plugin_record_intensities_using_preexisting_metadata.py

"""Uses a simple sphere of a given radius for segmentation"""
import math
import numpy
import random
from typing import Optional, Dict, Any, Tuple, List

import matplotlib.cm
import skimage.measure
from matplotlib.colors import Colormap, ListedColormap
from numpy import ndarray

from organoid_tracker.core import UserError, bounding_box, TimePoint
from organoid_tracker.core.experiment import Experiment
from organoid_tracker.core.image_loader import ImageChannel
from organoid_tracker.core.images import Image
from organoid_tracker.core.mask import Mask
from organoid_tracker.core.position import Position
from organoid_tracker.core.resolution import ImageResolution
from organoid_tracker.gui import dialog, option_choose_dialog
from organoid_tracker.gui.threading import Task
from organoid_tracker.gui.window import Window
from organoid_tracker.position_analysis import intensity_calculator
from organoid_tracker.visualizer import activate
from organoid_tracker.visualizer.exitable_image_visualizer import ExitableImageVisualizer


def get_menu_items(window: Window) -> Dict[str, Any]:
    return {
        "Intensity//Record-Record intensities//Record-Record using pre-existing metadata...": lambda: _record_intensities(window)
    }

def _record_intensities(window: Window):
    # Gather possible metadata and existing keys
    existing_keys = set()
    possible_keys = set()
    for experiment in window.get_active_experiments():
        existing_keys |= set(intensity_calculator.get_intensity_keys(experiment))

        # Find possible keys of intensities
        names_and_types = experiment.position_data.get_data_names_and_types()
        for data_name, data_type in names_and_types.items():
            if data_type != float:
                continue  # Skip non-numeric metadata

            if data_name.endswith("_volume") and data_name[:-len("_volume")] in names_and_types:
                continue  # Skip volume of an intensity

            possible_keys.add(data_name)

    # Remove existing keys from intensities
    for existing_key in existing_keys:
        if existing_key in possible_keys:
            possible_keys.remove(existing_key)

    # Raise error if nothing was found
    if len(possible_keys) == 0:
        raise UserError("No metadata found", "No suitable metadata found. Any numeric position metadata is fine."
                                             " You can import metadata through the File menu.")

    possible_keys = list(possible_keys)
    result = option_choose_dialog.prompt_list_multiple("Intensity keys", "Which metadata would you like to use as an intensity?"
          " Note: for normalization purposes, it is assumed that the intensity was measured using the same volume for all cells.", "Metadata keys", possible_keys)
    if result is None:
        return
    if len(result) == 0:
        raise UserError("No options selected", "No options were selected. Cannot do anything.")

    new_intensity_keys = [possible_keys[i] for i in result]
    for experiment in window.get_active_experiments():
        for new_intensity_key in new_intensity_keys:
            raw_intensities = dict(experiment.position_data.find_all_positions_with_data(new_intensity_key))
            volumes = dict(((position, 1) for position in raw_intensities.keys()))
            intensity_calculator.set_raw_intensities(experiment, raw_intensities, volumes, intensity_key=new_intensity_key)