annotate image_math.py @ 6:27edbb90ab2b draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

#!/usr/bin/env python

import argparse
import json

from cp_common_functions import (build_header, concat_conditional,
                                 get_json_value, get_pipeline_lines,
                                 get_total_number_of_modules,
                                 INDENTATION, update_module_count,
                                 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)