Mercurial > repos > iuc > imagej2_create_image
view imagej2_create_image.py @ 3:bb65623b90a8 draft
planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
| author | iuc |
|---|---|
| date | Tue, 04 Aug 2015 11:15:10 -0400 |
| parents | 26703988cdb3 |
| children | 48f25b8408e1 |
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#!/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( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' ) parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' ) 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 ) # Set the size of the memory allocation pool used by the JVM. memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size ) # 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( memory_size, 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 )
