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Adding metdata to tiled images

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This commit is contained in:
Martin Laasmaa
2026-01-16 10:39:14 +02:00
parent 31cb6a6c8e
commit eefda5b878
1 changed files with 25 additions and 10 deletions
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35
src/utils/image_splitter.py
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@@ -114,11 +114,12 @@ class Label:
return truth_val return truth_val
def to_string(self, bbox: list = None, polygon: list = None): def to_string(self, bbox: list = None, polygon: list = None):
coords = ""
if bbox is None: if bbox is None:
bbox = self.bbox bbox = self.bbox
# coords += " ".join([f"{x:.6f}" for x in self.bbox])
if polygon is None: if polygon is None:
polygon = self.polygon polygon = self.polygon
coords = " ".join([f"{x:.6f}" for x in self.bbox])
if self.polygon is not None: if self.polygon is not None:
coords += " " + " ".join([f"{x:.6f} {y:.6f}" for x, y in self.polygon]) coords += " " + " ".join([f"{x:.6f} {y:.6f}" for x, y in self.polygon])
return f"{self.class_id} {coords}" return f"{self.class_id} {coords}"
@@ -179,6 +180,13 @@ class ImageSplitter:
for i in range(patch_size[0]): for i in range(patch_size[0]):
for j in range(patch_size[1]): 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}" tile_reference = f"i{i}j{j}"
hrange = (i * hstep / h, (i + 1) * hstep / h) hrange = (i * hstep / h, (i + 1) * hstep / h)
wrange = (j * wstep / w, (j + 1) * wstep / w) wrange = (j * wstep / w, (j + 1) * wstep / w)
@@ -199,7 +207,7 @@ class ImageSplitter:
print(l.bbox) print(l.bbox)
# print(labels) # print(labels)
yield tile_reference, tile, labels yield tile_reference, tile, labels, metadata
def split_respective_to_label(self, padding: int = 67): def split_respective_to_label(self, padding: int = 67):
if self.labels is None: if self.labels is None:
@@ -208,6 +216,7 @@ class ImageSplitter:
for i, label in enumerate(self.labels): for i, label in enumerate(self.labels):
tile_reference = f"_lbl-{i+1:02d}" tile_reference = f"_lbl-{i+1:02d}"
# print(label.bbox) # 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_norm, yc_norm, h_norm, w_norm = label.bbox # normalized coords
xc, yc, h, w = [ xc, yc, h, w = [
@@ -246,17 +255,17 @@ class ImageSplitter:
# print("tile shape:", tile.shape) # print("tile shape:", tile.shape)
yolo_annotation = f"{label.class_id} {x_offset/nx} {y_offset/ny} {h_norm} {w_norm} " yolo_annotation = f"{label.class_id} " # {x_offset/nx} {y_offset/ny} {h_norm} {w_norm} "
print(yolo_annotation)
yolo_annotation += " ".join( yolo_annotation += " ".join(
[ [
f"{(x*self.image.shape[1]-(xc - x_offset))/nx:.6f} {(y*self.image.shape[0]-(yc-y_offset))/ny:.6f}" 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 for x, y in label.polygon
] ]
) )
print(yolo_annotation)
new_label = Label(yolo_annotation=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): def main(args):
@@ -278,9 +287,9 @@ def main(args):
else: else:
data = data.split_into_tiles(patch_size=args.patch_size) 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()
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
debug = False debug = False
@@ -310,15 +319,21 @@ def main(args):
# } debug # } debug
if args.output: 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 scale = 5
tile_zoomed = zoom(tile, zoom=scale) 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: if labels is not None:
with open(args.output / "labels" / f"{image_path.stem}_{tile_reference}.txt", "w") as f: with open(args.output / "labels" / f"{image_path.stem}_{tile_reference}.txt", "w") as f:
for label in labels: 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") f.write(label.to_string() + "\n")