \
for ik,key in enumerate( self.cellDataName ) }
for key in self.cellDataName:
self.cellDataDict[key].SetName(key)
self.ugrid.GetCellData().AddArray(self.cellDataDict[key])
# -- [4-2] pointData -- #
if (self.pointData is not None):
self.pointDataDict = { key: npv.numpy_to_vtk( self.pointData[:,ik], deep=True ) \
for ik,key in enumerate( self.pointDataName ) }
for key in self.pointDataName:
self.pointDataDict[key].SetName(key)
self.ugrid.GetPointData().AddArray(self.pointDataDict[key])
def array2vtkCellArray(num_array, vtk_array=None):
"""Given a nested Python list or a numpy array, this method
creates a vtkCellArray instance and returns it.
A variety of input arguments are supported as described in the
Parameter documentation. If numpy arrays are given, this method
is highly efficient. This function is most efficient if the
passed numpy arrays have a typecode `ID_TYPE_CODE`. Otherwise a
typecast is necessary and this involves an extra copy. This
method *always copies* the input data.
An alternative and more efficient way to build the connectivity
list is to create a vtkIdTypeArray having data of the form
(npts,p0,p1,...p(npts-1), repeated for each cell) and then call
<vtkCellArray_instance>.SetCells(n_cell, id_list).
Parameters
----------
- num_array : numpy array or Python list/tuple
Valid values are:
1. A Python list of 1D lists. Each 1D list can contain one
cell connectivity list. This is very slow and is to be
used only when efficiency is of no consequence.
2. A 2D numpy array with the cell connectivity list.
3. A Python list of 2D numpy arrays. Each numeric array can
have a different shape. This makes it easy to generate a
cell array having cells of different kinds.
- vtk_array : `vtkCellArray` (default: `None`)
If an optional `vtkCellArray` instance, is passed as an argument
then a new array is not created and returned. The passed array
is itself modified and returned.
Example
-------
>>> a = [[0], [1, 2], [3, 4, 5], [6, 7, 8, 9]]
>>> cells = array_handler.array2vtkCellArray(a)
>>> a = numpy.array([[0,1,2], [3,4,5], [6,7,8]], 'l')
>>> cells = array_handler.array2vtkCellArray(a)
>>> l_a = [a[:,:1], a[:2,:2], a]
>>> cells = array_handler.array2vtkCellArray(l_a)
"""
if vtk_array:
cells = vtk_array
else:
cells = vtk.vtkCellArray()
assert cells.GetClassName() == 'vtkCellArray', \
'Second argument must be a `vtkCellArray` instance.'
if len(num_array) == 0:
return cells
########################################
# Internal functions.
def _slow_array2cells(z, cells):
cells.Reset()
vtk_ids = vtk.vtkIdList()
for i in z:
vtk_ids.Reset()
for j in i:
vtk_ids.InsertNextId(j)
cells.InsertNextCell(vtk_ids)
def _get_tmp_array(arr):
try:
tmp_arr = numpy.asarray(arr, ID_TYPE_CODE)
except TypeError:
tmp_arr = arr.astype(ID_TYPE_CODE)
return tmp_arr
def _set_cells(cells, n_cells, id_typ_arr):
vtk_arr = vtk.vtkIdTypeArray()
array2vtk(id_typ_arr, vtk_arr)
cells.SetCells(n_cells, vtk_arr)
########################################
msg = "Invalid argument. Valid types are a Python list of lists,"\
" a Python list of numpy arrays, or a numpy array."
if issubclass(type(num_array), (types.ListType, types.TupleType)):
assert len(num_array[0]) > 0, "Input array must be 2D."
tp = type(num_array[0])
if issubclass(tp, types.ListType): # Pure Python list.
_slow_array2cells(num_array, cells)
return cells
elif issubclass(tp, numpy.ndarray): # List of arrays.
# Check shape of array and find total size.
tot_size = 0
n_cells = 0
for arr in num_array:
assert len(arr.shape) == 2, "Each array must be 2D"
shp = arr.shape
tot_size += shp[0]*(shp[1] + 1)
n_cells += shp[0]
# Create an empty array.
id_typ_arr = numpy.empty((tot_size,), ID_TYPE_CODE)
# Now populate it with the ids.
count = 0
for arr in num_array:
tmp_arr = _get_tmp_array(arr)
shp = arr.shape
sz = shp[0]*(shp[1] + 1)
set_id_type_array(tmp_arr, id_typ_arr[count:count+sz])
count += sz
# Now set them cells.
_set_cells(cells, n_cells, id_typ_arr)
return cells
else:
raise TypeError, msg
elif issubclass(type(num_array), numpy.ndarray):
assert len(num_array.shape) == 2, "Input array must be 2D."
tmp_arr = _get_tmp_array(num_array)
shp = tmp_arr.shape
id_typ_arr = numpy.empty((shp[0]*(shp[1] + 1),), ID_TYPE_CODE)
set_id_type_array(tmp_arr, id_typ_arr)
_set_cells(cells, shp[0], id_typ_arr)
return cells
else:
raise TypeError, msg
def straightenVolume(self,
outputStraightenedVolume,
curveNode,
volumeNode,
sliceSizeMm,
outputSpacingMm,
rotationAngleDeg=0.0):
"""
Compute straightened volume (useful for example for visualization of curved vessels)
"""
originalCurvePoints = curveNode.GetCurvePointsWorld()
sampledPoints = vtk.vtkPoints()
if not slicer.vtkMRMLMarkupsCurveNode.ResamplePoints(
originalCurvePoints, sampledPoints, outputSpacingMm[2], False):
return False
sliceExtent = [
int(sliceSizeMm[0] / outputSpacingMm[0]),
int(sliceSizeMm[1] / outputSpacingMm[1])
]
inputSpacing = volumeNode.GetSpacing()
lines = vtk.vtkCellArray()
lines.InsertNextCell(sampledPoints.GetNumberOfPoints())
for pointIndex in range(sampledPoints.GetNumberOfPoints()):
lines.InsertCellPoint(pointIndex)
sampledCurvePoly = vtk.vtkPolyData()
sampledCurvePoly.SetPoints(sampledPoints)
sampledCurvePoly.SetLines(lines)
# Get physical coordinates from voxel coordinates
volumeRasToIjkTransformMatrix = vtk.vtkMatrix4x4()
volumeNode.GetRASToIJKMatrix(volumeRasToIjkTransformMatrix)
transformWorldToVolumeRas = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(
None, volumeNode.GetParentTransformNode(),
transformWorldToVolumeRas)
transformWorldToIjk = vtk.vtkTransform()
transformWorldToIjk.Concatenate(transformWorldToVolumeRas)
transformWorldToIjk.Scale(inputSpacing)
transformWorldToIjk.Concatenate(volumeRasToIjkTransformMatrix)
transformPolydataWorldToIjk = vtk.vtkTransformPolyDataFilter()
transformPolydataWorldToIjk.SetInputData(sampledCurvePoly)
transformPolydataWorldToIjk.SetTransform(transformWorldToIjk)
reslicer = vtk.vtkSplineDrivenImageSlicer()
append = vtk.vtkImageAppend()
scaledImageData = vtk.vtkImageData()
scaledImageData.ShallowCopy(volumeNode.GetImageData())
scaledImageData.SetSpacing(inputSpacing)
reslicer.SetInputData(scaledImageData)
reslicer.SetPathConnection(transformPolydataWorldToIjk.GetOutputPort())
reslicer.SetSliceExtent(*sliceExtent)
reslicer.SetSliceSpacing(outputSpacingMm[0], outputSpacingMm[1])
reslicer.SetIncidence(vtk.vtkMath.RadiansFromDegrees(rotationAngleDeg))
nbPoints = sampledPoints.GetNumberOfPoints()
for ptId in reversed(range(nbPoints)):
reslicer.SetOffsetPoint(ptId)
reslicer.Update()
tempSlice = vtk.vtkImageData()
tempSlice.DeepCopy(reslicer.GetOutput(0))
append.AddInputData(tempSlice)
append.SetAppendAxis(2)
append.Update()
straightenedVolumeImageData = append.GetOutput()
straightenedVolumeImageData.SetOrigin(0, 0, 0)
straightenedVolumeImageData.SetSpacing(1.0, 1.0, 1.0)
dims = straightenedVolumeImageData.GetDimensions()
ijkToRas = vtk.vtkMatrix4x4()
ijkToRas.SetElement(0, 0, 0.0)
ijkToRas.SetElement(1, 0, 0.0)
ijkToRas.SetElement(2, 0, -outputSpacingMm[0])
ijkToRas.SetElement(0, 1, 0.0)
ijkToRas.SetElement(1, 1, outputSpacingMm[1])
ijkToRas.SetElement(2, 1, 0.0)
ijkToRas.SetElement(0, 2, outputSpacingMm[2])
ijkToRas.SetElement(1, 2, 0.0)
ijkToRas.SetElement(2, 2, 0.0)
outputStraightenedVolume.SetIJKToRASMatrix(ijkToRas)
outputStraightenedVolume.SetAndObserveImageData(
straightenedVolumeImageData)
outputStraightenedVolume.CreateDefaultDisplayNodes()
return True
# Create a selection window. We will display the point and cell ids # that lie within this window. xmin = 200 xLength = 100 xmax = xmin + xLength ymin = 200 yLength = 100 ymax = ymin + yLength pts = vtk.vtkPoints() pts.InsertPoint(0, xmin, ymin, 0) pts.InsertPoint(1, xmax, ymin, 0) pts.InsertPoint(2, xmax, ymax, 0) pts.InsertPoint(3, xmin, ymax, 0) rect = vtk.vtkCellArray() rect.InsertNextCell(5) rect.InsertCellPoint(0) rect.InsertCellPoint(1) rect.InsertCellPoint(2) rect.InsertCellPoint(3) rect.InsertCellPoint(0) selectRect = vtk.vtkPolyData() selectRect.SetPoints(pts) selectRect.SetLines(rect) rectMapper = vtk.vtkPolyDataMapper2D() rectMapper.SetInputData(selectRect) rectActor = vtk.vtkActor2D() rectActor.SetMapper(rectMapper) # Create a sphere and its associated mapper and actor.
def CreateFromArray(self, pc):
"""Create a point cloud visualization object from a given NumPy array
The NumPy array should have dimension Nxd where d >= 3
If d>3, the points will be colored according to the last column
in the supplied array (values should be between 0 and 1, where
0 is black and 1 is white)
"""
nCoords = pc.shape[0]
nElem = pc.shape[1]
if nElem < 3:
raise Exception(
"Number of elements must be greater than or equal to 3")
self.verts = vtk.vtkPoints()
self.cells = vtk.vtkCellArray()
self.scalars = None
self.pd = vtk.vtkPolyData()
# Optimized version of creating the vertices array
# - We need to be sure to keep the supplied NumPy array,
# because the numpy_support function creates a pointer into it
# - We need to take a copy to be sure the array is contigous
self.points_npy = pc[:, :3].copy()
self.verts.SetData(numpy_support.numpy_to_vtk(self.points_npy))
# Optimized version of creating the cell ID array
# - We need to be sure to keep the supplied NumPy array,
# because the numpy_support function creates a pointer into it
# - Note that the cell array looks like this: [1 vtx0 1 vtx1 1 vtx2 1 vtx3 ... ]
# because it consists of vertices with one primitive per cell
self.cells_npy = np.vstack([
np.ones(nCoords, dtype=np.int64),
np.arange(nCoords, dtype=np.int64)
]).T.flatten()
self.cells.SetCells(
nCoords, numpy_support.numpy_to_vtkIdTypeArray(self.cells_npy))
self.pd.SetPoints(self.verts)
self.pd.SetVerts(self.cells)
# Optimized version of creating the scalars array
# - We need to be sure to keep the NumPy array,
# because the numpy_support function creates a pointer into it
# - We need to take a copy to be sure the array is contigous
if nElem > 3:
self.scalars_npy = pc[:, -1].copy()
self.scalars = numpy_support.numpy_to_vtk(self.scalars_npy)
# Color the scalar data in gray values
self.LUT = vtk.vtkLookupTable()
self.LUT.SetNumberOfColors(255)
self.LUT.SetSaturationRange(0, 0)
self.LUT.SetHueRange(0, 0)
self.LUT.SetValueRange(0, 1)
self.LUT.Build()
self.scalars.SetLookupTable(self.LUT)
self.pd.GetPointData().SetScalars(self.scalars)
self.SetupPipelineCloud()
def add_faces(self, faces, color, opacity=0.35):
for face in faces:
if len(face) == 3:
points = vtk.vtkPoints()
triangle = vtk.vtkTriangle()
for ii in range(3):
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
triangle.GetPointIds().SetId(ii, ii)
triangles = vtk.vtkCellArray()
triangles.InsertNextCell(triangle)
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(points)
trianglePolyData.SetPolys(triangles)
mapper = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInputConnection(trianglePolyData.GetProducerPort())
else:
mapper.SetInputData(trianglePolyData)
# mapper.SetInput(trianglePolyData)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
elif False and len(face) == 4:
points = vtk.vtkPoints()
for ii in range(4):
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
line1 = vtk.vtkLine()
line1.GetPointIds().SetId(0, 0)
line1.GetPointIds().SetId(1, 2)
line2 = vtk.vtkLine()
line2.GetPointIds().SetId(0, 3)
line2.GetPointIds().SetId(1, 1)
lines = vtk.vtkCellArray()
lines.InsertNextCell(line1)
lines.InsertNextCell(line2)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetLines(lines)
ruledSurfaceFilter = vtk.vtkRuledSurfaceFilter()
ruledSurfaceFilter.SetInput(polydata)
ruledSurfaceFilter.SetResolution(15, 15)
ruledSurfaceFilter.SetRuledModeToResample()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(ruledSurfaceFilter.GetOutput())
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
elif len(face) > 3:
center = np.zeros(3, np.float)
for site in face:
center += site
center /= np.float(len(face))
for ii in range(len(face)):
points = vtk.vtkPoints()
triangle = vtk.vtkTriangle()
points.InsertNextPoint(face[ii][0], face[ii][1], face[ii][2])
ii2 = np.mod(ii+1, len(face))
points.InsertNextPoint(face[ii2][0], face[ii2][1], face[ii2][2])
points.InsertNextPoint(center[0], center[1], center[2])
for ii in range(3):
triangle.GetPointIds().SetId(ii, ii)
triangles = vtk.vtkCellArray()
triangles.InsertNextCell(triangle)
trianglePolyData = vtk.vtkPolyData()
trianglePolyData.SetPoints(points)
trianglePolyData.SetPolys(triangles)
mapper = vtk.vtkPolyDataMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
mapper.SetInputConnection(trianglePolyData.GetProducerPort())
else:
mapper.SetInputData(trianglePolyData)
# mapper.SetInput(trianglePolyData)
ac = vtk.vtkActor()
ac.SetMapper(mapper)
ac.GetProperty().SetOpacity(opacity)
ac.GetProperty().SetColor(color)
self.ren.AddActor(ac)
else:
raise ValueError("Number of points for a face should be >= 3")
def build_actors(self):
M = self.data_xyz.shape[0]
log.info('Plotting '+str(M)+' peaks.')
# Calculate points
max_rad = np.max(np.linalg.norm(self.data_ijk, axis=-1))
r = self.rad_scale/max_rad
starts = self.data_xyz - r*self.data_ijk
ends = self.data_xyz + r*self.data_ijk
# Interleave starts and ends
points_array = np.empty((2*M, 3))
points_array[0::2] = starts
points_array[1::2] = ends
# Calculate line connections
lines_array = []
for i in range(M):
lines_array += [2, 2*i, 2*i+1] # length, index0, index1
lines_array = np.array(lines_array)
# Set Points to vtk array format
vtk_points = vtk.vtkPoints()
vtk_points.SetData(ns.numpy_to_vtk(points_array, deep=True))
# Set Lines to vtk array format
vtk_lines = vtk.vtkCellArray()
vtk_lines.GetData().DeepCopy(ns.numpy_to_vtk(lines_array))
vtk_lines.SetNumberOfCells(M)
# Set poly_data
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(vtk_points)
poly_data.SetLines(vtk_lines)
# Set tube radius
tube_filter = vtk.vtkTubeFilter()
tube_filter.SetInputData(poly_data)
tube_filter.SetNumberOfSides(50)
tube_filter.SetRadius(0.5/np.min(self.shape))
tube_filter.CappingOn()
tube_filter.Update()
# Original
poly_mapper = vtk.vtkPolyDataMapper()
poly_mapper.SetInputConnection(tube_filter.GetOutputPort())
poly_mapper.ScalarVisibilityOn()
poly_mapper.SetScalarModeToUsePointFieldData()
poly_mapper.SelectColorArray("Colors")
poly_mapper.Update()
# Color
cols = np.zeros_like(points_array)
dirs = self.data_ijk/np.linalg.norm(self.data_ijk, axis=-1)[:,np.newaxis]
cols[0::2] = 255*np.abs(dirs)
cols[1::2] = 255*np.abs(dirs)
vtk_colors = ns.numpy_to_vtk(cols, deep=True, array_type=vtk.VTK_UNSIGNED_CHAR)
vtk_colors.SetName("Colors")
poly_data.GetPointData().SetScalars(vtk_colors)
# Set actor
actor = vtk.vtkActor()
actor.SetMapper(poly_mapper)
# actor.GetProperty().SetLineWidth(2)
# actor.GetProperty().SetLighting(0)
actor.GetProperty().SetAmbient(0.5)
self.ren.AddActor(actor)
# Draw extras
utilvtk.draw_origin_dot(self.ren)
utilvtk.draw_outer_box(self.ren, *self.shape)
utilvtk.draw_axes(self.ren, *self.shape)
# Set cameras
dist = 1.15*np.linalg.norm(self.shape)
self.ren.GetActiveCamera().SetPosition(np.array([1,-1,1])*dist)
self.ren.GetActiveCamera().SetViewUp([0,0,1])
def update(self):
if len(self.points) != len(self.stiffness):
return
points = self.points
scalars = self.stiffness
if np.all(self.points == self.oldPoints):
return
self.getNewPoints()
# Project points into UV space
texCoords = self.converter.toUVSpace(points)[:, 0:2]
# Flip y coordinates to match image space
texCoords[:, 1] *= -1
texCoords[:, 1] += 1
resolution = 100
grid = generateGrid(0, 1, 0, 1, resolution)
stiffMap = scipy.interpolate.griddata(texCoords,
scalars,
grid,
method="linear",
fill_value=-1)
stiffMap = stiffMap.reshape(resolution, resolution)
stiffMap[stiffMap == -1] = np.min(stiffMap[stiffMap != -1])
# print(np.min(stiffMap), np.max(stiffMap), np.min(stiffMat), np.max(stiffMat))
# Normalize
# stiffMap[stiffMap < np.mean(stiffMap)] = np.mean(stiffMap)
stiffMap -= np.min(stiffMap)
stiffMap /= np.max(stiffMap)
scale = 255 * 0.3
r = np.clip(stiffMap * 3, 0, 1) * scale
g = np.clip(stiffMap * 3 - 1, 0, 1) * scale
b = np.clip(stiffMap * 3 - 2, 0, 1) * scale
stiffImg = np.dstack((b, g, r)).astype(np.uint8)
shape = self.texture.shape
stiffImg = cv2.resize(stiffImg, (shape[1], shape[0]))
img = self.texture.copy()
img = np.subtract(img, stiffImg.astype(int))
img = np.clip(img, 0, 255).astype(np.uint8)
self.oldPoints = self.points
if self.visualize:
self.polyData.Reset()
vtkPoints = vtk.vtkPoints()
vtkCells = vtk.vtkCellArray()
# colors = vtk.vtkUnsignedCharArray()
# colors.SetNumberOfComponents(3)
# colors.SetName("Colors")
# minZ = np.min(scalars)
# maxZ = np.max(scalars)
# stiffness = (scalars - minZ) / (maxZ - minZ)
# r = np.clip(stiffness * 3, 0, 1) * 255
# g = np.clip(stiffness * 3 - 1, 0, 1) * 255
# b = np.clip(stiffness * 3 - 2, 0, 1) * 255
# for i, point in enumerate(np.hstack((points, r, g, b))):
for i, point in enumerate(points):
pointId = vtkPoints.InsertNextPoint(point)
vtkCells.InsertNextCell(1)
vtkCells.InsertCellPoint(pointId)
self.polyData.SetPoints(vtkPoints)
self.polyData.SetVerts(vtkCells)
self.polyData.Modified()
# self.polyData.GetPointData().SetScalars(colors)
self.actor_organ.setTexture(img)
print "made indexed image"
imageBounds = indexedImage.GetExtent()
dirs = (iPoint(-1, 0, 0), iPoint(1, 0, 0), iPoint(0, -1, 0), iPoint(0, 1, 0),
iPoint(0, 0, -1), iPoint(0, 0, 1))
poly = {
0: vtk.vtkPolyData(),
1: vtk.vtkPolyData(),
3: vtk.vtkPolyData(),
5: vtk.vtkPolyData(),
7: vtk.vtkPolyData()
}
faces = {
0: vtk.vtkCellArray(),
1: vtk.vtkCellArray(),
3: vtk.vtkCellArray(),
5: vtk.vtkCellArray(),
7: vtk.vtkCellArray()
}
imageGeoFilter = vtk.vtkImageDataGeometryFilter()
imageGeoFilter.SetInput(indexedImage)
imageGeoFilter.SetExtent(imageBounds)
imagePoints = imageGeoFilter.GetOutput()
imagePoints.Update()
# loop over voxels and add faces that border different pixel groups to polydata
for i in xrange(indexedImage.GetNumberOfCells()):
voxel = indexedImage.GetCell(i)
def convert(polydata, config=None, verbose=True, coords_only=False):
'''
Takes a vtk polydata and converts it to TKO.
'''
# remove degenerate (single point) lines
# see https://github.com/bostongfx/TRAKO/issues/8
cleaner = vtk.vtkCleanPolyData()
cleaner.PointMergingOff()
cleaner.SetInputData(polydata)
cleaner.Update()
polydata = cleaner.GetOutputDataObject(0)
polydata.SetVerts(vtk.vtkCellArray())
points = numpy_support.vtk_to_numpy(polydata.GetPoints().GetData())
lines = numpy_support.vtk_to_numpy(polydata.GetLines().GetData())
number_of_streamlines = polydata.GetLines().GetNumberOfCells()
#
# scalars are per point
#
pointdata = polydata.GetPointData()
number_of_scalars = pointdata.GetNumberOfArrays()
scalars = []
scalar_types = []
scalar_names = []
if not coords_only:
for i in range(number_of_scalars):
arr_name = pointdata.GetArrayName(i)
scalar_names.append(str(arr_name))
arr = pointdata.GetArray(i)
# arr.ComputeScalarRange()
# print(arr)
number_of_components = arr.GetNumberOfComponents()
data_type = arr.GetDataType()
scalar_types.append((data_type, number_of_components))
if verbose:
print('Loading scalar', arr_name)
scalars.append(numpy_support.vtk_to_numpy(arr))
#
# properties are per streamline
#
celldata = polydata.GetCellData()
number_of_properties = celldata.GetNumberOfArrays()
properties = []
property_types = []
property_names = []
if not coords_only:
for i in range(number_of_properties):
arr_name = celldata.GetArrayName(i)
property_names.append(str(arr_name))
arr = celldata.GetArray(i)
# print(i, arr)
number_of_components = arr.GetNumberOfComponents()
data_type = arr.GetDataType()
property_types.append((data_type, number_of_components))
if verbose:
print('Loading property', arr_name)
properties.append(numpy_support.vtk_to_numpy(arr))
#
# convert to streamlines
#
ordered_indices = []
ordered_scalars = []
i = 0
current_fiber_id = 0
line_length = 0
# sanity check
if len(lines) > 0:
line_length = lines[i]
line_index = 0
lines_just_length = []
while (line_index < number_of_streamlines):
lines_just_length.append(line_length)
i += line_length
line_index += 1
if line_index < number_of_streamlines:
line_length = lines[i + line_index]
#
# now, create fiber cluster data structure
#
fibercluster = {
'number_of_streamlines': number_of_streamlines,
'per_vertex_data': collections.OrderedDict(),
'indices': lines_just_length, #ordered_indices
'per_streamline_data': collections.OrderedDict()
}
fibercluster['per_vertex_data']['POSITION'] = {
'componentType':
vtkDataType_to_gltfComponentType[polydata.GetPoints().GetDataType()],
'type':
vtkNumberOfComponents_to_gltfType[
polydata.GetPoints().GetData().GetNumberOfComponents()],
'data':
points #ordered_vertices
}
for i, s in enumerate(scalar_names):
vtkdatatype = scalar_types[i][0]
vtknumberofcomponents = scalar_types[i][1]
thisdata = scalars[i] #[]
if vtknumberofcomponents in vtkNumberOfComponents_to_gltfType:
gltfType = vtkNumberOfComponents_to_gltfType[vtknumberofcomponents]
else:
# for now, we will just pass it through
gltfType = vtknumberofcomponents
fibercluster['per_vertex_data'][s] = {
'componentType': vtkDataType_to_gltfComponentType[vtkdatatype],
'type': gltfType,
'data': thisdata
}
for i, p in enumerate(property_names):
vtkdatatype = property_types[i][0]
vtknumberofcomponents = property_types[i][1]
thisdata = properties[i] #[]
if vtknumberofcomponents in vtkNumberOfComponents_to_gltfType:
gltfType = vtkNumberOfComponents_to_gltfType[vtknumberofcomponents]
else:
# for now, we will just pass it through
gltfType = vtknumberofcomponents
fibercluster['per_streamline_data'][p] = {
'componentType': vtkDataType_to_gltfComponentType[vtkdatatype],
'type': gltfType,
'data': thisdata
}
return fibercluster
import numpy
# Make a 32 x 32 grid
size = 32
# Define z values for the topography (random height)
topography = numpy.zeros([size, size])
for i in range(size):
for j in range(size):
topography[i][j] = random.randrange(0, 5)
# Define points, triangles and colors
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
points = vtk.vtkPoints()
triangles = vtk.vtkCellArray()
# Build the meshgrid manually
count = 0
for i in range(size - 1):
for j in range(size - 1):
z1 = topography[i][j]
z2 = topography[i][j + 1]
z3 = topography[i + 1][j]
# Triangle 1
points.InsertNextPoint(i, j, z1)
points.InsertNextPoint(i, (j + 1), z2)
points.InsertNextPoint((i + 1), j, z3)
Vessel = vtkReader(sys.argv[2])
numberOfBranches = 0
f = open(sys.argv[1])
ar = f.read().split('\n')
polyData_Container = []
for i in range(0, len(ar)):
v = ar[i].split(' ')
if (v[0]):
points = vtk.vtkPoints()
polyLine = vtk.vtkPolyLine()
polyLine.GetPointIds().SetNumberOfIds(int(v[0]))
cells = vtk.vtkCellArray()
polyData = vtk.vtkPolyData()
vtkFloatArray = vtk.vtkFloatArray()
vtkFloatArray.SetName("BranchIds")
vtkFloatArray.SetNumberOfTuples(int(v[0]))
for j in range(0, int(v[0])):
vtkFloatArray.SetTuple1(j, numberOfBranches)
for j in range(0, int(v[0])):
points.InsertNextPoint(float(v[j * 3 + 1]), float(v[j * 3 + 2]),
float(v[j * 3 + 3]))
for j in range(0, int(v[0])):
polyLine.GetPointIds().SetId(j, j)
def clean(pdata): # clean vtkPolyData
geoFilter = vtk.vtkGeometryFilter(
) # transform any entry in conform vtk (vertex, line, triangle and tetra)
geoFilter.SetInputData(pdata)
geoFilter.Update()
pdata.DeepCopy(geoFilter.GetOutput())
numCells = pdata.GetNumberOfCells() # store number of cells
vert = vtk.vtkCellArray() # see D1.py for explanation
line = vtk.vtkCellArray()
tri = vtk.vtkCellArray()
tetra = vtk.vtkCellArray()
for i in np.arange(numCells):
cell = pdata.GetCell(i)
if cell.GetCellType() == 1: # cell is a vertex (VTK_VERTEX = 1)
vert.InsertNextCell(cell)
elif cell.GetCellType() == 3: # cell is a line (VTK_LINE = 3)
line.InsertNextCell(cell)
elif cell.GetCellType() == 5: # cell is a triangle (VTK_TRIANGLE = 5)
tri.InsertNextCell(cell)
elif cell.GetCellType() == 10: # cell is a tetra (VTK_TETRA = 10)
tetra.InsertNextCell(cell)
numVertex = vert.GetNumberOfCells()
numLines = line.GetNumberOfCells()
numTri = tri.GetNumberOfCells()
numTetra = tetra.GetNumberOfCells()
if numTetra != 0: # if there is tetra, delete vertex, line and triangle
list = np.array([1, 3, 5])
elif numTri != 0: # elif there is triangle, delete vertex and line
list = np.array([1, 3])
elif numLines != 0: # elif there is line, delete vertex
list = np.array([1])
else: # elif there is only vertex, delete nothing
list = np.array([])
ids = vtk.vtkIdTypeArray() # array to store cell id to remove
ids.SetNumberOfComponents(1) # array with 1 2nd-size
it = pdata.NewCellIterator() # new cell iterator
it.InitTraversal()
while not it.IsDoneWithTraversal():
type = it.GetCellType()
for i in np.arange(list.shape[0]):
if list[i] == type: # the type of cell is in the the vector of type to delete
ids.InsertNextValue(it.GetCellId())
it.GoToNextCell()
selectionNode = vtk.vtkSelectionNode() # object to select things
selectionNode.SetFieldType(
vtk.vtkSelectionNode.CELL) # select things by cell
selectionNode.SetContentType(
vtk.vtkSelectionNode.INDICES) # select things through indices
selectionNode.SetSelectionList(ids) # select things by reference from ids
selection = vtk.vtkSelection() # object to select things
selection.AddNode(selectionNode) # select things through selectionNode
extractSelection = vtk.vtkExtractSelection() # extract wich are selected
extractSelection.SetInputData(0, pdata) # input data (base is pdata)
extractSelection.SetInputData(
1, selection) # input data to extract from base (selection)
selectionNode.GetProperties().Set(
vtk.vtkSelectionNode.INVERSE(),
1) # inverse selection (we want to keep wich are not selected)
extractSelection.Update() # update the extract selection
geoFilter.SetInputData(
extractSelection.GetOutput()) # convert any entry in vtkPolyData
geoFilter.Update()
pdata.DeepCopy(
geoFilter.GetOutput()) # replace pdata with the new vtkPolyData
return pdata
#!/usr/bin/env python # -*- coding: utf-8 -*- import vtk import sys # Test bounds computation for mixed cells in polydata. # Create some points that are unused by any cell as well. polyData = vtk.vtkPolyData() pts = vtk.vtkPoints() verts = vtk.vtkCellArray() lines = vtk.vtkCellArray() polys = vtk.vtkCellArray() strips = vtk.vtkCellArray() pts.SetNumberOfPoints(13) pts.SetPoint(0, 0,0,0) pts.SetPoint(1, 1,0,0) pts.SetPoint(2, 2,0,0) pts.SetPoint(3, 3,0,0) pts.SetPoint(4, 4,0,0) pts.SetPoint(5, 3,1,0) pts.SetPoint(6, 4,1,0) pts.SetPoint(7, 5,0,0) pts.SetPoint(8, 6,0,0) pts.SetPoint(9, 5,1,0) pts.SetPoint(10, 6,1,0) pts.SetPoint(11, 7,0,0) pts.SetPoint(12, 8,0,0) verts.InsertNextCell(1)
def testGlyphs(self):
"""Test if texturing of the glyphs works correctly."""
# The Glyph
cs = vtk.vtkCubeSource()
cs.SetXLength(2.0)
cs.SetYLength(1.0)
cs.SetZLength(0.5)
# Create input point data.
pts = vtk.vtkPoints()
pts.InsertPoint(0, (1, 1, 1))
pts.InsertPoint(1, (0, 0, 0))
pts.InsertPoint(2, (-1, -1, -1))
polys = vtk.vtkCellArray()
polys.InsertNextCell(1)
polys.InsertCellPoint(0)
polys.InsertNextCell(1)
polys.InsertCellPoint(1)
polys.InsertNextCell(1)
polys.InsertCellPoint(2)
pd = vtk.vtkPolyData()
pd.SetPoints(pts)
pd.SetPolys(polys)
# Orient the glyphs as per vectors.
vec = vtk.vtkFloatArray()
vec.SetNumberOfComponents(3)
vec.InsertTuple3(0, 1, 0, 0)
vec.InsertTuple3(1, 0, 1, 0)
vec.InsertTuple3(2, 0, 0, 1)
pd.GetPointData().SetVectors(vec)
# The glyph filter.
g = vtk.vtkGlyph3D()
g.SetScaleModeToDataScalingOff()
g.SetVectorModeToUseVector()
g.SetInputData(pd)
g.SetSourceConnection(cs.GetOutputPort())
m = vtk.vtkPolyDataMapper()
m.SetInputConnection(g.GetOutputPort())
a = vtk.vtkActor()
a.SetMapper(m)
# The texture.
img_file = os.path.join(VTK_DATA_ROOT, "Data", "masonry.bmp")
img_r = vtk.vtkBMPReader()
img_r.SetFileName(img_file)
t = vtk.vtkTexture()
t.SetInputConnection(img_r.GetOutputPort())
t.InterpolateOn()
a.SetTexture(t)
# Renderer, RenderWindow etc.
ren = vtk.vtkRenderer()
ren.SetBackground(0.5, 0.5, 0.5)
ren.AddActor(a)
ren.ResetCamera()
cam = ren.GetActiveCamera()
cam.Azimuth(-90)
cam.Zoom(1.4)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
rwi = vtk.vtkRenderWindowInteractor()
rwi.SetRenderWindow(renWin)
rwi.Initialize()
rwi.Render()
