81 lines
3.2 KiB
Python
81 lines
3.2 KiB
Python
#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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# ------------------------------------------------------------------- #
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# NOTE: #
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# 1. Not all output is defined in the DS_HDF5.xml, please add new #
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# new one to the system wide definition file #
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# <DAMASK_ROOT>/lib/damask/DS_HDF5.xml #
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# or specify your own when initializing HDF5 class #
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# ------------------------------------------------------------------- #
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import os
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import damask
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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desp_msg = "Convert DAMASK ascii table to HDF5 file"
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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description = desp_msg,
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version = scriptID)
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parser.add_option('-D', '--DefinitionFile',
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dest = 'storage definition file',
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type = 'string',
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metavar = 'string',
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help = 'definition file for H5 data storage')
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parser.add_option('-d','--debug',
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dest = 'debug output toggle',
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type = 'boolean',
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metavar = 'boolean',
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help = 'toggle on debug output') # not necessary for now
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parser.set_defaults(debug=False,
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DefinitionFile='default')
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(options,filenames) = parser.parse_args()
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if options.DefinitionFile == 'default':
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defFile = None
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else:
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defFile = options.DefinitionFile
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# ----- read in data using DAMASK ASCII table class ----- #
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asciiTable = damask.ASCIItable(name=filenames, buffered=False)
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asciiTable.head_read()
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asciiTable.data_readArray()
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incNum = int(asciiTable.data[asciiTable.label_index('inc'), 0])
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allData = np.copy(asciiTable.data) # deep copy all data, just to be safe
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featuresDim = [labels_idx[i+1] - labels_idx[i] for i in xrange(len(labels)-1)]
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featuresDim.append(fullTable.shape[1] - labels_idx[-1])
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# ----- create a new HDF5 file and save the data -----#
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# Will overwrite existing HDF5 file with the same name
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h5f = damask.H5Table(filenames.replace(".txt", ".h5"),
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new_file=True,
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dsXMLFile=defFile)
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# adding increment number as root level attributes
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h5f.add_attr('inc', incNum)
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for fi in xrange(len(labels)):
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featureName = labels[fi]
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if featureName == 'inc': continue
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# remove trouble maker "("" and ")"
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if "(" in featureName: featureName = featureName.replace("(", "")
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if ")" in featureName: featureName = featureName.replace(")", "")
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featureIdx = labels_idx[fi]
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featureDim = featuresDim[fi]
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# grab the data hook
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dataset = fullTable[:, featureIdx:featureIdx+featureDim]
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# reshape tensor to 3x3 --> just make life slightly easier
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if dataset.shape[1] == 9:
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dataset = dataset.reshape((dataset.shape[0], 3, 3))
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# write out data
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h5f.add_data(featureName, dataset)
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