--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/overlay_outlines.py	Sat Feb 06 09:58:52 2021 +0000
@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import get_json_value
+from cp_common_functions import get_pipeline_lines
+from cp_common_functions import get_total_number_of_modules
+from cp_common_functions import INDENTATION
+from cp_common_functions import update_module_count
+from cp_common_functions import write_pipeline
+
+MODULE_NAME = "OverlayOutlines"
+OUTPUT_FILENAME = "output.cppipe"
+
+
+def build_ctg_header(module_name, module_number):
+    """Creates the first line of a module given the name and module number"""
+    result = "|".join([f"{module_name}:[module_num:{module_number}",
+                       "svn_version:\\'Unknown\\'",
+                       "variable_revision_number:4",
+                       "show_window:True",
+                       "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
+
+    on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
+    # defaults
+    img_to_display = "None"
+    display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
+    method_brightness = "Max of image"
+    howto = get_json_value(input_params, 'howto_outline')
+    outline_color = "#FF0000"
+    obj_to_display = "None"
+
+    name_output_img = get_json_value(input_params, 'name_output_image')
+
+    if on_blank == "No":
+        img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
+         f"Name the output image:{name_output_img}\n",
+         f"Outline display mode:{display_mode}\n"
+         ])
+
+    if on_blank == "No" and display_mode == "Grayscale":
+        method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
+         f"How to outline:{howto}\n"
+         ])
+
+    obj_outline_str = ""
+
+    if display_mode == "Color":
+        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
+            outline_color = get_json_value(obj, 'outline_color')
+            obj_to_display = get_json_value(obj, 'obj_to_display')
+            obj_outline_str += INDENTATION.join(
+                [f"{INDENTATION}Select outline color:{outline_color}\n",
+                 f"Select objects to display:{obj_to_display}\n"
+                 ])
+    else:  # grayscale
+        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
+            obj_to_display = get_json_value(obj, 'obj_to_display')
+            obj_outline_str += INDENTATION.join(
+                [f"{INDENTATION}Select outline color:{outline_color}\n",
+                 f"Select objects to display:{obj_to_display}\n"
+                 ])
+    obj_outline_str = obj_outline_str.rstrip("\n")
+    result += f"{obj_outline_str}"
+
+    return result
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-p', '--pipeline',
+        help='CellProfiler pipeline'
+    )
+    parser.add_argument(
+        '-i', '--inputs',
+        help='JSON inputs from Galaxy'
+    )
+    args = parser.parse_args()
+
+    pipeline_lines = get_pipeline_lines(args.pipeline)
+    inputs_galaxy = json.load(open(args.inputs, "r"))
+
+    current_module_num = get_total_number_of_modules(pipeline_lines)
+    current_module_num += 1
+    pipeline_lines = update_module_count(pipeline_lines, current_module_num)
+
+    header_block = build_ctg_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)