Mercurial > repos > bgruening > cp_measure_texture
view image_math.py @ 2:8f3f8c94626f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 1907942bef43b20edfdbd1d1b5eb1cac3602848b"
author | bgruening |
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date | Thu, 16 Apr 2020 05:30:53 -0400 |
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children | 035a58c7f54a |
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#!/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)