--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_math.py	Sat Feb 06 10:06:16 2021 +0000
@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+from cp_common_functions import build_header
+from cp_common_functions import concat_conditional
+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 = "ImageMath"
+OUTPUT_FILENAME = "output.cppipe"
+
+operator_map = {
+    "add": "Add",
+    "subtract": "Subtract",
+    "multiply": "Multiply",
+    "divide": "Divide",
+    "average": "Average",
+    "minimum": "Minimum",
+    "maximum": "Maximum",
+    "invert": "Invert",
+    "log_2": "Log transform (base 2)",
+    "log_legacy": "Log transform (legacy)",
+    "and": "And",
+    "or": "Or",
+    "not": "Not",
+    "equals": "Equals"
+}
+
+
+def build_main_block(input_params):
+    """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
+    operation = operator_map[get_json_value(
+        input_params, 'operation.operation')]
+    result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
+                               f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
+                               f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
+                               f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
+                               f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
+                               f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
+                               f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
+                               f"Name the output image:{get_json_value(input_params,'name_output_image')}"
+                               ])
+    return result
+
+
+def build_variable_block(inputs_galaxy):
+    result = ""
+    first_image_block = build_first_image_block(
+        get_json_value(inputs_galaxy, 'operation.first_image'))
+    result += f"\n{first_image_block}"
+    second_image_block = build_second_image_block(
+        get_json_value(inputs_galaxy, 'operation.second_image'))
+    result += f"\n{second_image_block}"
+    return result
+
+
+def build_first_image_block(input_params):
+    """Creates the block of parameters for the first operator in operations"""
+
+    value_select = get_json_value(
+        input_params, 'image_or_measurement_first.image_or_measurement_first')
+    image_name = get_json_value(
+        input_params, 'image_or_measurement_first.select_the_first_image')
+    value_multiply = get_json_value(
+        input_params, 'multiply_the_first_image_by')
+    category = get_json_value(
+        input_params, 'image_or_measurement_first.category_first.category_first')
+    measurement = get_json_value(
+        input_params, 'image_or_measurement_first.category_first.measurement_first')
+
+    result = INDENTATION.join(
+        [f"{INDENTATION}Image or measurement?:{value_select}\n",
+         f"Select the first image:{image_name}\n",
+         f"Multiply the first image by:{value_multiply}\n",
+         f"Measurement:{concat_conditional(category, measurement)}"
+         ])
+    return result
+
+
+def build_second_image_block(input_params):
+    """Creates the block of parameters for the second operator in binary operations"""
+
+    value_select = get_json_value(
+        input_params, 'image_or_measurement_second.image_or_measurement_second')
+    image_name = get_json_value(
+        input_params, 'image_or_measurement_second.select_the_second_image')
+    value_multiply = get_json_value(
+        input_params, 'multiply_the_second_image_by')
+    category = get_json_value(
+        input_params, 'image_or_measurement_second.category_second.category_second')
+    measurement = get_json_value(
+        input_params, 'image_or_measurement_second.category_second.measurement_second')
+
+    result = INDENTATION.join(
+        [f"{INDENTATION}Image or measurement?:{value_select}\n",
+         f"Select the second image:{image_name}\n",
+         f"Multiply the second image by:{value_multiply}\n",
+         f"Measurement:{concat_conditional(category, measurement)}"
+         ])
+    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_header(MODULE_NAME, current_module_num)
+    main_block = build_main_block(inputs_galaxy)
+    variable_block = build_variable_block(inputs_galaxy)
+
+    module_pipeline = f"\n{header_block}{main_block}{variable_block}\n"
+    pipeline_lines.append(module_pipeline)
+
+    write_pipeline(OUTPUT_FILENAME, pipeline_lines)