--- a/imagej2_base_utils.py	Tue Aug 04 13:21:10 2015 -0400
+++ b/imagej2_base_utils.py	Wed Aug 26 14:38:12 2015 -0400
@@ -86,21 +86,6 @@
     os.symlink( input_file, image_path )
     return image_path
 
-def get_max_heap_size_value( max_heap_size_type, max_heap_size ):
-    """
-    Return a string that can be used by the javabridge to set the size
-    of the memory allocation pool used by the JVM.  The value must be
-    determined to be a multiple of 1024 or it will be ignored.
-    """
-    if max_heap_size_type == 'default':
-        return None
-    if max_heap_size_type == 'megabytes':
-        if int( max_heap_size ) % 1024 not in [ 0, 256, 512 ]:
-            return None
-        return '%sm' % str( max_heap_size )
-    if max_heap_size_type == 'gigabytes':
-        return '%sg' % str( max_heap_size )
-
 def get_platform_info_dict():
     '''Return a dict with information about the current platform.'''
     platform_dict = {}
@@ -172,6 +157,7 @@
             return ' %.1f' % val
         elif val_type == 'int':
             return ' %d' % val
+    return ' %s' % val
 
 def stop_err( msg ):
     sys.stderr.write( msg )

--- a/imagej2_bunwarpj_align.py	Tue Aug 04 13:21:10 2015 -0400
+++ b/imagej2_bunwarpj_align.py	Wed Aug 26 14:38:12 2015 -0400
@@ -35,8 +35,6 @@
 parser.add_argument( '--target_out', default=None, help='Output target image' )
 parser.add_argument( '--target_out_datatype', default=None, help='Output registered target image format' )
 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
-parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
-parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
 
 args = parser.parse_args()
 
@@ -66,9 +64,6 @@
     target_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_target_out_tiff_path )
     tmp_target_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % target_file_name )
 
-# Set the size of the memory allocation pool used by the JVM.
-memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
-
 # Define command response buffers.
 tmp_out = tempfile.NamedTemporaryFile().name
 tmp_stdout = open( tmp_out, 'wb' )
@@ -76,7 +71,7 @@
 tmp_stderr = open( tmp_err, 'wb' )
 
 # Build the command line to align the two images.
-cmd = imagej2_base_utils.get_base_cmd_bunwarpj( memory_size )
+cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
 if cmd is None:
     imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
 cmd += ' -align'
@@ -142,7 +137,7 @@
 tmp_stderr = open( tmp_err, 'wb' )
 
 # Build the command line to handle the multi-slice tiff images.
-cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script )
+cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
 if cmd is None:
     imagej2_base_utils.stop_err( "ImageJ not found!" )
 if args.mono:

--- a/imagej2_bunwarpj_align.xml	Tue Aug 04 13:21:10 2015 -0400
+++ b/imagej2_bunwarpj_align.xml	Wed Aug 26 14:38:12 2015 -0400
@@ -1,10 +1,10 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_bunwarpj_align" name="Align two images" version="1.0.0">
+<tool id="imagej2_bunwarpj_align" name="Align two images" version="@WRAPPER_VERSION@.0">
     <description>with bUnwarpJ</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_20141125_requirements" />
+    <expand macro="fiji_requirements" />
     <command>
 <![CDATA[
     python $__tool_directory__/imagej2_bunwarpj_align.py
@@ -44,7 +44,6 @@
         --target_out_datatype $target_out_datatype
     #end if
     --jython_script $__tool_directory__/jython_script.py
-    @max_heap_size_args@
 ]]>
     </command>
     <inputs>
@@ -119,7 +118,6 @@
             <when value="mono"/>
             <when value="save_transformation"/>
         </conditional>
-        <expand macro="max_heap_size_type_conditional" />
     </inputs>
     <outputs>
         <data name="source_out" format="png" label="${tool.name} on ${on_string}: Registered source image">

--- a/imagej2_macros.xml	Tue Aug 04 13:21:10 2015 -0400
+++ b/imagej2_macros.xml	Wed Aug 26 14:38:12 2015 -0400
@@ -1,11 +1,12 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <xml name="fiji_20141125_requirements">
+    <token name="@WRAPPER_VERSION@">1.0</token>
+    <xml name="fiji_requirements">
         <requirements>
             <requirement type="package" version="20141125">fiji</requirement>
         </requirements>
     </xml>
-    <xml name="python_bioformats_104_requirements">
+    <xml name="python_bioformats_requirements">
         <requirements>
             <requirement type="package" version="20141125">fiji</requirement>
             <requirement type="package" version="1.0.11">javabridge</requirement>
@@ -53,33 +54,27 @@
             <option value="yes">Yes</option>
         </param>
     </xml>
+    <xml name="black_background_param">
+        <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </xml>
     <token name="@make_binary_args@">
         --iterations $iterations
         --count $count
         --black_background $black_background
         --pad_edges_when_eroding $pad_edges_when_eroding
     </token>
-    <xml name="max_heap_size_type_conditional">
-        <conditional name="set_max_heap_size">
-            <param name="max_heap_size_type" type="select" label="Maximum size of the memory allocation pool used by the JVM" help="This value must be a multiple of 1024 or it will be ignored and the system default will be used.">
-                <option value="default" selected="True">Do not set</option>
-                <option value="megabytes">Set in megabytes</option>
-                <option value="gigabytes">Set in gigabytes</option>
-            </param>
-            <when value="default" >
-                <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/>
-            </when>
-            <when value="megabytes">
-                <param name="max_heap_size" type="integer" value="512" min="256" label="Maximum size, in megabytes, of the memory allocation pool" help="Examples: 256, 512, etc."/>
-            </when>
-            <when value="gigabytes">
-                <param name="max_heap_size" type="integer" value="1" min="1" label="Maximum size, in gigabytes, of the memory allocation pool" help="Examples: 1, 2, etc."/>
-            </when>
-        </conditional>
-    </xml>
-    <token name="@max_heap_size_args@">
-        --max_heap_size_type $set_max_heap_size.max_heap_size_type
-        --max_heap_size $set_max_heap_size.max_heap_size
+    <token name="@requires_binary_input@">
+.. class:: warningmark
+
+This tool works on binary images, so other image types will automatically be converted to binary
+before they are analyzed.  This step is performed using the ImageJ2 **Make Binary** command with
+the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No.  The tool
+allows you to choose the **Black background** setting.  If these settings are not appropriate,
+first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2**
+tool, which allows you to change them.
     </token>
     <xml name="image_datatypes">
         <option value="bmp">bmp</option>

--- a/jython_utils.py	Tue Aug 04 13:21:10 2015 -0400
+++ b/jython_utils.py	Wed Aug 26 14:38:12 2015 -0400
@@ -4,6 +4,9 @@
 IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32',
                                        '3':'COLOR_256', '4':'COLOR_RGB' }
 
+def asbool( val ):
+    return str( val ).lower() in [ 'yes', 'true' ]
+
 def convert_before_saving_as_tiff( image_plus ):
     # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
     # slices which can be viewed in ImageJ.  The 3 slices are: 1) the
@@ -26,6 +29,14 @@
     IJ.saveAs( image_plus, 'png', tmp_out_png_path )
     return IJ.openImage( tmp_out_png_path )
 
+def get_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ):
+    options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ]
+    if asbool( pad_edges_when_eroding ):
+        options.append( 'pad' )
+    if asbool( black_background ):
+        options.append( "black" )
+    return " ".join( options )
+
 def get_display_image_type( image_type ):
     return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None )