added script to produce VTK point cloud from seed file coordinates
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Philip Eisenlohr
parent
03633f7742
commit
0337b4f319
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@ -0,0 +1,169 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,numpy,vtk
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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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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parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
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Produce VTK point mesh from seed file
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-g', '--grid', dest='grid', type='int', nargs = 3, \
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help='a,b,c grid of hexahedral box [from seeds file]')
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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 hexahedral box [1.0 along largest grid point number]')
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parser.set_defaults(grid = [0,0,0])
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parser.set_defaults(size = [0.0,0.0,0.0])
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(options, filenames) = parser.parse_args()
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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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,
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'input':open(name),
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'output':sys.stdout,
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'croak':sys.stdout,
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})
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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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theTable = damask.ASCIItable(file['input'],file['output'])
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theTable.head_read()
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coords = theTable.data_asArray(['x','y','z'])
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if theTable.labels_index('microstructure') != -1:
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grain = theTable.data_asArray(['microstructure'])
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grainIDs = numpy.unique(grain).astype('i')
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else:
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grain = 1+numpy.arange(len(coords))
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grainIDs = grain
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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}
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for header in theTable.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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if 0 not in options.grid: # user-specified grid
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info['grid'] = numpy.array(options.grid)
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if numpy.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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for i in xrange(3):
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if info['size'][i] <= 0.0: # any invalid size?
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info['size'][i] = float(info['grid'][i])/max(info['grid'])
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file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
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#--- generate grid --------------------------------------------------------------------------------
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grid = vtk.vtkUnstructuredGrid()
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pts = vtk.vtkPoints()
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#--- process microstructure information --------------------------------------------------------------
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IDs = vtk.vtkIntArray()
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IDs.SetNumberOfComponents(1)
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IDs.SetName("GrainID")
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for coord,ID in zip(coords,grainIDs):
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pid = pts.InsertNextPoint(coord)
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pointIds = vtk.vtkIdList()
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pointIds.InsertId(0, pid)
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grid.InsertNextCell(1, pointIds)
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IDs.InsertNextValue(ID)
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grid.SetPoints(pts)
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grid.GetCellData().AddArray(IDs)
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#--- write data -----------------------------------------------------------------------------------
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if file['name'] == 'STDIN':
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outWriter = vtk.vtkUnstructuredGridWriter()
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outWriter.WriteToOutputStringOn()
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outWriter.SetFileTypeToASCII()
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outWriter.SetHeader('# powered by '+scriptID)
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outWriter.SetInputData(grid)
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outWriter.Write()
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sys.stdout.write(outWriter.GetOutputString()[0:outWriter.GetOutputStringLength()])
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else:
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(head,tail) = os.path.split(file['name'])
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outWriter = vtk.vtkXMLUnstructuredGridWriter()
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outWriter.SetDataModeToBinary()
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outWriter.SetCompressorTypeToZLib()
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outWriter.SetFileName(os.path.join(head,'seeds_'+os.path.splitext(tail)[0]
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+'.'+outWriter.GetDefaultFileExtension()))
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outWriter.SetInputData(grid)
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outWriter.Write()
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@ -17,6 +17,7 @@ bin_link = { \
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'OIMang_hex2cub.py',
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'patchFromReconstructedBoundaries.py',
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'randomSeeding.py',
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'seed_check.py',
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'geom_fromAng.py',
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'geom_fromVPSC.py',
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'geom_fromEuclideanDistance.py',
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