189 lines
6.7 KiB
Python
Executable File
189 lines
6.7 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,vtk
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import numpy as np
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from optparse import OptionParser
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import damask
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scriptID = '$Id$'
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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}
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'microstructures': lambda x: int(x),
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}
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Create hexahedral voxels around points in an ASCIItable.
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""", version = scriptID)
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parser.add_option('-p', '--positions', dest='pos', type='string',
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help = 'coordinate label')
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parser.add_option('-s', '--size', dest='size', type='float', nargs=3,
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help = 'x,y,z size of voxel')
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parser.add_option('-o', '--origin', dest='origin', type='float', nargs=3,
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help = 'x,y,z origin of coordinate system')
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parser.add_option('-g', '--geom', dest='geom', action='store_true',
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help = 'derive geometry from geom-file header information')
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parser.set_defaults(pos = 'pos')
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parser.set_defaults(origin = [0.0,0.0,0.0])
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parser.set_defaults(geom = False)
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(options, filenames) = parser.parse_args()
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if options.size == None and not options.geom:
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parser.error('no size sprecified.')
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datainfo = { # list of requested labels per datatype
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'vector': {'len':3,
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'label':[]},
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}
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if options.pos != None: datainfo['vector']['label'] += [options.pos]
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name), 'output':os.path.splitext(name)[0]+'.vtu', 'croak':sys.stderr})
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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table = damask.ASCIItable(file['input'],file['croak'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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if options.geom:
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for header in table.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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if np.any(info['grid'] < 1):
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file['croak'].write('invalid grid a b c.\n')
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continue
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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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else:
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info['size'] = np.ones(3)
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info['grid'] = info['size'] / options.size
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info['origin'] = options.origin
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# --------------- figure out columns to process
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active = {}
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column = {}
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head = []
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for datatype,infos in datainfo.items():
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for label in infos['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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if datatype not in active: active[datatype] = []
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if datatype not in column: column[datatype] = {}
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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# ------------------------------------------ process data ---------------------------------------
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hexPoints = np.array([[-1,-1,-1],
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[ 1,-1,-1],
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[ 1, 1,-1],
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[-1, 1,-1],
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[-1,-1, 1],
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[ 1,-1, 1],
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[ 1, 1, 1],
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[-1, 1, 1],
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])
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Points = vtk.vtkPoints()
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Hex = vtk.vtkHexahedron()
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uGrid = vtk.vtkUnstructuredGrid()
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table.data_readArray(range(column['vector'][options.pos],\
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column['vector'][options.pos]+datainfo['vector']['len']))
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table.data[:,0:3] *= info['size']
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table.data[:,0:3] += info['origin']
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# minD = np.array(options.size,dtype=float)
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# for i in xrange(3):
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# coords = np.unique(table.data[:,i])
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# minD[i] = coords[-1]-coords[0]
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# for j in xrange(len(coords)-1):
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# d = coords[j+1]-coords[j]
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# if d < minD[i]:
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# minD[i] = d
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for p in table.data:
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for i,h in enumerate(hexPoints):
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id = Points.InsertNextPoint(p+h*info['size']/info['grid']/2.)
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Hex.GetPointIds().SetId(i,id)
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uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
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uGrid.SetPoints(Points)
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLUnstructuredGridWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(file['output'])
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(uGrid)
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else:
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writer.SetInputData(uGrid)
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writer.Write()
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table.input_close() # close input ASCII table
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