195 lines
8.7 KiB
Python
Executable File
195 lines
8.7 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,string
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import numpy as np
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from optparse import OptionParser
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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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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'grid': lambda x: int(x),
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'size': lambda x: float(x),
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'origin': lambda x: float(x),
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'homogenization': lambda x: int(x),
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Changes the (three-dimensional) canvas of a spectral geometry description.
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""", version = scriptID)
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parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar=' '.join(['string']*3),
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, metavar=' '.join(['int']*3),
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help='a,b,c offset from old to new origin of grid %default')
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parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int',
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help='(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(offset = (0,0,0))
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parser.set_defaults(fill = 0)
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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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if filenames == []:
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files.append({'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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'croak':sys.stderr,
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})
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else:
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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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table = damask.ASCIItable(file['input'],file['output'],labels = False)
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table.head_read()
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#--- interpret header ----------------------------------------------------------------------------
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info = {
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'grid': np.zeros(3,'i'),
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'size': np.zeros(3,'d'),
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'origin': np.zeros(3,'d'),
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'homogenization': 0,
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'microstructures': 0,
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}
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newInfo = {
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'grid': np.zeros(3,'i'),
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'origin': np.zeros(3,'d'),
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'microstructures': 0,
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}
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extra_header = []
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for header in table.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue # skip blank lines
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if headitems[0] in mappings.keys():
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = \
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mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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else:
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extra_header.append(header)
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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'%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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#--- read data ------------------------------------------------------------------------------------
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microstructure = np.zeros(info['grid'].prod(),'i') # initialize as flat array
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i = 0
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while table.data_read():
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items = table.data
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if len(items) > 2:
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if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
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elif items[1].lower() == 'to': items = xrange(int(items[0]),1+int(items[2]))
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else: items = map(int,items)
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else: items = map(int,items)
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s = len(items)
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microstructure[i:i+s] = items
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i += s
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#--- do work ------------------------------------------------------------------------------------
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newInfo['grid'] = np.array([{True: int(o*float(n.translate(None,'xX'))),
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False: int(n.translate(None,'xX'))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
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newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure_cropped = np.zeros(newInfo['grid'],'i')
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microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0])
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xindex = list(set(xrange(options.offset[0],options.offset[0]+newInfo['grid'][0])) & \
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set(xrange(info['grid'][0])))
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yindex = list(set(xrange(options.offset[1],options.offset[1]+newInfo['grid'][1])) & \
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set(xrange(info['grid'][1])))
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zindex = list(set(xrange(options.offset[2],options.offset[2]+newInfo['grid'][2])) & \
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set(xrange(info['grid'][2])))
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translate_x = [i - options.offset[0] for i in xindex]
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translate_y = [i - options.offset[1] for i in yindex]
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translate_z = [i - options.offset[2] for i in zindex]
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microstructure_cropped[min(translate_x):(max(translate_x)+1),\
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min(translate_y):(max(translate_y)+1),\
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min(translate_z):(max(translate_z)+1)] \
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= microstructure[min(xindex):(max(xindex)+1),\
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min(yindex):(max(yindex)+1),\
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min(zindex):(max(zindex)+1)]
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newInfo['size'] = info['size']/info['grid']*newInfo['grid']
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newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset
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newInfo['microstructures'] = microstructure_cropped.max()
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#--- report ---------------------------------------------------------------------------------------
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if (any(newInfo['grid'] != info['grid'])):
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file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid']))))
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if (any(newInfo['size'] != info['size'])):
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file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size']))))
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if (any(newInfo['origin'] != info['origin'])):
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file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['origin']))))
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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if np.any(newInfo['grid'] < 1):
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file['croak'].write('invalid new grid a b c.\n')
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continue
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if np.any(newInfo['size'] <= 0.0):
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file['croak'].write('invalid new size x y z.\n')
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continue
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#--- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta %i\tb %i\tc %i"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2],),
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"size\tx %f\ty %f\tz %f"%(newInfo['size'][0],newInfo['size'][1],newInfo['size'][2],),
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"origin\tx %f\ty %f\tz %f"%(newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2],),
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"homogenization\t%i"%info['homogenization'],
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"microstructures\t%i"%(newInfo['microstructures']),
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])
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table.head_write()
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table.output_flush()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure_cropped.max())+1))
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table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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table.input_close()
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table.output_close()
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os.rename(file['name']+'_tmp',file['name'])
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