def exportToTable(self, table, nonEmptyKeysOnly = True):
"""
Export statistics to table node
"""
tableWasModified = table.StartModify()
table.RemoveAllColumns()
keys = self.getNonEmptyKeys() if nonEmptyKeysOnly else self.keys
columnHeaderNames, uniqueColumnHeaderNames = self.getHeaderNames(nonEmptyKeysOnly)
# Define table columns
statistics = self.getStatistics()
for key in keys:
# create table column appropriate for data type; currently supported: float, int, long, string
measurements = [statistics[segmentID, key] for segmentID in statistics["SegmentIDs"] if
(segmentID, key) in statistics]
if len(measurements)==0: # there were not measurements and therefore use the default "string" representation
col = table.AddColumn()
elif isinstance(measurements[0], int):
col = table.AddColumn(vtk.vtkLongArray())
elif isinstance(measurements[0], float):
col = table.AddColumn(vtk.vtkDoubleArray())
else: # default
col = table.AddColumn()
plugin = self.getPluginByKey(key)
columnName = uniqueColumnHeaderNames[key]
longColumnName = columnHeaderNames[key]
col.SetName( columnName )
if plugin:
table.SetColumnProperty(columnName, "Plugin", plugin.name)
longColumnName += '<br>Computed by '+plugin.name+' Statistics plugin'
table.SetColumnLongName(columnName, longColumnName)
measurementInfo = statistics["MeasurementInfo"][key] if key in statistics["MeasurementInfo"] else {}
if measurementInfo:
for mik, miv in measurementInfo.items():
if mik=='description':
table.SetColumnDescription(columnName, str(miv))
elif mik=='units':
table.SetColumnUnitLabel(columnName, str(miv))
else:
table.SetColumnProperty(columnName, str(mik), str(miv))
# Fill columns
for segmentID in statistics["SegmentIDs"]:
rowIndex = table.AddEmptyRow()
columnIndex = 0
for key in keys:
value = statistics[segmentID, key] if (segmentID, key) in statistics else None
if value is None and key!='Segment':
value = float('nan')
table.GetTable().GetColumn(columnIndex).SetValue(rowIndex, value)
columnIndex += 1
table.Modified()
table.EndModify(tableWasModified)
def testNumpyReduce(self):
"Test that reducing methods return scalars."
vtk_array = vtk.vtkLongArray()
for i in range(0, 10):
vtk_array.InsertNextValue(i)
numpy_vtk_array = dsa.vtkDataArrayToVTKArray(vtk_array)
s = numpy_vtk_array.sum()
self.assertEqual(s, 45)
self.assertEqual(type(s), numpy.int64)
m = numpy_vtk_array.mean()
self.assertEqual(m, 4.5)
self.assertEqual(type(m), numpy.float64)
def createLongArray(
name,
n_components=1,
n_tuples=0,
init_to_zero=0,
verbose=0):
larray = vtk.vtkLongArray()
larray.SetName(name)
larray.SetNumberOfComponents(n_components)
larray.SetNumberOfTuples(n_tuples)
if (init_to_zero):
for k_tuple in xrange(n_tuples):
iarray.SetTuple(k_tuple, [0]*n_components)
return larray
def extract_cell_field_data(self):
"""
Extracts basic information about cell field
:return:
"""
cellType = vtk.vtkIntArray()
cellType.SetName("celltype")
cellTypeIntAddr = extract_address_int_from_vtk_object(self.field_extractor, cellType)
# Also get the CellId
cellId = vtk.vtkLongArray()
cellId.SetName("cellid")
cellIdIntAddr = extract_address_int_from_vtk_object(self.field_extractor, cellId)
usedCellTypesList = self.field_extractor.fillCellFieldData3D(cellTypeIntAddr, cellIdIntAddr)
ret_val = {
'cell_type_array':cellType,
'cell_id_array':cellId,
'used_cell_types':usedCellTypesList
}
return ret_val
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):
"""Returns a VTK typecode given a numpy array."""
# This is a Mapping from numpy array types to VTK array types.
_np_vtk = {numpy.character:vtkConstants.VTK_UNSIGNED_CHAR,
numpy.uint8:vtkConstants.VTK_UNSIGNED_CHAR,
numpy.uint16:vtkConstants.VTK_UNSIGNED_SHORT,
numpy.uint32:vtkConstants.VTK_UNSIGNED_INT,
def vtk2array(vtk_array):
"""Converts a VTK data array to a numpy array.
Given a subclass of vtkDataArray, this function returns an
appropriate numpy array containing the same data. The function
is very efficient since it uses the VTK imaging pipeline to
convert the data. If a sufficiently new version of VTK (5.2) is
installed then it actually uses the buffer interface to return a
view of the VTK array in the returned numpy array.
Parameters
----------
- vtk_array : `vtkDataArray`
The VTK data array to be converted.
"""
typ = vtk_array.GetDataType()
assert typ in get_vtk_to_numeric_typemap().keys(), \
"Unsupported array type %s"%typ
shape = vtk_array.GetNumberOfTuples(), \
vtk_array.GetNumberOfComponents()
if shape[0] == 0:
dtype = get_numeric_array_type(typ)
return numpy.array([], dtype)
# First check if this array already has a numpy array cached,
# if it does and the array size has not been changed, reshape
# that and return it.
if vtk_array in _array_cache:
arr = _array_cache.get(vtk_array)
if shape[1] == 1:
shape = (shape[0], )
if arr.size == numpy.prod(shape):
arr = numpy.reshape(arr, shape)
return arr
# If VTK's new numpy support is available, use the buffer interface.
if numpy_support is not None and typ != vtkConstants.VTK_BIT:
dtype = get_numeric_array_type(typ)
result = numpy.frombuffer(vtk_array, dtype=dtype)
if shape[1] == 1:
shape = (shape[0], )
result.shape = shape
return result
# Setup an imaging pipeline to export the array.
img_data = vtk.vtkImageData()
img_data.SetDimensions(shape[0], 1, 1)
if typ == vtkConstants.VTK_BIT:
iarr = vtk.vtkCharArray()
iarr.DeepCopy(vtk_array)
img_data.GetPointData().SetScalars(iarr)
elif typ == vtkConstants.VTK_ID_TYPE:
# Needed since VTK_ID_TYPE does not work with VTK 4.5.
iarr = vtk.vtkLongArray()
iarr.SetNumberOfTuples(vtk_array.GetNumberOfTuples())
nc = vtk_array.GetNumberOfComponents()
iarr.SetNumberOfComponents(nc)
for i in range(nc):
iarr.CopyComponent(i, vtk_array, i)
img_data.GetPointData().SetScalars(iarr)
else:
img_data.GetPointData().SetScalars(vtk_array)
if is_old_pipeline():
img_data.SetNumberOfScalarComponents(shape[1])
if typ == vtkConstants.VTK_ID_TYPE:
# Hack necessary because vtkImageData can't handle VTK_ID_TYPE.
img_data.SetScalarType(vtkConstants.VTK_LONG)
r_dtype = get_numeric_array_type(vtkConstants.VTK_LONG)
elif typ == vtkConstants.VTK_BIT:
img_data.SetScalarType(vtkConstants.VTK_CHAR)
r_dtype = get_numeric_array_type(vtkConstants.VTK_CHAR)
else:
img_data.SetScalarType(typ)
r_dtype = get_numeric_array_type(typ)
img_data.Update()
else:
if typ == vtkConstants.VTK_ID_TYPE:
r_dtype = get_numeric_array_type(vtkConstants.VTK_LONG)
elif typ == vtkConstants.VTK_BIT:
r_dtype = get_numeric_array_type(vtkConstants.VTK_CHAR)
else:
r_dtype = get_numeric_array_type(typ)
img_data.Modified()
exp = vtk.vtkImageExport()
if is_old_pipeline():
exp.SetInput(img_data)
else:
exp.SetInputData(img_data)
# Create an array of the right size and export the image into it.
im_arr = numpy.empty((shape[0]*shape[1],), r_dtype)
exp.Export(im_arr)
# Now reshape it.
if shape[1] == 1:
shape = (shape[0], )
im_arr = numpy.reshape(im_arr, shape)
return im_arr
def topomesh_to_vtk_polydata(topomesh,degree=2,positions=None,topomesh_center=None,coef=1):
import numpy as np
import vtk
from time import time
from openalea.container import array_dict
if positions is None:
positions = topomesh.wisp_property('barycenter',0)
if topomesh_center is None:
topomesh_center = np.mean(positions.values(),axis=0)
# topomesh_center = np.array([0,0,0])
print topomesh_center
vtk_mesh = vtk.vtkPolyData()
vtk_points = vtk.vtkPoints()
vtk_edges = vtk.vtkCellArray()
vtk_triangles = vtk.vtkCellArray()
vtk_cells = vtk.vtkLongArray()
start_time = time()
print "--> Creating VTK PolyData"
if degree == 3:
for c in topomesh.wisps(3):
cell_points = []
cell_center = np.mean([positions[v] for v in topomesh.borders(3,c,3)],axis=0)
for v in topomesh.borders(3,c,3):
position = cell_center + coef*(positions[v]-cell_center) - topomesh_center
position[np.where(np.abs(position)<.001)] =0.
p = vtk_points.InsertNextPoint(position)
cell_points.append(p)
cell_points = array_dict(cell_points,list(topomesh.borders(3,c,3)))
for t in topomesh.borders(3,c):
poly = vtk_triangles.InsertNextCell(3)
for v in topomesh.borders(2,t,2):
vtk_triangles.InsertCellPoint(cell_points[v])
vtk_cells.InsertValue(poly,c)
elif degree == 2:
for t in topomesh.wisps(2):
triangle_points = []
triangle_center = np.mean([positions[v] for v in topomesh.borders(2,t,2)],axis=0)
for v in topomesh.borders(2,t,2):
position = triangle_center + coef*(positions[v]-triangle_center) - topomesh_center
position[np.where(np.abs(position)<.001)] =0.
p = vtk_points.InsertNextPoint(position)
triangle_points.append(p)
triangle_points = array_dict(triangle_points,list(topomesh.borders(2,t,2)))
poly = vtk_triangles.InsertNextCell(3)
for v in topomesh.borders(2,t,2):
vtk_triangles.InsertCellPoint(triangle_points[v])
vtk_cells.InsertValue(poly,list(topomesh.regions(2,t))[0])
elif degree == 1:
points = []
for v in topomesh.wisps(0):
position = positions[v]
position[np.where(np.abs(position)<.001)] =0.
p = vtk_points.InsertNextPoint(position)
points.append(p)
points = array_dict(points,list(topomesh.wisps(0)))
for e in topomesh.wisps(1):
# if topomesh.wisp_property('epidermis',1)[e]:
# if True:
if len(list(topomesh.regions(1,e))) > 2:
c = vtk_edges.InsertNextCell(2)
for v in topomesh.borders(1,e):
vtk_edges.InsertCellPoint(points[v])
print" --> Linking Mesh"
vtk_mesh.SetPoints(vtk_points)
vtk_mesh.SetPolys(vtk_triangles)
vtk_mesh.SetLines(vtk_edges)
vtk_mesh.GetCellData().SetScalars(vtk_cells)
end_time = time()
print "<-- Creating VTK PolyData [",end_time-start_time,"s]"
return vtk_mesh
def image_to_vtk_cell_polydata(img,considered_cells=None,mesh_center=None,coef=1.0,mesh_fineness=1.0,smooth_factor=1.0):
start_time = time()
print "--> Generating vtk mesh from image"
vtk_mesh = vtk.vtkPolyData()
vtk_points = vtk.vtkPoints()
vtk_triangles = vtk.vtkCellArray()
vtk_cells = vtk.vtkLongArray()
nx, ny, nz = img.shape
data_string = img.tostring('F')
reader = vtk.vtkImageImport()
reader.CopyImportVoidPointer(data_string, len(data_string))
if img.dtype == np.uint8:
reader.SetDataScalarTypeToUnsignedChar()
else:
reader.SetDataScalarTypeToUnsignedShort()
reader.SetNumberOfScalarComponents(1)
reader.SetDataExtent(0, nx - 1, 0, ny - 1, 0, nz - 1)
reader.SetWholeExtent(0, nx - 1, 0, ny - 1, 0, nz - 1)
reader.SetDataSpacing(*img.resolution)
reader.Update()
if considered_cells is None:
considered_cells = np.unique(img)[1:]
if mesh_center is None:
#mesh_center = np.array(img.resolution)*np.array(img.shape)/2.
mesh_center = np.array([0,0,0])
for label in considered_cells:
cell_start_time = time()
cell_volume = (img==label).sum()*np.array(img.resolution).prod()
# mask_data = vtk.vtkImageThreshold()
# mask_data.SetInputConnection(reader.GetOutputPort())
# mask_data.ThresholdBetween(label, label)
# mask_data.ReplaceInOn()
# mask_data.SetInValue(label)
# mask_data.SetOutValue(0)
contour = vtk.vtkDiscreteMarchingCubes()
# contour.SetInput(mask_data.GetOutput())
SetInput(contour,reader.GetOutput())
contour.ComputeNormalsOn()
contour.ComputeGradientsOn()
contour.SetValue(0,label)
contour.Update()
# print " --> Marching Cubes : ",contour.GetOutput().GetPoints().GetNumberOfPoints()," Points,",contour.GetOutput().GetNumberOfCells()," Triangles, 1 Cell"
# decimate = vtk.vtkDecimatePro()
# decimate.SetInputConnection(contour.GetOutputPort())
# # decimate.SetTargetReduction(0.75)
# decimate.SetTargetReduction(0.66)
# # decimate.SetTargetReduction(0.5)
# # decimate.SetMaximumError(2*np.sqrt(3))
# decimate.Update()
smooth_iterations = int(np.ceil(smooth_factor*8.))
smoother = vtk.vtkWindowedSincPolyDataFilter()
SetInput(smoother,contour.GetOutput())
smoother.BoundarySmoothingOn()
# smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOn()
# smoother.FeatureEdgeSmoothingOff()
smoother.SetFeatureAngle(120.0)
# smoother.SetPassBand(1)
smoother.SetPassBand(0.01)
smoother.SetNumberOfIterations(smooth_iterations)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
divisions = int(np.ceil(np.power(cell_volume,1/3.)*mesh_fineness))
decimate = vtk.vtkQuadricClustering()
# decimate = vtk.vtkQuadricDecimation()
# decimate = vtk.vtkDecimatePro()
# decimate.SetInput(contour.GetOutput())
SetInput(decimate,smoother.GetOutput())
# decimate.SetTargetReduction(0.95)
# decimate.AutoAdjustNumberOfDivisionsOff()
decimate.SetNumberOfDivisions(divisions,divisions,divisions)
decimate.SetFeaturePointsAngle(120.0)
# decimate.AttributeErrorMetricOn()
# decimate.ScalarsAttributeOn()
# decimate.PreserveTopologyOn()
# decimate.CopyCellDataOn()
# decimate.SetMaximumCost(1.0)
# decimate.SetMaximumCollapsedEdges(10000.0)
decimate.Update()
# print " --> Decimation : ",decimate.GetOutput().GetPoints().GetNumberOfPoints()," Points,",decimate.GetOutput().GetNumberOfCells()," Triangles, 1 Cell"
cell_polydata = decimate.GetOutput()
# cell_polydata = smoother.GetOutput()
polydata_points = np.array([cell_polydata.GetPoints().GetPoint(p) for p in xrange(cell_polydata.GetPoints().GetNumberOfPoints())])
polydata_center = polydata_points.mean(axis=0)
polydata_points = polydata_center + coef*(polydata_points-polydata_center) - mesh_center
cell_points = []
for p in xrange(cell_polydata.GetPoints().GetNumberOfPoints()):
pid = vtk_points.InsertNextPoint(polydata_points[p])
cell_points.append(pid)
cell_points = array_dict(cell_points,np.arange(cell_polydata.GetPoints().GetNumberOfPoints()))
for t in xrange(cell_polydata.GetNumberOfCells()):
poly = vtk_triangles.InsertNextCell(3)
for i in xrange(3):
pid = cell_polydata.GetCell(t).GetPointIds().GetId(i)
vtk_triangles.InsertCellPoint(cell_points[pid])
vtk_cells.InsertValue(poly,label)
cell_end_time = time()
print " --> Cell",label,":",decimate.GetOutput().GetNumberOfCells(),"triangles (",cell_volume," microm3 ) [",cell_end_time-cell_start_time,"s]"
vtk_mesh.SetPoints(vtk_points)
vtk_mesh.SetPolys(vtk_triangles)
vtk_mesh.GetCellData().SetScalars(vtk_cells)
print " <-- Cell Mesh : ",vtk_mesh.GetPoints().GetNumberOfPoints()," Points,",vtk_mesh.GetNumberOfCells()," Triangles, ",len(considered_cells)," Cells"
end_time = time()
print "<-- Generating vtk mesh from image [",end_time-start_time,"s]"
return vtk_mesh
def image_to_vtk_polydata(img,considered_cells=None,mesh_center=None,coef=1.0,mesh_fineness=1.0):
start_time = time()
print "--> Generating vtk mesh from image"
vtk_mesh = vtk.vtkPolyData()
vtk_points = vtk.vtkPoints()
vtk_triangles = vtk.vtkCellArray()
vtk_cells = vtk.vtkLongArray()
nx, ny, nz = img.shape
data_string = img.tostring('F')
reader = vtk.vtkImageImport()
reader.CopyImportVoidPointer(data_string, len(data_string))
if img.dtype == np.uint8:
reader.SetDataScalarTypeToUnsignedChar()
else:
reader.SetDataScalarTypeToUnsignedShort()
reader.SetNumberOfScalarComponents(1)
reader.SetDataExtent(0, nx - 1, 0, ny - 1, 0, nz - 1)
reader.SetWholeExtent(0, nx - 1, 0, ny - 1, 0, nz - 1)
reader.SetDataSpacing(*img.resolution)
if considered_cells is None:
considered_cells = np.unique(img)[1:]
if mesh_center is None:
mesh_center = np.array(img.resolution)*np.array(img.shape)/2.
marching_cube_start_time = time()
print " --> Marching Cubes"
contour = vtk.vtkDiscreteMarchingCubes()
SetInput(contour,reader.GetOutput())
contour.ComputeNormalsOn()
contour.ComputeGradientsOn()
contour.ComputeScalarsOn()
for i,label in enumerate(considered_cells):
contour.SetValue(i,label)
contour.Update()
marching_cube_end_time = time()
print " <-- Marching Cubes : ",contour.GetOutput().GetPoints().GetNumberOfPoints()," Points,",contour.GetOutput().GetNumberOfCells()," Triangles, ",len(np.unique(img)[1:])," Cells [",marching_cube_end_time - marching_cube_start_time,"s]"
marching_cubes = contour.GetOutput()
marching_cubes_cell_data = marching_cubes.GetCellData().GetArray(0)
triangle_cell_start_time = time()
print " --> Listing triangles"
print " - ",marching_cubes.GetNumberOfCells()," triangles"
marching_cubes_triangles = np.sort([[marching_cubes.GetCell(t).GetPointIds().GetId(i) for i in xrange(3)] for t in xrange(marching_cubes.GetNumberOfCells())])
triangle_cell_end_time = time()
print " <-- Listing triangles [",triangle_cell_end_time - triangle_cell_start_time,"s]"
triangle_cell_start_time = time()
print " --> Listing triangle cells"
triangle_cell = np.array([marching_cubes_cell_data.GetTuple(t)[0] for t in xrange(marching_cubes.GetNumberOfCells())],np.uint16)
triangle_cell_end_time = time()
print " <-- Listing triangle cells [",triangle_cell_end_time - triangle_cell_start_time,"s]"
triangle_cell_start_time = time()
print " --> Updating marching cubes mesh"
vtk_mesh = vtk.vtkPolyData()
vtk_points = vtk.vtkPoints()
vtk_triangles = vtk.vtkCellArray()
vtk_cells = vtk.vtkLongArray()
for label in considered_cells:
# cell_start_time = time()
cell_marching_cubes_triangles = marching_cubes_triangles[np.where(triangle_cell == label)]
marching_cubes_point_ids = np.unique(cell_marching_cubes_triangles)
marching_cubes_points = np.array([marching_cubes.GetPoints().GetPoint(p) for p in marching_cubes_point_ids])
marching_cubes_center = marching_cubes_points.mean(axis=0)
marching_cubes_points = marching_cubes_center + coef*(marching_cubes_points-marching_cubes_center) - mesh_center
cell_points = []
for p in xrange(marching_cubes_points.shape[0]):
pid = vtk_points.InsertNextPoint(marching_cubes_points[p])
cell_points.append(pid)
cell_points = array_dict(cell_points,marching_cubes_point_ids)
for t in xrange(cell_marching_cubes_triangles.shape[0]):
poly = vtk_triangles.InsertNextCell(3)
for i in xrange(3):
pid = cell_marching_cubes_triangles[t][i]
vtk_triangles.InsertCellPoint(cell_points[pid])
vtk_cells.InsertValue(poly,label)
# cell_end_time = time()
# print " --> Cell",label,":",cell_marching_cubes_triangles.shape[0],"triangles [",cell_end_time-cell_start_time,"s]"
vtk_mesh.SetPoints(vtk_points)
vtk_mesh.SetPolys(vtk_triangles)
vtk_mesh.GetCellData().SetScalars(vtk_cells)
triangle_cell_end_time = time()
print " <-- Updating marching cubes mesh [",triangle_cell_end_time - triangle_cell_start_time,"s]"
decimation_start_time = time()
print " --> Decimation"
smoother = vtk.vtkWindowedSincPolyDataFilter()
SetInput(smoother,vtk_mesh)
smoother.SetFeatureAngle(30.0)
smoother.SetPassBand(0.05)
smoother.SetNumberOfIterations(25)
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
decimate = vtk.vtkQuadricClustering()
SetInput(decimate,smoother.GetOutput())
decimate.SetNumberOfDivisions(*tuple(mesh_fineness*np.array(np.array(img.shape)*np.array(img.resolution)/2.,np.uint16)))
decimate.SetFeaturePointsAngle(30.0)
decimate.CopyCellDataOn()
decimate.Update()
decimation_end_time = time()
print " <-- Decimation : ",decimate.GetOutput().GetPoints().GetNumberOfPoints()," Points,",decimate.GetOutput().GetNumberOfCells()," Triangles, ",len(considered_cells)," Cells [",decimation_end_time - decimation_start_time,"s]"
end_time = time()
print "<-- Generating vtk mesh from image [",end_time-start_time,"s]"
return decimate.GetOutput()
Created by Prabhu Ramachandran in Feb. 2008.
"""
import vtk
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):
"""Returns a VTK typecode given a numpy array."""
# This is a Mapping from numpy array types to VTK array types.
_np_vtk = {numpy.character:vtk.VTK_UNSIGNED_CHAR,
numpy.uint8:vtk.VTK_UNSIGNED_CHAR,
numpy.uint16:vtk.VTK_UNSIGNED_SHORT,
numpy.uint32:vtk.VTK_UNSIGNED_INT,
def vtk2array(vtk_array):
"""Converts a VTK data array to a numpy array.
Given a subclass of vtkDataArray, this function returns an
appropriate numpy array containing the same data. The function
is very efficient since it uses the VTK imaging pipeline to
convert the data. If a sufficiently new version of VTK (5.2) is
installed then it actually uses the buffer interface to return a
view of the VTK array in the returned numpy array.
Parameters
----------
- vtk_array : `vtkDataArray`
The VTK data array to be converted.
"""
typ = vtk_array.GetDataType()
assert typ in get_vtk_to_numeric_typemap().keys(), \
"Unsupported array type %s"%typ
shape = vtk_array.GetNumberOfTuples(), \
vtk_array.GetNumberOfComponents()
if shape[0] == 0:
dtype = get_numeric_array_type(typ)
return numpy.array([], dtype)
# First check if this array already has a numpy array cached, if
# it does, reshape that and return it.
if vtk_array in _array_cache:
arr = _array_cache.get(vtk_array)
if shape[1] == 1:
shape = (shape[0], )
arr = numpy.reshape(arr, shape)
return arr
# If VTK's new numpy support is available, use the buffer interface.
if numpy_support is not None and typ != vtkConstants.VTK_BIT:
dtype = get_numeric_array_type(typ)
result = numpy.frombuffer(vtk_array, dtype=dtype)
if shape[1] == 1:
shape = (shape[0], )
result.shape = shape
return result
# Setup an imaging pipeline to export the array.
img_data = vtk.vtkImageData()
img_data.SetDimensions(shape[0], 1, 1)
if typ == vtkConstants.VTK_BIT:
iarr = vtk.vtkCharArray()
iarr.DeepCopy(vtk_array)
img_data.GetPointData().SetScalars(iarr)
elif typ == vtkConstants.VTK_ID_TYPE:
# Needed since VTK_ID_TYPE does not work with VTK 4.5.
iarr = vtk.vtkLongArray()
iarr.SetNumberOfTuples(vtk_array.GetNumberOfTuples())
nc = vtk_array.GetNumberOfComponents()
iarr.SetNumberOfComponents(nc)
for i in range(nc):
iarr.CopyComponent(i, vtk_array, i)
img_data.GetPointData().SetScalars(iarr)
else:
img_data.GetPointData().SetScalars(vtk_array)
img_data.SetNumberOfScalarComponents(shape[1])
if typ == vtkConstants.VTK_ID_TYPE:
# Hack necessary because vtkImageData can't handle VTK_ID_TYPE.
img_data.SetScalarType(vtkConstants.VTK_LONG)
r_dtype = get_numeric_array_type(vtkConstants.VTK_LONG)
elif typ == vtkConstants.VTK_BIT:
img_data.SetScalarType(vtkConstants.VTK_CHAR)
r_dtype = get_numeric_array_type(vtkConstants.VTK_CHAR)
else:
img_data.SetScalarType(typ)
r_dtype = get_numeric_array_type(typ)
img_data.Update()
exp = vtk.vtkImageExport()
exp.SetInput(img_data)
# Create an array of the right size and export the image into it.
im_arr = numpy.empty((shape[0]*shape[1],), r_dtype)
exp.Export(im_arr)
# Now reshape it.
if shape[1] == 1:
shape = (shape[0], )
im_arr = numpy.reshape(im_arr, shape)
return im_arr
def exportToTable(self, table, nonEmptyKeysOnly=True):
"""
Export statistics to table node
"""
tableWasModified = table.StartModify()
table.RemoveAllColumns()
keys = self.getNonEmptyKeys() if nonEmptyKeysOnly else self.keys
columnHeaderNames, uniqueColumnHeaderNames = self.getHeaderNames(
nonEmptyKeysOnly)
# Define table columns
statistics = self.getStatistics()
for key in keys:
# create table column appropriate for data type; currently supported: float, int, long, string
measurements = [
statistics[segmentID, key]
for segmentID in statistics["SegmentIDs"]
if statistics.has_key((segmentID, key))
]
if len(
measurements
) == 0: # there were not measurements and therefore use the default "string" representation
col = table.AddColumn()
elif type(measurements[0]) in [int, long]:
col = table.AddColumn(vtk.vtkLongArray())
elif type(measurements[0]) is float:
col = table.AddColumn(vtk.vtkDoubleArray())
else: # default
col = table.AddColumn()
plugin = self.getPluginByKey(key)
columnName = uniqueColumnHeaderNames[key]
longColumnName = columnHeaderNames[key]
col.SetName(columnName)
if plugin:
table.SetColumnProperty(columnName, "Plugin", plugin.name)
longColumnName += '<br>Computed by ' + plugin.name + ' Statistics plugin'
table.SetColumnLongName(columnName, longColumnName)
measurementInfo = statistics["MeasurementInfo"][
key] if key in statistics["MeasurementInfo"] else {}
if measurementInfo:
for mik, miv in measurementInfo.iteritems():
if mik == 'description':
table.SetColumnDescription(columnName, str(miv))
elif mik == 'units':
table.SetColumnUnitLabel(columnName, str(miv))
else:
table.SetColumnProperty(columnName, str(mik), str(miv))
# Fill columns
for segmentID in statistics["SegmentIDs"]:
rowIndex = table.AddEmptyRow()
columnIndex = 0
for key in keys:
value = statistics[segmentID, key] if statistics.has_key(
(segmentID, key)) else None
if value is None and key != 'Segment':
value = float('nan')
table.GetTable().GetColumn(columnIndex).SetValue(
rowIndex, value)
columnIndex += 1
table.Modified()
table.EndModify(tableWasModified)
import pytest
import vtk
from pytestvtk.assert_vtk import assert_vtk
@pytest.fixture(params=[
vtk.vtkDoubleArray(),
vtk.vtkFloatArray(),
vtk.vtkIntArray(),
vtk.vtkIdTypeArray(),
vtk.vtkLongArray(),
vtk.vtkShortArray(),
vtk.vtkUnsignedCharArray(),
vtk.vtkUnsignedIntArray(),
vtk.vtkUnsignedLongArray(),
vtk.vtkUnsignedLongLongArray(),
vtk.vtkUnsignedShortArray(),
vtk.vtkCharArray(),
])
def vtk_array(request):
array = request.param
array.SetName('testing_array')
array.SetNumberOfTuples(3)
array.SetNumberOfComponents(3)
array.InsertTuple3(0, 1, 2, 3)
array.InsertTuple3(1, 4, 5, 6)
array.InsertTuple3(2, 7, 8, 9)
return array
#!/usr/bin/env python
import vtk
import os
graph = vtk.vtkMutableDirectedGraph()
name = vtk.vtkStringArray()
name.SetName("path")
size = vtk.vtkLongArray()
size.SetName("size")
graph.GetVertexData().AddArray(name)
graph.GetVertexData().AddArray(size)
folder = "/home/bryan/Documents"
parent = graph.AddVertex()
name.InsertNextValue(folder)
id_map = {folder: parent}
for dirpath, dirnames, filenames in os.walk(folder):
parent = id_map[dirpath]
this_size = 0
for filename in filenames:
child_path = os.path.join(dirpath, filename)
try:
child_size = os.path.getsize(child_path)
except OSError:
child_size = 0