annotate imagej2_analyze_skeleton.py @ 0:bb84f130a4e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

#!/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( '--black_background', dest='black_background', help='Black background' )
parser.add_argument( '--prune_cycle_method', dest='prune_cycle_method', default='none', help='Prune cycle method' )
parser.add_argument( '--prune_ends', dest='prune_ends', default='no', help='Prune ends' )
parser.add_argument( '--calculate_largest_shortest_path', dest='calculate_largest_shortest_path', default='no', help='Calculate largest shortest path' )
parser.add_argument( '--show_detailed_info', dest='show_detailed_info', default='no', help='Show detailed info' )
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' )
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 )

# 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.black_background
cmd += ' %s' % args.prune_cycle_method
cmd += ' %s' % args.prune_ends
cmd += ' %s' % args.calculate_largest_shortest_path
cmd += ' %s' % args.show_detailed_info
cmd += ' %s' % args.output

# 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 )

imagej2_base_utils.cleanup_before_exit( tmp_dir )