Mercurial > repos > imgteam > imagej2_watershed_binary
diff imagej2_create_image.py @ 0:b143159845b4 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 17:02:55 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_create_image.py Tue Sep 17 17:02:55 2019 -0400 @@ -0,0 +1,40 @@ +#!/usr/bin/env python +import argparse +import shutil +import subprocess +import tempfile +import imagej2_base_utils + +if __name__=="__main__": + # Parse Command Line. + parser = argparse.ArgumentParser() + parser.add_argument( '--width', dest='width', type=int, help='Image width in pixels' ) + parser.add_argument( '--height', dest='height', type=int, help='Image height in pixels' ) + parser.add_argument( '--depth', dest='depth', type=int, help='Image depth (specifies the number of stack slices)' ) + parser.add_argument( '--image_type', dest='image_type', help='Image type' ) + parser.add_argument( '--image_title', dest='image_title', default='', help='Image title' ) + parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image format' ) + parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) + parser.add_argument( '--out_fname', help='Path to the output file' ) + args = parser.parse_args() + + tmp_dir = imagej2_base_utils.get_temp_dir() + tmp_image_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype ) + + # 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. + 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 %d %d %d %s %s' % ( args.image_title, args.width, args.height, args.depth, args.image_type, tmp_image_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 ) + shutil.move( tmp_image_path, args.out_fname ) + imagej2_base_utils.cleanup_before_exit( tmp_dir )