Qt widget for loading pose datasets as napari Points layers (#253)

* initialise napari plugin development * Create skeleton for napari plugin with collapsible widgets (#218) * initialise napari plugin development * initialise napari plugin development * create skeleton for napari plugin with collapsible widgets * add basic widget smoke tests and allow headless testing * do not depend on napari from pip * include napari option in install instructions * make meta_widget module private * pin atlasapi version to avoid unnecessary dependencies * pin napari >= 0.4.19 from conda-forge * switched to pip install of napari[all] * seperation of concerns in widget tests * add pytest-mock dev dependency * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * Added loader widget for poses * update widget tests * simplify dependency on brainglobe-utils * consistent monospace formatting for movement in public docstrings * get rid of code that's only relevant for displaying Tracks * enable visibility of napari layer tooltips * renamed widget to PosesLoader * make cmap optional in set_color_by method * wrote unit tests for napari convert module * wrote unit-tests for the layer styles module * linkcheck ignore zenodo redirects * move _sample_colormap out of PointsStyle class * small refactoring in the loader widget * Expand tests for loader widget * added comments and docstrings to napari plugin tests * refactored all napari tests into separate unit test folder * added napari-video to dependencies * replaced deprecated edge_width with border_width * got rid of widget pytest fixtures * remove duplicate word from docstring * remove napari-video dependency * include napari extras in docs requirements * add test for _on_browse_clicked method * getOpenFileName returns tuple, not str * simplify poses_to_napari_tracks Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * [pre-commit.ci] pre-commit autoupdate (#338) updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.2](astral-sh/ruff-pre-commit@v0.6.9...v0.7.2) - [github.com/pre-commit/mirrors-mypy: v1.11.2 → v1.13.0](pre-commit/mirrors-mypy@v1.11.2...v1.13.0) - [github.com/mgedmin/check-manifest: 0.49 → 0.50](mgedmin/check-manifest@0.49...0.50) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Implement `compute_speed` and `compute_path_length` (#280) * implement compute_speed and compute_path_length functions * added speed to existing kinematics unit test * rewrote compute_path_length with various nan policies * unit test compute_path_length across time ranges * fixed and refactor compute_path_length and its tests * fixed docstring for compute_path_length * Accept suggestion on docstring wording Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * Remove print statement from test Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * Ensure nan report is printed Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * adapt warning message match in test * change 'any' to 'all' * uniform wording across path length docstrings * (mostly) leave time range validation to xarray slice * refactored parameters for test across time ranges * simplified test for path lenght with nans * replace drop policy with ffill * remove B905 ruff rule * make pre-commit happy --------- Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * initialise napari plugin development * avoid redefining duplicate attributes in child dataclass * modify test case to match poses_to_napari_tracks simplification * expected_log_messages should be a subset of captured messages Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * fix typo Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * use names for Qwidgets * reorganised test_valid_poses_to_napari_tracks * parametrised layer style tests * delet integration test which was reintroduced after conflict resolution * added test about file filters * deleted obsolete loader widget file (had snuck back in due to conflict merging) * combine tests for button callouts Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> * Simplify test_layer_style_as_kwargs Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> --------- Co-authored-by: Chang Huan Lo <changhuan.lo@ucl.ac.uk> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
neuroinformatics-unit · Nov 20, 2024 · cc4155d · cc4155d
1 parent 9a91fc7
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diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,4 +1,4 @@
--e .
+-e .[napari]
 linkify-it-py
 myst-parser
 nbsphinx

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -178,6 +178,7 @@
     "https://opensource.org/license/bsd-3-clause/",  # to avoid odd 403 error
 ]
 
+
 myst_url_schemes = {
     "http": None,
     "https": None,

diff --git a/movement/napari/_loader_widget.py b/movement/napari/_loader_widget.py
diff --git a/movement/napari/_loader_widgets.py b/movement/napari/_loader_widgets.py
@@ -0,0 +1,161 @@
+"""Widgets for loading movement datasets from file."""
+
+import logging
+from pathlib import Path
+
+from napari.settings import get_settings
+from napari.utils.notifications import show_warning
+from napari.viewer import Viewer
+from qtpy.QtWidgets import (
+    QComboBox,
+    QFileDialog,
+    QFormLayout,
+    QHBoxLayout,
+    QLineEdit,
+    QPushButton,
+    QSpinBox,
+    QWidget,
+)
+
+from movement.io import load_poses
+from movement.napari.convert import poses_to_napari_tracks
+from movement.napari.layer_styles import PointsStyle
+
+logger = logging.getLogger(__name__)
+
+# Allowed poses file suffixes for each supported source software
+SUPPORTED_POSES_FILES = {
+    "DeepLabCut": ["*.h5", "*.csv"],
+    "LightningPose": ["*.csv"],
+    "SLEAP": ["*.h5", "*.slp"],
+}
+
+
+class PosesLoader(QWidget):
+    """Widget for loading movement poses datasets from file."""
+
+    def __init__(self, napari_viewer: Viewer, parent=None):
+        """Initialize the loader widget."""
+        super().__init__(parent=parent)
+        self.viewer = napari_viewer
+        self.setLayout(QFormLayout())
+        # Create widgets
+        self._create_source_software_widget()
+        self._create_fps_widget()
+        self._create_file_path_widget()
+        self._create_load_button()
+        # Enable layer tooltips from napari settings
+        self._enable_layer_tooltips()
+
+    def _create_source_software_widget(self):
+        """Create a combo box for selecting the source software."""
+        self.source_software_combo = QComboBox()
+        self.source_software_combo.setObjectName("source_software_combo")
+        self.source_software_combo.addItems(SUPPORTED_POSES_FILES.keys())
+        self.layout().addRow("source software:", self.source_software_combo)
+
+    def _create_fps_widget(self):
+        """Create a spinbox for selecting the frames per second (fps)."""
+        self.fps_spinbox = QSpinBox()
+        self.fps_spinbox.setObjectName("fps_spinbox")
+        self.fps_spinbox.setMinimum(1)
+        self.fps_spinbox.setMaximum(1000)
+        self.fps_spinbox.setValue(30)
+        self.layout().addRow("fps:", self.fps_spinbox)
+
+    def _create_file_path_widget(self):
+        """Create a line edit and browse button for selecting the file path.
+
+        This allows the user to either browse the file system,
+        or type the path directly into the line edit.
+        """
+        # File path line edit and browse button
+        self.file_path_edit = QLineEdit()
+        self.file_path_edit.setObjectName("file_path_edit")
+        self.browse_button = QPushButton("Browse")
+        self.browse_button.setObjectName("browse_button")
+        self.browse_button.clicked.connect(self._on_browse_clicked)
+        # Layout for line edit and button
+        self.file_path_layout = QHBoxLayout()
+        self.file_path_layout.addWidget(self.file_path_edit)
+        self.file_path_layout.addWidget(self.browse_button)
+        self.layout().addRow("file path:", self.file_path_layout)
+
+    def _create_load_button(self):
+        """Create a button to load the file and add layers to the viewer."""
+        self.load_button = QPushButton("Load")
+        self.load_button.setObjectName("load_button")
+        self.load_button.clicked.connect(lambda: self._on_load_clicked())
+        self.layout().addRow(self.load_button)
+
+    def _on_browse_clicked(self):
+        """Open a file dialog to select a file."""
+        file_suffixes = SUPPORTED_POSES_FILES[
+            self.source_software_combo.currentText()
+        ]
+
+        file_path, _ = QFileDialog.getOpenFileName(
+            self,
+            caption="Open file containing predicted poses",
+            filter=f"Poses files ({' '.join(file_suffixes)})",
+        )
+
+        # A blank string is returned if the user cancels the dialog
+        if not file_path:
+            return
+
+        # Add the file path to the line edit (text field)
+        self.file_path_edit.setText(file_path)
+
+    def _on_load_clicked(self):
+        """Load the file and add as a Points layer to the viewer."""
+        fps = self.fps_spinbox.value()
+        source_software = self.source_software_combo.currentText()
+        file_path = self.file_path_edit.text()
+        if file_path == "":
+            show_warning("No file path specified.")
+            return
+        ds = load_poses.from_file(file_path, source_software, fps)
+
+        self.data, self.props = poses_to_napari_tracks(ds)
+        logger.info("Converted poses dataset to a napari Tracks array.")
+        logger.debug(f"Tracks array shape: {self.data.shape}")
+
+        self.file_name = Path(file_path).name
+        self._add_points_layer()
+
+        self._set_playback_fps(fps)
+        logger.debug(f"Set napari playback speed to {fps} fps.")
+
+    def _add_points_layer(self):
+        """Add the predicted poses to the viewer as a Points layer."""
+        # Style properties for the napari Points layer
+        points_style = PointsStyle(
+            name=f"poses: {self.file_name}",
+            properties=self.props,
+        )
+        # Color the points by individual if there are multiple individuals
+        # Otherwise, color by keypoint
+        n_individuals = len(self.props["individual"].unique())
+        points_style.set_color_by(
+            prop="individual" if n_individuals > 1 else "keypoint"
+        )
+        # Add the points layer to the viewer
+        self.viewer.add_points(self.data[:, 1:], **points_style.as_kwargs())
+        logger.info("Added poses dataset as a napari Points layer.")
+
+    @staticmethod
+    def _set_playback_fps(fps: int):
+        """Set the playback speed for the napari viewer."""
+        settings = get_settings()
+        settings.application.playback_fps = fps
+
+    @staticmethod
+    def _enable_layer_tooltips():
+        """Toggle on tooltip visibility for napari layers.
+
+        This nicely displays the layer properties as a tooltip
+        when hovering over the layer in the napari viewer.
+        """
+        settings = get_settings()
+        settings.appearance.layer_tooltip_visibility = True
diff --git a/movement/napari/_meta_widget.py b/movement/napari/_meta_widget.py
@@ -3,7 +3,7 @@
 from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
 from napari.viewer import Viewer
 
-from movement.napari._loader_widget import Loader
+from movement.napari._loader_widgets import PosesLoader
 
 
 class MovementMetaWidget(CollapsibleWidgetContainer):
@@ -18,9 +18,9 @@ def __init__(self, napari_viewer: Viewer, parent=None):
         super().__init__()
 
         self.add_widget(
-            Loader(napari_viewer, parent=self),
+            PosesLoader(napari_viewer, parent=self),
             collapsible=True,
-            widget_title="Load data",
+            widget_title="Load poses",
         )
 
         self.loader = self.collapsible_widgets[0]

diff --git a/movement/napari/convert.py b/movement/napari/convert.py
@@ -0,0 +1,73 @@
+"""Conversion functions from ``movement`` datasets to napari layers."""
+
+import logging
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+
+# get logger
+logger = logging.getLogger(__name__)
+
+
+def _construct_properties_dataframe(ds: xr.Dataset) -> pd.DataFrame:
+    """Construct a properties DataFrame from a ``movement`` dataset."""
+    return pd.DataFrame(
+        {
+            "individual": ds.coords["individuals"].values,
+            "keypoint": ds.coords["keypoints"].values,
+            "time": ds.coords["time"].values,
+            "confidence": ds["confidence"].values.flatten(),
+        }
+    )
+
+
+def poses_to_napari_tracks(ds: xr.Dataset) -> tuple[np.ndarray, pd.DataFrame]:
+    """Convert poses dataset to napari Tracks array and properties.
+
+    Parameters
+    ----------
+    ds : xr.Dataset
+        ``movement`` dataset containing pose tracks, confidence scores,
+        and associated metadata.
+
+    Returns
+    -------
+    data : np.ndarray
+        napari Tracks array with shape (N, 4),
+        where N is n_keypoints * n_individuals * n_frames
+        and the 4 columns are (track_id, frame_idx, y, x).
+    properties : pd.DataFrame
+        DataFrame with properties (individual, keypoint, time, confidence).
+
+    Notes
+    -----
+    A corresponding napari Points array can be derived from the Tracks array
+    by taking its last 3 columns: (frame_idx, y, x). See the documentation
+    on the napari Tracks [1]_  and Points [2]_ layers.
+
+    References
+    ----------
+    .. [1] https://napari.org/stable/howtos/layers/tracks.html
+    .. [2] https://napari.org/stable/howtos/layers/points.html
+
+    """
+    n_frames = ds.sizes["time"]
+    n_individuals = ds.sizes["individuals"]
+    n_keypoints = ds.sizes["keypoints"]
+    n_tracks = n_individuals * n_keypoints
+    # Construct the napari Tracks array
+    # Reorder axes to (individuals, keypoints, frames, xy)
+    yx_cols = np.transpose(ds.position.values, (1, 2, 0, 3)).reshape(-1, 2)[
+        :, [1, 0]  # swap x and y columns
+    ]
+    # Each keypoint of each individual is a separate track
+    track_id_col = np.repeat(np.arange(n_tracks), n_frames).reshape(-1, 1)
+    time_col = np.tile(np.arange(n_frames), (n_tracks)).reshape(-1, 1)
+    data = np.hstack((track_id_col, time_col, yx_cols))
+    # Construct the properties DataFrame
+    # Stack 3 dimensions into a new single dimension named "tracks"
+    ds_ = ds.stack(tracks=("individuals", "keypoints", "time"))
+    properties = _construct_properties_dataframe(ds_)
+
+    return data, properties
diff --git a/movement/napari/layer_styles.py b/movement/napari/layer_styles.py
@@ -0,0 +1,64 @@
+"""Dataclasses containing layer styles for napari."""
+
+from dataclasses import dataclass, field
+
+import numpy as np
+import pandas as pd
+from napari.utils.colormaps import ensure_colormap
+
+DEFAULT_COLORMAP = "turbo"
+
+
+@dataclass
+class LayerStyle:
+    """Base class for napari layer styles."""
+
+    name: str
+    properties: pd.DataFrame
+    visible: bool = True
+    blending: str = "translucent"
+
+    def as_kwargs(self) -> dict:
+        """Return the style properties as a dictionary of kwargs."""
+        return self.__dict__
+
+
+@dataclass
+class PointsStyle(LayerStyle):
+    """Style properties for a napari Points layer."""
+
+    symbol: str = "disc"
+    size: int = 10
+    border_width: int = 0
+    face_color: str | None = None
+    face_color_cycle: list[tuple] | None = None
+    face_colormap: str = DEFAULT_COLORMAP
+    text: dict = field(default_factory=lambda: {"visible": False})
+
+    def set_color_by(self, prop: str, cmap: str | None = None) -> None:
+        """Set the face_color to a column in the properties DataFrame.
+
+        Parameters
+        ----------
+        prop : str
+            The column name in the properties DataFrame to color by.
+        cmap : str, optional
+            The name of the colormap to use, otherwise use the face_colormap.
+
+        """
+        if cmap is None:
+            cmap = self.face_colormap
+        self.face_color = prop
+        self.text["string"] = prop
+        n_colors = len(self.properties[prop].unique())
+        self.face_color_cycle = _sample_colormap(n_colors, cmap)
+
+
+def _sample_colormap(n: int, cmap_name: str) -> list[tuple]:
+    """Sample n equally-spaced colors from a napari colormap.
+
+    This includes the endpoints of the colormap.
+    """
+    cmap = ensure_colormap(cmap_name)
+    samples = np.linspace(0, len(cmap.colors) - 1, n).astype(int)
+    return [tuple(cmap.colors[i]) for i in samples]
diff --git a/pyproject.toml b/pyproject.toml
@@ -47,12 +47,8 @@ entry-points."napari.manifest".movement = "movement.napari:napari.yaml"
 
 [project.optional-dependencies]
 napari = [
-  "napari[all]>=0.4.19",
-  # the rest will be replaced by brainglobe-utils[qt]>=0.6 after release
-  "brainglobe-atlasapi>=2.0.7",
-  "brainglobe-utils>=0.5",
-  "qtpy",
-  "superqt",
+  "napari[all]>=0.5.0",
+  "brainglobe-utils[qt]>=0.6"  # needed for collapsible widgets
 ]
 dev = [
   "pytest",