Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
diff imagej2_bunwarpj_convert_to_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_convert_to_raw.py Tue Sep 17 17:06:56 2019 -0400 @@ -0,0 +1,47 @@ +#!/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( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' ) +parser.add_argument( '--raw_transformation', dest='raw_transformation', help='Raw transformation' ) + +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 ) +elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, '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 convert the B-spline (i.e., elastic) transformation to raw. +cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None ) +if cmd is None: + imagej2_base_utils.stop_err( "bUnwarpJ not found!" ) +cmd += ' -convert_to_raw' +# Target is sent before source. +cmd += ' %s' % target_image_path +cmd += ' %s' % source_image_path +cmd += ' %s' % elastic_transformation_path +cmd += ' %s' % args.raw_transformation + +# Convert the elastic transformation to raw using bUnwarpJ. +proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, 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 ) + +imagej2_base_utils.cleanup_before_exit( tmp_dir )