added qupath flag in CLI tool, create project if flag is true

.gitignore

@@ -172,5 +172,9 @@ cython_debug/
 # Version
 /wsinfer/_version.py
 
+#QuPath Project
+/QuPathProject
+*.backup
+
 # Extras
 .DS_Store

wsinfer/cli/infer.py

@@ -24,6 +24,7 @@
 from ..modellib.run_inference import run_inference
 from ..patchlib import segment_and_patch_directory_of_slides
 from ..write_geojson import write_geojsons
+from ..qupath import make_qupath_project
 
 
 def _num_cpus() -> int:
@@ -252,6 +253,13 @@ def get_stdout(args: list[str]) -> str:
     help="JIT-compile the model and apply inference optimizations. This imposes a"
     " startup cost but may improve performance overall.",
 )
+@click.option(
+    "--qupath",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Creates a QuPath project",
+)
 def run(
     ctx: click.Context,
     *,
@@ -263,6 +271,7 @@ def run(
     batch_size: int,
     num_workers: int = 0,
     speedup: bool = False,
+    qupath: bool = False
 ) -> None:
     """Run model inference on a directory of whole slide images.
 
@@ -378,3 +387,5 @@ def run(
 
     csvs = list((results_dir / "model-outputs-csv").glob("*.csv"))
     write_geojsons(csvs, results_dir, num_workers)
+    if qupath:
+        make_qupath_project(wsi_dir, results_dir)

wsinfer/qupath.py

@@ -0,0 +1,74 @@
+from __future__ import annotations
+
+import sys
+import json
+from pathlib import Path
+import subprocess
+import os
+import paquo
+from natsort import natsorted #add in dependencies?
+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
+    entry.hierarchy.load_geojson(geojson_features)  # type: ignore
+
+
+# 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)")
+
+    # csv_list = natsorted([str(file) for file in wsi_dir.iterdir() if file.is_file()])
+    # json_list = natsorted([str(file) for file in Path(f"{results_dir}/model-outputs-geojson").iterdir() if file.is_file()])
+
+    # slides_and_geojsons = [
+    #     (csv, json) for csv, json in zip(csv_list, json_list)
+    # ]
+
+    print(slides_and_geojsons)
+
+    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!")