WIP converting reader plugin to widget

movement/napari/_widget.py

@@ -0,0 +1,19 @@
+from brainglobe_utils.qtpy.collapsible_widget import CollapsibleWidgetContainer
+from napari.viewer import Viewer
+
+from movement.napari.loader_widgets import FileLoader
+
+
+class MovementWidgets(CollapsibleWidgetContainer):
+    def __init__(self, napari_viewer: Viewer, parent=None):
+        super().__init__()
+
+        self.add_widget(
+            FileLoader(napari_viewer, parent=self),
+            collapsible=True,
+            widget_title="Load files",
+        )
+
+        self.file_loader = self.collapsible_widgets[0]
+        # expand FileLoader widget by default
+        self.file_loader.expand()

movement/napari/loader_widgets.py

@@ -0,0 +1,147 @@
+import logging
+from pathlib import Path
+
+import numpy as np
+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 ds_to_napari_tracks
+
+logger = logging.getLogger(__name__)
+
+
+class FileLoader(QWidget):
+    """Widget for loading pose tracks from files into a napari viewer."""
+
+    loader_func_map = {
+        "DeepLabCut": load_poses.from_dlc_file,
+        "LightingPose": load_poses.from_lp_file,
+        "SLEAP": load_poses.from_sleap_file,
+    }
+
+    file_suffix_map = {
+        "DeepLabCut": "Files containing predicted poses (*.h5 *.csv)",
+        "LightingPose": "Files containing predicted poses (*.csv)",
+        "SLEAP": "Files containing predicted poses (*.h5 *.slp)",
+    }
+
+    def __init__(self, napari_viewer: Viewer, parent=None):
+        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()
+
+    def create_source_software_widget(self):
+        """Create a combo box for selecting the source software."""
+        self.source_software_combo = QComboBox()
+        self.source_software_combo.addItems(
+            ["DeepLabCut", "LightningPose", "SLEAP"]
+        )
+        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.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.browse_button = QPushButton("browse")
+        self.browse_button.clicked.connect(self.open_file_dialog)
+        self.file_path_edit.returnPressed.connect(self.load_file_from_edit)
+        # 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("Pose file:", self.file_path_layout)
+
+    def open_file_dialog(self):
+        dlg = QFileDialog()
+        dlg.setFileMode(QFileDialog.ExistingFile)
+        # Allowed file suffixes based on the source software
+        dlg.setNameFilter(
+            self.file_suffix_map[self.source_software_combo.currentText()]
+        )
+        if dlg.exec_():
+            file_paths = dlg.selectedFiles()
+            # Set the file path in the line edit
+            self.file_path_edit.setText(file_paths[0])
+            # Load the file immediately after selection
+            self.load_file(file_paths[0])
+
+    def load_file_from_edit(self):
+        # Load the file based on the path in the QLineEdit
+        file_path = self.file_path_edit.text()
+        self.load_file(file_path)
+
+    def load_file(self, file_path):
+        fps = self.fps_spinbox.value()
+        source_software = self.source_software_combo.currentText()
+        loader_func = self.loader_func_map[source_software]
+        logger.debug(f"Using {loader_func}.")
+        ds = loader_func(file_path, fps)
+
+        self.data, self.props = ds_to_napari_tracks(ds)
+        logger.info("Converted pose tracks to a napari Tracks array.")
+        logger.debug(f"Tracks data shape: {self.data.shape}")
+        logger.debug(f"{self.data[:5, :]}")
+
+        self.file_name = Path(file_path).name
+        n_individuals = len(np.unique(self.props["individual"]))
+        self.color_by = "individual" if n_individuals > 1 else "keypoint"
+
+        self.add_layers()
+
+    def add_layers(self):
+        """Add the predicted pose tracks and keypoints to the napari viewer."""
+
+        common_kwargs = {
+            "name": f"position {self.file_name}",
+            "properties": self.props,
+            "visible": True,
+            "blending": "translucent",
+        }
+
+        tracks_kwargs = {
+            **common_kwargs,
+            "tail_width": 5,
+            "tail_length": 60,
+            "head_length": 0,
+            "colormap": "turbo",
+            "color_by": self.color_by,
+        }
+
+        # Add the napari Tracks layer to the viewer
+        self.viewer.add_tracks(self.data, **tracks_kwargs)
+
+        # kwargs for the napari Points layer
+        points_kwargs = {
+            **common_kwargs,
+            "symbol": "ring",
+            "size": 15,
+            "face_color": "red",
+            "edge_width": 0,
+        }
+
+        # Add the napari Points layer to the viewer
+        self.viewer.add_points(self.data[:, 1:], **points_kwargs)

movement/napari/napari.yaml

@@ -5,6 +5,9 @@ contributions:
     - id: movement.get_reader
       python_name: movement.napari._reader:napari_get_reader
       title: Open data with movement
+    - id: movement.make_widget
+      python_name: movement.napari._widget:MovementWidgets
+      title: movement
   readers:
     - command: movement.get_reader
       accepts_directories: false
@@ -13,3 +16,6 @@ contributions:
       - "*.hdf5"
       - "*.slp"
       - "*.csv"
+  widgets:
+    - command: movement.make_widget
+      display_name: movement

pyproject.toml

@@ -44,7 +44,7 @@ entry-points."napari.manifest".movement = "movement.napari:napari.yaml"
 "User Support" = "https://neuroinformatics.zulipchat.com/#narrow/stream/406001-Movement"
 
 [project.optional-dependencies]
-napari = ["napari[all]>=0.4.18", "napari-video"]
+napari = ["napari[all]>=0.4.18", "napari-video", "brainglobe-utils[napari]"]
 
 dev = [
     "pytest",
@@ -64,6 +64,7 @@ dev = [
     "types-requests",
     "napari[all]>=0.4.18",
     "napari-video",
+    "brainglobe-utils[napari]",
 ]
 
 [build-system]