--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/measure_granularity.xml	Thu Mar 26 17:42:07 2020 -0400
@@ -0,0 +1,110 @@
+<tool id="cp_measure_granularity" name="MeasureGranularity" version="@CP_VERSION@">
+    <description>outputs spectra of size measurements of the textures in the image</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="py_requirements"/>
+    <expand macro="cmd_modules" />
+    
+    <configfiles>
+        <inputs name="inputs" />
+        <configfile name="script_file">
+import json
+import sys
+import os
+
+FOURSPACES=@SPACES@
+
+input_json_path = sys.argv[1]
+input_pipeline= sys.argv[2]
+
+params = json.load(open(input_json_path, "r"))
+
+def writemg():
+    _str = "\nMeasureGranularity:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\\'PARAMS\\x3A\\', \\'- Radius\\', \'- Range\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    image_count = len(params['rpt_image'])
+
+    _str += FOURSPACES + "Image count:%d\n" % image_count
+
+    for img in params['rpt_image']:
+        obj_count = len(img['rpt_object'])
+
+        _str += FOURSPACES + "Object count:%d\n" % obj_count
+
+        _str += FOURSPACES + "Select an image to measure:%s\n" % img['image_to_measure']
+
+        _str += FOURSPACES + "Subsampling factor for granularity measurements:%s\n" % img['subsampling_factor_granularity']
+
+        _str += FOURSPACES + "Subsampling factor for background reduction:%.2f\n" % img['subsampling_factor_background_reduction']
+
+        _str += FOURSPACES + "Radius of structuring element:%d\n" % img['radius']
+        _str += FOURSPACES + "Range of the granular spectrum:%d\n" % img['range_granular_spectrum']
+
+        for obj in img['rpt_object']:
+            _str += FOURSPACES + "Select objects to meausre:%s\n" % obj['object_to_measure']
+
+    return _str
+
+with open(input_pipeline) as fin:
+    lines = fin.readlines()
+
+    k, v = lines[4].strip().split(':')
+
+    module_count = int(v)
+    new_count = module_count + 1
+    lines[4] = k + ":%d\n" % new_count
+    with open("output", "w") as f:
+        f.writelines(lines)
+        f.write(writemg())
+
+f.close()
+        </configfile>
+    </configfiles>
+    
+    <inputs>
+        <expand macro="input_pipeline_macro" />
+        <repeat name="rpt_image" title="Add another image">
+            <param name="image_to_measure" type="text" label="Select an image to measure">
+                <expand macro="text_validator" />
+            </param>
+
+            <param name="subsampling_factor_granularity" type="float" value="0.25" label="Subsampling factor for granularity measurements" /> 
+
+            <param name="subsampling_factor_background_reduction" type="float" value="0.25" min="0.125" max="0.25" label="Subsampling factor for background reduction" /> 
+            
+            <param name="radius" type="integer" value="10" label="Radius of structuring element" /> 
+            
+            <param name="range_granular_spectrum" type="integer" value="16" label="Range of the granular spectrum" /> 
+
+            <repeat name="rpt_object" title="Add another object">
+                <param name="object_to_measure" type="text" label="Select object to measure" >
+                    <expand macro="text_validator" />
+                </param>
+            </repeat>
+        </repeat>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <repeat name="rpt_image">
+                <param name="image_to_measure" value="DNA" />
+                <param name="subsampling_factor_granularity" value="0.25" />
+                <param name="subsampling_factor_background_reduction" value="0.25" />
+                <param name="radius" value="10" />
+                <param name="range_granular_spectrum" value="16" />
+            </repeat>
+            <expand macro="test_out_file" file="measure_granularity.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="MeasureGranularity" />
+    <expand macro="citations" />
+</tool>