create a qupath project from the model inference results

[kaczmarj]

the wsinfer run cli should be able to generate a qupath project directly from the slides and model outputs. this would make qupath integration tighter and make it easier for users to visualize results in qupath.

qupath projects are described here https://qupath.readthedocs.io/en/0.4/docs/tutorials/projects.html

the project information is stored in a file and the goal here would be to generate this file.

[swaradgat19]

@kaczmarj This is the modified script. I'm mapping the svs and the geojson according to the output csvs. This script is working, although I'm currently doing minor changes wrt the suggestions given by flake8. Do let me know if any modification is required.

from __future__ import annotations

import sys
import json
from pathlib import Path
import os
import paquo

# os.environ["PAQUO_QUPATH_DIR"] = "/home/sggat/QuPath"

def add_image_and_geojson(
    qupath_proj: QuPathProject, *, image_path: Path | str, geojson_path: Path | str
) -> None:
    with open(geojson_path) as f:
        # FIXME: check that a 'features' key is present and raise a useful error if not
        geojson_features = json.load(f)["features"]

    entry = qupath_proj.add_image(image_path)
    # FIXME: test that the 'load_geojson' function exists. If not, raise a useful error
    try:
        entry.hierarchy.load_geojson(geojson_features)  # type: ignore
    except Exception as e:
        print(f"Failed to run load_geojson function with error:: {e}")

# Store a list of matched slides and geojson files. Linking the slides and geojson in
# this way prevents a potential mismatch by simply listing directories and relying on
# the order to be the same.

def make_qupath_project(wsi_dir, results_dir):
    try:
        from paquo.projects import QuPathProject
    except Exception as e:
        print(
            """QuPath is required to use this functionality but it cannot be found. 
If QuPath is installed, please use define the environment variable 
PAQUO_QUPATH_DIR with the location of the QuPath installation. 
If QuPath is not installed, please install it from https://qupath.github.io/."""
        )
        sys.exit(1)

    print("Found QuPath successfully!")
    QUPATH_PROJECT_DIRECTORY = "QuPathProject"

    csv_files = list((results_dir / "model-outputs-csv").glob("*.csv"))
    slides_and_geojsons = []

    for csv_file in csv_files:
        file_name = csv_file.stem

        json_file = results_dir / "model-outputs-geojson" / (file_name + ".json")
        image_file = wsi_dir / (file_name + ".svs")

        if json_file.exists() and image_file.exists():
            matching_pair = (image_file, json_file)
            slides_and_geojsons.append(matching_pair)
        else:
            print(f"Skipping CSV: {csv_file.name} (No corresponding JSON)")

    with QuPathProject(QUPATH_PROJECT_DIRECTORY, mode="w") as qp:
        for image_path, geojson_path in slides_and_geojsons:
            try:
                add_image_and_geojson(
                    qp, image_path=image_path, geojson_path=geojson_path
                )
            except Exception as e:
                print(f"Failed to add image/geojson with error:: {e}")
    print("Successfully created QuPath Project!")