comparison overlay_outlines.py @ 6:d3890df07463 draft default tip

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

5:6f4715b8540a

#!/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"))

6:d3890df07463

#!/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 = "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"))