script to produce ASCIItable from geom dataset.
contains best-practice for looping over multiple input files (to avoid error caused by too many open file handles!)
This commit is contained in:
Philip Eisenlohr
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deee3a175a
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,vtk
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import numpy as np
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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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class extendedOption(Option):
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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synonyms = {
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'grid': ['resolution'],
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'size': ['dimension'],
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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=extendedOption, usage='%prog [geomfile[s]]', description = """
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Produce ASCIItable of structure data from geom description
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""" + string.replace(scriptID,'\n','\\n')
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)
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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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'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':
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file['input'] = open(file['name'])
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file['output'] = open(os.path.splitext(file['name'])[0]+'.txt','w')
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file['croak'].write('\033[1m' + scriptName + '\033[0m' + (': '+file['name'] if file['name'] != 'STDIN' else '') + '\n')
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theTable = damask.ASCIItable(file['input'],file['output'],labels = False)
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theTable.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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for header in theTable.info:
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headitems = map(str.lower,header.split())
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if len(headitems) == 0: continue
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for synonym,alternatives in synonyms.iteritems():
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if headitems[0] in alternatives: headitems[0] = synonym
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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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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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# ------------------------------------------ assemble header ---------------------------------------
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theTable.labels_clear()
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theTable.labels_append(['%i_pos'%(i+1) for i in range(3)]+['microstructure'])
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theTable.head_write()
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#--- generate grid --------------------------------------------------------------------------------
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xx = np.arange(float(info['grid'][0]))/info['grid'][0]*info['size'][0]+info['origin'][0]
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yy = np.arange(float(info['grid'][1]))/info['grid'][1]*info['size'][1]+info['origin'][1]
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zz = np.arange(float(info['grid'][2]))/info['grid'][2]*info['size'][2]+info['origin'][2]
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#--- read microstructure information --------------------------------------------------------------
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i = 0
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outputAlive = True
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while outputAlive and theTable.data_read():
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items = theTable.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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for item in items:
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theTable.data = [xx[ i%info['grid'][0]],
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yy[(i/info['grid'][0])%info['grid'][1]],
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zz[ i/info['grid'][0]/info['grid'][1]],
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item]
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i += 1
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outputAlive = theTable.data_write() # output processed line
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if not outputAlive: break
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# ------------------------------------------ finalize output ---------------------------------------
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theTable.output_flush() # just in case of buffered ASCII table
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if file['name'] != 'STDIN':
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file['input'].close() # close input ASCII table
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file['output'].close() # close output ASCII table
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