# HG changeset patch
# User iuc
# Date 1440614261 14400
# Node ID d26f11339f08859abc1295c760d5fb620de4d874
# Parent  66d9e595dff29e46e6dc40656dcadf751eee6da3
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty

diff -r 66d9e595dff2 -r d26f11339f08 imagej2_base_utils.py
--- a/imagej2_base_utils.py	Tue Aug 04 13:20:29 2015 -0400
+++ b/imagej2_base_utils.py	Wed Aug 26 14:37:41 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 66d9e595dff2 -r d26f11339f08 imagej2_macros.xml
--- a/imagej2_macros.xml	Tue Aug 04 13:20:29 2015 -0400
+++ b/imagej2_macros.xml	Wed Aug 26 14:37:41 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>
diff -r 66d9e595dff2 -r d26f11339f08 imagej2_make_binary.py
--- a/imagej2_make_binary.py	Tue Aug 04 13:20:29 2015 -0400
+++ b/imagej2_make_binary.py	Wed Aug 26 14:37:41 2015 -0400
@@ -14,8 +14,6 @@
 parser.add_argument( '--black_background', dest='black_background', help='Black background' )
 parser.add_argument( '--pad_edges_when_eroding', dest='pad_edges_when_eroding', help='Pad edges when eroding' )
 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.' )
 parser.add_argument( '--output', dest='output', help='Path to the output file' )
 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
 args = parser.parse_args()
@@ -26,8 +24,6 @@
 # extension that points to the Galaxy dataset.  This symlink is used by ImageJ.
 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
-# 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' )
@@ -36,7 +32,7 @@
 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
 error_log = tempfile.NamedTemporaryFile( delete=False ).name
 # Build the command line.
-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!" )
 cmd += ' %s' % error_log
diff -r 66d9e595dff2 -r d26f11339f08 imagej2_make_binary.xml
--- a/imagej2_make_binary.xml	Tue Aug 04 13:20:29 2015 -0400
+++ b/imagej2_make_binary.xml	Wed Aug 26 14:37:41 2015 -0400
@@ -1,38 +1,27 @@
 <?xml version='1.0' encoding='UTF-8'?>
-<tool id="imagej2_make_binary" name="Convert to binary" version="1.0.0">
+<tool id="imagej2_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.0">
     <description>(black and white) with ImageJ2</description>
     <macros>
         <import>imagej2_macros.xml</import>
     </macros>
-    <expand macro="fiji_20141125_requirements" />
+    <expand macro="fiji_requirements" />
     <command>
 <![CDATA[
     python $__tool_directory__/imagej2_make_binary.py
     --input "$input"
     --input_datatype $input.ext
     @make_binary_args@
-    @max_heap_size_args@
     --jython_script $__tool_directory__/jython_script.py
-    --output_datatype $output_datatype
+    --output_datatype $output.ext
     --output "$output"
 ]]>
     </command>
     <inputs>
         <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
         <expand macro="make_binary_params" />
-        <param name="output_datatype" type="select" label="Save as format">
-            <expand macro="image_datatypes" />
-        </param>
-        <expand macro="max_heap_size_type_conditional" />
     </inputs>
     <outputs>
-        <data name="output" format_source="input" label="${tool.name} on ${on_string}">
-            <actions>
-                <action type="format">
-                    <option type="from_param" name="output_datatype" />
-                 </action>
-           </actions>
-       </data>
+        <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
diff -r 66d9e595dff2 -r d26f11339f08 jython_script.py
--- a/jython_script.py	Tue Aug 04 13:20:29 2015 -0400
+++ b/jython_script.py	Wed Aug 26 14:37:41 2015 -0400
@@ -1,40 +1,36 @@
 import jython_utils
 import sys
 from ij import IJ
-from ij import ImagePlus
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
 error_log = sys.argv[ -8 ]
 input = sys.argv[ -7 ]
-iterations = sys.argv[ -6 ]
-count = sys.argv[ -5 ]
-black_background = sys.argv[ -4 ]
-pad_edges_when_eroding = sys.argv[ -3 ]
+iterations = int( sys.argv[ -6 ] )
+count = int( sys.argv[ -5 ] )
+black_background = jython_utils.asbool( sys.argv[ -4 ] )
+pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
 tmp_output_path = sys.argv[ -2 ]
 output_datatype = sys.argv[ -1 ]
 
 # Open the input image file.
 input_image_plus = IJ.openImage( input )
-bit_depth = input_image_plus.getBitDepth()
-image_type = input_image_plus.getType()
 
 # Create a copy of the image.
-input_image_plus_copy = input_image_plus.createImagePlus()
-image_processor_copy = input_image_plus.getProcessor().duplicate()
-input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
 
 try:
-    options = [ "iterations=&iterations" "count=&count" ]
-    if black_background == "yes":
-        options.append( "black" )
-    if pad_edges_when_eroding == "yes":
-        options.append( "pad" )
-    # The following have no affect within this tool, but are necessary.
-    options.append( "edm=Overwrite" )
-    options.append( "do=Nothing" )
+    # Set binary options.
+    options = jython_utils.get_binary_options( black_background=black_background,
+                                               iterations=iterations,
+                                               count=count,
+                                               pad_edges_when_eroding=pad_edges_when_eroding )
+    IJ.run( input_image_plus_copy, "Options...", options )
+
     # Run the command.
-    IJ.run( input_image_plus_copy, "Make Binary", " ".join( options ) )
+    IJ.run( input_image_plus_copy, "Make Binary", "" )
+
     # Save the ImagePlus object as a new image.
     IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
 except Exception, e:
diff -r 66d9e595dff2 -r d26f11339f08 jython_utils.py
--- a/jython_utils.py	Tue Aug 04 13:20:29 2015 -0400
+++ b/jython_utils.py	Wed Aug 26 14:37:41 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 )