annotate image_math.py @ 2:3c3cd68d6d5a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"

#!/usr/bin/env python

import json
import sys
import os
import argparse
from cp_common_functions import *

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)