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annotate imagej2_find_maxima.py @ 0:7baf811ed973 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:59:39 -0400
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7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 #!/usr/bin/env python
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 import argparse
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 import os
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 import shutil
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 import subprocess
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6 import tempfile
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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7 import imagej2_base_utils
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8
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9 parser = argparse.ArgumentParser()
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 parser.add_argument( '--input', dest='input', help='Path to the input file' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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12 parser.add_argument( '--scale_when_converting', dest='scale_when_converting', help='Scale when converting RGB image' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 parser.add_argument( '--weighted_rgb_conversions', dest='weighted_rgb_conversions', help='Weighted RGB conversions for RGB image' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 parser.add_argument( '--noise_tolerance', dest='noise_tolerance', type=int, help='Noise tolerance' )
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15 parser.add_argument( '--output_type', dest='output_type', help='Output type' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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16 parser.add_argument( '--exclude_edge_maxima', dest='exclude_edge_maxima', help='Exclude edge maxima' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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17 parser.add_argument( '--light_background', dest='light_background', help='Light background' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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18 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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19 parser.add_argument( '--output', dest='output', help='Path to the output file' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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20 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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21 args = parser.parse_args()
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22
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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23 tmp_dir = imagej2_base_utils.get_temp_dir()
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 # work for some features. The following creates a symlink with an appropriate file
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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27 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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29
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30 # Define command response buffers.
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 tmp_out = tempfile.NamedTemporaryFile().name
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32 tmp_stdout = open( tmp_out, 'wb' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 tmp_err = tempfile.NamedTemporaryFile().name
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 tmp_stderr = open( tmp_err, 'wb' )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 error_log = tempfile.NamedTemporaryFile( delete=False ).name
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37
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38 # Build the command line.
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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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
7baf811ed973 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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43 cmd += ' %s' % tmp_input_path
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44 cmd += ' %s' % args.scale_when_converting
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45 cmd += ' %s' % args.weighted_rgb_conversions
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46 cmd += ' %d' % args.noise_tolerance
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47 cmd += ' %s' % args.output_type
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48 cmd += ' %s' % args.exclude_edge_maxima
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49 cmd += ' %s' % args.light_background
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50 cmd += ' %s' % tmp_output_path
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51 cmd += ' %s' % args.output_datatype
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52
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53 # Run the command.
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54 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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55 rc = proc.wait()
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57 # Handle execution errors.
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58 if rc != 0:
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59 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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60 imagej2_base_utils.stop_err( error_message )
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62 # Handle processing errors.
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63 if os.path.getsize( error_log ) > 0:
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64 error_message = open( error_log, 'r' ).read()
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65 imagej2_base_utils.stop_err( error_message )
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67 # Save the output image.
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68 shutil.move( tmp_output_path, args.output )
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69 imagej2_base_utils.cleanup_before_exit( tmp_dir )