Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic

annotate imagej2_noise.py @ 0:1bf7e70e67f9 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 16:56:02 -0400
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1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "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
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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9 if __name__=="__main__":
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10 # Parse Command Line.
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 parser = argparse.ArgumentParser()
1bf7e70e67f9 "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( '--input', dest='input', help='Path to the input file' )
1bf7e70e67f9 "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( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
1bf7e70e67f9 "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', dest='noise', help='Specified noise to add to or remove from the image' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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15 parser.add_argument( '--standard_deviation', dest='standard_deviation', type=float, default=None, help='Standard deviation' )
1bf7e70e67f9 "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( '--radius', dest='radius', type=float, default=None, help='Radius' )
1bf7e70e67f9 "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( '--threshold', dest='threshold', type=float, default=None, help='Threshold' )
1bf7e70e67f9 "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( '--which_outliers', dest='which_outliers', default=None, help='Which outliers' )
1bf7e70e67f9 "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( '--randomj', dest='randomj', default=None, help='RandomJ' )
1bf7e70e67f9 "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( '--trials', dest='trials', type=float, default=None, help='Trials' )
1bf7e70e67f9 "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( '--probability', dest='probability', type=float, default=None, help='Probability' )
1bf7e70e67f9 "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( '--lammbda', dest='lammbda', type=float, default=None, help='Lambda' )
1bf7e70e67f9 "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( '--order', dest='order', type=int, default=None, help='Order' )
1bf7e70e67f9 "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( '--mean', dest='mean', type=float, default=None, help='Mean' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 parser.add_argument( '--sigma', dest='sigma', type=float, default=None, help='Sigma' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 parser.add_argument( '--min', dest='min', type=float, default=None, help='Min' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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27 parser.add_argument( '--max', dest='max', type=float, default=None, help='Max' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 parser.add_argument( '--insertion', dest='insertion', default=None, help='Insertion' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
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30 parser.add_argument( '--output', dest='output', help='Path to the output file' )
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31 args = parser.parse_args()
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32
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33 tmp_dir = imagej2_base_utils.get_temp_dir()
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 # work for some features. The following creates a symlink with an appropriate file
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.input_datatype )
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39
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40 # Define command response buffers.
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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41 tmp_out = tempfile.NamedTemporaryFile().name
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42 tmp_stdout = open( tmp_out, 'wb' )
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43 tmp_err = tempfile.NamedTemporaryFile().name
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44 tmp_stderr = open( tmp_err, 'wb' )
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45 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
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46 error_log = tempfile.NamedTemporaryFile( delete=False ).name
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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47 # Build the command line.
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48 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
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49 if cmd is None:
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50 imagej2_base_utils.stop_err( "ImageJ not found!" )
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51 cmd += ' %s' % error_log
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52 cmd += ' %s' % tmp_input_path
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53 cmd += ' %s' % args.input_datatype
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54 cmd += ' %s ' % args.noise
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55 cmd += imagej2_base_utils.handle_none_type( args.standard_deviation )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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56 cmd += imagej2_base_utils.handle_none_type( args.radius )
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57 cmd += imagej2_base_utils.handle_none_type( args.threshold )
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58 cmd += ' %s' % args.which_outliers
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59 cmd += ' %s' % args.randomj
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60 cmd += imagej2_base_utils.handle_none_type( args.trials )
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61 cmd += imagej2_base_utils.handle_none_type( args.probability )
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62 cmd += imagej2_base_utils.handle_none_type( args.lammbda )
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63 cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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64 cmd += imagej2_base_utils.handle_none_type( args.mean )
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65 cmd += imagej2_base_utils.handle_none_type( args.sigma )
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66 cmd += imagej2_base_utils.handle_none_type( args.min )
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67 cmd += imagej2_base_utils.handle_none_type( args.max )
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68 cmd += ' %s' % args.insertion
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69 cmd += ' %s' % tmp_output_path
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71 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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72 rc = proc.wait()
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74 # Handle execution errors.
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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75 if rc != 0:
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
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76 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
77 imagej2_base_utils.stop_err( error_message )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
78 # Handle processing errors.
1bf7e70e67f9 "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 if os.path.getsize( error_log ) > 0:
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
80 error_message = open( error_log, 'r' ).read()
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
81 imagej2_base_utils.stop_err( error_message )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
82 # Save the output image.
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
83 shutil.move( tmp_output_path, args.output )
1bf7e70e67f9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
imgteam
parents:
diff changeset
84 imagej2_base_utils.cleanup_before_exit( tmp_dir )