Remove kwargs and mutable defaults (#48)

biogtr/inference/tracker.py

@@ -128,8 +128,7 @@ def sliding_inference(self, model: GlobalTrackingTransformer, frames: list[Frame
 
         Args:
             model: the pretrained GlobalTrackingTransformer to be used for inference
-            frames: A list of Frames (See `biogtr.io.data_structures.Frame` for more info).
-
+            frames: A list of Frames (See `biogtr.io.Frame` for more info).
 
         Returns:
             Frames: A list of Frames populated with pred_track_ids and asso_matrices

biogtr/io/association_matrix.py

@@ -173,7 +173,7 @@ def reduce(
                 Either "instance" (remains unchanged), or "track" (n_cols=n_traj)
            row_grouping: A str indicating how to group rows when aggregating. Either "pred" or "gt".
            col_grouping: A str indicating how to group columns when aggregating. Either "pred" or "gt".
-           method: A callable function that operates on numpy matrices and can take an `axis` arg for reducing.
+           reduce_method: A callable function that operates on numpy matrices and can take an `axis` arg for reducing.
 
         Returns:
             The association matrix reduced to an inst/traj x traj/inst association matrix as a dataframe.
@@ -199,7 +199,6 @@ def reduce(
 
         reduced_matrix = []
         for row_track, row_instances in row_tracks.items():
-
             for col_track, col_instances in col_tracks.items():
                 asso_matrix = self[row_instances, col_instances]
 
@@ -208,7 +207,6 @@ def reduce(
 
                 if row_dims == "track":
                     asso_matrix = reduce_method(asso_matrix, axis=0)
-
                 reduced_matrix.append(asso_matrix)
 
         reduced_matrix = np.array(reduced_matrix).reshape(n_cols, n_rows).T
@@ -234,7 +232,6 @@ def __getitem__(self, inds) -> np.ndarray:
 
         try:
             return self.numpy()[query_ind[:, None], ref_ind].squeeze()
-
         except IndexError as e:
             print(f"Query_insts: {type(query_inst)}")
             print(f"Query_inds: {query_ind}")

biogtr/io/config.py

@@ -78,6 +78,11 @@ def get_model(self) -> GlobalTrackingTransformer:
             A global tracking transformer with parameters indicated by cfg
         """
         model_params = self.cfg.model
+        ckpt_path = model_params.pop("ckpt_path", None)
+
+        if ckpt_path is not None and len(ckpt_path) > 0:
+            return GTRRunner.load_from_checkpoint(ckpt_path).model
+
         return GlobalTrackingTransformer(**model_params)
 
     def get_tracker_cfg(self) -> dict:
@@ -100,17 +105,21 @@ def get_gtr_runner(self):
         loss_params = self.cfg.loss
         gtr_runner_params = self.cfg.runner
 
-        if self.cfg.model.ckpt_path is not None and self.cfg.model.ckpt_path != "":
+        model_params = self.cfg.model
+
+        ckpt_path = model_params.pop("ckpt_path", None)
+
+        if ckpt_path is not None and ckpt_path != "":
+
             model = GTRRunner.load_from_checkpoint(
-                self.cfg.model.ckpt_path,
+                ckpt_path,
                 tracker_cfg=tracker_params,
                 train_metrics=self.cfg.runner.metrics.train,
                 val_metrics=self.cfg.runner.metrics.val,
                 test_metrics=self.cfg.runner.metrics.test,
             )
 
         else:
-            model_params = self.cfg.model
             model = GTRRunner(
                 model_params,
                 tracker_params,

biogtr/models/global_tracking_transformer.py

@@ -27,7 +27,6 @@ def __init__(
         embedding_meta: dict = None,
         return_embedding: bool = False,
         decoder_self_attn: bool = False,
-        **kwargs,
     ):
         """Initialize GTR.
 

biogtr/models/gtr_runner.py

@@ -18,23 +18,26 @@ class GTRRunner(LightningModule):
     Used for training, validation and inference.
     """
 
+    DEFAULT_METRICS = {
+        "train": [],
+        "val": ["num_switches"],
+        "test": ["num_switches"],
+    }
+    DEFAULT_TRACKING = {
+        "train": False,
+        "val": True,
+        "test": True,
+    }
+
     def __init__(
         self,
-        model_cfg: dict = {},
-        tracker_cfg: dict = {},
-        loss_cfg: dict = {},
+        model_cfg: dict = None,
+        tracker_cfg: dict = None,
+        loss_cfg: dict = None,
         optimizer_cfg: dict = None,
         scheduler_cfg: dict = None,
-        metrics: dict[str, list[str]] = {
-            "train": [],
-            "val": ["num_switches"],
-            "test": ["num_switches"],
-        },
-        persistent_tracking: dict[str, bool] = {
-            "train": False,
-            "val": True,
-            "test": True,
-        },
+        metrics: dict[str, list[str]] = None,
+        persistent_tracking: dict[str, bool] = None,
     ):
         """Initialize a lightning module for GTR.
 
@@ -51,15 +54,24 @@ def __init__(
         super().__init__()
         self.save_hyperparameters()
 
+        model_cfg = model_cfg if model_cfg else {}
+        loss_cfg = loss_cfg if loss_cfg else {}
+        tracker_cfg = tracker_cfg if tracker_cfg else {}
+
+        _ = model_cfg.pop("ckpt_path", None)
         self.model = GlobalTrackingTransformer(**model_cfg)
         self.loss = AssoLoss(**loss_cfg)
         self.tracker = Tracker(**tracker_cfg)
 
         self.optimizer_cfg = optimizer_cfg
         self.scheduler_cfg = scheduler_cfg
 
-        self.metrics = metrics
-        self.persistent_tracking = persistent_tracking
+        self.metrics = metrics if metrics is not None else self.DEFAULT_METRICS
+        self.persistent_tracking = (
+            persistent_tracking
+            if persistent_tracking is not None
+            else self.DEFAULT_TRACKING
+        )
 
     def forward(
         self, ref_instances: list[Instance], query_instances: list[Instance] = None
@@ -159,6 +171,7 @@ def _shared_eval_step(self, frames: list[Frame], mode: str) -> dict[str, float]:
         """
         try:
             instances = [instance for frame in frames for instance in frame.instances]
+
             if len(instances) == 0:
                 return None