Mercurial > repos > iuc > imagej2_noise

annotate imagej2_noise.py @ 2:c8fc3f34cbff draft

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planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author iuc
date Tue, 04 Aug 2015 11:15:16 -0400
parents da9a450c85b7
children d99cf938ad41
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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 if __name__=="__main__":
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10 # Parse Command Line.
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11 parser = argparse.ArgumentParser()
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12 parser.add_argument( '--input', dest='input', help='Path to the input file' )
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13 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' )
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14 parser.add_argument( '--noise', dest='noise', help='Specified noise to add to or remove from the image' )
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15 parser.add_argument( '--standard_deviation', dest='standard_deviation', type=float, default=None, help='Standard deviation' )
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16 parser.add_argument( '--radius', dest='radius', type=float, default=None, help='Radius' )
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17 parser.add_argument( '--threshold', dest='threshold', type=float, default=None, help='Threshold' )
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18 parser.add_argument( '--which_outliers', dest='which_outliers', default=None, help='Which outliers' )
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19 parser.add_argument( '--randomj', dest='randomj', default=None, help='RandomJ' )
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20 parser.add_argument( '--trials', dest='trials', type=float, default=None, help='Trials' )
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21 parser.add_argument( '--probability', dest='probability', type=float, default=None, help='Probability' )
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22 parser.add_argument( '--lammbda', dest='lammbda', type=float, default=None, help='Lambda' )
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23 parser.add_argument( '--order', dest='order', type=int, default=None, help='Order' )
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24 parser.add_argument( '--mean', dest='mean', type=float, default=None, help='Mean' )
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25 parser.add_argument( '--sigma', dest='sigma', type=float, default=None, help='Sigma' )
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26 parser.add_argument( '--min', dest='min', type=float, default=None, help='Min' )
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27 parser.add_argument( '--max', dest='max', type=float, default=None, help='Max' )
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28 parser.add_argument( '--insertion', dest='insertion', default=None, help='Insertion' )
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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( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
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31 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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32 parser.add_argument( '--output', dest='output', help='Path to the output file' )
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33 args = parser.parse_args()
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34
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35 tmp_dir = imagej2_base_utils.get_temp_dir()
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36 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
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37 # work for some features. The following creates a symlink with an appropriate file
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38 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
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39 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
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40 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.input_datatype )
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41 # Set the size of the memory allocation pool used by the JVM.
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42 memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
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43
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44 # Define command response buffers.
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45 tmp_out = tempfile.NamedTemporaryFile().name
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46 tmp_stdout = open( tmp_out, 'wb' )
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47 tmp_err = tempfile.NamedTemporaryFile().name
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48 tmp_stderr = open( tmp_err, 'wb' )
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49 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
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50 error_log = tempfile.NamedTemporaryFile( delete=False ).name
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51 # Build the command line.
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52 cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
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53 if cmd is None:
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54 imagej2_base_utils.stop_err( "ImageJ not found!" )
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55 cmd += ' %s' % error_log
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56 cmd += ' %s' % tmp_input_path
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57 cmd += ' %s' % args.input_datatype
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58 cmd += ' %s ' % args.noise
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59 cmd += imagej2_base_utils.handle_none_type( args.standard_deviation )
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60 cmd += imagej2_base_utils.handle_none_type( args.radius )
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61 cmd += imagej2_base_utils.handle_none_type( args.threshold )
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62 cmd += ' %s' % args.which_outliers
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63 cmd += ' %s' % args.randomj
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64 cmd += imagej2_base_utils.handle_none_type( args.trials )
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65 cmd += imagej2_base_utils.handle_none_type( args.probability )
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66 cmd += imagej2_base_utils.handle_none_type( args.lammbda )
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67 cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' )
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68 cmd += imagej2_base_utils.handle_none_type( args.mean )
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69 cmd += imagej2_base_utils.handle_none_type( args.sigma )
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70 cmd += imagej2_base_utils.handle_none_type( args.min )
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71 cmd += imagej2_base_utils.handle_none_type( args.max )
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72 cmd += ' %s' % args.insertion
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73 cmd += ' %s' % tmp_output_path
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74
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75 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
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76 rc = proc.wait()
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77
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78 # Handle execution errors.
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79 if rc != 0:
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80 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
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81 imagej2_base_utils.stop_err( error_message )
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82 # Handle processing errors.
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83 if os.path.getsize( error_log ) > 0:
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84 error_message = open( error_log, 'r' ).read()
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85 imagej2_base_utils.stop_err( error_message )
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86 # Save the output image.
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87 shutil.move( tmp_output_path, args.output )
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88 imagej2_base_utils.cleanup_before_exit( tmp_dir )