Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
view 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 |
---|---|
date | Tue, 17 Sep 2019 17:06:56 -0400 |
parents | |
children |
line wrap: on
line source
#!/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 )