def ReadPointCloud(filename):
print 'Reading file: ', filename
#vtkPoints here:
#method1: assign number of points, insert points by ID, ::SetPoint(ID, double[3])
#method2: assign no size, insert one after anther, ::InsertNextPoint(double[3])
points = vtk.vtkPoints()
poly = vtk.vtkPolyData()
glyphFilter = vtk.vtkVertexGlyphFilter(
) # I don't know what is the purpose
fp = open(filename, "rb+")
line = fp.readline()
while line != '':
line = line.strip()
if line == '':
continue
elif line.find('\t') < 0:
line = line.split(' ')
else:
line = line.split('\t')
points.InsertNextPoint(float(line[0]), float(line[1]), float(line[2]))
#read next line and return to loop
line = fp.readline()
#add point to poly data
poly.SetPoints(points)
glyphFilter.SetInputData(poly)
glyphFilter.Update()
#visualize
PolyVisualize(glyphFilter.GetOutputPort())
def create_path_geometry(self):
"""
Create geometry for the path.
"""
## Show path points.
#
for element in self.elements:
coords = element.points
num_pts = len(coords)
# Create path geometry points and line connectivity.
points = vtk.vtkPoints()
points.SetNumberOfPoints(num_pts)
lines = vtk.vtkCellArray()
lines.InsertNextCell(num_pts)
#lines.InsertNextCell(num_pts+1)
n = 0
for pt in coords:
points.SetPoint(n, pt[0], pt[1], pt[2])
lines.InsertCellPoint(n)
n += 1
#_for pt in coords
lines.InsertCellPoint(0)
geom = vtk.vtkPolyData()
geom.SetPoints(points)
geom.SetLines(lines)
#geom.BuildLinks()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(geom)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetLineWidth(4.0)
actor.GetProperty().SetColor(1.0, 0.0, 0.0)
self.graphics.add_actor(actor)
## Show control points.
#
for element in self.elements:
coords = element.control_points
points = vtk.vtkPoints()
points.SetNumberOfPoints(len(coords))
n = 0
for pt in coords:
points.SetPoint(n, pt[0], pt[1], pt[2])
n += 1
#_for pt in coords
geom = vtk.vtkPolyData()
geom.SetPoints(points)
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputData(geom)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(glyphFilter.GetOutputPort())
actor = vtk.vtkActor()
actor.GetProperty().SetColor(0.0, 0.0, 0.8)
actor.GetProperty().SetPointSize(10)
actor.SetMapper(mapper)
self.graphics.add_actor(actor)
def _colorPoints(plist, cols, r, alpha):
n = len(plist)
if n > len(cols):
colors.printc("~times Error: mismatch in colorPoints()",
n,
len(cols),
c=1)
exit()
if n != len(cols):
colors.printc("~lightning Warning: mismatch in colorPoints()", n,
len(cols))
src = vtk.vtkPointSource()
src.SetNumberOfPoints(n)
src.Update()
vgf = vtk.vtkVertexGlyphFilter()
vgf.SetInputData(src.GetOutput())
vgf.Update()
pd = vgf.GetOutput()
ucols = vtk.vtkUnsignedCharArray()
ucols.SetNumberOfComponents(3)
ucols.SetName("pointsRGB")
for i in range(len(plist)):
c = np.array(colors.getColor(cols[i])) * 255
ucols.InsertNextTuple3(c[0], c[1], c[2])
pd.GetPoints().SetData(numpy_to_vtk(plist, deep=True))
pd.GetPointData().SetScalars(ucols)
actor = Actor(pd, c, alpha)
actor.mapper.ScalarVisibilityOn()
actor.GetProperty().SetInterpolationToFlat()
actor.GetProperty().SetPointSize(r)
settings.collectable_actors.append(actor)
return actor
def generate_vertex_glyph_filter(self, poly):
glyph_filter = vtk.vtkVertexGlyphFilter()
glyph_filter.SetInput(poly)
return glyph_filter
def _add_nodes_to_cap(vtkPts, size):
"""
Add uniformed points to cap
"""
points = vtk_to_numpy(vtkPts.GetData())
num = points.shape[0]
#_plot_points(points)
ctr = np.mean(points, axis=0)
length = np.mean(np.linalg.norm(points - ctr, axis=1))
r = np.linspace(0.5 * size / length, (length - size * 0.8) / length,
int(np.floor(length / size)))
addedPts = vtk.vtkPoints()
for rf in r:
newPts = vtk.vtkPoints()
newPts.SetData(numpy_to_vtk((points - ctr) * rf + ctr))
addedPts.InsertPoints(addedPts.GetNumberOfPoints(),
newPts.GetNumberOfPoints(), 0, newPts)
ptsPly = vtk.vtkPolyData()
ptsPly.SetPoints(addedPts)
vertexFilter = vtk.vtkVertexGlyphFilter()
vertexFilter.SetInputData(ptsPly)
vertexFilter.Update()
ptsPly = vertexFilter.GetOutput()
cleanedPts = clean_polydata(ptsPly, size * 0.01)
vtkPts.InsertPoints(vtkPts.GetNumberOfPoints(),
cleanedPts.GetNumberOfPoints(), 0,
cleanedPts.GetPoints())
#_plot_points(vtk_to_numpy(vtkPts.GetData()))
return vtkPts
def _colorPoints(plist, cols, r, alpha, legend):
n = len(plist)
if n > len(cols):
colors.printc("Mismatch in colorPoints()", n, len(cols), c=1)
exit()
if n != len(cols):
colors.printc("Warning: mismatch in colorPoints()", n, len(cols))
src = vtk.vtkPointSource()
src.SetNumberOfPoints(n)
src.Update()
vertexFilter = vtk.vtkVertexGlyphFilter()
vertexFilter.SetInputData(src.GetOutput())
vertexFilter.Update()
pd = vertexFilter.GetOutput()
ucols = vtk.vtkUnsignedCharArray()
ucols.SetNumberOfComponents(3)
ucols.SetName("RGB")
for i, p in enumerate(plist):
c = np.array(colors.getColor(cols[i])) * 255
ucols.InsertNextTuple3(c[0], c[1], c[2])
pd.GetPoints().SetData(numpy_to_vtk(plist, deep=True))
pd.GetPointData().SetScalars(ucols)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(pd)
mapper.ScalarVisibilityOn()
actor = Actor() #vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetInterpolationToFlat()
actor.GetProperty().SetOpacity(alpha)
actor.GetProperty().SetPointSize(r)
return actor
def glyph_dot(centers, colors, radius=100):
if np.array(colors).ndim == 1:
colors = np.tile(colors, (len(centers), 1))
vtk_pnt = numpy_to_vtk_points(centers)
pnt_polydata = vtk.vtkPolyData()
pnt_polydata.SetPoints(vtk_pnt)
vertex_filter = vtk.vtkVertexGlyphFilter()
vertex_filter.SetInputData(pnt_polydata)
vertex_filter.Update()
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(vertex_filter.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydata)
mapper.SetScalarModeToUsePointFieldData()
pnt_actor = vtk.vtkActor()
pnt_actor.SetMapper(mapper)
pnt_actor.GetProperty().SetPointSize(radius)
cols = numpy_to_vtk_colors(255 * np.ascontiguousarray(colors))
cols.SetName('colors')
polydata.GetPointData().AddArray(cols)
mapper.SelectColorArray('colors')
return pnt_actor
def addPoints(self, points, color, thick=False, thickness=_DEFAULT_POINT_THICKNESS):
vtkPoints = vtk.vtkPoints()
for point in points:
vtkPoints.InsertNextPoint(point[0], point[1], point[2])
pointsPolyData = vtk.vtkPolyData()
pointsPolyData.SetPoints(vtkPoints)
if thick:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(thickness)
glyph3D = vtk.vtkGlyph3D()
glyph3D.SetSourceConnection(sphereSource.GetOutputPort())
glyph3D.SetInputData(pointsPolyData)
glyph3D.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(glyph3D.GetOutputPort())
else:
vertexFilter = vtk.vtkVertexGlyphFilter()
vertexFilter.SetInputData(pointsPolyData)
vertexFilter.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(vertexFilter.GetOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(color)
self._rendererScene.AddActor(actor)
def AdjustColor(self, flag):
if self.myactor is None:
self.selection = vtk.vtkExtractGeometry()
self.selection.SetInputConnection(self.input.GetOutputPort())
filter = vtk.vtkVertexGlyphFilter()
filter.SetInputConnection(self.selection.GetOutputPort())
self.myactor = PolyDataActor(filter.GetOutputPort())
self.renderer.AddMyActor(self.myactor)
polydata = vtk.vtkPolyData()
self.GetPolyData(polydata)
self.selection.SetImplicitFunction(polydata)
self.myactor.Update()
num_points = self.myactor.GetNumberOfPoints()
print("num of points: ", num_points)
num_cells = self.myactor.GetNumberOfCells()
f = self.GetEnabled() if flag else not self.GetEnabled()
if f:
color_name = "green"
else:
color_name = "red"
# generate colors
selected_colors = GenerateColors(num_points, color_name=color_name)
# set attribution of points
self.myactor.SetScalars(selected_colors)
def LeftButtonReleaseEvent(self, obj, event):
print("LEFT BUTTON RELEASED")
self.OnLeftButtonUp()
self.frustum = self.area_picker.GetFrustum()
self.extract_geometry = vtk.vtkExtractGeometry()
self.extract_geometry.SetImplicitFunction(self.frustum)
self.extract_geometry.SetInputData(self.pointcloud.cm_poly_data)
self.extract_geometry.Update()
self.glyph_filter = vtk.vtkVertexGlyphFilter()
self.glyph_filter.SetInputConnection(
self.extract_geometry.GetOutputPort())
self.glyph_filter.Update()
self.selected = self.glyph_filter.GetOutput()
self.p1 = self.selected.GetNumberOfPoints()
self.p2 = self.selected.GetNumberOfCells()
print("Number of points = %s" % self.p1)
print("Number of cells = %s" % self.p2)
'# % COLOR SELECTED POINTS RED'
self.selected_mapper.SetInputData(self.selected)
try:
self.selected_actor.GetProperty().SetPointSize(10)
self.selected_actor.GetProperty().SetColor(0, 0, 0) # (R, G, B)
self.color_picked()
except AttributeError:
pass
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkVertexGlyphFilter(), 'Processing.',
('vtkPointSet',), ('vtkPolyData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def AddFilter(self, func):
if not self.GetContinue():
# reset history
self.ResetHistory()
extract_geometry_filter = vtk.vtkExtractGeometry()
# set filter function
extract_geometry_filter.SetImplicitFunction(func)
# connect the last output
# some bug here, so I use SetInputData() instead.
# extract_geometry_filter.SetInputConnection(self.last_filters[-1].GetOutputPort())
extract_geometry_filter.SetInputConnection(
self.last_filter.GetOutputPort())
# save last_filter
self.last_filters.append(self.last_filter)
# update the last output
self.last_filter = vtk.vtkVertexGlyphFilter()
self.last_filter.SetInputConnection(
extract_geometry_filter.GetOutputPort())
# append to the list for saving
self.extract_geometry_filters.append(extract_geometry_filter)
# set the last filter to the input of mapper
self.selected_actor.SetInput(self.last_filter.GetOutputPort())
self.selected_actor.Update()
def create_node_labels(point_id_filter: vtk.vtkIdFilter,
grid: vtk.vtkUnstructuredGrid,
rend: vtk.vtkRenderer,
label_size: float = 10.0):
"""creates the node labels"""
# filter inner points, so only surface points will be available
geo = vtk.vtkUnstructuredGridGeometryFilter()
geo.SetInputData(grid)
# points
vertex_filter = vtk.vtkVertexGlyphFilter()
vertex_filter.SetInputConnection(geo.GetOutputPort())
vertex_filter.Update()
points_mapper = vtk.vtkPolyDataMapper()
points_mapper.SetInputConnection(vertex_filter.GetOutputPort())
points_mapper.ScalarVisibilityOn()
points_actor = vtk.vtkActor()
points_actor.SetMapper(points_mapper)
points_actor.GetProperty().SetPointSize(label_size)
# point labels
label_mapper = vtk.vtkLabeledDataMapper()
label_mapper.SetInputConnection(point_id_filter.GetOutputPort())
label_mapper.SetLabelModeToLabelFieldData()
label_actor = vtk.vtkActor2D()
label_actor.SetMapper(label_mapper)
return label_actor
def read_txt_points(filename):
'''
private function to read points from a file
return a point list
'''
print 'Reading file: ', filename
points = []
vtkpt = vtk.vtkPoints()
with open(filename, 'r') as ff:
for line in ff.readlines():
ss = line.strip().split(',')
if len(ss) == 3:
pp = [
string.atof(ss[0]),
string.atof(ss[1]),
string.atof(ss[2])
]
points.append(pp)
vtkpt.InsertNextPoint(pp)
poly = vtk.vtkPolyData()
poly.SetPoints(vtkpt)
vx = vtk.vtkVertexGlyphFilter()
vx.SetInputData(poly)
vx.Update()
poly = vx.GetOutput()
return poly
def ReadPointCloud(filename):
print 'Reading file: ', filename
#vtkPoints here:
#method1: assign number of points, insert points by ID, ::SetPoint(ID, double[3])
#method2: assign no size, insert one after anther, ::InsertNextPoint(double[3])
points = vtk.vtkPoints()
poly = vtk.vtkPolyData()
glyphFilter = vtk.vtkVertexGlyphFilter() # I don't know what is the purpose
fp = open(filename,"rb+")
line = fp.readline()
while line!='':
line = line.strip()
if line == '':
continue
elif line.find('\t') < 0:
line = line.split(' ')
else:
line = line.split('\t')
points.InsertNextPoint(float(line[0]),float(line[1]),float(line[2]))
#read next line and return to loop
line = fp.readline()
#add point to poly data
poly.SetPoints(points)
glyphFilter.SetInputData(poly)
glyphFilter.Update()
#visualize
PolyVisualize(glyphFilter.GetOutputPort())
def create_points_actor(points):
'''
points:array
'''
vtk_points = vtk.vtkPoints()
vtk_points.SetNumberOfPoints(len(points))
for i in range(len(points)):
vtk_points.SetPoint(i, points[i])
colors = vtk.vtkNamedColors()
polydata = vtk.vtkPolyData()
polydata.SetPoints(vtk_points)
vertexGlyphFilter = vtk.vtkVertexGlyphFilter()
vertexGlyphFilter.SetInputData(polydata)
vertexGlyphFilter.Update()
# Create a mapper and actor
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(vertexGlyphFilter.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetPointSize(1)
actor.GetProperty().SetColor(colors.GetColor3d("Yellow"))
return actor
def display_cloud(self, actorName, list_points, size, vec3_color):
# extract inlier points
vtk_points = vtk.vtkPoints()
for p in list_points:
vtk_points.InsertNextPoint(p[0], p[1], p[2])
temp_cloud = vtk.vtkPolyData()
temp_cloud.SetPoints(vtk_points)
# add 0D topology to every point
glfilter = vtk.vtkVertexGlyphFilter()
glfilter.SetInput(temp_cloud)
glfilter.Update()
cloud = glfilter.GetOutput()
cloudMapper = vtk.vtkPolyDataMapper()
cloudMapper.SetInput(cloud)
actor = vtk.vtkActor()
actor.SetMapper(cloudMapper)
actor.GetProperty().SetColor(vec3_color[0], vec3_color[1],
vec3_color[2])
actor.GetProperty().SetPointSize(size)
self.ren.AddActor(actor)
self.name2actor[actorName] = actor
pass
def onLeftButtonUp(self, obj, event):
# Forward events
self.OnLeftButtonUp()
frustum = self.GetInteractor().GetPicker().GetFrustum()
extractGeometry = vtk.vtkExtractGeometry()
extractGeometry.SetImplicitFunction(frustum)
extractGeometry.SetInputData(self.Points)
extractGeometry.Update()
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputConnection(extractGeometry.GetOutputPort())
glyphFilter.Update()
selected = glyphFilter.GetOutput()
print("Selected " + str(selected.GetNumberOfPoints()) + " points.")
print("Selected " + str(selected.GetNumberOfCells()) + " cells.")
self.SelectedMapper.SetInputData(selected)
self.SelectedMapper.ScalarVisibilityOff()
ids = selected.GetPointData().GetArray("OriginalIds")
for i in range(ids.GetNumberOfTuples()):
print("Id " + str(i) + str(ids.GetValue(i)))
self.SelectedActor.GetProperty().SetColor(1.0, 0.0, 0.0) #(R,G,B)
self.SelectedActor.GetProperty().SetPointSize(3)
self.GetCurrentRenderer().AddActor(self.SelectedActor)
self.GetInteractor().GetRenderWindow().Render()
self.HighlightProp(None)
def disk():
np.random.seed(42)
n_points = 1
centers = np.random.rand(n_points, 3)
colors = 255 * np.random.rand(n_points, 3)
vtk_points = numpy_to_vtk_points(centers)
points_polydata = vtk.vtkPolyData()
points_polydata.SetPoints(vtk_points)
vertex_filter = vtk.vtkVertexGlyphFilter()
vertex_filter.SetInputData(points_polydata)
vertex_filter.Update()
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(vertex_filter.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydata)
points_actor = vtk.vtkActor()
points_actor.SetMapper(mapper)
points_actor.GetProperty().SetPointSize(1000)
points_actor.GetProperty().SetRenderPointsAsSpheres(True)
return points_actor
def main():
colors = vtk.vtkNamedColors()
# Create points on an XY grid with random Z coordinate
points = vtk.vtkPoints()
gridSize = 10
seed = 0
randomSequence = vtk.vtkMinimalStandardRandomSequence()
randomSequence.Initialize(seed)
for x in range(0, gridSize):
for y in range(0, gridSize):
d = randomSequence.GetValue()
randomSequence.Next()
points.InsertNextPoint(x, y, d * 3)
# Add the grid points to a polydata object
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputData(polydata)
glyphFilter.Update()
# Create a mapper and actor
pointsMapper = vtk.vtkPolyDataMapper()
pointsMapper.SetInputConnection(glyphFilter.GetOutputPort())
pointsActor = vtk.vtkActor()
pointsActor.SetMapper(pointsMapper)
pointsActor.GetProperty().SetPointSize(3)
pointsActor.GetProperty().SetColor(colors.GetColor3d("Red"))
# Triangulate the grid points
delaunay = vtk.vtkDelaunay2D()
delaunay.SetInputData(polydata)
delaunay.Update()
# Create a mapper and actor
triangulatedMapper = vtk.vtkPolyDataMapper()
triangulatedMapper.SetInputConnection(delaunay.GetOutputPort())
triangulatedActor = vtk.vtkActor()
triangulatedActor.SetMapper(triangulatedMapper)
# Create a renderer, render window, and interactor
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Add the actor to the scene
renderer.AddActor(pointsActor)
renderer.AddActor(triangulatedActor)
renderer.SetBackground(colors.GetColor3d("Green")) # Background color green
# Render and interact
renderWindow.SetWindowName('TriangulateTerrainMap')
renderWindow.Render()
renderWindowInteractor.Start()
def draw_points(self, points):
points_data = vtk.vtkPolyData()
vertex_filter = vtk.vtkVertexGlyphFilter()
points_data.SetPoints(points)
vertex_filter.SetInputData(points_data)
vertex_filter.Update()
return vertex_filter.GetOutput()
def numpy2PolyData(data):
vtkArr = dsa.numpyTovtkDataArray(data)
pts = v.vtkPoints()
pts.SetData(vtkArr)
pd = v.vtkPolyData()
pd.SetPoints(pts)
vgf = v.vtkVertexGlyphFilter()
vgf.SetInputData(pd)
vgf.Update()
return vgf.GetOutput()
def point2vertexglyph(point):
points = vtk.vtkPoints()
points.InsertNextPoint(point[0],point[1],point[2])
poly = vtk.vtkPolyData()
poly.SetPoints(points)
glyph = vtk.vtkVertexGlyphFilter()
glyph.SetInputData(poly)
glyph.Update()
return glyph.GetOutput()
def main():
colors = vtk.vtkNamedColors()
# Create a set of heights on a grid.
# This is often called a "terrain map".
points = vtk.vtkPoints()
gridSize = 10
for x in range(gridSize):
for y in range(gridSize):
points.InsertNextPoint(x, y, int((x + y) / (y + 1)))
# Add the grid points to a polydata object
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
delaunay = vtk.vtkDelaunay2D()
delaunay.SetInputData(polydata)
# Visualize
meshMapper = vtk.vtkPolyDataMapper()
meshMapper.SetInputConnection(delaunay.GetOutputPort())
meshActor = vtk.vtkActor()
meshActor.SetMapper(meshMapper)
meshActor.GetProperty().SetColor(colors.GetColor3d('Banana'))
meshActor.GetProperty().EdgeVisibilityOn()
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputData(polydata)
pointMapper = vtk.vtkPolyDataMapper()
pointMapper.SetInputConnection(glyphFilter.GetOutputPort())
pointActor = vtk.vtkActor()
pointActor.GetProperty().SetColor(colors.GetColor3d('Tomato'))
pointActor.GetProperty().SetPointSize(5)
pointActor.SetMapper(pointMapper)
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderer.AddActor(meshActor)
renderer.AddActor(pointActor)
renderer.SetBackground(colors.GetColor3d('Mint'))
renderWindowInteractor.Initialize()
renderWindow.SetWindowName('Delaunay2D')
renderWindow.Render()
renderWindowInteractor.Start()
def add_glyph_points(renderer, points, color=[1.0, 1.0, 1.0], size=2):
geom = vtk.vtkPolyData()
geom.SetPoints(points)
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputData(geom)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(glyphFilter.GetOutputPort())
actor = vtk.vtkActor()
actor.GetProperty().SetColor(color)
actor.GetProperty().SetPointSize(size)
actor.SetMapper(mapper)
renderer.AddActor(actor)
def p2actor(pp):
pPoly = vtk.vtkPolyData()
pPoly.SetPoints(pp)
vx = vtk.vtkVertexGlyphFilter()
vx.SetInputData(pPoly)
vx.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(vx.GetOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
#actor.GetProperty().SetPointSize(10)
return actor
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()
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(0.0, 1.0, 0.0)
pointsPolydata = vtk.vtkPolyData()
pointsPolydata.SetPoints(points)
vertexFilter = vtk.vtkVertexGlyphFilter()
vertexFilter.SetInputConnection(pointsPolydata.GetProducerPort())
vertexFilter.Update()
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(vertexFilter.GetOutput())
# Setup colors
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("Colors")
colors.InsertNextTupleValue((255, 0, 0))
colors.InsertNextTupleValue((0, 255, 0))
colors.InsertNextTupleValue((0, 0, 255))
polydata.GetPointData().SetScalars(colors)
# Create a mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(polydata.GetProducerPort())
# Create an actor
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetPointSize(5)
self.ren.AddActor(actor)
self.ren.ResetCamera()
self._initialized = False
def setPoints(self, points_xyz, points_rgb):
points_polyd = vtk.vtkPolyData()
vtk_points = numpy_support.numpy_to_vtk(points_xyz)
self.vtkPoints.SetData(vtk_points)
vtk_pntcols = numpy_support.numpy_to_vtk(
(points_rgb * 255).astype(np.uint8))
self.vtkColors = vtk_pntcols
points_polyd.SetPoints(self.vtkPoints)
vertexfilter = vtk.vtkVertexGlyphFilter()
vertexfilter.SetInputData(points_polyd)
vertexfilter.Update()
self.vtkPolyData.ShallowCopy(vertexfilter.GetOutput())
self.vtkPolyData.GetPointData().SetScalars(self.vtkColors)
self.vtkPolyData.Modified()
def visualize_crop(self, LAA_surface):
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputData(self.pred_surface)
actor2 = vtk.vtkActor()
actor2.SetMapper(mapper2)
actor2.GetProperty().SetColor(0.5, 0.5, 0.5)
# LAA only
polyDataMapper = vtk.vtkPolyDataMapper()
polyDataMapper.SetInputData(LAA_surface)
actor = vtk.vtkActor()
actor.SetMapper(polyDataMapper)
actor.GetProperty().SetColor(1, 1, 1)
# Add points as glyphs
ostium_ids = np.load(self.path_ostiumIDs)
vtk_points = vtk.vtkPoints()
for ostium_id in ostium_ids:
vtk_points.InsertNextPoint(
self.surface_in_correspondance.GetPoint(ostium_id))
pd_points = vtk.vtkPolyData()
pd_points.SetPoints(vtk_points)
vertexGlyphFilter = vtk.vtkVertexGlyphFilter()
vertexGlyphFilter.AddInputData(pd_points)
vertexGlyphFilter.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(vertexGlyphFilter.GetOutputPort())
actor1 = vtk.vtkActor()
actor1.SetMapper(mapper)
actor1.GetProperty().SetPointSize(3)
actor1.GetProperty().SetColor(1, 0, 0)
# RENDER
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(800, 600)
renderWindow.SetWindowName("VTK")
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderer = vtk.vtkRenderer()
renderer.AddActor(actor2) #Full Surface
renderer.AddActor(actor) #Clipped surface
renderer.AddActor(actor1) #Points
#renderer.AddActor(planeActor) #PLane
renderer.SetBackground(1, 1, 1)
renderWindow.AddRenderer(renderer)
renderWindow.Render()
renderWindowInteractor.Start()
def try_point_surface():
'''
Workflow proved valid:
src_surface: source surface to be moved
src_points: points selected from src_surface
tgt_surface: fixed surface, src_surface will transform to this
moved_surface: src_surface applied transform
Workflow:
register src_points to tgt_surface, get a matrix Mat
apply Mat to src_surface, get moved_surface
Result:
moved_surface apply perfectly to tgt_surface
'''
pt_list = read_txt('data/point.txt')
points = vtk.vtkPoints()
for pt in pt_list:
points.InsertNextPoint(pt)
# points as source
point_poly = vtk.vtkPolyData()
point_poly.SetPoints(points)
vertex = vtk.vtkVertexGlyphFilter()
vertex.SetInputData(point_poly)
vertex.Update()
point_poly = vertex.GetOutput()
# surface patch as target
reg = icp_register()
surface = reg._read_poly('data/tcut.stl')
src_surface = reg._read_poly('data/cut.stl')
mat = reg.register(point_poly, surface, 5000)
transform = vtk.vtkTransform()
transform.SetMatrix(mat)
transFilter = vtk.vtkTransformFilter()
transFilter.SetTransform(transform)
#transFilter.SetInputData(point_poly)
transFilter.SetInputData(src_surface)
transFilter.Update()
pp = transFilter.GetOutput()
reg._write_poly(src_surface, 'data/src_tr.stl')
writer = vtk.vtkXMLPolyDataWriter()
writer.SetInputData(pp)
writer.SetFileName('data/transed_P.vtp')
def clip_area(poly, bounds):
new_pts = vtk.vtkPoints()
for id in range(poly.GetNumberOfPoints()):
pt = poly.GetPoint(id)
if ((pt[0] > bounds[0] - 10) & (pt[0] < bounds[1] + 10) &
(pt[1] > bounds[2] - 10) & (pt[1] < bounds[3] + 10) &
(pt[2] > bounds[4] - 10) & (pt[2] < bounds[5] + 10)):
new_pts.InsertNextPoint(pt)
poly = vtk.vtkPolyData()
poly.SetPoints(new_pts)
vx = vtk.vtkVertexGlyphFilter()
vx.SetInputData(poly)
vx.Update()
new_pts = vx.GetOutput()
return new_pts
def __init__(self):
# References to the converted numpy arrays to avoid seg faults
# self.np_to_vtk_points = None
# self.np_to_vtk_cells = None
# VTK Data
self.vtk_poly_data = vtk.vtkPolyData()
self.vtk_points = vtk.vtkPoints()
# self.vtk_points.SetNumberOfPoints(500000)
# self.vtk_cells = vtk.vtkCellArray()
# Colours for each point in the point cloud
self.vtk_colours = None
self.vtk_points_temp = vtk.vtkPoints()
# self.something = None
self.vtk_id_list = vtk.vtkIdList()
# self.ranges = None
# self.vtk_id_list = vtk.vtkIdList()
# self.vtk_colours = vtk.vtkUnsignedCharArray()
# self.vtk_colours.SetNumberOfComponents(3)
# self.vtk_colours.SetName("Colours")
self.points = np.zeros((0, 3))
self.colours = []
self.point_idx = 0
# Poly Data
self.vtk_poly_data.SetPoints(self.vtk_points)
# self.vtk_poly_data.SetVerts(self.vtk_cells)
self.glyphFilter = vtk.vtkVertexGlyphFilter()
self.glyphFilter.AddInputData(self.vtk_poly_data)
self.glyphFilter.Update()
# Poly Data Mapper
self.vtk_poly_data_mapper = vtk.vtkPolyDataMapper()
# self.vtk_poly_data_mapper.SetInputData(self.vtk_poly_data)
self.vtk_poly_data_mapper.SetInputConnection(
self.glyphFilter.GetOutputPort())
# Actor
self.vtk_actor = vtk.vtkActor()
self.vtk_actor.SetMapper(self.vtk_poly_data_mapper)
def main():
colors = vtk.vtkNamedColors()
points = vtk.vtkPoints()
points.InsertNextPoint(10, 10, 0)
points.InsertNextPoint(100, 100, 0)
points.InsertNextPoint(200, 200, 0)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputData(polydata)
glyphFilter.Update()
mapper = vtk.vtkPolyDataMapper2D()
mapper.SetInputConnection(glyphFilter.GetOutputPort())
mapper.Update()
actor = vtk.vtkActor2D()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(colors.GetColor3d('Gold'))
actor.GetProperty().SetPointSize(8)
# Create a renderer, render window, and interactor
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
# Add the actor to the scene
renderer.AddActor(actor)
renderWindow.SetSize(300, 300)
renderer.SetBackground(colors.GetColor3d('DarkSlateGray'))
renderWindow.SetWindowName('Actor2D')
# Render and interact
renderWindow.Render()
# w2if = vtk.vtkWindowToImageFilter()
# w2if.SetInput(renderWindow)
# w2if.Update()
#
# writer = vtk.vtkPNGWriter()
# writer.SetFileName('TestActor2D.png')
# writer.SetInputConnection(w2if.GetOutputPort())
# writer.Write()
renderWindowInteractor.Start()
def FiducialsToPolyData(self, fiducials, polyData):
#create polydata from fiducial list
points = vtk.vtkPoints()
n = fiducials.GetNumberOfFiducials()
for fiducialIndex in range( 0, n ):
p = [0, 0, 0]
fiducials.GetNthFiducialPosition(fiducialIndex, p)
points.InsertNextPoint(p)
tempPolyData = vtk.vtkPolyData()
tempPolyData.SetPoints(points)
vertex = vtk.vtkVertexGlyphFilter()
vertex.SetInputData(tempPolyData)
vertex.Update()
polyData.ShallowCopy(vertex.GetOutput())
def VertexGlyphFilter(self, currentElement):
gFilter = vtk.vtkVertexGlyphFilter()
AlgorithmElement = ''
for childElement in currentElement.getchildren():
if childElement.tag in vtkTypes['Algorithm']:
self.logger.debug('VertexGlyphFilter trying to add: %s' % (childElement.tag))
AlgorithmElement = childElement
if AlgorithmElement != '':
dataset = self.namesToFunctions[AlgorithmElement.tag](AlgorithmElement)
try:
gFilter.SetInputConnection(dataset.GetOutputPort())
except Exception as err:
self.logger.error(" .. <VertexGlyphFilter> failed to SetInputConnection")
self.logger.error(err)
else:
self.logger.error(' .. <VertexGlyphFilter> needs an Algorithm-type childElement')
return gFilter
def create_actor_pts(pts, color, **kwargs):
""" Creates a VTK actor for rendering scatter plots.
:param pts: points
:type pts: vtkFloatArray
:param color: actor color
:type color: list
:return: a VTK actor
:rtype: vtkActor
"""
# Keyword arguments
array_name = kwargs.get('name', "")
array_index = kwargs.get('index', 0)
point_size = kwargs.get('size', 5)
point_sphere = kwargs.get('point_as_sphere', True)
# Create points
points = vtk.vtkPoints()
points.SetData(pts)
# Create a PolyData object and add points
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
# Run vertex glyph filter on the points array
vertex_filter = vtk.vtkVertexGlyphFilter()
vertex_filter.SetInputData(polydata)
# Map ploy data to the graphics primitives
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(vertex_filter.GetOutputPort())
mapper.SetArrayName(array_name)
mapper.SetArrayId(array_index)
# Create an actor and set its properties
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(*color)
actor.GetProperty().SetPointSize(point_size)
actor.GetProperty().SetRenderPointsAsSpheres(point_sphere)
# Return the actor
return actor
def OnLeftButtonUp(self):
# Forward events
vtkInteractorStyleRubberBandPick.OnLeftButtonUp()
frustum = vtk.vtkAreaPicker(self.GetInteractor().GetPicker()).GetFrustum()
extractGeometry = vtk.vtkExtractGeometry.New()
extractGeometry.SetImplicitFunction(frustum)
if VTK_MAJOR_VERSION <= 5:
extractGeometry.SetInput(this.Points)
else:
extractGeometry.SetInputData(this.Points)
extractGeometry.Update()
glyphFilter = vtk.vtkVertexGlyphFilter()
glyphFilter.SetInputConnection(extractGeometry.GetOutputPort())
glyphFilter.Update()
selected = glyphFilter.GetOutput()
print("Selected %s points" % selected.GetNumberOfPoints())
print("Selected %s cells" % selected.GetNumberOfCells())
if vtk.VTK_MAJOR_VERSION <= 5:
self.SelectedMapper.SetInput(selected)
else:
self.SelectedMapper.SetInputData(selected)
self.SelectedMapper.ScalarVisibilityOff()
ids = vtkIdTypeArray.SafeDownCast(selected.GetPointData().GetArray("OriginalIds"))
for i in range(ids.GetNumberOfTuples()):
print("Id %s : %s" % (i, ids.GetValue(i)))
self.SelectedActor.GetProperty().SetColor(1.0, 0.0, 0.0) #(R,G,B)
self.SelectedActor.GetProperty().SetPointSize(3)
self.CurrentRenderer.AddActor(SelectedActor)
self.GetInteractor().GetRenderWindow().Render()
def buildATPMesh():
# Report our CWD just for testing purposes.
print "CWD:", os.getcwd()
# Read in the mesh.
print 'Reading', meshFile
meshReader = vtk.vtkXMLPolyDataReader()
meshReader.SetFileName(meshFile)
meshReader.Update()
ecMesh = meshReader.GetOutput()
# Read in the centreline.
print 'Reading', centrelineFile
centrelineReader = vtk.vtkPolyDataReader()
centrelineReader.SetFileName(centrelineFile)
centrelineReader.Update()
centreline = centrelineReader.GetOutput()
origin = centreline.GetPoint(0)
print 'origin:', origin
# Put the ecMesh through centroids filter.
centroidFilter = vtk.vtkCellCenters()
centroidFilter.SetInputData(ecMesh)
centroidFilter.Update()
centroids = centroidFilter.GetOutput()
# Iterate over each centroid and find the closest segment
centroidPoints = centroids.GetPoints()
# Only for DEBUG output.
distArray = vtk.vtkDoubleArray()
distArray.SetName("Dist")
# For each point calculate the distance from origin.
totalPoints = centroidPoints.GetNumberOfPoints()
for ptId in range(totalPoints):
distance = vtk.vtkMath.Distance2BetweenPoints(origin, centroidPoints.GetPoint(ptId))
distArray.InsertNextValue(math.sqrt(distance))
# Get the range of the distance values.
inMin, inMax = distArray.GetRange()
atpArray = vtk.vtkFloatArray()
atpArray.SetName('initialATP')
# Normalise distance values.
for i in range(distArray.GetNumberOfTuples()):
dist = distArray.GetTuple(i)[0]
distRescaled = rescale(dist, inMin, inMax)
atpVal = sigmoidATP(distRescaled)
atpArray.InsertNextValue(atpVal)
# Prepare debug ATP mesh.
debugAtpDataset = ecMesh
debugAtpDataset.GetCellData().AddArray(distArray)
debugAtpDataset.GetCellData().AddArray(atpArray)
# Save the debug ATP mesh.
debugAtpMapWriter = vtk.vtkXMLPolyDataWriter()
debugAtpMapWriter.SetFileName(debugAtpFile)
debugAtpMapWriter.SetInputData(debugAtpDataset)
debugAtpMapWriter.Update()
# Prepare the ATP mesh by converting all points to vercices.
pointsToVerticesFilter = vtk.vtkVertexGlyphFilter()
pointsToVerticesFilter.SetInputData(centroids)
pointsToVerticesFilter.Update()
atpDataset = pointsToVerticesFilter.GetOutput()
atpDataset.GetCellData().AddArray(atpArray)
# Assert the number of cells is equal to the number of items in the cell arrays.
assert atpArray.GetNumberOfTuples() == debugAtpDataset.GetNumberOfCells(), "Number of cells (%d) and cell data values (%d) mismatch." % (atpArray.GetNumberOfTuples(), debugAtpDataset.GetNumberOfCells())
atpMapWriter = vtk.vtkXMLPolyDataWriter()
atpMapWriter.SetFileName(atpFile)
atpMapWriter.SetInputData(atpDataset)
atpMapWriter.Update()
# Provide a quick visualisation of the ATP profile for validation.
pointsX = numpy.arange(outMin, outMax, 0.001)
pointsY = []
for pt in pointsX:
pointsY.append(sigmoidATP(pt))
pyplot.plot(pointsX, pointsY, 'b')
pyplot.show()
edgeActor.GetProperty().SetLineWidth(theme.GetLineWidth())
edgeActor.SetPosition(0, 0, -0.003);
edgeActor.SetVisibility(0)
lut = vtk.vtkLookupTable()
lutNum = 256
lut.SetNumberOfTableValues(lutNum)
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0, 0, 1.0)
ctf.AddRGBPoint(1.0, 1.0, 0, 0)
for ii,ss in enumerate([float(xx)/float(lutNum) for xx in range(lutNum)]):
cc = ctf.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
vertGlyph = vtk.vtkVertexGlyphFilter()
vertGlyph.SetInputConnection(subgraph.GetOutputPort())
vertMapper = vtk.vtkPolyDataMapper()
vertMapper.SetInputConnection(vertGlyph.GetOutputPort())
vertMapper.SetImmediateModeRendering(True)
vertMapper.SetScalarModeToUsePointFieldData()
vertMapper.SetLookupTable(lut)
vertMapper.SelectColorArray('ExtBasis')
vertMapper.Update()
vertRange = vertMapper.GetInput().GetPointData().GetArray(vertMapper.GetArrayName()).GetRange()
vertMapper.SetScalarRange(-1.0*vertRange[1], vertRange[1])
vertActor = vtk.vtkActor()
vertActor.SetMapper(vertMapper)
# vertActor.GetProperty().SetColor(theme.GetPointColor())
# vertActor.GetProperty().SetOpacity(theme.GetPointOpacity())
vertActor.GetProperty().SetPointSize(theme.GetPointSize())
def scatterplot_3d(data, color=None, point_size=None, cmap="jet", point_shape=None):
if len(data.shape) != 2 or data.shape[1] != 3:
raise ValueError("data must have shape (n, 3) where n is the number of points.")
if point_shape is None:
if len(data) <= 1000:
point_shape = "spheres"
else:
point_shape = "squares"
data = _numpy.float32(data)
data_vtk = array_to_float_array(data)
point_data = _vtk.vtkPoints()
point_data.SetData(data_vtk)
points_poly_data = _vtk.vtkPolyData()
points_poly_data.SetPoints(point_data)
if not color is None:
lut = get_lookup_table(color.min(), color.max())
color_scalars = array_to_vtk(_numpy.float32(color.copy()))
color_scalars.SetLookupTable(lut)
points_poly_data.GetPointData().SetScalars(color_scalars)
if point_shape == "spheres":
if point_size is None:
point_size = _numpy.array(data).std() / len(data)**(1./3.) / 3.
glyph_filter = _vtk.vtkGlyph3D()
glyph_filter.SetInputData(points_poly_data)
sphere_source = _vtk.vtkSphereSource()
sphere_source.SetRadius(point_size)
glyph_filter.SetSourceConnection(sphere_source.GetOutputPort())
glyph_filter.SetScaleModeToDataScalingOff()
if not color is None:
glyph_filter.SetColorModeToColorByScalar()
else:
glyph_filter.SetColorMode(0)
glyph_filter.Update()
elif point_shape == "squares":
if point_size is None:
point_size = 3
glyph_filter = _vtk.vtkVertexGlyphFilter()
glyph_filter.SetInputData(points_poly_data)
glyph_filter.Update()
else:
raise ValueError("{0} is not a valid entry for points".format(points))
poly_data = _vtk.vtkPolyData()
poly_data.ShallowCopy(glyph_filter.GetOutput())
renderer, render_window, interactor = setup_window()
mapper = _vtk.vtkPolyDataMapper()
mapper.SetInputData(poly_data)
if not color is None:
mapper.SetLookupTable(lut)
mapper.SetUseLookupTableScalarRange(True)
points_actor = _vtk.vtkActor()
points_actor.SetMapper(mapper)
points_actor.GetProperty().SetPointSize(point_size)
points_actor.GetProperty().SetColor(0., 0., 0.)
axes_actor = _vtk.vtkCubeAxesActor()
axes_actor.SetBounds(points_actor.GetBounds())
axes_actor.SetCamera(renderer.GetActiveCamera())
axes_actor.SetFlyModeToStaticTriad()
#axes_actor.GetProperty().SetColor(0., 0., 0.)
axes_actor.GetXAxesLinesProperty().SetColor(0., 0., 0.)
axes_actor.GetYAxesLinesProperty().SetColor(0., 0., 0.)
axes_actor.GetZAxesLinesProperty().SetColor(0., 0., 0.)
for i in range(3):
axes_actor.GetLabelTextProperty(i).SetColor(0., 0., 0.)
axes_actor.GetTitleTextProperty(i).SetColor(0., 0., 0.)
renderer.AddActor(points_actor)
renderer.AddActor(axes_actor)
render_window.Render()
interactor.Start()
def loadGraph():
# ----------
# Load and construct whole graph and multi-resolution data from Matlab structure
dataDir = '/Users/emonson/Programming/Matlab/EMonson/Fodava/DocumentAnalysis/Analysis/'
filename = dataDir + 'X20_042709b.mat'
# filename = '/Users/emonson/Programming/Python/VTK/X20_040609b.mat'
X = scipy.io.loadmat(filename)
# Get graph structure G out of matlab variables
G = X['G']
# ----------
# Set multi-resolution level bounds in GUI sliders
levelMax = G.Tree.shape[0]-1
ui_window.hSlider_level.setMinimum(1)
ui_window.hSlider_level.setMaximum(levelMax)
ui_window.spinBox_level.setMinimum(1)
ui_window.spinBox_level.setMaximum(levelMax)
# Start setting up basis function for display as subgraph
ExtBasis = GTree[level,0]['ExtBasis'][0][0][0]
basisMax = ExtBasis.shape[1]-1 # zero-based indices
# Set particular level basis function bounds in GUI sliders
ui_window.hSlider_basisIndex.setMinimum(0)
ui_window.hSlider_basisIndex.setMaximum(basisMax)
ui_window.spinBox_basisIndex.setMinimum(0)
ui_window.spinBox_basisIndex.setMaximum(basisMax)
# Build table which will become graph
table = vtk.vtkTable()
col0 = vtk.vtkIntArray()
col0.SetName('index1')
col1 = vtk.vtkIntArray()
col1.SetName('index2')
val = vtk.vtkDoubleArray()
val.SetName('weight')
Tmat = G.T
# Tmat = G.W
for ii in range(Tmat.nzmax):
col0.InsertNextValue(Tmat.rowcol(ii)[0])
col1.InsertNextValue(Tmat.rowcol(ii)[1])
val.InsertNextValue(abs(Tmat.getdata(ii)))
table.AddColumn(col0)
table.AddColumn(col1)
table.AddColumn(val)
# Vertex links need to be done with index2 first or indexing won't be right...
# TODO: Make this foolproof so that graph always ends up with correct ordering of indices...
tgraph = vtk.vtkTableToGraph()
tgraph.SetInput(table)
tgraph.AddLinkVertex('index2', 'stuff', False)
tgraph.AddLinkVertex('index1', 'stuff', False)
tgraph.AddLinkEdge('index2', 'index1')
rawGraph = tgraph.GetOutput()
rawGraph.Update()
# print graph
# Load and assign whole graph pre-layout coordinates
ptsFile = os.path.splitext(filename)[0] + '_pts.vtp'
if os.path.exists(ptsFile):
polyreader = vtk.vtkXMLPolyDataReader()
polyreader.SetFileName(ptsFile)
polyreader.Update()
pts = polyreader.GetOutput().GetPoints()
rawGraph.SetPoints(pts)
# print pts
strategy = vtk.vtkPassThroughLayoutStrategy()
layout = vtk.vtkGraphLayout()
layout.SetInput(rawGraph)
layout.SetLayoutStrategy(strategy)
edgeLayout = vtk.vtkEdgeLayout()
edgeStrategy = vtk.vtkArcParallelEdgeStrategy()
edgeStrategy.SetNumberOfSubdivisions(50)
edgeLayout.SetInputConnection(layout.GetOutputPort())
edgeLayout.SetLayoutStrategy(edgeStrategy)
graph = edgeLayout.GetOutput()
graph.Update()
# --------
# Add ExtBasis to graph data & Select particular basis function
# print 'ExtBasis shape: ' + str(ExtBasis[:,basisNum].data.shape) + ' (level,basis) (' + str(level) + ',' + str(basisNum) + ')'
# Indexing of ExtBasis is backwards from graph, so need to reverse with [::-1]
# and array not "contiguous" if don't do .copy()
Esub = ExtBasis[:,basisNum].data[::-1].copy()
EsubSq = Esub**2
# Esub = N.random.random(ExtBasis[:,basisNum].data.shape[0])
# SubIdxs = (Esub > 0.001).nonzero()
# SubIdxs = (Esub**2 > 0.8).nonzero()
# Set ExtBasis vertex data from numpy array
basisFunc = VN.numpy_to_vtk(Esub)
basisFunc.SetName('ExtBasis')
basisFuncSq = VN.numpy_to_vtk(EsubSq)
basisFuncSq.SetName('ExtBasisSq')
vertexData = graph.GetVertexData()
vertexData.AddArray(basisFunc)
vertexData.AddArray(basisFuncSq)
selection = vtk.vtkSelectionSource()
selection.SetContentType(7) # vtkSelection::THRESHOLDS
# selection.SetContentType(2) # vtkSelection::PEDIGREE_IDS
selection.SetFieldType(3) # vtkSelection::VERTEX
selection.SetArrayName("ExtBasisSq")
selection.AddThreshold(basisCutoff, 10)
# TODO: There was something wrong with the indexing in the PEDIGREE_IDS selection...
# for ii in SubIdxs[0]:
# selection.AddID(0,ii)
minmax = "(%3.2e, %3.2e)" % (EsubSq.min(), EsubSq.max())
ui_window.label_basisCutoff_minmax.setText(minmax)
selection.Update()
# ----------
# Back to pipeline
degree = vtk.vtkVertexDegree()
degree.SetInput(graph)
subgraph = vtk.vtkExtractSelectedGraph()
subgraph.SetRemoveIsolatedVertices(False)
subgraph.SetInputConnection(degree.GetOutputPort())
subgraph.SetSelectionConnection(selection.GetOutputPort())
# +++++++++++++
graphToPoly = vtk.vtkGraphToPolyData()
graphToPoly.SetInputConnection(subgraph.GetOutputPort())
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.SetInputConnection(graphToPoly.GetOutputPort())
edgeMapper.SetScalarModeToUseCellData()
edgeMapper.SetScalarVisibility(False)
edgeMapper.SetImmediateModeRendering(True)
edgeActor = vtk.vtkActor()
edgeActor.SetMapper(edgeMapper)
edgeActor.SetPosition(0, 0, -0.003);
lut = vtk.vtkLookupTable()
lutNum = 256
lut.SetNumberOfTableValues(lutNum)
ctf = vtk.vtkColorTransferFunction()
ctf.SetColorSpaceToDiverging()
ctf.AddRGBPoint(0.0, 0, 0, 1.0)
ctf.AddRGBPoint(1.0, 1.0, 0, 0)
for ii,ss in enumerate([float(xx)/float(lutNum) for xx in range(lutNum)]):
cc = ctf.GetColor(ss)
lut.SetTableValue(ii,cc[0],cc[1],cc[2],1.0)
vertGlyph = vtk.vtkVertexGlyphFilter()
vertGlyph.SetInputConnection(subgraph.GetOutputPort())
vertMapper = vtk.vtkPolyDataMapper()
vertMapper.SetInputConnection(vertGlyph.GetOutputPort())
vertMapper.SetImmediateModeRendering(True)
vertMapper.SetScalarModeToUsePointFieldData()
vertMapper.SetLookupTable(lut)
vertMapper.SelectColorArray('ExtBasis')
vertMapper.Update()
vertRange = vertMapper.GetInput().GetPointData().GetArray(vertMapper.GetArrayName()).GetRange()
vertMapper.SetScalarRange(-1.0*vertRange[1], vertRange[1])
vertActor = vtk.vtkActor()
vertActor.SetMapper(vertMapper)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetScalarVisibility(False)
outlineMapper.SetImmediateModeRendering(True)
outlineMapper.SetInputConnection(vertGlyph.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.PickableOff()
outlineActor.SetPosition(0, 0, -0.001)
outlineActor.GetProperty().SetRepresentationToWireframe()
outlineActor.SetMapper(outlineMapper)
# Create an Actor Collection for applying visibility to group
basisActorCollection = vtk.vtkActorCollection()
basisActorCollection.AddItem(vertActor)
# basisActorCollection.AddItem(edgeActor)
basisActorCollection.AddItem(outlineActor)
# Apply a theme to the views
theme = vtk.vtkViewTheme.CreateMellowTheme()
theme.SetLineWidth(3)
theme.SetPointSize(5)
theme.SetSelectedCellColor(1,1,1)
theme.SetSelectedPointColor(1,1,1)
theme.SetOutlineColor(0.8, 0.8, 0.8)
# theme.SetPointColor(0.9, 0.7, 0.3)
theme.SetCellColor(0.9, 0.7, 0.3)
# theme.SetPointOpacity(0.5)
# theme.SetPointHueRange(0.0, 0.15)
# theme.SetPointSaturationRange(0.6, 0.8)
# theme.SetPointValueRange(0.4,0.8)
# theme.SetPointAlphaRange(0.2,0.8)
# theme.SetPointAlphaRange(1.0,1.0)
# Apply theme
# vertActor.GetProperty().SetColor(theme.GetPointColor())
# vertActor.GetProperty().SetOpacity(theme.GetPointOpacity())
vertActor.GetProperty().SetPointSize(theme.GetPointSize())
outlineActor.GetProperty().SetPointSize(vertActor.GetProperty().GetPointSize()+2)
outlineActor.GetProperty().SetColor(theme.GetOutlineColor())
outlineActor.GetProperty().SetOpacity(theme.GetPointOpacity())
edgeActor.GetProperty().SetColor(theme.GetCellColor())
edgeActor.GetProperty().SetOpacity(theme.GetCellOpacity())
edgeActor.GetProperty().SetLineWidth(theme.GetLineWidth())
# ----------
# Background graph skeleton
graphMapper = vtk.vtkGraphMapper()
graphMapper.SetInputConnection(0, degree.GetOutputPort(0))
# Apply a theme to the background graph
gtheme = vtk.vtkViewTheme()
gtheme.SetLineWidth(1)
gtheme.SetPointSize(0)
gtheme.SetCellColor(0.8, 0.8, 0.8)
gtheme.SetCellOpacity(0.2)
gtheme.SetOutlineColor(0.8, 0.8, 0.8)
gtheme.SetPointColor(0.8, 0.8, 0.8)
gtheme.SetPointOpacity(0.0)
graphMapper.ApplyViewTheme(gtheme)
graphActor = vtk.vtkActor()
graphActor.SetMapper(graphMapper)
graphActor.SetPosition(0,0,-0.005)
# ----------
# Background vertices
graphPoly = vtk.vtkGraphToPolyData()
graphPoly.SetInputConnection(0, tgraph.GetOutputPort(0))
vertGlyph = vtk.vtkGlyph3D()
vertGlyph.SetInputConnection(0, graphPoly.GetOutputPort())
glyphSource = vtk.vtkGlyphSource2D()
glyphSource.SetGlyphTypeToVertex()
# glyphSource.SetGlyphTypeToCircle()
# glyphSource.SetScale(0.025)
vertGlyph.SetInputConnection(1, glyphSource.GetOutputPort())
vertexMapper = vtk.vtkPolyDataMapper()
vertexMapper.SetInputConnection(vertGlyph.GetOutputPort())
vertexActor = vtk.vtkActor()
vertexActor.SetMapper(vertexMapper)
vertexActor.GetProperty().SetPointSize(4)
vertexActor.GetProperty().SetOpacity(0.5)
vertexActor.GetProperty().SetColor(0.6, 0.6, 0.6)
vertexActor.SetPosition(0, 0, -0.004)
# ----------
# Vertex index labels
labelMapper = vtk.vtkDynamic2DLabelMapper()
labelMapper.SetInputConnection(0, graphPoly.GetOutputPort(0))
labelMapper.SetLabelModeToLabelFieldData()
labelMapper.SetFieldDataName("label")
labelMapper.SetLabelFormat("%s")
labelMapper.GetLabelTextProperty().SetColor(0.0, 0.0, 0.0)
labelActor = vtk.vtkActor2D()
labelActor.SetMapper(labelMapper)
# ----------
# MultiScale Graph
msGraph = buildSubGraph(level)
msMapper = vtk.vtkGraphMapper()
msMapper.SetInput(msGraph)
msMapper.SetColorEdges(True)
msMapper.SetEdgeColorArrayName('weight')
# Apply a theme to the background graph
mtheme = vtk.vtkViewTheme()
mtheme.SetLineWidth(3)
mtheme.SetPointSize(11)
# mtheme.SetCellColor(0.5, 0.5, 0.7)
# mtheme.SetCellOpacity(0.5)
mtheme.SetOutlineColor(0.8, 0.8, 0.8)
mtheme.SetPointColor(0.3, 0.3, 0.6)
mtheme.SetPointOpacity(1.0)
mtheme.SetCellHueRange(0.67, 0.67)
mtheme.SetCellSaturationRange(0.6, 0.1)
mtheme.SetCellValueRange(0.5,1.0)
mtheme.SetCellAlphaRange(0.2,0.8)
msMapper.ApplyViewTheme(mtheme)
msActor = vtk.vtkActor()
msActor.SetMapper(msMapper)
msActor.SetPosition(0,0,-0.002)
# ----------
# Set up window and add actors
view.SetLayoutStrategyToPassThrough()
# view.ApplyViewTheme(theme)
# view.SetupRenderWindow(win)
view.GetRenderer().SetBackground(theme.GetBackgroundColor())
view.GetRenderer().SetBackground2(theme.GetBackgroundColor2())
view.GetRenderer().SetGradientBackground(True)
view.GetRenderer().AddActor(vertActor)
view.GetRenderer().AddActor(outlineActor)
view.GetRenderer().AddActor(edgeActor)
view.GetRenderer().AddActor(graphActor)
view.GetRenderer().AddActor(vertexActor)
view.GetRenderer().AddActor(labelActor)
view.GetRenderer().AddActor(msActor)
# ----------
# General interactor
isty = vtk.vtkInteractorStyleRubberBand2D()
# RubberBand2D assumes/needs parallel projection ON
view.GetRenderer().GetActiveCamera().ParallelProjectionOn()
iren = view.GetRenderWindow().GetInteractor()
iren.SetInteractorStyle(isty)
# Interactor style must be set before scalar bar can be shown
# view.SetVertexScalarBarVisibility(True)
sbActor = vtk.vtkScalarBarActor()
sbActor.SetLookupTable(vertMapper.GetLookupTable())
sbActor.SetTitle(vertMapper.GetArrayName())
sbActor.SetNumberOfLabels(3)
vertexScalarBar = vtk.vtkScalarBarWidget()
vertexScalarBar.SetScalarBarActor(sbActor)
vertexScalarBar.SetInteractor(iren)
vertexScalarBar.SetDefaultRenderer(view.GetRenderer())
vertexScalarBar.SetCurrentRenderer(view.GetRenderer())
vertexScalarBar.SetEnabled(True)
scalarBarRep = vertexScalarBar.GetRepresentation()
scalarBarRep.SetOrientation(1) # 0 = Horizontal, 1 = Vertical
scalarBarRep.GetPositionCoordinate().SetValue(0.05,0.05)
scalarBarRep.GetPosition2Coordinate().SetValue(0.15,0.25)
# Adding it this way gets it to show up, but it's not interactive
view.GetRenderer().AddActor(sbActor)
view.ResetCamera()
view.Render()
# ----------
# Add Actors to QListWidget to allow check and uncheck for visibility
listItem0 = QtGui.QListWidgetItem()
listItem0.setText('Index Labels')
listItem0.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
labelActor.SetVisibility(0)
listItem0.setCheckState(QtCore.Qt.Unchecked)
# Put actor it in as data in the list widget item
listItem0.setData(QtCore.Qt.UserRole, QtCore.QVariant(labelActor))
ui_window.listWidget.insertItem(0,listItem0)
# Test retrieval of actor from list widget item
# tmpItem = ui_window.listWidget.item(0)
# tmpQtActor = tmpItem.data(QtCore.Qt.UserRole)
# tmpActor = tmpQtActor.toPyObject()
# tmpActor.SetVisibility(0)
# Shorter way to add item to list widget
listItem1 = QtGui.QListWidgetItem('Vertices (background)', ui_window.listWidget)
listItem1.setData(QtCore.Qt.UserRole, QtCore.QVariant(vertexActor))
listItem1.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem1.setCheckState(QtCore.Qt.Checked)
listItem2 = QtGui.QListWidgetItem('Graph (background)', ui_window.listWidget)
listItem2.setData(QtCore.Qt.UserRole, QtCore.QVariant(graphActor))
listItem2.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem2.setCheckState(QtCore.Qt.Checked)
listItem3 = QtGui.QListWidgetItem()
listItem3.setText('Basis Function Vertices')
listItem3.setData(QtCore.Qt.UserRole, QtCore.QVariant(basisActorCollection))
listItem3.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem3.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(1,listItem3)
listItem6 = QtGui.QListWidgetItem()
listItem6.setText('Basis Function Edges')
listItem6.setData(QtCore.Qt.UserRole, QtCore.QVariant(edgeActor))
listItem6.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem6.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(2,listItem6)
listItem4 = QtGui.QListWidgetItem()
listItem4.setText('MultiScale Graph')
listItem4.setData(QtCore.Qt.UserRole, QtCore.QVariant(msActor))
listItem4.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem4.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(3,listItem4)
listItem5 = QtGui.QListWidgetItem()
listItem5.setText('Basis Function Scale Bar')
listItem5.setData(QtCore.Qt.UserRole, QtCore.QVariant(sbActor))
listItem5.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
listItem5.setCheckState(QtCore.Qt.Checked)
ui_window.listWidget.insertItem(3,listItem5)
iren.Initialize()
iren.Start()
# Add distances to each point
signedDistances = vtk.vtkFloatArray()
signedDistances.SetNumberOfComponents(1)
signedDistances.SetName("SignedDistances")
# Evaluate the signed distance function at all of the grid points
for pointId in range(points.GetNumberOfPoints()):
p = points.GetPoint(pointId)
signedDistance = implicitPolyDataDistance.EvaluateFunction(p)
signedDistances.InsertNextValue(signedDistance)
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
polyData.GetPointData().SetScalars(signedDistances)
vertexGlyphFilter = vtk.vtkVertexGlyphFilter()
vertexGlyphFilter.SetInputData(polyData)
vertexGlyphFilter.Update()
signedDistanceMapper = vtk.vtkPolyDataMapper()
signedDistanceMapper.SetInputConnection(vertexGlyphFilter.GetOutputPort())
signedDistanceMapper.ScalarVisibilityOn()
signedDistanceActor = vtk.vtkActor()
signedDistanceActor.SetMapper(signedDistanceMapper)
renderer = vtk.vtkRenderer()
renderer.AddViewProp(sphereActor)
renderer.AddViewProp(signedDistanceActor)
renderWindow = vtk.vtkRenderWindow()
def writeLegacyVTK():
# This is where the data is for testing purposes.
print "Current working directory:", os.getcwd()
if os.path.isdir("vtk") == False:
os.makedirs("vtk")
print "Cretated vtk output directory..."
if os.path.isdir("files") == False:
os.makedirs("files")
print "Created files ouptut directory..."
# Working with the task mesh.
taskMeshReader = vtk.vtkXMLPolyDataReader()
taskMeshReader.SetFileName(meshSet[0])
taskMeshReader.Update()
taskMesh = taskMeshReader.GetOutput()
# Get the range of branch labels.
labelRange = [0, 0]
taskMesh.GetCellData().GetScalars().GetRange(labelRange, 0)
# Convert label range to a list of labels.
labelRange = range(int(labelRange[0]), int(labelRange[1]) + 1)
print "Labels found in task mesh:", labelRange
# Store the number of rings for each label.
numRingsPerLabel = {}
# For every label in the range of labels we want to extract all cells/quads.
for label in labelRange:
# Use this filter to extract the cells for a given label value.
branchSelector = vtk.vtkThreshold()
branchSelector.SetInputData(taskMesh)
branchSelector.ThresholdBetween(label,label);
branchSelector.Update()
taskMeshBranch = branchSelector.GetOutput()
# New vtkPoints for storing reordered points.
reorderedPoints = vtk.vtkPoints()
# New vtkCellArray for storing reordeced cells.
reorderedCellArray = vtk.vtkCellArray()
numQuadRowsPerBranch = taskMeshBranch.GetNumberOfCells() / numQuadsPerRing;
numRingsPerLabel[label] = numQuadRowsPerBranch
ringIds = range(0, numQuadRowsPerBranch);
# Working with rows in reverse order: UPSTREAM.
ringIds.reverse()
rowBase = 0
# Iterate over the rings in reverse order.
for ringNum in ringIds:
# Iterate over the cells in normal order.
for cellNum in range(0, numQuadsPerRing):
# Calculate the 'real' cell id and get the corresponding cell.
cellId = ringNum * numQuadsPerRing + cellNum
cell = taskMeshBranch.GetCell(cellId)
# The ids to be written to the TXT file.
pointIdList = [cell.GetNumberOfPoints()]
# Write the appropriate points to TXT file.
for pPos in range(0, cell.GetNumberOfPoints()):
newPoint = False
if ringNum == ringIds[0]:
if cellNum == 0:
newPoint = True
elif pPos == 1 or pPos == 2:
newPoint = True
else:
if cellNum == 0:
if pPos == 0 or pPos == 1:
newPoint = True
else:
if pPos == 1:
newPoint = True
if newPoint == True:
# Inserting a new point...
point = taskMeshBranch.GetPoint(cell.GetPointId(pPos))
# ... with a new id.
newId = reorderedPoints.InsertNextPoint(point)
pointIdList.append(newId)
# To make it easier for remembering the number of points instered in a row.
if cellNum == 0 and pPos == 0:
rowBasePrev = newId
else:
# Perhaps this can be done in a nicer way.
# Calculate the id of a previously inserted point.
if ringNum == ringIds[0]:
if cellNum == 1:
if pPos == 0:
pointIdList.append(1L)
elif pPos == 3:
pointIdList.append(2L)
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 2))
elif pPos == 3:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 3))
elif ringNum == ringIds[1]:
if cellNum == 0:
if pPos == 2:
pointIdList.append(1L)
elif pPos == 3:
pointIdList.append(0L)
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(cellNum * 2 + 2))
elif pPos == 3:
if cellNum == 1:
pointIdList.append(1L)
else:
pointIdList.append(long(cellNum * 2))
else:
if cellNum == 0:
if pPos == 2:
pointIdList.append(long(rowBase + 1))
elif pPos == 3:
pointIdList.append(long(rowBase))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(rowBase + cellNum + 1))
elif pPos == 3:
pointIdList.append(long(rowBase + cellNum))
# print pointIdList, rowBase
# Insert the ids into the cell array.
newCell = vtk.vtkQuad()
newCell.GetPointIds().Reset()
for id in pointIdList[1:]:
newCell.GetPointIds().InsertNextId(id)
reorderedCellArray.InsertNextCell(newCell)
rowBase = rowBasePrev
# print '\n'
print "Inserted", reorderedPoints.GetNumberOfPoints(), "task mesh points for label", label, "..."
print "Inserted", reorderedCellArray.GetNumberOfCells(), "task mesh cells for label", label, "..."
# Create new vtkPolyData object for the new reordered mesh.
reorderedTaskMeshBranch = vtk.vtkPolyData()
# Put the reordered points and cells into the reordered mesh.
reorderedTaskMeshBranch.SetPoints(reorderedPoints)
reorderedTaskMeshBranch.SetPolys(reorderedCellArray)
# Write the VTK file.
reorderedMeshWriter = vtk.vtkXMLPolyDataWriter()
reorderedMeshWriter.SetInputData(reorderedTaskMeshBranch)
reorderedMeshWriter.SetFileName(taskVTKFiles[label])
reorderedMeshWriter.Update()
print "Rings per label:", numRingsPerLabel, "..."
ringsPerLabelVals = numRingsPerLabel.values()
# Check all rings per label values are the same.
assert ringsPerLabelVals[1:] == ringsPerLabelVals[:-1], "All values of rings per label must be identical. Generated output is invalid ..."
# Working with EC mesh.
ecMeshReader = vtk.vtkXMLPolyDataReader()
ecMeshReader.SetFileName(meshSet[1])
ecMeshReader.Update()
# Original ECs mesh to work with.
ecMesh = ecMeshReader.GetOutput()
print "There are", ecMesh.GetNumberOfCells(), "ECs in total ..."
# For every label in the range of labels we want to extract all ECs.
for label in labelRange:
# Keep track of how many branches we need to skip.
numECsPerLabel = numQuadsPerRing * numRingsPerLabel[label] * numECsPerQuad
ecCellOffset = label * numECsPerLabel
print "ecCellOffset", ecCellOffset
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, numECsPerLabel):
selectionIds.InsertNextValue(ecCellOffset + sId)
# Create selecion node.
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(selectionNode.CELL)
selectionNode.SetContentType(selectionNode.INDICES)
selectionNode.SetSelectionList(selectionIds)
# Create selection.
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
# Use vtkSelection filter.
selectionExtractor = vtk.vtkExtractSelection()
selectionExtractor.SetInputData(0, ecMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedECs = selectionExtractor.GetOutput()
# Ring ids list for traversal.
ringIds = range(0, numRingsPerLabel[label])
ringIds.reverse()
# Number of ECs rows is the number of ECs per quad.
rowIds = range(0, numECsPerCol)
rowIds.reverse()
# The ECs are organised in rings of blocks of cells.
# New vtkCellArray for storing reordeced cells.
reorderedCellArray = vtk.vtkCellArray()
# Iterate over the rings in reverse order.
for ringNum in ringIds:
# Iterate over the 'imaginary' quads of cells in normal order.
for quadNum in range(0, numQuadsPerRing):
# Iterate over the rows of cells in reverse order.
# Calculate the 'real' id for the 'imaginary' quad.
quadId = ringNum * numQuadsPerRing + quadNum
# Iterate over rows of cells in reverse order.
for rowNum in rowIds:
# Iterate over the rows of cells in normal order.
for ecNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
ecId = quadId * numECsPerQuad + rowNum * numECsPerRow + ecNum
ecCell = extractedECs.GetCell(ecId)
reorderedCellArray.InsertNextCell(ecCell)
# Create new vtkPolyData object for the new reordered mesh.
reorderedECMeshBranch = vtk.vtkPolyData()
# Insert our new points.
reorderedECMeshBranch.SetPoints(extractedECs.GetPoints())
# Set the reordered cells to the reordered ECs mesh.
reorderedECMeshBranch.SetPolys(reorderedCellArray)
# New vtkPoints for storing reordered points.
reorderedPoints = vtk.vtkPoints()
# New vtkCellArray for storing reordeced cells.
reorderedCellArray = vtk.vtkCellArray()
rowBase = 0
# Iterate over quads in normal order because they have been reordered.
for quadNum in range(0, numRingsPerLabel[label] * numQuadsPerRing):
# Iterate over rows in normal order because they have been reordered.
for rowNum in range(0, numECsPerCol):
# Iterate over the ECs in the row in normal order.
for ecNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
ecId = quadNum * numECsPerQuad + rowNum * numECsPerRow + ecNum
ecCell = reorderedECMeshBranch.GetCell(ecId)
# The ids to be written to the TXT file.
pointIdList = [ecCell.GetNumberOfPoints()]
# Write the appropriate points to the TXT file.
for pPos in range(0, ecCell.GetNumberOfPoints()):
newPoint = False
if rowNum == 0:
if ecNum == 0:
newPoint = True
elif pPos == 1 or pPos == 2:
newPoint = True
else:
if ecNum == 0:
if pPos == 0 or pPos == 1:
newPoint = True
else:
if pPos == 1:
newPoint = True
if newPoint == True:
# Inserting a new point...
point = reorderedECMeshBranch.GetPoint(ecCell.GetPointId(pPos))
# ... with a new id.
newId = reorderedPoints.InsertNextPoint(point)
pointIdList.append(newId)
if ecNum == 0 and pPos == 0:
rowBasePrev = newId
else:
# Perhaps this can be done in a nicer way.
# Calculate the ide of a previously inserted point.
if rowNum == 0:
if ecNum == 1:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 3))
elif pPos == 3:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 4))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 2))
elif pPos == 3:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 3))
elif rowNum == 1:
if ecNum == 0:
if pPos == 2:
pointIdList.append(long(rowBase + 1))
elif pPos == 3:
pointIdList.append(long(rowBase))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(rowBase + ecNum * 2 + 2))
elif pPos == 3:
if ecNum == 1:
pointIdList.append(long(rowBase + 1))
else:
pointIdList.append(long(rowBase + ecNum * 2))
else:
if ecNum == 0:
if pPos == 2:
pointIdList.append(long(rowBase + 1))
elif pPos == 3:
pointIdList.append(long(rowBase))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(rowBase + ecNum + 1))
elif pPos == 3:
pointIdList.append(long(rowBase + ecNum))
# print pointIdList, rowBase
# Insert the ids into the cell array.
newCell = vtk.vtkQuad()
newCell.GetPointIds().Reset()
for id in pointIdList[1:]:
newCell.GetPointIds().InsertNextId(id)
reorderedCellArray.InsertNextCell(newCell)
rowBase = rowBasePrev
# print '\n'
print "There are", reorderedPoints.GetNumberOfPoints(), "ECs points for label", label, "..."
print "There are", reorderedCellArray.GetNumberOfCells(), "ECs cells for label", label, "..."
# Create new vtkPolyData object for the new reordered mesh.
reorderedECs = vtk.vtkPolyData()
# Put the reordered points and cells into the mesh.
reorderedECs.SetPoints(reorderedPoints)
reorderedECs.SetPolys(reorderedCellArray)
# Write the VTK EC mesh file.
reorderedMeshWriter = vtk.vtkXMLPolyDataWriter()
reorderedMeshWriter.SetInputData(reorderedECs)
reorderedMeshWriter.SetFileName(ecVTKFiles[label])
reorderedMeshWriter.Update()
# Use VTK centroid filter to get the centroids in the right order
# from the reorderedECMeshBranch.
centroidFilter = vtk.vtkCellCenters()
centroidFilter.SetInputData(reorderedECs)
centroidFilter.Update()
# Create a vertex cell for each point.
pointsToVerticesFilter = vtk.vtkVertexGlyphFilter()
pointsToVerticesFilter.SetInputData(centroidFilter.GetOutput())
pointsToVerticesFilter.Update()
reorderedCentroidBranch = pointsToVerticesFilter.GetOutput()
# Write the VTK EC centrouid file.
centroidWriter = vtk.vtkXMLPolyDataWriter()
centroidWriter.SetInputData(reorderedCentroidBranch)
centroidWriter.SetFileName(ecCentroidVTKFiles[label])
centroidWriter.Update()
# Write the centroids to the TXT points and cells files.
for cId in range(0, reorderedCentroidBranch.GetNumberOfCells()):
centCell = reorderedCentroidBranch.GetCell(cId)
centIds = [centCell.GetNumberOfPoints()]
# Write centroid ids.
ptId = centCell.GetPointId(0)
centIds.append(ptId)
# Write centroid points.
point = reorderedCentroidBranch.GetPoint(ptId)
# Working with SMC mesh.
# Working with SMC mesh.
# Working with SMC mesh.
smcMeshReader = vtk.vtkXMLPolyDataReader()
smcMeshReader.SetFileName(meshSet[2])
smcMeshReader.Update()
# Original SMCs mesh to work with.
smcMesh = smcMeshReader.GetOutput()
print "There are", smcMesh.GetNumberOfCells(), "SMCs in total ..."
# For every label in the range of labels we want to extract all SMCs.
for label in labelRange:
# Keep track of how many branches we need to skip.
numSMCsPerLabel = numQuadsPerRing * numRingsPerLabel[label] * numSMCsPerQuad
smcCellOffset = label * numSMCsPerLabel
print "smcCellOffset", smcCellOffset
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, numSMCsPerLabel):
selectionIds.InsertNextValue(smcCellOffset + sId)
# Create selecion node.
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(selectionNode.CELL)
selectionNode.SetContentType(selectionNode.INDICES)
selectionNode.SetSelectionList(selectionIds)
# Create selection.
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
# Use vtkSelection filter.
selectionExtractor = vtk.vtkExtractSelection()
selectionExtractor.SetInputData(0, smcMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedSMCs = selectionExtractor.GetOutput()
# Ring ids list for traversal.
ringIds = range(0, numRingsPerLabel[label])
ringIds.reverse()
# Number of SMCs rows is the number of ECs per quad times 13.
rowIds = range(0, numSMCsPerCol)
rowIds.reverse()
# The SMCs are organised in rings of blocks of cells.
# New vtkCellArray for storing reordeced cells.
reorderedCellArray = vtk.vtkCellArray()
# Iterate over the rings in reverse order.
for ringNum in ringIds:
# Iterate over the 'imaginary' quads of cells in normal order.
for quadNum in range(0, numQuadsPerRing):
# Iterate over the rows of cells in reverse order.
# Calculate the 'real' id for the 'imaginary' quad.
quadId = ringNum * numQuadsPerRing + quadNum
# Iterate over rows of cells in reverse order.
for rowNum in rowIds:
# Iterate over the rows of cells in normal order.
for smcNum in range(0, numSMCsPerRow):
# Calculate the 'real' smc cell id and get the corresponding cell.
smcId = quadId * numSMCsPerQuad + rowNum * numSMCsPerRow + smcNum
smcCell = extractedSMCs.GetCell(smcId)
reorderedCellArray.InsertNextCell(smcCell)
# Create new vtkPolyData object for the new reordered mesh.
reorderedSMCMeshBranch = vtk.vtkPolyData()
# Insert our new points.
reorderedSMCMeshBranch.SetPoints(extractedSMCs.GetPoints())
# Set the reordered cells to the reordered SMCs mesh.
reorderedSMCMeshBranch.SetPolys(reorderedCellArray)
# New vtkPoints for storing reordered points.
reorderedPoints = vtk.vtkPoints()
# New vtkCellArray for storing reordeced cells.
reorderedCellArray = vtk.vtkCellArray()
rowBase = 0
# Iterate over quads in normal order because they have been reordered.
for quadNum in range(0, numRingsPerLabel[label] * numQuadsPerRing):
# Iterate over rows in normal order because they have been reordered.
for rowNum in range(0, numSMCsPerCol):
# Iterate over the SMCs in the row in normal order.
for smcNum in range(0, numSMCsPerRow):
# Calculate the 'real' smc cell id and get the corresponding cell.
smcId = quadNum * numSMCsPerQuad + rowNum * numSMCsPerRow + smcNum
smcCell = reorderedSMCMeshBranch.GetCell(smcId)
# The ids to be written to the TXT file.
pointIdList = [smcCell.GetNumberOfPoints()]
# Write the appropriate points to the TXT file.
for pPos in range(0, smcCell.GetNumberOfPoints()):
newPoint = False
if rowNum == 0:
if smcNum == 0:
newPoint = True
elif pPos == 1 or pPos == 2:
newPoint = True
else:
if smcNum == 0:
if pPos == 0 or pPos == 1:
newPoint = True
else:
if pPos == 1:
newPoint = True
if newPoint == True:
# Inserting a new point...
point = reorderedSMCMeshBranch.GetPoint(smcCell.GetPointId(pPos))
# with a new id.
newId = reorderedPoints.InsertNextPoint(point)
pointIdList.append(newId)
if smcNum == 0 and pPos == 0:
rowBasePrev = newId
else:
# Perhaps this can be done in a nicer way.
# Calculate the ide of a previously inserted point.
if rowNum == 0:
if smcNum == 1:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 3))
elif pPos == 3:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 4))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 2))
elif pPos == 3:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 3))
elif rowNum == 1:
if smcNum == 0:
if pPos == 2:
pointIdList.append(long(rowBase + 1))
elif pPos == 3:
pointIdList.append(long(rowBase))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(rowBase + smcNum * 2 + 2))
elif pPos == 3:
if smcNum == 1:
pointIdList.append(long(rowBase + 1))
else:
pointIdList.append(long(rowBase + smcNum * 2))
else:
if smcNum == 0:
if pPos == 2:
pointIdList.append(long(rowBase + 1))
elif pPos == 3:
pointIdList.append(long(rowBase))
else:
if pPos == 0:
pointIdList.append(long(reorderedPoints.GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(long(rowBase + smcNum + 1))
elif pPos == 3:
pointIdList.append(long(rowBase + smcNum))
# print pointIdList, rowBase
# Insert the ids into the cell array.
newCell = vtk.vtkQuad()
newCell.GetPointIds().Reset()
for id in pointIdList[1:]:
newCell.GetPointIds().InsertNextId(id)
reorderedCellArray.InsertNextCell(newCell)
rowBase = rowBasePrev
# print '\n'
print "There are", reorderedPoints.GetNumberOfPoints(), "SMCs points for label", label, "..."
print "There are", reorderedCellArray.GetNumberOfCells(), "SMCs cells for label", label, "..."
# Create new vtkPolyData object for the new reordered mesh.
reorderedSMCs = vtk.vtkPolyData()
# Put the reordered points and cells in to the mesh.
reorderedSMCs.SetPoints(reorderedPoints)
reorderedSMCs.SetPolys(reorderedCellArray)
# Write the VTK SMC mesh file.
reorderedMeshWriter = vtk.vtkXMLPolyDataWriter()
reorderedMeshWriter.SetInputData(reorderedSMCs)
reorderedMeshWriter.SetFileName(smcVTKFiles[label])
reorderedMeshWriter.Update()
print "All done ..."
print "... Except the last configuration_info.txt file ..."
configFile = open("files/configuration_info.txt", 'w')
configFile.write("Processors information\n")
configFile.write("Total number of points per branch (vtk points) = %d\t\tm = %d n = %d\n" \
% ((numQuadsPerRing + 1) * (numRingsPerLabel[0] + 1), (numQuadsPerRing + 1), (numRingsPerLabel[0] + 1)))
configFile.write("Total number of cells per branch (vtk cells) = %d\t\tm = %d n = %d\n" \
% (numQuadsPerRing * numRingsPerLabel[0], numQuadsPerRing, numRingsPerLabel[0]))
configFile.write("Total number of SMC mesh points per processor mesh (vtk points) = %d\t\tm = %d n = %d\n" \
% ((numSMCsPerCol + 1) * (numSMCsPerRow + 1), (numSMCsPerCol + 1), (numSMCsPerRow + 1)))
configFile.write("Total number of SMC mesh cells per processor mesh (vtk cells) = %d\t\tm = %d n = %d\n" \
% (numSMCsPerCol * numSMCsPerRow, numSMCsPerCol, numSMCsPerRow))
configFile.write("Total number of EC mesh points per processor mesh (vtk points) = %d\t\tm = %d n = %d\n" \
% ((numECsPerCol + 1) * (numECsPerRow + 1), (numECsPerCol + 1), (numECsPerRow + 1)))
configFile.write("Total number of EC mesh cells per processor mesh (vtk cells) = %d\t\tm = %d n = %d\n" \
% (numECsPerCol *numECsPerRow, numECsPerCol, numECsPerRow))
configFile.write("Total number of EC mesh centeroid points per processor mesh (vtk points) = %d\t\tm = %d n = %d\n" \
% (numECsPerCol *numECsPerRow, numECsPerCol, numECsPerRow))
configFile.write("Total number of EC mesh centeroid cells per processor mesh (vtk cells) = %d\t\tm = %d n = %d\n" \
% (numECsPerCol *numECsPerRow, numECsPerCol, numECsPerRow))
configFile.close()
print "Now it is all done for real ..."
def buildATPMesh():
# Report our CWD just for testing purposes.
print "CWD:", os.getcwd()
# Read in the mesh.
meshReader = vtk.vtkXMLPolyDataReader()
meshReader.SetFileName(meshFile)
meshReader.Update()
mesh = meshReader.GetOutput()
print mesh.GetNumberOfCells()
# Put it through centroids filter.
# Use VTK centroid filter to get the centroids in the right order
# from the reorderedECMeshBranch.
centroidFilter = vtk.vtkCellCenters()
centroidFilter.SetInput(mesh)
# Create a vertex cell for each point.
pointsToVerticesFilter = vtk.vtkVertexGlyphFilter()
pointsToVerticesFilter.SetInputConnection(centroidFilter.GetOutputPort())
pointsToVerticesFilter.Update()
atpDataset = pointsToVerticesFilter.GetOutput()
# Here we are assuming that cell ordering has been preserved.
gridCoords = mesh.GetCellData().GetArray("gridCoords")
# Create a new cell data array "parametricDistance" in the centroids
# dataset with the values from the previous step. This array is really not
# needed for any computations but is good to have for verification. Also,
# it is useful to know the max value for each branch.
axialDist = vtk.vtkIntArray()
axialDist.SetName("parametriDistance")
# Iterate over all quad cells in the mesh and pull out the first component
# of the "gridCoords" cell data array. Here we assuming the mesh contains
# only quad cells.
# If the branches were labelled properly here, it would be much simpler
# to set the neganive axial distance values by examining the range first.
for cellId in range(0, mesh.GetNumberOfCells()):
axialDist.InsertNextValue(gridCoords.GetTuple(cellId)[0])
atpArray = vtk.vtkDoubleArray()
atpArray.SetName("initialATP")
axialDistRange = [0, 0]
axialDist.GetRange(axialDistRange, 0)
# Iterate over the "axialDist" cell array and for each value call
# the agonistValue function and store the computed values in the new
# "initialATP" cell data array.
for cellId in range(0, axialDist.GetNumberOfTuples()):
# Figure out the current branch id.
branchId = cellId / (axialDist.GetNumberOfTuples() / 3)
# For the first branch the parametric distance value must be in the
# range [maxDist - 1, 0). Range values are required for this.
# TODO: The ATP calculations here are repeated many times for the same value
# of the parametric distnace. It would make sense to have a lookup table (dictionary)
# for previously calculated values.
if branchId == 0:
distVal = axialDist.GetValue(cellId) - axialDistRange[1] - 1
atpVal = sigmoidATP(distVal)
else:
# This is for the 'normal' atp map.
distVal = axialDist.GetValue(cellId)
atpVal = sigmoidATP(distVal)
atpArray.InsertNextValue(atpVal)
# Assert the number of cells is equal to the number of items in the cell arrays.
assert axialDist.GetNumberOfTuples() == atpDataset.GetNumberOfCells(), "Number of cells (%d) and cell data values (%d) mismatch." % (axialDist.GetNumberOfTuples(), atpDataset.GetNumberOfCells)
assert atpArray.GetNumberOfTuples() == atpDataset.GetNumberOfCells(), "Number of cells (%d) and cell data values (%d) mismatch." % (atpArray.GetNumberOfTuples(), atpDataset.GetNumberOfCells())
atpDataset.GetCellData().AddArray(axialDist)
atpDataset.GetCellData().AddArray(atpArray)
atpMapWriter = vtk.vtkXMLPolyDataWriter()
atpMapWriter.SetFileName(atpFile)
atpMapWriter.SetInput(atpDataset)
atpMapWriter.Update()
# Provide a quick visualisation of the ATP profile for validation.
pointsX = range(-int(axialDistRange[1] - 1), int(axialDistRange[1]))
pointsY = []
for pt in pointsX:
pointsY.append(sigmoidATP(pt))
pyplot.plot(pointsX, pointsY, 'b')
pyplot.show()
