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import sys, subprocess
import os
import os.path
import shutil
import re
import glob
from optparse import OptionParser
#-------------------------------------------------------------------------------
# the main function
# Below we deform the moving image segmentation by the current result as well as
# by a previous stored result. This makes this test a regression test.
#
# We could instead compare with a fixed image segmentation, but that would require
# the tested registrations to be relatively good, which they are not to save time.
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( "-d", "--directory", dest="directory", help="elastix output directory" );
parser.add_option( "-m", "--movingsegmentation", dest="mseg", help="moving image segmentation" );
parser.add_option( "-b", "--baselinetp", dest="btp", help="baseline transform parameter file" );
parser.add_option( "-p", "--path", dest="path", help="path where executables can be found" );
(options, args) = parser.parse_args();
# Check if option -d and -m and -b are given
if options.directory == None :
parser.error( "The option directory (-d) should be given" );
if options.mseg == None :
parser.error( "The option directory (-m) should be given" );
if options.btp == None :
parser.error( "The option directory (-b) should be given" );
# Get the transform parameters files
tpFileName_in = os.path.join( options.directory, "TransformParameters.0.txt" );
tpFileName = os.path.join( options.directory, "TransformParameters.seg.txt" );
tpFileName_b_in = options.btp;
tpFileName_b = os.path.join( options.directory, "TransformParameters.baseline.seg.txt" );
# Sanity checks
if not os.path.exists( tpFileName_in ) :
print( "ERROR: the file " + tpFileName_in + " does not exist" );
return 1;
# Below we use programs that are compiled with elastix, and are thus available
# in the binary directory. The user of this script has to supply the path
# to the binary directory via the command line.
# In order to make sure that python is able to find these programs we add
# the paths to the local environment.
_path = os.path.dirname( options.path );
_path += os.pathsep + os.getenv('PATH');
os.environ['PATH'] = _path;
#
# Deform the moving image segmentation by the current result
#
print( "Deforming moving image segmentation using " + tpFileName_in );
# Make the transform parameters file suitable for binary images
f1 = open( tpFileName_in, 'r' ); f2 = open( tpFileName, 'w' );
for line in f1 :
lineout = line.replace( '(FinalBSplineInterpolationOrder 3)', '(FinalBSplineInterpolationOrder 0)' );
lineout = re.sub( "(ResultImageFormat \"mhd\")", "ResultImageFormat \"mha\"", lineout );
lineout = re.sub( "(ResultImagePixelType \"short\")", "ResultImagePixelType \"unsigned char\"", lineout );
lineout = re.sub( "(CompressResultImage \"false\")", "CompressResultImage \"true\"", lineout );
f2.write( lineout );
f1.close(); f2.close();
# Transform the moving image segmentation to mimick the baseline result
seg = os.path.join( options.directory, "result.mha" );
seg_defm = os.path.join( options.directory, "segmentation_deformed.mha" );
subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName ],
stdout=subprocess.PIPE );
if( os.path.exists( seg_defm ) ) : os.remove( seg_defm );
shutil.move( seg, seg_defm );
#
# Deform the moving image segmentation by the baseline result
#
print( "Deforming moving image segmentation using " + tpFileName_b_in );
# Make the transform parameters file suitable for binary images
f1 = open( tpFileName_b_in, 'r' ); f2 = open( tpFileName_b, 'w' );
for line in f1 :
lineout = line.replace( '(FinalBSplineInterpolationOrder 3)', '(FinalBSplineInterpolationOrder 0)' );
lineout = re.sub( "(ResultImageFormat \"mhd\")", "ResultImageFormat \"mha\"", lineout );
lineout = re.sub( "(ResultImagePixelType \"short\")", "ResultImagePixelType \"unsigned char\"", lineout );
lineout = re.sub( "(CompressResultImage \"false\")", "CompressResultImage \"true\"", lineout );
f2.write( lineout );
f1.close(); f2.close();
# Transform the moving image segmentation to mimick the fixed image segmentation
seg_defb = os.path.join( options.directory, "segmentation_baseline.mha" );
subprocess.call( [ "transformix", "-in", options.mseg, "-out", options.directory, "-tp", tpFileName_b ],
stdout=subprocess.PIPE );
if( os.path.exists( seg_defb ) ) : os.remove( seg_defb );
shutil.move( seg, seg_defb );
# Compute the overlap between baseline segmentation and deformed moving segmentation
try :
# This will work from python 2.7 on
outputAsString = subprocess.check_output( [ "elxComputeOverlap", "-in", seg_defm, seg_defb ] ).decode("utf-8");
except :
# Workaround for python 2.6 and lower. For MacMini specifically.
outputAsString = subprocess.Popen( [ "elxComputeOverlap", "-in", seg_defm, seg_defb ], stdout=subprocess.PIPE ).communicate()[0].decode("utf-8");
overlap = outputAsString[ outputAsString.find( "Overlap" ) : ].strip( "Overlap: " );
# Report
print( "The segmentation overlap between current and baseline is " + overlap );
if float( overlap ) > 0.99 :
print( "SUCCESS: overlap is higher than 0.99" );
return 0;
else :
print( "FAILURE: overlap is lower than 0.99" );
return 1;
#-------------------------------------------------------------------------------
if __name__ == '__main__':
sys.exit(main())
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