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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| *.m linguist-vendored | ||
| *.dat linguist-vendored | ||
| *.tab linguist-vendored | ||
| *.txt linguist-vendored | ||
| *.C linguist-language=C++ | ||
| *.h linguist-language=C++ | ||
| *.cpp linguist-language=C++ |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,147 @@ | ||
| """ | ||
| -----------------------------------------------------------------------bl- | ||
| -------------------------------------------------------------------------- | ||
| QUESO - a library to support the Quantification of Uncertainty | ||
| for Estimation, Simulation and Optimization | ||
| Copyright (C) 2008,2009,2010,2011,2012,2013 The PECOS Development Team | ||
| This library is free software; you can redistribute it and/or | ||
| modify it under the terms of the Version 2.1 GNU Lesser General | ||
| Public License as published by the Free Software Foundation. | ||
| This library is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | ||
| Lesser General Public License for more details. | ||
| You should have received a copy of the GNU Lesser General Public | ||
| License along with this library; if not, write to the Free Software | ||
| Foundation, Inc. 51 Franklin Street, Fifth Floor, | ||
| Boston, MA 02110-1301 USA | ||
| -----------------------------------------------------------------------el- | ||
| This module contains a utility funtion, convertMFile, for converting m-files | ||
| generated by QUESO into regular text. See the convertMFile help string for more | ||
| specific information on usage and output. Conversion can also be accomplished | ||
| by invoking convertQuesoMFileToTxt.py on the command line. In this case, | ||
| the script will parse a list of input m-files and create text file output | ||
| for each m-file. The script separates the chain data, likelihood data, and | ||
| target data into separate output files. For more information on the command | ||
| version, run: python convertQuesoMFileToTxt.py --help | ||
| """ | ||
|
|
||
| import re | ||
| import sys | ||
|
|
||
| def convertMFile(mFileName, getChain=True, getLike=True, | ||
| getTarget=True, chainIdent='[cC]hain', | ||
| likeIdent='[lL]ikelihood', targetIdent='[tT]arget'): | ||
| """ | ||
| This function parses chain, likelihood, and target data from a single m-file. | ||
| mFileName specifies the name of m-file to parse. The get{Chain,Like,Target} | ||
| optional inputs take boolean values indicating if the function should parse | ||
| that particular item from the file. The {chain,like,target}Ident optional | ||
| inputs allow the user to specify a regular expression that identifies that | ||
| particular item in the m-file. This function returns a dictionary | ||
| containing keys, 'chain', 'logLikelihood', and 'logTarget'. The value | ||
| associated with a particular key is the data for that item in character | ||
| string format. If the data for an item cannot be found in the file, the | ||
| key for that item will not be present in the dictionary. | ||
| """ | ||
|
|
||
| # tokens delimiting the data | ||
| dataEncloseTokens = ('[', ']') | ||
|
|
||
| # Read file into string buffer | ||
| fIn = open(mFileName,'r') | ||
| fileBuf = fIn.read() | ||
| fIn.close() | ||
|
|
||
| outputMap = dict() | ||
| parseMap = {'chain': (getChain, chainIdent), 'logLikelihood': (getLike, likeIdent), | ||
| 'logTarget': (getTarget, targetIdent)} | ||
|
|
||
| # iterate over wanted items and parse them from the buffer | ||
| for item in parseMap: | ||
| if parseMap[item][0] == False: | ||
| continue | ||
|
|
||
| # Find tag for current item via search with regex: identString\w*\s*=\s*(?=\[) | ||
| parseTagRegEx = parseMap[item][1] + r'\w*\s*=\s*' + '(?=' + re.escape(dataEncloseTokens[0]) + ')' | ||
| match = re.search(parseTagRegEx, fileBuf) | ||
| tag = '' | ||
| if match: | ||
| tag = match.group(0) + re.escape(dataEncloseTokens[0]) | ||
| else: | ||
| print 'Error: Could not find identifier {0} in {1}. Regex string: {2}'.format(item, mFileName, parseTagRegEx) | ||
| return outputMap | ||
|
|
||
| # Extract current item data between [ ] via search with regex: (?<=tag)[^\]]+ | ||
| parseDataRegEx = '(?<=' + tag + ')[^' + re.escape(dataEncloseTokens[1]) + ']+' | ||
| match = re.search(parseDataRegEx, fileBuf) | ||
| if match: | ||
| outputMap[item] = match.group(0) | ||
| else: | ||
| print 'Error: Could not find {0} data in {1}. Regex string: {2}'.format(item, mFileName, parseDataRegEx) | ||
| return outputMap | ||
|
|
||
| return outputMap | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| import argparse | ||
|
|
||
| parser = argparse.ArgumentParser(description='Convert a list of m-files generated by QUESO into text files.') | ||
| parser.add_argument('-c', '--chain', type=str, choices=['yes','no'], default='yes', | ||
| help='Parse chain data from m-file (default: yes)') | ||
| parser.add_argument('-l', '--likelihood', type=str, choices=['yes','no'], default='yes', | ||
| help='Parse likelihood data from m-file (default: yes)') | ||
| parser.add_argument('-t', '--target', type=str, choices=['yes','no'], default='yes', | ||
| help='Parse target data from m-file (default: yes)') | ||
|
|
||
| parser.add_argument('-ci', '--chain_identifier', type=str, default='[cC]hain', | ||
| help='RegEx string identifying chain entry in the m-file (default: [cC]hain)') | ||
| parser.add_argument('-li', '--likelihood_identifier', type=str, default='[lL]ikelihood', | ||
| help='RegEx string identifying likelihood entry in the m-file (default: [lL]ikelihood)') | ||
| parser.add_argument('-ti', '--target_identifier', type=str, default='[tT]arget', | ||
| help='RegEx string identifying target entry in the m-file (default: [tT]arget)') | ||
|
|
||
| parser.add_argument('mFileList', nargs='+', help='List of m-files to convert') | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| if args.chain == 'yes': | ||
| getChainOpt = True | ||
| else: | ||
| getChainOpt = False | ||
|
|
||
| if args.likelihood == 'yes': | ||
| getLikeOpt = True | ||
| else: | ||
| getLikeOpt = False | ||
|
|
||
| if args.target == 'yes': | ||
| getTargetOpt = True | ||
| else: | ||
| getTargetOpt = False | ||
|
|
||
| # process files one-by-one | ||
| for mFileName in args.mFileList: | ||
| outputMap = convertMFile(mFileName, getChain=getChainOpt, getLike=getLikeOpt, getTarget=getTargetOpt, \ | ||
| chainIdent=args.chain_identifier, likeIdent=args.likelihood_identifier, \ | ||
| targetIdent=args.target_identifier) | ||
|
|
||
| # Write the data out to text files | ||
| mFileNameBase = mFileName.rstrip('.m') | ||
| for item in outputMap: | ||
| outFileName = mFileNameBase + '_' + item + '.txt' | ||
| fOut = open(outFileName, 'w') | ||
| fOut.write(outputMap[item]) | ||
| fOut.close() | ||
| print 'Created file {0}...'.format(outFileName) |
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