Mercurial > repos > iuc > imagej2_analyze_skeleton

annotate imagej2_analyze_skeleton.py @ 0:a989ca433027 draft

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planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author iuc
date Tue, 04 Aug 2015 11:14:30 -0400
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children 9631aab7da53
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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4 import shutil
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5 import subprocess
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6 import tempfile
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7 import imagej2_base_utils
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8
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9 parser = argparse.ArgumentParser()
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10 parser.add_argument( '--input', dest='input', help='Path to the input file' )
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11 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
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12 parser.add_argument( '--prune_cycle_method', dest='prune_cycle_method', default='none', help='Prune cycle method' )
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13 parser.add_argument( '--prune_ends', dest='prune_ends', default='no', help='Prune ends' )
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14 parser.add_argument( '--calculate_largest_shortest_path', dest='calculate_largest_shortest_path', default='no', help='Calculate largest shortest path' )
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15 parser.add_argument( '--show_detailed_info', dest='show_detailed_info', default='no', help='Show detailed info' )
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16 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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17 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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18 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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19 parser.add_argument( '--output', dest='output', help='Path to the output file' )
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20 args = parser.parse_args()
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21
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22 tmp_dir = imagej2_base_utils.get_temp_dir()
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23 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
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24 # work for some features. The following creates a symlink with an appropriate file
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25 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
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26 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
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27 # Set the size of the memory allocation pool used by the JVM.
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28 memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
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29
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30 # Define command response buffers.
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31 tmp_out = tempfile.NamedTemporaryFile().name
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32 tmp_stdout = open( tmp_out, 'wb' )
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33 tmp_err = tempfile.NamedTemporaryFile().name
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34 tmp_stderr = open( tmp_err, 'wb' )
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35 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
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36 error_log = tempfile.NamedTemporaryFile( delete=False ).name
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37
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38 # Build the command line.
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39 cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
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40 if cmd is None:
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41 imagej2_base_utils.stop_err( "ImageJ not found!" )
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42 cmd += ' %s' % error_log
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43 cmd += ' %s' % tmp_input_path
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44 cmd += ' %s' % args.prune_cycle_method
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45 cmd += ' %s' % args.prune_ends
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46 cmd += ' %s' % args.calculate_largest_shortest_path
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47 cmd += ' %s' % args.show_detailed_info
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48 cmd += ' %s' % args.output
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49
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50 # Run the command.
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51 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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52 rc = proc.wait()
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53
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54 # Handle execution errors.
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55 if rc != 0:
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56 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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57 imagej2_base_utils.stop_err( error_message )
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58 # Handle processing errors.
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59 if os.path.getsize( error_log ) > 0:
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60 error_message = open( error_log, 'r' ).read()
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61 imagej2_base_utils.stop_err( error_message )
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62
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63 imagej2_base_utils.cleanup_before_exit( tmp_dir )