Merge pull request #87 from MilagrosMarin/train_bug

Fix project path in the pose config file

Author: kabilar

CHANGELOG.md

@@ -3,6 +3,10 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and 
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
+## [0.2.7] - 2023-08-04
+
++ Fix - Update the project path in the pose config file to train the model
+
 ## [0.2.6] - 2023-05-22
 
 + Add - DeepLabCut, NWB, and DANDI citations
@@ -68,6 +72,7 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
   graciously provided by the Mathis Lab.
 + Add - Support for 2d single-animal models
 
+[0.2.7]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.7
 [0.2.6]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.6
 [0.2.5]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.5
 [0.2.4]: https://github.com/datajoint/element-deeplabcut/releases/tag/0.2.4

element_deeplabcut/train.py

@@ -241,13 +241,17 @@ class ModelTraining(dj.Computed):
     # https://github.com/DeepLabCut/DeepLabCut/issues/70
 
     def make(self, key):
-        from deeplabcut import train_network # isort:skip
+        from deeplabcut import train_network  # isort:skip
+
         try:
-            from deeplabcut.utils.auxiliaryfunctions import get_model_folder # isort:skip
+            from deeplabcut.utils.auxiliaryfunctions import (
+                get_model_folder,
+                edit_config,
+            )  # isort:skip
         except ImportError:
             from deeplabcut.utils.auxiliaryfunctions import (
-                GetModelFolder as get_model_folder
-            ) # isort:skip
+                GetModelFolder as get_model_folder,
+            )  # isort:skip
 
         """Launch training for each train.TrainingTask training_id via `.populate()`."""
         project_path, model_prefix = (TrainingTask & key).fetch1(
@@ -275,11 +279,26 @@ def make(self, key):
         # Write dlc config file to base project folder
         dlc_cfg_filepath = dlc_reader.save_yaml(project_path, dlc_config)
 
+        # ---- Update the project path in the DLC pose configuration (yaml) files ----
+        model_folder = get_model_folder(
+            trainFraction=dlc_config["train_fraction"],
+            shuffle=dlc_config["shuffle"],
+            cfg=dlc_config,
+            modelprefix=dlc_config["modelprefix"],
+        )
+        model_train_folder = project_path / model_folder / "train"
+
+        edit_config(
+            model_train_folder / "pose_cfg.yaml",
+            {"project_path": project_path.as_posix()},
+        )
+
         # ---- Trigger DLC model training job ----
         train_network_input_args = list(inspect.signature(train_network).parameters)
         train_network_kwargs = {
-            k: int(v) if k in ("shuffle", "trainingsetindex", "maxiters") else v 
-            for k, v in dlc_config.items() if k in train_network_input_args
+            k: int(v) if k in ("shuffle", "trainingsetindex", "maxiters") else v
+            for k, v in dlc_config.items()
+            if k in train_network_input_args
         }
         for k in ["shuffle", "trainingsetindex", "maxiters"]:
             train_network_kwargs[k] = int(train_network_kwargs[k])
@@ -289,18 +308,7 @@ def make(self, key):
         except KeyboardInterrupt:  # Instructions indicate to train until interrupt
             print("DLC training stopped via Keyboard Interrupt")
 
-        snapshots = list(
-            (
-                project_path
-                / get_model_folder(
-                    trainFraction=dlc_config["train_fraction"],
-                    shuffle=dlc_config["shuffle"],
-                    cfg=dlc_config,
-                    modelprefix=dlc_config["modelprefix"],
-                )
-                / "train"
-            ).glob("*index*")
-        )
+        snapshots = list(model_train_folder.glob("*index*"))
         max_modified_time = 0
         # DLC goes by snapshot magnitude when judging 'latest' for evaluation
         # Here, we mean most recently generated

element_deeplabcut/version.py

@@ -1,4 +1,4 @@
 """
 Package metadata
 """
-__version__ = "0.2.6"
+__version__ = "0.2.7"