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
#--------------------------------------------------------------------------------------------------
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.add_option('-p','--position',
dest = 'position',
type = 'string', metavar = 'string',
help = 'column label for coordinates [%default]')
parser.set_defaults(size = [0.0,0.0,0.0],
position = 'pos',
)
(options, filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = ['STDIN']
for name in filenames:
if not (name == 'STDIN' or os.path.exists(name)): continue
table = damask.ASCIItable(name = name, outname = None,
buffered = False, readonly = True)
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name != 'STDIN' else ''))
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
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'],
])
remarks = []
errors = []
if np.any(info['grid'] < 1): remarks.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0) \
and np.all(info['grid'] < 1): errors.append('invalid size x y z.')
else:
for i in xrange(3):
if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
remarks.append('rescaling size {} to {}...'.format({0:'x',1:'y',2:'z'}[i],info['size'][i]))
if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
table.label_dimension(options.position)))
if remarks != []: table.croak(remarks)
if errors != []:
table.croak(errors)
table.close(dismiss=True)
continue
labels = ['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in xrange(3)]
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
# --- 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):
IDs.InsertNextValue(grain[i])
pid = pts.InsertNextPoint(item[0:3])
pointIds = vtk.vtkIdList()
pointIds.InsertId(0, pid)
grid.InsertNextCell(1, pointIds)
grid.SetPoints(pts)
grid.GetCellData().AddArray(IDs)
# --- write data -----------------------------------------------------------------------------------
if 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:
(dir,filename) = os.path.split(name)
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
writer.SetFileName(os.path.join(dir,'seeds_'+os.path.splitext(filename)[0]
+'.'+writer.GetDefaultFileExtension()))
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
else: writer.SetInputData(grid)
writer.Write()
table.close()