simplified processing of ASCIItables by utilizing the improved class methods.
modernized file looping. updated help.
This commit is contained in:
Philip Eisenlohr
parent
c089ff9256
commit
d57c7568dd
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@ -36,78 +36,67 @@ Examples:
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""", version = scriptID)
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parser.add_option('-p', '--positions', dest = 'pos', metavar='string',
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parser.add_option('-p', '--positions', dest = 'pos', metavar = 'string',
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help = 'coordinate label')
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parser.add_option('--boundingbox', dest = 'box', type = 'float', nargs = 6,
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help = 'min (x,y,z) and max (x,y,z) to specify bounding box [auto]')
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parser.add_option('-i', '--index', dest = 'index', type = 'string',
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parser.add_option('--boundingbox', dest = 'box', type = 'float', nargs = 6, metavar = ' '.join(['float']*6),
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help = 'min (x,y,z) and max (x,y,z) coordinates of bounding box [auto]')
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parser.add_option('-i', '--index', dest = 'index', type = 'string', metavar = 'string',
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help = 'microstructure index label')
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parser.add_option('-w','--white', dest = 'whitelist', action = 'extend',\
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parser.add_option('-w','--white', dest = 'whitelist', action = 'extend',
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help = 'white list of microstructure indices', metavar = '<LIST>')
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parser.add_option('-b','--black', dest = 'blacklist', action = 'extend',\
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parser.add_option('-b','--black', dest = 'blacklist', action = 'extend',
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help = 'black list of microstructure indices', metavar = '<LIST>')
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parser.set_defaults(pos = 'pos')
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parser.set_defaults(index = 'microstructure')
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parser.set_defaults(pos = 'pos',
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index ='microstructure',
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)
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(options,filenames) = parser.parse_args()
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datainfo = { # list of requested labels per datatype
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'scalar': {'len':1,
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'label':[]},
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'vector': {'len':3,
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'label':[]},
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}
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datainfo['vector']['label'] += [options.pos]
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datainfo['scalar']['label'] += [options.index]
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if options.whitelist != None: options.whitelist = map(int,options.whitelist)
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if options.blacklist != None: options.blacklist = map(int,options.blacklist)
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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# --- loop over input 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(os.path.splitext(name)[0]+'.seeds','w'),
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'croak':sys.stdout,
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})
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filenames = ['STDIN']
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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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for name in filenames:
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if name == 'STDIN':
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file = {'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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else:
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if not os.path.exists(name): continue
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file = {'name':name,
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'input':open(name),
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'output':open(os.path.splitext(name)[0]+ \
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('' if options.label == None else '_'+options.label)+ \
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'.png','w'),
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'croak':sys.stderr}
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file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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table = damask.ASCIItable(file['input'],file['output'],
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buffered = False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table = damask.ASCIItable(file['input'],file['output'],buffered = False)
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table.head_read()
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# --------------- figure out columns to process
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active = defaultdict(list)
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column = defaultdict(dict)
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for datatype,info in datainfo.items():
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for label in info['label']:
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foundIt = False
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for key in ['1_'+label,label]:
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if key in table.labels:
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foundIt = True
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active[datatype].append(label)
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column[datatype][label] = table.labels.index(key) # remember columns of requested data
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if not foundIt:
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file['croak'].write('column %s not found...\n'%label)
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break
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray(list(itertools.chain.from_iterable(map(lambda x:[x+i for i in range(datainfo['vector']['len'])],
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[column['vector'][label] for label in active['vector']]))) +
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[column['scalar'][label] for label in active['scalar']])
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# ------------------------------------------ process data ------------------------------------------
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errors = []
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missing_labels = table.data_readArray(options.pos,options.label)
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if len(missing_labels) > 0:
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errors.append('column%s %s not found'%('s' if len(missing_labels) > 1 else '',
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', '.join(missing_labels)))
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for label, dim in {options.pos: 3,
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options.label: 1}.iteritems():
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if table.label_dimension(label) != dim:
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errors.append('column %s has wrong dimension'%label)
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if errors != []:
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file['croak'].write('\n'.join(errors))
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table.close(dismiss = True) # close ASCII table file handles and delete output file
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continue
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#--- finding bounding box ------------------------------------------------------------------------------------
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boundingBox = np.array((np.amin(table.data[:,0:3],axis = 0),np.amax(table.data[:,0:3],axis = 0)))
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if options.box:
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@ -126,7 +115,7 @@ for file in files:
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else np.in1d(table.data[:,3].ravel(), options.whitelist).reshape(table.data[:,3].shape),
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np.ones_like(table.data[:,3],bool) \
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if options.blacklist == None \
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else np.invert(np.in1d(table.data[:,3].ravel(), options.blacklist).reshape(table.data[:,3].shape))
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else np.invert(np.in1d(table.data[:,3].ravel(), options.blacklist).reshape(table.data[:,3].shape))
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)
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table.data = table.data[mask]
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@ -135,10 +124,10 @@ for file in files:
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# ------------------------------------------ assemble header ---------------------------------------
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table.info = [
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scriptID,
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'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
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map(str,boundingBox[1,:]-boundingBox[0,:])))))),
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]
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scriptID,
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'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'],
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map(str,boundingBox[1,:]-boundingBox[0,:])))))),
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]
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table.labels_clear()
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table.labels_append(['1_coords','2_coords','3_coords','microstructure']) # implicitly switching label processing/writing on
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table.head_write()
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@ -146,6 +135,4 @@ for file in files:
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table.data_writeArray()
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table.output_flush()
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table.input_close() # close input ASCII table
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if file['name'] != 'STDIN':
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table.output_close() # close output ASCII table
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table.close() # close ASCII tables
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