changeset 3:169cde4adbdb draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 11:40:39 +0000
parents b7014aafa455
children fab70e70cf7b
files enhance_or_suppress_features.xml macros.xml starting_modules.py starting_modules_groups.xml starting_modules_image.xml starting_modules_images.xml starting_modules_metadata.xml starting_modules_nameandtypes.xml test-data/common-complicated.cppipe test-data/common-nogroup.cppipe test-data/common.cppipe test-data/common.txt test-data/convert_objects_to_image.cppipe test-data/convert_objects_to_image.txt test-data/display_data_on_image.cppipe test-data/display_data_on_image.txt test-data/enhance_or_suppress_features.cppipe test-data/enhance_or_suppress_features.txt test-data/export_to_spreadsheet.cppipe test-data/export_to_spreadsheet.txt test-data/export_to_spreadsheet_create_gene.cppipe test-data/export_to_spreadsheet_create_gene_image_filename.cppipe test-data/export_to_spreadsheet_create_gene_metadata.cppipe test-data/export_to_spreadsheet_multi.cppipe test-data/gray_to_color.cppipe test-data/gray_to_color.txt test-data/identify_primary_objects.cppipe test-data/identify_primary_objects.txt test-data/identify_primary_objects_adv_adaptive_otsu.cppipe test-data/identify_primary_objects_adv_global_manual.cppipe test-data/identify_primary_objects_adv_global_mce.cppipe test-data/identify_primary_objects_adv_global_measurement.cppipe test-data/identify_primary_objects_adv_global_rb.cppipe test-data/identify_primary_objects_noadv.cppipe test-data/image_math.xml test-data/images.tar test-data/mask_image.cppipe test-data/mask_image.txt test-data/measure_granularity.cppipe test-data/measure_granularity.txt test-data/measure_image_area_occupied.cppipe test-data/measure_image_area_occupied.txt test-data/measure_image_intensity.cppipe test-data/measure_image_intensity.txt test-data/measure_image_quality.cppipe test-data/measure_image_quality.txt test-data/measure_object_intensity.cppipe test-data/measure_object_intensity.txt test-data/measure_object_size.txt test-data/measure_object_size_shape.cppipe test-data/measure_object_size_shape.txt test-data/measure_texture.cppipe test-data/measure_texture.txt test-data/relate_objects.cppipe test-data/relate_objects.txt test-data/save_images.cppipe test-data/save_images.txt
diffstat 53 files changed, 2682 insertions(+), 1220 deletions(-) [+]
line wrap: on
line diff
--- a/enhance_or_suppress_features.xml	Thu Apr 16 09:19:53 2020 +0000
+++ b/enhance_or_suppress_features.xml	Mon May 11 11:40:39 2020 +0000
@@ -5,8 +5,15 @@
         <import>macros.xml</import>
 
         <xml name="feature_speckles">
-            <param name="speckles_feature_size" label="Feature size" type="integer" value="10" />
+            <param name="speckles_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size." />
             <param name="speed_accuracy" label="Speed and accuracy" type="select">
+                <help>
+                    <![CDATA[
+                        Speckles can use a fast or slow algorithm to find speckles.
+                        <br> - Fast: Select this option for speckles that have a large radius (greater than 10 pixels) and need not be exactly circular.
+                        <br> - Slow: Use for speckles of small radius.
+                        ]]>
+                </help>
                 <option value="Fast">Fast</option>
                 <option value="Slow">Slow</option>
             </param>
@@ -14,36 +21,43 @@
         <xml name="feature_neurites">
             <conditional name="con_feature_neurites">
                 <param name="enhancement_method" label="Enhancement method" type="select">
+                    <help>
+                        <![CDATA[
+                            Two methods can be used to enhance neurites:
+                            <br> - Tubeness: This method is an adaptation of the method used by the ImageJ Tubeness plugin. The image is smoothed with a Gaussian. The Hessian is then computed at every point to measure the intensity gradient and the eigenvalues of the Hessian are computed to determine the magnitude of the intensity. The absolute maximum of the two eigenvalues gives a measure of the ratio of the intensity of the gradient in the direction of its most rapid descent versus in the orthogonal direction. The output image is the absolute magnitude of the highest eigenvalue if that eigenvalue is negative (white neurite on dark background), otherwise, zero.
+                            <br> - Line structures: The module takes the difference of the white and black tophat filters (a white tophat filtering is the image minus the morphological grayscale opening of the image; a black tophat filtering is the morphological grayscale closing of the image minus the image). The effect is to enhance lines whose width is the feature size.
+                            ]]>
+                    </help>
                     <option value="Tubeness">Tubeness</option>
                     <option value="Line structures">Line structures</option>
                 </param>
                 <when value="Tubeness">
-                    <param name="tube_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" />
+                    <param name="tube_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" help="The Tubeness option uses this scale as the sigma of the Gaussian used to smooth the image prior to gradient detection." />
                 </when>
                 <when value="Line structures">
-                    <param name="line_structures_feature_size" label="Feature size" type="integer" value="10" />
+                    <param name="line_structures_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size."/>
                 </when>
             </conditional>
         </xml>
         <xml name="feature_darkholes">
             <param name="min_hole_size" label="Minimum hole size" type="integer" value="1" min="0"/>
-            <param name="max_hole_size" label="Maximum hole size" type="integer" value="15"/>
-        </xml>  
+            <param name="max_hole_size" label="Maximum hole size" type="integer" value="10" min="0"/>
+        </xml>
         <xml name="feature_circle">
-            <param name="circle_feature_size" label="Feature size" type="integer" value="10"/>
-        </xml>     
+            <param name="circle_feature_size" label="Feature size" type="integer" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size."/>
+        </xml>
         <xml name="feature_texture">
-            <param name="texture_smoothing_scale" label="Smoothing scale" type="float" value="2.0"  min="0.0"/>
+            <param name="texture_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" help="This is roughly the scale of the texture features, in pixels. The algorithm uses the smoothing value entered as the sigma of the Gaussian used to weight nearby pixels by distance in the variance calculation." />
         </xml>
         <xml name="feature_dic">
-            <param name="dic_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" />
-            <param name="dic_shear_angle" label="Shear angle" type="float" value="0.0" min="0.0" />
-            <param name="dic_decay" label="Decay" type="float" value="0.95" min="0.0" />
-        </xml>      
+            <param name="dic_smoothing_scale" label="Smoothing scale" type="float" value="2.0" min="0.0" help="Specifies the amount of smoothing of the image in the direction parallel to the shear axis of the image. The line integration method will leave streaks in the image without smoothing as it encounters noisy pixels during the course of the integration. The smoothing takes contributions from nearby pixels, which decreases the noise but smooths the resulting image. Increase the smoothing to eliminate streakiness and decrease the smoothing to sharpen the image." />
+            <param name="dic_shear_angle" label="Shear angle" type="float" value="0.0" min="0.0" help="The shear angle is the direction of constant value for the shadows and highlights in a DIC image. The gradients in a DIC image run in the direction perpendicular to the shear angle." />
+            <param name="dic_decay" label="Decay" type="float" value="0.95" min="0.0" help="The decay setting applies an exponential decay during the process of integration by multiplying the accumulated sum by the decay at each step. This lets the integration recover from accumulated error during the course of the integration, but it also results in diminished intensities in the middle of large objects. Set the decay to a large value, on the order of 1 - 1/diameter of your objects if the intensities decrease toward the middle. Set the decay to a small value if there appears to be a bias in the integration direction." />
+        </xml>
     </macros>
 
     <expand macro="py_requirements"/>
-    <expand macro="cmd_modules" /> 
+    <expand macro="cmd_modules" />
 
     <configfiles>
         <inputs name="inputs" />
@@ -151,7 +165,6 @@
 
     return _str
 
-
 with open(input_pipeline) as fin:
     lines = fin.readlines()
 
@@ -161,89 +174,101 @@
     new_count = module_count + 1
     lines[4] = k + ":%d\n" % new_count
 
-    with open("output", "w") as f:
+    with open("output.cppipe", "w") as f:
         f.writelines(lines)
         f.write(writeesf())
 
 f.close()
-        </configfile>    
+        </configfile>
     </configfiles>
 
     <inputs>
-
-      <expand macro="input_pipeline_macro"/>
-      <param name="input_image" type="text" label="Select the input image" />
-
-      <param name="name_output_image" type="text" label="Name the output image" />
-
-      <conditional name="con_enhance_suppress">
-        <param name="select_operation" label="Select the operation" type="select">
-          <option value="Enhance">Enhance</option>
-          <option value="Suppress">Suppress</option>
-        </param>
-
-        <when value="Enhance">
-           <conditional name="con_feature_type">
-            <param name="feature_type" type="select" label="Feature type">
-              <option value="Speckles">Speckles</option>
-              <option value="Neurites">Neurites</option>
-              <option value="Dark holes">Dark holes</option>
-              <option value="Circles">Circles</option>
-              <option value="Texture">Texture</option>
-              <option value="DIC">DIC</option>
+        <expand macro="input_pipeline_param"/>
+        <param name="input_image" type="text" label="Enter the name of the input image" />
+        <param name="name_output_image" type="text" label="Enter a name for the resulting image" />
+        <conditional name="con_enhance_suppress">
+            <param name="select_operation" label="Select the operation" type="select" help="Enhance produces an image whose intensity is largely composed of the features of interest and Supress produces an image with the features largely removed.">
+                <option value="Enhance">Enhance</option>
+                <option value="Suppress">Suppress</option>
             </param>
-             <when value="Speckles">
-              <expand macro="feature_speckles" />
-            </when>
-            <when value="Neurites">
-              <expand macro="feature_neurites" />
-            </when>
-            <when value="Dark holes">
-              <expand macro="feature_darkholes" />
-            </when>
-            <when value="Circles">
-              <expand macro="feature_circle" />
-            </when>
-            <when value="Texture">
-              <expand macro="feature_texture" />
+            <when value="Enhance">
+                <conditional name="con_feature_type">
+                    <param name="feature_type" type="select" label="Feature type">
+                        <help>
+                            <![CDATA[
+                                - Speckles: A speckle is an area of enhanced intensity relative to its immediate neighborhood. This option enhances speckles using a white tophat filter, which is the image minus the morphological grayscale opening of the image. The opening operation first suppresses the speckles by applying a grayscale erosion to reduce everything within a given radius to the lowest value within that radius, then uses a grayscale dilation to restore objects larger than the radius to an approximation of their former shape. The white tophat filter enhances speckles by subtracting the effects of opening from the original image.
+                                <br>- Neurites: Neurites are taken to be long, thin features of enhanced intensity. Choose this option to enhance the intensity of the neurites using the Line structures or Tubeness methods described in a later setting.
+                                <br>- Dark holes: This option uses morphological reconstruction (the rolling-ball algorithm) to identify dark holes within brighter areas, or brighter ring shapes. The image is inverted so that the dark holes turn into bright peaks. The image is successively eroded and the eroded image is reconstructed at each step, resulting in an image that is missing the peaks. Finally, the reconstructed image is subtracted from the previous reconstructed image. This leaves circular bright spots with a radius equal to the number of iterations performed.
+                                <br>- Circles: This option calculates the circular Hough transform of the image at the diameter given by the feature size. The Hough transform will have the highest intensity at points that are centered within a ring of high intensity pixels where the ring diameter is the feature size. You may want to use the EnhanceEdges module to find the edges of your circular object and then process the output by enhancing circles. You can use IdentifyPrimaryObjects to find the circle centers and then use these centers as seeds in IdentifySecondaryObjects to find whole, circular objects using a watershed.
+                                <br>- Texture: This option produces an image whose intensity is the variance among nearby pixels. The method weights pixel contributions by distance using a Gaussian to calculate the weighting. You can use this method to separate foreground from background if the foreground is textured and the background is not.
+                                <br>- DIC: This method recovers the optical density of a DIC image by integrating in a direction perpendicular to the shear direction of the image.
+                                ]]>
+                        </help>
+                        <option value="Speckles">Speckles</option>
+                        <option value="Neurites">Neurites</option>
+                        <option value="Dark holes">Dark holes</option>
+                        <option value="Circles">Circles</option>
+                        <option value="Texture">Texture</option>
+                        <option value="DIC">DIC</option>
+                    </param>
+                    <when value="Speckles">
+                        <expand macro="feature_speckles" />
+                    </when>
+                    <when value="Neurites">
+                        <expand macro="feature_neurites" />
+                    </when>
+                    <when value="Dark holes">
+                        <expand macro="feature_darkholes" />
+                    </when>
+                    <when value="Circles">
+                        <expand macro="feature_circle" />
+                    </when>
+                    <when value="Texture">
+                        <expand macro="feature_texture" />
+                    </when>
+                    <when value="DIC">
+                        <expand macro="feature_dic" />
+                    </when>
+                </conditional>
             </when>
-            <when value="DIC">
-              <expand macro="feature_dic" />
-            </when> 
-          </conditional>
-        </when>
+            <when value="Suppress">
+                <param name="feature_size" type="integer" label="Feature size" value="10" help="Enter the diameter of the largest speckle, the width of the circle, or the width of the neurites to be enhanced or suppressed, which will be used to calculate an appropriate filter size." />
+            </when>
+        </conditional>
+    </inputs>
 
-        <when value="Suppress">
-          <param name="feature_size" type="integer" label="Feature size" value="10"/>
-        </when>
-
-      </conditional>
-      
-  </inputs>
-
-  <outputs>
-      <expand macro="output_pipeline_macro" />
-  </outputs>
-
+    <outputs>
+        <expand macro="output_pipeline_param" />
+    </outputs>
 
-  <tests>
-      <test>
-        <expand macro="test_input_pipeline_param" />
-        <param name="input_image" value="DNA" />
-        <param name="name_output_image" value="DNAdarkholes" />
-        <conditional name="con_enhance_suppress">
-            <param name="select_operation" value="Enhance" />
-            <conditional name="con_feature_type">
-                <param name="feature_type" value="Dark holes" />
-                <param name="min_hole_size" value="1" />
-                <param name="max_hole_size" value="15" />
+    <tests>
+        <test>
+            <expand macro="test_input_pipeline_param" />
+            <param name="input_image" value="DNA" />
+            <param name="name_output_image" value="DNAdarkholes" />
+            <conditional name="con_enhance_suppress">
+                <param name="select_operation" value="Enhance" />
+                <conditional name="con_feature_type">
+                    <param name="feature_type" value="Dark holes" />
+                    <param name="min_hole_size" value="1" />
+                    <param name="max_hole_size" value="15" />
+                </conditional>
             </conditional>
-        </conditional>
+            <expand macro="test_out_file" file="enhance_or_suppress_features.cppipe" />
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+            .. class:: infomark
 
-        <expand macro="test_out_file" file="enhance_or_suppress_features.txt" />
-      </test>
-  </tests>
+            **What it does**
+
+            This tool enhances or suppresses the intensity of certain pixels relative to the rest of the image, by applying image processing filters to the image. It produces a grayscale image in which objects can be identified using an Identify module.
 
-  <expand macro="help" module="EnhanceOrSuppressFeatures" />
-  <expand macro="citations" />
+            @COMMON_HELP@
+            ]]>
+    </help>
+
+    <expand macro="citations" />
 </tool>
--- a/macros.xml	Thu Apr 16 09:19:53 2020 +0000
+++ b/macros.xml	Mon May 11 11:40:39 2020 +0000
@@ -25,12 +25,12 @@
     </token>
 
 
-    <xml name="output_pipeline_macro">
-        <data name="out_file" from_work_dir="output" format="txt"/>
+    <xml name="output_pipeline_param">
+        <data name="output_pipeline" from_work_dir="output.cppipe" format="txt"/>
     </xml>
 
 
-    <xml name="input_pipeline_macro">
+    <xml name="input_pipeline_param">
         <param name="input_pipeline" type="data" format="data" label="Select the input CellProfiler pipeline"/>
     </xml>
 
@@ -81,25 +81,13 @@
 
 
     <xml name="test_input_pipeline_param">
-        <param name="input_pipeline" value="common.txt" />
-    </xml>
-
-
-    <xml name="test_out_file" token_file="common.txt">
-        <output name="out_file" ftype="txt" file="@FILE@" lines_diff="0"/>
+        <param name="input_pipeline" value="common.cppipe" />
     </xml>
 
 
-    <xml name="help" token_module="common">
-        <help>
-            This tool appends the inputs of the @MODULE@ module to an existing pipeline file (.cppipe)
-
-            Input: existing pipeline file
-
-            Output: new pipeline file
-
-            Combine this tool with "Common" tool and "CellProfiler" tool together to run the current module alone.
-        </help>
+    <xml name="test_out_file" token_file="common.cppipe">
+        <output name="output_pipeline" ftype="txt" file="@FILE@" lines_diff="0"/>
     </xml>
+    
 </macros>
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules.py	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,227 @@
+import json
+import sys
+import os
+
+FOURSPACES = "    "
+
+input_json_path = sys.argv[1]
+
+params = json.load(open(input_json_path, "r"))
+
+
+def write_images():
+    filter_images = params['images']['filter_images']
+
+    _str = "\nImages:[module_num:1|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES+":\n"
+    _str += FOURSPACES + "Filter images?:%s\n" % filter_images
+    _str += FOURSPACES + "Select the rule criteria:and (extension does isimage) (directory doesnot startwith \".\")\n"
+
+    return _str
+
+
+def write_metadata():
+    metadata_extraction = params['metadata']['con_metadata_extraction']
+    extract = metadata_extraction['extract']
+
+    if 'extraction_method' in metadata_extraction:
+        method_count = len(metadata_extraction['extraction_method'])
+    else:
+        method_count = 1
+
+    _str = "\nMetadata:[module_num:2|svn_version:\\'Unknown\\'|variable_revision_number:4|show_window:False|notes:\\x5B\\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+    _str += FOURSPACES + "Extract metadata?:%s\n" % extract
+
+    if extract == "No":
+        _str += FOURSPACES + "Metadata data type:Text\n"
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+        _str += FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
+        _str += FOURSPACES + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
+        _str += FOURSPACES + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
+        _str += FOURSPACES + "Extract metadata from:All images\n"
+        _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
+        _str += FOURSPACES + "Metadata file location:\n"
+        _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+        _str += FOURSPACES + "Use case insensitive matching?:No\n"
+    else:
+        _str += FOURSPACES + "Metadata data type:Text\n"  #default Text,not possible to select in Galaxy
+        _str += FOURSPACES + "Metadata types:{}\n"
+        _str += FOURSPACES + "Extraction method count:%d\n" % method_count
+
+        for methods in metadata_extraction["extraction_method"]:
+            _str += FOURSPACES + "Metadata extraction method:%s\n" % methods["metadata_extraction_method"]
+            _str += FOURSPACES + "Metadata source:%s\n" % methods["con_metadata_source"]["metadata_source"]
+
+            if "file_name_regex" in methods["con_metadata_source"]:
+                file_regex = methods["con_metadata_source"]["file_name_regex"]
+                folder_regex = "(?P<folderField1>.*)"
+            elif "folder_name_regex" in methods["con_metadata_source"]:
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = methods["con_metadata_source"]["folder_name_regex"]
+            else:
+                # default regex
+                file_regex = "(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)"
+                folder_regex = "(?P<folderField1>.*)"
+
+            _str += FOURSPACES + "Regular expression to extract from file name:%s\n" % file_regex
+            _str += FOURSPACES + "Regular expression to extract from folder name:%s\n" % folder_regex
+
+            _str += FOURSPACES + "Extract metadata from:%s\n" % methods["con_metadata_extract_from"]["extract_metadata_from"]
+
+            if methods["con_metadata_extract_from"]["extract_metadata_from"] == "Images matching a rule":
+                rule_str =""
+                for r in methods["con_metadata_extract_from"]["r_match"]:
+                    if r["con_match"]["rule_type"] == "extension":
+                        rule_str += " (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                                    r["con_match"]["match_type"]+")"
+                    else:
+                        rule_str +=" (" + r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " +\
+                                   r["con_match"]["contain"] + " \"" + r["con_match"]["match_value"] +"\")"
+
+
+                _str += FOURSPACES + "Select the filtering criteria:" + methods["con_metadata_extract_from"]["match_all_any"] + rule_str +"\n"
+            else:
+                _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n" #this line is required even if it's not used
+
+            _str += FOURSPACES + "Metadata file location:\n"
+            _str += FOURSPACES + "Match file and image metadata:\x5B\x5D\n"
+            _str += FOURSPACES + "Use case insensitive matching?:No\n"
+
+    return _str
+
+
+def write_nameandtypes():
+    nameandtypes = params['nameandtypes']
+    assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
+
+    if "con_select_image_type" in nameandtypes['con_assign_a_name_to']:
+        con_set_intensity = nameandtypes['con_assign_a_name_to']['con_select_image_type']['con_set_intensity']
+        max_intensity = con_set_intensity['maximum_intensity'] if "maximum_intensity" in con_set_intensity else 255.0
+    else:
+        max_intensity = 255.0
+
+    pixel_space = nameandtypes['pixel_space']
+
+    rule_count = len(nameandtypes['con_assign_a_name_to']['r_match_rule']) if "r_match_rule" in nameandtypes['con_assign_a_name_to'] else 1
+
+    process_3d = nameandtypes['pixel_space']['process_3d']
+    x_spacing = 1.0 if "x_spacing" not in pixel_space else pixel_space["x_spacing"]
+    y_spacing = 1.0 if "y_spacing" not in pixel_space else pixel_space["y_spacing"]
+    z_spacing = 1.0 if "z_spacing" not in pixel_space else pixel_space["z_spacing"]
+
+    _str = "\nNamesAndTypes:[module_num:3|svn_version:\\'Unknown\\'|variable_revision_number:8|show_window:False|notes:\\x5B\\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    _str += FOURSPACES + "Assign a name to:%s\n" % assign_a_name
+
+    if assign_a_name == "All images":
+        _str += FOURSPACES + "Select the image type:%s\n" % nameandtypes['con_assign_a_name_to']['con_select_image_type']['select_image_type']
+        _str += FOURSPACES + "Name to assign these images:%s\n" % nameandtypes['con_assign_a_name_to']['name_to_assign']
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:Order\n"
+        _str += FOURSPACES + "Set intensity range from:%s\n" % con_set_intensity['set_intensity_range_from']
+        _str += FOURSPACES + "Assignments count:%s\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    else:
+        #the below lines are not relevant to "images matching rules", but needed in pipeline file
+        _str += FOURSPACES + "Select the image type:Grayscale image\n"
+        _str += FOURSPACES + "Name to assign these images:DNA\n"
+        _str += FOURSPACES + "Match metadata:[]\n"
+
+        _str += FOURSPACES + "Image set matching method:%s\n" % nameandtypes['con_assign_a_name_to']['matching_method']
+        _str += FOURSPACES + "Set intensity range from:Image metadata\n"
+        _str += FOURSPACES + "Assignments count:%d\n" % rule_count
+        _str += FOURSPACES + "Single images count:0\n"
+        _str += FOURSPACES + "Maximum intensity:%.1f\n" % max_intensity
+        _str += FOURSPACES + "Process as 3D?:%s\n" % process_3d
+
+    _str += FOURSPACES + "Relative pixel spacing in X:%.1f\n" % x_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Y:%.1f\n" % y_spacing
+    _str += FOURSPACES + "Relative pixel spacing in Z:%.1f\n" % z_spacing
+
+    if assign_a_name == "Images matching rules":
+        for rule in nameandtypes["con_assign_a_name_to"]["r_match_rule"]:
+
+            rule_str = ""
+            if len(rule["r_match"]) >0 :
+                for r in rule["r_match"]:
+                        if r["con_match"]["rule_type"] == "file" or r["con_match"]["rule_type"] == "directory":
+                            rule_str += " (" + r["con_match"]["rule_type"] + " "+r["con_match"]["operator"]+" "+\
+                                        r["con_match"]["contain"]+" \"" + r["con_match"]["match_value"] +"\")"
+                        else:
+                            rule_str += " ("+ r["con_match"]["rule_type"] + " " + r["con_match"]["operator"] + " " + \
+                                        r["con_match"]["match_type"] + ")"
+            else:
+                rule_str = " (file does contain \"\")"  #need to have a value even if it is not used
+
+            _str += FOURSPACES + "Select the rule criteria:" + rule["match_all_any"] + rule_str +"\n"
+
+            img_or_obj = rule["con_select_image_type"]["select_image_type"]
+
+            if img_or_obj == "Objects":
+                _str += FOURSPACES + "Name to assign these images:DNA\n"
+                _str += FOURSPACES + "Name to assign these objects:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+            else:
+                _str += FOURSPACES + "Name to assign these images:%s\n" % rule["con_select_image_type"]["name_to_assign"]
+                _str += FOURSPACES + "Name to assign these objects:Cell\n"
+
+            _str += FOURSPACES + "Select the image type:%s\n" % img_or_obj
+
+
+            intensity_range="Image metadata" #default value
+            if img_or_obj == "Grayscale image" or img_or_obj == "Color image":
+                intensity_range = rule["con_select_image_type"]["con_set_intensity"]["set_intensity_range_from"]
+
+            _str += FOURSPACES + "Set intensity range from:%s\n" % intensity_range
+
+            if intensity_range == "Manual":
+                _str += FOURSPACES + "Maximum intensity:%s\n" % rule["con_select_image_type"]["con_set_intensity"]["maximum_intensity"]
+            else:
+                _str += FOURSPACES + "Maximum intensity:255.0\n"
+
+
+    return _str
+
+
+def write_groups():
+    groups = params['groups']
+
+    _str = "\nGroups:[module_num:4|svn_version:\\'Unknown\\'|variable_revision_number:2|show_window:False|notes:\\x5B\\\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n"
+
+    group_images =  groups["con_groups"]["group_images"]
+
+    _str += FOURSPACES + "Do you want to group your images?:%s\n" % group_images
+    _str += FOURSPACES + "grouping metadata count:1\n"
+
+    if group_images == "Yes":
+        _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
+    else:
+        _str += FOURSPACES + "Metadata category:None\n"
+
+    return _str
+
+
+with open("output.cppipe", "w") as f:
+    headers = ["CellProfiler Pipeline: http://www.cellprofiler.org\n",
+               "Version:3\n",
+               "DateRevision:319\n",
+               "GitHash:\n",
+               "ModuleCount:4\n",
+               "HasImagePlaneDetails:False",
+               "\n"]
+
+    f.writelines(headers)
+
+    img_str = write_images()
+    metadata_str = write_metadata()
+    nameandtypes_str = write_nameandtypes()
+    groups_str = write_groups()
+
+    output_str = img_str + metadata_str + nameandtypes_str + groups_str
+
+    f.write(output_str)
+    f.close()
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_groups.xml	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,32 @@
+<macros>
+    <xml name="starting_modules_groups">
+        <section name="groups" title="Groups" expanded="false">
+        <conditional name="con_groups">
+            <param name="group_images" type="select" value="No" label="Do you want to group your images?">
+                <option value="Yes">Yes, group the images</option>
+                <option value="No" selected="true">No, do not group images</option>
+            </param>
+            <when value="Yes">
+                <param name="group_category" type="select" label="Metadata category">
+                    <option value="None" selected="true">None</option>
+                    <option value="ChannelNumber">Channel number</option>
+                    <option value="FileLocation">File location</option>
+                    <option value="Plate">Plate</option>
+                    <option value="Frame">Frame</option>
+                    <option value="Series">Series</option>
+                    <option value="Site">Site</option>
+                    <option value="Well">Well</option>
+                    <option value="field1">field1</option>
+                    <option value="field2">field2</option>
+                    <option value="field3">field3</option>
+                    <option value="field4">field4</option>
+                    <option value="field5">field5</option>
+                    <option value="field6">field6</option>
+                </param>
+            </when>
+            <when value="No">
+            </when>
+        </conditional>
+    </section>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_images.xml	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,10 @@
+<macros>
+    <xml name="starting_modules_images">
+        <section name="images" title="Images" expanded="false">
+            <param name="filter_images" type="select" label="Do you want to filter only the images?" help="Enabling file filtering is useful if, for example, you drag-and-dropped a folder onto the file list panel which contains a mixture of images that you want to analyze and other files that you want to ignore.">
+                <option value="Images only">Select the images only</option>
+                <option value="No filtering">Select all the files</option>
+            </param>
+        </section>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_metadata.xml	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,92 @@
+<macros>
+    <xml name="image_matching_rules_metadata">
+        <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+            <option value="and">All</option>
+            <option value="or">Any</option>
+        </param>
+        <repeat name="r_match" title="filtering rules">
+            <conditional name="con_match">
+                <param name="rule_type" type="select" label="Select the filtering criteria">
+                    <option value="file">File</option>
+                    <option value="directory">Directory</option>
+                    <option value="extension">Extension</option>
+                </param>
+                <when value="file">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="directory">
+                    <expand macro="name_type_rule_matching_file"/>
+                </when>
+                <when value="extension">
+                    <expand macro="name_type_rule_ext" />
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_metadata">
+        <section name="metadata" title="Metadata" expanded="false">
+            <conditional name="con_metadata_extraction">
+                <param name="extract" type="select" label="Do you want to extract the metadata?">
+                    <option value="Yes">Yes, specify metadata</option>
+                    <option value="No" selected="true">No, do not specify metadata</option>
+                </param>
+                <when value="Yes">
+                    <repeat name="extraction_method" title="new metadata" min="1">
+                        <param name="metadata_extraction_method" type="select" label="Metadata extraction method" help="Metadata can be stored in either or both of two ways: internally (through the file naming, directory structuring, or the file header information) or externally (external index, such as spreadsheet or database of some kind). " >
+                            <option value="Extract from file/folder names">Extract from file/folder names</option>
+                            <option value="Import from file">Import from file</option>
+                            <option value="Extract from image file headers">Extract from image file headers</option>
+                        </param>
+                        <conditional name="con_metadata_source">
+                            <param name="metadata_source" type="select" label="Metadata source" help="You can extract the metadata from the image file name or from its folder name.">
+                                <option value="File name">File name</option>
+                                <option value="Folder name">Folder name</option>
+                            </param>
+                            <when value="File name">
+                                <param name="file_name_regex" type="select" label="Select the pattern to extract metadata from the file name" help="Image file names must comply with one of the patterns. For example, plate_reagent_timepoint.tif matches the pattern field1_field2_field3. If none of the patterns is suitable, please use other Galaxy tools to rename your files first.">
+
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;field1>.*)">field1</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)">field1_field2</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)">field1__field2</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)">field1-field2-field3</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)">field1_field2_field3</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)">field1__field2__field3</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)">field1-field2-field3-field4</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)">field1_field2_field3_field4</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)">field1__field2__field3__field4</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5</option>
+                                    <option value="(?P&lt;field1>.*)-(?P&lt;field2>[a-zA-Z0-9]+)-(?P&lt;field3>[a-zA-Z0-9]+)-(?P&lt;field4>[a-zA-Z0-9]+)-(?P&lt;field5>[a-zA-Z0-9]+)-(?P&lt;field6>[a-zA-Z0-9]+)">field1-field2-field3-field4-field5-field6</option>
+                                    <option value="(?P&lt;field1>.*)_(?P&lt;field2>[a-zA-Z0-9]+)_(?P&lt;field3>[a-zA-Z0-9]+)_(?P&lt;field4>[a-zA-Z0-9]+)_(?P&lt;field5>[a-zA-Z0-9]+)_(?P&lt;field6>[a-zA-Z0-9]+)">field1_field2_field3_field4_field5_field6</option>
+                                    <option value="(?P&lt;field1>.*)__(?P&lt;field2>[a-zA-Z0-9]+)__(?P&lt;field3>[a-zA-Z0-9]+)__(?P&lt;field4>[a-zA-Z0-9]+)__(?P&lt;field5>[a-zA-Z0-9]+)__(?P&lt;field6>[a-zA-Z0-9]+)">field1__field2__field3__field4__field5__field6</option>
+                                </param>
+                            </when>
+                            <when value="Folder name">
+                                <param name="folder_name_regex" type="select" label="Select the pattern to extract metadata from the folder name" help="Folder names must comply with one of the patterns. For example, folder name exp1-channel_name matches the pattern field1-field2. If none of the patterns is suitable, please use other Galaxy tools to rename your folder first.">
+                                    <sanitizer sanitize="false"/>
+                                    <option value="(?P&lt;folderField1>.*)">field1</option>
+                                    <option value="(?P&lt;folderField1>.*)-(?P&lt;folderField2>[a-zA-Z0-9]+)">field1-field2</option>
+                                    <option value="(?P&lt;folderField1>.*)_(?P&lt;folderField2>[a-zA-Z0-9]+)">field1_field2</option>
+                                </param>
+                            </when>
+                        </conditional>
+                        <conditional name="con_metadata_extract_from">
+                            <param name="extract_metadata_from" type="select" label="Extract metadata from">
+                                <option value="All images">All images</option>
+                                <option value="Images matching a rule">Images matching a rule</option>
+                            </param>
+                            <when value="Images matching a rule">
+                                <expand macro="image_matching_rules_metadata" />
+                            </when>
+                            <when value="All images" />
+                        </conditional>
+                    </repeat>
+                </when>
+                <when value="No" />
+            </conditional>
+        </section>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/starting_modules_nameandtypes.xml	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,182 @@
+<macros>
+    <xml name="macro_image_type" token_thing="images">
+        <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" />
+    </xml>
+    
+    <xml name="image_type_condition"> 
+        <conditional name="con_set_intensity">
+            <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0.">
+                <option value="Image metadata">Image metadata</option>
+                <option value="Image bit-depth">Image bit-depth</option>
+                <option value="Manual">Manual</option>
+            </param>
+            <when value="Manual">
+                <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." />
+
+            </when>
+            <when value="Image metadata" />
+            <when value="Image bit-depth" />
+        </conditional>
+    </xml>
+    <xml name="name_type_rule_matching_file">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="contain" type="select">
+            <option value="contain">Contain</option>
+            <option value="Contain regular expression">Contain regular expression</option>
+            <option value="startwith">Start with</option>
+            <option value="endwith">End with</option>
+            <option value="Exactly match">Exactly match</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_image">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="iscolor">Color</option>
+            <option value="ismonochrome">Monochrome</option>
+            <option value="isstack">Stack</option>
+            <option value="isstackframe">Stack frame</option>
+        </param>
+    </xml>
+    <xml name="name_type_rule_metadata">
+        <param name="operator" type="select">
+            <option value="does">Does</option>
+            <option value="doesnot">Does not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="FileLocation">Have FileLocation matching</option>
+            <option value="Frame">Have Frame matching</option>
+            <option value="Screen">Have Screen matching</option>
+            <option value="Series">Have Series matching</option>
+        </param>
+        <param name="match_value" type="text"/>
+    </xml>
+    <xml name="name_type_rule_ext">
+        <param name="operator" type="select">
+            <option value="does">Is</option>
+            <option value="doesnot">Is not</option>
+        </param>
+        <param name="match_type" type="select">
+            <option value="istif">tif, tiff, ome.tif or ome.tiff</option>
+            <option value="isjpeg">jpg, jpeg</option>
+            <option value="ispng">png</option>
+            <option value="isimage">the extension of an image file</option>
+            <option value="isflex">flex</option>
+            <option value="ismovie">mov, avi</option>
+
+        </param>
+    </xml>
+    <xml name="image_matching_rules">
+        <repeat name="r_match_rule" title="Another image">
+            <param name="match_all_any" type="select" display="radio" label="Match the following rules">
+                <option value="and">All</option>
+                <option value="or">Any</option>
+            </param>
+            <repeat name="r_match" title="rule">
+                <conditional name="con_match">
+                    <param name="rule_type" type="select" label="Select rule criteria">
+                        <option value="file">File</option>
+                        <option value="directory">Directory</option>
+                        <option value="extension">Extension</option>
+                        <option value="image">Image</option>
+                        <option value="metadata">Metadata</option>
+                    </param>
+                    <when value="file">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="directory">
+                        <expand macro="name_type_rule_matching_file"/>
+                    </when>
+                    <when value="extension">
+                        <expand macro="name_type_rule_ext" />
+                    </when>
+                    <when value="image">
+                        <expand macro="name_type_rule_image" />
+                    </when>
+                    <when value="metadata">
+                        <expand macro="name_type_rule_metadata" />
+                    </when>
+                </conditional>
+            </repeat>
+            <conditional name="con_select_image_type">
+                <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated">
+                    <option value="Grayscale image">Grayscale image</option>
+                    <option value="Color image">Color image</option>
+                    <option value="Binary mask">Binary mask</option>
+                    <option value="Illumination function">Illumination function</option>
+                    <option value="Objects">Objects</option>
+
+                </param>
+                <when value ="Grayscale image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Color image">
+                    <expand macro="macro_image_type" thing="images"/>
+                    <expand macro="image_type_condition" />
+                </when>
+                <when value="Binary mask">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Illumination function">
+                    <expand macro="macro_image_type" thing="images"/>
+                </when>
+                <when value="Objects">
+                    <expand macro="macro_image_type" thing="objects"/>
+                </when>
+            </conditional>
+        </repeat>
+    </xml>
+    <xml name="starting_modules_nameandtypes">
+        <section name="nameandtypes" title="NamesAndTypes" expanded="false">
+            <conditional name="pixel_space">
+                <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images.">
+                    <option value="Yes">Yes, process 3D data</option>
+                    <option value="No">No, do not process 3D data</option>
+                </param>  
+                <when value="Yes">
+                    <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." />
+                    <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/>
+                    <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/>
+                </when>
+                <when value="No"/>
+            </conditional>
+            <conditional name="con_assign_a_name_to">
+                <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools.">
+                    <option value="All images">Give every image the same name</option>
+                    <option value="Images matching rules">Give images one of several names depending on the metadata</option>
+                </param>
+                <when value="All images">
+                    <expand macro="macro_image_type" thing="images" />
+                    <conditional name="con_select_image_type">
+                        <param name="select_image_type" type="select" label="Select the image type">
+                            <option value="Grayscale image">Grayscale image</option>
+                            <option value="Color image">Color image</option>
+                            <option value="Binary mask">Binary mask</option>
+                        </param>
+                        <when value ="Grayscale image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Color image">
+                            <expand macro="image_type_condition" />
+                        </when>
+                        <when value="Binary mask" />
+                    </conditional>
+                </when>
+            <when value="Images matching rules">
+                <expand macro="image_matching_rules"/>
+                <param name="matching_method" type="select" label="Image set matching method">
+                    <option value="Order">Order</option>
+                    <option value="Metadata">Metadata</option>
+                </param>
+            </when>
+        </conditional>
+    </section>
+</xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-complicated.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common-nogroup.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,73 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:2
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:Images matching a rule
+    Select the filtering criteria:and (file does contain "im") (extension does istif)
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:Folder name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)_(?P<folderField2>[a-zA-Z0-9]+)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:3
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does contain "im") (image doesnot ismonochrome)
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Objects
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:and (file does contain "")
+    Name to assign these images:GFP
+    Name to assign these objects:Cell
+    Select the image type:Illumination function
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+    Select the rule criteria:or (extension does istif)
+    Name to assign these images:Actin
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:No
+    grouping metadata count:1
+    Metadata category:None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/common.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,53 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:4
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
--- a/test-data/common.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:4
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/convert_objects_to_image.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,59 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input objects:Nuclei
+    Name the output image:MaskNuclei
+    Select the color format:Binary (black & white)
+    Select the colormap:Default
--- a/test-data/convert_objects_to_image.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,59 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-ConvertObjectsToImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input objects:Nuclei
-    Name the output image:MaskNuclei
-    Select the color format:Binary (black & white)
-    Select the colormap:Default
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/display_data_on_image.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,70 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Display object or image measurements?:Object
+    Select the input objects:Nuclei
+    Measurement to display:Number_Object_Number
+    Select the image on which to display the measurements:DNA
+    Text color:#ff0000
+    Name the output image that has the measurements displayed:ImageDisplay
+    Font size (points):11
+    Number of decimals:0
+    Image elements to save:Image
+    Annotation offset (in pixels):0
+    Display mode:Text
+    Color map:Default
+    Display background image?:Yes
+    Color map scale:Use this image's measurement range
+    Color map range:0.0,1.0
--- a/test-data/display_data_on_image.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-DisplayDataOnImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Add nuclei id as label\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Display object or image measurements?:Object
-    Select the input objects:Nuclei
-    Measurement to display:Number_Object_Number
-    Select the image on which to display the measurements:DNA
-    Text color:#ff0000
-    Name the output image that has the measurements displayed:ImageDisplay
-    Font size (points):11
-    Number of decimals:0
-    Image elements to save:Image
-    Annotation offset (in pixels):0
-    Display mode:Text
-    Color map:Default
-    Display background image?:Yes
-    Color map scale:Use this image's measurement range
-    Color map range:0.0,1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/enhance_or_suppress_features.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,66 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNA
+    Name the output image:DNAdarkholes
+    Select the operation:Enhance
+    Feature size:10
+    Feature type:Dark holes
+    Range of hole sizes:1,15
+    Smoothing scale:2.0
+    Shear angle:0.0
+    Decay:0.95
+    Enhancement method:Tubeness
+    Speed and accuracy:Fast
--- a/test-data/enhance_or_suppress_features.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,66 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-EnhanceOrSuppressFeatures:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:6|show_window:False|notes:\x5B\'Identify nucleoli\', \'PARAMS\x3A Range of hole sizes'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input image:DNA
-    Name the output image:DNAdarkholes
-    Select the operation:Enhance
-    Feature size:10
-    Feature type:Dark holes
-    Range of hole sizes:1,15
-    Smoothing scale:2.0
-    Shear angle:0.0
-    Decay:0.95
-    Enhancement method:Tubeness
-    Speed and accuracy:Fast
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:No
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- a/test-data/export_to_spreadsheet.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the column delimiter:Tab
-    Add image metadata columns to your object data file?:Yes
-    Select the measurements to export:No
-    Calculate the per-image mean values for object measurements?:Yes
-    Calculate the per-image median values for object measurements?:Yes
-    Calculate the per-image standard deviation values for object measurements?:Yes
-    Output file location:Default Output Folder\x7C
-    Create a GenePattern GCT file?:No
-    Select source of sample row name:Metadata
-    Select the image to use as the identifier:None
-    Select the metadata to use as the identifier:None
-    Export all measurement types?:Yes
-    Press button to select measurements:
-    Representation of Nan/Inf:NaN
-    Add a prefix to file names?:No
-    Filename prefix:MyPrefix_
-    Overwrite existing files without warning?:Yes
-    Data to export:Do not use
-    Combine these object measurements with those of the previous object?:No
-    File name:DATA.csv
-    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_image_filename.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_create_gene_metadata.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,76 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Metadata
+    Select the image to use as the identifier:None
+    Select the metadata to use as the identifier:FileName_DNA
+    Export all measurement types?:Yes
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:No
+    Filename prefix:MyPrefix_
+    Overwrite existing files without warning?:Yes
+    Data to export:Do not use
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_to_spreadsheet_multi.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,80 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+ExportToSpreadsheet:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:12|show_window:True|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the column delimiter:Tab
+    Add image metadata columns to your object data file?:Yes
+    Select the measurements to export:No
+    Calculate the per-image mean values for object measurements?:Yes
+    Calculate the per-image median values for object measurements?:Yes
+    Calculate the per-image standard deviation values for object measurements?:Yes
+    Output file location:Default Output Folder\x7C
+    Create a GenePattern GCT file?:Yes
+    Select source of sample row name:Image filename
+    Select the image to use as the identifier:DNA
+    Select the metadata to use as the identifier:None
+    Export all measurement types?:No
+    Press button to select measurements:
+    Representation of Nan/Inf:NaN
+    Add a prefix to file names?:Yes
+    Filename prefix:MyExpt_
+    Overwrite existing files without warning?:Yes
+    Data to export:Image
+    Combine these object measurements with those of the previous object?:No
+    File name:data.csv
+    Use the object name for the file name?:No
+    Data to export:Experiment
+    Combine these object measurements with those of the previous object?:No
+    File name:DATA.csv
+    Use the object name for the file name?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gray_to_color.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,75 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
+    Select a color scheme:RGB
+    Select the image to be colored red:MaskNucleoli
+    Select the image to be colored green:Leave this black
+    Select the image to be colored blue:MaskNuclei
+    Name the output image:CombinedMask
+    Relative weight for the red image:0.8
+    Relative weight for the green image:1.0
+    Relative weight for the blue image:0.5
+    Select the image to be colored cyan:Leave this black
+    Select the image to be colored magenta:Leave this black
+    Select the image to be colored yellow:Leave this black
+    Select the image that determines brightness:Leave this black
+    Relative weight for the cyan image:1.0
+    Relative weight for the magenta image:1.0
+    Relative weight for the yellow image:1.0
+    Relative weight for the brightness image:1.0
+    Hidden:1
+    Image name:None
+    Color:#FF0000
+    Weight:1.0
--- a/test-data/gray_to_color.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-GrayToColor:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\'Combine masks nuclei + nucleoli with colors\'\x5D|batch_state:array(\x5B], dtype=uint8)|enabled:True|wants_pause:False]
-    Select a color scheme:RGB
-    Select the image to be colored red:MaskNucleoli
-    Select the image to be colored green:Leave this black
-    Select the image to be colored blue:MaskNuclei
-    Name the output image:CombinedMask
-    Relative weight for the red image:0.8
-    Relative weight for the green image:1.0
-    Relative weight for the blue image:0.5
-    Select the image to be colored cyan:Leave this black
-    Select the image to be colored magenta:Leave this black
-    Select the image to be colored yellow:Leave this black
-    Select the image that determines brightness:Leave this black
-    Relative weight for the cyan image:1.0
-    Relative weight for the magenta image:1.0
-    Relative weight for the yellow image:1.0
-    Relative weight for the brightness image:1.0
-    Hidden:1
-    Image name:None
-    Color:#FF0000
-    Weight:1.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:0.9
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:500
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.0
+    Thresholding method:Otsu
--- a/test-data/identify_primary_objects.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-IdentifyPrimaryObjects:[module_num:5|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]
-    Select the input image:DNA
-    Name the primary objects to be identified:Nuclei
-    Typical diameter of objects, in pixel units (Min,Max):15,200
-    Discard objects outside the diameter range?:Yes
-    Discard objects touching the border of the image?:Yes
-    Method to distinguish clumped objects:Shape
-    Method to draw dividing lines between clumped objects:Shape
-    Size of smoothing filter:0
-    Suppress local maxima that are closer than this minimum allowed distance:7
-    Speed up by using lower-resolution image to find local maxima?:Yes
-    Fill holes in identified objects?:After both thresholding and declumping
-    Automatically calculate size of smoothing filter for declumping?:Yes
-    Automatically calculate minimum allowed distance between local maxima?:Yes
-    Handling of objects if excessive number of objects identified:Continue
-    Maximum number of objects:500
-    Use advanced settings?:Yes
-    Threshold settings version:10
-    Threshold strategy:Global
-    Thresholding method:Otsu
-    Threshold smoothing scale:1.3488
-    Threshold correction factor:0.9
-    Lower and upper bounds on threshold:0.0,1.0
-    Manual threshold:0
-    Select the measurement to threshold with:None
-    Two-class or three-class thresholding?:Two classes
-    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
-    Size of adaptive window:500
-    Lower outlier fraction:0.05
-    Upper outlier fraction:0.05
-    Averaging method:Mean
-    Variance method:Standard deviation
-    # of deviations:2.0
-    Thresholding method:Otsu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_adaptive_otsu.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Adaptive
+    Thresholding method:Otsu
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Three classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Otsu
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_manual.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:No
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:1
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Erase
+    Maximum number of objects:499
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Manual
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:1
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Manual
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_mce.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.5000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_measurement.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):5,20
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:No
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:0
+    Suppress local maxima that are closer than this minimum allowed distance:6
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Measurement
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.1,0.4
+    Manual threshold:0
+    Select the measurement to threshold with:FileName_DNA
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Measurement
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_adv_global_rb.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):10,40
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Shape
+    Method to draw dividing lines between clumped objects:Shape
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:No
+    Automatically calculate minimum allowed distance between local maxima?:No
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:Yes
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:RobustBackground
+    Threshold smoothing scale:1.4000
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.06
+    Upper outlier fraction:0.07
+    Averaging method:Median
+    Variance method:Median absolute deviation
+    # of deviations:3.00
+    Thresholding method:RobustBackground
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/identify_primary_objects_noadv.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,88 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+IdentifyPrimaryObjects:[module_num:5|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]
+    Select the input image:DNA
+    Name the primary objects to be identified:Nuclei
+    Typical diameter of objects, in pixel units (Min,Max):15,200
+    Discard objects outside the diameter range?:Yes
+    Discard objects touching the border of the image?:Yes
+    Method to distinguish clumped objects:Intensity
+    Method to draw dividing lines between clumped objects:Intensity
+    Size of smoothing filter:1
+    Suppress local maxima that are closer than this minimum allowed distance:7
+    Speed up by using lower-resolution image to find local maxima?:Yes
+    Fill holes in identified objects?:After both thresholding and declumping
+    Automatically calculate size of smoothing filter for declumping?:Yes
+    Automatically calculate minimum allowed distance between local maxima?:Yes
+    Handling of objects if excessive number of objects identified:Continue
+    Maximum number of objects:500
+    Use advanced settings?:No
+    Threshold settings version:10
+    Threshold strategy:Global
+    Thresholding method:Minimum cross entropy
+    Threshold smoothing scale:1.3488
+    Threshold correction factor:1.0
+    Lower and upper bounds on threshold:0.0,1.0
+    Manual threshold:0
+    Select the measurement to threshold with:None
+    Two-class or three-class thresholding?:Two classes
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
+    Size of adaptive window:50
+    Lower outlier fraction:0.05
+    Upper outlier fraction:0.05
+    Averaging method:Mean
+    Variance method:Standard deviation
+    # of deviations:2.00
+    Thresholding method:Minimum cross entropy
Binary file test-data/images.tar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mask_image.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the input image:DNAdarkholes
+    Name the output image:MaskDNAdarkholes
+    Use objects or an image as a mask?:Objects
+    Select object for mask:Nuclei
+    Select image for mask:None
+    Invert the mask?:No
--- a/test-data/mask_image.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MaskImage:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B'Keep only nucleoli inside the nuclei\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the input image:DNAdarkholes
-    Name the output image:MaskDNAdarkholes
-    Use objects or an image as a mask?:Objects
-    Select object for mask:Nuclei
-    Select image for mask:None
-    Invert the mask?:No
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_granularity.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureGranularity:[module_num:5|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]
+    Image count:1
+    Object count:0
+    Select an image to measure:DNA
+    Subsampling factor for granularity measurements:0.25
+    Subsampling factor for background reduction:0.25
+    Radius of structuring element:10
+    Range of the granular spectrum:16
--- a/test-data/measure_granularity.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureGranularity:[module_num:5|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]
-    Image count:1
-    Object count:0
-    Select an image to measure:DNA
-    Subsampling factor for granularity measurements:0.25
-    Subsampling factor for background reduction:0.25
-    Radius of structuring element:10
-    Range of the granular spectrum:16
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_area_occupied.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:2
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nuclei
+    Select a binary image to measure:None
+    Measure the area occupied in a binary image, or in objects?:Objects
+    Select objects to measure:Nucleoli
+    Select a binary image to measure:None
--- a/test-data/measure_image_area_occupied.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageAreaOccupied:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:2
-    Measure the area occupied in a binary image, or in objects?:Objects
-    Select objects to measure:Nuclei
-    Select a binary image to measure:None
-    Measure the area occupied in a binary image, or in objects?:Objects
-    Select objects to measure:Nucleoli
-    Select a binary image to measure:None
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_intensity.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,61 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:No
+    Select the input objects:None
+    Select the image to measure:DNA
+    Measure the intensity only from areas enclosed by objects?:Yes
+    Select the input objects:Nuclei
--- a/test-data/measure_image_intensity.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the image to measure:DNA
-    Measure the intensity only from areas enclosed by objects?:No
-    Select the input objects:None
-    Select the image to measure:DNA
-    Measure the intensity only from areas enclosed by objects?:Yes
-    Select the input objects:Nuclei
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_image_quality.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,72 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Calculate metrics for which images?:All loaded images
+    Image count:1
+    Scale count:1
+    Threshold count:1
+    Select the images to measure:
+    Include the image rescaling value?:Yes
+    Calculate blur metrics?:Yes
+    Spatial scale for blur measurements:20
+    Calculate saturation metrics?:Yes
+    Calculate intensity metrics?:Yes
+    Calculate thresholds?:Yes
+    Use all thresholding methods?:No
+    Select a thresholding method:Otsu
+    Typical fraction of the image covered by objects:0.1
+    Two-class or three-class thresholding?:Two classes
+    Minimize the weighted variance or the entropy:Weighted variance
+    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
--- a/test-data/measure_image_quality.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureImageQuality:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Calculate metrics for which images?:All loaded images
-    Image count:1
-    Scale count:1
-    Threshold count:1
-    Select the images to measure:
-    Include the image rescaling value?:Yes
-    Calculate blur metrics?:Yes
-    Spatial scale for blur measurements:20
-    Calculate saturation metrics?:Yes
-    Calculate intensity metrics?:Yes
-    Calculate thresholds?:Yes
-    Use all thresholding methods?:No
-    Select a thresholding method:Otsu
-    Typical fraction of the image covered by objects:0.1
-    Two-class or three-class thresholding?:Two classes
-    Minimize the weighted variance or the entropy:Weighted variance
-    Assign pixels in the middle intensity class to the foreground or the background?:Foreground
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_intensity.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
--- a/test-data/measure_object_intensity.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureObjectIntensity:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:3|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:1
-    Select an image to measure:DNA
-    Select objects to measure:Nuclei
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_object_size_shape.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,58 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select objects to measure:Nuclei
+    Select objects to measure:Nucleoli
+    Calculate the Zernike features?:Yes
--- a/test-data/measure_object_size_shape.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureObjectSizeShape:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:1|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select objects to measure:Nuclei
-    Select objects to measure:Nucleoli
-    Calculate the Zernike features?:Yes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/measure_texture.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Hidden:1
+    Hidden:1
+    Hidden:1
+    Select an image to measure:DNA
+    Select objects to measure:Nuclei
+    Texture scale to measure:3
+    Measure images or objects?:Objects
--- a/test-data/measure_texture.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-MeasureTexture:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\'PARAMS\x3A\', \'- Texture scale']|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Hidden:1
-    Hidden:1
-    Hidden:1
-    Select an image to measure:DNA
-    Select objects to measure:Nuclei
-    Texture scale to measure:3
-    Measure images or objects?:Objects
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/relate_objects.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,62 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Parent objects:Nuclei
+    Child objects:Nucleoli
+    Calculate child-parent distances?:Both
+    Calculate per-parent means for all child measurements?:Yes
+    Calculate distances to other parents?:No
+    Do you want to save the children with parents as a new object set?:Yes
+    Name the output object:RelateObjects
--- a/test-data/relate_objects.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-RelateObjects:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:5|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Parent objects:Nuclei
-    Child objects:Nucleoli
-    Calculate child-parent distances?:Both
-    Calculate per-parent means for all child measurements?:Yes
-    Calculate distances to other parents?:No
-    Do you want to save the children with parents as a new object set?:Yes
-    Name the output object:RelateObjects
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/save_images.cppipe	Mon May 11 11:40:39 2020 +0000
@@ -0,0 +1,71 @@
+CellProfiler Pipeline: http://www.cellprofiler.org
+Version:3
+DateRevision:319
+GitHash:
+ModuleCount:5
+HasImagePlaneDetails:False
+
+Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    :
+    Filter images?:Images only
+    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
+
+Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
+    Extract metadata?:Yes
+    Metadata data type:Text
+    Metadata types:{}
+    Extraction method count:1
+    Metadata extraction method:Extract from file/folder names
+    Metadata source:File name
+    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
+    Regular expression to extract from folder name:(?P<folderField1>.*)
+    Extract metadata from:All images
+    Select the filtering criteria:and (file does contain "")
+    Metadata file location:
+    Match file and image metadata:[]
+    Use case insensitive matching?:No
+
+NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Assign a name to:Images matching rules
+    Select the image type:Grayscale image
+    Name to assign these images:DNA
+    Match metadata:[]
+    Image set matching method:Order
+    Set intensity range from:Image metadata
+    Assignments count:1
+    Single images count:0
+    Maximum intensity:255.0
+    Process as 3D?:No
+    Relative pixel spacing in X:1.0
+    Relative pixel spacing in Y:1.0
+    Relative pixel spacing in Z:1.0
+    Select the rule criteria:and (file does startwith "im")
+    Name to assign these images:DNA
+    Name to assign these objects:Cell
+    Select the image type:Grayscale image
+    Set intensity range from:Image metadata
+    Select the image type:Grayscale image
+    Maximum intensity:255.0
+
+Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Do you want to group your images?:Yes
+    grouping metadata count:1
+    Metadata category:field1
+
+SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
+    Select the type of image to save:Image
+    Select the image to save:ImageDisplay
+    Select method for constructing file names:From image filename
+    Select image name for file prefix:DNA
+    Enter single file name:OrigBlue
+    Number of digits:4
+    Append a suffix to the image file name?:Yes
+    Text to append to the image name:_nucleiNumbers
+    Saved file format:tiff
+    Output file location:Default Output Folder\x7Coutput
+    Image bit depth:8-bit integer
+    Overwrite existing files without warning?:Yes
+    When to save:Every cycle
+    Record the file and path information to the saved image?:No
+    Create subfolders in the output folder?:No
+    Base image folder:Elsewhere...
--- a/test-data/save_images.txt	Thu Apr 16 09:19:53 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-CellProfiler Pipeline: http://www.cellprofiler.org
-Version:3
-DateRevision:319
-GitHash:
-ModuleCount:5
-HasImagePlaneDetails:False
-
-Images:[module_num:1|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'To begin creating your project, use the Images module to compile a list of files and/or folders that you want to analyze. You can also specify a set of rules to include only the desired files in your selected folders.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    :
-    Filter images?:Images only
-    Select the rule criteria:and (extension does isimage) (directory doesnot startwith ".")
-
-Metadata:[module_num:2|svn_version:\'Unknown\'|variable_revision_number:4|show_window:False|notes:\x5B\'The Metadata module optionally allows you to extract information describing your images (i.e, metadata) which will be stored along with your measurements. This information can be contained in the file name and/or location, or in an external file.\']|batch_state:array([], dtype=uint8)|enabled:True|wants_pause:False]
-    Extract metadata?:Yes
-    Metadata data type:Text
-    Metadata types:{}
-    Extraction method count:1
-    Metadata extraction method:Extract from file/folder names
-    Metadata source:File name
-    Regular expression to extract from file name:(?P<field1>.*)_(?P<field2>[a-zA-Z0-9]+)_(?P<field3>[a-zA-Z0-9]+)_(?P<field4>[a-zA-Z0-9]+)
-    Regular expression to extract from folder name:(?P<field1>.*)
-    Extract metadata from:All images
-    Select the filtering criteria:and (file does contain "")
-    Metadata file location:
-    Match file and image metadata:[]
-    Use case insensitive matching?:No
-
-NamesAndTypes:[module_num:3|svn_version:\'Unknown\'|variable_revision_number:8|show_window:False|notes:\x5B\'The NamesAndTypes module allows you to assign a meaningful name to each image by which other modules will refer to it.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Assign a name to:Images matching rules
-    Select the image type:Grayscale image
-    Name to assign these images:DNA
-    Match metadata:[]
-    Image set matching method:Order
-    Set intensity range from:Image metadata
-    Assignments count:1
-    Single images count:0
-    Maximum intensity:255.0
-    Process as 3D?:No
-    Relative pixel spacing in X:1.0
-    Relative pixel spacing in Y:1.0
-    Relative pixel spacing in Z:1.0
-    Select the rule criteria:and (file does startwith "im")
-    Name to assign these images:DNA
-    Name to assign these objects:Cell
-    Select the image type:Grayscale image
-    Set intensity range from:Image metadata
-    Select the image type:Grayscale image
-    Maximum intensity:255.0
-
-Groups:[module_num:4|svn_version:\'Unknown\'|variable_revision_number:2|show_window:False|notes:\x5B\'The Groups module optionally allows you to split your list of images into image subsets (groups) which will be processed independently of each other. Examples of groupings include screening batches, microtiter plates, time-lapse movies, etc.\'\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Do you want to group your images?:Yes
-    grouping metadata count:1
-    Metadata category:Screen
-
-SaveImages:[module_num:5|svn_version:\'Unknown\'|variable_revision_number:13|show_window:False|notes:\x5B\x5D|batch_state:array(\x5B\x5D, dtype=uint8)|enabled:True|wants_pause:False]
-    Select the type of image to save:Image
-    Select the image to save:ImageDisplay
-    Select method for constructing file names:From image filename
-    Select image name for file prefix:DNA
-    Enter single file name:OrigBlue
-    Number of digits:4
-    Append a suffix to the image file name?:Yes
-    Text to append to the image name:_nucleiNumbers
-    Saved file format:tiff
-    Output file location:Default Output Folder\x7Coutput
-    Image bit depth:8-bit integer
-    Overwrite existing files without warning?:Yes
-    When to save:Every cycle
-    Record the file and path information to the saved image?:No
-    Create subfolders in the output folder?:No
-    Base image folder:Elsewhere...