202 lines
8.4 KiB
Python
Executable File
202 lines
8.4 KiB
Python
Executable File
#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,math
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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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Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
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Either absolute values or relative factors (like "0.25x") can be used.
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""", version = scriptID)
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parser.add_option('-g', '--grid', dest='grid', nargs = 3, metavar = 'string string string', \
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help='a,b,c grid of hexahedral box [unchanged]')
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parser.add_option('-s', '--size', dest='size', nargs = 3, metavar = 'string string string', \
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help='x,y,z size of hexahedral box [unchanged]')
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parser.add_option('-r', '--renumber', dest='renumber', action='store_true', \
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help='renumber microstructure indices from 1...N [%default]')
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parser.set_defaults(renumber = False)
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parser.set_defaults(grid = ['0','0','0'])
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parser.set_defaults(size = ['0.0','0.0','0.0'])
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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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if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\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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'size': 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
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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')
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i = 0
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table.data_rewind()
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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:round(o*float(n.translate(None,'xX'))), False: round(float(n.translate(None,'xX')))}[n[-1].lower() == 'x'] for o,n in zip(info['grid'],options.grid)],'i')
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newInfo['size'] = np.array([{True: o*float(n.translate(None,'xX')) , False: float(n.translate(None,'xX')) }[n[-1].lower() == 'x'] for o,n in zip(info['size'],options.size)],'d')
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newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
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newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
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multiplicity = []
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for j in xrange(3):
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multiplicity.append([])
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last = 0
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for i in xrange(info['grid'][j]):
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this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
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multiplicity[j].append(this-last)
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last = this
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microstructure = microstructure.reshape(info['grid'],order='F')
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microstructure = np.repeat(
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np.repeat(
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np.repeat(microstructure,multiplicity[0], axis=0),
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multiplicity[1], axis=1),
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multiplicity[2], axis=2)
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# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
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# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
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if options.renumber:
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newID=0
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for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))):
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if count != 0:
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newID+=1
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microstructure=np.where(microstructure==microstructureID,newID,microstructure).reshape(microstructure.shape)
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newInfo['microstructures'] = microstructure.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 (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"%(info['origin'][0],info['origin'][1],info['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.max())+1))
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table.data = microstructure.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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