DAMASK_EICMD/processing/pre/seeds_check.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,vtk
import numpy as np
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
2014-11-18 21:01:39 +05:30
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
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),
}
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [seedsfile[s]]', description = """
Produce VTK point mesh from seeds file
""", version = scriptID)
parser.add_option('-s', '--size', dest='size', type='float', nargs = 3, metavar='float float float',\
help='x,y,z size of hexahedral box [1.0 along largest grid point number]')
parser.set_defaults(size = [0.0,0.0,0.0])
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []:
filenames = ['STDIN']
for name in filenames:
if name == 'STDIN':
file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
else:
if not os.path.exists(name): continue
file = {'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr}
file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
table = damask.ASCIItable(file['input'],file['output'],buffered = False)
table.head_read()
if np.all(table.label_index(['1_coords','2_coords','3_coords']) != -1):
labels = ['1_coords','2_coords','3_coords']
elif np.all(table.label_index(['x','y','z']) != -1):
labels = ['x','y','z']
else:
file['croak'].write('no coordinate data (1/2/3_coords | x/y/z) found ...')
continue
hasGrains = table.label_index('microstructure') != -1
labels += ['microstructure'] if hasGrains else []
table.data_readArray(labels) # read ASCIItable columns
coords = table.data[:,:3] # assign coordinates
grain = table.data[:,3].astype('i') if hasGrains else 1+np.arange(len(coords),dtype='i') # assign grains
grainIDs = np.unique(grain).astype('i') # find all grainIDs present
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': np.zeros(3,'i'),
'size': np.array(options.size),
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
for header in table.info:
headitems = map(str.lower,header.split())
if len(headitems) == 0: continue
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])
if info['microstructures'] != len(grainIDs):
file['croak'].write('grain data not matching grain count (%i)...\n'%(len(grainIDs)))
info['microstructures'] = len(grainIDs)
if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
for i in xrange(3):
if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid'])
file['croak'].write('rescaling size %s...\n'%{0:'x',1:'y',2:'z'}[i])
#--- generate grid --------------------------------------------------------------------------------
grid = vtk.vtkUnstructuredGrid()
pts = vtk.vtkPoints()
#--- process microstructure information --------------------------------------------------------------
IDs = vtk.vtkIntArray()
IDs.SetNumberOfComponents(1)
IDs.SetName("GrainID")
for i,item in enumerate(coords):
pid = pts.InsertNextPoint(item[0:3])
pointIds = vtk.vtkIdList()
pointIds.InsertId(0, pid)
grid.InsertNextCell(1, pointIds)
IDs.InsertNextValue(grain[i])
grid.SetPoints(pts)
grid.GetCellData().AddArray(IDs)
#--- write data -----------------------------------------------------------------------------------
if file['name'] == 'STDIN':
writer = vtk.vtkUnstructuredGridWriter()
writer.WriteToOutputStringOn()
writer.SetFileTypeToASCII()
writer.SetHeader('# powered by '+scriptID)
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(grid)
else:
writer.SetInputData(grid)
writer.Write()
sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
else:
table.close(dismiss=True)
(head,tail) = os.path.split(file['name'])
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(head,'seeds_'+os.path.splitext(tail)[0]
+'.'+writer.GetDefaultFileExtension()))
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(grid)
else:
writer.SetInputData(grid)
writer.Write()