From 8dbaaf2b94fe4d2cf5dfba9dcc91cb1881154510 Mon Sep 17 00:00:00 2001
From: guillaumejaume <gjaume@bwh.harvard.edu>
Date: Tue, 18 Feb 2025 11:50:49 -0500
Subject: [PATCH] mem: gdf contours not in self od wsi

---
 trident/wsi_objects/WSI.py        | 24 ++++++++++++++++--------
 trident/wsi_objects/WSIPatcher.py |  2 +-
 2 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/trident/wsi_objects/WSI.py b/trident/wsi_objects/WSI.py
index 79186a2..d289d34 100644
--- a/trident/wsi_objects/WSI.py
+++ b/trident/wsi_objects/WSI.py
@@ -127,12 +127,6 @@ def _lazy_initialize(self) -> None:
                 self.mag = self._fetch_magnification(self.custom_mpp_keys)
                 self.lazy_init = True
 
-                if self.tissue_seg_path is not None:
-                    try:
-                        # self.mask = cv2.imread(self.tissue_seg_path, cv2.IMREAD_GRAYSCALE)
-                        self.gdf_contours = gpd.read_file(self.tissue_seg_path)
-                    except FileNotFoundError:
-                        raise FileNotFoundError(f"Tissue segmentation file not found: {self.tissue_seg_path}")
             except Exception as e:
                 raise Exception(f"Error initializing WSI: {e}")
 
@@ -513,7 +507,6 @@ def segment_tissue(
         )
         gdf_contours.set_crs("EPSG:3857", inplace=True)  # used to silent warning // Web Mercator
         gdf_contours.to_file(gdf_saveto, driver="GeoJSON")
-        self.gdf_contours = gdf_contours
         self.tissue_seg_path = gdf_saveto
 
         # Draw the contours on the thumbnail image
@@ -586,6 +579,20 @@ def get_best_level_and_custom_downsample(
         # If no suitable level is found, raise an error
         raise ValueError(f"No suitable level found for downsample {downsample}.")
 
+    def load_gdf_contours(self):
+        """
+        Load geodataframe with tissue vs. background contours.
+
+        Returns:
+        --------
+        gpd: Geodataframe. Each entry is a contour.
+        """
+        try:
+            gdf_contours = gpd.read_file(self.tissue_seg_path)
+        except FileNotFoundError:
+            raise FileNotFoundError(f"Tissue segmentation file not found: {self.tissue_seg_path}")
+        return gdf_contours
+
     def extract_tissue_coords(
         self,
         target_mag: int,
@@ -625,12 +632,13 @@ def extract_tissue_coords(
         """
 
         self._lazy_initialize()
+        gdf_contours = self.load_gdf_contours()
 
         patcher = self.create_patcher(
             patch_size=patch_size,
             src_mag=self.mag,
             dst_mag=target_mag,
-            mask=self.gdf_contours,
+            mask=gdf_contours,
             coords_only=True,
             overlap=overlap,
             threshold=min_tissue_proportion,
diff --git a/trident/wsi_objects/WSIPatcher.py b/trident/wsi_objects/WSIPatcher.py
index 02e7224..9e5bfda 100644
--- a/trident/wsi_objects/WSIPatcher.py
+++ b/trident/wsi_objects/WSIPatcher.py
@@ -27,7 +27,7 @@ def __init__(
         """ Initialize patcher, compute number of (masked) rows, columns.
 
         Args:
-            wsi (WSI): wsi to patch
+            wsi (OpenSlideWSI): wsi to patch
             patch_size (int): patch width/height in pixel on the slide after rescaling
             src_pixel_size (float, optional): pixel size in um/px of the slide before rescaling. Defaults to None.
             dst_pixel_size (float, optional): pixel size in um/px of the slide after rescaling. Defaults to None.