Add SuggestionFrame

sleap_io/__init__.py

@@ -10,6 +10,7 @@
     Instance,
     PredictedInstance,
 )
+from sleap_io.model.suggestions import SuggestionFrame
 from sleap_io.model.labeled_frame import LabeledFrame
 from sleap_io.model.labels import Labels
 from sleap_io.io.main import (

sleap_io/io/slp.py

@@ -12,6 +12,7 @@
     Symmetry,
     Node,
     Track,
+    SuggestionFrame,
     Point,
     PredictedPoint,
     Instance,
@@ -161,6 +162,55 @@ def write_tracks(labels_path: str, tracks: list[Track]):
         f.create_dataset("tracks_json", data=tracks_json, maxshape=(None,))
 
 
+def read_suggestions(labels_path: str, videos: list[Video]) -> list[SuggestionFrame]:
+    """Read `SuggestionFrame` dataset in a SLEAP labels file.
+
+    Args:
+        labels_path: A string path to the SLEAP labels file.
+        videos: A list of `Video` objects.
+
+    Returns:
+        A list of `SuggestionFrame` objects.
+    """
+    suggestions = [
+        json.loads(x) for x in read_hdf5_dataset(labels_path, "suggestions_json")
+    ]
+    suggestions_objects = []
+    for suggestion in suggestions:
+        suggestions_objects.append(
+            SuggestionFrame(
+                video=videos[int(suggestion["video"])],
+                frame_idx=suggestion["frame_idx"],
+            )
+        )
+    return suggestions_objects
+
+
+def write_suggestions(
+    labels_path: str, suggestions: list[SuggestionFrame], videos: list[Video]
+):
+    """Write track metadata to a SLEAP labels file.
+
+    Args:
+        labels_path: A string path to the SLEAP labels file.
+        suggestions: A list of `SuggestionFrame` objects to store the metadata for.
+        videos: A list of `Video` objects.
+    """
+    GROUP = 0  # TODO: Handle storing extraneous metadata.
+    suggestions_json = []
+    for suggestion in suggestions:
+        suggestion_dict = {
+            "video": str(videos.index(suggestion.video)),
+            "frame_idx": suggestion.frame_idx,
+            "group": GROUP,
+        }
+        suggestion_json = np.string_(json.dumps(suggestion_dict, separators=(",", ":")))
+        suggestions_json.append(suggestion_json)
+
+    with h5py.File(labels_path, "a") as f:
+        f.create_dataset("suggestions_json", data=suggestions_json, maxshape=(None,))
+
+
 def read_metadata(labels_path: str) -> dict:
     """Read metadata from a SLEAP labels file.
 
@@ -649,6 +699,7 @@ def read_labels(labels_path: str) -> Labels:
     instances = read_instances(
         labels_path, skeletons, tracks, points, pred_points, format_id
     )
+    suggestions = read_suggestions(labels_path, videos)
     metadata = read_metadata(labels_path)
     provenance = metadata.get("provenance", dict())
 
@@ -668,6 +719,7 @@ def read_labels(labels_path: str) -> Labels:
         videos=videos,
         skeletons=skeletons,
         tracks=tracks,
+        suggestions=suggestions,
         provenance=provenance,
     )
 
@@ -685,5 +737,6 @@ def write_labels(labels_path: str, labels: Labels):
         Path(labels_path).unlink()
     write_videos(labels_path, labels.videos)
     write_tracks(labels_path, labels.tracks)
+    write_suggestions(labels_path, labels.suggestions, labels.videos)
     write_metadata(labels_path, labels)
     write_lfs(labels_path, labels)

sleap_io/model/labels.py

@@ -12,7 +12,14 @@
 """
 
 from __future__ import annotations
-from sleap_io import LabeledFrame, Instance, PredictedInstance, Video, Track
+from sleap_io import (
+    LabeledFrame,
+    Instance,
+    PredictedInstance,
+    Video,
+    Track,
+    SuggestionFrame,
+)
 from attrs import define, field
 from typing import Union, Optional, Any
 import numpy as np
@@ -32,6 +39,7 @@ class Labels:
         skeletons: A list of `Skeleton`s that are associated with this dataset. This
             should generally only contain a single skeleton.
         tracks: A list of `Track`s that are associated with this dataset.
+        suggestions: A list of `SuggestionFrame`s that are associated with this dataset.
         provenance: Dictionary of arbitrary metadata providing additional information
             about where the dataset came from.
 
@@ -44,6 +52,7 @@ class Labels:
     videos: list[Video] = field(factory=list)
     skeletons: list[Skeleton] = field(factory=list)
     tracks: list[Track] = field(factory=list)
+    suggestions: list[SuggestionFrame] = field(factory=list)
     provenance: dict[str, Any] = field(factory=dict)
 
     def __attrs_post_init__(self):

sleap_io/model/suggestions.py

@@ -0,0 +1,19 @@
+"""Data module for suggestions."""
+
+from __future__ import annotations
+from sleap_io.model.video import Video
+import attrs
+from typing import Optional
+
+
+@attrs.define(auto_attribs=True)
+class SuggestionFrame:
+    """Data structure for a single frame of suggestions.
+
+    Attributes:
+        video: The video associated with the frame.
+        frame_idx: The index of the frame in the video.
+    """
+
+    video: Video
+    frame_idx: int

tests/io/test_slp.py

@@ -186,6 +186,7 @@ def test_write_labels(centered_pair, slp_real_data, tmp_path):
         assert len(saved_labels.skeletons) == len(labels.skeletons) == 1
         assert saved_labels.skeleton.name == labels.skeleton.name
         assert saved_labels.skeleton.node_names == labels.skeleton.node_names
+        assert len(saved_labels.suggestions) == len(labels.suggestions)
 
 
 def test_load_multi_skeleton(tmpdir):