def addblockid(ug):
# get number of elements in ug:
nele = int(ug.GetNumberOfCells())
# add blockID to ug (required by the ensight format)
blockIDs = vtk.vtkUnsignedIntArray()
blockIDs.SetNumberOfTuples(nele)
blockIDs.SetNumberOfComponents(1)
blockIDs.SetName("BlockId")
for j in range(nele):
blockIDs.SetValue(j,1)
ug.GetCellData().AddArray(blockIDs)
return ug
def addblockid(ug):
# get number of elements in ug:
nele = int(ug.GetNumberOfCells())
# add blockID to ug (required by the ensight format)
blockIDs = vtk.vtkUnsignedIntArray()
blockIDs.SetNumberOfTuples(nele)
blockIDs.SetNumberOfComponents(1)
blockIDs.SetName("BlockId")
for j in range(nele):
blockIDs.SetValue(j,1)
ug.GetCellData().AddArray(blockIDs)
return ug
def createUnsignedIntArray(name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=0):
uiarray = vtk.vtkUnsignedIntArray()
uiarray.SetName(name)
uiarray.SetNumberOfComponents(n_components)
uiarray.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_tuple in xrange(n_tuples):
uiarray.SetTuple(k_tuple, [0] * n_components)
return uiarray
def createUnsignedIntArray(name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=0):
array = vtk.vtkUnsignedIntArray()
array.SetName(name)
array.SetNumberOfComponents(n_components)
array.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_component in range(n_components):
array.FillComponent(k_component, 0.)
return array
def createUnsignedIntArray(
name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=0):
uiarray = vtk.vtkUnsignedIntArray()
uiarray.SetName(name)
uiarray.SetNumberOfComponents(n_components)
uiarray.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_tuple in xrange(n_tuples):
uiarray.SetTuple(k_tuple, [0]*n_components)
return uiarray
def prepareDelaunayData(dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
dim = len(global_nodecoords[0])
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0, len(agg_globalnodeidx)):
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
if dimension == 2:
id = Points.InsertNextPoint(nodecoords[0], nodecoords[1], 0.0)
elif dimension == 3:
id = Points.InsertNextPoint(
nodecoords[0] + 0.001 * random.random(),
nodecoords[1] + 0.001 * random.random(),
nodecoords[2] + 0.001 * random.random(),
)
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
# create polygon for current aggregate
polydata = vtk.vtkPolyData()
polydata.SetPoints(Points)
polydata.SetVerts(Vertices)
polydata.Modified()
polydata.Update()
polydata2 = vtk.vtkPolyData()
if Points.GetNumberOfPoints() > 2: # todo: avoid error messages + add support for lines/surfaces
# create delaunay object
if dimension == 2:
delaunay = vtk.vtkDelaunay2D()
elif dimension == 3:
delaunay = vtk.vtkDelaunay3D()
# delaunay.SetAlpha(0.1)
delaunay.SetInput(polydata)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
polydata2 = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0, Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0, Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata2.SetPoints(Points)
polydata2.SetVerts(Vertices)
polydata2.GetPointData().SetScalars(Ids)
polydata2.GetPointData().AddArray(Procs)
polydata2.Modified()
polydata2.Update()
aggpolygons.AddInput(polydata2)
def om_display_vtk(f,d = 0,n = 0):
"""
This function displays a VTK::vtk file generated with OpenMEEG.
Such a file defines a polydata, containing points and triangles of a single
mesh. Most often a EEG helmet mesh and associated leadfield.
"""
welcome = """Welcome\n\n
Move the slider to see all sources (columns of the input matrix)\n
Press 'r': To select points/cells.\n"""
# This callback function does updates the mappers for where n is the slider value
def CleanPickData(object, event):
ren.RemoveActor(selactor)
PickData(object, event, selactor, 0, view, text_init)
def SelectSource(object, event): # object will be the slider2D
slidervalue = int(round(object.GetRepresentation().GetValue()))
mapper.GetInput().GetPointData().SetActiveScalars("Potentials-"+str(slidervalue))
renWin.SetWindowName(renWin.GetWindowName()[0:(renWin.GetWindowName().find('-')+1)]+str(slidervalue))
UpdateColorBar(colorBar, mapper)
# A window with an interactor
renWin = vtk.vtkRenderWindow()
renWin.SetSize(600, 600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.SetInteractorStyle(vtk.vtkInteractorStyleRubberBandPick())
# A picker (to pick points/cells)
picker = vtk.vtkRenderedAreaPicker()
iren.SetPicker(picker)
# Read the input file
reader = vtk.vtkPolyDataReader()
reader.SetFileName(f); reader.Update()
poly = reader.GetOutput()
renWin.SetWindowName(f+' Potentials-'+str(n))
# determine the number of sources
nb_sources = 0
for i in range(poly.GetPointData().GetNumberOfArrays()):
if poly.GetPointData().GetGlobalIds('Potentials-'+str(i)):
nb_sources += 1
if nb_sources == 0: #the file doesn't provide potentials
if not d.__class__ == int:
assert(d.shape[0] == poly.GetNumberOfPoints())
nb_sources = d.shape[1]
pot = [vtk.vtkDoubleArray() for j in range(d.shape[1])]
for j in range(d.shape[1]):
pot[j].SetName('Potentials-'+str(j))
for i in range(d.shape[0]):
pot[j].InsertNextValue(d[i,j])
poly.GetPointData().AddArray(pot[j])
poly.Update()
if not poly.GetPointData().GetGlobalIds('Indices'):
ind = vtk.vtkUnsignedIntArray()
ind.SetName('Indices')
for i in range(poly.GetNumberOfPoints()):
ind.InsertNextValue(i)
poly.GetPointData().AddArray(ind)
poly.GetPointData().SetActiveScalars('Potentials-'+str(n))
mapper = vtk.vtkPolyDataMapper()
colorBar = vtk.vtkScalarBarActor()
actor = vtk.vtkActor()
ren = vtk.vtkRenderer()
mapper.SetInput(poly)
mapper.SetScalarModeToUsePointData(); mapper.Update()
actor.SetMapper(mapper)
ren.AddActor(actor)
if nb_sources:
ren.AddActor2D(colorBar)
UpdateColorBar(colorBar, mapper)
renWin.AddRenderer(ren)
renWin.Render()
if nb_sources > 1:
# Slider
sliderWidget = vtk.vtkSliderWidget()
slider = vtk.vtkSliderRepresentation2D(); slider.SetMaximumValue(nb_sources-1)
slider.SetValue(n); slider.SetEndCapLength(0.01); slider.SetLabelFormat('%1.0f')
slider.SetSliderWidth(0.05); slider.SetSliderLength(1./nb_sources)
slider.GetPoint1Coordinate().SetCoordinateSystemToNormalizedViewport()
slider.GetPoint1Coordinate().SetValue(.0, 0.02)
slider.GetPoint2Coordinate().SetCoordinateSystemToNormalizedViewport()
slider.GetPoint2Coordinate().SetValue(1., 0.02);
sliderWidget.SetInteractor(iren); sliderWidget.SetRepresentation(slider);
sliderWidget.SetAnimationModeToAnimate(); sliderWidget.EnabledOn();
sliderWidget.AddObserver("InteractionEvent", SelectSource);
# Selection
selactor = vtk.vtkActor()
view = vtk.vtkContextView(); view.GetRenderWindow().SetWindowName('Plot')
view.GetRenderWindow().SetPosition(600, 0); view.GetRenderWindow().SetSize(600, 600)
# Welcome text
text_init = vtk.vtkTextActor()
text_init.SetPosition(10, 300)
text_init.SetInput(welcome)
text_init.GetTextProperty().SetColor(1.0, 0.0, 0.0)
view.GetRenderer().AddActor2D(text_init)
view.GetInteractor().Initialize()
iren.AddObserver(vtk.vtkCommand.EndPickEvent,CleanPickData)
iren.Initialize()
iren.Start()
def morphology_polydata(compartments,
soma_compartment,
color_fn,
minRadius=0.0):
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
radii = vtk.vtkDoubleArray()
radii.SetNumberOfComponents(1)
radii.SetName("radius")
types = vtk.vtkUnsignedCharArray()
types.SetNumberOfComponents(1)
types.SetName("type")
colors = vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3)
colors.SetName("colors")
compartment_ids = vtk.vtkUnsignedIntArray()
compartment_ids.SetNumberOfComponents(1)
compartment_ids.SetName("compartment_id")
pidmap = {}
soma_pid = -1
soma_radius = 0
roots = [c for c in compartments.values() if c['parent'] == -1]
for ri, root in enumerate(roots):
print "root", ri
nodelist = preorder_traversal(root, compartments)
line = []
for node in nodelist:
if len(line) == 0 and node['parent'] != -1:
line.append(pidmap[node['parent']])
pid = points.InsertNextPoint(node['x'], node['y'], node['z'])
# keep track of the pid of the root node, as well as the radius of
# one of its children. We'll use that radius as a surrogate radius,
# since dendrites don't actually have a cone shape
if node == soma_compartment:
soma_pid = pid
if node['parent'] == soma_compartment['id']:
soma_radius = node['radius']
radii.InsertNextTuple1(max(node['radius'], minRadius))
types.InsertNextTuple1(node['type'])
color = color_fn(node)
colors.InsertNextTuple3(color[0], color[1], color[2])
compartment_ids.InsertNextTuple1(int(node['id']))
pidmap[node['id']] = pid
line.append(pid)
if len(node['children']) == 0:
lines.InsertNextCell(len(line))
for i in line:
lines.InsertCellPoint(i)
line = []
for p in xrange(1, points.GetNumberOfPoints()):
p1 = points.GetPoint(p - 1)
p2 = points.GetPoint(p)
# assuming we found a root, update its radius
if soma_radius > 0 and soma_pid >= 0:
radii.SetTuple1(soma_pid, soma_radius)
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
polyData.SetLines(lines)
polyData.GetPointData().AddArray(radii)
polyData.GetPointData().AddArray(types)
polyData.GetPointData().AddArray(colors)
polyData.GetPointData().AddArray(compartment_ids)
polyData.GetPointData().SetActiveScalars("radius")
return polyData
# Sanity check to ensure we are in the build tree
test_cost_data_file = os.path.join('Testing', 'Temporary', 'CTestCostData.txt')
if not os.path.exists(test_cost_data_file):
print('Run this script from the build tree after running ctest ' +
'at least once.')
sys.exit(1)
# Read the input data
with open(test_cost_data_file, 'r') as fp:
test_cost_data_lines = fp.readlines()
failed_tests_index = test_cost_data_lines.index('---\n')
# Import the data into a vtkTable
table = vtk.vtkTable()
id_array = vtk.vtkUnsignedIntArray()
id_array.SetName('Pedigree Id')
table.AddColumn(id_array)
attributes = table.GetAttributes(vtk.vtkDataObject.ROW)
attributes.SetActivePedigreeIds('Pedigree Id')
test_name_array = vtk.vtkStringArray()
test_name_array.SetName('Test Name')
table.AddColumn(test_name_array)
number_of_runs_array = vtk.vtkUnsignedIntArray()
number_of_runs_array.SetName('Number of Runs')
table.AddColumn(number_of_runs_array)
test_time_array = vtk.vtkFloatArray()
test_time_array.SetName('Test Time')
table.AddColumn(test_time_array)
runs_long_array = vtk.vtkStringArray()
runs_long_array.SetName('RUNS_LONG Label')
def prepareDelaunayData3d(dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0,len(agg_globalnodeidx)):
id = -1
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
id = Points.InsertNextPoint(nodecoords[0]+ 0.0001 * random.random(),nodecoords[1]+ 0.0001 * random.random(),nodecoords[2]+ 0.0001 * random.random())
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
polydata2 = vtk.vtkPolyData()
polydata2.SetPoints(Points)
polydata2.Modified()
polydata2.Update()
delaunay = vtk.vtkDelaunay3D()
delaunay.SetInput(polydata2)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
pt_polydata = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0,Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0,Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata3 = vtk.vtkPolyData()
polydata3 = surfaceFilter.GetOutput()
polydata3.GetPointData().SetScalars(Ids)
polydata3.GetPointData().AddArray(Procs)
polydata4 = vtk.vtkPolyData()
polydata4.SetPoints(Points)
polydata4.SetVerts(Vertices)
polydata4.GetPointData().SetScalars(Ids)
polydata4.GetPointData().AddArray(Procs)
#datamapper = vtk.vtkDataSetMapper()
#datamapper.SetInputConnection(delaunay.GetOutputPort())
#datamapper.SetInput(polydata3)
#actor = vtk.vtkActor()
#actor.SetMapper(datamapper)
#renderer = vtk.vtkRenderer()
#renderWindow = vtk.vtkRenderWindow()
#renderWindow.AddRenderer(renderer)
#renderWindowInteractor = vtk.vtkRenderWindowInteractor()
#renderWindowInteractor.SetRenderWindow(renderWindow)
#renderer.AddActor(actor)
#renderWindow.Render()
#renderWindowInteractor.Start()
#print polydata.GetVertices()
aggpolygons.AddInput(polydata3)
aggpolygons.AddInput(polydata4)
# Sanity check to ensure we are in the build tree
test_cost_data_file = os.path.join('Testing', 'Temporary', 'CTestCostData.txt')
if not os.path.exists(test_cost_data_file):
print('Run this script from the build tree after running ctest ' +
'at least once.')
sys.exit(1)
# Read the input data
with open(test_cost_data_file, 'r') as fp:
test_cost_data_lines = fp.readlines()
failed_tests_index = test_cost_data_lines.index('---\n')
# Import the data into a vtkTable
table = vtk.vtkTable()
id_array = vtk.vtkUnsignedIntArray()
id_array.SetName('Pedigree Id')
table.AddColumn(id_array)
attributes = table.GetAttributes(vtk.vtkDataObject.ROW)
attributes.SetActivePedigreeIds('Pedigree Id')
test_name_array = vtk.vtkStringArray()
test_name_array.SetName('Test Name')
table.AddColumn(test_name_array)
number_of_runs_array = vtk.vtkUnsignedIntArray()
number_of_runs_array.SetName('Number of Runs')
table.AddColumn(number_of_runs_array)
test_time_array = vtk.vtkFloatArray()
test_time_array.SetName('Test Time')
table.AddColumn(test_time_array)
runs_long_array = vtk.vtkStringArray()
runs_long_array.SetName('RUNS_LONG Label')
def getvtkarray(attribute_type):
# assume ints are positive
if attribute_type is int:
return vtk.vtkUnsignedIntArray()
elif attribute_type is float:
return vtk.vtkDoubleArray()
def generate_polydata(compartments, root_compartment, minRadius=.25):
import vtk
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
radii = vtk.vtkDoubleArray()
radii.SetNumberOfComponents(1)
radii.SetName("radius")
types = vtk.vtkUnsignedCharArray()
types.SetNumberOfComponents(1)
types.SetName("type")
compartment_ids = vtk.vtkUnsignedIntArray()
compartment_ids.SetNumberOfComponents(1)
compartment_ids.SetName("compartment_id")
nodelist = preorder_traversal(root_compartment, compartments)
pidmap = {}
line = []
root_pid = -1
root_radius = 0
for node in nodelist:
if len(line) == 0 and node['parent'] != "-1":
line.append(pidmap[node['parent']])
pid = points.InsertNextPoint(node['x'], node['y'], node['z'])
# keep track of the pid of the root node, as well as the radius of
# one of its children. We'll use that radius as a surrogate radius,
# since dendrites don't actually have a cone shape
if node['parent'] == "-1":
root_pid = pid
try:
child = compartments[node['children'][0]]
root_radius = child['radius']
except BaseException as e:
print(e)
pass
radii.InsertNextTuple1(max(node['radius'], minRadius))
types.InsertNextTuple1(node['type'])
compartment_ids.InsertNextTuple1(int(node['id']))
pidmap[node['id']] = pid
line.append(pid)
if len(node['children']) == 0:
lines.InsertNextCell(len(line))
for i in line:
lines.InsertCellPoint(i)
line = []
for p in xrange(1,points.GetNumberOfPoints()):
p1 = points.GetPoint(p-1)
p2 = points.GetPoint(p)
# assuming we found a root, update its radius
if root_radius > 0 and root_pid >= 0:
radii.SetTuple1(root_pid, root_radius)
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
polyData.SetLines(lines)
polyData.GetPointData().AddArray(radii)
polyData.GetPointData().AddArray(types)
polyData.GetPointData().AddArray(compartment_ids)
polyData.GetPointData().SetActiveScalars("radius")
return polyData
import pytest
import vtk
from pytestvtk.assert_vtk import assert_vtk
@pytest.fixture(params=[
vtk.vtkDoubleArray(),
vtk.vtkFloatArray(),
vtk.vtkIntArray(),
vtk.vtkIdTypeArray(),
vtk.vtkLongArray(),
vtk.vtkShortArray(),
vtk.vtkUnsignedCharArray(),
vtk.vtkUnsignedIntArray(),
vtk.vtkUnsignedLongArray(),
vtk.vtkUnsignedLongLongArray(),
vtk.vtkUnsignedShortArray(),
vtk.vtkCharArray(),
])
def vtk_array(request):
array = request.param
array.SetName('testing_array')
array.SetNumberOfTuples(3)
array.SetNumberOfComponents(3)
array.InsertTuple3(0, 1, 2, 3)
array.InsertTuple3(1, 4, 5, 6)
array.InsertTuple3(2, 7, 8, 9)
return array
def prepareDelaunayData3d(
dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs
):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0, len(agg_globalnodeidx)):
id = -1
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
id = Points.InsertNextPoint(
nodecoords[0] + 0.0001 * random.random(),
nodecoords[1] + 0.0001 * random.random(),
nodecoords[2] + 0.0001 * random.random(),
)
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
polydata2 = vtk.vtkPolyData()
polydata2.SetPoints(Points)
polydata2.Modified()
polydata2.Update()
delaunay = vtk.vtkDelaunay3D()
delaunay.SetInput(polydata2)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
pt_polydata = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0, Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0, Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata3 = vtk.vtkPolyData()
polydata3 = surfaceFilter.GetOutput()
polydata3.GetPointData().SetScalars(Ids)
polydata3.GetPointData().AddArray(Procs)
polydata4 = vtk.vtkPolyData()
polydata4.SetPoints(Points)
polydata4.SetVerts(Vertices)
polydata4.GetPointData().SetScalars(Ids)
polydata4.GetPointData().AddArray(Procs)
# datamapper = vtk.vtkDataSetMapper()
# datamapper.SetInputConnection(delaunay.GetOutputPort())
# datamapper.SetInput(polydata3)
# actor = vtk.vtkActor()
# actor.SetMapper(datamapper)
# renderer = vtk.vtkRenderer()
# renderWindow = vtk.vtkRenderWindow()
# renderWindow.AddRenderer(renderer)
# renderWindowInteractor = vtk.vtkRenderWindowInteractor()
# renderWindowInteractor.SetRenderWindow(renderWindow)
# renderer.AddActor(actor)
# renderWindow.Render()
# renderWindowInteractor.Start()
# print polydata.GetVertices()
aggpolygons.AddInput(polydata3)
aggpolygons.AddInput(polydata4)
def generate_polydata(compartments, root_compartment, minRadius=.25):
import vtk
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
radii = vtk.vtkDoubleArray()
radii.SetNumberOfComponents(1)
radii.SetName("radius")
types = vtk.vtkUnsignedCharArray()
types.SetNumberOfComponents(1)
types.SetName("type")
compartment_ids = vtk.vtkUnsignedIntArray()
compartment_ids.SetNumberOfComponents(1)
compartment_ids.SetName("compartment_id")
nodelist = preorder_traversal(root_compartment, compartments)
pidmap = {}
line = []
root_pid = -1
root_radius = 0
for node in nodelist:
if len(line) == 0 and node['parent'] != "-1":
line.append(pidmap[node['parent']])
pid = points.InsertNextPoint(node['x'], node['y'], node['z'])
# keep track of the pid of the root node, as well as the radius of
# one of its children. We'll use that radius as a surrogate radius,
# since dendrites don't actually have a cone shape
if node['parent'] == "-1":
root_pid = pid
try:
child = compartments[node['children'][0]]
root_radius = child['radius']
except BaseException as e:
print(e)
pass
radii.InsertNextTuple1(max(node['radius'], minRadius))
types.InsertNextTuple1(node['type'])
compartment_ids.InsertNextTuple1(int(node['id']))
pidmap[node['id']] = pid
line.append(pid)
if len(node['children']) == 0:
lines.InsertNextCell(len(line))
for i in line:
lines.InsertCellPoint(i)
line = []
for p in xrange(1, points.GetNumberOfPoints()):
p1 = points.GetPoint(p - 1)
p2 = points.GetPoint(p)
# assuming we found a root, update its radius
if root_radius > 0 and root_pid >= 0:
radii.SetTuple1(root_pid, root_radius)
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
polyData.SetLines(lines)
polyData.GetPointData().AddArray(radii)
polyData.GetPointData().AddArray(types)
polyData.GetPointData().AddArray(compartment_ids)
polyData.GetPointData().SetActiveScalars("radius")
return polyData
def prepareDelaunayData(dimension, agg_globalnodeidx, global_nodecoords, aggpolygons, aggid, aggid2nodes, aggid2procs):
local_nodeidx2global_nodeidx = {}
no_of_aggnodes = len(agg_globalnodeidx)
dim = len(global_nodecoords[0])
no_aggs = len(aggid2nodes)
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for i in range(0,len(agg_globalnodeidx)):
local_nodeidx2global_nodeidx[i] = agg_globalnodeidx[i]
nodecoords = global_nodecoords[int(agg_globalnodeidx[i])]
if dimension==2:
id = Points.InsertNextPoint(nodecoords[0],nodecoords[1],0.0)
elif dimension==3:
id = Points.InsertNextPoint(nodecoords[0]+ 0.001 * random.random(),nodecoords[1]+ 0.001 * random.random(),nodecoords[2]+ 0.001 * random.random())
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(id)
# create polygon for current aggregate
polydata = vtk.vtkPolyData()
polydata.SetPoints(Points)
polydata.SetVerts(Vertices)
polydata.Modified()
polydata.Update()
polydata2 = vtk.vtkPolyData()
if Points.GetNumberOfPoints()>2: # todo: avoid error messages + add support for lines/surfaces
# create delaunay object
if dimension==2:
delaunay = vtk.vtkDelaunay2D()
elif dimension==3:
delaunay = vtk.vtkDelaunay3D()
#delaunay.SetAlpha(0.1)
delaunay.SetInput(polydata)
delaunay.Update()
# create surfaceFilter
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
surfaceFilter.Update()
polydata2 = surfaceFilter.GetOutput()
lookupTable = vtk.vtkLookupTable()
lookupTable.SetNumberOfTableValues(no_aggs)
lookupTable.Build()
Ids = vtk.vtkUnsignedIntArray()
Ids.SetNumberOfComponents(1)
Ids.SetName("Ids")
for i in range(0,Points.GetNumberOfPoints()):
Ids.InsertNextTuple1(int(aggid))
Ids.SetLookupTable(lookupTable)
Procs = vtk.vtkUnsignedCharArray()
Procs.SetNumberOfComponents(1)
Procs.SetName("proc")
for i in range(0,Points.GetNumberOfPoints()):
Procs.InsertNextTuple1(aggid2procs[aggid])
polydata2.SetPoints(Points)
polydata2.SetVerts(Vertices)
polydata2.GetPointData().SetScalars(Ids)
polydata2.GetPointData().AddArray(Procs)
polydata2.Modified()
polydata2.Update()
aggpolygons.AddInput(polydata2)
