diff --git a/processing/pre/seeds_fromTable.py b/processing/pre/seeds_fromTable.py index 45a2b386b..fd45a954b 100755 --- a/processing/pre/seeds_fromTable.py +++ b/processing/pre/seeds_fromTable.py @@ -23,29 +23,38 @@ Examples: """, version = scriptID) -parser.add_option('-p', '--positions', - dest = 'pos', - type = 'string', metavar = 'string', - help = 'coordinate label [%default]') +parser.add_option('-p', + '--pos', '--seedposition', + dest = 'pos', + type = 'string', metavar = 'string', + help = 'label of coordinates [%default]') parser.add_option('--boundingbox', dest = 'box', type = 'float', nargs = 6, metavar = ' '.join(['float']*6), help = 'min (x,y,z) and max (x,y,z) coordinates of bounding box [tight]') -parser.add_option('-i', '--index', - dest = 'index', +parser.add_option('-m', + '--microstructure', + dest = 'microstructure', type = 'string', metavar = 'string', - help = 'microstructure index label [%default]') -parser.add_option('-w','--white', + help = 'label of microstructures [%default]') +parser.add_option('--weight', + dest = 'weight', + type = 'string', metavar = 'string', + help = 'label of weights [%default]') +parser.add_option('-w', + '--white', dest = 'whitelist', action = 'extend', metavar = '', help = 'whitelist of microstructure indices') -parser.add_option('-b','--black', +parser.add_option('-b', + '--black', dest = 'blacklist', action = 'extend', metavar = '', help = 'blacklist of microstructure indices') -parser.set_defaults(pos = 'pos', - index ='microstructure', +parser.set_defaults(pos = 'pos', + microstructure = 'microstructure', + weight = None, ) (options,filenames) = parser.parse_args() @@ -58,10 +67,9 @@ if options.blacklist is not None: options.blacklist = map(int,options.blacklist) if filenames == []: filenames = [None] for name in filenames: - try: - table = damask.ASCIItable(name = name, - outname = os.path.splitext(name)[0]+'.seeds' if name else name, - buffered = False) + try: table = damask.ASCIItable(name = name, + outname = os.path.splitext(name)[0]+'.seeds' if name else name, + buffered = False) except: continue damask.util.report(scriptName,name) @@ -69,14 +77,17 @@ for name in filenames: # ------------------------------------------ sanity checks --------------------------------------- - missing_labels = table.data_readArray([options.pos,options.index]) + missing_labels = table.data_readArray([options.pos,options.microstructure] + + ([options.weight] if options.weight else [])) errors = [] if len(missing_labels) > 0: errors.append('column{} {} not found'.format('s' if len(missing_labels) > 1 else '', ', '.join(missing_labels))) - for label, dim in {options.pos: 3, - options.index: 1}.iteritems(): + input = {options.pos: 3, + options.microstructure: 1,} + if options.weight: input.update({options.weight: 1}) + for label, dim in input.iteritems(): if table.label_dimension(label) != dim: errors.append('column {} has wrong dimension'.format(label)) @@ -113,11 +124,12 @@ for name in filenames: table.info = [ scriptID, - 'size %s'%(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'], + 'size {}'.format(' '.join(list(itertools.chain.from_iterable(zip(['x','y','z'], map(str,boundingBox[1,:]-boundingBox[0,:])))))), ] table.labels_clear() - table.labels_append(['1_pos','2_pos','3_pos','microstructure']) # implicitly switching label processing/writing on + table.labels_append(['1_pos','2_pos','3_pos','microstructure'] + + ['weight'] if options.weight else []) # implicitly switching label processing/writing on table.head_write() # ------------------------------------------ output result ---------------------------------------