Mercurial > repos > imgteam > imagej2_sharpen

annotate imagej2_analyze_particles_binary.py @ 0:a84f2cbf091b 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 17:08:08 -0400
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a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "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
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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9 parser = argparse.ArgumentParser()
a84f2cbf091b "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' )
a84f2cbf091b "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' )
a84f2cbf091b "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( '--black_background', dest='black_background', help='Black background' )
a84f2cbf091b "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( '--size', dest='size', help='Size (pixel^2)' )
a84f2cbf091b "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( '--circularity_min', dest='circularity_min', type=float, help='Circularity minimum' )
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15 parser.add_argument( '--circularity_max', dest='circularity_max', type=float, help='Circularity maximum' )
a84f2cbf091b "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( '--show', dest='show', help='Show' )
a84f2cbf091b "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( '--display_results', dest='display_results', help='Display results' )
a84f2cbf091b "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( '--all_results', dest='all_results', help='All results' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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19 parser.add_argument( '--exclude_edges', dest='exclude_edges', help='Exclude edges' )
a84f2cbf091b "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( '--include_holes', dest='include_holes', help='Include holes' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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21 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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22 parser.add_argument( '--results', dest='results', default=None, help='Path to the output results file' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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23 parser.add_argument( '--output', dest='output', default=None, help='Path to the output image file' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 parser.add_argument( '--output_datatype', dest='output_datatype', default='data', help='Datatype of the output image' )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 args = parser.parse_args()
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a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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27 tmp_dir = imagej2_base_utils.get_temp_dir()
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 # work for some features. The following creates a symlink with an appropriate file
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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30 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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32 if args.output is None:
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 tmp_output_path = None
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 else:
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35 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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36
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37 # Define command response buffers.
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 tmp_out = tempfile.NamedTemporaryFile().name
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39 tmp_stdout = open( tmp_out, 'wb' )
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40 tmp_err = tempfile.NamedTemporaryFile().name
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41 tmp_stderr = open( tmp_err, 'wb' )
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42 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
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43 error_log = tempfile.NamedTemporaryFile( delete=False ).name
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44
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45 # Build the command line.
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
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47 if cmd is None:
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48 imagej2_base_utils.stop_err( "ImageJ not found!" )
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49 cmd += ' %s' % error_log
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50 cmd += ' %s' % tmp_input_path
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51 cmd += ' %s' % args.black_background
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52 cmd += ' %s' % args.size
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53 cmd += ' %.3f' % args.circularity_min
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54 cmd += ' %.3f' % args.circularity_max
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55 cmd += ' %s' % args.show
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56 cmd += ' %s' % args.display_results
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57 cmd += '%s' % imagej2_base_utils.handle_none_type( args.all_results, val_type='str' )
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58 cmd += ' %s' % args.exclude_edges
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59 cmd += ' %s' % args.include_holes
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60 cmd += '%s' % imagej2_base_utils.handle_none_type( tmp_output_path, val_type='str' )
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61 cmd += ' %s' % args.output_datatype
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62 cmd += '%s' % imagej2_base_utils.handle_none_type( args.results, val_type='str' )
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63
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64 # Run the command.
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65 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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66 rc = proc.wait()
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67
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68 # Handle execution errors.
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69 if rc != 0:
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70 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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71 imagej2_base_utils.stop_err( error_message )
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73 # Handle processing errors.
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74 if os.path.getsize( error_log ) > 0:
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75 error_message = open( error_log, 'r' ).read()
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76 imagej2_base_utils.stop_err( error_message )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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77
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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parents:
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78 if tmp_output_path is not None:
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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79 # Save the output image.
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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80 shutil.move( tmp_output_path, args.output )
a84f2cbf091b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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81 imagej2_base_utils.cleanup_before_exit( tmp_dir )