Mercurial > repos > iuc > imagej2_convert_format

annotate imagej2_utils.py @ 5:a3806b0a32ed draft default tip

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planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:30:31 -0400
parents 312e8ce708b1
children
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1 import bioformats
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2 import javabridge
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3 import os
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4 import shutil
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5
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6 FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None )
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7 FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None )
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8 FIJI_PLUGIN_DIR = os.environ.get( 'FIJI_PLUGIN_DIR', None )
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9 FIJI_ROOT_DIR = os.environ.get( 'FIJI_ROOT_DIR', None )
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10
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11 def get_java_class_path():
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12 """
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13 Return the Java class path for use when starting the JVM via Javabridge.
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14 This function expects the following environment variable settings:
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15 FIJI_JAR_DIR, FIJI_PLUGIN_DIR, FIJI_OSX_JAVA3D_DIR.
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16 """
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17 class_path_list = []
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18 # Handle javabridge.JARS setting.
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19 for jar_file in javabridge.JARS:
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20 class_path_list.append( jar_file )
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21 if FIJI_JAR_DIR is not None and os.path.isdir( FIJI_JAR_DIR ):
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22 for filename in os.listdir( FIJI_JAR_DIR ):
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23 if filename.endswith( '.jar' ):
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24 class_path_list.append( os.path.join( FIJI_JAR_DIR, filename ) )
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25 fiji_bioformats_jar_dir = os.path.join( FIJI_JAR_DIR, 'bio-formats' )
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26 if os.path.isdir( fiji_bioformats_jar_dir ):
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27 for filename in os.listdir( fiji_bioformats_jar_dir ):
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28 if filename.endswith( '.jar' ):
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29 class_path_list.append( os.path.join( fiji_bioformats_jar_dir, filename ) )
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30 if FIJI_PLUGIN_DIR is not None and os.path.isdir( FIJI_PLUGIN_DIR ):
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31 for filename in os.listdir( FIJI_PLUGIN_DIR ):
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32 if filename.endswith( '.jar' ):
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33 class_path_list.append( os.path.join( FIJI_PLUGIN_DIR, filename ) )
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34 if FIJI_OSX_JAVA3D_DIR is not None and os.path.isdir( FIJI_OSX_JAVA3D_DIR ):
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35 for filename in os.listdir( FIJI_OSX_JAVA3D_DIR ):
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36 if filename.endswith( '.jar' ):
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37 class_path_list.append( os.path.join( FIJI_OSX_JAVA3D_DIR, filename ) )
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38 return class_path_list
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39
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40 def kill_vm():
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41 javabridge.detach()
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42 javabridge.kill_vm()
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43
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44 def load_image( image_path, c=None, z=0, t=0, series=None, index=None,
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45 rescale=True, wants_max_intensity=False, channel_names=None ):
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46 """
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47 Load in image from a file using bioformats, always returning a tuple of
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48 (image, scale) where the image is a numpy.ndarray object, and the scale
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49 is an integer or None.
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50 """
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51 result = bioformats.load_image( path=image_path,
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52 c=c,
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53 z=z,
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54 t=t,
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55 series=series,
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56 index=index,
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57 rescale=rescale,
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58 wants_max_intensity=wants_max_intensity,
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59 channel_names=channel_names )
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60 if wants_max_intensity:
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61 # The value of result is a tuple: ( image, scale )
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62 image, scale = result
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63 else:
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64 image = result
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65 scale = None
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66 # The image is a numpy.ndarray object, and the scale is an integer or None.
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67 return image, scale
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68
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69 def start_vm( args=None, class_path=None, max_heap_size=None, run_headless=False ):
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70 """
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71 Start the JVM via Javabridge.
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72 """
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73 if class_path is None:
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74 class_path = get_java_class_path()
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75 # Start the JVM.
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76 javabridge.start_vm( args=args, class_path=class_path, max_heap_size=max_heap_size, run_headless=run_headless )
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77 # Suppress Java logging to stdout.
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78 java_stack = javabridge.make_instance( 'java/io/ByteArrayOutputStream', "()V" )
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79 java_stack_ps = javabridge.make_instance( 'java/io/PrintStream', "(Ljava/io/OutputStream;)V", java_stack )
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80 javabridge.static_call( 'Ljava/lang/System;', "setErr", '(Ljava/io/PrintStream;)V', java_stack_ps )
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81 java_out = javabridge.make_instance( 'java/io/ByteArrayOutputStream', "()V" )
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82 java_out_ps = javabridge.make_instance( 'java/io/PrintStream', "(Ljava/io/OutputStream;)V", java_out )
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83 javabridge.static_call( 'Ljava/lang/System;', "setOut", '(Ljava/io/PrintStream;)V', java_out_ps )
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84 javabridge.attach()
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85
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86 def write_image( image_path, pixels, pixel_type, c=0, z=0, t=0,
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87 size_c=1, size_z=1, size_t=1, channel_names=None,
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88 move_to=None ):
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89 """
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90 Write an image file using bioformats. Bioformats uses file extensions
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91 (e.g., .job, .gif, etc) when reading and writing image files, so the
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92 Galaxy dataset naming convention of setting all file extensions as .dat
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93 is handled by setting the move_to parameter to the value of the Galaxy
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94 dataset path.
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95 """
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96 bioformats.write_image( pathname=image_path,
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97 pixels=pixels,
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98 pixel_type=pixel_type,
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99 c=c,
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100 z=z,
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101 t=t,
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102 size_c=size_c,
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103 size_z=size_z,
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104 size_t=size_t,
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105 channel_names=channel_names )
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106 if move_to is not None and os.path.exists( move_to ):
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107 shutil.move( image_path, os.path.abspath( move_to ) )