DAMASK_EICMD/processing/pre/geom_fromImage.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,ImageOps
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Generate geometry description from (multilayer) images.
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 [%default]')
parser.set_defaults(homogenization = 1,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
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table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.geom' if name else name,
buffered = False, labeled = False)
except: continue
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name else ''))
# --- read image ------------------------------------------------------------------------------------
img = Image.open(name).convert(mode = 'L') # open and convert to grayscale 8bit
slice = 0
while True:
try:
img.seek(slice) # advance to slice
layer = np.expand_dims(1+np.array(img,dtype = 'uint16'),axis = 0) # read image layer
microstructure = layer if slice == 0 else np.vstack((microstructure,layer)) # add to microstructure data
slice += 1 # advance to next slice
except EOFError:
break
# http://docs.scipy.org/doc/scipy/reference/ndimage.html
# http://scipy-lectures.github.io/advanced/image_processing/
info = {
'grid': np.array(microstructure.shape,'i')[::-1],
'size': np.array(microstructure.shape,'d')[::-1],
'origin': np.zeros(3,'d'),
'microstructures': len(np.unique(microstructure)),
'homogenization': options.homogenization,
}
# --- report ---------------------------------------------------------------------------------------
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'],
])
errors = []
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
if errors != []:
table.croak(errors)
table.close(dismiss = True)
continue
# --- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
])
table.labels_clear()
table.head_write()
table.output_flush()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((info['grid'][1]*info['grid'][2],info['grid'][0]),order='C')
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table