100 lines
4.0 KiB
Python
Executable File
100 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math,string
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import numpy as np
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from optparse import OptionParser
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from PIL import Image
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import damask
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Generate geometry description and from stacked 8bit tiff images. No orientation info is used.
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Microstructure index is based on gray scale value (1...256).
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""", version = scriptID)
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parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
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help='homogenization index for <microstructure> configuration [%default]')
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parser.set_defaults(homogenization = 1)
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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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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':open(name+'_tmp','w'),
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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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file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n')
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info = {
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'grid': np.ones (3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': options.homogenization,
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}
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ImageFile=Image.open(file['input'])
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i=0
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a=[]
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while True:
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try:
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ImageFile.seek(i)
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a.append(np.array(ImageFile.transpose(Image.FLIP_TOP_BOTTOM)))
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i+=1
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except EOFError:
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break
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# http://docs.scipy.org/doc/scipy/reference/ndimage.html
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# http://scipy-lectures.github.io/advanced/image_processing/
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imarray=np.asarray(a)
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info['grid'] = np.array(imarray.shape)[::-1]
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info['size'] = np.array(imarray.shape,'d')[::-1]
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info['microstructures']=len(np.unique(imarray))
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#--- report ---------------------------------------------------------------------------------------
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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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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) +
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'homogenization: %i\n'%info['homogenization'] +
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'microstructures: %i\n\n'%info['microstructures'])
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if np.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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if np.any(info['size'] <= 0.0):
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file['croak'].write('invalid size x y z.\n')
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continue
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#--- write data -----------------------------------------------------------------------------------
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header = [' '.join([scriptID] + sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2]),
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"size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2]),
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"origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2]),
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"microstructures\t%i"%info['microstructures'],
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"homogenization\t%i"%info['homogenization'],
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]
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file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n')
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np.savetxt(file['output'],imarray.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]),
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fmt='%0'+str(1+int(math.log10(np.amax(imarray))))+'d'
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close()
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os.rename(file['name']+'_tmp', os.path.splitext(file['name'])[0] +'.geom')
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