remove unnecessary for loop, adjust tests, change default threshold

docs/guides/cli.md

@@ -36,8 +36,8 @@ optional arguments:
 
 ```none
 usage: sleap-train [-h] [--video-paths VIDEO_PATHS] [--val_labels VAL_LABELS]
-                   [--test_labels TEST_LABELS] [--tensorboard] [--save_viz]
-                   [--zmq] [--run_name RUN_NAME] [--prefix PREFIX]
+                   [--test_labels TEST_LABELS] [--tensorboard] [--save_viz] 
+                   [--keep_viz] [--zmq] [--run_name RUN_NAME] [--prefix PREFIX]
                    [--suffix SUFFIX]
                    training_job_path [labels_path]
 
@@ -68,6 +68,8 @@ optional arguments:
   --save_viz            Enable saving of prediction visualizations to the run
                         folder if not already specified in the training job
                         config.
+  --keep_viz            Keep prediction visualization images in the run
+                        folder after training if --save_viz is enabled.
   --zmq                 Enable ZMQ logging (for GUI) if not already specified
                         in the training job config.
   --run_name RUN_NAME   Run name to use when saving file, overrides other run

docs/notebooks/Training_and_inference_on_an_example_dataset.ipynb

@@ -335,7 +335,7 @@
       "        \"runs_folder\": \"models\",\n",
       "        \"tags\": [],\n",
       "        \"save_visualizations\": true,\n",
-      "        \"delete_viz_images\": true,\n",
+      "        \"keep_viz_images\": true,\n",
       "        \"zip_outputs\": false,\n",
       "        \"log_to_csv\": true,\n",
       "        \"checkpointing\": {\n",
@@ -727,7 +727,7 @@
       "        \"runs_folder\": \"models\",\n",
       "        \"tags\": [],\n",
       "        \"save_visualizations\": true,\n",
-      "        \"delete_viz_images\": true,\n",
+      "        \"keep_viz_images\": true,\n",
       "        \"zip_outputs\": false,\n",
       "        \"log_to_csv\": true,\n",
       "        \"checkpointing\": {\n",

sleap/config/pipeline_form.yaml

@@ -286,6 +286,11 @@ training:
   type: bool
   default: true
 
+- name: _keep_viz
+  label: Keep Prediction Visualization Images After Training
+  type: bool
+  default: false
+
 - name: _predict_frames
   label: Predict On
   type: list

sleap/gui/learning/runners.py

@@ -1,4 +1,5 @@
 """Run training/inference in background process via CLI."""
+
 import abc
 import attr
 import os
@@ -500,9 +501,11 @@ def write_pipeline_files(
                 "data_path": os.path.basename(data_path),
                 "models": [Path(p).as_posix() for p in new_cfg_filenames],
                 "output_path": prediction_output_path,
-                "type": "labels"
-                if type(item_for_inference) == DatasetItemForInference
-                else "video",
+                "type": (
+                    "labels"
+                    if type(item_for_inference) == DatasetItemForInference
+                    else "video"
+                ),
                 "only_suggested_frames": only_suggested_frames,
                 "tracking": tracking_args,
             }
@@ -544,6 +547,7 @@ def run_learning_pipeline(
     """
 
     save_viz = inference_params.get("_save_viz", False)
+    keep_viz = inference_params.get("_keep_viz", False)
 
     if "movenet" in inference_params["_pipeline"]:
         trained_job_paths = [inference_params["_pipeline"]]
@@ -557,6 +561,7 @@ def run_learning_pipeline(
             inference_params=inference_params,
             gui=True,
             save_viz=save_viz,
+            keep_viz=keep_viz,
         )
 
         # Check that all the models were trained
@@ -585,6 +590,7 @@ def run_gui_training(
     inference_params: Dict[str, Any],
     gui: bool = True,
     save_viz: bool = False,
+    keep_viz: bool = False,
 ) -> Dict[Text, Text]:
     """
     Runs training for each training job.
@@ -594,6 +600,7 @@ def run_gui_training(
         config_info_list: List of ConfigFileInfo with configs for training.
         gui: Whether to show gui windows and process gui events.
         save_viz: Whether to save visualizations from training.
+        keep_viz: Whether to keep prediction visualization images after training.
 
     Returns:
         Dictionary, keys are head name, values are path to trained config.
@@ -683,6 +690,7 @@ def waiting():
                 video_paths=video_path_list,
                 waiting_callback=waiting,
                 save_viz=save_viz,
+                keep_viz=keep_viz,
             )
 
             if ret == "success":
@@ -825,6 +833,7 @@ def train_subprocess(
     video_paths: Optional[List[Text]] = None,
     waiting_callback: Optional[Callable] = None,
     save_viz: bool = False,
+    keep_viz: bool = False,
 ):
     """Runs training inside subprocess."""
     run_path = job_config.outputs.run_path
@@ -853,6 +862,8 @@ def train_subprocess(
 
         if save_viz:
             cli_args.append("--save_viz")
+        if keep_viz:
+            cli_args.append("--keep_viz")
 
         # Use cli arg since cli ignores setting in config
         if job_config.outputs.tensorboard.write_logs:

sleap/nn/config/outputs.py

@@ -151,8 +151,8 @@ class OutputsConfig:
         save_visualizations: If True, will render and save visualizations of the model
             predictions as PNGs to "{run_folder}/viz/{split}.{epoch:04d}.png", where the
             split is one of "train", "validation", "test".
-        delete_viz_images: If True, delete the saved visualizations after training
-            completes. This is useful to reduce the model folder size if you do not need
+        keep_viz_images: If True, keep the saved visualization images after training
+            completes. This is useful unchecked to reduce the model folder size if you do not need
             to keep the visualization images.
         zip_outputs: If True, compress the run folder to a zip file. This will be named
             "{run_folder}.zip".
@@ -170,7 +170,7 @@ class OutputsConfig:
     runs_folder: Text = "models"
     tags: List[Text] = attr.ib(factory=list)
     save_visualizations: bool = True
-    delete_viz_images: bool = True
+    keep_viz_images: bool = False
     zip_outputs: bool = False
     log_to_csv: bool = True
     checkpointing: CheckpointingConfig = attr.ib(factory=CheckpointingConfig)

sleap/nn/training.py

@@ -946,7 +946,7 @@ def train(self):
         if self.config.outputs.save_outputs:
             if (
                 self.config.outputs.save_visualizations
-                and self.config.outputs.delete_viz_images
+                and not self.config.outputs.keep_viz_images
             ):
                 self.cleanup()
 
@@ -997,7 +997,7 @@ def cleanup(self):
 
     def package(self):
         """Package model folder into a zip file for portability."""
-        if self.config.outputs.delete_viz_images:
+        if not self.config.outputs.keep_viz_images:
             self.cleanup()
         logger.info(f"Packaging results to: {self.run_path}.zip")
         shutil.make_archive(
@@ -1864,6 +1864,14 @@ def create_trainer_using_cli(args: Optional[List] = None):
             "already specified in the training job config."
         ),
     )
+    parser.add_argument(
+        "--keep_viz",
+        action="store_true",
+        help=(
+            "Keep prediction visualization images in the run folder after training when "
+            "--save_viz is enabled."
+        ),
+    )
     parser.add_argument(
         "--zmq",
         action="store_true",
@@ -1949,6 +1957,7 @@ def create_trainer_using_cli(args: Optional[List] = None):
     if args.suffix != "":
         job_config.outputs.run_name_suffix = args.suffix
     job_config.outputs.save_visualizations |= args.save_viz
+    job_config.outputs.keep_viz_images = args.keep_viz
     if args.labels_path == "":
         args.labels_path = None
     args.video_paths = args.video_paths.split(",")

sleap/training_profiles/baseline.centroid.json

@@ -116,6 +116,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_large_rf.bottomup.json

@@ -125,6 +125,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_large_rf.single.json

@@ -116,6 +116,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_large_rf.topdown.json

@@ -117,6 +117,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_medium_rf.bottomup.json

@@ -125,6 +125,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_medium_rf.single.json

@@ -116,6 +116,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/baseline_medium_rf.topdown.json

@@ -117,6 +117,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/pretrained.bottomup.json

@@ -122,6 +122,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/pretrained.centroid.json

@@ -113,6 +113,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/pretrained.single.json

@@ -113,6 +113,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

sleap/training_profiles/pretrained.topdown.json

@@ -114,6 +114,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/min_tracks_2node.UNet.bottomup_multiclass/initial_config.json

@@ -128,6 +128,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/min_tracks_2node.UNet.bottomup_multiclass/training_config.json

@@ -191,6 +191,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/min_tracks_2node.UNet.topdown_multiclass/initial_config.json

@@ -141,7 +141,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
-        "delete_viz_images": true,
+        "keep_viz_images": false,
         "zip_outputs": false,
         "log_to_csv": true,
         "checkpointing": {

tests/data/models/min_tracks_2node.UNet.topdown_multiclass/training_config.json

@@ -208,7 +208,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
-        "delete_viz_images": true,
+        "keep_viz_images": false,
         "zip_outputs": false,
         "log_to_csv": true,
         "checkpointing": {

tests/data/models/minimal_instance.UNet.bottomup/initial_config.json

@@ -127,6 +127,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_instance.UNet.bottomup/training_config.json

@@ -192,6 +192,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_instance.UNet.centered_instance/initial_config.json

@@ -119,6 +119,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_instance.UNet.centered_instance/training_config.json

@@ -179,6 +179,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_instance.UNet.centroid/initial_config.json

@@ -118,6 +118,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_instance.UNet.centroid/training_config.json

@@ -175,6 +175,7 @@
         "runs_folder": "models",
         "tags": [],
         "save_visualizations": false,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_robot.UNet.single_instance/initial_config.json

@@ -120,6 +120,7 @@
             ""
         ],
         "save_visualizations": false,
+        "keep_viz_images": true,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/data/models/minimal_robot.UNet.single_instance/training_config.json

@@ -180,6 +180,7 @@
             ""
         ],
         "save_visualizations": false,
+        "keep_viz_images": true,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

tests/gui/test_dialogs.py

@@ -1,6 +1,5 @@
 """Module to test the dialogs of the GUI (contained in sleap/gui/dialogs)."""
 
-
 import os
 from pathlib import Path