From eefda5b878bf10bbc93fdbff8dead5e53eb5e7d7 Mon Sep 17 00:00:00 2001
From: Martin Laasmaa <martin@sysbio.ioc.ee>
Date: Fri, 16 Jan 2026 10:39:14 +0200
Subject: [PATCH] Adding metdata to tiled images

---
 src/utils/image_splitter.py | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/utils/image_splitter.py b/src/utils/image_splitter.py
index 5f01d6e..0cf22f9 100644
--- a/src/utils/image_splitter.py
+++ b/src/utils/image_splitter.py
@@ -114,11 +114,12 @@ class Label:
         return truth_val
 
     def to_string(self, bbox: list = None, polygon: list = None):
+        coords = ""
         if bbox is None:
             bbox = self.bbox
+            # coords += " ".join([f"{x:.6f}" for x in self.bbox])
         if polygon is None:
             polygon = self.polygon
-        coords = " ".join([f"{x:.6f}" for x in self.bbox])
         if self.polygon is not None:
             coords += " " + " ".join([f"{x:.6f} {y:.6f}" for x, y in self.polygon])
         return f"{self.class_id} {coords}"
@@ -179,6 +180,13 @@ class ImageSplitter:
 
         for i in range(patch_size[0]):
             for j in range(patch_size[1]):
+                metadata = {
+                    "image_path": str(self.image_path),
+                    "label_path": str(self.label_path),
+                    "tile_section": f"{i}, {j}",
+                    "tile_size": f"{hstep}, {wstep}",
+                    "patch_size": f"{patch_size[0]}, {patch_size[1]}",
+                }
                 tile_reference = f"i{i}j{j}"
                 hrange = (i * hstep / h, (i + 1) * hstep / h)
                 wrange = (j * wstep / w, (j + 1) * wstep / w)
@@ -199,7 +207,7 @@ class ImageSplitter:
                             print(l.bbox)
 
                 # print(labels)
-                yield tile_reference, tile, labels
+                yield tile_reference, tile, labels, metadata
 
     def split_respective_to_label(self, padding: int = 67):
         if self.labels is None:
@@ -208,6 +216,7 @@ class ImageSplitter:
         for i, label in enumerate(self.labels):
             tile_reference = f"_lbl-{i+1:02d}"
             # print(label.bbox)
+            metadata = {"image_path": str(self.image_path), "label_path": str(self.label_path), "label_index": str(i)}
 
             xc_norm, yc_norm, h_norm, w_norm = label.bbox  # normalized coords
             xc, yc, h, w = [
@@ -246,17 +255,17 @@ class ImageSplitter:
 
             # print("tile shape:", tile.shape)
 
-            yolo_annotation = f"{label.class_id} {x_offset/nx} {y_offset/ny} {h_norm} {w_norm} "
-            print(yolo_annotation)
+            yolo_annotation = f"{label.class_id} "  # {x_offset/nx} {y_offset/ny} {h_norm} {w_norm} "
             yolo_annotation += " ".join(
                 [
                     f"{(x*self.image.shape[1]-(xc - x_offset))/nx:.6f} {(y*self.image.shape[0]-(yc-y_offset))/ny:.6f}"
                     for x, y in label.polygon
                 ]
             )
+            print(yolo_annotation)
             new_label = Label(yolo_annotation=yolo_annotation)
 
-            yield tile_reference, tile, [new_label]
+            yield tile_reference, tile, [new_label], metadata
 
 
 def main(args):
@@ -278,9 +287,9 @@ def main(args):
         else:
             data = data.split_into_tiles(patch_size=args.patch_size)
 
-        for tile_reference, tile, labels in data:
+        for tile_reference, tile, labels, metadata in data:
             print()
-            print(tile_reference, tile.shape, labels)  # len(labels) if labels else None)
+            print(tile_reference, tile.shape, labels, metadata)  # len(labels) if labels else None)
 
             # { debug
             debug = False
@@ -310,15 +319,21 @@ def main(args):
             # } debug
 
             if args.output:
-                imwrite(args.output / "images" / f"{image_path.stem}_{tile_reference}.tif", tile)
+                # imwrite(args.output / "images" / f"{image_path.stem}_{tile_reference}.tif", tile, metadata=metadata)
                 scale = 5
                 tile_zoomed = zoom(tile, zoom=scale)
-                imwrite(args.output / "images-zoomed" / f"{image_path.stem}_{tile_reference}.tif", tile_zoomed)
+                metadata["scale"] = scale
+                imwrite(
+                    args.output / "images" / f"{image_path.stem}_{tile_reference}.tif",
+                    tile_zoomed,
+                    metadata=metadata,
+                    imagej=True,
+                )
 
                 if labels is not None:
                     with open(args.output / "labels" / f"{image_path.stem}_{tile_reference}.txt", "w") as f:
                         for label in labels:
-                            label.offset_label(tile.shape[1], tile.shape[0])
+                            # label.offset_label(tile.shape[1], tile.shape[0])
                             f.write(label.to_string() + "\n")