annotate overlay_outlines.py @ 4:f8fa0f6718a3 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"

#!/usr/bin/env python

import argparse
import json

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 = "OverlayOutlines"
OUTPUT_FILENAME = "output.cppipe"


def build_ctg_header(module_name, module_number):
    """Creates the first line of a module given the name and module number"""
    result = "|".join([f"{module_name}:[module_num:{module_number}",
                       "svn_version:\\'Unknown\\'",
                       "variable_revision_number:4",
                       "show_window:True",
                       "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
                       "batch_state:array(\\x5B\\x5D, dtype=uint8)",
                       "enabled:True",
                       "wants_pause:False]\n"])
    return result


def build_main_block(input_params):
    result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"

    on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
    # defaults
    img_to_display = "None"
    display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
    method_brightness = "Max of image"
    howto = get_json_value(input_params, 'howto_outline')
    outline_color = "#FF0000"
    obj_to_display = "None"

    name_output_img = get_json_value(input_params, 'name_output_image')

    if on_blank == "No":
        img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')

    result += INDENTATION.join(
        [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
         f"Name the output image:{name_output_img}\n",
         f"Outline display mode:{display_mode}\n"
         ])

    if on_blank == "No" and display_mode == "Grayscale":
        method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')

    result += INDENTATION.join(
        [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
         f"How to outline:{howto}\n"
         ])

    obj_outline_str = ""

    if display_mode == "Color":
        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
            outline_color = get_json_value(obj, 'outline_color')
            obj_to_display = get_json_value(obj, 'obj_to_display')
            obj_outline_str += INDENTATION.join(
                [f"{INDENTATION}Select outline color:{outline_color}\n",
                 f"Select objects to display:{obj_to_display}\n"
                 ])
    else:  # grayscale
        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
            obj_to_display = get_json_value(obj, 'obj_to_display')
            obj_outline_str += INDENTATION.join(
                [f"{INDENTATION}Select outline color:{outline_color}\n",
                 f"Select objects to display:{obj_to_display}\n"
                 ])
    obj_outline_str = obj_outline_str.rstrip("\n")
    result += f"{obj_outline_str}"

    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_ctg_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)