Mercurial > repos > imgteam > imagej2_find_maxima
diff imagej2_math.py @ 0:29b39f5b0e69 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 17:01:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_math.py Tue Sep 17 17:01:44 2019 -0400 @@ -0,0 +1,69 @@ +#!/usr/bin/env python +import argparse +import os +import shutil +import subprocess +import tempfile +import imagej2_base_utils + +parser = argparse.ArgumentParser() +parser.add_argument( '--input', dest='input', help='Path to the input file' ) +parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) +parser.add_argument( '--operation', dest='operation', help='Operation' ) +parser.add_argument( '--expression', dest='expression', default=None, help='Expression' ) +parser.add_argument( '--bin_constant', dest='bin_constant', type=int, default=None, help='Constant of type binary integer' ) +parser.add_argument( '--float_constant', dest='float_constant', type=float, default=None, help='Constant of type float' ) +parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) +parser.add_argument( '--output', dest='output', help='Path to the output file' ) +parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' ) +args = parser.parse_args() + +tmp_dir = imagej2_base_utils.get_temp_dir() +# ImageJ expects valid image file extensions, so the Galaxy .dat extension does not +# work for some features. The following creates a symlink with an appropriate file +# extension that points to the Galaxy dataset. This symlink is used by ImageJ. +tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) +tmp_output_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' ) +# Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. +error_log = tempfile.NamedTemporaryFile( delete=False ).name + +# 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' % error_log +cmd += ' %s' % tmp_input_path +cmd += ' %s' % args.operation +# Handle the expression, which must be enclosed in " if not None. +if args.expression in [ None, 'None' ]: + cmd += ' None' +else: + cmd += ' "%s"' % args.expression +cmd += imagej2_base_utils.handle_none_type( args.bin_constant, val_type='int' ) +cmd += imagej2_base_utils.handle_none_type( args.float_constant ) +cmd += ' %s' % tmp_output_path +cmd += ' %s' % args.output_datatype + +# Run the command. +proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) +rc = proc.wait() + +# Handle execution errors. +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 ) + +# Handle processing errors. +if os.path.getsize( error_log ) > 0: + error_message = open( error_log, 'r' ).read() + imagej2_base_utils.stop_err( error_message ) + +# Save the output image. +shutil.move( tmp_output_path, args.output ) +imagej2_base_utils.cleanup_before_exit( tmp_dir )