Mercurial > repos > iuc > imagej2_create_image

annotate imagej2_create_image.py @ 0:dfe318d97378 draft

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planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
author iuc
date Tue, 09 Jun 2015 12:22:03 -0400
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children 26703988cdb3
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1 #!/usr/bin/env python
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2 # Galaxy wrapper for use with Imagej2 by Greg Von Kuster
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3 """
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4 A wrapper script for running ImageJ2 Jython scripts.
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5 """
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6 import argparse
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7 import shutil
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8 import subprocess
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9 import tempfile
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10 import imagej2_base_utils
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11
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12 if __name__=="__main__":
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13 # Parse Command Line.
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14 parser = argparse.ArgumentParser()
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15 parser.add_argument( '--width', dest='width', type=int, help='Image width in pixels' )
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16 parser.add_argument( '--height', dest='height', type=int, help='Image height in pixels' )
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17 parser.add_argument( '--depth', dest='depth', type=int, help='Image depth (specifies the number of stack slices)' )
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18 parser.add_argument( '--image_type', dest='image_type', help='Image type' )
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19 parser.add_argument( '--image_title', dest='image_title', default='', help='Image title' )
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20 parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
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21 parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
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22 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image format' )
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23 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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24 parser.add_argument( '--out_fname', help='Path to the output file' )
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25 args = parser.parse_args()
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26
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27 tmp_dir = imagej2_base_utils.get_temp_dir()
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28 tmp_image_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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29 # Set the size of the memory allocation pool used by the JVM.
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30 memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
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31
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32 # Define command response buffers.
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33 tmp_out = tempfile.NamedTemporaryFile().name
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34 tmp_stdout = open( tmp_out, 'wb' )
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35 tmp_err = tempfile.NamedTemporaryFile().name
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36 tmp_stderr = open( tmp_err, 'wb' )
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37 # Build the command line.
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38 cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
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39 if cmd is None:
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40 imagej2_base_utils.stop_err( "ImageJ not found!" )
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41 cmd += ' %s %d %d %d %s %s' % ( args.image_title, args.width, args.height, args.depth, args.image_type, tmp_image_path )
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42 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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43 rc = proc.wait()
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44 if rc != 0:
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45 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_stdout )
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46 imagej2_base_utils.stop_err( error_message )
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47 shutil.move( tmp_image_path, args.out_fname )
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48 imagej2_base_utils.cleanup_before_exit( tmp_dir )