--- a/starting_modules.py	Fri Feb 26 14:11:48 2021 +0000
+++ b/starting_modules.py	Sun Nov 05 09:31:44 2023 +0000
@@ -9,22 +9,25 @@
 
 
 def write_images():
-    filter_images = params['images']['filter_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"
+    _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']
+    metadata_extraction = params["metadata"]["con_metadata_extraction"]
+    extract = metadata_extraction["extract"]
 
-    if 'extraction_method' in metadata_extraction:
-        method_count = len(metadata_extraction['extraction_method'])
+    if "extraction_method" in metadata_extraction:
+        method_count = len(metadata_extraction["extraction_method"])
     else:
         method_count = 1
 
@@ -35,22 +38,42 @@
         _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})$\n"
+        _str += (
+            FOURSPACES + "Metadata extraction method:Extract from file/folder names\n"
+        )
+        _str += (
+            FOURSPACES
+            + "Regular expression to extract from file name:^(?P<Plate>.*)_(?P<Well>\x5BA-P\x5D\x5B0-9\x5D{2})_s(?P<Site>\x5B0-9\x5D)_w(?P<ChannelNumber>\x5B0-9\x5D)\n"
+        )
+        _str += (
+            FOURSPACES
+            + "Regular expression to extract from folder name:(?P<Date>\x5B0-9\x5D{4}_\x5B0-9\x5D{2}_\x5B0-9\x5D{2})$\n"
+        )
         _str += FOURSPACES + "Extract metadata from:All images\n"
-        _str += FOURSPACES + "Select the filtering criteria:and (file does contain \"\")\n"
+        _str += (
+            FOURSPACES + '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 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"]
+            _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"]
@@ -63,24 +86,62 @@
                 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
+                + "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"]
+            _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":
+            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"] + ")"
+                        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"] + "\")"
+                        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"
+                _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
+                    + '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"
@@ -90,20 +151,30 @@
 
 
 def write_nameandtypes():
-    nameandtypes = params['nameandtypes']
-    assign_a_name = nameandtypes['con_assign_a_name_to']['assign_a_name_to']
+    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
+    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']
+    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
+    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']
+    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"]
@@ -113,12 +184,26 @@
     _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
+            + "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
+            + "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
@@ -130,7 +215,11 @@
         _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
+            + "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"
@@ -147,36 +236,77 @@
             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"] + "\")"
+                    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"] + ")"
+                        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
+                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"
+            _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"]
+                _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 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"]
+                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"]
+                _str += (
+                    FOURSPACES
+                    + "Maximum intensity:%s\n"
+                    % rule["con_select_image_type"]["con_set_intensity"][
+                        "maximum_intensity"
+                    ]
+                )
             else:
                 _str += FOURSPACES + "Maximum intensity:255.0\n"
 
@@ -184,9 +314,9 @@
 
 
 def write_groups():
-    groups = params['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"
+    _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"]
 
@@ -194,7 +324,10 @@
     _str += FOURSPACES + "grouping metadata count:1\n"
 
     if group_images == "Yes":
-        _str += FOURSPACES + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
+        _str += (
+            FOURSPACES
+            + "Metadata category:%s\n" % groups["con_groups"]["group_category"]
+        )
     else:
         _str += FOURSPACES + "Metadata category:None\n"
 
@@ -202,13 +335,15 @@
 
 
 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"]
+    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)