Tracking: rebased and refactored Cotracker integration

pyproject.toml

@@ -52,6 +52,9 @@ dev = [
   "pytest-qt",
   "tox",
 ]
+tracking = [
+  "torch",
+]
 [project.urls]
 "Bug Tracker" = "https://github.com/DeepLabCut/napari-deeplabcut/issues"
 Documentation = "https://github.com/DeepLabCut/napari-deeplabcut#README.md"

src/napari_deeplabcut/_reader.py

@@ -4,9 +4,11 @@
 from __future__ import annotations
 
 import logging
+from functools import partial
 from pathlib import Path
 
 from napari_deeplabcut.config._autostart import maybe_install_keypoint_controls_autostart
+from napari_deeplabcut.config.models import DLCProjectContext
 from napari_deeplabcut.core.discovery import discover_annotations
 from napari_deeplabcut.core.io import (
     SUPPORTED_IMAGES,
@@ -17,11 +19,41 @@
     read_images,
     read_video,
 )
-from napari_deeplabcut.core.project_paths import looks_like_dlc_labeled_folder
+from napari_deeplabcut.core.project_paths import (
+    infer_dlc_project_from_labeled_folder,
+    infer_dlc_project_from_video_path,
+    looks_like_dlc_labeled_folder,
+    session_key_from_project_context,
+)
 
 logger = logging.getLogger(__name__)
 
 
+def _build_dlc_layer_meta(
+    *,
+    session_role: str | None,
+    project_context: DLCProjectContext | None,
+) -> dict:
+    """
+    Build explicit DLC lifecycle metadata for image/video layers.
+
+    If session_role is None or project_context is None, the layer should be
+    treated as a non-session image/video by lifecycle code.
+    """
+    if session_role is None or project_context is None:
+        return {
+            "session_role": None,
+            "project_context": None,
+            "session_key": None,
+        }
+
+    return {
+        "session_role": session_role,
+        "project_context": project_context.model_dump(mode="python", exclude_none=True),
+        "session_key": session_key_from_project_context(project_context),
+    }
+
+
 def get_hdf_reader(path):
     if isinstance(path, list):
         path = path[0]
@@ -40,9 +72,28 @@ def get_image_reader(path):
 
 
 def get_video_reader(path):
-    if isinstance(path, str) and any(path.lower().endswith(ext) for ext in SUPPORTED_VIDEOS):
-        return read_video
-    return None
+    if not isinstance(path, str) or not any(path.lower().endswith(ext) for ext in SUPPORTED_VIDEOS):
+        return None
+
+    ctx = infer_dlc_project_from_video_path(path)
+    if ctx is None:
+        # Generic non-DLC video layer: allowed, but ignored by lifecycle session context.
+        return partial(
+            read_video,
+            dlc_meta=_build_dlc_layer_meta(
+                session_role=None,
+                project_context=None,
+            ),
+        )
+
+    maybe_install_keypoint_controls_autostart()
+    return partial(
+        read_video,
+        dlc_meta=_build_dlc_layer_meta(
+            session_role="video",
+            project_context=ctx,
+        ),
+    )
 
 
 def get_config_reader(path):
@@ -87,7 +138,17 @@ def get_folder_parser(path):
             )
         return None
 
-    layers.extend(read_images(images))
+    ctx = infer_dlc_project_from_labeled_folder(path)
+
+    layers.extend(
+        read_images(
+            images,
+            dlc_meta=_build_dlc_layer_meta(
+                session_role="image",
+                project_context=ctx,
+            ),
+        )
+    )
 
     # Deterministic discovery: load ALL H5 artifacts
     artifacts = discover_annotations(path)

src/napari_deeplabcut/_tests/config/test_keybinds.py

@@ -23,8 +23,12 @@ def bind_key(self, key, callback, overwrite=False):
 
 def test_iter_shortcuts_returns_registry():
     shortcuts = tuple(keybinds.iter_shortcuts())
-    assert shortcuts == keybinds.SHORTCUTS
-    assert shortcuts, "SHORTCUTS should not be empty"
+    expected = keybinds.SHORTCUTS
+    if keybinds.TRACKING_SHORTCUTS_ENABLED:
+        expected = expected + keybinds.TRACKING_SHORTCUTS
+
+    assert shortcuts == expected
+    assert keybinds.SHORTCUTS, "SHORTCUTS should not be empty"
 
 
 def test_shortcuts_registry_points_layer_entries_have_callbacks():

src/napari_deeplabcut/_tests/conftest.py

@@ -8,6 +8,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+from napari.utils.events import Event
 from qtpy.QtWidgets import QApplication, QDockWidget
 from skimage.io import imsave
 
@@ -199,9 +200,43 @@ def images(tmp_path_factory, viewer, fake_image):
     return viewer.open(output_path, plugin="napari-deeplabcut")[0]
 
 
+class DummyDimsForStore:
+    def __init__(self, nsteps=5, current_step=0):
+        self.nsteps = (nsteps,)
+        self.current_step = (current_step,)
+        self.set_calls = []
+
+    def set_current_step(self, axis, value):
+        self.set_calls.append((axis, value))
+        steps = list(self.current_step)
+        while len(steps) <= axis:
+            steps.append(0)
+        steps[axis] = value
+        self.current_step = tuple(steps)
+
+
+class DummyViewerForStore:
+    def __init__(self, nsteps=5, current_step=0):
+        self.dims = DummyDimsForStore(nsteps=nsteps, current_step=current_step)
+
+
 @pytest.fixture
-def store(viewer, points):
-    return keypoints.KeypointStore(viewer, points)
+def store(points):
+    try:
+        data = np.asarray(points.data)
+        nsteps = int(np.nanmax(data[:, 0])) + 1 if data.size else 1
+    except Exception:
+        nsteps = 1
+
+    viewer = DummyViewerForStore(nsteps=nsteps)
+    store = keypoints.KeypointStore(viewer, points)
+
+    # Mimic the minimal runtime wiring used by LOOP mode
+    if not hasattr(points.events, "query_next_frame"):
+        points.events.add(query_next_frame=Event)
+    points.events.query_next_frame.connect(store._advance_step)
+
+    return store
 
 
 @pytest.fixture

src/napari_deeplabcut/_tests/core/io/test_hdf_reader.py

@@ -29,7 +29,7 @@ def _write_h5_single_animal(
     )
     df = pd.DataFrame([values], index=list(index), columns=cols)
     path.parent.mkdir(parents=True, exist_ok=True)
-    df.to_hdf(path, key="keypoints", mode="w")
+    df.to_hdf(path, key="df_with_missing", mode="w")
     return df
 
 

src/napari_deeplabcut/_tests/core/io/test_write_routing.py

@@ -18,7 +18,7 @@ def test_resolve_output_path_returns_none_for_machine_without_save_target():
                 "project_root": str(Path.cwd()),
                 "source_relpath_posix": "machinelabels-iter0.h5",
                 "kind": AnnotationKind.MACHINE,
-                "dataset_key": "keypoints",
+                "dataset_key": "df_with_missing",
             }
         }
     }
@@ -39,7 +39,7 @@ def test_write_hdf_refuses_machine_without_promotion(tmp_path: Path):
                 "project_root": str(tmp_path),
                 "source_relpath_posix": "machinelabels-iter0.h5",
                 "kind": AnnotationKind.MACHINE,
-                "dataset_key": "keypoints",
+                "dataset_key": "df_with_missing",
             },
             # header is required by writer
             "header": {
@@ -84,7 +84,7 @@ def test_write_hdf_aborts_machine_without_promotion_target(tmp_path: Path):
                 "project_root": str(tmp_path),
                 "source_relpath_posix": "machinelabels-iter0.h5",
                 "kind": AnnotationKind.MACHINE,
-                "dataset_key": "keypoints",
+                "dataset_key": "df_with_missing",
             },
             "header": {"columns": [("S", "", "bp1", "x"), ("S", "", "bp1", "y")]},
         },