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
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
|
# pylint: disable=line-too-long
import copy
import re
from numpy import dtype, array, invert, take
__all__ = ('generate_xdmf',)
xdmffile = """<?xml version="1.0" encoding="utf-8"?>
<Xdmf xmlns:xi="http://www.w3.org/2001/XInclude" Version="2.1">
<Domain>
<Grid Name="Structured Grid" GridType="Collection" CollectionType="Temporal">
<Time TimeType="List"><DataItem Format="XML" Dimensions="{1}"> {0} </DataItem></Time>
{2}
</Grid>
</Domain>
</Xdmf>
"""
def get_grid(geometry, topology, attrs):
return """<Grid GridType="Uniform">
{0}
{1}
{2}
</Grid>
""".format(geometry, topology, attrs)
def get_geometry(kind=0, dim=2):
assert kind in (0, 1)
assert dim in (2, 3)
if dim == 2:
if kind == 0:
return """<Geometry Type="ORIGIN_DXDY">
<DataItem Format="XML" NumberType="Float" Dimensions="2">
{0} {1}
</DataItem>
<DataItem Format="XML" NumberType="Float" Dimensions="2">
{2} {3}
</DataItem>
</Geometry>"""
return """<Geometry Type="VXVYVZ">
<DataItem Format="HDF" NumberType="Float" Precision="{0}" Dimensions="{1}">
{3}:{6}/mesh/{4}
</DataItem>
<DataItem Format="HDF" NumberType="Float" Precision="{0}" Dimensions="{2}">
{3}:{6}/mesh/{5}
</DataItem>
<DataItem Format="XML" NumberType="Float" Precision="8" Dimensions="1">
0
</DataItem>
</Geometry>"""
if dim == 3:
if kind == 0:
return """<Geometry Type="ORIGIN_DXDYDZ">
<DataItem Format="XML" NumberType="Float" Dimensions="3">
{0} {1} {2}
</DataItem>
<DataItem Format="XML" NumberType="Float" Dimensions="3">
{3} {4} {5}
</DataItem>
</Geometry>"""
return """<Geometry Type="VXVYVZ">
<DataItem Format="HDF" NumberType="Float" Precision="{0}" Dimensions="{3}">
{4}:{8}/mesh/{5}
</DataItem>
<DataItem Format="HDF" NumberType="Float" Precision="{0}" Dimensions="{2}">
{4}:{8}/mesh/{6}
</DataItem>
<DataItem Format="HDF" NumberType="Float" Precision="{0}" Dimensions="{1}">
{4}:{8}/mesh/{7}
</DataItem>
</Geometry>"""
def get_topology(dims, kind=0):
assert len(dims) in (2, 3)
co = 'Co' if kind == 0 else ''
if len(dims) == 2:
return """<Topology Dimensions="1 {0} {1}" Type="3D{2}RectMesh"/>""".format(dims[0], dims[1], co)
if len(dims) == 3:
return """<Topology Dimensions="{0} {1} {2}" Type="3D{3}RectMesh"/>""".format(dims[0], dims[1], dims[2], co)
def get_attribute(attr, h5filename, dims, prec):
name = attr.split("/")[0]
assert len(dims) in (2, 3)
if len(dims) == 2:
return """<Attribute Name="{0}" Center="Node">
<DataItem Format="HDF" NumberType="Float" Precision="{5}" Dimensions="1 {1} {2}">
{3}:/{4}
</DataItem>
</Attribute>
""".format(name, dims[0], dims[1], h5filename, attr, prec)
return """<Attribute Name="{0}" Center="Node">
<DataItem Format="HDF" NumberType="Float" Precision="{6}" Dimensions="{1} {2} {3}">
{4}:/{5}
</DataItem>
</Attribute>
""".format(name, dims[0], dims[1], dims[2], h5filename, attr, prec)
def generate_xdmf(h5filename, periodic=True, order='paraview'):
"""Generate XDMF-files
Parameters
----------
h5filename : str
Name of hdf5-file that we want to decorate with xdmf
periodic : bool or dim-sequence of bools, optional
If true along axis i, assume data is periodic.
Only affects the calculation of the domain size and only if the
domain is given as 2-tuple of origin+dx.
order : str
``paraview`` or ``visit``
For some reason Paraview and Visit requires the mesh stored in
opposite order in the XDMF-file for 2D slices. Make choice of
order here.
"""
import h5py
f = h5py.File(h5filename, 'a')
keys = []
f.visit(keys.append)
assert order.lower() in ('paraview', 'visit')
# Find unique scalar groups of 2D and 3D datasets
datasets = {2:{}, 3:{}}
for key in keys:
if f[key.split('/')[0]].attrs['rank'] > 0:
continue
if isinstance(f[key], h5py.Dataset):
if not ('mesh' in key or 'domain' in key or 'Vector' in key):
tstep = int(key.split("/")[-1])
ndim = int(key.split("/")[1][0])
if ndim in (2, 3):
ds = datasets[ndim]
if tstep in ds:
ds[tstep] += [key]
else:
ds[tstep] = [key]
if periodic is True:
periodic = [0]*5
elif periodic is False:
periodic = [1]*5
else:
assert isinstance(periodic, (tuple, list))
periodic = list(array(invert(periodic), int))
coor = ['x0', 'x1', 'x2', 'x3', 'x4']
for ndim, dsets in datasets.items():
timesteps = list(dsets.keys())
per = copy.copy(periodic)
if not timesteps:
continue
timesteps.sort(key=int)
tt = ""
for i in timesteps:
tt += "%s " %i
datatype = f[dsets[timesteps[0]][0]].dtype
assert datatype.char not in 'FDG', "Cannot use generate_xdmf to visualize complex data."
prec = 4 if datatype is dtype('float32') else 8
xff = {}
geometry = {}
topology = {}
attrs = {}
grid = {}
NN = {}
for name in dsets[timesteps[0]]:
group = name.split('/')[0]
if 'slice' in name:
slices = name.split("/")[2]
else:
slices = 'whole'
cc = copy.copy(coor)
if slices not in xff:
xff[slices] = copy.copy(xdmffile)
N = list(f[name].shape)
kk = 0
sl = 0
if 'slice' in slices:
ss = slices.split("_")
ii = []
for i, sx in enumerate(ss):
if 'slice' in sx:
ii.append(i)
else:
if len(f[group].attrs.get('shape')) == 3: # 2D slice in 3D domain
kk = i
sl = int(sx)
N.insert(i, 1)
cc = take(coor, ii)
else:
ii = list(range(ndim))
NN[slices] = N
if 'domain' in f[group].keys():
if ndim == 2 and ('slice' not in slices or len(f[group].attrs.get('shape')) > 3):
geo = get_geometry(kind=0, dim=2)
assert len(ii) == 2
i, j = ii
if order.lower() == 'paraview':
data = [f[group+'/domain/{}'.format(coor[i])][0],
f[group+'/domain/{}'.format(coor[j])][0],
f[group+'/domain/{}'.format(coor[i])][1]/(N[0]-per[i]),
f[group+'/domain/{}'.format(coor[j])][1]/(N[1]-per[j])]
geometry[slices] = geo.format(*data)
else:
data = [f[group+'/domain/{}'.format(coor[j])][0],
f[group+'/domain/{}'.format(coor[i])][0],
f[group+'/domain/{}'.format(coor[j])][1]/(N[0]-per[j]),
f[group+'/domain/{}'.format(coor[i])][1]/(N[1]-per[i])]
geometry[slices] = geo.format(*data)
else:
if ndim == 2:
ii.insert(kk, kk)
per[kk] = 0
i, j, k = ii
geo = get_geometry(kind=0, dim=3)
data = [f[group+'/domain/{}'.format(coor[i])][0],
f[group+'/domain/{}'.format(coor[j])][0],
f[group+'/domain/{}'.format(coor[k])][0],
f[group+'/domain/{}'.format(coor[i])][1]/(N[0]-per[i]),
f[group+'/domain/{}'.format(coor[j])][1]/(N[1]-per[j]),
f[group+'/domain/{}'.format(coor[k])][1]/(N[2]-per[k])]
if ndim == 2:
origin, dx = f[group+'/domain/x{}'.format(kk)]
M = f[group].attrs.get('shape')
pos = origin+dx/(M[kk]-per[kk])*sl
data[kk] = pos
data[kk+3] = pos
geometry[slices] = geo.format(*data)
topology[slices] = get_topology(N, kind=0)
elif 'mesh' in f[group].keys():
if ndim == 2 and ('slice' not in slices or len(f[group].attrs.get('shape')) > 3):
geo = get_geometry(kind=1, dim=2)
else:
geo = get_geometry(kind=1, dim=3)
if ndim == 2 and ('slice' not in slices or len(f[group].attrs.get('shape')) > 3):
if order.lower() == 'paraview':
sig = (prec, N[0], N[1], h5filename, cc[0], cc[1], group)
else:
sig = (prec, N[1], N[0], h5filename, cc[1], cc[0], group)
else:
if ndim == 2: # 2D slice in 3D domain
pos = f[group+"/mesh/x{}".format(kk)][sl]
z = re.findall(r'<DataItem(.*?)</DataItem>', geo, re.DOTALL)
geo = geo.replace(z[2-kk], ' Format="XML" NumberType="Float" Precision="{0}" Dimensions="{%d}">\n {%d}\n '%(1+kk, 7-kk))
cc = list(cc)
cc.insert(kk, pos)
sig = (prec, N[0], N[1], N[2], h5filename, cc[2], cc[1], cc[0], group)
geometry[slices] = geo.format(*sig)
topology[slices] = get_topology(N, kind=1)
grid[slices] = ''
# if slice of data, need to know along which axes
# Since there may be many different slices, we need to create
# one xdmf-file for each composition of slices
attrs = {}
for tstep in timesteps:
d = dsets[tstep]
slx = set()
for i, x in enumerate(d):
slices = x.split("/")[2]
if not 'slice' in slices:
slices = 'whole'
N = NN[slices]
if slices not in attrs:
attrs[slices] = ''
attrs[slices] += get_attribute(x, h5filename, N, prec)
slx.add(slices)
for slices in slx:
grid[slices] += get_grid(geometry[slices], topology[slices],
attrs[slices].rstrip())
attrs[slices] = ''
for slices, ff in xff.items():
if 'slice' in slices:
fname = h5filename[:-3]+"_"+slices+".xdmf"
else:
fname = h5filename[:-3]+".xdmf"
xfl = open(fname, "w")
h = ff.format(tt, len(timesteps), grid[slices].rstrip())
xfl.write(h)
xfl.close()
f.close()
if __name__ == "__main__":
import sys
generate_xdmf(sys.argv[-1])
|
