talmolab · keyaloding · Jun 28, 2024 · Jul 12, 2024 · Jul 16, 2024 · Jul 16, 2024
diff --git a/pyproject.toml b/pyproject.toml
@@ -24,7 +24,7 @@ dependencies = [
     "attrs",
     "h5py>=3.8.0",
     "pynwb",
-    "ndx-pose",
+    "ndx-pose @ git+https://github.com/rly/ndx-pose@a847ad4be75e60ef9e413b8cbfc99c616fc9fd05",
     "pandas",
     "simplejson",
     "imageio",

diff --git a/sleap_io/io/main.py b/sleap_io/io/main.py
@@ -47,34 +47,50 @@ def save_slp(
     return slp.write_labels(filename, labels, embed=embed)
 
 
-def load_nwb(filename: str) -> Labels:
+def load_nwb(filename: str, as_training: Optional[bool]=None) -> Labels:
     """Load an NWB dataset as a SLEAP `Labels` object.
 
     Args:
         filename: Path to a NWB file (`.nwb`).
+        as_training: If `True`, load the dataset as a training dataset.
 
     Returns:
         The dataset as a `Labels` object.
     """
-    return nwb.read_nwb(filename)
+    if as_training is None:
+        return 
+
+    if as_training:
+        return nwb.read_nwb_training(filename)
+    else:
+        return nwb.read_nwb(filename)
-def load_nwb(filename: str, as_training: Optional[bool]=None) -> Labels:
-    """Load an NWB dataset as a SLEAP `Labels` object.
-
-    Args:
-        filename: Path to a NWB file (`.nwb`).
-        as_training: If `True`, load the dataset as a training dataset.
-
-    Returns:
-        The dataset as a `Labels` object.
-    """
-    return nwb.read_nwb(filename)
-    if as_training is None:
-        return 
-
-    if as_training:
-        return nwb.read_nwb_training(filename)
-    else:
-        return nwb.read_nwb(filename)
+    if as_training:
+        return nwb.read_nwb_training(filename)
+    else:
+        return nwb.read_nwb(filename)
-def load_nwb(filename: str, as_training: Optional[bool]=None) -> Labels:
-    """Load an NWB dataset as a SLEAP `Labels` object.
-
-    Args:
-        filename: Path to a NWB file (`.nwb`).
-        as_training: If `True`, load the dataset as a training dataset.
-
-    Returns:
-        The dataset as a `Labels` object.
-    """
-    return nwb.read_nwb(filename)
-    if as_training is None:
-        return 
-
-    if as_training:
-        return nwb.read_nwb_training(filename)
-    else:
-        return nwb.read_nwb(filename)
+    if as_training:
+        return nwb.read_nwb_training(filename)
+    else:
+        return nwb.read_nwb(filename)
 
 
-def save_nwb(labels: Labels, filename: str, append: bool = True):
+def save_nwb(labels: Labels, filename: str, as_training: bool = None, append: bool = True, **kwargs):
     """Save a SLEAP dataset to NWB format.
 
     Args:
         labels: A SLEAP `Labels` object (see `load_slp`).
         filename: Path to NWB file to save to. Must end in `.nwb`.
+        as_training: If `True`, save the dataset as a training dataset.
         append: If `True` (the default), append to existing NWB file. File will be
             created if it does not exist.
 
     See also: nwb.write_nwb, nwb.append_nwb
     """
-    if append and Path(filename).exists():
-        nwb.append_nwb(labels, filename)
-    else:
-        nwb.write_nwb(labels, filename)
+    if as_training:
+        pose_training = nwb.labels_to_pose_training(labels, **kwargs)
+        if append and Path(filename).exists():
+            nwb.append_nwb_training(pose_training, filename, **kwargs)
+        else:
+            nwb.write_nwb_training(pose_training, filename, **kwargs)
 
+    else:
+        if append and Path(filename).exists():
+            nwb.append_nwb(labels, filename, **kwargs)
+        else:
+            nwb.write_nwb(labels, filename)
-def save_nwb(labels: Labels, filename: str, as_training: bool = None, append: bool = True, **kwargs):
-    """Save a SLEAP dataset to NWB format.
-
-    Args:
-        labels: A SLEAP `Labels` object (see `load_slp`).
-        filename: Path to NWB file to save to. Must end in `.nwb`.
-        as_training: If `True`, save the dataset as a training dataset.
-        append: If `True` (the default), append to existing NWB file. File will be
-            created if it does not exist.
-
-    See also: nwb.write_nwb, nwb.append_nwb
-    """
-    if append and Path(filename).exists():
-        nwb.append_nwb(labels, filename)
-    else:
-        nwb.write_nwb(labels, filename)
-    if as_training:
-        pose_training = nwb.labels_to_pose_training(labels, **kwargs)
-        if append and Path(filename).exists():
-            nwb.append_nwb_training(pose_training, filename, **kwargs)
-        else:
-            nwb.write_nwb_training(pose_training, filename, **kwargs)
-
-    else:
-        if append and Path(filename).exists():
-            nwb.append_nwb(labels, filename, **kwargs)
-        else:
-            nwb.write_nwb(labels, filename)
+def save_nwb(labels: Labels, filename: str, as_training: bool = None, append: bool = True, **kwargs):
+    """Save a SLEAP dataset to NWB format.
+
+    Args:
+        labels: A SLEAP `Labels` object (see `load_slp`).
+        filename: Path to NWB file to save to. Must end in `.nwb`.
+        as_training: If `True`, save the dataset as a training dataset.
+        append: If `True` (the default), append to existing NWB file. File will be
+            created if it does not exist.
+
+    See also: nwb.write_nwb, nwb.append_nwb
+    """
+    func = nwb.labels_to_pose_training if as_training else lambda l, **kw: l
+    action = nwb.append_nwb_training if as_training else nwb.append_nwb
+    write = nwb.write_nwb_training if as_training else nwb.write_nwb
+
+    data = func(labels, **kwargs)
+    if append and Path(filename).exists():
+        action(data, filename, **kwargs)
+    else:
+        write(data, filename, **kwargs)
-def save_nwb(labels: Labels, filename: str, as_training: bool = None, append: bool = True, **kwargs):
-    """Save a SLEAP dataset to NWB format.
-
-    Args:
-        labels: A SLEAP `Labels` object (see `load_slp`).
-        filename: Path to NWB file to save to. Must end in `.nwb`.
-        as_training: If `True`, save the dataset as a training dataset.
-        append: If `True` (the default), append to existing NWB file. File will be
-            created if it does not exist.
-
-    See also: nwb.write_nwb, nwb.append_nwb
-    """
-    if append and Path(filename).exists():
-        nwb.append_nwb(labels, filename)
-    else:
-        nwb.write_nwb(labels, filename)
-    if as_training:
-        pose_training = nwb.labels_to_pose_training(labels, **kwargs)
-        if append and Path(filename).exists():
-            nwb.append_nwb_training(pose_training, filename, **kwargs)
-        else:
-            nwb.write_nwb_training(pose_training, filename, **kwargs)
-
-    else:
-        if append and Path(filename).exists():
-            nwb.append_nwb(labels, filename, **kwargs)
-        else:
-            nwb.write_nwb(labels, filename)
+def save_nwb(labels: Labels, filename: str, as_training: bool = None, append: bool = True, **kwargs):
+    """Save a SLEAP dataset to NWB format.
+
+    Args:
+        labels: A SLEAP `Labels` object (see `load_slp`).
+        filename: Path to NWB file to save to. Must end in `.nwb`.
+        as_training: If `True`, save the dataset as a training dataset.
+        append: If `True` (the default), append to existing NWB file. File will be
+            created if it does not exist.
+
+    See also: nwb.write_nwb, nwb.append_nwb
+    """
+    func = nwb.labels_to_pose_training if as_training else lambda l, **kw: l
+    action = nwb.append_nwb_training if as_training else nwb.append_nwb
+    write = nwb.write_nwb_training if as_training else nwb.write_nwb
+
+    data = func(labels, **kwargs)
+    if append and Path(filename).exists():
+        action(data, filename, **kwargs)
+    else:
+        write(data, filename, **kwargs)
+
 
 def load_labelstudio(
     filename: str, skeleton: Optional[Union[Skeleton, list[str]]] = None
@@ -190,6 +206,8 @@ def load_file(
         return load_jabs(filename, **kwargs)
     elif format == "video":
         return load_video(filename, **kwargs)
+    else:
+        raise ValueError(f"Unknown format '{format}' for filename: '{filename}'.")
 
 
 def save_file(
@@ -219,7 +237,7 @@ def save_file(
 
     if format == "slp":
         save_slp(labels, filename, **kwargs)
-    elif format == "nwb":
+    elif format in ("nwb", "nwb_training", "nwb_predictions"):
         save_nwb(labels, filename, **kwargs)
     elif format == "labelstudio":
         save_labelstudio(labels, filename, **kwargs)