# HG changeset patch
# User iuc
# Date 1440614232 14400
# Node ID 7a8b05b111f9f51db42d2c12e5aa5bf9844d9649
# Parent  9a24b7e6801090a68df01b1fa3ba0114538c7d9c
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty

diff -r 9a24b7e68010 -r 7a8b05b111f9 imagej2_base_utils.py
--- a/imagej2_base_utils.py	Tue Aug 04 11:15:04 2015 -0400
+++ b/imagej2_base_utils.py	Wed Aug 26 14:37:12 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 )
diff -r 9a24b7e68010 -r 7a8b05b111f9 imagej2_convert_format.py
--- a/imagej2_convert_format.py	Tue Aug 04 11:15:04 2015 -0400
+++ b/imagej2_convert_format.py	Wed Aug 26 14:37:12 2015 -0400
@@ -8,15 +8,12 @@
     parser = argparse.ArgumentParser()
     parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' )
     parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' )
-    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.' )
     parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' )
     parser.add_argument( '--out_fname', help='Path to the output file' )
     args = parser.parse_args()
-    # Set the size of the memory allocation pool used by the JVM.
-    max_heap_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
+
     # Start the JVM via the Javabridge.
-    imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=max_heap_size, run_headless=True )
+    imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=None, run_headless=True )
     try:
         tmp_dir = imagej2_base_utils.get_temp_dir()
         in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype )
diff -r 9a24b7e68010 -r 7a8b05b111f9 imagej2_convert_format.xml
--- a/imagej2_convert_format.xml	Tue Aug 04 11:15:04 2015 -0400
+++ b/imagej2_convert_format.xml	Wed Aug 26 14:37:12 2015 -0400
@@ -1,22 +1,20 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_convert_format" name="Convert image format" version="1.0.0">
+<tool id="imagej2_convert_format" name="Convert image format" version="@WRAPPER_VERSION@.0">
     <description>with bioformats</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="python_bioformats_104_requirements" />
+    <expand macro="python_bioformats_requirements" />
     <command interpreter="python">
 <![CDATA[
         imagej2_convert_format.py
         --in_fname "$input"
         --input_datatype $input.ext
-        @max_heap_size_args@
         --output_datatype $output_datatype
         --out_fname "$output"
 ]]>
     </command>
     <inputs>
-        <expand macro="max_heap_size_type_conditional" />
         <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
         <param name="output_datatype" type="select" label="Convert to format">
             <option value="jpg" selected="true">jpg</option>
diff -r 9a24b7e68010 -r 7a8b05b111f9 imagej2_macros.xml
--- a/imagej2_macros.xml	Tue Aug 04 11:15:04 2015 -0400
+++ b/imagej2_macros.xml	Wed Aug 26 14:37:12 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>