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vtk_file.py
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"""
Read/Write VTK files
Part of weio library: https://github.com/ebranlard/weio
"""
import pandas as pd
import numpy as np
import numpy
import os
from functools import reduce
import collections
try:
from .file import File, EmptyFileError, WrongFormatError, BrokenFormatError
except ImportError:
EmptyFileError = type('EmptyFileError', (Exception,),{})
WrongFormatError = type('WrongFormatError', (Exception,),{})
BrokenFormatError = type('BrokenFormatError', (Exception,),{})
File=dict
class VTKFile(File):
"""
Read/write a VTK file (.vtk).
Main attributes for grids:
---------
- xp_grid, yp_grid, zp_grid: vectors of points locations
- point_data_grid: dictionary containing data at the grid points
Main attributes for mesh:
---------
- points
- point_data
- cells
- cell_data
Main methods
------------
- read, write
Examples
--------
vtk = VTKFile('DisXZ1.vtk')
x = vtk.x_grid
z = vtk.z_grid
Ux = vtk.point_data_grid['DisXZ'][:,0,:,0]
"""
@staticmethod
def defaultExtensions():
return ['.vtk','.vtp']
@staticmethod
def formatName():
return 'VTK file'
def __init__(self,filename=None,**kwargs):
self.filename = None
# For regular grid
self.xp_grid=None # location of points
self.yp_grid=None
self.zp_grid=None
self.point_data_grid = None
# Main Data
self.points = None
self.field_data = {}
self.point_data = {}
self.dataset = {}
# Data for reading only
self.cell_data_raw = {}
self.c = None # Cell
self.ct = None # CellTypes
self.active = None
self.is_ascii = False
self.split = []
self.num_items = 0
self.section = None
# Propagate read
if filename:
self.read(filename=filename,**kwargs)
def read(self, filename=None):
""" read a VTK file """
if filename:
self.filename = filename
if not self.filename:
raise Exception('No filename provided')
if not os.path.isfile(self.filename):
raise OSError(2,'File not found:',self.filename)
if os.stat(self.filename).st_size == 0:
raise EmptyFileError('File is empty:',self.filename)
with open(filename, "rb") as f:
# initialize output data
# skip header and title
f.readline()
f.readline()
data_type = f.readline().decode("utf-8").strip().upper()
if data_type not in ["ASCII", "BINARY"]:
raise ReadError('Unknown VTK data type ',data_type)
self.is_ascii = data_type == "ASCII"
while True:
line = f.readline().decode("utf-8")
if not line:
# EOF
break
line = line.strip()
if len(line) == 0:
continue
self.split = line.split()
self.section = self.split[0].upper()
if self.section in vtk_sections:
_read_section(f, self)
else:
_read_subsection(f, self)
# --- Postpro
_check_mesh(self) # generate points if needed
cells, cell_data = translate_cells(self.c, self.ct, self.cell_data_raw)
self.cells = cells
self.cell_data = cell_data
if self.dataset['type']=='STRUCTURED_POINTS':
self.point_data_grid = {}
# We provide point_data_grid, corresponds to point_data but reshaped
for k,PD in self.point_data.items():
# NOTE: tested foe len(y)=1, len(z)=1
self.point_data_grid[k]=PD.reshape(len(self.xp_grid), len(self.yp_grid), len(self.zp_grid),PD.shape[1], order='F')
def write(self, filename=None, binary=True):
"""
Write to unstructured grid
TODO structured grid
"""
if filename:
self.filename = filename
if not self.filename:
raise Exception('No filename provided')
def pad(array):
return np.pad(array, ((0, 0), (0, 1)), "constant")
if self.points.shape[1] == 2:
points = pad(self.points)
else:
points = self.points
if self.point_data:
for name, values in self.point_data.items():
if len(values.shape) == 2 and values.shape[1] == 2:
self.point_data[name] = pad(values)
for name, data in self.cell_data.items():
for k, values in enumerate(data):
if len(values.shape) == 2 and values.shape[1] == 2:
data[k] = pad(data[k])
with open(filename, "wb") as f:
f.write(b"# vtk DataFile Version 4.2\n")
f.write("written \n".encode("utf-8"))
f.write(("BINARY\n" if binary else "ASCII\n").encode("utf-8"))
f.write(b"DATASET UNSTRUCTURED_GRID\n")
# write points and cells
_write_points(f, points, binary)
_write_cells(f, self.cells, binary)
# write point data
if self.point_data:
num_points = self.points.shape[0]
f.write("POINT_DATA {}\n".format(num_points).encode("utf-8"))
_write_field_data(f, self.point_data, binary)
# write cell data
if self.cell_data:
total_num_cells = sum(len(c.data) for c in self.cells)
f.write("CELL_DATA {}\n".format(total_num_cells).encode("utf-8"))
_write_field_data(f, self.cell_data, binary)
def __repr__(self):
s='<{} object> with keys:\n'.format(type(self).__name__)
for k,v in self.items():
s+=' - {}: {}\n'.format(k,v)
return s
def __repr__(self):
""" print function """
def show_grid(v,s):
if v is None:
return
if len(v)==0:
return
if len(v)==1:
lines.append('- {}: [{}], n: {}'.format(s,v[0],len(v)))
else:
lines.append('- {}: [{} ... {}], dx: {}, n: {}'.format(s,v[0],v[-1],v[1]-v[0],len(v)))
lines = ['<{} object> with attributes:'.format(type(self).__name__)]
show_grid(self.xp_grid, 'xp_grid')
show_grid(self.yp_grid, 'yp_grid')
show_grid(self.zp_grid, 'zp_grid')
if self.point_data_grid:
lines.append('- point_data_grid:')
for k,v in self.point_data_grid.items():
lines.append(' "{}" : {}'.format(k,v.shape))
lines.append('- points {}'.format(len(self.points)))
if len(self.cells) > 0:
lines.append("- cells:")
for tpe, elems in self.cells:
lines.append(" {}: {}".format(tpe,len(elems)))
else:
lines.append(" No cells.")
if self.point_data:
lines.append('- point_data:')
for k,v in self.point_data.items():
lines.append(' "{}" : {}'.format(k,v.shape))
if self.cell_data:
names = ", ".join(self.cell_data.keys())
lines.append(" Cell data: {}".format(names))
return "\n".join(lines)
def toDataFrame(self):
return None
# Save FlowData Object to vtk
# """
# n_points = self.dimensions.x1 * self.dimensions.x2 * self.dimensions.x3
# vtk_file = Output(filename)
#self.file = open(self.filename, "w")
#self.ln = "\n"
# vtk_file.write_line('# vtk DataFile Version 3.0')
# vtk_file.write_line('array.mean0D')
# vtk_file.write_line('ASCII')
# vtk_file.write_line('DATASET STRUCTURED_POINTS')
# vtk_file.write_line('DIMENSIONS {}'.format(self.dimensions))
# vtk_file.write_line('ORIGIN {}'.format(self.origin))
# vtk_file.write_line('SPACING {}'.format(self.spacing))
# vtk_file.write_line('POINT_DATA {}'.format(n_points))
# vtk_file.write_line('FIELD attributes 1')
# vtk_file.write_line('UAvg 3 {} float'.format(n_points))
# for u, v, w in zip(self.u, self.v, self.w):
# vtk_file.write_line('{}'.format(Vec3(u, v, w)))
# --- Paraview
# except: from paraview.simple import *
# sliceFile = sliceDir + '/' + tStartStr + '/' + sliceName
# print ' Slice file 1a: ' + sliceFile
# slice_1a_vtk = LegacyVTKReader( FileNames=[sliceFile] )
# sliceFile = sliceDir + '/' + tEndStr + '/' + sliceName
# DataRepresentation3 = GetDisplayProperties(slice_1a_vtk)
# DataRepresentation3.Visibility = 0
# SetActiveSource(slice_1a_vtk)
# --- VTK
# import np
# from vtk import vtkStructuredPointsReader
# from vtk.util import np as VN
#
# reader = vtkStructuredPointsReader()
# reader.SetFileName(filename)
# reader.ReadAllVectorsOn()
# reader.ReadAllScalarsOn()
# reader.Update()
#
# data = reader.GetOutput()
#
# dim = data.GetDimensions()
# vec = list(dim)
# vec = [i-1 for i in dim]
# vec.append(3)
#
# u = VN.vtk_to_np(data.GetCellData().GetArray('velocity'))
# b = VN.vtk_to_numpy(data.GetCellData().GetArray('cell_centered_B'))
#
# u = u.reshape(vec,order='F')
# b = b.reshape(vec,order='F')
#
# x = zeros(data.GetNumberOfPoints())
# y = zeros(data.GetNumberOfPoints())
# z = zeros(data.GetNumberOfPoints())
#
# for i in range(data.GetNumberOfPoints()):
# x[i],y[i],z[i] = data.GetPoint(i)
#
# x = x.reshape(dim,order='F')
# y = y.reshape(dim,order='F')
# z = z.reshape(dim,order='F')
# --- vtk
# import vtk
# import numpy
# import vtk_demo.version as version
#
#
# def main():
# """
# :return: The render window interactor.
# """
#
# chessboard_resolution = 5
# n_lut_colors = 256
# data_max_value = 1
#
# # Provide some geometry
# chessboard = vtk.vtkPlaneSource()
# chessboard.SetXResolution(chessboard_resolution)
# chessboard.SetYResolution(chessboard_resolution)
# num_squares = chessboard_resolution * chessboard_resolution
# # Force an update so we can set cell data
# chessboard.Update()
#
# # Make some arbitrary data to show on the chessboard geometry
# data = vtk.vtkFloatArray()
# for i in range(num_squares):
# if i == 4:
# # This square should in principle light up with color given by SetNanColor below
# data.InsertNextTuple1(numpy.nan)
# else:
# thing = (i * data_max_value) / (num_squares - 1)
# data.InsertNextTuple1(thing)
#
# # Make a LookupTable
# lut = vtk.vtkLookupTable()
# lut.SetNumberOfColors(n_lut_colors)
# lut.Build()
# lut.SetTableRange(0, data_max_value)
# lut.SetNanColor(.1, .5, .99, 1.0) # <------ This color gets used
# for i in range(n_lut_colors):
# # Fill it with arbitrary colors, e.g. grayscale
# x = data_max_value*i/(n_lut_colors-1)
# lut.SetTableValue(i, x, x, x, 1.0)
# lut.SetNanColor(.99, .99, .1, 1.0) # <----- This color gets ignored! ...except by GetNanColor
#
# print(lut.GetNanColor()) # <-- Prints the color set by the last SetNanColor call above!
#
# chessboard.GetOutput().GetCellData().SetScalars(data)
#
# mapper = vtk.vtkPolyDataMapper()
# mapper.SetInputConnection(chessboard.GetOutputPort())
# mapper.SetScalarRange(0, data_max_value)
# mapper.SetLookupTable(lut)
# mapper.Update()
#
# actor = vtk.vtkActor()
# actor.SetMapper(mapper)
#
# renderer = vtk.vtkRenderer()
# ren_win = vtk.vtkRenderWindow()
# ren_win.AddRenderer(renderer)
# renderer.SetBackground(vtk.vtkNamedColors().GetColor3d('MidnightBlue'))
# renderer.AddActor(actor)
#
# iren = vtk.vtkRenderWindowInteractor()
# --- pyvtk
# """Read vtk-file stored previously with tovtk."""
# p = pyvtk.VtkData(filename)
# xn = array(p.structure.points)
# dims = p.structure.dimensions
# try:
# N = eval(p.header.split(" ")[-1])
# --- Extract
# # Convert the center of the turbine coordinate in m to High-Resolution domains left most corner in (i,j)
# xe_index = int(origin_at_precusr[0]/10)
# ye_index = int(origin_at_precusr[1]/10)
#
# # Read the full domain from VTK
# reader = vtk.vtkStructuredPointsReader()
# reader.SetFileName(in_vtk)
# reader.Update()
#
# # Extract the High Resolution domain at same spacial spacing by specifying the (i,i+14),(j,j+14),(k,k+20) tuples
# extract = vtk.vtkExtractVOI()
# extract.SetInputConnection(reader.GetOutputPort())
# extract.SetVOI(xe_index, xe_index+14, ye_index, ye_index+14, 0, 26)
# extract.SetSampleRate(1, 1, 1)
# extract.Update()
#
# # Write the extract as VTK
# points = extract.GetOutput()
# vec = points.GetPointData().GetVectors('Amb')
#
# with open(out_vtk, 'a') as the_file:
# the_file.write('# vtk DataFile Version 3.0\n')
# the_file.write('High\n')
# the_file.write('ASCII\n')
# the_file.write('DATASET STRUCTURED_POINTS\n')
# the_file.write('DIMENSIONS %d %d %d\n' % points.GetDimensions())
# the_file.write('ORIGIN %f %f %f\n' % origin_at_stitch)
# the_file.write('SPACING %f %f %f\n' % points.GetSpacing())
# the_file.write('POINT_DATA %d\n' % points.GetNumberOfPoints())
# the_file.write('VECTORS Amb float\n')
# for i in range(points.GetNumberOfPoints()):
# the_file.write('%f %f %f\n' % vec.GetTuple(i) )
# --- Stitch
# reader = vtk.vtkStructuredPointsReader()
# reader.SetFileName(in_vtk)
# reader.Update()
#
# hAppend = vtk.vtkImageAppend()
# hAppend.SetAppendAxis(0)
# for i in range(nx):
# hAppend.AddInputData(reader.GetOutput())
# hAppend.Update()
#
# vAppend = vtk.vtkImageAppend()
# vAppend.SetAppendAxis(1)
# for i in range(ny):
# vAppend.AddInputData(hAppend.GetOutput())
# vAppend.Update()
#
# points = vAppend.GetOutput()
# vec = points.GetPointData().GetVectors('Amb')
#
# with open(out_vtk, 'a') as the_file:
# the_file.write('# vtk DataFile Version 3.0\n')
# the_file.write('Low\n')
# the_file.write('ASCII\n')
# the_file.write('DATASET STRUCTURED_POINTS\n')
# the_file.write('DIMENSIONS %d %d %d\n' % points.GetDimensions())
# the_file.write('ORIGIN %f %f %f\n' % points.GetOrigin())
# the_file.write('SPACING %f %f %f\n' % points.GetSpacing())
# the_file.write('POINT_DATA %d\n' % points.GetNumberOfPoints())
# the_file.write('VECTORS Amb float\n')
# for i in range(points.GetNumberOfPoints()):
# the_file.write('%f %f %f\n' % vec.GetTuple(i) )
#
# --------------------------------------------------------------------------------}
# --- The code below is taken from meshio
# https://github.com/nschloe/meshio
# The MIT License (MIT)
# Copyright (c) 2015-2020 meshio developers
# --------------------------------------------------------------------------------{
ReadError = BrokenFormatError
WriteError = BrokenFormatError
def _vtk_to_meshio_order(vtk_type, numnodes, dtype=int):
# meshio uses the same node ordering as VTK for most cell types. However, for the
# linear wedge, the ordering of the gmsh Prism [1] is adopted since this is found in
# most codes (Abaqus, Ansys, Nastran,...). In the vtkWedge [2], the normal of the
# (0,1,2) triangle points outwards, while in gmsh this normal points inwards.
# [1] http://gmsh.info/doc/texinfo/gmsh.html#Node-ordering
# [2] https://vtk.org/doc/nightly/html/classvtkWedge.html
if vtk_type == 13:
return numpy.array([0, 2, 1, 3, 5, 4], dtype=dtype)
else:
return numpy.arange(0, numnodes, dtype=dtype)
def _meshio_to_vtk_order(meshio_type, numnodes, dtype=int):
if meshio_type == "wedge":
return numpy.array([0, 2, 1, 3, 5, 4], dtype=dtype)
else:
return numpy.arange(0, numnodes, dtype=dtype)
vtk_to_meshio_type = {
0: "empty",
1: "vertex",
# 2: 'poly_vertex',
3: "line",
# 4: 'poly_line',
5: "triangle",
# 6: 'triangle_strip',
7: "polygon",
8: "pixel",
9: "quad",
10: "tetra",
# 11: 'voxel',
12: "hexahedron",
13: "wedge",
14: "pyramid",
15: "penta_prism",
16: "hexa_prism",
21: "line3",
22: "triangle6",
23: "quad8",
24: "tetra10",
25: "hexahedron20",
26: "wedge15",
27: "pyramid13",
28: "quad9",
29: "hexahedron27",
30: "quad6",
31: "wedge12",
32: "wedge18",
33: "hexahedron24",
34: "triangle7",
35: "line4",
42: "polyhedron",
#
# 60: VTK_HIGHER_ORDER_EDGE,
# 61: VTK_HIGHER_ORDER_TRIANGLE,
# 62: VTK_HIGHER_ORDER_QUAD,
# 63: VTK_HIGHER_ORDER_POLYGON,
# 64: VTK_HIGHER_ORDER_TETRAHEDRON,
# 65: VTK_HIGHER_ORDER_WEDGE,
# 66: VTK_HIGHER_ORDER_PYRAMID,
# 67: VTK_HIGHER_ORDER_HEXAHEDRON,
# Arbitrary order Lagrange elements
68: "VTK_LAGRANGE_CURVE",
69: "VTK_LAGRANGE_TRIANGLE",
70: "VTK_LAGRANGE_QUADRILATERAL",
71: "VTK_LAGRANGE_TETRAHEDRON",
72: "VTK_LAGRANGE_HEXAHEDRON",
73: "VTK_LAGRANGE_WEDGE",
74: "VTK_LAGRANGE_PYRAMID",
# Arbitrary order Bezier elements
75: "VTK_BEZIER_CURVE",
76: "VTK_BEZIER_TRIANGLE",
77: "VTK_BEZIER_QUADRILATERAL",
78: "VTK_BEZIER_TETRAHEDRON",
79: "VTK_BEZIER_HEXAHEDRON",
80: "VTK_BEZIER_WEDGE",
81: "VTK_BEZIER_PYRAMID",
}
meshio_to_vtk_type = {v: k for k, v in vtk_to_meshio_type.items()}
# --------------------------------------------------------------------------------}
# --- Mesh
# --------------------------------------------------------------------------------{
class CellBlock(collections.namedtuple("CellBlock", ["type", "data"])):
def __repr__(self):
return "<meshio CellBlock, type: {}, num cells: {}>".format(self.type,len(self.data))
# --------------------------------------------------------------------------------}
# --- File _vtk.py from meshio
# --------------------------------------------------------------------------------{
vtk_type_to_numnodes = numpy.array(
[
0, # empty
1, # vertex
-1, # poly_vertex
2, # line
-1, # poly_line
3, # triangle
-1, # triangle_strip
-1, # polygon
-1, # pixel
4, # quad
4, # tetra
-1, # voxel
8, # hexahedron
6, # wedge
5, # pyramid
10, # penta_prism
12, # hexa_prism
-1,
-1,
-1,
-1,
3, # line3
6, # triangle6
8, # quad8
10, # tetra10
20, # hexahedron20
15, # wedge15
13, # pyramid13
9, # quad9
27, # hexahedron27
6, # quad6
12, # wedge12
18, # wedge18
24, # hexahedron24
7, # triangle7
4, # line4
]
)
# These are all VTK data types.
# One sometimes finds 'vtktypeint64', but this is ill-formed.
vtk_to_numpy_dtype_name = {
"bit": "bool",
"unsigned_char": "uint8",
"char": "int8",
"unsigned_short": "uint16",
"short": "int16",
"unsigned_int": "uint32",
"int": "int32",
"unsigned_long": "uint64",
"long": "int64",
"float": "float32",
"double": "float64",
"vtktypeint32": "int32", # vtk DataFile Version 5.1
"vtktypeint64": "int64", # vtk DataFile Version 5.1
"vtkidtype": "int32", # may be either 32-bit or 64-bit (VTK_USE_64BIT_IDS)
}
numpy_to_vtk_dtype = {
v: k for k, v in vtk_to_numpy_dtype_name.items() if "vtk" not in k
}
# supported vtk dataset types
vtk_dataset_types = [
"UNSTRUCTURED_GRID",
"STRUCTURED_POINTS",
"STRUCTURED_GRID",
"RECTILINEAR_GRID",
]
# additional infos per dataset type
vtk_dataset_infos = {
"UNSTRUCTURED_GRID": [],
"STRUCTURED_POINTS": [
"DIMENSIONS",
"ORIGIN",
"SPACING",
"ASPECT_RATIO", # alternative for SPACING in version 1.0 and 2.0
],
"STRUCTURED_GRID": ["DIMENSIONS"],
"RECTILINEAR_GRID": [
"DIMENSIONS",
"X_COORDINATES",
"Y_COORDINATES",
"Z_COORDINATES",
],
}
# all main sections in vtk
vtk_sections = [
"METADATA",
"DATASET",
"POINTS",
"CELLS",
"CELL_TYPES",
"POINT_DATA",
"CELL_DATA",
"LOOKUP_TABLE",
"COLOR_SCALARS",
]
def read(filename):
"""Reads a VTK vtk file."""
with open(filename, "rb") as f:
out = read_buffer(f)
return out
def read_buffer(f):
# initialize output data
info = VTKFile()
# skip header and title
f.readline()
f.readline()
data_type = f.readline().decode("utf-8").strip().upper()
if data_type not in ["ASCII", "BINARY"]:
raise WrongFormatError("Unknown VTK data type ",data_type)
info.is_ascii = data_type == "ASCII"
while True:
line = f.readline().decode("utf-8")
if not line:
# EOF
break
line = line.strip()
if len(line) == 0:
continue
info.split = line.split()
info.section = info.split[0].upper()
if info.section in vtk_sections:
_read_section(f, info)
else:
_read_subsection(f, info)
_check_mesh(info)
cells, cell_data = translate_cells(info.c, info.ct, info.cell_data_raw)
info.cells = cells
info.cell_data = cell_data
return info
def _read_section(f, info):
if info.section == "METADATA":
_skip_meta(f)
elif info.section == "DATASET":
info.active = "DATASET"
info.dataset["type"] = info.split[1].upper()
if info.dataset["type"] not in vtk_dataset_types:
raise BrokenFormatError(
"Only VTK '{}' supported (not {}).".format(
"', '".join(vtk_dataset_types), info.dataset["type"]
)
)
elif info.section == "POINTS":
info.active = "POINTS"
info.num_points = int(info.split[1])
data_type = info.split[2].lower()
info.points = _read_points(f, data_type, info.is_ascii, info.num_points)
elif info.section == "CELLS":
info.active = "CELLS"
last_pos = f.tell()
try:
line = f.readline().decode("utf-8")
except UnicodeDecodeError:
line = ""
if "OFFSETS" in line:
# vtk DataFile Version 5.1 - appearing in Paraview 5.8.1 outputs
# No specification found for this file format.
# See the question on ParaView Discourse Forum:
# <https://discourse.paraview.org/t/specification-of-vtk-datafile-version-5-1/5127>.
info.num_offsets = int(info.split[1])
info.num_items = int(info.split[2])
dtype = numpy.dtype(vtk_to_numpy_dtype_name[line.split()[1]])
offsets = _read_cells(f, info.is_ascii, info.num_offsets, dtype)
line = f.readline().decode("utf-8")
assert "CONNECTIVITY" in line
dtype = numpy.dtype(vtk_to_numpy_dtype_name[line.split()[1]])
connectivity = _read_cells(f, info.is_ascii, info.num_items, dtype)
info.c = (offsets, connectivity)
else:
f.seek(last_pos)
info.num_items = int(info.split[2])
info.c = _read_cells(f, info.is_ascii, info.num_items)
elif info.section == "CELL_TYPES":
info.active = "CELL_TYPES"
info.num_items = int(info.split[1])
info.ct = _read_cell_types(f, info.is_ascii, info.num_items)
elif info.section == "POINT_DATA":
info.active = "POINT_DATA"
info.num_items = int(info.split[1])
elif info.section == "CELL_DATA":
info.active = "CELL_DATA"
info.num_items = int(info.split[1])
elif info.section == "LOOKUP_TABLE":
info.num_items = int(info.split[2])
numpy.fromfile(f, count=info.num_items * 4, sep=" ", dtype=float)
# rgba = data.reshape((info.num_items, 4))
elif info.section == "COLOR_SCALARS":
nValues = int(info.split[2])
# re-use num_items from active POINT/CELL_DATA
num_items = info.num_items
dtype = numpy.ubyte
if info.is_ascii:
dtype = float
numpy.fromfile(f, count=num_items * nValues, dtype=dtype)
def _read_subsection(f, info):
if info.active == "POINT_DATA":
d = info.point_data
elif info.active == "CELL_DATA":
d = info.cell_data_raw
elif info.active == "DATASET":
d = info.dataset
else:
d = info.field_data
if info.section in vtk_dataset_infos[info.dataset["type"]]:
if info.section[1:] == "_COORDINATES":
info.num_points = int(info.split[1])
data_type = info.split[2].lower()
d[info.section] = _read_coords(f, data_type, info.is_ascii, info.num_points)
else:
if info.section == "DIMENSIONS":
d[info.section] = list(map(int, info.split[1:]))
else:
d[info.section] = list(map(float, info.split[1:]))
if len(d[info.section]) != 3:
raise BrokenFormatError(
"Wrong number of info in section '{}'. Need 3, got {}.".format(
info.section, len(d[info.section])
)
)
elif info.section == "SCALARS":
d.update(_read_scalar_field(f, info.num_items, info.split, info.is_ascii))
elif info.section == "VECTORS":
d.update(_read_field(f, info.num_items, info.split, [3], info.is_ascii))
elif info.section == "TENSORS":
d.update(_read_field(f, info.num_items, info.split, [3, 3], info.is_ascii))
elif info.section == "FIELD":
d.update(_read_fields(f, int(info.split[2]), info.is_ascii))
else:
raise WrongFormatError("Unknown section ",info.section)
def _check_mesh(info):
if info.dataset["type"] == "UNSTRUCTURED_GRID":
if info.c is None:
raise ReadError("Required section CELLS not found.")
if info.ct is None:
raise ReadError("Required section CELL_TYPES not found.")
elif info.dataset["type"] == "STRUCTURED_POINTS":
dim = info.dataset["DIMENSIONS"]
ori = info.dataset["ORIGIN"]
spa = (
info.dataset["SPACING"]
if "SPACING" in info.dataset
else info.dataset["ASPECT_RATIO"]
)
axis = [
numpy.linspace(ori[i], ori[i] + (dim[i] - 1.0) * spa[i], dim[i])
for i in range(3)
]
info.xp_grid=axis[0]
info.yp_grid=axis[1]
info.zp_grid=axis[2]
info.points = _generate_points(axis)
info.c, info.ct = _generate_cells(dim=info.dataset["DIMENSIONS"])
elif info.dataset["type"] == "RECTILINEAR_GRID":
axis = [
info.dataset["X_COORDINATES"],
info.dataset["Y_COORDINATES"],
info.dataset["Z_COORDINATES"],
]
info.xp_grid=axis[0]
info.yp_grid=axis[1]
info.zp_grid=axis[2]
info.points = _generate_points(axis)
info.c, info.ct = _generate_cells(dim=info.dataset["DIMENSIONS"])
elif info.dataset["type"] == "STRUCTURED_GRID":
info.c, info.ct = _generate_cells(dim=info.dataset["DIMENSIONS"])
# TODO x_grid, y_grid, z_grid points
def _generate_cells(dim):
ele_dim = [d - 1 for d in dim if d > 1]
ele_no = numpy.prod(ele_dim, dtype=int)
spatial_dim = len(ele_dim)
if spatial_dim == 1:
# cells are lines in 1D
cells = numpy.empty((ele_no, 3), dtype=int)
cells[:, 0] = 2
cells[:, 1] = numpy.arange(ele_no, dtype=int)
cells[:, 2] = cells[:, 1] + 1
cell_types = numpy.full(ele_no, 3, dtype=int)
elif spatial_dim == 2:
# cells are quad in 2D
cells = numpy.empty((ele_no, 5), dtype=int)
cells[:, 0] = 4
cells[:, 1] = numpy.arange(0, ele_no, dtype=int)
cells[:, 1] += numpy.arange(0, ele_no, dtype=int) // ele_dim[0]
cells[:, 2] = cells[:, 1] + 1
cells[:, 3] = cells[:, 1] + 2 + ele_dim[0]
cells[:, 4] = cells[:, 3] - 1
cell_types = numpy.full(ele_no, 9, dtype=int)
else:
# cells are hex in 3D
cells = numpy.empty((ele_no, 9), dtype=int)
cells[:, 0] = 8
cells[:, 1] = numpy.arange(ele_no)
cells[:, 1] += (ele_dim[0] + ele_dim[1] + 1) * (
numpy.arange(ele_no) // (ele_dim[0] * ele_dim[1])
)
cells[:, 1] += (numpy.arange(ele_no) % (ele_dim[0] * ele_dim[1])) // ele_dim[0]
cells[:, 2] = cells[:, 1] + 1
cells[:, 3] = cells[:, 1] + 2 + ele_dim[0]
cells[:, 4] = cells[:, 3] - 1
cells[:, 5] = cells[:, 1] + (1 + ele_dim[0]) * (1 + ele_dim[1])
cells[:, 6] = cells[:, 5] + 1
cells[:, 7] = cells[:, 5] + 2 + ele_dim[0]
cells[:, 8] = cells[:, 7] - 1
cell_types = numpy.full(ele_no, 12, dtype=int)
return cells.reshape(-1), cell_types
def _generate_points(axis):
x_dim = len(axis[0])
y_dim = len(axis[1])
z_dim = len(axis[2])
pnt_no = x_dim * y_dim * z_dim
x_id, y_id, z_id = numpy.mgrid[0:x_dim, 0:y_dim, 0:z_dim]
points = numpy.empty((pnt_no, 3), dtype=axis[0].dtype)
# VTK sorts points and cells in Fortran order
points[:, 0] = axis[0][x_id.reshape(-1, order="F")]
points[:, 1] = axis[1][y_id.reshape(-1, order="F")]
points[:, 2] = axis[2][z_id.reshape(-1, order="F")]
return points
def _read_coords(f, data_type, is_ascii, num_points):
dtype = numpy.dtype(vtk_to_numpy_dtype_name[data_type])
if is_ascii:
coords = numpy.fromfile(f, count=num_points, sep=" ", dtype=dtype)
else:
# Binary data is big endian, see
# <https://www.vtk.org/Wiki/VTK/Writing_VTK_files_using_python#.22legacy.22>.
dtype = dtype.newbyteorder(">")
coords = numpy.fromfile(f, count=num_points, dtype=dtype)
line = f.readline().decode("utf-8")
if line != "\n":
raise ReadError()
return coords
def _read_points(f, data_type, is_ascii, num_points):
dtype = numpy.dtype(vtk_to_numpy_dtype_name[data_type])
if is_ascii:
points = numpy.fromfile(f, count=num_points * 3, sep=" ", dtype=dtype)
else:
# Binary data is big endian, see
# <https://www.vtk.org/Wiki/VTK/Writing_VTK_files_using_python#.22legacy.22>.
dtype = dtype.newbyteorder(">")
points = numpy.fromfile(f, count=num_points * 3, dtype=dtype)
line = f.readline().decode("utf-8")
if line != "\n":
raise ReadError()
return points.reshape((num_points, 3))
def _read_cells(f, is_ascii, num_items, dtype=numpy.dtype("int32")):
if is_ascii:
c = numpy.fromfile(f, count=num_items, sep=" ", dtype=dtype)
else:
dtype = dtype.newbyteorder(">")
c = numpy.fromfile(f, count=num_items, dtype=dtype)
line = f.readline().decode("utf-8")
if line != "\n":
raise ReadError()
return c
def _read_cell_types(f, is_ascii, num_items):
if is_ascii:
ct = numpy.fromfile(f, count=int(num_items), sep=" ", dtype=int)
else:
# binary
ct = numpy.fromfile(f, count=int(num_items), dtype=">i4")
line = f.readline().decode("utf-8")
# Sometimes, there's no newline at the end
if line.strip() != "":
raise ReadError()
return ct
def _read_scalar_field(f, num_data, split, is_ascii):
data_name = split[1]
data_type = split[2].lower()
try:
num_comp = int(split[3])
except IndexError:
num_comp = 1
# The standard says:
# > The parameter numComp must range between (1,4) inclusive; [...]
if not (0 < num_comp < 5):
raise ReadError("The parameter numComp must range between (1,4) inclusive")
dtype = numpy.dtype(vtk_to_numpy_dtype_name[data_type])
lt, _ = f.readline().decode("utf-8").split()
if lt.upper() != "LOOKUP_TABLE":
raise ReadError()
if is_ascii:
data = numpy.fromfile(f, count=num_data * num_comp, sep=" ", dtype=dtype)