Call this function to launch a napari window with a given image to begin annotating true positives, false positives, and false negatives on the image with points layers.

napari_count_tfpn.py

import os
import napari
from skimage.io import imread, imsave

def napari_count_tfpn(screenshot_file, point_size=20, save_screenshot=True):
    """
    Opens a napari window and initializes three points layers:
        - "True Positives" with green points
        - "False Positives" with red points
        - "False Negatives" with yellow points

    The user is then able to annotate their image with the points to count instances of each class in the image provided
    by the "screenshot_file" parameter.

    To complete the count, close the napari window. A dictionary is returned with counts for true positives, false
    positives, and false negatives. 

    "tfpn" stands for true/false postive/negative and is a terrible function name. I am open to better alternatives.

    Note that this script has dependencies as shown below:
        import os
        import napari
        from skimage.io import imread, imsave

    :param screenshot_file: (string) Path to image you wish to count true and false positive and negatives for.

    :param point_size: (int) Size of points to use for annotations in napari.

    :param save_screenshot" (bool) Whether or not to save a screenshot of the annotated image in the same location
        as the original image, with "_Annotated" added to the filename before the file extension.

    :return: A dictionary with tallies for true positives, false positives, and false negatives.
    """

    screenshot_file = os.path.abspath(screenshot_file)
    screenshot_directory = os.path.dirname(screenshot_file)
    screenshot_filename = os.path.basename(screenshot_file)
    screenshot_annotated = os.path.join(screenshot_directory, screenshot_filename.replace('.', '_Annotated.'))

    try:
        with napari.gui_qt():
            viewer = napari.view_image(imread(screenshot_file), rgb=True)

            TP_layer = viewer.add_points(size=point_size, name='True Positives', face_color='green')
            FP_layer = viewer.add_points(size=point_size, name='False Positives', face_color='red')
            FN_layer = viewer.add_points(size=point_size, name='False Negatives', face_color='yellow')

            TP_layer.mode = 'add'
            FP_layer.mode = 'add'
            FN_layer.mode = 'add'

            TP_layer.selected = True
            FP_layer.selected = False
            FN_layer.selected = False

    finally:
        tfpn_stats = {'True Positives': len(TP_layer.data),
                      'False Positives': len(FP_layer.data),
                      'False Negatives': len(FN_layer.data)}

        if save_screenshot is True:
            imsave(screenshot_annotated, viewer.screenshot())

    return tfpn_stats