/usr/lib/python2.7/dist-packages/PySPH-1.0a4.dev0-py2.7-linux-x86_64.egg/pysph/tools/pysph_to_vtk.py is in python-pysph 0~20160514.git91867dc-4build1.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 | ''' convert pysph .npz output to vtk file format '''
from __future__ import print_function
import os
import re
from enthought.tvtk.api import tvtk, write_data
from numpy import array, c_, ravel, load, zeros_like
def write_vtk(data, filename, scalars=None, vectors={'V':('u','v','w')}, tensors={},
coords=('x','y','z'), dims=None, **kwargs):
''' write data in to vtk file
Parameters
----------
data : dict
mapping of variable name to their numpy array
filename : str
the file to write to (can be any recognized vtk extension)
if extension is missing .vts extension is appended
scalars : list
list of arrays to write as scalars (defaults to data.keys())
vectors : dict
mapping of vector name to vector component names to take from data
tensors : dict
mapping of tensor name to tensor component names to take from data
coords : list
the name of coordinate data arrays (default=('x','y','z'))
dims : 3 tuple
the size along the dimensions for (None means x.shape)
**kwargs : extra arguments for the file writer
example file_type=binary/ascii
'''
x = data[coords[0]]
y = data.get(coords[1], zeros_like(x))
z = data.get(coords[2], zeros_like(x))
if dims is None:
dims = array([1,1,1])
dims[:x.ndim] = x.shape
else:
dims = array(dims)
sg = tvtk.StructuredGrid(points=c_[x.flat,y.flat,z.flat],dimensions=array(dims))
pd = tvtk.PointData()
if scalars is None:
scalars = [i for i in data.keys() if i not in coords]
for v in scalars:
pd.scalars = ravel(data[v])
pd.scalars.name = v
sg.point_data.add_array(pd.scalars)
for vec,vec_vars in vectors.items():
u,v,w = [data[i] for i in vec_vars]
pd.vectors = c_[ravel(u),ravel(v),ravel(w)]
pd.vectors.name = vec
sg.point_data.add_array(pd.vectors)
for ten,ten_vars in tensors.items():
vars = [data[i] for i in ten_vars]
tensors = c_[[ravel(i) for i in vars]].T
pd.tensors = tensors
pd.tensors.name = ten
sg.point_data.add_array(pd.tensors)
write_data(sg, filename, **kwargs)
def detect_vectors_tensors(keys):
''' detect the vectors and tensors from given array names
Vectors are identified as the arrays with common prefix followed by
0,1 and 2 in their names
Tensors are identified as the arrays with common prefix followed by
two character codes representing ij indices
(00,01,02,11,12,22) for a symmetric tensor
(00,01,02,10,11,12,20,21,22) for a tensor
Arrays not belonging to vectors or tensors are returned as scalars
Returns scalars,vectors,tensors in a format suitable to be used as arguments
for :py:func:`write_vtk`
'''
d = {}
for k in keys:
d[len(k)] = d.get(len(k), [])
d[len(k)].append(k)
scalars = []
vectors = {}
tensors = {}
for n,l in d.items():
if n<2:
continue
l.sort()
idx = -1
while idx<len(l)-1:
idx += 1
k = l[idx]
# check if last char is 0
if k[-1] == '0':
# check for tensor
if k[-2] == '0':
# check for 9 tensor
ten = []
for i in range(3):
for j in range(3):
ten.append(k[:-2]+str(j)+str(i))
ten.sort()
if l[idx:idx+9] == ten:
tensors[k[:-2]] = ten
idx += 8
continue
# check for symm 6 tensor
ten2 = []
for i in range(3):
for j in range(i+1):
ten2.append(k[:-2]+str(j)+str(i))
ten2.sort()
if l[idx:idx+6] == ten2:
ten = []
for i in range(3):
for j in range(3):
ten.append(k[:-2]+str(min(i,j))+str(max(i,j)))
tensors[k[:-2]] = ten
idx += 5
continue
# check for vector
vec = []
for i in range(3):
vec.append(k[:-1] + str(i))
if l[idx:idx+3] == vec:
vectors[k[:-1]] = vec
idx += 2
continue
scalars.append(k)
return scalars, vectors, tensors
def get_output_details(path):
solvers = {}
if not os.path.isdir(path):
path = os.path.dirname(path)
files = os.listdir(path)
files.sort()
pat = re.compile(r'(?P<solver>.+)_(?P<rank>\d+)_(?P<entity>.+)_(?P<time>[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?).npz')
matches = [(f,pat.match(f)) for f in files]
files = []
for filename,match in matches:
if match is None:
continue
files.append(filename)
groups = match.groupdict()
solvername = groups['solver']
solver = solvers.get(solvername)
if solver is None:
solver = [set([]),set([]),set([])]
solvers[solvername] = solver
solver[0].add(groups['rank'])
solver[1].add(groups['entity'])
solver[2].add(groups['time'])
# {solver:(entities,procs,times)}
return solvers
def pysph_to_vtk(path, merge_procs=False, skip_existing=True, binary=True):
''' convert pysph output .npz files into vtk format
Parameters
----------
path : str
directory where .npz files are located
merge_procs : bool
whether to merge the data from different procs into a single file
(not yet implemented)
skip_existing : bool
skip files where corresponding vtk already exist
this is useful if you've converted vtk files while a solver is running
only want to convert the newly added files
binary : bool
whether to use binary format in vtk file
The output vtk files are stored in a directory `solver_name` _vtk within
the `path` directory
'''
if binary:
data_mode = 'binary'
else:
data_mode = 'ascii'
if merge_procs is True:
# FIXME: implement
raise NotImplementedError('merge_procs=True not implemented yet')
solvers = get_output_details(path)
for solver, (procs, entities, times) in solvers.items():
print('converting solver:', solver)
dir = os.path.join(path,solver+'_vtk')
if not os.path.exists(dir):
os.mkdir(dir)
procs = sorted(procs)
entities = sorted(entities)
times = sorted(times, key=float)
times_file = open(os.path.join(dir,'times'), 'w')
for entity in entities:
print(' entity:', entity)
for proc in procs:
print(' proc:', proc)
print(' timesteps:', len(times))
f = '%s_%s_%s_'%(solver,proc,entity)
of = os.path.join(dir,f)
for i, time in enumerate(times):
print('\r',i,)
if skip_existing and os.path.exists(f+str(i)):
continue
d = load(os.path.join(path, f+time+'.npz'))
arrs = {}
for nam,val in d.items():
if val.ndim > 0:
arrs[nam] = val
d.close()
scalars, vectors, tensors = detect_vectors_tensors(arrs)
vectors['V'] = ['u','v','w']
z = zeros_like(arrs['x'])
if 'v' not in arrs:
arrs['v'] = z
if 'w' not in arrs:
arrs['w'] = z
write_vtk(arrs, of+str(i),
scalars=scalars, vectors=vectors, tensors=tensors,
data_mode=data_mode)
times_file.write('%d\t%s\n'%(i,time))
times_file.close()
def extract_text(path, particle_idx, props=['x','y','u','v','p','rho','sigma00','sigma01','sigma11'], ent=None, solvers=None):
if solvers:
raise NotImplementedError
else:
solvers = get_output_details(path)
for solver, (procs, entities, times) in solvers.items():
print('converting solver:', solver)
dir = os.path.join(path,solver+'_vtk')
if not os.path.exists(dir):
os.mkdir(dir)
procs = sorted(procs)
entities = sorted(entities)
times = sorted(times, key=float)
times_file = open(os.path.join(dir,'times'), 'w')
e = ent
if ent is None:
e = entities
for entity in entities:
if entity not in e:
continue
print(' entity:', entity)
for proc in procs:
print(' proc:', proc)
print(' timesteps:', len(times))
f = '%s_%s_%s_'%(solver,proc,entity)
of = os.path.join(dir,f)
files = [open(os.path.join(path,f+'%d.dat'%particle_id), 'w') for particle_id in particle_idx]
print(files)
for file in files:
file.write('i\tt\t'+'\t'.join(props))
for i, time in enumerate(times):
print('\r',i,)
d = load(os.path.join(path, f+time+'.npz'))
s = '\n%d\t%s'%(i,time)
for j,file in enumerate(files):
file.write(s)
for prop in props:
file.write('\t')
file.write(str(d[prop][particle_idx[j]]))
d.close()
for file in files:
file.close()
def test():
l = ['x'+str(i) for i in range(3)]
l.append('a0')
l.append('a1')
for i in range(3):
for j in range(3):
if i == j:
l.append('XX%d'%i)
if i <= j:
l.append('S%d%d'%(i,j))
l.append('T%d%d'%(i,j))
scalars, vectors, tensors = detect_vectors_tensors(l)
assert set(scalars) == set(['a0','a1'])
assert set(vectors) == set(['x','XX'])
assert set(tensors) == set(['S','T'])
if __name__ == '__main__':
import sys
pysph_to_vtk(path=sys.argv[1])
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