DAMASK_EICMD/processing/pre/geom_fromTIFF.py

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#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,math,string
import numpy as np
from optparse import OptionParser
from PIL import Image
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description and from stacked 8bit tiff images. No orientation info is used.
Microstructure index is based on gray scale value (1...256).
""", version = scriptID)
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
help='homogenization index for <microstructure> configuration [%default]')
parser.set_defaults(homogenization = 1)
(options,filenames) = parser.parse_args()
#--- setup file handles ---------------------------------------------------------------------------
files = []
for name in filenames:
if os.path.exists(name):
files.append({'name':name,
'input':open(name),
'output':open(name+'_tmp','w'),
'croak':sys.stdout,
})
#--- loop over input files ------------------------------------------------------------------------
for file in files:
file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
info = {
'grid': np.ones (3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization,
}
ImageFile=Image.open(file['input'])
i=0
a=[]
while True:
try:
ImageFile.seek(i)
a.append(np.array(ImageFile.transpose(Image.FLIP_TOP_BOTTOM)))
i+=1
except EOFError:
break
# http://docs.scipy.org/doc/scipy/reference/ndimage.html
# http://scipy-lectures.github.io/advanced/image_processing/
imarray=np.asarray(a)
info['grid'] = np.array(imarray.shape)[::-1]
info['size'] = np.array(imarray.shape,'d')[::-1]
info['microstructures']=len(np.unique(imarray))
#--- report ---------------------------------------------------------------------------------------
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) +
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) +
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
'homogenization: %i\n'%info['homogenization'] +
'microstructures: %i\n\n'%info['microstructures'])
if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
#--- write data -----------------------------------------------------------------------------------
header = [' '.join([scriptID] + sys.argv[1:]),
"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2]),
"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2]),
"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2]),
"microstructures\t%i"%info['microstructures'],
"homogenization\t%i"%info['homogenization'],
]
file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n')
np.savetxt(file['output'],imarray.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]),fmt='%03d')
#--- output finalization --------------------------------------------------------------------------
if file['name'] != 'STDIN':
file['output'].close()
os.rename(file['name']+'_tmp', os.path.splitext(file['name'])[0] +'.geom')