From 540dabf8073ab8e3abf8618d2c59f9b8006027df Mon Sep 17 00:00:00 2001
From: swaradgat19 <swarad2000@gmail.com>
Date: Wed, 3 Jan 2024 17:08:48 -0500
Subject: [PATCH] handled paquo import using global variable HAS_PAQUO

---
 .gitignore        |  2 +-
 wsinfer/qupath.py | 72 +++++++++++++++++++++++++----------------------
 2 files changed, 40 insertions(+), 34 deletions(-)

diff --git a/.gitignore b/.gitignore
index 17e8df1..fb560af 100644
--- a/.gitignore
+++ b/.gitignore
@@ -173,7 +173,7 @@ cython_debug/
 /wsinfer/_version.py
 
 #QuPath Project
-/QuPathProject
+model-outputs-qupath/
 *.backup
 
 # Extras
diff --git a/wsinfer/qupath.py b/wsinfer/qupath.py
index a761f94..10f919b 100644
--- a/wsinfer/qupath.py
+++ b/wsinfer/qupath.py
@@ -4,62 +4,68 @@
 import json
 from pathlib import Path
 
+try:
+    from paquo.projects import QuPathProject
+
+    HAS_PAQUO = True
+except Exception:
+    HAS_PAQUO = False
+
 
 def add_image_and_geojson(
-    qupath_proj,
+    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"]
+        try:
+            geojson_features = json.load(f)["features"]
+        except Exception as e:
+            print(f"Unable to find features key:: {e}")
 
     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
+        entry.hierarchy.load_geojson(geojson_features)
     except Exception as e:
         print(f"Failed to run load_geojson function with error:: {e}")
 
 
-def make_qupath_project(wsi_dir, results_dir):
-    try:
-        from paquo.projects import QuPathProject
-    except Exception as e:
+def make_qupath_project(wsi_dir: Path, results_dir: Path) -> None:
+    if not HAS_PAQUO:
         print(
-            f"""Cannot find QuPath with error:: {e}.
+            """Cannot find QuPath.
 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)
+    else:
+        print("Found QuPath successfully!")
+        QUPATH_PROJECT_DIRECTORY = results_dir / "model-outputs-qupath"
 
-    print("Found QuPath successfully!")
-    QUPATH_PROJECT_DIRECTORY = results_dir / "model-outputs-qupath"
-
-    csv_files = list((results_dir / "model-outputs-csv").glob("*.csv"))
-    slides_and_geojsons = []
+        csv_files = list((results_dir / "model-outputs-csv").glob("*.csv"))
+        slides_and_geojsons = []
 
-    for csv_file in csv_files:
-        file_name = csv_file.stem
+        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")
+            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)")
+            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!")
+        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!")