Merge branch 'develop' into arlo/max_instances

sleap/config/pipeline_form.yaml

@@ -271,6 +271,16 @@ inference:
       label: Elapsed Frame Window
       type: int
       default: 5
+    - name: tracking.robust
+      label: 'Robust quantile of similarity scores'
+      help: 'For a value between 0 and 1 (excluded), use a robust quantile
+      of the similarity scores to assign a track to an instance.<br />If equal to 1,
+      use the max similarity score (non-robust).'
+      type: optional_double
+      default_disabled: true
+      none_label: Use max (non-robust)
+      range: 0,1
+      default: 0.95
     - name: tracking.save_shifted_instances
       label: Save shifted instances
       type: bool
@@ -333,6 +343,16 @@ inference:
       label: Elapsed Frame Window
       type: int
       default: 5
+    - name: tracking.robust
+      label: 'Robust quantile of similarity scores'
+      help: 'For a value between 0 and 1 (excluded), use a robust quantile
+      of the similarity scores to assign a track to an instance.<br />If equal to 1,
+      use the max similarity score (non-robust).'
+      type: optional_double
+      default_disabled: true
+      none_label: Use max (non-robust)
+      range: 0,1
+      default: 0.95
     - type: text
       text: '<b>Kalman filter-based tracking</b>:<br />
         Uses the above tracking options to track instances for an initial

sleap/gui/learning/runners.py

@@ -239,6 +239,7 @@ def make_predict_cli_call(
         optional_items_as_nones = (
             "tracking.target_instance_count",
             "tracking.kf_init_frame_count",
+            "tracking.robust",
         )
 
         for key in optional_items_as_nones:

sleap/nn/tracker/components.py

@@ -410,8 +410,23 @@ def from_candidate_instances(
         candidate_instances: List[InstanceType],
         similarity_function: Callable,
         matching_function: Callable,
+        robust_best_instance: float = 1.0,
     ):
+        """Calculates (and stores) matches for a frame from candidate instance.
+
+        Args:
+            untracked_instances: list of untracked instances in the frame.
+            candidate_instances: list of instances use as match.
+            similarity_function: a function that returns the similarity between
+                two instances (untracked and candidate).
+            matching_function: function used to find the best match from the
+                cost matrix. See the classmethod `from_cost_matrix`.
+            robust_best_instance (float): if the value is between 0 and 1
+                (excluded), use a robust quantile similarity score for the
+                track. If the value is 1, use the max similarity (non-robust).
+                For selecting a robust score, 0.95 is a good value.
 
+        """
         cost = np.ndarray((0,))
         candidate_tracks = []
 
@@ -425,9 +440,8 @@ def from_candidate_instances(
             # Compute similarity matrix between untracked instances and best
             # candidate for each track.
             candidate_tracks = list(candidate_instances_by_track.keys())
-            matching_similarities = np.full(
-                (len(untracked_instances), len(candidate_tracks)), np.nan
-            )
+            dims = (len(untracked_instances), len(candidate_tracks))
+            matching_similarities = np.full(dims, np.nan)
 
             for i, untracked_instance in enumerate(untracked_instances):
 
@@ -443,19 +457,27 @@ def from_candidate_instances(
                         for candidate_instance in track_instances
                     ]
 
-                    # Keep the best scoring instance for this track.
-                    best_ind = np.argmax(track_matching_similarities)
-
-                    # Use the best similarity score for matching.
-                    best_similarity = track_matching_similarities[best_ind]
+                    if 0 < robust_best_instance < 1:
+                        # Robust, use the similarity score in the q-quantile for matching.
+                        best_similarity = np.quantile(
+                            track_matching_similarities,
+                            robust_best_instance,
+                        )
+                    else:
+                        # Non-robust, use the max similarity score for matching.
+                        best_similarity = np.max(track_matching_similarities)
+                    # Keep the best similarity score for this track.
                     matching_similarities[i, j] = best_similarity
 
             # Perform matching between untracked instances and candidates.
             cost = -matching_similarities
             cost[np.isnan(cost)] = np.inf
 
         return cls.from_cost_matrix(
-            cost, untracked_instances, candidate_tracks, matching_function
+            cost,
+            untracked_instances,
+            candidate_tracks,
+            matching_function,
         )
 
     @classmethod

sleap/nn/tracking.py

@@ -403,6 +403,10 @@ class Tracker(BaseTracker):
             after the other tracking has run for all frames.
         min_new_track_points: We won't spawn a new track for an instance with
             fewer than this many points.
+        robust_best_instance (float): if the value is between 0 and 1 (excluded),
+            use a robust quantile similarity score for the track. If the value is 1,
+            use the max similarity (non-robust). For selecting a robust score,
+            0.95 is a good value.
     """
 
     track_window: int = 5
@@ -414,6 +418,7 @@ class Tracker(BaseTracker):
     target_instance_count: int = 0
     pre_cull_function: Optional[Callable] = None
     post_connect_single_breaks: bool = False
+    robust_best_instance: float = 1.0
 
     min_new_track_points: int = 0
 
@@ -510,6 +515,7 @@ def track(
                 candidate_instances=candidate_instances,
                 similarity_function=self.similarity_function,
                 matching_function=self.matching_function,
+                robust_best_instance=self.robust_best_instance,
             )
 
             # Store the most recent match data (for outside inspection).
@@ -596,6 +602,7 @@ def make_tracker_by_name(
         similarity: str = "instance",
         match: str = "greedy",
         track_window: int = 5,
+        robust: float = 1.0,
         min_new_track_points: int = 0,
         min_match_points: int = 0,
         # Optical flow options
@@ -663,6 +670,7 @@ def pre_cull_function(inst_list):
 
         tracker_obj = cls(
             track_window=track_window,
+            robust_best_instance=robust,
             min_new_track_points=min_new_track_points,
             similarity_function=similarity_function,
             matching_function=matching_function,
@@ -751,6 +759,14 @@ def get_by_name_factory_options(cls):
         option["options"] = list(match_policies.keys())
         options.append(option)
 
+        option = dict(name="robust", default=1)
+        option["type"] = float
+        option["help"] = (
+            "Robust quantile of similarity score for instance matching. "
+            "If equal to 1, keep the max similarity score (non-robust)."
+        )
+        options.append(option)
+
         option = dict(name="track_window", default=5)
         option["type"] = int
         option["help"] = "How many frames back to look for matches"