--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_utils.py	Tue Jun 09 12:21:40 2015 -0400
@@ -0,0 +1,107 @@
+import bioformats
+import javabridge
+import os
+import shutil
+
+FIJI_JAR_DIR = os.environ.get( 'FIJI_JAR_DIR', None )
+FIJI_OSX_JAVA3D_DIR = os.environ.get( 'FIJI_OSX_JAVA3D_DIR', None )
+FIJI_PLUGIN_DIR = os.environ.get( 'FIJI_PLUGIN_DIR', None )
+FIJI_ROOT_DIR = os.environ.get( 'FIJI_ROOT_DIR', None )
+
+def get_java_class_path():
+    """
+    Return the Java class path for use when starting the JVM via Javabridge.
+    This function expects the following environment variable settings:
+    FIJI_JAR_DIR, FIJI_PLUGIN_DIR, FIJI_OSX_JAVA3D_DIR.
+    """
+    class_path_list = []
+    # Handle javabridge.JARS setting.
+    for jar_file in javabridge.JARS:
+        class_path_list.append( jar_file )
+    if FIJI_JAR_DIR is not None and os.path.isdir( FIJI_JAR_DIR ):
+        for filename in os.listdir( FIJI_JAR_DIR ):
+            if filename.endswith( '.jar' ):
+                class_path_list.append( os.path.join( FIJI_JAR_DIR, filename ) )
+        fiji_bioformats_jar_dir = os.path.join( FIJI_JAR_DIR, 'bio-formats' )
+        if os.path.isdir( fiji_bioformats_jar_dir ):
+            for filename in os.listdir( fiji_bioformats_jar_dir ):
+                if filename.endswith( '.jar' ):
+                    class_path_list.append( os.path.join( fiji_bioformats_jar_dir, filename ) )
+    if FIJI_PLUGIN_DIR is not None and os.path.isdir( FIJI_PLUGIN_DIR ):
+        for filename in os.listdir( FIJI_PLUGIN_DIR ):
+            if filename.endswith( '.jar' ):
+                class_path_list.append( os.path.join( FIJI_PLUGIN_DIR, filename ) )
+    if FIJI_OSX_JAVA3D_DIR is not None and os.path.isdir( FIJI_OSX_JAVA3D_DIR ):
+        for filename in os.listdir( FIJI_OSX_JAVA3D_DIR ):
+            if filename.endswith( '.jar' ):
+                class_path_list.append( os.path.join( FIJI_OSX_JAVA3D_DIR, filename ) )
+    return class_path_list
+
+def kill_vm():
+    javabridge.detach()
+    javabridge.kill_vm()
+
+def load_image( image_path, c=None, z=0, t=0, series=None, index=None,
+                rescale=True, wants_max_intensity=False, channel_names=None ):
+    """
+    Load in image from a file using bioformats, always returning a tuple of
+    (image, scale) where the image is a numpy.ndarray object, and the scale
+    is an integer or None.
+    """
+    result = bioformats.load_image( path=image_path,
+                                    c=c,
+                                    z=z,
+                                    t=t,
+                                    series=series,
+                                    index=index,
+                                    rescale=rescale,
+                                    wants_max_intensity=wants_max_intensity,
+                                    channel_names=channel_names )
+    if wants_max_intensity:
+        # The value of result is a tuple: ( image, scale )
+        image, scale = result
+    else:
+        image = result
+        scale = None
+     # The image is a numpy.ndarray object, and the scale is an integer or None.
+    return image, scale
+
+def start_vm( args=None, class_path=None, max_heap_size=None, run_headless=False ):
+    """
+    Start the JVM via Javabridge.
+    """
+    if class_path is None:
+        class_path = get_java_class_path()
+    # Start the JVM.
+    javabridge.start_vm( args=args, class_path=class_path, max_heap_size=max_heap_size, run_headless=run_headless )
+    # Suppress Java logging to stdout.
+    java_stack = javabridge.make_instance( 'java/io/ByteArrayOutputStream', "()V" )
+    java_stack_ps = javabridge.make_instance( 'java/io/PrintStream', "(Ljava/io/OutputStream;)V", java_stack )
+    javabridge.static_call( 'Ljava/lang/System;', "setErr", '(Ljava/io/PrintStream;)V', java_stack_ps )
+    java_out = javabridge.make_instance( 'java/io/ByteArrayOutputStream', "()V" )
+    java_out_ps = javabridge.make_instance( 'java/io/PrintStream', "(Ljava/io/OutputStream;)V", java_out )
+    javabridge.static_call( 'Ljava/lang/System;', "setOut", '(Ljava/io/PrintStream;)V', java_out_ps )
+    javabridge.attach()
+
+def write_image( image_path, pixels, pixel_type, c=0, z=0, t=0,
+                 size_c=1, size_z=1, size_t=1, channel_names=None,
+                 move_to=None ):
+    """
+    Write an image file using bioformats.  Bioformats uses file extensions
+    (e.g., .job, .gif, etc) when reading and writing image files, so the
+    Galaxy dataset naming convention of setting all file extensions as .dat
+    is handled by setting the move_to parameter to the value of the Galaxy
+    dataset path.
+    """
+    bioformats.write_image( pathname=image_path,
+                            pixels=pixels,
+                            pixel_type=pixel_type,
+                            c=c,
+                            z=z,
+                            t=t,
+                            size_c=size_c,
+                            size_z=size_z,
+                            size_t=size_t,
+                            channel_names=channel_names )
+    if move_to is not None and os.path.exists( move_to ):
+        shutil.move( image_path, os.path.abspath( move_to ) )