Mercurial > repos > imgteam > imagej2_bunwarpj_raw_transform
view imagej2_bunwarpj_raw_transform.py @ 0:95b7592729e2 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 17:03:42 -0400 |
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#!/usr/bin/env python import argparse import shutil 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( '--raw_transformation', dest='raw_transformation', help='Raw transformation as saved by bUnwarpJ' ) parser.add_argument( '--source_out', help='Output source image' ) parser.add_argument( '--source_out_datatype', help='Output registered source image format' ) parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) 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 ) tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' ) tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype ) target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format ) raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.raw_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 apply the raw transformation. cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None ) if cmd is None: imagej2_base_utils.stop_err( "bUnwarpJ not found!" ) cmd += ' -raw_transform' # Target is sent before source. cmd += ' %s' % target_image_path cmd += ' %s' % source_image_path cmd += ' %s' % raw_transformation_path cmd += ' %s' % tmp_source_out_tiff_path # Apply the raw transformation 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 ) # Convert the registered image to the specified output format. tmp_out = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) if cmd is None: imagej2_base_utils.stop_err( "ImageJ not found!" ) cmd += ' %s %s %s' % ( tmp_source_out_tiff_path, args.source_out_datatype, tmp_source_out_path ) 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 ) # Save the Registered Source Image to the defined output. shutil.move( tmp_source_out_path, args.source_out ) imagej2_base_utils.cleanup_before_exit( tmp_dir )