add implementation for label-studio annotations and DeepLabCut

.vscode/settings.json

@@ -2,10 +2,11 @@
     "python.testing.unittestEnabled": false,
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": [
-        "-v",
+        "-vv",
         "--cov=sleap_io/",
         "--cov-report=xml",
         "--pdb",
         "tests/"
-    ]
+    ],
+    "python.formatting.provider": "black"
 }

setup.cfg

@@ -23,6 +23,8 @@ install_requires =
     pynwb
     ndx-pose
     pandas
+    tables
+    ruamel.yaml
 
 [options.extras_require]
 dev =

sleap_io/io/dlc.py

@@ -0,0 +1,328 @@
+import math
+import os
+from typing import Dict, List, Optional, Tuple, Union
+
+import numpy as np
+import pandas as pd
+from sleap_io import Instance, LabeledFrame, Labels, Node, Point, Skeleton, Video
+
+
+def is_multianimal(dlc_config: dict) -> bool:
+    """Returns True if `dlc_config` is configured for a multi-animal project, otherwise False
+
+    Parameters:
+    dlc_config (dict): DLC project configuration data
+
+    Returns:
+    bool: True if the config is setup for multi-animal projects, otherwise false
+    """
+    return "multianimalproject" in dlc_config and dlc_config["multianimalproject"]
+
+
+def load_skeletons(dlc_config: dict) -> List[Skeleton]:
+    """Load skeletons from a DLC configuration
+
+    Parameters:
+    dlc_config (dict): DLC project configuration data
+
+    Returns:
+    List of Sekeletons found in the DLC configuration
+    """
+
+    out = []
+    if is_multianimal(dlc_config):
+        ma_nodes = [Node(bp) for bp in dlc_config["multianimalbodyparts"]]
+        out.append(Skeleton(ma_nodes, name="multi"))
+
+        uq_nodes = [Node(bp) for bp in dlc_config["uniquebodyparts"]]
+        out.append(Skeleton(uq_nodes, name="unique"))
+
+    else:
+        nodes = [Node(bp) for bp in dlc_config["bodyparts"]]
+        out.append(Skeleton(nodes, name="single"))
+
+    return out
+
+
+def load_dlc(dlc_config: dict) -> Labels:
+    """Given a DLC configuration, load all labels from the training set.
+
+    Parameters:
+    dlc_config: DLC project configuration data
+
+    Returns:
+    Labels loaded from the DLC project
+    """
+
+    videos = dlc_config["video_sets"].keys()
+    video_basenames = [os.path.splitext(os.path.basename(v))[0] for v in videos]
+
+    all_annots = []
+    for vb in video_basenames:
+        annot_path = os.path.join(
+            dlc_config["project_path"],
+            "labeled-data",
+            vb,
+            f'CollectedData_{dlc_config["scorer"]}.h5',
+        )
+        if not os.path.exists(annot_path):
+            raise FileExistsError(
+                f'Unable to locate annotations, was expecting to find it here: "{annot_path}'
+            )
+
+        annots = pd.read_hdf(annot_path)
+        all_annots.append(annots)
+
+    return dlc_to_labels(pd.concat(all_annots), dlc_config)
+
+
+def write_dlc(dlc_config: dict, labels: Labels):
+    """Write Labels to a DLC project on disk
+        writes both the csv format as well as the HDF5 format
+
+    Parameters:
+    dlc_config: DLC project configuration data
+    labels: Labels to be written to the DLC project
+    """
+
+    split_labels = split_labels_by_directory(labels)
+
+    grouped_dlc: Dict[str, pd.DataFrame] = {}
+    for group, glabels in split_labels.items():
+        grouped_dlc[group] = labels_to_dlc(glabels, dlc_config)
+
+    for group, group_df in grouped_dlc.items():
+        dest = os.path.join(
+            dlc_config["project_path"],
+            "labeled-data",
+            group,
+            f"CollectedData_{dlc_config['scorer']}",
+        )
+
+        group_df.to_csv(f"{dest}.csv")
+        group_df.to_hdf(f"{dest}.h5", key="df_with_missing", mode="w")
+
+
+def make_index_from_dlc_config(dlc_config: dict) -> pd.MultiIndex:
+    """Given a DLC configuration, prepare a pandas multi-index
+
+    Parameters:
+    dlc_config: DLC project configuration data
+
+    Returns:
+    multiindex for dataframe columns
+    """
+    if is_multianimal(dlc_config):
+        cols = []
+        for individual in dlc_config["individuals"]:
+            for mabp in dlc_config["multianimalbodyparts"]:
+                cols.append((dlc_config["scorer"], individual, mabp, "x"))
+                cols.append((dlc_config["scorer"], individual, mabp, "y"))
+        for unbp in dlc_config["uniquebodyparts"]:
+            cols.append((dlc_config["scorer"], "single", unbp, "x"))
+            cols.append((dlc_config["scorer"], "single", unbp, "y"))
+
+        return pd.MultiIndex.from_tuples(
+            cols, names=("scorer", "individuals", "bodyparts", "coords")
+        )
+
+    else:
+        return pd.MultiIndex.from_product(
+            [[dlc_config["scorer"]], dlc_config["bodyparts"], ["x", "y"]],
+            names=["scorer", "bodyparts", "coords"],
+        )
+
+
+def split_labels_by_directory(labels: Labels) -> Dict[str, Labels]:
+    """Split annotations into groups according to their file name
+
+    Parameters:
+    intermediate_annotations (List[dict]): "intermediate-style" annotations
+
+    Returns:
+    list of labels grouped by underlying video source
+    """
+    grouped: Dict[str, List[LabeledFrame]] = {}
+    labels
+
+    for labeled_frame in labels.labeled_frames:
+        path, _ = os.path.split(labeled_frame.video.filename)
+        _, group = os.path.split(path)
+        if group not in grouped:
+            grouped[group] = []
+        grouped[group].append(labeled_frame)
+
+    return {group: Labels(frames) for group, frames in grouped.items()}
+
+
+def dlc_to_labels(annots: pd.DataFrame, dlc_config: dict) -> Labels:
+    """Convert a dlc-style dataframe to a Labels object"""
+    skeletons = load_skeletons(dlc_config)
+    frames: List[LabeledFrame] = []
+    if is_multianimal(dlc_config):
+        # Iterate over frames
+        for frame in annots.index.values:
+            ma_instances: List[Instance] = []
+
+            # Iterate over individuals
+            for indv in annots.columns.levels[1].values:
+
+                # pick the correct skeleton to use
+                skel: Skeleton
+                if indv == "single":
+                    # `single` is a sentinal for unique bodyparts
+                    skel = next(filter(lambda s: s.name == "unique", skeletons))
+
+                else:
+                    # otherwise we are in a multi-animal context
+                    skel = next(filter(lambda s: s.name == "multi", skeletons))
+
+                points = {}
+                # Iterate over this individual's body parts
+                bodyparts = list(
+                    set(
+                        bp
+                        for _, bp, _ in annots.columns.get_loc_level(
+                            indv, level="individuals"
+                        )[1].values
+                    )
+                )
+                for node in bodyparts:
+                    x_pos = (
+                        annots.loc[frame, (dlc_config["scorer"], indv, node, "x")]
+                        or np.nan
+                    )
+                    y_pos = (
+                        annots.loc[frame, (dlc_config["scorer"], indv, node, "y")]
+                        or np.nan
+                    )
+
+                    # If the value is a NAN, the user did not mark this keypoint
+                    if math.isnan(x_pos) or math.isnan(y_pos):
+                        continue
+
+                    points[skel[node]] = Point(x_pos, y_pos)
+
+                ma_instances.append(Instance(points, skel))
+
+            ma_video, ma_frame_idx = video_from_index(frame, dlc_config)
+            frames.append(LabeledFrame(ma_video, ma_frame_idx, ma_instances))
+
+    else:
+        # fetch the skeleton to use
+        skel = next(filter(lambda s: s.name == "single", skeletons))
+        # Iterate over frames
+        for frame in annots.index.values:
+            uq_instances: List[Instance] = []
+            points = {}
+            # Iterate over this individual's body parts
+            for node in annots.columns.levels[1].values:
+                x_pos = (
+                    annots.loc[frame, (dlc_config["scorer"], indv, node, "x")] or np.nan
+                )
+                y_pos = (
+                    annots.loc[frame, (dlc_config["scorer"], indv, node, "y")] or np.nan
+                )
+
+                # If the value is a NAN, the user did not mark this keypoint
+                if math.isnan(x_pos) or math.isnan(y_pos):
+                    continue
+
+                points[skel[node]] = Point(x_pos, y_pos)
+
+            uq_instances.append(Instance(points, skel))
+
+            uq_video, uq_frame_idx = video_from_index(frame, dlc_config)
+            frames.append(LabeledFrame(uq_video, uq_frame_idx, ma_instances))
+
+    return Labels(frames)
+
+
+def video_from_index(
+    index: Union[str, Tuple[str]], dlc_config: dict
+) -> Tuple[Video, int]:
+    """Given an index from DLC-style dataframe, construct a video instance and the frame number"""
+    vfname: str
+    if isinstance(index, tuple):
+        vfname = "/".join(index)
+    else:
+        vfname = str(index)
+    video = Video(vfname)  # TODO: find a better way to represent the data
+    frame_idx = (
+        0  # TODO: Just putting zero for now. Maybe we can parse from the filename???
+    )
+
+    return video, frame_idx
+
+
+def labels_to_dlc(labels: Labels, dlc_config: dict) -> pd.DataFrame:
+    """Convert a `Labels` instance to a DLC-format `pandas.DataFrame`"""
+
+    is_ma = is_multianimal(dlc_config)
+    col_idx = make_index_from_dlc_config(dlc_config)
+    row_idx = []
+    dlc_data: Dict[Tuple, List[float]] = {idx_val: [] for idx_val in col_idx.values}
+
+    errors_found = 0
+    for labeled_frame in labels.labeled_frames:
+        row_idx.append(
+            tuple(labeled_frame.video.filename.replace(r"\\", "/").split("/"))
+        )
+        # fill across the board with None
+        for value in dlc_data.values():
+            value.append(np.nan)
+
+        instance_names = list(dlc_config["individuals"]).copy()
+
+        for instance in labeled_frame.instances:
+
+            # determine individual type / identity
+            instance_name: Optional[str] = None
+            if is_ma:
+                if instance.skeleton.name == "unique":
+                    instance_name = "single"
+
+                elif instance.skeleton.name == "multi":
+                    instance_name = instance_names.pop(0)
+
+                else:
+                    raise ValueError(
+                        "Type of instance is ambiguous. Skeleton should be named `unique` for unique body parts, or `multi` for multi-animal body parts!"
+                    )
+
+            for node, point in instance.points.items():
+                key: Tuple
+                if is_ma:
+                    key = (
+                        dlc_config["scorer"],
+                        instance_name,
+                        node.name,
+                    )  # TODO - need to represent the unique bodyparts somehow!!
+
+                else:
+                    key = (dlc_config["scorer"], node.name)
+
+                try:
+                    dlc_data[(*key, "x")][-1] = point.x
+                    dlc_data[(*key, "y")][-1] = point.y
+                except KeyError:
+                    errors_found += 1
+                    # if annot['bodypart'] in dlc_config['multianimalbodyparts'] and annot['individual'] is None:
+                    #     rationale = 'bodypart is a multianimal bodypart, but no relationship to an individual was found!'
+                    # elif annot['bodypart'] in dlc_config['uniquebodyparts'] and annot['individual'] is not None:
+                    #     rationale = 'bodypart is a unique bodypart and should not have a relationship with an individual, but one was found'
+                    # else:
+                    #     rationale = 'Unknown'
+
+                    # message = 'ERROR! Data seems to violate the DLC annotation schema!\n' \
+                    #         f' -> Task: {annot["task_id"]}\n' \
+                    #         f' -> Image: "{annot["file_name"]}"\n' \
+                    #         f' -> Bodypart: {annot["bodypart"]}\n'
+                    # if is_ma:
+                    #     message += f' -> Individual: {annot.get("individual", None)}\n'
+                    # message += f' -> Rationale: {rationale}\n'
+                    # print(message)
+    row_index = pd.MultiIndex.from_tuples(row_idx)
+    dlc_df = pd.DataFrame(dlc_data, index=row_index, columns=col_idx)
+
+    return dlc_df