def GetTree(self):
"""Returns a full vtkTree based on data loaded in LoadData()."""
if self.data_loaded:
vertex_id = vtk.vtkIdTypeArray()
vertex_id.SetName('vertex_ids')
for ii in range(len(self.cp)):
vertex_id.InsertNextValue(ii)
NINvtk = VN.numpy_to_vtk(self.NumberInNet, deep=True)
NINvtk.SetName('num_in_vertex')
SCALESvtk = VN.numpy_to_vtk(self.Scales, deep=True)
SCALESvtk.SetName('scale')
# This array will default to empty strings
BLANKvtk = vtk.vtkStringArray()
BLANKvtk.SetNumberOfComponents(1)
BLANKvtk.SetNumberOfTuples(self.NumberInNet.shape[0])
BLANKvtk.SetName('blank')
# Build tree out of CP list of "is a child of"
# remembering that Matlab indices are 1-based and numpy/VTK 0-based
print 'Building graph'
dg = vtk.vtkMutableDirectedGraph()
edge_id = vtk.vtkIdTypeArray()
edge_id.SetName('edge_ids')
for ii in range(self.cp.size):
dg.AddVertex()
for ii in range(self.cp.size):
if self.cp[ii] > 0: # CP already zero-based
dg.AddGraphEdge(self.cp[ii],ii) # Method for use with wrappers -- AddEdge() in C++
edge_id.InsertNextValue(ii)
dg.GetVertexData().AddArray(NINvtk)
dg.GetVertexData().AddArray(SCALESvtk)
dg.GetVertexData().AddArray(vertex_id)
dg.GetVertexData().SetActiveScalars('scale')
dg.GetVertexData().SetActivePedigreeIds('vertex_ids')
dg.GetEdgeData().AddArray(edge_id)
dg.GetEdgeData().SetActivePedigreeIds('edge_ids')
tree = vtk.vtkTree()
tree.CheckedShallowCopy(dg)
return tree
else:
raise IOError, "Can't get tree until data is loaded successfully"
def selectCell(self, cellId):
if cellId in (None, -1):
return
ids = vtk.vtkIdTypeArray();
ids.SetNumberOfComponents(1);
ids.InsertNextValue(cellId);
selectionNode = vtk.vtkSelectionNode();
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL);
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES);
selectionNode.SetSelectionList(ids);
selection = vtk.vtkSelection();
selection.AddNode(selectionNode);
extractSelection = vtk.vtkExtractSelection();
extractSelection.SetInputData(0, self.actor.GetMapper().GetInput());
extractSelection.SetInputData(1, selection);
extractSelection.Update();
selected = vtk.vtkUnstructuredGrid();
selected.ShallowCopy(extractSelection.GetOutput());
self.selectedMapper.SetInputData(selected);
self.selectedMapper.Update()
def test_id_array(self):
"""Test if a vtkIdTypeArray is converted correctly."""
arr = vtk.vtkIdTypeArray()
arr.SetNumberOfTuples(10)
for i in range(10):
arr.SetValue(i, i)
np = array_handler.vtk2array(arr)
self.assertEqual(numpy.all(np == range(10)), True)
def numpy_to_vtkIdTypeArray(num_array, deep=0):
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
dtype = num_array.dtype
if isize == 4:
if dtype != numpy.int32:
raise ValueError, \
'Expecting a numpy.int32 array, got %s instead.' % (str(dtype))
else:
if dtype != numpy.int64:
raise ValueError, \
'Expecting a numpy.int64 array, got %s instead.' % (str(dtype))
return numpy_to_vtk(num_array, deep, vtkConstants.VTK_ID_TYPE)
def __init__(self, times, slider_repres):
self._stimes = set(times)
self._opacity = 1.0
self._time_step = (max(self._stimes) - min(self._stimes)) \
/ len(self._stimes)
self._time = min(times)
self._slider_repres = slider_repres
self._current_id = vtk.vtkIdTypeArray()
self._renderer = renderer
self._renderer_window = renderer_window
self._times = times
self._image_counter = 0
self._recording = False
def WriteTecplotMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing Tecplot file.')
triangleFilter = vtk.vtkDataSetTriangleFilter()
triangleFilter.SetInputData(self.Mesh)
triangleFilter.Update()
self.Mesh = triangleFilter.GetOutput()
f=open(self.OutputFileName, 'w')
line = "VARIABLES = X,Y,Z"
arrayNames = []
for i in range(self.Mesh.GetPointData().GetNumberOfArrays()):
array = self.Mesh.GetPointData().GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if (arrayName[-1]=='_'):
continue
arrayNames.append(arrayName)
if (array.GetNumberOfComponents() == 1):
line = line + ',' + arrayName
else:
for j in range(array.GetNumberOfComponents()):
line = line + ',' + arrayName + str(j)
line = line + '\n'
f.write(line)
tetraCellIdArray = vtk.vtkIdTypeArray()
tetraCellType = 10
self.Mesh.GetIdsOfCellsOfType(tetraCellType,tetraCellIdArray)
numberOfTetras = tetraCellIdArray.GetNumberOfTuples()
line = "ZONE " + "N=" + str(self.Mesh.GetNumberOfPoints()) + ',' + "E=" + str(numberOfTetras) + ',' + "F=FEPOINT" + ',' + "ET=TETRAHEDRON" + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = self.Mesh.GetPointData().GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + str(array.GetComponent(i,j))
line = line + '\n'
f.write(line)
for i in range(numberOfTetras):
cellPointIds = self.Mesh.GetCell(tetraCellIdArray.GetValue(i)).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if (j>0):
line = line + ' '
line = line + str(cellPointIds.GetId(j)+1)
line = line + '\n'
f.write(line)
def numpy2vtkDataArrayInt(npa):
# print npa[1][0]
size0, size1 = npa.shape
data = vtk.vtkIdTypeArray()
data.SetNumberOfComponents(4)
# data.SetName("CELLS")
for i in range(size0):
n0 = int(npa[i, 0])
n1 = int(npa[i, 1])
n2 = int(npa[i, 2])
n3 = int(npa[i, 3])
data.InsertNextTuple4(n0, n1, n2, n3)
return data
def build_2d_grid(parent_bit_mask, parent_id, origin, spacing, ndims, chunk_info, grid_desc):
if "slice" in grid_desc:
return cells_on_slice_planes(parent_bit_mask, parent_id, origin, \
spacing, ndims, chunk_info, grid_desc)
ug = vtk.vtkUnstructuredGrid()
points = vtk.vtkPoints()
for j in range(ndims[1]):
j_offset = j*spacing[1]
for i in range(ndims[0]):
points.InsertNextPoint(origin[0] + i*spacing[0], \
origin[1] + j_offset, \
0.0)
ug.SetPoints(points)
quad = vtk.vtkQuad()
for j in range(ndims[1]-1):
jl_offset = j*ndims[0]
ju_offset = (j+1)*ndims[0]
for i in range(ndims[0]-1):
quad.GetPointIds().SetId(0, i + jl_offset)
quad.GetPointIds().SetId(1, i + 1 + jl_offset)
quad.GetPointIds().SetId(2, i + 1 + ju_offset)
quad.GetPointIds().SetId(3, i + ju_offset)
ug.InsertNextCell(quad.GetCellType(), quad.GetPointIds())
gids = vtk.vtkIdTypeArray()
gids.SetName("GlobalIds")
if parent_id == 0:
Dx = grid_desc["create_grid"][1]["Cx"]
xc = range(chunk_info["x"][0], chunk_info["x"][1]+1)
yc = range(chunk_info["y"][0], chunk_info["y"][1]+1)
for j in range(ndims[1]-1):
yindex = (yc[j]-1)*Dx
for i in range(ndims[0]-1):
gids.InsertNextTuple1(xc[i]+yindex)
else:
for i in range(ug.GetNumberOfCells()):
if parent_bit_mask == -1:
gids.InsertNextTuple1(parent_id)
else:
gids.InsertNextTuple1((i+1)*(2**parent_bit_mask) + parent_id)
ug.GetCellData().AddArray(gids)
ug.GetCellData().SetActiveGlobalIds("GlobalIds")
return ug
def trimesh_to_vtk(trimesh):
r"""Return a `vtkPolyData` representation of a :map:`TriMesh` instance
Parameters
----------
trimesh : :map:`TriMesh`
The menpo :map:`TriMesh` object that needs to be converted to a
`vtkPolyData`
Returns
-------
`vtk_mesh` : `vtkPolyData`
A VTK mesh representation of the Menpo :map:`TriMesh` data
Raises
------
ValueError:
If the input trimesh is not 3D.
"""
import vtk
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
if trimesh.n_dims != 3:
raise ValueError("trimesh_to_vtk() only works on 3D TriMesh instances")
mesh = vtk.vtkPolyData()
points = vtk.vtkPoints()
points.SetData(numpy_to_vtk(trimesh.points, deep=1))
mesh.SetPoints(points)
cells = vtk.vtkCellArray()
# Seemingly, VTK may be compiled as 32 bit or 64 bit.
# We need to make sure that we convert the trilist to the correct dtype
# based on this. See numpy_to_vtkIdTypeArray() for details.
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
req_dtype = np.int32 if isize == 4 else np.int64
cells.SetCells(
trimesh.n_tris,
numpy_to_vtkIdTypeArray(
np.hstack((np.ones(trimesh.n_tris)[:, None] * 3,
trimesh.trilist)).astype(req_dtype).ravel(),
deep=1,
),
)
mesh.SetPolys(cells)
return mesh
def picker_callback(self,obj,event):
extract = vtk.vtkExtractSelectedFrustum()
fPlanes=obj.GetFrustum() #collection of planes based on unscaled display
#scale frustum to account for the zaspect
scaledPlanes=vtk.vtkPlanes()
scaledNormals=vtk.vtkDoubleArray()
scaledNormals.SetNumberOfComponents(3)
scaledNormals.SetNumberOfTuples(6)
scaledOrigins=vtk.vtkPoints()
for j in range(6):
i=fPlanes.GetPlane(j)
k=i.GetOrigin()
q=i.GetNormal()
scaledOrigins.InsertNextPoint(k[0],k[1],k[2]/float(self.Zaspect))
scaledNormals.SetTuple(j,(q[0],q[1],q[2]*float(self.Zaspect)))
scaledPlanes.SetNormals(scaledNormals)
scaledPlanes.SetPoints(scaledOrigins)
extract.SetFrustum(scaledPlanes)
extract.SetInputData(self.vtkPntsPolyData)
extract.Update()
extracted = extract.GetOutput()
ids = vtk.vtkIdTypeArray()
ids = extracted.GetPointData().GetArray("vtkOriginalPointIds")
if ids:
#store them in an array for an undo operation
self.lastSelectedIds=ids
for i in range(ids.GetNumberOfTuples()):
#turn them red
self.colors.SetTuple(ids.GetValue(i),(255,0,0))
self.bool_pnt[ids.GetValue(i)]=False
self.vtkPntsPolyData.GetPointData().SetScalars(self.colors)
self.vtkPntsPolyData.Modified()
self.ui.vtkWidget.update()
#set flag on ui to show that data has been modified
self.unsaved_changes=True
def _highlight_picker_node(self, cell_id, grid, node_xyz):
"""won't handle multiple cell_ids/node_xyz"""
point_id = find_point_id_closest_to_xyz(grid, cell_id, node_xyz)
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
ids.InsertNextValue(point_id)
selection_node = vtk.vtkSelectionNode()
#selection_node.SetContainingCellsOn()
#selection_node.Initialize()
selection_node.SetFieldType(vtk.vtkSelectionNode.POINT)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(ids)
actor = self._highlight_picker_by_selection_node(
grid, selection_node, representation='points')
return actor
def picker_callback(self,obj,event):
extract = vtk.vtkExtractSelectedFrustum()
fPlanes=obj.GetFrustum() #collection of planes based on unscaled display
#scale frustum to account for the zaspect
scaledPlanes=vtk.vtkPlanes()
scaledNormals=vtk.vtkDoubleArray()
scaledNormals.SetNumberOfComponents(3)
scaledNormals.SetNumberOfTuples(6)
scaledOrigins=vtk.vtkPoints()
for j in range(6):
i=fPlanes.GetPlane(j)
k=i.GetOrigin()
q=i.GetNormal()
scaledOrigins.InsertNextPoint(k[0],k[1],k[2]/float(self.Zaspect))
scaledNormals.SetTuple(j,(q[0],q[1],q[2]*float(self.Zaspect)))
scaledPlanes.SetNormals(scaledNormals)
scaledPlanes.SetPoints(scaledOrigins)
extract.SetFrustum(scaledPlanes)
extract.SetInputData(self.vtkPntsPolyData)
extract.Update()
extracted = extract.GetOutput()
ids = vtk.vtkIdTypeArray()
ids = extracted.GetPointData().GetArray("vtkOriginalPointIds")
if ids:
#store them in an array for an undo operation
self.lastSelectedIds=ids
for i in range(ids.GetNumberOfTuples()):
#turn them red
self.colors.SetTuple(ids.GetValue(i),(255,0,0))
self.bool_pnt[ids.GetValue(i)]=False
self.vtkPntsPolyData.GetPointData().SetScalars(self.colors)
self.vtkPntsPolyData.Modified()
self.ui.vtkWidget.update()
#set flag on ui to show that data has been modified
self.unsaved_changes=True
def GetSelection(ids, inverse=False):
selNode = vtk.vtkSelectionNode()
selNode.SetContentType(vtk.vtkSelectionNode.BLOCKS)
idArray = vtk.vtkIdTypeArray()
idArray.SetNumberOfTuples(len(ids))
for i in range(len(ids)):
idArray.SetValue(i, ids[i])
selNode.SetSelectionList(idArray)
if inverse:
selNode.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
sel = vtk.vtkSelection()
sel.AddNode(selNode)
return sel
def GetSelection(ids, inverse=False):
selNode = vtk.vtkSelectionNode()
selNode.SetContentType(vtk.vtkSelectionNode.BLOCKS)
idArray = vtk.vtkIdTypeArray()
idArray.SetNumberOfTuples(len(ids))
for i in range(len(ids)):
idArray.SetValue(i, ids[i])
selNode.SetSelectionList(idArray)
if inverse:
selNode.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
sel = vtk.vtkSelection()
sel.AddNode(selNode)
return sel
def create_vtk_selection_node_by_cell_ids(cell_ids):
if isinstance(cell_ids, integer_types):
cell_ids = [cell_ids]
else:
for cell_id in cell_ids:
assert isinstance(cell_id, integer_types), type(cell_id)
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
for cell_id in cell_ids:
ids.InsertNextValue(cell_id)
selection_node = vtk.vtkSelectionNode()
selection_node.SetFieldType(vtk.vtkSelectionNode.CELL)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(ids)
return selection_node
def setPoints( self, point_data ):
self.vtkPoints.SetData( point_data )
ncells = point_data.GetNumberOfTuples()
cells = vtk.vtkIdTypeArray()
cell_data_array = np.empty( 2*ncells, dtype=np.int64 )
cell_data_array[1:2*ncells:2] = range( ncells )
cell_data_array[0:2*ncells:2] = 1
# cell_data_array = np.array( range( ncells ), dtype=np.int64 )
cells.SetVoidArray( cell_data_array, 2*ncells, 1 )
self.vtkCells.SetCells ( ncells, cells )
# self.vtkCells.InsertNextCell( cell )
# for iCell in range( ncells ):
# self.vtkCells.InsertNextCell( 1 )
# self.vtkCells.InsertCellPoint( iCell )
cellData = self.vtkCells.GetData ()
print " Cell Data:\n %s " % str( [ cellData.GetValue(iCell) for iCell in range(cellData.GetNumberOfTuples())] )
self.vtkCells.Modified()
self.vtkPoints.Modified()
def numpy_to_vtkIdTypeArray(num_array, deep=0):
"""
Notes
-----
This was pulled from VTK and modified to eliminate numpy 1.14 warnings.
VTK uses a BSD license, so it's OK to do that.
"""
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
dtype = num_array.dtype
if isize == 4:
if dtype != np.int32:
raise ValueError('Expecting a numpy.int32 array, got %s instead.' %
(str(dtype)))
else:
if dtype != np.int64:
raise ValueError('Expecting a numpy.int64 array, got %s instead.' %
(str(dtype)))
return numpy_to_vtk(num_array, deep, vtkConstants.VTK_ID_TYPE)
def setPoints( self, point_data ):
self.vtkPoints.SetData( point_data )
ncells = point_data.GetNumberOfTuples()
cells = vtk.vtkIdTypeArray()
cell_data_array = np.empty( 2*ncells, dtype=np.int64 )
cell_data_array[1:2*ncells:2] = range( ncells )
cell_data_array[0:2*ncells:2] = 1
# cell_data_array = np.array( range( ncells ), dtype=np.int64 )
cells.SetVoidArray( cell_data_array, 2*ncells, 1 )
self.vtkCells.SetCells ( ncells, cells )
# self.vtkCells.InsertNextCell( cell )
# for iCell in range( ncells ):
# self.vtkCells.InsertNextCell( 1 )
# self.vtkCells.InsertCellPoint( iCell )
cellData = self.vtkCells.GetData ()
print " Cell Data:\n %s " % str( [ cellData.GetValue(iCell) for iCell in range(cellData.GetNumberOfTuples())] )
self.vtkCells.Modified()
self.vtkPoints.Modified()
def readUnstructuredGrid(filename, tets_only=False):
extension = os.path.splitext(filename)[1]
if extension == ".vtk":
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
#return reader.GetOutput()
elif extension == ".vtu":
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
#return reader.GetOutput()
else:
print("Bad extension: %s", extension)
return None
if tets_only: # may renumber points!
print("reading unstructured grid keeping only tets -> this may result in renumbered points!")
# select tets only
ug = reader.GetOutput()
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
for i in range(ug.GetNumberOfCells()):
if ug.GetCellType(i) == vtk.VTK_TETRA:
ids.InsertNextValue(i)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0, ug)
extractSelection.SetInputData(1, selection)
extractSelection.Update()
return extractSelection.GetOutput()
else:
return reader.GetOutput()
def create_vtk_selection_node_by_point_ids(point_ids):
if isinstance(point_ids, integer_types):
point_ids = [point_ids]
else:
for point_id in point_ids:
assert isinstance(point_id, integer_types), type(point_id)
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
for point_id in point_ids:
ids.InsertNextValue(point_id)
selection_node = vtk.vtkSelectionNode()
#selection_node.SetContainingCellsOn()
#selection_node.Initialize()
selection_node.SetFieldType(vtk.vtkSelectionNode.POINT)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(ids)
return selection_node
def trimesh_to_vtk(trimesh):
r"""Return a `vtkPolyData` representation of a :map:`TriMesh` instance
Parameters
----------
trimesh : :map:`TriMesh`
The menpo :map:`TriMesh` object that needs to be converted to a
`vtkPolyData`
Returns
-------
`vtk_mesh` : `vtkPolyData`
A VTK mesh representation of the Menpo :map:`TriMesh` data
Raises
------
ValueError:
If the input trimesh is not 3D.
"""
import vtk
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
if trimesh.n_dims != 3:
raise ValueError('trimesh_to_vtk() only works on 3D TriMesh instances')
mesh = vtk.vtkPolyData()
points = vtk.vtkPoints()
points.SetData(numpy_to_vtk(trimesh.points, deep=1))
mesh.SetPoints(points)
cells = vtk.vtkCellArray()
# Seemingly, VTK may be compiled as 32 bit or 64 bit.
# We need to make sure that we convert the trilist to the correct dtype
# based on this. See numpy_to_vtkIdTypeArray() for details.
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
req_dtype = np.int32 if isize == 4 else np.int64
cells.SetCells(trimesh.n_tris,
numpy_to_vtkIdTypeArray(
np.hstack((np.ones(trimesh.n_tris)[:, None] * 3,
trimesh.trilist)).astype(req_dtype).ravel(),
deep=1))
mesh.SetPolys(cells)
return mesh
def set_polydata_triangles(polydata, triangles):
"""Set polydata triangles with a numpy array (ndarrays Nx3 int).
Parameters
----------
polydata : vtkPolyData
triangles : array (N, 3)
triangles, represented as 2D ndarrays (Nx3)
"""
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
req_dtype = np.int32 if isize == 4 else np.int64
vtk_triangles = np.hstack(np.c_[np.ones(len(triangles), dtype=req_dtype) *
3,
triangles.astype(req_dtype)])
vtk_triangles = numpy_support.numpy_to_vtkIdTypeArray(vtk_triangles,
deep=True)
vtk_cells = vtk.vtkCellArray()
vtk_cells.SetCells(len(triangles), vtk_triangles)
polydata.SetPolys(vtk_cells)
return polydata
def set_polydata_triangles(polydata, triangles):
"""Set polydata triangles with a numpy array (ndarrays Nx3 int).
Parameters
----------
polydata : vtkPolyData
triangles : array (N, 3)
triangles, represented as 2D ndarrays (Nx3)
"""
vtk_cells = vtk.vtkCellArray()
if vtk.vtkVersion.GetVTKMajorVersion() >= 9:
vtk_cells = numpy_to_vtk_cells(triangles, is_coords=False)
else:
isize = vtk.vtkIdTypeArray().GetDataTypeSize()
req_dtype = np.int32 if isize == 4 else np.int64
all_triangles =\
np.insert(triangles, 0, 3, axis=1).astype(req_dtype).flatten()
vtk_triangles = numpy_support.numpy_to_vtkIdTypeArray(all_triangles,
deep=True)
vtk_cells.SetCells(len(triangles), vtk_triangles)
polydata.SetPolys(vtk_cells)
return polydata
xM = data2[:,1].max()
ym = data2[:,0].min()
yM = data2[:,0].max()
N = data2.shape[0]
m2 = numpy.ascontiguousarray(numpy.transpose(data2,(0,2,1)))
nVertices = m2.shape[-2]
m2.resize((m2.shape[0]*m2.shape[1],m2.shape[2]))
m2=m2[...,::-1]
# here we add dummy levels, might want to reconsider converting "trimData" to "reOrderData" and use actual levels?
m3=numpy.concatenate((m2,numpy.zeros((m2.shape[0],1))),axis=1)
except Exception,err: # Ok no mesh on file, will do with lat/lon
pass
if m3 is not None:
#Create unstructured grid points
vg = vtk.vtkUnstructuredGrid()
lst = vtk.vtkIdTypeArray()
cells = vtk.vtkCellArray()
numberOfCells = N
lst.SetNumberOfComponents(nVertices + 1)
lst.SetNumberOfTuples(numberOfCells)
for i in range(N):
tuple = [None] * (nVertices + 1)
tuple[0] = nVertices
for j in range(nVertices):
tuple[j + 1] = i * nVertices + j
lst.SetTuple(i, tuple)
## ??? TODO ??? when 3D use CUBE?
cells.SetCells(numberOfCells, lst)
vg.SetCells(vtk.VTK_POLYGON, cells)
else:
#Ok a simple structured grid is enough
def main():
pointSource = vtk.vtkPointSource()
pointSource.SetNumberOfPoints(50)
pointSource.Update()
print("There are %s input points\n" % pointSource.GetOutput().GetNumberOfPoints())
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
# Set values
i = 10
while i < 20:
ids.InsertNextValue(i)
i += 1
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(1) # POINT
# CELL_DATA = 0
# POINT_DATA = 1
# FIELD_DATA = 2
# VERTEX_DATA = 3
# EDGE_DATA = 4
selectionNode.SetContentType(4) # INDICES
#SELECTIONS = 0
#GLOBALIDS = 1
#PEDIGREEIDS = 2
#VALUES = 3
#INDICES = 4
#FRUSTUM = 5
#LOCATIONS = 6
#THRESHOLDS = 7
#BLOCKS = 8
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputConnection(0, pointSource.GetOutputPort())
if vtk.VTK_MAJOR_VERSION <= 5:
extractSelection.SetInput(1, selection)
else:
extractSelection.SetInputData(1, selection)
extractSelection.Update()
# In selection
selected = vtk.vtkUnstructuredGrid()
selected.ShallowCopy(extractSelection.GetOutput())
print("There are %s points in the selection" % selected.GetNumberOfPoints())
print("There are %s cells in the selection" %selected.GetNumberOfCells())
# Get points that are NOT in the selection
# invert the selection
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
extractSelection.Update()
notSelected = vtk.vtkUnstructuredGrid()
notSelected.ShallowCopy(extractSelection.GetOutput())
print("There are %s points NOT in the selection" % notSelected.GetNumberOfPoints())
print("There are %s cells NOT in the selection" % notSelected.GetNumberOfCells())
inputMapper = vtk.vtkDataSetMapper()
inputMapper.SetInputConnection(pointSource.GetOutputPort())
inputActor = vtk.vtkActor()
inputActor.SetMapper(inputMapper)
selectedMapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
selectedMapper.SetInputConnection(selected.GetProducerPort())
else:
selectedMapper.SetInputData(selected)
selectedActor = vtk.vtkActor()
selectedActor.SetMapper(selectedMapper)
notSelectedMapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
notSelectedMapper.SetInputConnection(notSelected.GetProducerPort())
else:
notSelectedMapper.SetInputData(notSelected)
notSelectedActor = vtk.vtkActor()
notSelectedActor.SetMapper(notSelectedMapper)
# There will be one render window
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(900, 300)
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
leftViewport = [0.0, 0.0, 0.33, 1.0]
centerViewport = [0.33, 0.0, .66, 1.0]
rightViewport = [0.66, 0.0, 1.0, 1.0]
# Setup the renderers
leftRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(leftRenderer)
leftRenderer.SetViewport(leftViewport)
leftRenderer.SetBackground(.6, .5, .4)
centerRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(centerRenderer)
centerRenderer.SetViewport(centerViewport)
centerRenderer.SetBackground(.3, .1, .4)
rightRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(rightRenderer)
rightRenderer.SetViewport(rightViewport)
rightRenderer.SetBackground(.4, .5, .6)
leftRenderer.AddActor(inputActor)
centerRenderer.AddActor(selectedActor)
rightRenderer.AddActor(notSelectedActor)
leftRenderer.ResetCamera()
centerRenderer.ResetCamera()
rightRenderer.ResetCamera()
renderWindow.Render()
interactor.Start()
# Get variables out of Matlab structure
print 'Transferring variables from Matlab structures'
gW = MatInput['gW']
Data = MatInput['Data']
X = MatInput['X']
# WC = MatInput['WavCoeffs']
# Instead of using WC, which has already been ordered within Matlab
WavCoeffsOrig = Data['MatWavCoeffs'][0,0].T
# Structures are accessed like this:
PROJ = Data['Projections'][0,0]
CP = gW['cp'][0,0][0] # CP ends up as 'uint16'... Not sure why 16-bit...
# Making a list of numpy arrays because cell array structure is a pain...
PIN = [] # Points In Net
NIN = [] # Number In Net
vertex_id = vtk.vtkIdTypeArray()
vertex_id.SetName('vertex_ids')
for ii in range(gW['PointsInNet'][0,0].shape[1]):
PIN.append(gW['PointsInNet'][0,0][0,ii][0]-1) # 0-based indices
NIN.append(gW['PointsInNet'][0,0][0,ii][0].size)
vertex_id.InsertNextValue(ii)
NINarray = N.array(NIN)
NINvtk = VN.numpy_to_vtk(NINarray)
NINvtk.SetName('num_in_vertex')
SCALESvtk = VN.numpy_to_vtk(gW['Scales'][0,0][0])
SCALESvtk.SetName('scale')
# Build tree out of CP list of "is a child of"
# remembering that Matlab indices are 1-based and numpy/VTK 0-based
print 'Building graph'
def ReducePolyData2D(inPoly, outPoly, closed):
"""
FIXME
"""
inPts = inPoly.GetPoints()
if inPts is None:
return 0
n = inPts.GetNumberOfPoints()
if (n < 3):
return 0
p0 = inPts.GetPoint(0)
p1 = inPts.GetPoint(n-1)
minusNth = p0[0] == p1[0] and p0[1] == p1[1] and p0[2] == p1[2]
if ( minusNth and closed == 1):
n = n - 1
# frenet unit tangent vector and state of kappa (zero or non-zero)
f = n*[frenet((0.0,0.0,0.0), False)]
# calculate the tangent vector by forward differences
for i in range(n):
p0 = inPts.GetPoint(i)
p1 = inPts.GetPoint( ( i + 1 ) % n)
tL = math.sqrt(vtk.vtkMath.Distance2BetweenPoints( p0, p1 ) )
if ( tL == 0.0 ):
tL = 1.0
f[i].t = ((p1[0] - p0[0])/tL,
(p1[1] - p0[1])/tL,
(p1[2] - p0[2])/tL)
# calculate kappa from tangent vectors by forward differences
# mark those points that have very low curvature
eps = 1.0e-10
for i in range(n):
t0 = f[i].t
t1 = f[(i+1) % n].t
f[i].state = math.fabs(vtk.vtkMath.Dot(t0,t1) - 1.0) < eps
tempPts = vtk.vtkPoints()
# mark keepers
ids = vtk.vtkIdTypeArray()
# for now, insist on keeping the first point for closure
ids.InsertNextValue(0)
for i in range(1, n):
pre = f[( i - 1 + n ) % n].state # means fik != 1
cur = f[i].state # means fik = 1
nex = f[( i + 1 ) % n].state
# possible vertex bend patterns for keep: pre cur nex
# 0 0 1
# 0 1 1
# 0 0 0
# 0 1 0
# definite delete pattern
# 1 1 1
keep = False
if ( pre and cur and nex ):
keep = False
elif (not pre and not cur and nex ):
keep = True
elif (not pre and cur and nex ):
keep = True
elif ( not pre and not cur and not nex ):
keep = True
elif ( not pre and cur and not nex ):
keep = True
if ( keep ):
ids.InsertNextValue( i )
for i in range(ids.GetNumberOfTuples()):
tempPts.InsertNextPoint( inPts.GetPoint( ids.GetValue( i ) ) )
if ( closed == 1):
tempPts.InsertNextPoint( inPts.GetPoint( ids.GetValue( 0 ) ) )
outPoly = ConvertPointSequenceToPolyData( tempPts, closed)
ids = None#.Delete()
tempPts = None#.Delete()
return 1
def writeHdf5():
if timeStep < 0.01:
exit("Timestep is too small, choose 0.01 or larger")
# This is where the data is for testing purposes.
print "Current working directory:", os.getcwd()
print taskMeshIn
numQuadsPerRing = circQuads
# Working with the task mesh junt to figure out the quads and rows numbers.
taskMeshReader = vtk.vtkXMLPolyDataReader()
taskMeshReader.SetFileName(taskMeshIn)
taskMeshReader.Update()
taskMesh = taskMeshReader.GetOutput()
print taskMesh.GetNumberOfPoints()
# 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()
numQuadRowsPerBranch = taskMeshBranch.GetNumberOfCells() / numQuadsPerRing;
numRingsPerLabel[label] = numQuadRowsPerBranch
atpFiles = glob.glob(atpMeshPattern)
parentFile = h5py.File(atpHdf5Files[0], 'w')
leftBranchFile = h5py.File(atpHdf5Files[1], 'w')
rightBranchFile = h5py.File(atpHdf5Files[2], 'w')
for atpIndex in range(0, len(atpFiles), int(timeStep / originalTimeStep)):
print "Time step " + str(atpIndex * timeStep )
atpMeshReader = vtk.vtkXMLPolyDataReader()
atpMeshReader.SetFileName(atpFiles[atpIndex])
atpMeshReader.Update()
atpMesh = atpMeshReader.GetOutput()
# 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
atpCellOffset = label * numECsPerLabel
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, numECsPerLabel):
selectionIds.InsertNextValue(atpCellOffset + 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, atpMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedCells = 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()
# Decide which h5 files to write to.
pointsOf = ''
if label == 0:
pointsOf = parentFile
elif label == 1:
pointsOf = leftBranchFile
elif label == 2:
pointsOf = rightBranchFile
dset = pointsOf.create_dataset("/" + str(atpIndex), (numECsPerLabel,), 'f')
i = 0
# 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 cellNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
realId = quadId * numECsPerQuad + rowNum * numECsPerRow + cellNum
atpVal = extractedCells.GetCellData().GetArray("ATP").GetValue(realId)
# Write the value to the txt file.
dset[i] = atpVal
i += 1
parentFile.close()
leftBranchFile.close()
rightBranchFile.close()
print "All done ..."
def _generate_vtk_mesh(points, cells):
import vtk
from vtk.util import numpy_support
mesh = vtk.vtkUnstructuredGrid()
# set points
vtk_points = vtk.vtkPoints()
# Not using a deep copy here results in a segfault.
vtk_array = numpy_support.numpy_to_vtk(points, deep=True)
vtk_points.SetData(vtk_array)
mesh.SetPoints(vtk_points)
# Set cells.
meshio_to_vtk_type = {y: x for x, y in vtk_to_meshio_type.items()}
# create cell_array. It's a one-dimensional vector with
# (num_points2, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
cell_types = []
cell_offsets = []
cell_connectivity = []
len_array = 0
for meshio_type, data in cells.items():
numcells, num_local_nodes = data.shape
if meshio_type[:7] == "polygon":
vtk_type = meshio_to_vtk_type[meshio_type[:7]]
else:
vtk_type = meshio_to_vtk_type[meshio_type]
# add cell types
cell_types.append(numpy.empty(numcells, dtype=numpy.ubyte))
cell_types[-1].fill(vtk_type)
# add cell offsets
cell_offsets.append(
numpy.arange(
len_array,
len_array + numcells * (num_local_nodes + 1),
num_local_nodes + 1,
dtype=numpy.int64,
))
cell_connectivity.append(
numpy.c_[num_local_nodes * numpy.ones(numcells, dtype=data.dtype),
data].flatten())
len_array += len(cell_connectivity[-1])
cell_types = numpy.concatenate(cell_types)
cell_offsets = numpy.concatenate(cell_offsets)
cell_connectivity = numpy.concatenate(cell_connectivity)
connectivity = vtk.util.numpy_support.numpy_to_vtkIdTypeArray(
cell_connectivity.astype(numpy.int64), deep=1)
# wrap the data into a vtkCellArray
cell_array = vtk.vtkCellArray()
cell_array.SetCells(len(cell_types), connectivity)
# Add cell data to the mesh
mesh.SetCells(
numpy_support.numpy_to_vtk(
cell_types,
deep=1,
array_type=vtk.vtkUnsignedCharArray().GetDataType()),
numpy_support.numpy_to_vtk(
cell_offsets,
deep=1,
array_type=vtk.vtkIdTypeArray().GetDataType()),
cell_array,
)
return mesh
def node_pick(self, pos):
picker = vtk.vtkPointPicker()
picker.SetTolerance(0.005)
picker.Pick(pos[0], pos[1], 0, self.GetDefaultRenderer())
_id = picker.GetPointId()
if _id != -1:
if _id < self.node_count:
if self.last_selection == 'Node %s' % str(_id):
self.should_it_render = False
self.did_it_render = True
return True
self.last_selection = 'Node %s' % str(_id)
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
ids.InsertNextValue(_id)
self.picked_type = 'Node'
self.picked_id = self.node_ids[_id]
#print 'picked type = %s, id = %s' % (self.picked_type, self.picked_id)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0, self.Data)
extractSelection.SetInputData(1, selection)
extractSelection.Update()
selected = vtk.vtkUnstructuredGrid()
selected.ShallowCopy(extractSelection.GetOutput())
self.selectedMapper.SetInputData(selected)
#self.selectedActor = vtk_widget.vtkActor()
self.selectedActor.SetMapper(self.selectedMapper)
self.selectedActor.GetProperty().EdgeVisibilityOn() # this makes cells not blue?
#self.selectedActor.GetProperty().SetColor(0, 0.5, 0)
self.selectedActor.GetProperty().SetEdgeColor(0.5, 0.5, 0)
self.selectedActor.GetProperty().SetPointSize(6)
self.should_it_render = True
return True
else:
self.picked_id = None
return False
return self.cell_pick(_id)
else:
self.picked_id = None
return False
def WriteLifeVMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing LifeV file.')
self.Mesh.BuildLinks()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.DeepCopy(self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName))
tetraCellType = 10
triangleCellType = 5
f=open(self.OutputFileName, 'w')
line = "MeshVersionFormatted 1\n\n"
line += "Dimension\n"
line += "3\n\n"
line += "Vertices\n"
line += "%d\n" % self.Mesh.GetNumberOfPoints()
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
pointCells = vtk.vtkIdList()
self.Mesh.GetPointCells(i,pointCells)
minTriangleCellEntityId = -1
tetraCellEntityId = -1
for j in range(pointCells.GetNumberOfIds()):
cellId = pointCells.GetId(j)
if self.Mesh.GetCellType(cellId) == triangleCellType:
cellEntityId = cellEntityIdsArray.GetValue(cellId)
if cellEntityId < minTriangleCellEntityId or minTriangleCellEntityId == -1:
minTriangleCellEntityId = cellEntityId
else:
tetraCellEntityId = cellEntityIdsArray.GetValue(cellId)
cellEntityId = tetraCellEntityId
if minTriangleCellEntityId != -1:
cellEntityId = minTriangleCellEntityId
line = "%f %f %f %d\n" % (point[0], point[1], point[2], cellEntityId)
f.write(line)
line = "\n"
tetraCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(tetraCellType,tetraCellIdArray)
numberOfTetras = tetraCellIdArray.GetNumberOfTuples()
line += "Tetrahedra\n"
line += "%d\n" % numberOfTetras
f.write(line)
for i in range(numberOfTetras):
tetraCellId = tetraCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(tetraCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
line += ' %d\n' % 1
f.write(line)
line = "\n"
triangleCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(triangleCellType,triangleCellIdArray)
numberOfTriangles = triangleCellIdArray.GetNumberOfTuples()
line += "Triangles\n"
line += "%d\n" % numberOfTriangles
f.write(line)
for i in range(numberOfTriangles):
triangleCellId = triangleCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(triangleCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
cellEntityId = cellEntityIdsArray.GetValue(triangleCellId)
line += ' %d\n' % cellEntityId
f.write(line)
def _generate_vtk_mesh(points, cells):
mesh = vtk.vtkUnstructuredGrid()
# set points
vtk_points = vtk.vtkPoints()
# Not using a deep copy here results in a segfault.
vtk_array = numpy_support.numpy_to_vtk(points, deep=True)
vtk_points.SetData(vtk_array)
mesh.SetPoints(vtk_points)
# Set cells.
meshio_to_vtk_type = {
'vertex': vtk.VTK_VERTEX,
'line': vtk.VTK_LINE,
'triangle': vtk.VTK_TRIANGLE,
'quad': vtk.VTK_QUAD,
'tetra': vtk.VTK_TETRA,
'hexahedron': vtk.VTK_HEXAHEDRON,
'wedge': vtk.VTK_WEDGE,
'pyramid': vtk.VTK_PYRAMID
}
# create cell_array. It's a one-dimensional vector with
# (num_points2, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
cell_types = []
cell_offsets = []
cell_connectivity = []
len_array = 0
for meshio_type, data in cells.iteritems():
numcells, num_local_nodes = data.shape
vtk_type = meshio_to_vtk_type[meshio_type]
# add cell types
cell_types.append(numpy.empty(numcells, dtype=numpy.ubyte))
cell_types[-1].fill(vtk_type)
# add cell offsets
cell_offsets.append(
numpy.arange(
len_array,
len_array + numcells * num_local_nodes,
num_local_nodes + 1,
dtype=numpy.int64))
cell_connectivity.append(
numpy.c_[num_local_nodes *
numpy.ones(numcells, dtype=data.dtype), data].flatten())
len_array += len(cell_connectivity[-1])
cell_types = numpy.concatenate(cell_types)
cell_offsets = numpy.concatenate(cell_offsets)
cell_connectivity = numpy.concatenate(cell_connectivity)
connectivity = vtk.util.numpy_support.numpy_to_vtkIdTypeArray(
cell_connectivity.astype(numpy.int64), deep=1)
# wrap the data into a vtkCellArray
cell_array = vtk.vtkCellArray()
cell_array.SetCells(len(cell_types), connectivity)
# Add cell data to the mesh
mesh.SetCells(
numpy_support.numpy_to_vtk(
cell_types,
deep=1,
array_type=vtk.vtkUnsignedCharArray().GetDataType()),
numpy_support.numpy_to_vtk(
cell_offsets,
deep=1,
array_type=vtk.vtkIdTypeArray().GetDataType()), cell_array)
return mesh
def main():
pointSource = vtk.vtkPointSource()
pointSource.SetNumberOfPoints(50)
pointSource.Update()
print("There are %s input points\n" %
pointSource.GetOutput().GetNumberOfPoints())
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
# Set values
i = 10
while i < 20:
ids.InsertNextValue(i)
i += 1
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(1) # POINT
# CELL_DATA = 0
# POINT_DATA = 1
# FIELD_DATA = 2
# VERTEX_DATA = 3
# EDGE_DATA = 4
selectionNode.SetContentType(4) # INDICES
# SELECTIONS = 0
# GLOBALIDS = 1
# PEDIGREEIDS = 2
# VALUES = 3
# INDICES = 4
# FRUSTUM = 5
# LOCATIONS = 6
# THRESHOLDS = 7
# BLOCKS = 8
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputConnection(0, pointSource.GetOutputPort())
if vtk.VTK_MAJOR_VERSION <= 5:
extractSelection.SetInput(1, selection)
else:
extractSelection.SetInputData(1, selection)
extractSelection.Update()
# In selection
selected = vtk.vtkUnstructuredGrid()
selected.ShallowCopy(extractSelection.GetOutput())
print("There are %s points in the selection" %
selected.GetNumberOfPoints())
print("There are %s cells in the selection" % selected.GetNumberOfCells())
# Get points that are NOT in the selection
# invert the selection
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
extractSelection.Update()
notSelected = vtk.vtkUnstructuredGrid()
notSelected.ShallowCopy(extractSelection.GetOutput())
print("There are %s points NOT in the selection" %
notSelected.GetNumberOfPoints())
print("There are %s cells NOT in the selection" %
notSelected.GetNumberOfCells())
inputMapper = vtk.vtkDataSetMapper()
inputMapper.SetInputConnection(pointSource.GetOutputPort())
inputActor = vtk.vtkActor()
inputActor.SetMapper(inputMapper)
selectedMapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
selectedMapper.SetInputConnection(selected.GetProducerPort())
else:
selectedMapper.SetInputData(selected)
selectedActor = vtk.vtkActor()
selectedActor.SetMapper(selectedMapper)
notSelectedMapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
notSelectedMapper.SetInputConnection(notSelected.GetProducerPort())
else:
notSelectedMapper.SetInputData(notSelected)
notSelectedActor = vtk.vtkActor()
notSelectedActor.SetMapper(notSelectedMapper)
# There will be one render window
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(900, 300)
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
leftViewport = [0.0, 0.0, 0.33, 1.0]
centerViewport = [0.33, 0.0, .66, 1.0]
rightViewport = [0.66, 0.0, 1.0, 1.0]
# Setup the renderers
leftRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(leftRenderer)
leftRenderer.SetViewport(leftViewport)
leftRenderer.SetBackground(.6, .5, .4)
centerRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(centerRenderer)
centerRenderer.SetViewport(centerViewport)
centerRenderer.SetBackground(.3, .1, .4)
rightRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(rightRenderer)
rightRenderer.SetViewport(rightViewport)
rightRenderer.SetBackground(.4, .5, .6)
leftRenderer.AddActor(inputActor)
centerRenderer.AddActor(selectedActor)
rightRenderer.AddActor(notSelectedActor)
leftRenderer.ResetCamera()
centerRenderer.ResetCamera()
rightRenderer.ResetCamera()
renderWindow.Render()
interactor.Start()
lsv_reader = vtk.vtkArrayReader()
lsv_reader.SetFileName(os.path.join(lsa_data_path,"CH_LeftSingularVectors.txt"))
rsv_reader = vtk.vtkArrayReader()
rsv_reader.SetFileName(os.path.join(lsa_data_path,"CH_RightSingularVectors.txt"))
sv_reader = vtk.vtkArrayReader()
sv_reader.SetFileName(os.path.join(lsa_data_path,"CH_SingluarValues.txt"))
power_weighting = vtk.vtkPowerWeighting()
power_weighting.SetInputConnection(0, sv_reader.GetOutputPort())
power_weighting.SetPower(-0.5)
# Setup the query pipeline ...
query_document_array = vtk.vtkIdTypeArray()
query_document_array.SetName("document")
query_text_array = vtk.vtkUnicodeStringArray()
query_text_array.SetName("text")
query_document_array.InsertNextValue(query_document_array.GetNumberOfTuples())
query_text_array.InsertNextValue(unicode(query_string))
query_document_table = vtk.vtkTable()
query_document_table.AddColumn(query_document_array)
query_document_table.AddColumn(query_text_array)
query_document_reader = vtk.vtkPassThrough()
query_document_reader.SetInputConnection(0, query_document_table.GetProducerPort())
def remove_non_visible_faces(
polydata,
positions=[[1, 0, 0], [-1, 0, 0], [0, 1, 0], [0, -1, 0], [0, 0, 1], [0, 0, -1]],
remove_visible=False,
):
polydata.BuildLinks()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(polydata)
mapper.Update()
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
render_window = vtk.vtkRenderWindow()
render_window.AddRenderer(renderer)
render_window.SetSize(800, 800)
render_window.OffScreenRenderingOn()
camera = renderer.GetActiveCamera()
renderer.ResetCamera()
pos = np.array(camera.GetPosition())
fp = np.array(camera.GetFocalPoint())
v = pos - fp
mag = np.linalg.norm(v)
vn = v / mag
id_filter = vtk.vtkIdFilter()
id_filter.SetInputData(polydata)
id_filter.PointIdsOn()
id_filter.Update()
set_points = None
for position in positions:
pos = fp + np.array(position) * mag
camera.SetPosition(pos.tolist())
renderer.ResetCamera()
render_window.Render()
select_visible_points = vtk.vtkSelectVisiblePoints()
select_visible_points.SetInputData(id_filter.GetOutput())
select_visible_points.SetRenderer(renderer)
# select_visible_points.SelectInvisibleOn()
select_visible_points.Update()
output = select_visible_points.GetOutput()
id_points = numpy_support.vtk_to_numpy(
output.GetPointData().GetAbstractArray("vtkIdFilter_Ids")
)
if set_points is None:
set_points = set(id_points.tolist())
else:
set_points.update(id_points.tolist())
# id_list = vtk.vtkIdList()
# output.GetVerts().GetCell(1000, id_list)
if remove_visible:
set_points = set(range(polydata.GetNumberOfPoints())) - set_points
cells_ids = set()
for p_id in set_points:
id_list = vtk.vtkIdList()
polydata.GetPointCells(p_id, id_list)
for i in range(id_list.GetNumberOfIds()):
cells_ids.add(id_list.GetId(i))
try:
id_list = numpy_support.numpy_to_vtkIdTypeArray(np.array(list(cells_ids), dtype=np.int64))
except ValueError:
id_list = vtk.vtkIdTypeArray()
selection_node = vtk.vtkSelectionNode()
selection_node.SetFieldType(vtk.vtkSelectionNode.CELL)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(id_list)
selection = vtk.vtkSelection()
selection.AddNode(selection_node)
extract_selection = vtk.vtkExtractSelection()
extract_selection.SetInputData(0, polydata)
extract_selection.SetInputData(1, selection)
extract_selection.Update()
geometry_filter = vtk.vtkGeometryFilter()
geometry_filter.SetInputData(extract_selection.GetOutput())
geometry_filter.Update()
clean_polydata = vtk.vtkCleanPolyData()
clean_polydata.SetInputData(geometry_filter.GetOutput())
clean_polydata.Update()
return clean_polydata.GetOutput()
def main():
"""
^y
|
8----9----10---11
| / | / | / |
4----5----6----7
| / | / | / |
0----1----2----3 --> x
"""
ugrid = vtk.vtkUnstructuredGrid()
xyzs = [
[0., 0., 0.],
[1., 0., 0.],
[2., 0., 0.],
[3., 0., 0.],
[0., 1., 0.],
[1., 1., 0.],
[2., 1., 0.],
[3., 1., 0.],
[0., 2., 0.],
[1., 2., 0.],
[2., 2., 0.],
[3., 2., 0.],
]
# we make the lower triangle first, then the upper one to finish off the quad
# go accross each row, left to right
tris = [
[0, 1, 5],
[0, 5, 4],
[1, 2, 6],
[1, 6, 5],
[2, 3, 7],
[2, 7, 6],
[4, 5, 9],
[4, 9, 8],
[5, 6, 10],
[5, 10, 9],
[6, 7, 11],
[6, 11, 10],
]
ids_to_show = [0, 1, #2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12]
ids_to_show_updated = [
0, 1, #2, 3,
#4, 5,
6, 7, 8, 9, 10, 11, 12]
nnodes = len(xyzs)
points = vtk.vtkPoints()
points.SetNumberOfPoints(nnodes)
nid = 0
for i, xyz in enumerate(xyzs):
points.InsertPoint(nid, *xyz)
nid += 1
for tri in tris:
elem = vtk.vtkTriangle()
(n1, n2, n3) = tri
elem.GetPointIds().SetId(0, n1)
elem.GetPointIds().SetId(1, n2)
elem.GetPointIds().SetId(2, n3)
ugrid.InsertNextCell(elem.GetCellType(), elem.GetPointIds())
ugrid.SetPoints(points)
grid_mapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
grid_mapper.SetInputConnection(ugrid.GetProducerPort())
else:
grid_mapper.SetInputData(ugrid)
input_actor = vtk.vtkActor()
input_actor.SetMapper(grid_mapper)
render_window = vtk.vtkRenderWindow()
camera = vtk.vtkCamera()
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
print("There are %s input points" % ugrid.GetNumberOfPoints())
print("There are %s input cells" % ugrid.GetNumberOfCells())
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
ids.Allocate(len(ids_to_show))
for id_to_show in ids_to_show:
ids.InsertNextValue(id_to_show)
selection_node = vtk.vtkSelectionNode()
selection_node.SetFieldType(vtk.vtkSelectionNode.CELL)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selection_node)
extract_selection = vtk.vtkExtractSelection()
if vtk.VTK_MAJOR_VERSION <= 5:
extract_selection.SetInput(0, ugrid)
extract_selection.SetInput(1, selection)
else:
extract_selection.SetInputData(0, ugrid)
extract_selection.SetInputData(1, selection)
extract_selection.Update()
# In selection
grid_selected = vtk.vtkUnstructuredGrid()
grid_selected.ShallowCopy(extract_selection.GetOutput())
print("There are %s points in the selection" % grid_selected.GetNumberOfPoints())
print("There are %s cells in the selection" % grid_selected.GetNumberOfCells())
# Get points that are NOT in the selection
# invert the selection
selection_node.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
extract_selection.Update()
not_selected = vtk.vtkUnstructuredGrid()
not_selected.ShallowCopy(extract_selection.GetOutput())
print("There are %s points NOT in the selection" % not_selected.GetNumberOfPoints())
print("There are %s cells NOT in the selection" % not_selected.GetNumberOfCells())
selected_mapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
selected_mapper.SetInputConnection(grid_selected.GetProducerPort())
else:
selected_mapper.SetInputData(grid_selected)
selected_actor = vtk.vtkActor()
selected_actor.SetMapper(selected_mapper)
not_selected_mapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
not_selected_mapper.SetInputConnection(not_selected.GetProducerPort())
else:
not_selected_mapper.SetInputData(not_selected)
not_selected_actor = vtk.vtkActor()
not_selected_actor.SetMapper(not_selected_mapper)
# There will be one render window
render_window = vtk.vtkRenderWindow()
render_window.SetSize(900, 300)
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
left_viewport = [0.0, 0.0, 0.5, 1.0]
right_viewport = [0.5, 0.0, 1.0, 1.0]
# Create a camera for all renderers
camera = vtk.vtkCamera()
# Setup the renderers
left_renderer = vtk.vtkRenderer()
render_window.AddRenderer(left_renderer)
left_renderer.SetViewport(left_viewport)
left_renderer.SetBackground(.6, .5, .4)
left_renderer.SetActiveCamera(camera)
right_renderer = vtk.vtkRenderer()
render_window.AddRenderer(right_renderer)
right_renderer.SetViewport(right_viewport)
right_renderer.SetBackground(.3, .1, .4)
right_renderer.SetActiveCamera(camera)
right_renderer.AddActor(selected_actor)
left_renderer.AddActor(input_actor)
right_renderer.AddActor(not_selected_actor)
right_renderer.ResetCamera()
interactor.Start()
#-----------------
ids.Reset()
ids.Allocate(len(ids_to_show_updated))
for id_to_show in ids_to_show_updated:
ids.InsertNextValue(id_to_show)
ids.Modified()
grid_selected.Modified()
#ids.Update()
ids.Modified()
#selection_node.Update()
selection_node.Modified()
#selection.Update()
selection.Modified()
extract_selection.Update()
extract_selection.Modified()
#grid_selected.Update()
grid_selected.Modified()
selected_mapper.Update()
selected_mapper.Modified()
#selected_actor.Update()
selected_actor.Modified()
right_renderer.Modified()
#right_renderer.Update()
interactor.Modified()
#interactor.Update()
#-----------------
render_window.Render()
render_window.Modified()
def writeHdf5():
if timeStep < 0.01:
exit("Timestep is too small, choose 0.01 or larger")
# This is where the data is for testing purposes.
print("Current working directory:", os.getcwd())
numQuadsPerRing = circQuads
# Working with the task mesh junt to figure out the quads and rows numbers.
taskMeshReader = vtk.vtkXMLPolyDataReader()
taskMeshReader.SetFileName(taskMeshIn)
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()
numQuadRowsPerBranch = taskMeshBranch.GetNumberOfCells(
) / numQuadsPerRing
numRingsPerLabel[label] = numQuadRowsPerBranch
atpFiles = sorted(glob.glob(atpMeshPattern))
parentFile = h5py.File(atpHdf5Files[0], 'w')
leftBranchFile = h5py.File(atpHdf5Files[1], 'w')
rightBranchFile = h5py.File(atpHdf5Files[2], 'w')
for atpIndex in range(0, len(atpFiles), int(timeStep / originalTimeStep)):
print("Time step" + str(atpIndex * timeStep))
print("Reading", atpFiles[atpIndex], "at index", atpIndex)
atpMeshReader = vtk.vtkXMLPolyDataReader()
atpMeshReader.SetFileName(atpFiles[atpIndex])
atpMeshReader.Update()
atpMesh = atpMeshReader.GetOutput()
# 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
atpCellOffset = label * numECsPerLabel
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, int(numECsPerLabel)):
selectionIds.InsertNextValue(int(atpCellOffset) + 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, atpMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedCells = selectionExtractor.GetOutput()
# Ring ids list for traversal.
ringIds = range(0, int(numRingsPerLabel[label]))
ringIds = list(ringIds)
ringIds.reverse()
# Number of ECs rows is the number of ECs per quad.
rowIds = range(0, numECsPerCol)
rowIds = list(rowIds)
rowIds.reverse()
# Decide which h5 files to write to.
pointsOf = ''
if label == 0:
pointsOf = parentFile
elif label == 1:
pointsOf = leftBranchFile
elif label == 2:
pointsOf = rightBranchFile
dset = pointsOf.create_dataset("/" + str(atpIndex),
(numECsPerLabel, ), 'f')
i = 0
# 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 cellNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
realId = quadId * numECsPerQuad + rowNum * numECsPerRow + cellNum
atpVal = extractedCells.GetCellData().GetArray(
"ATP").GetValue(realId)
# Insert the value into the dataset.
dset[i] = atpVal
i += 1
parentFile.close()
leftBranchFile.close()
rightBranchFile.close()
print("All done ...")
def cell_pick(self, _id):
if _id != -1:
if self.last_selection == 'Element %s' % str(_id):
self.should_it_render = False
self.did_it_render = True
return True
camera_pos = self.camera.GetPosition()
self.last_selection = 'Element %s' % str(_id)
cell = self.Data.GetCell(_id)
points = cell.GetPoints()
count = points.GetNumberOfPoints()
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
ids.InsertNextValue(_id)
self.picked_type = 'Element'
self.picked_id = self.element_ids[_id]
point_list = vtk.vtkPoints()
cell_list = vtk.vtkCellArray()
f = 0.05
if count == 4:
xyz = points.GetPoint(0)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(1)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(2)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(3)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
cell = vtk.vtkQuad()
point_ids = cell.GetPointIds()
point_ids.SetId(0, 0)
point_ids.SetId(1, 1)
point_ids.SetId(2, 2)
point_ids.SetId(3, 3)
elif count == 3:
xyz = points.GetPoint(0)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(1)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(2)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
cell = vtk.vtkTriangle()
point_ids = cell.GetPointIds()
point_ids.SetId(0, 0)
point_ids.SetId(1, 1)
point_ids.SetId(2, 2)
elif count == 2:
xyz = points.GetPoint(0)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
xyz = points.GetPoint(1)
xyz = [camera_pos[0] + (xyz[0] - camera_pos[0])*f,
camera_pos[1] + (xyz[1] - camera_pos[1])*f,
camera_pos[2] + (xyz[2] - camera_pos[2])*f]
point_list.InsertNextPoint(xyz)
cell = vtk.vtkLine()
point_ids = cell.GetPointIds()
point_ids.SetId(0, 0)
point_ids.SetId(1, 1)
cell_list.InsertNextCell(cell)
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(point_list)
poly_data.SetPolys(cell_list)
poly_data.SetLines(cell_list)
idFilter = vtk.vtkIdFilter()
idFilter.SetInputData(poly_data)
idFilter.SetIdsArrayName("SelectedIds")
idFilter.Update()
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(idFilter.GetOutputPort())
surfaceFilter.Update()
input = surfaceFilter.GetOutput()
self.selectedMapper.SetInputData(input)
self.selectedMapper.ScalarVisibilityOff()
self.selectedActor.SetMapper(self.selectedMapper)
self.selectedActor.GetProperty().EdgeVisibilityOn() # this makes cells not blue?
#self.selectedActor.GetProperty().SetColor(0, 0.5, 0)
self.selectedActor.GetProperty().SetEdgeColor(0.5, 0.5, 0)
self.selectedActor.GetProperty().SetLineWidth(3)
self.selectedActor.GetProperty().SetOpacity(0.5)
self.should_it_render = True
return True
else:
return False
- You need to make sure you hold a reference to a Numpy array you want
to import into VTK. If not you'll get a segfault (in the best case).
The same holds in reverse when you convert a VTK array to a numpy
array -- don't delete the VTK array.
Created by Prabhu Ramachandran in Feb. 2008.
"""
import vtk
import vtkConstants
import numpy
# Useful constants for VTK arrays.
VTK_ID_TYPE_SIZE = vtk.vtkIdTypeArray().GetDataTypeSize()
if VTK_ID_TYPE_SIZE == 4:
ID_TYPE_CODE = numpy.int32
elif VTK_ID_TYPE_SIZE == 8:
ID_TYPE_CODE = numpy.int64
VTK_LONG_TYPE_SIZE = vtk.vtkLongArray().GetDataTypeSize()
if VTK_LONG_TYPE_SIZE == 4:
LONG_TYPE_CODE = numpy.int32
ULONG_TYPE_CODE = numpy.uint32
elif VTK_LONG_TYPE_SIZE == 8:
LONG_TYPE_CODE = numpy.int64
ULONG_TYPE_CODE = numpy.uint64
def get_vtk_array_type(numpy_array_type):
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 to_vtk(bdf):
# type: (BDF) -> VTKData
import vtk
# TODO: use pynastran numpy_to_vtk
from vtk.util.numpy_support import numpy_to_vtk
nid_list = []
nid_dict = {}
node_pos = np.empty((len(bdf.nodes), 3), dtype=np.float64)
i = 0
for node in itervalues(bdf.nodes):
node_pos[i] = node.get_position()
nid = node.nid
nid_list.append(nid)
nid_dict[nid] = i
i += 1
_points = vtk.vtkPoints()
_points.SetData(numpy_to_vtk(node_pos))
points = vtk.vtkPoints()
points.DeepCopy(_points)
cells = []
cell_types = []
cell_count = 0
elem_types = []
eid_list = []
eid_dict = {}
_nastran_to_vtk = nastran_to_vtk
bdf_data_to_plot = chain(itervalues(bdf.nodes), itervalues(bdf.elements),
itervalues(bdf.rigid_elements))
category_list = []
for elem in bdf_data_to_plot:
elem_type = elem.type
cell_type, add_method, category = _nastran_to_vtk.get(
elem_type, (None, None, None))
if cell_type is None:
continue
cell_types.append(cell_type)
elem_types.append(elem_type)
eid = add_method(elem, cells, nid_dict) # returns element/grid id
eid_list.append(eid)
eid_dict[eid] = cell_count
category_list.append(categories[category])
cell_count += 1
cells = np.array(cells, dtype=np.int64)
id_array = vtk.vtkIdTypeArray()
id_array.SetVoidArray(cells, len(cells), 1)
vtk_cells = vtk.vtkCellArray()
vtk_cells.SetCells(cell_count, id_array)
cell_types = np.array(cell_types, 'B')
vtk_cell_types = numpy_to_vtk(cell_types)
cell_locations = np.array([i for i in range(cell_count)])
vtk_cell_locations = numpy_to_vtk(cell_locations,
deep=1,
array_type=vtk.VTK_ID_TYPE)
ugrid = vtk.vtkUnstructuredGrid()
ugrid.SetPoints(points)
ugrid.SetCells(vtk_cell_types, vtk_cell_locations, vtk_cells)
vtk_cell_locations.SetName('index')
ugrid.GetCellData().AddArray(vtk_cell_locations)
_elem_types = vtk.vtkStringArray()
_elem_types.SetName('element_type')
_elem_types.SetNumberOfValues(len(elem_types))
for i in range(len(elem_types)):
_elem_types.SetValue(i, elem_types[i])
ugrid.GetCellData().AddArray(_elem_types)
_cat_arr = np.array(category_list, dtype=np.int64)
_cat = vtk.vtkIdTypeArray()
_cat.SetNumberOfValues(len(category_list))
_cat.SetVoidArray(_cat_arr, len(_cat_arr), 1)
_cat.SetName('category')
ugrid.GetCellData().AddArray(_cat)
id_array = numpy_to_vtk(np.array(eid_list),
deep=1,
array_type=vtk.VTK_ID_TYPE)
# id_array = vtk.vtkIdTypeArray()
# id_array.SetVoidArray(eid_list, len(eid_list), 1)
id_array.SetName('element_id')
ugrid.GetCellData().AddArray(id_array)
copy = vtk.vtkUnstructuredGrid()
copy.DeepCopy(ugrid)
vtk_data = VTKData(copy, nid_list, nid_dict, eid_list, eid_dict)
return vtk_data
def main():
colors = vtk.vtkNamedColors()
# colors.SetColor('leftBkg', [0.6, 0.5, 0.4, 1.0])
# colors.SetColor('centreBkg', [0.3, 0.1, 0.4, 1.0])
# colors.SetColor('rightBkg', [0.4, 0.5, 0.6, 1.0])
sphereSource = vtk.vtkSphereSource()
sphereSource.Update()
print('There are %s input points' % sphereSource.GetOutput().GetNumberOfPoints())
print('There are %s input cells' % sphereSource.GetOutput().GetNumberOfCells())
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
# Specify that we want to extract cells 10 through 19
i = 10
while i < 20:
ids.InsertNextValue(i)
i += 1
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputConnection(0, sphereSource.GetOutputPort())
extractSelection.SetInputData(1, selection)
extractSelection.Update()
# In selection
selected = vtk.vtkUnstructuredGrid()
selected.ShallowCopy(extractSelection.GetOutput())
print('There are %s points in the selection' % selected.GetNumberOfPoints())
print('There are %s cells in the selection' % selected.GetNumberOfCells())
# Get points that are NOT in the selection
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1) # invert the selection
extractSelection.Update()
notSelected = vtk.vtkUnstructuredGrid()
notSelected.ShallowCopy(extractSelection.GetOutput())
print('There are %s points NOT in the selection' % notSelected.GetNumberOfPoints())
print('There are %s cells NOT in the selection' % notSelected.GetNumberOfCells())
backfaces = vtk.vtkProperty()
backfaces.SetColor(colors.GetColor3d('Gold'))
inputMapper = vtk.vtkDataSetMapper()
inputMapper.SetInputConnection(sphereSource.GetOutputPort())
inputActor = vtk.vtkActor()
inputActor.SetMapper(inputMapper)
inputActor.SetBackfaceProperty(backfaces)
inputActor.GetProperty().SetColor(colors.GetColor3d('MistyRose'))
selectedMapper = vtk.vtkDataSetMapper()
selectedMapper.SetInputData(selected)
selectedActor = vtk.vtkActor()
selectedActor.SetMapper(selectedMapper)
selectedActor.SetBackfaceProperty(backfaces)
selectedActor.GetProperty().SetColor(colors.GetColor3d('MistyRose'))
notSelectedMapper = vtk.vtkDataSetMapper()
notSelectedMapper.SetInputData(notSelected)
notSelectedActor = vtk.vtkActor()
notSelectedActor.SetMapper(notSelectedMapper)
notSelectedActor.SetBackfaceProperty(backfaces)
notSelectedActor.GetProperty().SetColor(colors.GetColor3d('MistyRose'))
# There will be one render window
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(900, 300)
renderWindow.SetWindowName('ExtractSelectionCells')
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
leftViewport = [0.0, 0.0, 0.33, 1.0]
centerViewport = [0.33, 0.0, 0.66, 1.0]
rightViewport = [0.66, 0.0, 1.0, 1.0]
# Create a camera for all renderers
camera = vtk.vtkCamera()
# Setup the renderers
leftRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(leftRenderer)
leftRenderer.SetViewport(leftViewport)
leftRenderer.SetBackground(colors.GetColor3d('BurlyWood'))
leftRenderer.SetActiveCamera(camera)
centerRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(centerRenderer)
centerRenderer.SetViewport(centerViewport)
centerRenderer.SetBackground(colors.GetColor3d('orchid_dark'))
centerRenderer.SetActiveCamera(camera)
rightRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(rightRenderer)
rightRenderer.SetViewport(rightViewport)
rightRenderer.SetBackground(colors.GetColor3d('CornflowerBlue'))
rightRenderer.SetActiveCamera(camera)
leftRenderer.AddActor(inputActor)
centerRenderer.AddActor(selectedActor)
rightRenderer.AddActor(notSelectedActor)
leftRenderer.ResetCamera()
renderWindow.Render()
interactor.Start()
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
# Working with rows in reverse order: UPSTREAM.
ringIds = range(0, int(numQuadRowsPerBranch))
ringIds = list(ringIds)
ringIds.reverse()
rowBase = 0
# Iterate over the rings in reverse order.
for ringNum in ringIds:
# print("ringNum", ringNum)
# Iterate over the cells in normal order.
for cellNum in range(0, int(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(1)
elif pPos == 3:
pointIdList.append(2)
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.GetNumberOfPoints(
) - 2))
elif pPos == 3:
pointIdList.append(
int(reorderedPoints.GetNumberOfPoints(
) - 3))
elif ringNum == ringIds[1]:
if cellNum == 0:
if pPos == 2:
pointIdList.append(1)
elif pPos == 3:
pointIdList.append(0)
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.GetNumberOfPoints(
) - 1))
elif pPos == 2:
pointIdList.append(int(cellNum * 2 + 2))
elif pPos == 3:
if cellNum == 1:
pointIdList.append(1)
else:
pointIdList.append(int(cellNum * 2))
else:
if cellNum == 0:
if pPos == 2:
pointIdList.append(int(rowBase + 1))
elif pPos == 3:
pointIdList.append(int(rowBase))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.GetNumberOfPoints(
) - 1))
elif pPos == 2:
pointIdList.append(
int(rowBase + cellNum + 1))
elif pPos == 3:
pointIdList.append(int(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 ..."
print(ringsPerLabelVals)
# 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, int(numECsPerLabel)):
selectionIds.InsertNextValue(int(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, int(numRingsPerLabel[label]))
ringIds = list(ringIds)
ringIds.reverse()
# Number of ECs rows is the number of ECs per quad.
rowIds = range(0, numECsPerCol)
rowIds = list(rowIds)
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,
int(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(
int(reorderedPoints.
GetNumberOfPoints() - 3))
elif pPos == 3:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 4))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 2))
elif pPos == 3:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 3))
elif rowNum == 1:
if ecNum == 0:
if pPos == 2:
pointIdList.append(int(rowBase + 1))
elif pPos == 3:
pointIdList.append(int(rowBase))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(
int(rowBase + ecNum * 2 + 2))
elif pPos == 3:
if ecNum == 1:
pointIdList.append(int(rowBase +
1))
else:
pointIdList.append(
int(rowBase + ecNum * 2))
else:
if ecNum == 0:
if pPos == 2:
pointIdList.append(int(rowBase + 1))
elif pPos == 3:
pointIdList.append(int(rowBase))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(
int(rowBase + ecNum + 1))
elif pPos == 3:
pointIdList.append(int(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, int(numSMCsPerLabel)):
selectionIds.InsertNextValue(int(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, int(numRingsPerLabel[label]))
ringIds = list(ringIds)
ringIds.reverse()
# Number of SMCs rows is the number of ECs per quad times 13.
rowIds = range(0, numSMCsPerCol)
rowIds = list(rowIds)
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,
int(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(
int(reorderedPoints.
GetNumberOfPoints() - 3))
elif pPos == 3:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 4))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 2))
elif pPos == 3:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 3))
elif rowNum == 1:
if smcNum == 0:
if pPos == 2:
pointIdList.append(int(rowBase + 1))
elif pPos == 3:
pointIdList.append(int(rowBase))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(
int(rowBase + smcNum * 2 + 2))
elif pPos == 3:
if smcNum == 1:
pointIdList.append(int(rowBase +
1))
else:
pointIdList.append(
int(rowBase + smcNum * 2))
else:
if smcNum == 0:
if pPos == 2:
pointIdList.append(int(rowBase + 1))
elif pPos == 3:
pointIdList.append(int(rowBase))
else:
if pPos == 0:
pointIdList.append(
int(reorderedPoints.
GetNumberOfPoints() - 1))
elif pPos == 2:
pointIdList.append(
int(rowBase + smcNum + 1))
elif pPos == 3:
pointIdList.append(
int(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 ...")
if (trilabel[tri_id] == 0): #if not labeled yet
trilabel[tri_id] = region_id
neighb = find_celledge_neighbors(tri_id, tri)
#print('Neighbors ', neighb)
for j in range(len(neighb)):
if trilabel[neighb[j]] == 0:
#see if the triangles tri_id and neighb[j] are on the different sides of the line
#i.e. if they share any pair of points of the line
if not triangles_on_any_line(tri_id, neighb[j], tri,
lines):
tri_stack.append(neighb[j])
# In[11]:
array = vtk.vtkIdTypeArray()
array.SetName(array_name)
array.SetNumberOfComponents(1)
array.SetNumberOfTuples(trilabel.shape[0])
for i in range(trilabel.shape[0]):
array.SetTuple1(i, trilabel[i])
mesh.GetCellData().AddArray(array)
wr = vtk.vtkPolyDataWriter()
wr.SetFileName(output_mesh)
wr.SetInputData(mesh)
wr.Write()
def rasterizeFibers(self,fiberNode,labelNode,labelValue=1,samplingDistance=0.1):
"""Trace through the given fiber bundles and
set the corresponding pixels in the given labelNode volume"""
print('rasterizing...')
rasToIJK = vtk.vtkMatrix4x4()
labelNode.GetRASToIJKMatrix(rasToIJK)
labelArray = slicer.util.array(labelNode.GetID())
polyData = fiberNode.GetPolyData()
cellCount = polyData.GetNumberOfCells()
selection = vtk.vtkSelection()
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.CELL)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
extractor = vtk.vtkExtractSelectedPolyDataIds()
extractor.SetInputData(0, polyData)
resampler = vtk.vtkPolyDataPointSampler()
resampler.GenerateEdgePointsOn()
resampler.GenerateVertexPointsOff()
resampler.GenerateInteriorPointsOff()
resampler.GenerateVerticesOff()
resampler.SetDistance(samplingDistance)
cellIds = vtk.vtkIdTypeArray()
# as a compromise between memory blowup (for large fiberbundles) and not
# eating time in the python loop, resample CELLS_TO_PROCESS at once.
CELLS_TO_PROCESS = 100
for startCellId in xrange(0, cellCount, CELLS_TO_PROCESS):
# generate list of cell Ids to sample
cellIdsAr = numpy.arange(startCellId,
min(cellCount, startCellId + CELLS_TO_PROCESS))
cellIds.SetVoidArray(cellIdsAr, cellIdsAr.size, 1)
# update the selection node to extract those cells
selectionNode.SetSelectionList(cellIds)
selection.AddNode(selectionNode)
selection.Modified()
extractor.SetInputData(1, selection)
extractor.Update()
resampler.SetInputConnection(extractor.GetOutputPort())
resampler.Update()
# get the resampler output
# note: to test without resampling, just use
# `pdSubset = extractor.GetOutput()` instead
pdSubset = resampler.GetOutput()
pointCount = pdSubset.GetNumberOfPoints()
points = pdSubset.GetPoints()
for pointIndex in xrange(pointCount):
point = points.GetPoint(pointIndex)
ijkFloat = rasToIJK.MultiplyPoint(point+(1,))[:3]
# skip any negative indices to avoid wrap-around
# to the other side of the image.
if (any(coord < 0 for coord in ijkFloat)):
continue
ijk = [int(round(element)) for element in ijkFloat]
ijk.reverse()
try:
# paint the voxels
labelArray[tuple(ijk)] = labelValue
except IndexError:
pass
# reset the selection node
selection.RemoveAllNodes()
labelNode.GetImageData().Modified()
labelNode.Modified()
print('finished')
def buildPolyData(vertices, faces=None, lines=None, indexOffset=0, fast=True):
"""
Build a ``vtkPolyData`` object from a list of vertices
where faces represents the connectivity of the polygonal mesh.
E.g. :
- ``vertices=[[x1,y1,z1],[x2,y2,z2], ...]``
- ``faces=[[0,1,2], [1,2,3], ...]``
Use ``indexOffset=1`` if face numbering starts from 1 instead of 0.
if fast=False the mesh is built "manually" by setting polygons and triangles
one by one. This is the fallback case when a mesh contains faces of
different number of vertices.
"""
if len(vertices[0]) < 3: # make sure it is 3d
vertices = np.c_[np.array(vertices), np.zeros(len(vertices))]
if len(vertices[0]) == 2:
vertices = np.c_[np.array(vertices), np.zeros(len(vertices))]
poly = vtk.vtkPolyData()
sourcePoints = vtk.vtkPoints()
sourcePoints.SetData(
numpy_to_vtk(np.ascontiguousarray(vertices), deep=True))
poly.SetPoints(sourcePoints)
if lines is not None:
# Create a cell array to store the lines in and add the lines to it
linesarr = vtk.vtkCellArray()
for i in range(1, len(lines) - 1):
vline = vtk.vtkLine()
vline.GetPointIds().SetId(0, lines[i])
vline.GetPointIds().SetId(1, lines[i + 1])
linesarr.InsertNextCell(vline)
poly.SetLines(linesarr)
if faces is None:
sourceVertices = vtk.vtkCellArray()
for i in range(len(vertices)):
sourceVertices.InsertNextCell(1)
sourceVertices.InsertCellPoint(i)
poly.SetVerts(sourceVertices)
return poly ###################
# faces exist
sourcePolygons = vtk.vtkCellArray()
faces = np.array(faces)
if len(faces.shape) == 2 and indexOffset == 0 and fast:
#################### all faces are composed of equal nr of vtxs, FAST
ast = np.int32
if vtk.vtkIdTypeArray().GetDataTypeSize() != 4:
ast = np.int64
nf, nc = faces.shape
hs = np.hstack((np.zeros(nf)[:, None] + nc, faces)).astype(ast).ravel()
arr = numpy_to_vtkIdTypeArray(hs, deep=True)
sourcePolygons.SetCells(nf, arr)
else: ########################################## manually add faces, SLOW
showbar = False
if len(faces) > 25000:
showbar = True
pb = ProgressBar(0, len(faces), ETA=False)
for f in faces:
n = len(f)
if n == 3:
ele = vtk.vtkTriangle()
pids = ele.GetPointIds()
for i in range(3):
pids.SetId(i, f[i] - indexOffset)
sourcePolygons.InsertNextCell(ele)
elif n == 4:
# do not use vtkTetra() because it fails
# with dolfin faces orientation
ele0 = vtk.vtkTriangle()
ele1 = vtk.vtkTriangle()
ele2 = vtk.vtkTriangle()
ele3 = vtk.vtkTriangle()
if indexOffset:
for i in [0, 1, 2, 3]:
f[i] -= indexOffset
f0, f1, f2, f3 = f
pid0 = ele0.GetPointIds()
pid1 = ele1.GetPointIds()
pid2 = ele2.GetPointIds()
pid3 = ele3.GetPointIds()
pid0.SetId(0, f0)
pid0.SetId(1, f1)
pid0.SetId(2, f2)
pid1.SetId(0, f0)
pid1.SetId(1, f1)
pid1.SetId(2, f3)
pid2.SetId(0, f1)
pid2.SetId(1, f2)
pid2.SetId(2, f3)
pid3.SetId(0, f2)
pid3.SetId(1, f3)
pid3.SetId(2, f0)
sourcePolygons.InsertNextCell(ele0)
sourcePolygons.InsertNextCell(ele1)
sourcePolygons.InsertNextCell(ele2)
sourcePolygons.InsertNextCell(ele3)
else:
ele = vtk.vtkPolygon()
pids = ele.GetPointIds()
pids.SetNumberOfIds(n)
for i in range(n):
pids.SetId(i, f[i] - indexOffset)
sourcePolygons.InsertNextCell(ele)
if showbar:
pb.print("converting mesh... ")
poly.SetPolys(sourcePolygons)
return poly
def _generate_vtk_mesh(points, cells):
import vtk
from vtk.util import numpy_support
mesh = vtk.vtkUnstructuredGrid()
# set points
vtk_points = vtk.vtkPoints()
# Not using a deep copy here results in a segfault.
vtk_array = numpy_support.numpy_to_vtk(points, deep=True)
vtk_points.SetData(vtk_array)
mesh.SetPoints(vtk_points)
# Set cells.
meshio_to_vtk_type = {y: x for x, y in vtk_to_meshio_type.items()}
# create cell_array. It's a one-dimensional vector with
# (num_points2, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
cell_types = []
cell_offsets = []
cell_connectivity = []
len_array = 0
for meshio_type, data in cells.items():
numcells, num_local_nodes = data.shape
if meshio_type[:7] == "polygon":
vtk_type = meshio_to_vtk_type[meshio_type[:7]]
else:
vtk_type = meshio_to_vtk_type[meshio_type]
# add cell types
cell_types.append(numpy.empty(numcells, dtype=numpy.ubyte))
cell_types[-1].fill(vtk_type)
# add cell offsets
cell_offsets.append(
numpy.arange(
len_array,
len_array + numcells * (num_local_nodes + 1),
num_local_nodes + 1,
dtype=numpy.int64,
)
)
cell_connectivity.append(
numpy.c_[
num_local_nodes * numpy.ones(numcells, dtype=data.dtype), data
].flatten()
)
len_array += len(cell_connectivity[-1])
cell_types = numpy.concatenate(cell_types)
cell_offsets = numpy.concatenate(cell_offsets)
cell_connectivity = numpy.concatenate(cell_connectivity)
connectivity = vtk.util.numpy_support.numpy_to_vtkIdTypeArray(
cell_connectivity.astype(numpy.int64), deep=1
)
# wrap the data into a vtkCellArray
cell_array = vtk.vtkCellArray()
cell_array.SetCells(len(cell_types), connectivity)
# Add cell data to the mesh
mesh.SetCells(
numpy_support.numpy_to_vtk(
cell_types, deep=1, array_type=vtk.vtkUnsignedCharArray().GetDataType()
),
numpy_support.numpy_to_vtk(
cell_offsets, deep=1, array_type=vtk.vtkIdTypeArray().GetDataType()
),
cell_array,
)
return mesh
def _set_cells(cells, n_cells, id_typ_arr):
vtk_arr = vtk.vtkIdTypeArray()
array2vtk(id_typ_arr, vtk_arr)
cells.SetCells(n_cells, vtk_arr)
def convert2VPD(M,clean=False):
"""Convert pyFormex data to vtkPolyData.
Convert a pyFormex Mesh or Coords object into vtkPolyData.
This is limited to vertices, lines, and polygons.
Lines should already be ordered (with connectedLineElems for instance).
Parameters:
- `M`: a Mesh or Coords type. If M is a Coords type it will be saved as
VERTS. Else...
- `clean`: if True, the resulting vtkdata will be cleaned by calling
cleanVPD.
Returns a vtkPolyData.
"""
from vtk import vtkPolyData,vtkPoints,vtkIdTypeArray,vtkCellArray
print('STARTING CONVERSION FOR DATA OF TYPE %s '%type(M))
if type(M) == Coords:
M = Mesh(M,arange(M.ncoords()))
Nelems = M.nelems() # Number of elements
Ncxel = M.nplex() # # Number of nodes per element
# create a vtkPolyData variable
vpd=vtkPolyData()
# creating vtk coords
pts = vtkPoints()
ntype=gnat(pts.GetDataType())
coordsv = n2v(asarray(M.coords,order='C',dtype=ntype),deep=1) #.copy() # deepcopy array conversion for C like array of vtk, it is necessary to avoid memry data loss
pts.SetNumberOfPoints(M.ncoords())
pts.SetData(coordsv)
vpd.SetPoints(pts)
# create vtk connectivity
elms = vtkIdTypeArray()
ntype=gnat(vtkIdTypeArray().GetDataType())
elmsv = concatenate([Ncxel*ones(Nelems).reshape(-1,1),M.elems],axis=1)
elmsv = n2v(asarray(elmsv,order='C',dtype=ntype),deep=1) #.copy() # deepcopy array conversion for C like array of vtk, it is necessary to avoid memry data loss
elms.DeepCopy(elmsv)
# set vtk Cell data
datav = vtkCellArray()
datav.SetCells(Nelems,elms)
if Ncxel == 1:
try:
print("setting VERTS for data with %s maximum number of point for cell "%Ncxel)
vpd.SetVerts(datav)
except:
raise ValueError,"Error in saving VERTS"
elif Ncxel == 2:
try:
print ("setting LINES for data with %s maximum number of point for cell "%Ncxel)
vpd.SetLines(datav)
except:
raise ValueError,"Error in saving LINES"
else:
try:
print ("setting POLYS for data with %s maximum number of point for cell "%Ncxel)
vpd.SetPolys(datav)
except:
raise ValueError,"Error in saving POLYS"
vpd.Update()
if clean:
vpd=cleanVPD(vpd)
return vpd
def Pick(self, selectionX, selectionY, selectionZ, renderer=None):
self.ids.Reset()
if renderer is None:
print "Renderer has not been set!"
return
self.Renderer = renderer
ray_result = picking_ray([selectionX, selectionY, selectionZ],
renderer)
if ray_result != -1:
self.selection_point = ray_result[0]
self.PickPosition = ray_result[1]
self.p1World = ray_result[2]
self.p2World = ray_result[3]
else:
return
tol = self.Tolerance
self.FindCellsAlongLine(self.p1World[:3], self.p2World[:3], tol,
self.ids)
self.ClosestCellId = -1
self.ClosestCellGlobalId = -1
# determine which cells are actually intersected
data = self.GetDataSet()
global_ids = data.GetCellData().GetGlobalIds()
self.id_array.Reset()
self.global_id_array.Reset()
self.id_list = []
self.global_id_list = []
t = mutable(0.)
x = [0, 0, 0]
pcoords = [0, 0, 0]
subId = mutable(0)
OFFSET_ELEMENT = vtk_globals.OFFSET_ELEMENT
my_int = int
for i in xrange(self.ids.GetNumberOfIds()):
id = self.ids.GetId(i)
cell = data.GetCell(id)
try:
if not self.cells_to_pick_from[cell.GetCellType()]:
continue
except IndexError:
continue
nodes_exist = False
if cell.IntersectWithLine(self.p1World[:3], self.p2World[:3], tol,
t, x, pcoords, subId):
self.id_array.InsertNextValue(id)
self.id_list.append(id)
global_id = my_int(global_ids.GetTuple(id)[0])
self.global_id_list.append(global_id)
self.global_id_array.InsertNextValue(global_id)
#print global_id
if global_id < OFFSET_ELEMENT:
nodes_exist = True
if nodes_exist:
new_id_array = vtk.vtkIdTypeArray()
new_id_array.ShallowCopy(self.id_array)
new_global_id_array = vtk.vtkIdTypeArray()
new_global_id_array.ShallowCopy(self.global_id_array)
for i in xrange(self.id_array.GetNumberOfTuples()):
global_id = my_int(self.global_id_array.GetTuple(i)[0])
id = my_int(self.id_array.GetTuple(i)[0])
if global_id < OFFSET_ELEMENT:
new_global_id_array.InsertNextValue(global_id)
new_id_array.InsertNextValue(id)
new_global_id_array.Squeeze()
new_id_array.Squeeze()
self.id_array.Reset()
self.global_id_array.Reset()
self.id_array.ShallowCopy(new_id_array)
self.global_id_array.ShallowCopy(new_global_id_array)
else:
self.id_array.Squeeze()
self.global_id_array.Squeeze()
self.update_ids()
- You need to make sure you hold a reference to a Numpy array you want
to import into VTK. If not you'll get a segfault (in the best case).
The same holds in reverse when you convert a VTK array to a numpy
array -- don't delete the VTK array.
Created by Prabhu Ramachandran in Feb. 2008.
"""
import vtk
import vtkConstants
import numpy
# Useful constants for VTK arrays.
VTK_ID_TYPE_SIZE = vtk.vtkIdTypeArray().GetDataTypeSize()
if VTK_ID_TYPE_SIZE == 4:
ID_TYPE_CODE = numpy.int32
elif VTK_ID_TYPE_SIZE == 8:
ID_TYPE_CODE = numpy.int64
VTK_LONG_TYPE_SIZE = vtk.vtkLongArray().GetDataTypeSize()
if VTK_LONG_TYPE_SIZE == 4:
LONG_TYPE_CODE = numpy.int32
ULONG_TYPE_CODE = numpy.uint32
elif VTK_LONG_TYPE_SIZE == 8:
LONG_TYPE_CODE = numpy.int64
ULONG_TYPE_CODE = numpy.uint64
def get_vtk_array_type(numpy_array_type):
def writeHdf5():
# This is where the data is for testing purposes.
print("Current working directory:", os.getcwd())
print(taskMeshIn)
numQuadsPerRing = circQuads
# Working with the task mesh junt to figure out the quads and rows numbers.
taskMeshReader = vtk.vtkXMLPolyDataReader()
taskMeshReader.SetFileName(taskMeshIn)
taskMeshReader.Update()
taskMesh = taskMeshReader.GetOutput()
print(taskMesh.GetNumberOfPoints())
ecMeshReader = vtk.vtkXMLPolyDataReader()
ecMeshReader.SetFileName(ecMeshIn)
ecMeshReader.Update()
ecMesh = ecMeshReader.GetOutput()
print(ecMesh.GetNumberOfPoints())
# 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()
numQuadRowsPerBranch = taskMeshBranch.GetNumberOfCells(
) / numQuadsPerRing
numRingsPerLabel[label] = numQuadRowsPerBranch
# Working with EC mesh only
atpMeshReader = vtk.vtkXMLPolyDataReader()
atpMeshReader.SetFileName(atpMeshIn)
atpMeshReader.Update()
# Original ECs mesh to work with.
atpMesh = atpMeshReader.GetOutput()
print("There are", atpMesh.GetNumberOfCells(), "ATP values in total ...")
parentFile = h5py.File(atpHdf5Files[0], 'w')
leftBranchFile = h5py.File(atpHdf5Files[1], 'w')
rightBranchFile = h5py.File(atpHdf5Files[2], 'w')
appendPolyData = vtk.vtkAppendPolyData()
# For every label in the range of labels we want to extract all ECs.
for label in labelRange:
ecMeshReader = vtk.vtkXMLPolyDataReader()
ecMeshReader.SetFileName(ecVTPFiles[label])
ecMeshReader.Update()
tmpPolyData = ecMeshReader.GetOutput()
# Keep track of how many branches we need to skip.
numECsPerLabel = numQuadsPerRing * numRingsPerLabel[
label] * numECsPerQuad
atpCellOffset = label * numECsPerLabel
print("atpCellOffset", atpCellOffset)
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, int(numECsPerLabel)):
selectionIds.InsertNextValue(int(atpCellOffset) + 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, atpMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedCells = selectionExtractor.GetOutput()
# Ring ids list for traversal.
ringIds = range(0, int(numRingsPerLabel[label]))
ringIds = list(ringIds)
ringIds.reverse()
# Number of ECs rows is the number of ECs per quad.
rowIds = range(0, numECsPerCol)
rowIds = list(rowIds)
rowIds.reverse()
reorderedATPArray = vtk.vtkDoubleArray()
reorderedATPArray.SetName("initialATP")
# Decide which TXT files to write to.
pointsOf = ''
if label == 0:
pointsOf = parentFile
elif label == 1:
pointsOf = leftBranchFile
elif label == 2:
pointsOf = rightBranchFile
print("Writing H5 file for ECs ATP:")
print(pointsOf)
dset = pointsOf.create_dataset("/atp", (numECsPerLabel, ), 'f')
i = 0
# 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 cellNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
realId = quadId * numECsPerQuad + rowNum * numECsPerRow + cellNum
atpVal = extractedCells.GetCellData().GetArray(
"initialATP").GetValue(realId)
reorderedATPArray.InsertNextValue(atpVal)
# Write the value to the txt file.
dset[i] = atpVal
i += 1
tmpPolyData.GetCellData().SetScalars(reorderedATPArray)
appendPolyData.AddInputData(tmpPolyData)
parentFile.close()
leftBranchFile.close()
rightBranchFile.close()
print("Writing reorderd ATP map for verification...")
appendPolyData.Update()
reorderedATPWriter = vtk.vtkXMLPolyDataWriter()
reorderedATPWriter.SetInputData(appendPolyData.GetOutput())
reorderedATPWriter.SetFileName("vtk/reordered_atp.vtp")
reorderedATPWriter.Update()
print("All done ...")
neighb = find_celledge_neighbors(tri_id, tri)
#print('Neighbors ', neighb)
for j in range( len(neighb) ):
if trilabel[neighb[j]]==0:
#see if the triangles tri_id and neighb[j] are on the different sides of the line
#i.e. if they share any pair of points of the line
if not triangles_on_any_line(tri_id, neighb[j], tri, lines):
tri_stack.append(neighb[j])
# In[11]:
array = vtk.vtkIdTypeArray()
array.SetName(array_name)
array.SetNumberOfComponents(1)
array.SetNumberOfTuples(trilabel.shape[0])
for i in range(trilabel.shape[0]):
array.SetTuple1(i, trilabel[i])
mesh.GetCellData().AddArray(array)
wr = vtk.vtkPolyDataWriter()
wr.SetFileName(output_mesh)
wr.SetInputData(mesh)
wr.Write()
def GenerateTetrInFile(self):
self.PrintLog('Generating Tetr .in file.')
f=open(self.OutputFileName, 'w')
line = '$title' + '\n'
f.write(line)
line = self.OutputFileName + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$compress' + '\n'
f.write(line)
line = 'gzip -f' + '\n'
f.write(line)
line = '\n'
f.write(line)
self.NormalizationTransform.Identity()
if (self.NormalizationEntity != ''):
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(self.NormalizationEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.Execute()
self.NormalizationRadius = sectionProperties.Radius
if (self.NormalizationRadius != 0.0) & (self.NormalizationRadius != 1.0):
self.NormalizationTransform.Scale(1.0/self.NormalizationRadius,1.0/self.NormalizationRadius,1.0/self.NormalizationRadius)
line = '$radius' + '\n'
f.write(line)
line = str(self.NormalizationRadius) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$viscosity' + '\n'
f.write(line)
line = str(0.035) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$density' + '\n'
f.write(line)
line = str(1.06) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$red' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$alpha' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$nsolve' + '\n'
f.write(line)
line = '22' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$Uzawa_PC' + '\n'
f.write(line)
line = '1' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$node' + '\n'
f.write(line)
line = str(self.Mesh.GetNumberOfPoints()) + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = [0.0,0.0,0.0]
self.NormalizationTransform.TransformPoint(self.Mesh.GetPoint(i),point)
line = str(i+1) + ' ' + str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2]) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$elem' + '\n'
f.write(line)
quadratidTetraCellType = 24
quadraticTetraCellIds = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(quadratidTetraCellType,quadraticTetraCellIds)
line = str(quadraticTetraCellIds.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(quadraticTetraCellIds.GetNumberOfTuples()):
line = str(i+1) + ' '
cell = self.Mesh.GetCell(quadraticTetraCellIds.GetValue(i))
line += str(cell.GetPointId(0)+1) + ' '
line += str(cell.GetPointId(4)+1) + ' '
line += str(cell.GetPointId(1)+1) + ' '
line += str(cell.GetPointId(5)+1) + ' '
line += str(cell.GetPointId(2)+1) + ' '
line += str(cell.GetPointId(6)+1) + ' '
line += str(cell.GetPointId(7)+1) + ' '
line += str(cell.GetPointId(8)+1) + ' '
line += str(cell.GetPointId(9)+1) + ' '
line += str(cell.GetPointId(3)+1) + ' '
line += '\n'
f.write(line)
# inletEntities = self.InletEntities
# reversedInlets = self.ReverseInlets
# inletEntitiesReversed = zip(inletEntities,reversedInlets)
# for inletEntityReversed in inletEntitiesReversed:
# inletEntity = inletEntityReversed[0]
# reversedInlet = inletEntityReversed[1]
# if (inletEntity == ''):
# continue
for inletEntity in self.InletEntities:
reversedInlet = inletEntity in self.ReverseInletEntities
line = '\n'
f.write(line)
line = '$binlet' + ' (' + inletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(inletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(inletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
if not reversedInlet:
sectionProperties.FlipOutwardNormal = 1
else:
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(sectionProperties.Origin[1]) + ' ' + str(sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(sectionProperties.Normal[1]) + ' ' + str(sectionProperties.Normal[2]) + '\n'
f.write(line)
#TODO: for every inlet insert fourier coefficients given points of waveform (spline-interpolate points beforehands to get them equispaced).
if (self.OutletEntity != ''):
line = '\n'
f.write(line)
line = '$boutlet' + ' (' + self.OutletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.OutletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(self.OutletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(sectionProperties.Origin[1]) + ' ' + str(sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(sectionProperties.Normal[1]) + ' ' + str(sectionProperties.Normal[2]) + '\n'
f.write(line)
if (self.WallEntity != ''):
line = '\n'
f.write(line)
line = '$bwall' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.WallEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
wallPointIdsMap = vtk.vtkIdList()
if (self.WriteWNodeSection == 1):
line = '\n'
f.write(line)
line = '$wnode' + '\n'
f.write(line)
line = str(numberOfEntityNodes) + '\n'
f.write(line)
count = 0
wallPointIdsMap.SetNumberOfIds(entityArray.GetNumberOfTuples())
extractSurface = vtk.vtkGeometryFilter()
extractSurface.SetInput(self.Mesh)
extractSurface.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInput(extractSurface.GetOutput())
normalsFilter.AutoOrientNormalsOn()
normalsFilter.ConsistencyOn()
normalsFilter.Update()
normalsSurface = normalsFilter.GetOutput()
locator = vtk.vtkMergePoints()
locator.SetDataSet(normalsSurface)
locator.BuildLocator()
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
wallPointIdsMap.SetId(i,-1)
continue
wallPointIdsMap.SetId(i,count)
point = self.Mesh.GetPoint(i)
surfacePointId = locator.FindClosestPoint(point)
normal = normalsSurface.GetPointData().GetNormals().GetTuple3(surfacePointId)
line = str(count+1) + ' ' + str(i+1) + ' ' + str(normal[0]) + ' ' + str(normal[1]) + ' ' + str(normal[2]) + '\n'
f.write(line)
count += 1
if (self.WriteWElemSection == 1):
line = '\n'
f.write(line)
line = '$welem' + '\n'
f.write(line)
dataArray = vtk.vtkIntArray()
dataArray.SetNumberOfComponents(8)
for i in range(self.Mesh.GetNumberOfCells()):
qtetra = self.Mesh.GetCell(i)
for j in range(qtetra.GetNumberOfFaces()):
face = qtetra.GetFace(j)
isBoundaryFace = 1
for k in range(face.GetNumberOfPoints()):
if (entityArray.GetComponent(face.GetPointId(k),0) != 1.0):
isBoundaryFace = 0
break
if (isBoundaryFace == 0):
continue
dataArray.InsertNextValue(i)
dataArray.InsertNextValue(j)
for k in range(face.GetNumberOfPoints()):
dataArray.InsertNextValue(face.GetPointId(k))
line = str(dataArray.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(dataArray.GetNumberOfTuples()):
line = str(i+1) + ' '
line += str(int(dataArray.GetComponent(i,0))+1) + ' '
faceId = int(dataArray.GetComponent(i,1))
newTetrFaceIdsMap = [2, 4, 3, 1]
line += str(newTetrFaceIdsMap[faceId]) + ' '
for j in range(2,dataArray.GetNumberOfComponents()):
line += str(wallPointIdsMap.GetId(int(dataArray.GetComponent(i,j)))+1) + ' '
line += '\n'
f.write(line)
if (self.HistoryEntity != ''):
line = '\n'
f.write(line)
line = '$history' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.HistoryEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i,0) != 1.0):
continue
line = str(i+1) + '\n'
f.write(line)
self.WriteTimeSteps(f)
def ExtractSelection(fileList):
# Report our CWD just for testing purposes.
print "CWD:", os.getcwd()
ringOffset = numQuadsPerRing * numSMCsPerCol * 4
branchOffset = numRingsPerBranch * ringOffset
# Prepare selection id array.
selectionIds = vtk.vtkIdTypeArray()
for branch in branches:
thisBranchOffset = branch * branchOffset
# print thisBranchOffset,
for ring in range(numRingsPerBranch):
thisRingOffset = ring * ringOffset
# print thisRingOffset,
for cell in range(numSMCsPerCol):
thisOffset = start + thisBranchOffset + thisRingOffset + cell
# print thisOffset,
selectionIds.InsertNextValue(thisOffset)
# Create selection node.
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(selectionNode.CELL)
selectionNode.SetContentType(selectionNode.INDICES)
selectionNode.SetSelectionList(selectionIds)
# Create selection.
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
sortNicely(fileList)
# Process every file by extracting selection.
for inFile in fileList:
print 'Reading file', inFile
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(inFile)
print '\tExtracting ', selectionIds.GetNumberOfTuples(), 'cells...'
selectionExtractor = vtk.vtkExtractSelection()
selectionExtractor.SetInputConnection(reader.GetOutputPort())
if vtk.vtkVersion().GetVTKMajorVersion() > 5:
selectionExtractor.SetInputData(1, selection)
else:
selectionExtractor.SetInput(1, selection)
baseName = os.path.basename(inFile)
number = [int(s) for s in re.split('([0-9]+)', baseName) if s.isdigit()]
outFile = outputPattern + str(number[0]) + '.vtu'
print '\t\tSaving file', outFile
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetInputConnection(selectionExtractor.GetOutputPort())
writer.SetFileName(outFile)
writer.Update()
print '\n'
print 'All done...'
def GenerateTetrInFile(self):
self.PrintLog('Generating Tetr .in file.')
f = open(self.OutputFileName, 'w')
line = '$title' + '\n'
f.write(line)
line = self.OutputFileName + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$compress' + '\n'
f.write(line)
line = 'gzip -f' + '\n'
f.write(line)
line = '\n'
f.write(line)
self.NormalizationTransform.Identity()
if (self.NormalizationEntity != ''):
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
self.NormalizationEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.Execute()
self.NormalizationRadius = sectionProperties.Radius
if (self.NormalizationRadius != 0.0) & (self.NormalizationRadius !=
1.0):
self.NormalizationTransform.Scale(1.0 / self.NormalizationRadius,
1.0 / self.NormalizationRadius,
1.0 / self.NormalizationRadius)
line = '$radius' + '\n'
f.write(line)
line = str(self.NormalizationRadius) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$viscosity' + '\n'
f.write(line)
line = str(0.035) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$density' + '\n'
f.write(line)
line = str(1.06) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$red' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$alpha' + '\n'
f.write(line)
line = str(0) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$nsolve' + '\n'
f.write(line)
line = '22' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$Uzawa_PC' + '\n'
f.write(line)
line = '1' + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$node' + '\n'
f.write(line)
line = str(self.Mesh.GetNumberOfPoints()) + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = [0.0, 0.0, 0.0]
self.NormalizationTransform.TransformPoint(self.Mesh.GetPoint(i),
point)
line = str(i + 1) + ' ' + str(point[0]) + ' ' + str(
point[1]) + ' ' + str(point[2]) + '\n'
f.write(line)
line = '\n'
f.write(line)
line = '$elem' + '\n'
f.write(line)
quadratidTetraCellType = 24
quadraticTetraCellIds = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(quadratidTetraCellType,
quadraticTetraCellIds)
line = str(quadraticTetraCellIds.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(quadraticTetraCellIds.GetNumberOfTuples()):
line = str(i + 1) + ' '
cell = self.Mesh.GetCell(quadraticTetraCellIds.GetValue(i))
line += str(cell.GetPointId(0) + 1) + ' '
line += str(cell.GetPointId(4) + 1) + ' '
line += str(cell.GetPointId(1) + 1) + ' '
line += str(cell.GetPointId(5) + 1) + ' '
line += str(cell.GetPointId(2) + 1) + ' '
line += str(cell.GetPointId(6) + 1) + ' '
line += str(cell.GetPointId(7) + 1) + ' '
line += str(cell.GetPointId(8) + 1) + ' '
line += str(cell.GetPointId(9) + 1) + ' '
line += str(cell.GetPointId(3) + 1) + ' '
line += '\n'
f.write(line)
# inletEntities = self.InletEntities
# reversedInlets = self.ReverseInlets
# inletEntitiesReversed = zip(inletEntities,reversedInlets)
# for inletEntityReversed in inletEntitiesReversed:
# inletEntity = inletEntityReversed[0]
# reversedInlet = inletEntityReversed[1]
# if (inletEntity == ''):
# continue
for inletEntity in self.InletEntities:
reversedInlet = inletEntity in self.ReverseInletEntities
line = '\n'
f.write(line)
line = '$binlet' + ' (' + inletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(inletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
inletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
if not reversedInlet:
sectionProperties.FlipOutwardNormal = 1
else:
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(
sectionProperties.Origin[1]) + ' ' + str(
sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(
sectionProperties.Normal[1]) + ' ' + str(
sectionProperties.Normal[2]) + '\n'
f.write(line)
#TODO: for every inlet insert fourier coefficients given points of waveform (spline-interpolate points beforehands to get them equispaced).
if (self.OutletEntity != ''):
line = '\n'
f.write(line)
line = '$boutlet' + ' (' + self.OutletEntity + ') ' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.OutletEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
sectionBoundaryPointIds = self.GetSectionBoundaryPointIds(
self.OutletEntity)
sectionProperties = SectionProperties()
sectionProperties.Mesh = self.Mesh
sectionProperties.NormalizationTransform = self.NormalizationTransform
sectionProperties.SectionBoundaryPointIds = sectionBoundaryPointIds
sectionProperties.FlipOutwardNormal = 0
sectionProperties.Execute()
line = str(sectionProperties.Radius) + '\n'
f.write(line)
line = str(sectionProperties.Origin[0]) + ' ' + str(
sectionProperties.Origin[1]) + ' ' + str(
sectionProperties.Origin[2]) + '\n'
f.write(line)
line = str(sectionProperties.Normal[0]) + ' ' + str(
sectionProperties.Normal[1]) + ' ' + str(
sectionProperties.Normal[2]) + '\n'
f.write(line)
if (self.WallEntity != ''):
line = '\n'
f.write(line)
line = '$bwall' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.WallEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
wallPointIdsMap = vtk.vtkIdList()
if (self.WriteWNodeSection == 1):
line = '\n'
f.write(line)
line = '$wnode' + '\n'
f.write(line)
line = str(numberOfEntityNodes) + '\n'
f.write(line)
count = 0
wallPointIdsMap.SetNumberOfIds(entityArray.GetNumberOfTuples())
extractSurface = vtk.vtkGeometryFilter()
extractSurface.SetInputData(self.Mesh)
extractSurface.Update()
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputConnection(
extractSurface.GetOutputPort())
normalsFilter.AutoOrientNormalsOn()
normalsFilter.ConsistencyOn()
normalsFilter.Update()
normalsSurface = normalsFilter.GetOutput()
locator = vtk.vtkMergePoints()
locator.SetDataSet(normalsSurface)
locator.BuildLocator()
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
wallPointIdsMap.SetId(i, -1)
continue
wallPointIdsMap.SetId(i, count)
point = self.Mesh.GetPoint(i)
surfacePointId = locator.FindClosestPoint(point)
normal = normalsSurface.GetPointData().GetNormals(
).GetTuple3(surfacePointId)
line = str(count + 1) + ' ' + str(i + 1) + ' ' + str(
normal[0]) + ' ' + str(normal[1]) + ' ' + str(
normal[2]) + '\n'
f.write(line)
count += 1
if (self.WriteWElemSection == 1):
line = '\n'
f.write(line)
line = '$welem' + '\n'
f.write(line)
dataArray = vtk.vtkIntArray()
dataArray.SetNumberOfComponents(8)
for i in range(self.Mesh.GetNumberOfCells()):
qtetra = self.Mesh.GetCell(i)
for j in range(qtetra.GetNumberOfFaces()):
face = qtetra.GetFace(j)
isBoundaryFace = 1
for k in range(face.GetNumberOfPoints()):
if (entityArray.GetComponent(
face.GetPointId(k), 0) != 1.0):
isBoundaryFace = 0
break
if (isBoundaryFace == 0):
continue
dataArray.InsertNextValue(i)
dataArray.InsertNextValue(j)
for k in range(face.GetNumberOfPoints()):
dataArray.InsertNextValue(face.GetPointId(k))
line = str(dataArray.GetNumberOfTuples()) + '\n'
f.write(line)
for i in range(dataArray.GetNumberOfTuples()):
line = str(i + 1) + ' '
line += str(int(dataArray.GetComponent(i, 0)) + 1) + ' '
faceId = int(dataArray.GetComponent(i, 1))
newTetrFaceIdsMap = [2, 4, 3, 1]
line += str(newTetrFaceIdsMap[faceId]) + ' '
for j in range(2, dataArray.GetNumberOfComponents()):
line += str(
wallPointIdsMap.GetId(
int(dataArray.GetComponent(i, j))) + 1) + ' '
line += '\n'
f.write(line)
if (self.HistoryEntity != ''):
line = '\n'
f.write(line)
line = '$history' + '\n'
f.write(line)
entityArray = self.Mesh.GetPointData().GetArray(self.HistoryEntity)
numberOfEntityNodes = 0
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
numberOfEntityNodes += 1
line = str(numberOfEntityNodes) + '\n'
f.write(line)
for i in range(entityArray.GetNumberOfTuples()):
if (entityArray.GetComponent(i, 0) != 1.0):
continue
line = str(i + 1) + '\n'
f.write(line)
self.WriteTimeSteps(f)
def WriteLifeVMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing LifeV file.')
self.Mesh.BuildLinks()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.DeepCopy(self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName))
tetraCellType = 10
triangleCellType = 5
f=open(self.OutputFileName, 'w')
line = "MeshVersionFormatted 1\n\n"
line += "Dimension\n"
line += "3\n\n"
line += "Vertices\n"
line += "%d\n" % self.Mesh.GetNumberOfPoints()
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
pointCells = vtk.vtkIdList()
self.Mesh.GetPointCells(i,pointCells)
minTriangleCellEntityId = -1
tetraCellEntityId = -1
for j in range(pointCells.GetNumberOfIds()):
cellId = pointCells.GetId(j)
if self.Mesh.GetCellType(cellId) == triangleCellType:
cellEntityId = cellEntityIdsArray.GetValue(cellId)
if cellEntityId < minTriangleCellEntityId or minTriangleCellEntityId == -1:
minTriangleCellEntityId = cellEntityId
else:
tetraCellEntityId = cellEntityIdsArray.GetValue(cellId)
cellEntityId = tetraCellEntityId
if minTriangleCellEntityId != -1:
cellEntityId = minTriangleCellEntityId
line = "%f %f %f %d\n" % (point[0], point[1], point[2], cellEntityId)
f.write(line)
line = "\n"
tetraCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(tetraCellType,tetraCellIdArray)
numberOfTetras = tetraCellIdArray.GetNumberOfTuples()
line += "Tetrahedra\n"
line += "%d\n" % numberOfTetras
f.write(line)
for i in range(numberOfTetras):
tetraCellId = tetraCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(tetraCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
line += ' %d\n' % 1
f.write(line)
line = "\n"
triangleCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(triangleCellType,triangleCellIdArray)
numberOfTriangles = triangleCellIdArray.GetNumberOfTuples()
line += "Triangles\n"
line += "%d\n" % numberOfTriangles
f.write(line)
for i in range(numberOfTriangles):
triangleCellId = triangleCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(triangleCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
cellEntityId = cellEntityIdsArray.GetValue(triangleCellId)
line += ' %d\n' % cellEntityId
f.write(line)
def writeHdf5():
# This is where the data is for testing purposes.
print "Current working directory:", os.getcwd()
print taskMeshIn
numQuadsPerRing = circQuads
# Working with the task mesh junt to figure out the quads and rows numbers.
taskMeshReader = vtk.vtkXMLPolyDataReader()
taskMeshReader.SetFileName(taskMeshIn)
taskMeshReader.Update()
taskMesh = taskMeshReader.GetOutput()
print taskMesh.GetNumberOfPoints()
ecMeshReader = vtk.vtkXMLPolyDataReader()
ecMeshReader.SetFileName(ecMeshIn)
ecMeshReader.Update()
ecMesh = ecMeshReader.GetOutput()
print ecMesh.GetNumberOfPoints()
# 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()
numQuadRowsPerBranch = taskMeshBranch.GetNumberOfCells() / numQuadsPerRing;
numRingsPerLabel[label] = numQuadRowsPerBranch
# Working with EC mesh only
atpMeshReader = vtk.vtkXMLPolyDataReader()
atpMeshReader.SetFileName(atpMeshIn)
atpMeshReader.Update()
# Original ECs mesh to work with.
atpMesh = atpMeshReader.GetOutput()
print "There are", atpMesh.GetNumberOfCells(), "ATP values in total ..."
parentFile = h5py.File(atpHdf5Files[0], 'w')
leftBranchFile = h5py.File(atpHdf5Files[1], 'w')
rightBranchFile = h5py.File(atpHdf5Files[2], 'w')
appendPolyData = vtk.vtkAppendPolyData();
# For every label in the range of labels we want to extract all ECs.
for label in labelRange:
ecMeshReader = vtk.vtkXMLPolyDataReader()
ecMeshReader.SetFileName(ecVTPFiles[label])
ecMeshReader.Update()
tmpPolyData = ecMeshReader.GetOutput()
# Keep track of how many branches we need to skip.
numECsPerLabel = numQuadsPerRing * numRingsPerLabel[label] * numECsPerQuad
atpCellOffset = label * numECsPerLabel
print "atpCellOffset", atpCellOffset
# Collect cell ids to select.
selectionIds = vtk.vtkIdTypeArray()
for sId in range(0, numECsPerLabel):
selectionIds.InsertNextValue(atpCellOffset + 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, atpMesh)
selectionExtractor.SetInputData(1, selection)
selectionExtractor.Update()
extractedCells = 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()
reorderedATPArray = vtk.vtkDoubleArray()
reorderedATPArray.SetName("initialATP")
# Decide which TXT files to write to.
pointsOf = ''
if label == 0:
pointsOf = parentFile
elif label == 1:
pointsOf = leftBranchFile
elif label == 2:
pointsOf = rightBranchFile
print "Writing H5 file for ECs ATP:"
print pointsOf
dset = pointsOf.create_dataset("/atp", (numECsPerLabel,), 'f')
i = 0
# 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 cellNum in range(0, numECsPerRow):
# Calculate the 'real' ec cell id and get the corresponding cell.
realId = quadId * numECsPerQuad + rowNum * numECsPerRow + cellNum
atpVal = extractedCells.GetCellData().GetArray("initialATP").GetValue(realId)
reorderedATPArray.InsertNextValue(atpVal)
# Write the value to the txt file.
dset[i] = atpVal
i += 1
tmpPolyData.GetCellData().SetScalars(reorderedATPArray)
appendPolyData.AddInputData(tmpPolyData)
parentFile.close()
leftBranchFile.close()
rightBranchFile.close()
print "Writing reorderd ATP map for verification..."
appendPolyData.Update()
reorderedATPWriter = vtk.vtkXMLPolyDataWriter()
reorderedATPWriter.SetInputData(appendPolyData.GetOutput())
reorderedATPWriter.SetFileName("vtk/reordered_atp.vtp")
reorderedATPWriter.Update()
print "All done ..."
def main():
sphere_source = vtk.vtkSphereSource()
sphere_source.Update()
print("There are %s input points" % sphere_source.GetOutput().GetNumberOfPoints())
print("There are %s input cells" % sphere_source.GetOutput().GetNumberOfCells())
ids = vtk.vtkIdTypeArray()
ids.SetNumberOfComponents(1)
# Specify that we want to extract cells 10 through 19
i = 10
while i < 20:
ids.InsertNextValue(i)
i += 1
selection_node = vtk.vtkSelectionNode()
selection_node.SetFieldType(vtk.vtkSelectionNode.CELL)
selection_node.SetContentType(vtk.vtkSelectionNode.INDICES)
selection_node.SetSelectionList(ids)
selection = vtk.vtkSelection()
selection.AddNode(selection_node)
extract_selection = vtk.vtkExtractSelection()
if vtk.VTK_MAJOR_VERSION <= 5:
extract_selection.SetInputConnection(0, sphere_source.GetOutputPort())
extract_selection.SetInput(1, selection)
else:
extract_selection.SetInputConnection(0, sphere_source.GetOutputPort())
extract_selection.SetInputData(1, selection)
extract_selection.Update()
# In selection
grid_selected = vtk.vtkUnstructuredGrid()
grid_selected.ShallowCopy(extract_selection.GetOutput())
print("There are %s points in the selection" % grid_selected.GetNumberOfPoints())
print("There are %s cells in the selection" % grid_selected.GetNumberOfCells())
# Get points that are NOT in the selection
# invert the selection
selection_node.GetProperties().Set(vtk.vtkSelectionNode.INVERSE(), 1)
extract_selection.Update()
not_selected = vtk.vtkUnstructuredGrid()
not_selected.ShallowCopy(extract_selection.GetOutput())
print("There are %s points NOT in the selection" % not_selected.GetNumberOfPoints())
print("There are %s cells NOT in the selection" % not_selected.GetNumberOfCells())
backfaces = vtk.vtkProperty()
backfaces.SetColor(1, 0, 0)
input_mapper = vtk.vtkDataSetMapper()
input_mapper.SetInputConnection(sphere_source.GetOutputPort())
input_actor = vtk.vtkActor()
input_actor.SetMapper(input_mapper)
input_actor.SetBackfaceProperty(backfaces)
selected_mapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
selected_mapper.SetInputConnection(grid_selected.GetProducerPort())
else:
selected_mapper.SetInputData(grid_selected)
selected_actor = vtk.vtkActor()
selected_actor.SetMapper(selected_mapper)
selected_actor.SetBackfaceProperty(backfaces)
not_selected_mapper = vtk.vtkDataSetMapper()
if vtk.VTK_MAJOR_VERSION <= 5:
not_selected_mapper.SetInputConnection(not_selected.GetProducerPort())
else:
not_selected_mapper.SetInputData(not_selected)
not_selected_actor = vtk.vtkActor()
not_selected_actor.SetMapper(not_selected_mapper)
not_selected_actor.SetBackfaceProperty(backfaces)
# There will be one render window
render_window = vtk.vtkRenderWindow()
render_window.SetSize(900, 300)
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(render_window)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
left_viewport = [0.0, 0.0, 0.5, 1.0]
center_viewport = [0.33, 0.0, .66, 1.0]
right_viewport = [0.66, 0.0, 1.0, 1.0]
# Create a camera for all renderers
camera = vtk.vtkCamera()
# Setup the renderers
left_renderer = vtk.vtkRenderer()
render_window.AddRenderer(left_renderer)
left_renderer.SetViewport(left_viewport)
left_renderer.SetBackground(.6, .5, .4)
left_renderer.SetActiveCamera(camera)
center_renderer = vtk.vtkRenderer()
render_window.AddRenderer(center_renderer)
center_renderer.SetViewport(center_viewport)
center_renderer.SetBackground(.3, .1, .4)
center_renderer.SetActiveCamera(camera)
right_renderer = vtk.vtkRenderer()
render_window.AddRenderer(right_renderer)
right_renderer.SetViewport(right_viewport)
right_renderer.SetBackground(.4, .5, .6)
right_renderer.SetActiveCamera(camera)
left_renderer.AddActor(input_actor)
center_renderer.AddActor(selected_actor)
right_renderer.AddActor(not_selected_actor)
left_renderer.ResetCamera()
render_window.Render()
interactor.Start()
