--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/identify_primary_objects.xml	Thu Mar 26 16:57:05 2020 -0400
@@ -0,0 +1,367 @@
+<tool id="cp_identify_primary_objects" name="IdentifyPrimaryObjects" version="@CP_VERSION@">
+    <description>module of CellProfiler</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <xml name="ipo_common"> 
+            <param name="input_from_nat" type="text" label="Select the input image (from NamesAndTypes)">
+                <expand macro="text_validator" />
+            </param>
+            <param name="name_to_be_identified" type="text" label="Name the primary objects to be identified">
+                <expand macro="text_validator" />
+            </param>
+            <param name="min_diameter" type="integer" label="Typical minimum diameter of objects, in pixel units (Min)" value="15" min="0" />
+            <param name="max_diameter" type="integer" label="Typical maximum diameter of objects, in pixel units (Max)" value="200" min="0" />
+            <param name="discard_outside_border" type="select" display="radio" label="Discard objects outside the diameter range?">
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <param name="discard_touching_border" type="select" display="radio" label="Discard objects touching the border of the image?">
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>
+            </param>
+        </xml>
+
+        <xml name="clumped_objects_params">
+            <conditional name="con_smoothing_filter">
+                <param name="smoothing_filter" type="select" label="Automatically calculate size of smoothing filter for decluping?">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="No">
+                    <param name="size_smoothing_filter" type="integer" label="Size of smoothing filter" value="1"/>
+                </when>
+                <when value="Yes" />
+            </conditional>
+            <conditional name="con_min_distance">
+                <param name="min_distance" type="select" label="Automatically calculate minimum allowed distance between local maxima?">
+                    <option value="Yes">Yes</option>
+                    <option value="No">No</option>
+                </param>
+                <when value="No">
+                    <param name="min_allowed_distance" type="integer" label="Supress local maxima that are closer than this minimum allowed distance" value="1" />
+                </when>
+                <when value="Yes" />
+            </conditional>  
+            <param name="speed_up" type="select" display="radio" label="Speed up by using lower-resolution image to find local maxima?">    
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>        
+            </param>
+        </xml>
+
+        <xml name="clumped_objects">
+            <conditional name="con_dividing_lines">
+                <param name="dividing_lines" type="select" label="Method to draw dividing lines between clumped objects">
+                    <option value="Intensity">Intensity</option>
+                    <option value="Shape">Shape</option>
+                    <option value="Propagate">Propagate</option>
+                    <option value="None">None</option>
+                </param>
+                <when value="Shape">
+                    <expand macro="clumped_objects_params"/>
+                </when>
+                <when value="Intensity">
+                    <expand macro="clumped_objects_params"/>
+                </when>
+                <when value="Propagate"/>
+                <when value="None"/>
+            </conditional>
+        </xml>   
+    </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"))
+
+ipo = params['con_advanced']
+
+adv = params['con_advanced']['advanced']
+
+
+def write_ipo():
+    _str = "\nIdentifyPrimaryObjects:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:13|show_window:True|notes:\\x5B\\'Identify the nuclei from the DNA channel.\\', \\'PARAMS\\x3A\\', \\'- Typical diameter of objects (Min,Max)\\', \\'- Method to distinguish clumped objects\\x3A Shape/None. With Shape, the distance between the 2 centers can be changed.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
+
+    if adv == "Yes":
+        _str += FOURSPACES + "Select the input image:%s\n" % ipo['input_from_nat']
+        _str += FOURSPACES + "Name the primary objects to be identified:%s\n" % ipo['name_to_be_identified']
+        _str += FOURSPACES + "Typical diameter of objects, in pixel units (Min,Max):%d,%d\n" % (ipo['min_diameter'], ipo['max_diameter'])
+        _str += FOURSPACES + "Discard objects outside the diameter range?:%s\n" % ipo['discard_outside_border']
+        _str += FOURSPACES + "Discard objects touching the border of the image?:%s\n" % ipo['discard_touching_border']
+
+        _str += FOURSPACES + "Method to distinguish clumped objects:%s\n" % ipo['con_distinguish_clumped_objects']['distinguish_clumped_objects']
+
+        if "con_dividing_lines" in ipo['con_distinguish_clumped_objects']:
+            smoothing = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter'][
+                'smoothing_filter']
+            supress = ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance']['min_distance']
+
+            _str += FOURSPACES + "Method to draw dividing lines between clumped objects:%s\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['dividing_lines']
+
+            if smoothing == "Yes":
+                _str += FOURSPACES + "Size of smoothing filter:0\n"
+            else:
+                _str += FOURSPACES + "Size of smoothing filter:%d\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter']['size_smoothing_filter']
+
+            if supress == "Yes":
+                _str += FOURSPACES + "Suppress local maxima that are closer than this minimum allowed distance:7\n"
+            else:
+                _str += FOURSPACES + "Suppress local maxima that are closer than this minimum allowed distance:%d\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance']['min_allowed_distance']
+
+            _str += FOURSPACES + "Speed up by using lower-resolution image to find local maxima?:%s\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['speed_up']
+
+        _str += FOURSPACES + "Fill holes in identified objects?:%s\n" % ipo['fill_hole']
+
+        if "con_dividing_lines" in ipo['con_distinguish_clumped_objects']:
+            _str += FOURSPACES + "Automatically calculate size of smoothing filter for declumping?:%s\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_smoothing_filter']['smoothing_filter']
+            _str += FOURSPACES + "Automatically calculate minimum allowed distance between local maxima?:%s\n" % ipo['con_distinguish_clumped_objects']['con_dividing_lines']['con_min_distance']['min_distance']
+
+        if "con_handling_excessive" in ipo:
+            excessive = ipo['con_handling_excessive']['excessive_handling']
+
+            _str += FOURSPACES + "Handling of objects if excessive number of objects identified:%s\n" % ipo['con_handling_excessive']['excessive_handling']
+            if excessive == "Continue":
+                _str += FOURSPACES + "Maximum number of objects:500\n"
+            else:
+                _str += FOURSPACES + "Maximum number of objects:%d\n" + ipo['con_handling_excessive']['max_obj']
+
+        _str += FOURSPACES + "Use advanced settings?:%s\n" % ipo['advanced']
+        _str += FOURSPACES + "Threshold settings version:10\n"
+        _str += FOURSPACES + "Threshold strategy:%s\n" % ipo['con_threshold_strategy']['threshold_strategy']
+
+        threshold_method = ipo['con_threshold_method']['threshold_method']
+        _str += FOURSPACES + "Thresholding method:%s\n" % threshold_method
+
+        _str += FOURSPACES + "Threshold smoothing scale:%.4f\n" % ipo['threshold_smoothing_scale']
+        _str += FOURSPACES + "Threshold correction factor:%.1f\n" % ipo['threshold_correction_factor']
+        _str += FOURSPACES + "Lower and upper bounds on threshold:%.1f,%.1f\n" % (ipo['threshold_lower'], ipo['threshold_upper'])
+
+        if threshold_method == "Manual":
+            _str += FOURSPACES + "Manual threshold:%d\n" % ipo['con_threshold_method']['manual_threshold']
+        else:
+            _str += FOURSPACES + "Manual threshold:0\n"
+
+        if threshold_method == "Measurement":
+            _str += FOURSPACES + "Select the measurement to threshold with:%s\n" % ipo['con_threshold_method']['threshold_measurement']
+        else:
+            _str += FOURSPACES + "Select the measurement to threshold with:None\n"
+
+        threshold_class = ipo['con_threshold_method']['con_threshold_class']['threshold_class']
+        _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % threshold_class
+
+        if threshold_class == "Three classes":
+            _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % threshold_class['assign_pixel']
+        else:
+            _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:Foreground\n"
+
+        if ipo['con_threshold_strategy']['threshold_strategy'] == "Adaptive":
+            _str += FOURSPACES + "Size of adaptive window:%d\n" + ipo['con_threshold_strategy']['adaptive_window']
+        else:
+            _str += FOURSPACES + "Size of adaptive window:500\n"
+
+        if threshold_method == "RobustBackground":
+            _str += FOURSPACES + "Lower outlier fraction:%.2f\n" % ipo['con_threshold_method']['lower_outlier_fraction']
+            _str += FOURSPACES + "Upper outlier fraction:%.2f\n" % ipo['con_threshold_method']['upper_outlier_fraction']
+            _str += FOURSPACES + "Averaging method:%s\n" % ipo['con_threshold_method']['avg_method']
+            _str += FOURSPACES + "Variance method:%s\n" % ['variance_method']
+            _str += FOURSPACES + "# of deviations:%.2f\n" % ipo['con_threshold_method']['no_of_deviations']
+        else:
+            _str += FOURSPACES + "Lower outlier fraction:0.05\n"
+            _str += FOURSPACES + "Upper outlier fraction:0.05\n"
+            _str += FOURSPACES + "Averaging method:Mean\n"
+            _str += FOURSPACES + "Variance method:Standard deviation\n"
+            _str += FOURSPACES + "# of deviations:2.0\n"
+
+        _str += FOURSPACES + "Thresholding method:%s\n" % threshold_method    # This is a repeated entry, but needed for pipeline file
+
+    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(write_ipo())
+
+f.close()
+      </configfile>
+    </configfiles>
+
+    <inputs>
+        <expand macro="input_pipeline_macro" /> 
+        <conditional name="con_advanced">
+            <param name="advanced" type="select"  display="radio" label="Use advanced settings?">
+                <option value="No">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="No">
+                <expand macro="ipo_common" />
+            </when>
+            <when value="Yes">
+                <expand macro="ipo_common" />
+                <conditional name="con_threshold_strategy">
+                    <param name="threshold_strategy" type="select" label="Threshold strategy">
+                        <option value="Global">Global</option>
+                        <option value="Adaptive">Adaptive</option>
+                    </param>
+                    <when value="Adaptive">
+                        <param name="adaptive_window" type="integer" label="Size of adaptive window" value="500"/>
+                    </when>
+                    <when value="Global" />
+                </conditional>
+                <conditional name="con_threshold_method">
+                    <param name="threshold_method" type="select" label="Thresholding method">
+                        <option value="Manual">Manual</option>
+                        <option value="Measurement">Measurement</option>
+                        <option value="Minimum cross entropy">Minimum cross entropy</option>
+                        <option value="Otsu">Otsu</option>
+                        <option value="RobustBackground">RobustBackground</option>
+                    </param>
+                    <when value="Otsu">
+                        <conditional name="con_threshold_class">
+                            <param name="threshold_class" type="select" label="Two-class or three-class thresholding?">
+                                <option value="Two classes">Two classes</option>
+                                <option value="Three classes">Three classes</option>
+                            </param>
+                            <when value="Three classes">
+                                <param name="assign_pixel" type="select" label="Assign pixels in the middle intensity class to the foreground or the background?">
+                                    <option value="Foreground">Foreground</option>
+                                    <option value="Background">Background</option>
+                                </param>
+                            </when>
+                            <when value="Two classes" />
+                        </conditional>
+                    </when>
+                    <when value="Manual">
+                        <param name="manual_threshold" type="integer" label="Manual threshold" value="0" />
+                    </when>
+                    <when value="RobustBackground">
+                        <param name="lower_outlier_fraction" type="float" value="0.05" label="Lower outlier fraction" />
+                        <param name="upper_outlier_fraction" type="float" value="0.05" label="Upper outlier fraction" />
+                        <param name="avg_method" type="select" label="Averaging method">
+                            <option value="Mean">Mean</option>
+                            <option value="Median">Median</option>
+                            <option value="Mode">Mode</option>
+                        </param>
+                        <param name="variance_method" type="select" label="Variance">
+                            <option value="Standard deviation">Standard deviation</option>
+                            <option value="Median absolute deviation">Median absolute deviation</option>                
+                        </param>
+                        <param name="no_of_deviations" type="float" value="2.0" label="# of deviations" />
+                    </when>
+                    <when value="Measurement"/>
+                    <when value="Minimum cross entropy"/>
+                </conditional>
+                <param name="threshold_smoothing_scale" type="float" value="0.0" label="Threshold smoothing scale"/>
+                <param name="threshold_correction_factor" type="float" value="0.0" label="Threshold correction factor"/>
+                <param name="threshold_lower" type="float" value="0.0" label="Lower bounds on threshold"/>
+                <param name="threshold_upper" type="float" value="1.0" label="Upper bounds on threshold"/>
+                <conditional name="con_distinguish_clumped_objects">
+                    <param name="distinguish_clumped_objects" type="select" label="Method to distinguish clumped objects">
+                        <option value="Shape">Shape</option>
+                        <option value="Intensity">Intensity</option>
+                        <option value="None">None</option>
+                    </param>
+                    <when value="Shape">
+                        <expand macro="clumped_objects"/>
+                    </when>
+                    <when value="Intensity">
+                        <expand macro="clumped_objects"/>
+                    </when>
+                    <when value="None"/>
+                </conditional>
+                <param name="fill_hole" type="select" label="Fill holes in identified objects">
+                    <option value="Never">Never</option>
+                    <option value="After both thresholding and declumping">After both thresholding and declumping</option>
+                    <option value="After declumping only">After declumping only</option>
+                </param>
+
+                <conditional name="con_handling_excessive">
+                    <param name="excessive_handling" type="select" label="Handling of objects if excessive number of objects identified">
+                        <option value="Continue">Continue</option>
+                        <option value="Erase">Erase</option>
+                    </param>
+                    <when value="Erase">
+                        <param name="max_obj" type="integer" value="500" label="Maximum number of objects" />
+                    </when>
+                    <when value="Continue" />
+                </conditional>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <expand macro="output_pipeline_macro" />
+    </outputs>
+
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <conditional name="con_advanced">
+                <param name="advanced" value="Yes" />
+                <param name="input_from_nat" value="DNA" />
+                <param name="name_to_be_identified" value="Nuclei" />
+                <param name="min_diameter" value="15" />
+                <param name="max_diameter" value="200" />
+                <param name="discard_outside_border" value="Yes" />
+                <param name="discard_touching_border" value="Yes" />
+                <conditional name="con_threshold_strategy">
+                    <param name="threshold_strategy" value="Global" />
+                </conditional>
+                <conditional name="con_threshold_method">
+                    <param name="threshold_method" value="Otsu" />
+                    <conditional name="con_threshold_class" >
+                        <param name="threshold_class" value="Two classes" />
+                    </conditional>
+                </conditional>
+                <param name="threshold_smoothing_scale" value="1.3488" />
+                <param name="threshold_correction_factor" value="0.9" />
+                <param name="threshold_lower" value="0.0" />
+                <param name="threshold_upper" value="1.0" />
+                <conditional name="con_distinguish_clumped_objects">
+                    <param name="distinguish_clumped_objects" value="Shape" />
+                    <conditional name="con_dividing_lines">
+                        <param name="dividing_lines" value="Shape" />
+                        <conditional name="con_smoothing_filter">
+                            <param name="smoothing_filter" value="Yes" />
+                        </conditional>
+                        <conditional name="con_min_distance">
+                            <param name="min_distance" value="Yes" />
+                        </conditional>     
+                        <param name="speed_up" value="Yes" />             
+                    </conditional>
+                </conditional>
+                <conditional name="con_handling_excessive">
+                        <param name="excessive_handling" value="Continue" />
+                </conditional>
+                <param name="fill_hole" value="After both thresholding and declumping" />
+            </conditional>
+            <expand macro="test_out_file" file="identify_primary_objects.txt" />
+        </test>
+    </tests>
+
+    <expand macro="help" module="IdentifyPrimaryObjects"/>
+
+    <expand macro="citations" />
+
+</tool>
+