-
Notifications
You must be signed in to change notification settings - Fork 2
/
hl.py
243 lines (208 loc) · 9.64 KB
/
hl.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
# ***********************************************************************************
# * Copyright 2010 Paulo A. Herrera. All rights reserved. *
# * *
# * Redistribution and use in source and binary forms, with or without *
# * modification, are permitted provided that the following conditions are met: *
# * *
# * 1. Redistributions of source code must retain the above copyright notice, *
# * this list of conditions and the following disclaimer. *
# * *
# * 2. Redistributions in binary form must reproduce the above copyright notice, *
# * this list of conditions and the following disclaimer in the documentation *
# * and/or other materials provided with the distribution. *
# * *
# * THIS SOFTWARE IS PROVIDED BY PAULO A. HERRERA ``AS IS'' AND ANY EXPRESS OR *
# * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF *
# * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO *
# * EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, *
# * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, *
# * BUT NOT LIMITED TO, PROCUREMEN OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, *
# * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY *
# * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING *
# * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS *
# * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. *
# ***********************************************************************************
# **************************************
# * High level Python library to *
# * export data to binary VTK file. *
# **************************************
from vtk import * # VtkFile, VtkUnstructuredGrid, etc.
import numpy as np
# =================================
# Helper functions
# =================================
def _addDataToFile(vtkFile, cellData, pointData):
# Point data
if pointData <> None:
keys = pointData.keys()
vtkFile.openData("Point", scalars = keys[0])
for key in keys:
data = pointData[key]
vtkFile.addData(key, data)
vtkFile.closeData("Point")
# Cell data
if cellData <> None:
keys = cellData.keys()
vtkFile.openData("Cell", scalars = keys[0])
for key in keys:
data = cellData[key]
vtkFile.addData(key, data)
vtkFile.closeData("Cell")
def _appendDataToFile(vtkFile, cellData, pointData):
# Append data to binary section
if pointData <> None:
keys = pointData.keys()
for key in keys:
data = pointData[key]
vtkFile.appendData(data)
if cellData <> None:
keys = cellData.keys()
for key in keys:
data = cellData[key]
vtkFile.appendData(data)
# =================================
# High level functions
# =================================
def imageToVTK(path, origin = (0.0,0.0,0.0), spacing = (1.0,1.0,1.0), cellData = None, pointData = None ):
""" Exports data values as a rectangular image.
PARAMETERS:
path: name of the file without extension where data should be saved.
origin: grid origin (default = (0,0,0))
spacing: grid spacing (default = (1,1,1))
cellData: dictionary containing arrays with cell centered data.
Keys should be the names of the data arrays.
Arrays must have the same dimensions in all directions and must contain
only scalar data.
nodeData: dictionary containing arrays with node centered data.
Keys should be the names of the data arrays.
Arrays must have same dimension in each direction and
they should be equal to the dimensions of the cell data plus one and
must contain only scalar data.
RETURNS:
Full path to saved file.
NOTE: At least, cellData or pointData must be present to infer the dimensions of the image.
"""
assert (cellData <> None or pointData <> None)
# Extract dimensions
start = (0,0,0)
end = None
if cellData <> None:
keys = cellData.keys()
data = cellData[keys[0]]
end = data.shape
elif pointData <> None:
keys = pointData.keys()
data = pointData[keys[0]]
end = data.shape
end = (end[0] - 1, end[1] - 1, end[1] - 1)
# Write data to file
w = VtkFile(path, VtkImageData)
w.openGrid(start = start, end = end, origin = origin, spacing = spacing)
w.openPiece(start = start, end = end)
_addDataToFile(w, cellData, pointData)
w.closePiece()
w.closeGrid()
_appendDataToFile(w, cellData, pointData)
w.save()
return w.getFileName()
def gridToVTK(path, x, y, z, cellData = None, pointData = None):
"""
Writes data values as a rectilinear or rectangular grid.
PARAMETERS:
path: name of the file without extension where data should be saved.
x, y, z: coordinates of the nodes of the grid. They can be 1D or 3D depending if
the grid should be saved as a rectilinear or logically structured grid, respectively.
Arrays should contain coordinates of the nodes of the grid.
If arrays are 1D, then the grid should be Cartesian, i.e. faces in all cells are orthogonal.
If arrays are 3D, then the grid should be logically structured with hexahedral cells.
In both cases the arrays dimenions should be equal to the number of nodes of the grid.
cellData: dictionary containing arrays with cell centered data.
Keys should be the names of the data arrays.
Arrays must have the same dimensions in all directions and must contain
only scalar data.
nodeData: dictionary containing arrays with node centered data.
Keys should be the names of the data arrays.
Arrays must have same dimension in each direction and
they should be equal to the dimensions of the cell data plus one and
must contain only scalar data.
RETURNS:
Full path to saved file.
"""
# Extract dimensions
start = (0,0,0)
isRect = False
nx = ny = nz = 0
ftype = VtkStructuredGrid
if (x.ndim == 1 and y.ndim == 1 and z.ndim == 1):
nx, ny, nz = x.size - 1, y.size - 1, z.size - 1
isRect = True
ftype = VtkRectilinearGrid
elif (x.ndim == 3 and y.ndim == 3 and z.ndim == 3):
s = x.shape
nx, ny, nz = s[0] - 1, s[1] - 1, s[2] - 1
else:
assert(False)
end = (nx, ny, nz)
w = VtkFile(path, ftype)
w.openGrid(start = start, end = end)
w.openPiece(start = start, end = end)
if isRect:
w.openElement("Coordinates")
w.addData("x_coordinates", x)
w.addData("y_coordinates", y)
w.addData("z_coordinates", z)
w.closeElement("Coordinates")
else:
w.openElement("Points")
w.addData("points", (x,y,z))
w.closeElement("Points")
_addDataToFile(w, cellData, pointData)
w.closePiece()
w.closeGrid()
# Write coordinates
if isRect:
w.appendData(x).appendData(y).appendData(z)
else:
w.appendData( (x,y,z) )
# Write data
_appendDataToFile(w, cellData, pointData)
w.save()
return w.getFileName()
def pointsToVTK(path, x, y, z, data):
"""
Export points and associated data as an unstructured grid.
PARAMETERS:
path: name of the file without extension where data should be saved.
x, y, z: 1D arrays with coordinates of the points.
data: dictionary with variables associated to each point.
Keys should be the names of the variable stored in each array.
All arrays must have the same number of elements.
RETURNS:
Full path to saved file.
"""
assert (x.size == y.size == z.size)
npoints = x.size
# create some temporary arrays to write grid topology
offsets = np.arange(start = 1, stop = npoints + 1, dtype = 'int32') # index of last node in each cell
connectivity = np.arange(npoints, dtype = 'int32') # each point is only connected to itself
cell_types = np.empty(npoints, dtype = 'uint8')
cell_types[:] = VtkVertex.tid
w = VtkFile(path, VtkUnstructuredGrid)
w.openGrid()
w.openPiece(ncells = npoints, npoints = npoints)
w.openElement("Points")
w.addData("points", (x,y,z))
w.closeElement("Points")
w.openElement("Cells")
w.addData("connectivity", connectivity)
w.addData("offsets", offsets)
w.addData("types", cell_types)
w.closeElement("Cells")
_addDataToFile(w, cellData = None, pointData = data)
w.closePiece()
w.closeGrid()
w.appendData( (x,y,z) )
w.appendData(connectivity).appendData(offsets).appendData(cell_types)
_appendDataToFile(w, cellData = None, pointData = data)
w.save()
return w.getFileName()