Mercurial > repos > bgruening > cp_mask_image
view tile.py @ 6:667a513e67e4 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | bgruening |
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date | Sun, 05 Nov 2023 09:24:38 +0000 |
parents | b178453ea8d1 |
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#!/usr/bin/env python import argparse import json from cp_common_functions import (get_json_value, get_pipeline_lines, get_total_number_of_modules, INDENTATION, update_module_count, write_pipeline) MODULE_NAME = "Tile" OUTPUT_FILENAME = "output.cppipe" def build_header(module_name, module_number): result = "|".join( [ f"{module_name}:[module_num:{module_number}", "svn_version:\\'Unknown\\'", "variable_revision_number:1", "show_window:True", "notes:\\x5B\\'Tile the original color image, the outlined image and the image of tracked labels together.\\'\\x5D", "batch_state:array(\\x5B\\x5D, dtype=uint8)", "enabled:True", "wants_pause:False]\n", ] ) return result def build_main_block(input_params): result = INDENTATION.join( [ f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n", f"Name the output image:{get_json_value(input_params,'output_image_name')}\n", f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n", ] ) calc_rows = get_json_value( input_params, "con_assembly_method.con_calc_no_row.calc_no_row" ) no_of_rows = 8 calc_cols = get_json_value( input_params, "con_assembly_method.con_calc_no_cols.calc_no_cols" ) no_of_cols = 12 if calc_rows == "No": no_of_rows = get_json_value( input_params, "con_assembly_method.con_calc_no_row.no_of_row" ) if calc_cols == "No": no_of_cols = get_json_value( input_params, "con_assembly_method.con_calc_no_cols.no_of_cols" ) corner_to_begin = get_json_value( input_params, "con_assembly_method.corner_to_begin" ) direction_tiling = get_json_value(input_params, "con_assembly_method.direction") meander = get_json_value(input_params, "con_assembly_method.meander_mode") assembly_method = get_json_value( input_params, "con_assembly_method.assembly_method" ) result += INDENTATION.join( [ f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n", f"Final number of columns:{str(no_of_cols)}\n", f"Image corner to begin tiling:{corner_to_begin}\n", f"Direction to begin tiling:{direction_tiling}\n", f"Use meander mode?:{meander}\n", f"Automatically calculate number of rows?:{calc_rows}\n", f"Automatically calculate number of columns?:{calc_cols}\n", ] ) if assembly_method == "Within cycles": additionals = input_params["con_assembly_method"]["rpt_additional_image"] for img in additionals: result += INDENTATION.join( [ f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n" ] ) result = result.rstrip("\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_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)