def __init__(self, vtifname, parallel=False, dtype=np.float64):
if not os.path.isfile(vtifname):
raise FileNotFoundError(vtifname)
if parallel:
self.reader = vtk.vtkXMLPImageDataReader()
else:
self.reader = vtk.vtkXMLImageDataReader()
self.reader.SetFileName(vtifname)
self.reader.Update()
self.data = self.reader.GetOutput()
self.dim = self.data.GetDimensions()
self.trim_0 = [0, 0, 0]
self.trim_1 = [x - 1 for x in self.dim]
self.s_vec = [self.dim[2] - 1, self.dim[1] - 1, self.dim[0] - 1]
if self.dim[2] > 2:
self.subspace = np.meshgrid(
*[range(self.trim_0[i], self.trim_1[i]) for i in range(3)])
self.s_scal = [self.dim[2] - 1, self.dim[1] - 1, self.dim[0] - 1]
else:
self.s_scal = [self.dim[1] - 1, self.dim[0] - 1]
self.subspace = np.meshgrid(
*[range(self.trim_0[i], self.trim_1[i]) for i in range(2)])
self.dtype = dtype
def read_vti(file):
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(file)
reader.Update()
data = reader.GetOutput()
pointData = data.GetPointData()
sh = data.GetDimensions()[::-1]
ndims = len(sh)
# get vector field
v = np.array(pointData.GetVectors("Velocity")).reshape(sh + (ndims, ))
vec = []
for d in range(ndims):
a = v[..., d]
vec.append(a)
# get scalar field
sca = np.array(pointData.GetScalars('Pressure')).reshape(sh + (1, ))
# Generate grid
# nPoints = dat.GetNumberOfPoints()
(xmin, xmax, ymin, ymax, zmin, zmax) = data.GetBounds()
grid3D = np.mgrid[xmin:xmax + 1, ymin:ymax + 1, zmin:zmax + 1]
return np.transpose(np.array(vec),
(0, 3, 2, 1)), np.transpose(sca, (0, 3, 2, 1)), grid3D
def import_vtk(self, filename, varname, log=False):
if (not os.path.isfile(filename)):
print("Can't find file: " + filename)
else:
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(filename)
reader.Update()
data = reader.GetOutput()
dim = data.GetDimensions()
v = vtk_np.vtk_to_numpy(data.GetCellData().GetArray(0))
if (log):
v = 10**v
n_comp = data.GetCellData().GetArray(0).GetNumberOfComponents()
vec = [int(i - 1) for i in dim]
if (n_comp > 1):
vec.append(n_comp)
self.arr[varname] = v.reshape(vec, order='F')
def pvti_readin(filename):
'''
Reads in data from pvti with filename, use this to read in electron number density data
'''
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(filename)
reader.Update()
data = reader.GetOutput()
dim = data.GetDimensions()
spacing = np.array(data.GetSpacing())
v = vtk_np.vtk_to_numpy(data.GetCellData().GetArray(0))
n_comp = data.GetCellData().GetArray(0).GetNumberOfComponents()
vec = [int(i - 1) for i in dim]
if (n_comp > 1):
vec.append(n_comp)
if (n_comp > 2):
img = v.reshape(vec, order="F")[0:dim[0] - 1, 0:dim[1] - 1,
0:dim[2] - 1, :]
else:
img = v.reshape(vec, order="F")[0:dim[0] - 1, 0:dim[1] - 1,
0:dim[2] - 1]
dim = img.shape
return img, dim, spacing
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkXMLPImageDataReader(), 'Reading vtkXMLPImageData.',
(), ('vtkXMLPImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkXMLPImageDataReader(),
'Reading vtkXMLPImageData.', (),
('vtkXMLPImageData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self, vtifname, parallel=False):
if parallel:
self.reader = vtk.vtkXMLPImageDataReader()
else:
self.reader = vtk.vtkXMLImageDataReader()
self.reader.SetFileName(vtifname)
self.reader.Update()
self.data = self.reader.GetOutput()
self.dim = self.data.GetDimensions()
self.s_scal = [self.dim[1]-1, self.dim[0]-1]
self.s_vec = [self.dim[1]-1, self.dim[0]-1,3]
def __init__(self, vtifname, parallel=False, dtype=np.float64):
if parallel:
self.reader = vtk.vtkXMLPImageDataReader()
else:
self.reader = vtk.vtkXMLImageDataReader()
self.reader.SetFileName(vtifname)
self.reader.Update()
self.data = self.reader.GetOutput()
self.dim = self.data.GetDimensions()
self.s_scal = [self.dim[2]-1, self.dim[1]-1, self.dim[0]-1]
self.s_vec = [self.dim[2]-1, self.dim[1]-1, self.dim[0]-1,3]
self.trim_0 = [0,0,0]
self.trim_1 = [x-1 for x in self.dim]
self.dtype = dtype
def __init__(self, vtifname, parallel=False, dtype=np.float64):
if parallel:
self.reader = vtk.vtkXMLPImageDataReader()
else:
self.reader = vtk.vtkXMLImageDataReader()
self.reader.SetFileName(vtifname)
self.reader.Update()
self.data = self.reader.GetOutput()
self.dim = self.data.GetDimensions()
self.s_scal = [self.dim[2]-1, self.dim[1]-1, self.dim[0]-1]
self.s_vec = [self.dim[2]-1, self.dim[1]-1, self.dim[0]-1,3]
self.trim_0 = [0,0,0]
self.trim_1 = [x-1 for x in self.dim]
self.dtype = dtype
def import_space(self, filename):
if (not os.path.isfile(filename)):
print("Can't find file: " + filename)
else:
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(filename)
reader.Update()
data = reader.GetOutput()
bounds = np.array(data.GetBounds())
spacing = np.array(data.GetSpacing())
self.d = spacing
self.xc = -np.array([bounds[0], bounds[2], bounds[4]])
self.x = np.arange(bounds[0], bounds[1], spacing[0])
self.y = np.arange(bounds[2], bounds[3], spacing[1])
self.z = np.arange(bounds[4], bounds[5], spacing[2])
def revti(name):
in_vtifname = name
out_vtifname = "/tmp/"+os.path.basename( os.path.splitext(name)[0] )+'.vti'
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(in_vtifname)
reader.Update()
data = reader.GetOutput()
cd = data.GetCellData()
k = 0
bc = cd.GetNumberOfArrays()
while cd.GetNumberOfArrays() > len(save) or k > 10:
k = k + 1
for i in range(cd.GetNumberOfArrays()):
if not ( cd.GetArrayName(i) in save ):
# print "Removing:", cd.GetArrayName(i)
cd.RemoveArray(cd.GetArrayName(i))
break
# else:
# print "Keeping:", cd.GetArrayName(i)
print out_vtifname +" : ", bc, '/', cd.GetNumberOfArrays()
writer = vtk.vtkXMLImageDataWriter()
writer.SetFileName(out_vtifname)
writer.SetInputData(data)
writer.Write()
if rank == 0:
print(da2.GetValue(0))
import os
os.remove(filename)
for i in range(npieces):
if not useSubdir:
os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))
else:
os.remove(VTK_TEMP_DIR + "/%s/%s_%d.%s" %
(dataType, dataType, i, ext))
assert da2.GetValue(0) == numTris
TestDataType('ImageData', vtk.vtkXMLPImageDataReader(),
vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(),
vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(),
vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(),
vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)
# Test writers with UseSubdirectory on
TestDataType('ImageData',
vtk.vtkXMLPImageDataReader(),
vtk.vtkXMLPImageDataWriter(),
'vti',
4924,
useSubdir=True)
da.InsertNextValue(ntris)
da2 = vtk.vtkIntArray()
da2.SetNumberOfTuples(1)
contr.AllReduce(da, da2, vtk.vtkCommunicator.SUM_OP)
if rank == 0:
print(da2.GetValue(0))
import os
os.remove(filename)
for i in range(npieces):
if not useSubdir:
os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))
else:
os.remove(VTK_TEMP_DIR + "/%s/%s_%d.%s" %(dataType, dataType, i, ext))
assert da2.GetValue(0) == numTris
TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)
TestDataType('Table', vtk.vtkXMLPTableReader(), vtk.vtkXMLPTableWriter(), 'vtt', 18522)
# Test writers with UseSubdirectory on
TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924, useSubdir=True)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924, useSubdir=True)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924, useSubdir=True)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856, useSubdir=True)
TestDataType('Table', vtk.vtkXMLPTableReader(), vtk.vtkXMLPTableWriter(), 'vtt', 18522, useSubdir=True)
import os
import vtk
from vtk.util.misc import vtkGetDataRoot
from vtk.util.misc import vtkGetTempDir
VTK_DATA_ROOT = vtkGetDataRoot()
VTK_TEMP_DIR = vtkGetTempDir()
rt = vtk.vtkRTAnalyticSource()
rt.Update()
inp = rt.GetOutput()
inp.GetInformation().Set(vtk.vtkDataObject.DATA_TIME_STEP(), 11)
file_root = VTK_TEMP_DIR + '/testpxmlfield'
file0 = file_root + ".pvti"
w = vtk.vtkXMLPImageDataWriter()
w.SetInputData(inp)
w.SetFileName(file0)
w.Write()
r = vtk.vtkXMLPImageDataReader()
r.SetFileName(file0)
r.UpdateInformation()
assert (r.GetOutputInformation(0).Get(
vtk.vtkStreamingDemandDrivenPipeline.TIME_STEPS(), 0) == 11.0)
os.remove(file0)
os.remove(file_root + "_0.vti")
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 19 11:57:07 2010
@author: VBaidin
"""
import vtk
import array
import numpy as np
DATA_ROOT = 'f:/data/Bank/Constant Speed 001/RESULTS_MPI4-50ms/IM'
reader = vtk.vtkXMLPImageDataReader()
reader.SetFileName(DATA_ROOT + "/image.pvti")
reader.Update()
#reader.SetFileName(DATA_ROOT + "/node_0_0.vti")
#darray = vtk.vtkDoubleArray()
#coords = [0,0,0]
#reader.GetOutput().GetArrayPointer(darray,coords)
D = reader.GetOutput().GetDimensions()
image = reader.GetOutput().GetPointData().GetArray ('IMAGE')
func = lambda i,j: image.GetTuple1(i+D[0]*j)
Img = np.zeros ((D[0],D[1]),dtype=float)
for i in xrange(D[0]):
for j in xrange(D[1]):
Img[i,j]=func(i,j)
np.savez ("%s/IMAGE.npz"%DATA_ROOT,Img)
cf.SetValue(0, 130)
cf.SetComputeNormals(0)
cf.SetComputeGradients(0)
cf.SetInputConnection(reader.GetOutputPort())
cf.UpdateInformation()
cf.GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_PIECES(), nranks)
cf.GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_PIECE_NUMBER(), rank)
cf.Update()
ntris = cf.GetOutput().GetNumberOfCells()
da = vtk.vtkIntArray()
da.InsertNextValue(ntris)
da2 = vtk.vtkIntArray()
da2.SetNumberOfTuples(1)
contr.AllReduce(da, da2, vtk.vtkCommunicator.SUM_OP)
if rank == 0:
print(da2.GetValue(0))
import os
os.remove(filename)
for i in range(npieces):
os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))
assert da2.GetValue(0) == numTris
TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)
