now works with recent changes of ASCIItable and with STDIN to STDOUT.
This commit is contained in:
Philip Eisenlohr
parent
afc88c7029
commit
c215139ce1
|
|
@ -9,21 +9,6 @@ import damask
|
|||
scriptID = '$Id$'
|
||||
scriptName = os.path.splitext(scriptID.split()[1])[0]
|
||||
|
||||
synonyms = {
|
||||
'grid': ['resolution'],
|
||||
'size': ['dimension'],
|
||||
}
|
||||
identifiers = {
|
||||
'grid': ['a','b','c'],
|
||||
'size': ['x','y','z'],
|
||||
'origin': ['x','y','z'],
|
||||
}
|
||||
mappings = {
|
||||
'grid': lambda x: int(x),
|
||||
'size': lambda x: float(x),
|
||||
'origin': lambda x: float(x),
|
||||
'microstructures': lambda x: int(x),
|
||||
}
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
|
|
@ -34,138 +19,96 @@ Create hexahedral voxels around points in an ASCIItable.
|
|||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-p', '--positions', dest='pos', type='string', metavar = 'string',
|
||||
parser.add_option('-p', '--positions',
|
||||
dest = 'position',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'coordinate label [%default]')
|
||||
parser.add_option('-s', '--size', dest='size', type='float', nargs=3, metavar = 'float float float',
|
||||
parser.add_option('-s', '--size',
|
||||
dest = 'size',
|
||||
type = 'float', nargs = 3, metavar = 'float float float',
|
||||
help = 'x,y,z size of voxel')
|
||||
parser.add_option('-o', '--origin', dest='origin', type='float', nargs=3, metavar = 'float float float',
|
||||
parser.add_option('-o', '--origin',
|
||||
dest = 'origin',
|
||||
type = 'float', nargs = 3, metavar = 'float float float',
|
||||
help = 'x,y,z origin of coordinate system')
|
||||
parser.add_option('-g', '--geom', dest='geom', action='store_true',
|
||||
help = 'derive geometry from geom-file header information')
|
||||
parser.set_defaults(pos = 'pos')
|
||||
parser.set_defaults(origin = (0.0,0.0,0.0))
|
||||
parser.set_defaults(geom = False)
|
||||
parser.add_option('-g', '--geom',
|
||||
dest = 'geom', action='store_true',
|
||||
help = 'derive geometry from geom-file header information [%default]')
|
||||
parser.set_defaults(position = 'pos',
|
||||
origin = (0.0,0.0,0.0),
|
||||
geom = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
if options.size == None and not options.geom:
|
||||
parser.error('no size sprecified.')
|
||||
parser.error('no size specified.')
|
||||
|
||||
datainfo = { # list of requested labels per datatype
|
||||
'vector': {'len':3,
|
||||
'label':[]},
|
||||
}
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if options.pos != None: datainfo['vector']['label'] += [options.pos]
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
# ------------------------------------------ setup file handles ---------------------------------------
|
||||
|
||||
files = []
|
||||
for name in filenames:
|
||||
if os.path.exists(name):
|
||||
files.append({'name':name, 'input':open(name), 'output':os.path.splitext(name)[0]+'.vtu', 'croak':sys.stderr})
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, readonly = True)
|
||||
except: continue
|
||||
table.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
|
||||
|
||||
#--- loop over input files ------------------------------------------------------------------------
|
||||
for file in files:
|
||||
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
|
||||
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
|
||||
|
||||
table = damask.ASCIItable(file['input'],file['croak'],False) # make unbuffered ASCII_table
|
||||
table.head_read() # read ASCII header info
|
||||
#--- interpret header ----------------------------------------------------------------------------
|
||||
info = {
|
||||
'grid': np.zeros(3,'i'),
|
||||
'size': np.zeros(3,'d'),
|
||||
'origin': np.zeros(3,'d'),
|
||||
'homogenization': 0,
|
||||
'microstructures': 0,
|
||||
}
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
|
||||
if options.geom:
|
||||
for header in table.info:
|
||||
headitems = map(str.lower,header.split())
|
||||
if len(headitems) == 0: continue
|
||||
for synonym,alternatives in synonyms.iteritems():
|
||||
if headitems[0] in alternatives: headitems[0] = synonym
|
||||
if headitems[0] in mappings.keys():
|
||||
if headitems[0] in identifiers.keys():
|
||||
for i in xrange(len(identifiers[headitems[0]])):
|
||||
info[headitems[0]][i] = \
|
||||
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
|
||||
else:
|
||||
info[headitems[0]] = mappings[headitems[0]](headitems[1])
|
||||
|
||||
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
|
||||
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
|
||||
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
|
||||
'homogenization: %i\n'%info['homogenization'] + \
|
||||
'microstructures: %i\n'%info['microstructures'])
|
||||
|
||||
if np.any(info['grid'] < 1):
|
||||
file['croak'].write('invalid grid a b c.\n')
|
||||
continue
|
||||
if np.any(info['size'] <= 0.0):
|
||||
file['croak'].write('invalid size x y z.\n')
|
||||
continue
|
||||
|
||||
info,extra_header = table.head_getGeom()
|
||||
|
||||
table.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
else:
|
||||
info = {}
|
||||
info['size'] = np.ones(3)
|
||||
info['grid'] = info['size'] / options.size
|
||||
info['origin'] = options.origin
|
||||
|
||||
# --------------- figure out columns to process
|
||||
active = {}
|
||||
column = {}
|
||||
head = []
|
||||
|
||||
for datatype,infos in datainfo.items():
|
||||
for label in infos['label']:
|
||||
foundIt = False
|
||||
for key in ['1_'+label,label]:
|
||||
if key in table.labels:
|
||||
foundIt = True
|
||||
if datatype not in active: active[datatype] = []
|
||||
if datatype not in column: column[datatype] = {}
|
||||
active[datatype].append(label)
|
||||
column[datatype][label] = table.labels.index(key) # remember columns of requested data
|
||||
if not foundIt:
|
||||
file['croak'].write('column %s not found...\n'%label)
|
||||
break
|
||||
|
||||
|
||||
errors = []
|
||||
if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
|
||||
table.label_dimension(options.position)))
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
|
||||
if errors != []:
|
||||
table.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
hexPoints = np.array([[-1,-1,-1],
|
||||
[ 1,-1,-1],
|
||||
[ 1, 1,-1],
|
||||
[-1, 1,-1],
|
||||
[-1,-1, 1],
|
||||
[ 1,-1, 1],
|
||||
[ 1, 1, 1],
|
||||
[-1, 1, 1],
|
||||
])
|
||||
Points = vtk.vtkPoints()
|
||||
Hex = vtk.vtkHexahedron()
|
||||
uGrid = vtk.vtkUnstructuredGrid()
|
||||
|
||||
table.data_readArray(range(column['vector'][options.pos],\
|
||||
column['vector'][options.pos]+datainfo['vector']['len']))
|
||||
|
||||
table.data_readArray(options.position)
|
||||
table.data[:,0:3] *= info['size']
|
||||
table.data[:,0:3] += info['origin']
|
||||
|
||||
# minD = np.array(options.size,dtype=float)
|
||||
# for i in xrange(3):
|
||||
# coords = np.unique(table.data[:,i])
|
||||
# minD[i] = coords[-1]-coords[0]
|
||||
# for j in xrange(len(coords)-1):
|
||||
# d = coords[j+1]-coords[j]
|
||||
# if d < minD[i]:
|
||||
# minD[i] = d
|
||||
hexPoints = np.array([[-1,-1,-1],
|
||||
[ 1,-1,-1],
|
||||
[ 1, 1,-1],
|
||||
[-1, 1,-1],
|
||||
[-1,-1, 1],
|
||||
[ 1,-1, 1],
|
||||
[ 1, 1, 1],
|
||||
[-1, 1, 1],
|
||||
])
|
||||
|
||||
halfDelta = 0.5*info['size']/info['grid']
|
||||
|
||||
Points = vtk.vtkPoints()
|
||||
Hex = vtk.vtkHexahedron()
|
||||
uGrid = vtk.vtkUnstructuredGrid()
|
||||
|
||||
for p in table.data:
|
||||
for i,h in enumerate(hexPoints):
|
||||
id = Points.InsertNextPoint(p+h*info['size']/info['grid']/2.)
|
||||
id = Points.InsertNextPoint(p+h*halfDelta)
|
||||
Hex.GetPointIds().SetId(i,id)
|
||||
|
||||
uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
|
||||
|
|
@ -174,14 +117,26 @@ for file in files:
|
|||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(file['output'])
|
||||
if vtk.VTK_MAJOR_VERSION <= 5:
|
||||
writer.SetInput(uGrid)
|
||||
else:
|
||||
writer.SetInputData(uGrid)
|
||||
writer.Write()
|
||||
if name:
|
||||
(dir,filename) = os.path.split(name)
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.join(dir,os.path.splitext(filename)[0]+'_{}'.format(options.position) \
|
||||
+'.'+writer.GetDefaultFileExtension()))
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
|
||||
else: writer.SetInputData(uGrid)
|
||||
writer.Write()
|
||||
|
||||
else:
|
||||
writer = vtk.vtkUnstructuredGridWriter()
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetFileTypeToASCII()
|
||||
writer.SetHeader('# powered by '+scriptID)
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
|
||||
else: writer.SetInputData(uGrid)
|
||||
writer.Write()
|
||||
sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
|
||||
|
||||
table.close() # close input ASCII table
|
||||
|
||||
table.input_close() # close input ASCII table
|
||||
|
|
|
|||
Loading…
Reference in New Issue