Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
diff imagej2_bunwarpj_compare_elastic_raw.py @ 0:95fb6fa70c2f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 17:06:56 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_bunwarpj_compare_elastic_raw.py Tue Sep 17 17:06:56 2019 -0400 @@ -0,0 +1,64 @@ +#!/usr/bin/env python +import argparse +import subprocess +import tempfile +import imagej2_base_utils + +# Parse Command Line. +parser = argparse.ArgumentParser() +parser.add_argument( '--source_image', dest='source_image', help='Source image' ) +parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' ) +parser.add_argument( '--target_image', dest='target_image', help='Target image' ) +parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' ) +parser.add_argument( '--target_elastic_transformation', dest='target_elastic_transformation', help='Target elastic transformation matrix' ) +parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Source raw transformation matrix' ) +parser.add_argument( '--output', dest='output', help='Warping index' ) + +args = parser.parse_args() + +tmp_dir = imagej2_base_utils.get_temp_dir() +source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format ) +target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format ) +target_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_elastic_transformation, 'txt' ) +source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' ) +# bUnwarpJ produces several lines of output that we need to discard, so +# we'll use a temporary output file from which we'll read only the last line. +tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' ) + +# Define command response buffers. +tmp_out = tempfile.NamedTemporaryFile().name +tmp_stdout = open( tmp_out, 'wb' ) +tmp_err = tempfile.NamedTemporaryFile().name +tmp_stderr = open( tmp_err, 'wb' ) + +# Build the command line to calculate the warping index. +cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None ) +if cmd is None: + imagej2_base_utils.stop_err( "bUnwarpJ not found!" ) +cmd += ' -compare_elastic_raw' +cmd += ' %s' % target_image_path +cmd += ' %s' % source_image_path +cmd += ' %s' % target_elastic_transformation_path +cmd += ' %s' % source_raw_transformation_path +cmd += ' > %s' % tmp_output_path + +# Calculate the warping index of elastic and raw transformations using bUnwarpJ. +proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True ) +rc = proc.wait() +if rc != 0: + error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) + imagej2_base_utils.stop_err( error_message ) + +# Example contents of tmp_output_path: +# ['Target image : ~/tmpHdt9Cs.jpg\n', +# 'Source image : ~/tmpu6kyfc.gif\n', +# 'Elastic Transformation file : ~/tmp4vZurG.txt\n', +# 'Raw Transformation file : ~/tmp2PNQcT.txt\n', +# ' Warping index = 25.007467512204983\n'] +results = open( tmp_output_path, 'r' ).readlines() +warp_index = results[ -1 ].split( ' ' )[ -1 ] +outf = open( args.output, 'wb' ) +outf.write( '%s' % warp_index ) +outf.close() + +imagej2_base_utils.cleanup_before_exit( tmp_dir )