new scripts for:
-generating vtk point cloud from x,y,z ASCIItable data -adding scalar values and color tuples from ASCIItable to vtk point cloud -permuting data in ASCIItable columns (used to shuffle ordered grain indices)
This commit is contained in:
Philip Eisenlohr
parent
a45c7dbb62
commit
b63d2eafe8
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#!/usr/bin/env python
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import os,re,sys,math,numpy,string
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import damask
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from collections import defaultdict
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from optparse import OptionParser, Option
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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# -----------------------------
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class extendableOption(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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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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Permute all values in given column(s).
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-l','--label', dest='label', action='extend', type='string',
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help='heading(s) of column to permute',
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metavar='<label>')
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parser.set_defaults(label = [])
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(options,filenames) = parser.parse_args()
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if len(options.label)== 0:
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parser.error('no data column specified...')
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datainfo = { # list of requested labels per datatype
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'scalar': {'len':1,
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'label':[]},
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}
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if options.label != None: datainfo['scalar']['label'] += options.label
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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', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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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, 'input':open(name), 'output':open(name+'_tmp','w'), '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['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptName,'\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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# --------------- figure out columns to process
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active = defaultdict(list)
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column = defaultdict(dict)
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for datatype,info in datainfo.items():
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for label in info['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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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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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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permutation = {}
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theColumns = table.data_asArray([column['scalar'][label] for label in active['scalar']])
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print 'shape:',theColumns.shape
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for i,label in enumerate(active['scalar']):
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unique = list(set(theColumns[:,i]))
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permutated = numpy.random.permutation(unique)
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permutation[label] = dict(zip(unique,permutated))
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table.data_rewind()
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over vector,tensor
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for label in labels: # loop over all requested stiffnesses
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for c in xrange(column[datatype][label],
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column[datatype][label]+datainfo[datatype]['len']):
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table.data[c] = permutation[label][float(table.data[c])] # apply permutation
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table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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table.output_flush() # just in case of buffered ASCII table
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if file['name'] != 'STDIN':
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file['input'].close() # close input ASCII table
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file['output'].close() # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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@ -0,0 +1,155 @@
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#!/usr/bin/env python
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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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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).
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""" + string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-v', '--vtk', dest='vtk', type='string', \
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help = 'VTK file name')
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parser.add_option('-s', '--scalar', dest='scalar', action='extend', \
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help = 'scalar values')
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parser.add_option('-c', '--color', dest='color', action='extend', \
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help = 'RGB color tuples')
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parser.set_defaults(scalar = [])
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parser.set_defaults(color = [])
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(options, filenames) = parser.parse_args()
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datainfo = { # list of requested labels per datatype
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'scalar': {'len':1,
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'label':[]},
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'color': {'len':3,
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'label':[]},
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}
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if not os.path.exists(options.vtk):
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options.error('VTK file does not exist'); sys.exit()
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reader = vtk.vtkXMLPolyDataReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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Npoints = reader.GetNumberOfPoints()
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Ncells = reader.GetNumberOfCells()
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Nvertices = reader.GetNumberOfVerts()
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Polydata = reader.GetOutput()
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if Npoints != Ncells or Npoints != Nvertices:
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options.error('Number of points, cells, and vertices in VTK differ from each other'); sys.exit()
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if options.scalar != None: datainfo['scalar']['label'] += options.scalar
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if options.color != None: datainfo['color']['label'] += options.color
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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', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
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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, 'input':open(name), 'output':sys.stderr, '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['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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# --------------- figure out columns to process
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active = {}
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column = {}
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array = {}
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for datatype,info in datainfo.items():
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for label in info['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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if datatype not in array: array[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 datatype == 'scalar':
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array[datatype][label] = vtk.vtkDoubleArray()
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array[datatype][label].SetNumberOfComponents(1)
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array[datatype][label].SetName(label)
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elif datatype == 'color':
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array[datatype][label] = vtk.vtkUnsignedCharArray()
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array[datatype][label].SetNumberOfComponents(3)
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array[datatype][label].SetName(label)
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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# ------------------------------------------ process data ---------------------------------------
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while table.data_read(): # read next data line of ASCII table
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for datatype,labels in active.items(): # loop over scalar,color
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for label in labels: # loop over all requested items
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theData = table.data[column[datatype][label]:\
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column[datatype][label]+datainfo[datatype]['len']] # read strings
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if datatype == 'color':
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theData = map(lambda x: int(255.*float(x)),theData)
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array[datatype][label].InsertNextTuple3(theData[0],theData[1],theData[2],)
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elif datatype == 'scalar':
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array[datatype][label].InsertNextValue(float(theData[0]))
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file['input'].close() # close input ASCII table
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# ------------------------------------------ add data ---------------------------------------
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for datatype,labels in active.items(): # loop over scalar,color
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if datatype == 'color':
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Polydata.GetPointData().SetScalars(array[datatype][labels[0]])
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Polydata.GetCellData().SetScalars(array[datatype][labels[0]])
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for label in labels: # loop over all requested items
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Polydata.GetPointData().AddArray(array[datatype][label])
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Polydata.GetCellData().AddArray(array[datatype][label])
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Polydata.Modified()
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if vtk.VTK_MAJOR_VERSION <= 5:
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Polydata.Update()
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLPolyDataWriter()
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtp')
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if vtk.VTK_MAJOR_VERSION <= 5:
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writer.SetInput(Polydata)
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else:
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writer.SetInputData(Polydata)
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writer.Write()
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@ -0,0 +1,116 @@
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#!/usr/bin/env python
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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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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Add grain index based on similitude of crystal lattice orientation.
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""" + string.replace(scriptID,'\n','\\n')
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)
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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.set_defaults(pos = 'pos')
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(options, filenames) = parser.parse_args()
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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]+'.vtp', '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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# --------------- 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,info in datainfo.items():
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for label in info['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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Polydata = vtk.vtkPolyData()
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Points = vtk.vtkPoints()
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Vertices = vtk.vtkCellArray()
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pos = table.data_asArray(range(column['vector'][options.pos],\
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column['vector'][options.pos]+datainfo['vector']['len']))
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print range(column['vector'][options.pos],\
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column['vector'][options.pos]+datainfo['vector']['len']),len(pos),pos[0]
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for p in pos:
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id = Points.InsertNextPoint(p)
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Vertices.InsertNextCell(1)
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Vertices.InsertCellPoint(id)
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Polydata.SetPoints(Points)
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Polydata.SetVerts(Vertices)
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Polydata.Modified()
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if vtk.VTK_MAJOR_VERSION <= 5:
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Polydata.Update()
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# ------------------------------------------ output result ---------------------------------------
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writer = vtk.vtkXMLPolyDataWriter()
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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(Polydata)
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else:
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writer.SetInputData(Polydata)
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writer.Write()
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file['input'].close() # close input ASCII table
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@ -36,6 +36,7 @@ bin_link = { \
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],
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'post' : [
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'3Dvisualize.py',
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'permuteData.py'
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'addCalculation.py',
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'addCauchy.py',
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'addCompatibilityMismatch.py',
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@ -71,6 +72,8 @@ bin_link = { \
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'tagLabel.py',
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'vtk2ang.py',
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'vtk_addData.py',
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'vtk_pointcloud.py',
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'vtk_addPointcloudData.py'
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],
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}
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