Use converted frame filenames in COCO JSON output

examples/EPM_to_benchmark.py

@@ -13,6 +13,8 @@
 import shutil
 from pathlib import Path
 
+import sleap_io as sio
+
 from poseinterface.io import annotations_to_coco
 
 # %%
@@ -75,11 +77,8 @@
     print(f"Video already exists at: {target_video_path}")
 
 # %%
-# Convert DLC annotations to COCO format
-# --------------------------------------
-# Here we use the :func:`annotations_to_coco` function from `poseinterface.io`
-# which wraps around `sleap_io` functionality to perform the conversion.
-#
+# Define source annotations path
+# ------------------------------
 # The first attempt failed because the paths in the DLC annotations
 # csv file were given as
 # ``labeled-data,<video-name>,<filename-with-frame-number>.<extension>``
@@ -99,9 +98,43 @@
 # Save COCO annotations inside the Frames directory
 target_annotations_path = target_frames_dir / f"{video_id}_framelabels.json"
 
+# %%
+# Build new filenames for COCO annotations
+# ----------------------------------------
+# We need to determine the new filenames before calling annotations_to_coco.
+# This ensures the JSON file references the renamed frame files,
+# not the original source filenames.
+
+# Load annotations to get the order of labeled frames
+labels = sio.load_file(source_annotations_path)
+
+# Build list of new filenames matching the order of labeled frames
+coco_image_filenames = []
+for lf in labels.labeled_frames:
+    # Extract the original image path from the labeled frame
+    # For DLC, video.filename is a list of all image paths;
+    # use frame_idx to get the correct one for this labeled frame
+    filename = lf.video.filename
+    if isinstance(filename, list):
+        filename = filename[lf.frame_idx]
+    original_path = Path(filename)
+    # Extract frame number from filename, e.g. "img0042.png" -> "0042"
+    frame_number = original_path.stem.replace("img", "")
+    # Create new filename following the naming convention
+    new_filename = f"{video_id}_frame-{frame_number}.png"
+    coco_image_filenames.append(new_filename)
+
+# %%
+# Convert DLC annotations to COCO format
+# --------------------------------------
+# Here we use the :func:`annotations_to_coco` function from `poseinterface.io`
+# which wraps around `sleap_io` functionality to perform the conversion.
+# We pass the new filenames so the JSON references the renamed frames.
+
 annotations_to_coco(
     input_path=source_annotations_path,
     output_json_path=target_annotations_path,
+    coco_image_filenames=coco_image_filenames,
     coco_visibility_encoding="ternary",
 )
 print(f"Saved COCO annotations to: {target_annotations_path}")