Reverted �iew_ back to save_ and changed new training checkbox to Kee…

…p visualization images after training.
talmolab · Jul 1, 2024 · c75a0ef · c75a0ef
1 parent ad06cf5
commit c75a0ef
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Showing 29 changed files with 91 additions and 91 deletions.
diff --git a/docs/guides/cli.md b/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] [--view_viz] 
-                   [--delete_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]
 
@@ -65,11 +65,11 @@ optional arguments:
                         to resume training from.
   --tensorboard         Enable TensorBoard logging to the run path if not
                         already specified in the training job config.
-  --view_viz            Enable saving of prediction visualizations to the run
+  --save_viz            Enable saving of prediction visualizations to the run
                         folder if not already specified in the training job
                         config.
-  --delete_viz          Delete prediction visualizations in the run
-                        folder after training if view_viz is enabled.
+  --keep_viz            Keep prediction visualization images in the run
+                        folder after training when 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

diff --git a/docs/notebooks/Training_and_inference_on_an_example_dataset.ipynb b/docs/notebooks/Training_and_inference_on_an_example_dataset.ipynb
@@ -190,7 +190,7 @@
       "    \"test_labels\": null,\n",
       "    \"base_checkpoint\": null,\n",
       "    \"tensorboard\": false,\n",
-      "    \"view_viz\": false,\n",
+      "    \"save_viz\": false,\n",
       "    \"zmq\": false,\n",
       "    \"run_name\": \"courtship.centroid\",\n",
       "    \"prefix\": \"\",\n",
@@ -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",
@@ -581,7 +581,7 @@
       "    \"test_labels\": null,\n",
       "    \"base_checkpoint\": null,\n",
       "    \"tensorboard\": false,\n",
-      "    \"view_viz\": false,\n",
+      "    \"save_viz\": false,\n",
       "    \"zmq\": false,\n",
       "    \"run_name\": \"courtship.topdown_confmaps\",\n",
       "    \"prefix\": \"\",\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",

diff --git a/sleap/config/pipeline_form.yaml b/sleap/config/pipeline_form.yaml
@@ -281,15 +281,15 @@ training:
   name: outputs.tensorboard.write_logs
   type: bool
 
-- name: _view_viz
+- name: _save_viz
   label: Visualize Predictions During Training
   type: bool
   default: true
 
-- name: _delete_viz
-  label: Delete Prediction Visualizations After Training
+- name: _keep_viz
+  label: Keep Prediction Visualization Images After Training
   type: bool
-  default: true
+  default: false
 
 - name: _predict_frames
   label: Predict On

diff --git a/sleap/gui/learning/runners.py b/sleap/gui/learning/runners.py
@@ -546,8 +546,8 @@ def run_learning_pipeline(
 
     """
 
-    view_viz = inference_params.get("_view_viz", False)
-    delete_viz = inference_params.get("_delete_viz", False)
+    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"]]
@@ -560,8 +560,8 @@ def run_learning_pipeline(
             config_info_list=config_info_list,
             inference_params=inference_params,
             gui=True,
-            view_viz=view_viz,
-            delete_viz=delete_viz,
+            save_viz=save_viz,
+            keep_viz=keep_viz,
         )
 
         # Check that all the models were trained
@@ -589,8 +589,8 @@ def run_gui_training(
     config_info_list: List[ConfigFileInfo],
     inference_params: Dict[str, Any],
     gui: bool = True,
-    view_viz: bool = False,
-    delete_viz: bool = True,
+    save_viz: bool = False,
+    keep_viz: bool = False,
 ) -> Dict[Text, Text]:
     """
     Runs training for each training job.
@@ -599,8 +599,8 @@ def run_gui_training(
         labels: Labels object from which we'll get training data.
         config_info_list: List of ConfigFileInfo with configs for training.
         gui: Whether to show gui windows and process gui events.
-        view_viz: Whether to save visualizations from training.
-        delete_viz: Whether to delete prediction visualizations after training.
+        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.
@@ -667,7 +667,7 @@ def run_gui_training(
                 win.reset(what=str(model_type), config=job)
                 win.setWindowTitle(f"Training Model - {str(model_type)}")
                 win.set_message(f"Preparing to run training...")
-                if view_viz:
+                if save_viz:
                     viz_window = QtImageDirectoryWidget.make_training_vizualizer(
                         job.outputs.run_path
                     )
@@ -689,8 +689,8 @@ def waiting():
                 labels_filename=labels_filename,
                 video_paths=video_path_list,
                 waiting_callback=waiting,
-                view_viz=view_viz,
-                delete_viz=delete_viz,
+                save_viz=save_viz,
+                keep_viz=keep_viz,
             )
 
             if ret == "success":
@@ -832,8 +832,8 @@ def train_subprocess(
     inference_params: Dict[str, Any],
     video_paths: Optional[List[Text]] = None,
     waiting_callback: Optional[Callable] = None,
-    view_viz: bool = False,
-    delete_viz: bool = True,
+    save_viz: bool = False,
+    keep_viz: bool = False,
 ):
     """Runs training inside subprocess."""
     run_path = job_config.outputs.run_path
@@ -860,10 +860,10 @@ def train_subprocess(
             str(inference_params["publish_port"]),
         ]
 
-        if view_viz:
-            cli_args.append("--view_viz")
-        if delete_viz:
-            cli_args.append("--delete_viz")
+        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:

diff --git a/sleap/nn/config/outputs.py b/sleap/nn/config/outputs.py
@@ -148,11 +148,11 @@ class OutputsConfig:
         tags: A list of strings to use as "tags" that can be used to organize multiple
             runs. These are not used for anything during training or inference, so they
             can be used to store arbitrary user-specified metadata.
-        view_visualizations: If True, will render and save visualizations of the model
+        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".
@@ -169,8 +169,8 @@ class OutputsConfig:
     run_name_suffix: Optional[Text] = None
     runs_folder: Text = "models"
     tags: List[Text] = attr.ib(factory=list)
-    view_visualizations: bool = True
-    delete_viz_images: bool = True
+    save_visualizations: bool = True
+    keep_viz_images: bool = False
     zip_outputs: bool = False
     log_to_csv: bool = True
     checkpointing: CheckpointingConfig = attr.ib(factory=CheckpointingConfig)

diff --git a/sleap/nn/training.py b/sleap/nn/training.py
@@ -515,7 +515,7 @@ def setup_visualization(
             "This probably means Qt is running headless."
         )
 
-    if config.view_visualizations and config.save_outputs:
+    if config.save_visualizations and config.save_outputs:
         callbacks.append(
             MatplotlibSaver(
                 save_folder=os.path.join(run_path, "viz"), plot_fn=viz_fn, prefix=name
@@ -945,8 +945,8 @@ def train(self):
         # Run post-training actions.
         if self.config.outputs.save_outputs:
             if (
-                self.config.outputs.view_visualizations
-                and self.config.outputs.delete_viz_images
+                self.config.outputs.save_visualizations
+                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(
@@ -1857,19 +1857,19 @@ def create_trainer_using_cli(args: Optional[List] = None):
         ),
     )
     parser.add_argument(
-        "--view_viz",
+        "--save_viz",
         action="store_true",
         help=(
             "Enable saving of prediction visualizations to the run folder if not "
             "already specified in the training job config."
         ),
     )
     parser.add_argument(
-        "--delete_viz",
+        "--keep_viz",
         action="store_true",
         help=(
-            "Delete prediction visualizations in the run folder after training if "
-            "view_viz is enabled."
+            "Keep prediction visualization images in the run folder after training when "
+            "save_viz is enabled."
         ),
     )
     parser.add_argument(
@@ -1956,8 +1956,8 @@ def create_trainer_using_cli(args: Optional[List] = None):
         job_config.outputs.run_name_prefix = args.prefix
     if args.suffix != "":
         job_config.outputs.run_name_suffix = args.suffix
-    job_config.outputs.view_visualizations |= args.view_viz
-    job_config.outputs.delete_viz_images |= args.delete_viz
+    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(",")

diff --git a/sleap/training_profiles/baseline.centroid.json b/sleap/training_profiles/baseline.centroid.json
@@ -115,8 +115,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_large_rf.bottomup.json b/sleap/training_profiles/baseline_large_rf.bottomup.json
@@ -124,8 +124,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_large_rf.single.json b/sleap/training_profiles/baseline_large_rf.single.json
@@ -115,8 +115,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_large_rf.topdown.json b/sleap/training_profiles/baseline_large_rf.topdown.json
@@ -116,8 +116,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_medium_rf.bottomup.json b/sleap/training_profiles/baseline_medium_rf.bottomup.json
@@ -124,8 +124,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_medium_rf.single.json b/sleap/training_profiles/baseline_medium_rf.single.json
@@ -115,8 +115,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/baseline_medium_rf.topdown.json b/sleap/training_profiles/baseline_medium_rf.topdown.json
@@ -116,8 +116,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/pretrained.bottomup.json b/sleap/training_profiles/pretrained.bottomup.json
@@ -121,8 +121,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/pretrained.centroid.json b/sleap/training_profiles/pretrained.centroid.json
@@ -112,8 +112,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/pretrained.single.json b/sleap/training_profiles/pretrained.single.json
@@ -112,8 +112,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/sleap/training_profiles/pretrained.topdown.json b/sleap/training_profiles/pretrained.topdown.json
@@ -113,8 +113,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": true,
-        "delete_viz_images": true,
+        "save_visualizations": true,
+        "keep_viz_images": false,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,

diff --git a/tests/data/models/min_tracks_2node.UNet.bottomup_multiclass/initial_config.json b/tests/data/models/min_tracks_2node.UNet.bottomup_multiclass/initial_config.json
@@ -127,8 +127,8 @@
         "run_name_suffix": null,
         "runs_folder": "models",
         "tags": [],
-        "view_visualizations": false,
-        "delete_viz_images": false,
+        "save_visualizations": false,
+        "keep_viz_images": true,
         "log_to_csv": true,
         "checkpointing": {
             "initial_model": false,