--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/color_to_gray.py	Sat Feb 06 10:00:59 2021 +0000
@@ -0,0 +1,159 @@
+#!/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 = "ColorToGray"
+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\\'Convert the color image to grayscale.\\'\\x5D",
+                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+                       "enabled:True",
+                       "wants_pause:False]\n"])
+    return result
+
+
+def build_main_block(input_params):
+    """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
+    result = INDENTATION.join([f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
+                               f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
+                               f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
+                               ])
+
+    conversion_method = get_json_value(input_params, 'con_conversion_method.conversion_method')
+
+    image_type = get_json_value(input_params, 'con_conversion_method.con_image_type.image_type')
+    rgb_comb_name_out = "OrigGray"
+    combine_w_red = 1.0
+    combine_w_green = 1.0
+    combine_w_blue = 1.0
+
+    split_red = "Yes"
+    split_green = "Yes"
+    split_blue = "Yes"
+    red_output_name = "OrigRed"
+    green_output_name = "OrigGreen"
+    blue_output_name = "OrigBlue"
+
+    split_hue = "Yes"
+    split_saturation = "Yes"
+    split_value = "Yes"
+    hue_output_name = "OrigHue"
+    saturation_output_name = "OrigSaturation"
+    value_output_name = "OrigValue"
+
+    channel_count = 1
+    if conversion_method == "Combine":
+        if image_type == "RGB" or image_type == "HSV":
+            rgb_comb_name_out = get_json_value(input_params, 'con_conversion_method.name_output_image')
+            combine_w_red = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_red_channel')
+            combine_w_green = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_green_channel')
+            combine_w_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_blue_channel')
+    elif conversion_method == "Split":
+        if image_type == "RGB":
+            split_red = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.yes_no')
+            red_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.name_output_image')
+            split_green = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.yes_no')
+            green_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.name_output_image')
+            split_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.yes_no')
+            blue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.name_output_image')
+        elif image_type == "HSV":
+            split_hue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.yes_no')
+            hue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.name_output_image')
+            split_saturation = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.yes_no')
+            saturation_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.name_output_image')
+            split_value = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.yes_no')
+            value_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.name_output_image')
+
+    result += INDENTATION.join(
+        [f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
+         f"Relative weight of the red channel:{str(combine_w_red)}\n",
+         f"Relative weight of the green channel:{str(combine_w_green)}\n",
+         f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
+
+         f"Convert red to gray?:{split_red}\n",
+         f"Name the output image:{red_output_name}\n",
+         f"Convert green to gray?:{split_green}\n",
+         f"Name the output image:{green_output_name}\n",
+         f"Convert blue to gray?:{split_blue}\n",
+         f"Name the output image:{blue_output_name}\n",
+
+         f"Convert hue to gray?:{split_hue}\n",
+         f"Name the output image:{hue_output_name}\n",
+         f"Convert saturation to gray?:{split_saturation}\n",
+         f"Name the output image:{saturation_output_name}\n",
+         f"Convert value to gray?:{split_value}\n",
+         f"Name the output image:{value_output_name}\n"
+         ])
+
+    channel_count = 1
+    if image_type == "Channels":
+        channels = input_params['con_conversion_method']['con_image_type']['rpt_channel']
+        channel_count = len(channels)
+        result += INDENTATION.join(
+            [f"{INDENTATION}Channel count:{channel_count}\n"
+             ])
+
+        for ch in channels:
+            rel_weight_ch = 1.0
+            image_name = "Channel1"
+            if conversion_method == "Combine":
+                rel_weight_ch = get_json_value(ch, 'weight_of_channel')
+            else:
+                image_name = get_json_value(ch, 'image_name')
+            result += INDENTATION.join(
+                [f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n",
+                 f"Relative weight of the channel:{str(rel_weight_ch)}\n",
+                 f"Image name:{image_name}\n"
+                 ])
+    else:
+        result += INDENTATION.join(
+            [f"{INDENTATION}Channel count:{channel_count}\n",
+             "Channel number:Red\\x3A 1\n",
+             "Relative weight of the channel:1.0\n",
+             "Image name:Channel1\n"
+             ])
+
+    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)