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import sys
import os
import re
import os.path
import glob
import shutil
from optparse import OptionParser
#-------------------------------------------------------------------------------
# the main function
# cd bin_VS2010
# ctest -C Release
# cd Testing
# python ../../Testing/elx_get_tp_list.py -l elastix_run* -o ../../Testing/Baselines
# cd ..
# cmake .
# ctest -C Release -R COMPARE_TP
# cd ..
# git add Testing/Baselines/TransformParameters_*
# git commit -m "ENH: updating baselines after recent change X"
# git push
def main():
# usage, parse parameters
usage = "usage: %prog [options] arg";
parser = OptionParser( usage );
# option to debug and verbose
parser.add_option( "-v", "--verbose",
action="store_true", dest="verbose" );
# options to control files
parser.add_option( "-l", "--list", type="string", dest="directoryList", help="list of elastix output directories" );
parser.add_option( "-o", "--output", type="string", dest="outputDirectory", help="output base directory" );
(options, args) = parser.parse_args();
# Check if option -l is given
if options.directoryList == None :
parser.error( "The option directory list (-l) should be given" );
# Check if option -d is given
if options.outputDirectory == None :
parser.error( "The option output directory (-o) should be given" );
if not os.path.exists( options.outputDirectory ) :
print( "The output directory " + options.outputDirectory + " does not exist. Create it before running" );
# Convert string -l to list
dirList = options.directoryList.split( ' ' );
# Add everything not processed
dirList.extend( args );
for directory in dirList :
# Skip directories with "Threads" in the name
if "Threads" in directory : continue;
# Find the largest TransformParameters.?.txt
inputFileNames = glob.glob( os.path.join( directory, "TransformParameters.?.txt" ) );
inputFileNames.sort( reverse = True );
inputFileName = inputFileNames[0];
# Create a name for the output file name
directory = re.sub( '\/$', '', directory );
dir_part = list( os.path.split( directory ) ).pop();
dir_part = dir_part.replace( "elastix_run_", "", 1 );
outputFileName = "TransformParameters_" + dir_part + ".txt.in";
outputFileName = os.path.join( options.outputDirectory, outputFileName );
print( outputFileName );
# Copy the results as the new baselines, while replacing
# the initial transform to point to the correct path.
f1 = open( inputFileName, 'rU' );
f2 = open( outputFileName, 'w' );
for oldline in f1 :
newline = oldline;
if "InitialTransformParametersFileName" in oldline :
oldFileName = os.path.basename( oldline.split()[1][1:-2] );
newFileName = os.path.join( "@ELASTIX_DATA_DIR@", oldFileName );
if not "NoInitialTransform" in oldFileName :
newline = "(InitialTransformParametersFileName \"" + newFileName + "\")\n";
f2.write( newline );
f1.close(); f2.close();
return 0
#-------------------------------------------------------------------------------
if __name__ == '__main__':
sys.exit(main())
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