ethograph 0.2.3__tar.gz → 0.2.4__tar.gz

{ethograph-0.2.3 → ethograph-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ethograph
-Version: 0.2.3
+Version: 0.2.4
 Summary: A multimodal timeseries GUI for neuroethology
 Author-email: Akseli Ilmanen <akseli.ilmanen@gmail.com>
 License-Expression: BSD-3-Clause
@@ -26,6 +26,7 @@ Requires-Dist: pandas
 Requires-Dist: xarray
 Requires-Dist: netcdf4
 Requires-Dist: scipy
+Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: pynapple
 Requires-Dist: pyyaml

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/cli.py

@@ -32,13 +32,9 @@ def _ensure_qt_plugins():
 
 
 def _fix_wayland_opengl():
-    """Force XCB/GLX on Linux+Wayland to avoid OpenGL crashes with napari.
+    """Force XCB/GLX on GNOME+Wayland to avoid OpenGL crashes with napari.
 
-    Wayland's EGL/native-OpenGL path segfaults with vispy on both Nvidia and
-    AMD hardware across PyQt6 and PySide6.  XCB (X11 via XWayland) is the
-    recommended workaround per napari's own troubleshooting guide.  We only
-    apply this when Wayland is actually active and the user has not already
-    set a preference via the environment.
+    See https://github.com/Akseli-Ilmanen/ethograph/issues/1
     """
     if sys.platform != "linux":
         return
@@ -47,6 +43,9 @@ def _fix_wayland_opengl():
     )
     if not wayland_active:
         return
+    desktop = os.environ.get("XDG_CURRENT_DESKTOP", "").upper()
+    if "GNOME" not in desktop:
+        return
     os.environ.setdefault("QT_QPA_PLATFORM", "xcb")
     os.environ.setdefault("PYOPENGL_PLATFORM", "glx")
 

ethograph-0.2.4/ethograph/gui/grid_section_container.py

@@ -0,0 +1,227 @@
+"""3x3 grid tab bar replacing the collapsible accordion headers.
+
+GridSectionContainer is a drop-in replacement for CollapsibleWidgetContainer.
+Instead of 9 stacked clickable header rows it shows a compact 3-column grid of
+buttons at the top; clicking one expands that section's content below (one at a
+time, same accordion semantics as before).
+"""
+
+from __future__ import annotations
+
+from qtpy.QtCore import QObject, QSize, Qt, Signal
+from qtpy.QtWidgets import (
+    QGridLayout,
+    QPushButton,
+    QSizePolicy,
+    QStackedWidget,
+    QVBoxLayout,
+    QWidget,
+)
+
+_GRID_COLS = 3
+
+# Short labels shown on the buttons; order must match add_widget call order in
+# widgets_meta.py.
+_SHORT_LABELS = ["Help", "I/O", "Data", "Neural", "Label", "CP", "Plots", "Trials", "Nav"]
+
+_STATUS_CHARS = set("✅❌🎯⭕")
+
+_BTN_STYLE = """
+QPushButton {{
+    padding: 3px 2px;
+    font-size: 7pt;
+    border: 1px solid rgba(255,255,255,35);
+    border-radius: 3px;
+    background: rgba(255,255,255,12);
+    color: #cccccc;
+    min-height: 22px;
+}}
+QPushButton:hover {{
+    background: rgba(255,255,255,25);
+    color: #ffffff;
+    border: 1px solid rgba(255,255,255,60);
+}}
+QPushButton:checked {{
+    background: rgba(65,125,195,160);
+    border: 1px solid rgba(90,150,220,200);
+    color: #ffffff;
+    font-weight: bold;
+}}
+"""
+
+
+class _AdaptiveStack(QStackedWidget):
+    """QStackedWidget that reports only the *current* page's size hint.
+
+    The default QStackedWidget always sizes itself to the largest of all its
+    pages.  That causes the content area to be over-tall when a short section
+    is active, which makes QVBoxLayout distribute the spare pixels as blank
+    gaps between the section's own widgets.  Overriding sizeHint / minimumSizeHint
+    so they reflect the current page fixes this entirely.
+    """
+
+    def sizeHint(self) -> QSize:
+        w = self.currentWidget()
+        return w.sizeHint() if w is not None else super().sizeHint()
+
+    def minimumSizeHint(self) -> QSize:
+        w = self.currentWidget()
+        return w.minimumSizeHint() if w is not None else super().minimumSizeHint()
+
+
+class SectionProxy(QObject):
+    """Duck-type stand-in for qt_niu.CollapsibleWidget.
+
+    Exposes the subset of the QCollapsible API used by MetaWidget so that
+    widgets_meta.py needs no structural changes.
+    """
+
+    toggled = Signal(bool)
+
+    def __init__(self, container: GridSectionContainer, index: int) -> None:
+        super().__init__()
+        self._c = container
+        self._i = index
+
+    # --- QCollapsible-compatible API ---
+
+    def expand(self, animate: bool = True) -> None:
+        self._c._expand(self._i)
+
+    def collapse(self, animate: bool = False) -> None:
+        self._c._collapse(self._i)
+
+    def isExpanded(self) -> bool:
+        return self._c._active == self._i
+
+    def content(self) -> QWidget | None:
+        widgets = self._c._content_widgets
+        return widgets[self._i] if self._i < len(widgets) else None
+
+    def setText(self, full_title: str) -> None:
+        self._c._update_button_label(self._i, full_title)
+
+    def setTitle(self, full_title: str) -> None:
+        self.setText(full_title)
+
+    def _expand_collapse(self, *_args, **_kwargs) -> None:
+        """No-op: _AdaptiveStack + updateGeometry handles sizing."""
+
+    def _emit_toggled(self, state: bool) -> None:
+        self.toggled.emit(state)
+
+
+class GridSectionContainer(QWidget):
+    """Container with a 3-column grid of tab buttons + a single content area.
+
+    API mirrors CollapsibleWidgetContainer so MetaWidget.add_widget() and
+    MetaWidget.collapsible_widgets work unchanged.
+    """
+
+    def __init__(self, parent: QWidget | None = None) -> None:
+        super().__init__(parent)
+
+        outer = QVBoxLayout(self)
+        outer.setContentsMargins(0, 0, 0, 0)
+        outer.setSpacing(2)
+        outer.setAlignment(Qt.AlignTop)
+
+        # ── 3×3 grid of buttons ──────────────────────────────────────────────
+        self._grid_widget = QWidget()
+        self._grid_layout = QGridLayout(self._grid_widget)
+        self._grid_layout.setContentsMargins(2, 2, 2, 2)
+        self._grid_layout.setSpacing(2)
+        for col in range(_GRID_COLS):
+            self._grid_layout.setColumnStretch(col, 1)
+        outer.addWidget(self._grid_widget)
+
+        # ── Content area: shows the active section ───────────────────────────
+        # _AdaptiveStack reports only the current page's sizeHint so the outer
+        # layout never allocates more vertical space than the content needs.
+        self._stack = _AdaptiveStack()
+        self._stack.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Preferred)
+        self._stack.hide()
+        outer.addWidget(self._stack, 0, Qt.AlignTop)
+
+        self._buttons: list[QPushButton] = []
+        self._content_widgets: list[QWidget] = []
+        self._active: int | None = None
+
+        # Public list of proxy objects (replaces CollapsibleWidgetContainer.collapsible_widgets)
+        self.collapsible_widgets: list[SectionProxy] = []
+
+    # ── Public API (mirrors CollapsibleWidgetContainer) ──────────────────────
+
+    def add_widget(
+        self,
+        widget: QWidget,
+        collapsible: bool = True,
+        widget_title: str = "",
+    ) -> None:
+        index = len(self._content_widgets)
+        label = _SHORT_LABELS[index] if index < len(_SHORT_LABELS) else widget_title
+
+        btn = QPushButton(label)
+        btn.setCheckable(True)
+        btn.setToolTip(widget_title)
+        btn.setStyleSheet(_BTN_STYLE)
+        btn.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
+        btn.clicked.connect(lambda _, i=index: self._on_btn_clicked(i))
+
+        row, col = divmod(index, _GRID_COLS)
+        self._grid_layout.addWidget(btn, row, col)
+        self._buttons.append(btn)
+
+        self._stack.addWidget(widget)
+        self._content_widgets.append(widget)
+
+        proxy = SectionProxy(self, index)
+        self.collapsible_widgets.append(proxy)
+
+    def notify_content_resized(self) -> None:
+        """Call this when the active section's content changes height.
+
+        EphysWidget and PlotSettingsWidget call meta_widget.refresh_widget_layout()
+        after toggling their sub-panels; that call routes here so the adaptive
+        stack recalculates its size hint.
+        """
+        self._stack.updateGeometry()
+        self.updateGeometry()
+
+    # ── Internal expand / collapse ───────────────────────────────────────────
+
+    def _on_btn_clicked(self, index: int) -> None:
+        if self._active == index:
+            self._collapse(index)
+        else:
+            self._expand(index)
+
+    def _expand(self, index: int) -> None:
+        if self._active is not None and self._active != index:
+            prev = self._active
+            self._buttons[prev].setChecked(False)
+            self.collapsible_widgets[prev]._emit_toggled(False)
+        self._active = index
+        self._buttons[index].setChecked(True)
+        self._stack.setCurrentIndex(index)
+        self._stack.show()
+        self._stack.updateGeometry()
+        self.updateGeometry()
+        self.collapsible_widgets[index]._emit_toggled(True)
+
+    def _collapse(self, index: int) -> None:
+        self._active = None
+        self._buttons[index].setChecked(False)
+        self._stack.hide()
+        self._stack.updateGeometry()
+        self.updateGeometry()
+        self.collapsible_widgets[index]._emit_toggled(False)
+
+    def _update_button_label(self, index: int, full_title: str) -> None:
+        """Keep the short base label but append a trailing status character."""
+        if not (0 <= index < len(self._buttons)):
+            return
+        base = _SHORT_LABELS[index] if index < len(_SHORT_LABELS) else ""
+        label = f"{base} {full_title[-1]}" if full_title and full_title[-1] in _STATUS_CHARS else base
+        self._buttons[index].setText(label)
+        self._buttons[index].setToolTip(full_title)

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/gui/widgets_changepoints.py

@@ -205,7 +205,7 @@ class ChangepointsWidget(QWidget):
         row1_layout = QHBoxLayout()
         row1_layout.setContentsMargins(0, 0, 0, 0)
 
-        self.show_cp_checkbox = QCheckBox("Show changepoints")
+        self.show_cp_checkbox = QCheckBox("Show changepoints (CPs)")
         self.show_cp_checkbox.setToolTip("Display changepoints on plot")
         self.show_cp_checkbox.setChecked(True)
         self.show_cp_checkbox.stateChanged.connect(self._on_show_changepoints_changed)

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/gui/widgets_ephys.py

@@ -780,7 +780,7 @@ class EphysWidget(QWidget):
         toggle_widget.setLayout(toggle_layout)
 
         toggle_defs = [
-            ("traceview_toggle", "TraceView", self._toggle_traceview),
+            ("traceview_toggle", "Phy TraceView", self._toggle_traceview),
             ("firing_rate_toggle", "Firing rates", self._toggle_firing_rate),
         ]
         for attr, label, callback in toggle_defs:
@@ -848,6 +848,8 @@ class EphysWidget(QWidget):
 
         group = QGroupBox("Ephys trace controls")
         group_layout = QVBoxLayout()
+        group_layout.setSpacing(2)
+        group_layout.setContentsMargins(2, 2, 2, 2)
         group.setLayout(group_layout)
         layout.addWidget(group)
 
@@ -2244,8 +2246,8 @@ class EphysWidget(QWidget):
 
         group = QGroupBox("Firing rates")
         group_layout = QVBoxLayout()
-        group_layout.setSpacing(6)
-        group_layout.setContentsMargins(8, 12, 8, 8)
+        group_layout.setSpacing(2)
+        group_layout.setContentsMargins(2, 2, 2, 2)
         group.setLayout(group_layout)
         layout.addWidget(group)
 
@@ -2291,8 +2293,8 @@ class EphysWidget(QWidget):
 
         pca_group = QGroupBox("PCA")
         pca_layout = QVBoxLayout()
-        pca_layout.setSpacing(6)
-        pca_layout.setContentsMargins(8, 12, 8, 8)
+        pca_layout.setSpacing(2)
+        pca_layout.setContentsMargins(2, 2, 2, 2)
         pca_group.setLayout(pca_layout)
         layout.addWidget(pca_group)
 

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/gui/widgets_meta.py

@@ -3,7 +3,6 @@
 import logging
 
 from napari.viewer import Viewer
-from qt_niu.collapsible_widget import CollapsibleWidgetContainer
 from qtpy.QtCore import Qt, QTimer
 from qtpy.QtWidgets import (
     QMessageBox,
@@ -26,6 +25,7 @@ from .app_constants import (
     SIDEBAR_MIN_WIDTH_PX,
 )
 from .app_state import ObservableAppState
+from .grid_section_container import GridSectionContainer
 from .make_pretty import LayoutManager
 from .plots_container import UnifiedPanelContainer
 from .shortcuts import bind_global_shortcuts
@@ -42,7 +42,7 @@ from .widgets_plot_settings import PlotSettingsWidget
 logger = logging.getLogger(__name__)
 
 
-class MetaWidget(CollapsibleWidgetContainer):
+class MetaWidget(GridSectionContainer):
     def __init__(self, napari_viewer: Viewer):
         """Initialize the meta-widget."""
         super().__init__()
@@ -226,11 +226,11 @@ class MetaWidget(CollapsibleWidgetContainer):
             widget_title="Data",
         )
 
-        # Index 3: Phy extension
+        # Index 3: Phy TraceView
         self.add_widget(
             self.ephys_widget,
             collapsible=True,
-            widget_title="Phy extension",
+            widget_title="Phy TraceView",
         )
 
         # Index 4: Labelling
@@ -323,6 +323,7 @@ class MetaWidget(CollapsibleWidgetContainer):
 
     def refresh_widget_layout(self, widget: QWidget):
         self._schedule_layout_refresh()
+        self.notify_content_resized()
 
     def _cycle_channel(self, direction: int):
         if not self.app_state.ready:

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/gui/widgets_navigation.py

@@ -100,6 +100,8 @@ class NavigationWidget(QWidget):
         # ── Navigate (unified prev/next + mode) ──────────────────────
         navigate_group = QGroupBox("Navigate")
         navigate_layout = QVBoxLayout()
+        navigate_layout.setSpacing(2)
+        navigate_layout.setContentsMargins(2, 2, 2, 2)
         navigate_group.setLayout(navigate_layout)
 
         filter_hint = QLabel("Only navigates trials visible in the Trials tab")
@@ -234,6 +236,8 @@ class NavigationWidget(QWidget):
         # ── Playback ─────────────────────────────────────────────────
         playback_group = QGroupBox("Playback")
         playback_layout = QGridLayout()
+        playback_layout.setSpacing(2)
+        playback_layout.setContentsMargins(2, 2, 2, 2)
         playback_group.setLayout(playback_layout)
 
         self.fps_label = QLabel("Playback FPS:")

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/gui/widgets_plot_settings.py

@@ -145,6 +145,8 @@ class PlotSettingsWidget(QWidget):
 
         group_box = QGroupBox("Axes Controls")
         group_layout = QGridLayout()
+        group_layout.setSpacing(2)
+        group_layout.setContentsMargins(2, 2, 2, 2)
         group_box.setLayout(group_layout)
         layout.addWidget(group_box)
 
@@ -297,6 +299,8 @@ class PlotSettingsWidget(QWidget):
 
         group_box = QGroupBox("Space Plot Controls")
         group_layout = QGridLayout()
+        group_layout.setSpacing(2)
+        group_layout.setContentsMargins(2, 2, 2, 2)
         group_box.setLayout(group_layout)
         layout.addWidget(group_box)
 
@@ -410,8 +414,8 @@ class PlotSettingsWidget(QWidget):
 
         group_box = QGroupBox("Spectrogram Controls")
         group_layout = QGridLayout()
-        group_layout.setVerticalSpacing(6)
-        group_layout.setContentsMargins(6, 10, 6, 6)
+        group_layout.setSpacing(2)
+        group_layout.setContentsMargins(2, 2, 2, 2)
         group_box.setLayout(group_layout)
         layout.addWidget(group_box)
 
@@ -740,6 +744,8 @@ class PlotSettingsWidget(QWidget):
 
         hm_group = QGroupBox("Heatmap Display")
         hm_layout = QGridLayout()
+        hm_layout.setSpacing(2)
+        hm_layout.setContentsMargins(2, 2, 2, 2)
         hm_group.setLayout(hm_layout)
         layout.addWidget(hm_group)
 

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph/labels/intervals.py

@@ -201,17 +201,24 @@ _LABEL_COLORS = [
 _GAP_COLOR = [128 / 255.0, 128 / 255.0, 128 / 255.0]
 
 
-def load_label_mapping(mapping_file: str | Path = "mapping.txt") -> Dict[int, Dict]:
+def load_label_mapping(
+    mapping_file: str | Path = "mapping.txt",
+    order: list[int] | None = None,
+) -> Dict[int, Dict]:
     """Load a label mapping with colors for visualization.
 
     Parameters
     ----------
     mapping_file : str or Path
-        Path to the mapping file.  Each line is
+        Path to the mapping file. Each line is
         ``<id> <name> [<branch>] [<event_type>]`` where *branch* is an
         optional integer (default 0) grouping labels into branches for
         independent labeling, and *event_type* is ``"state"`` (default) or
-        ``"point"``.  Missing trailing columns inherit their defaults.
+        ``"point"``.
+    order : list[int] or None
+        Label IDs in the desired display sequence. If provided, overrides
+        the default order (which follows label ID). Any ID not listed
+        retains its default position.
 
     Returns
     -------
@@ -229,10 +236,12 @@ def load_label_mapping(mapping_file: str | Path = "mapping.txt") -> Dict[int, Di
     >>> mappings = load_label_mapping("mapping.txt")
     >>> mappings[1]["name"]
     'walk'
-    >>> mappings[1]["color"].shape
-    (3,)
 
-    Use the RGB colors to draw labelled rectangles on a plot::
+    Reorder labels for display without changing the file::
+
+        mappings = load_label_mapping("mapping.txt", order=[0, 3, 1, 2])
+
+    Draw labelled intervals on a plot::
 
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
@@ -240,12 +249,9 @@ def load_label_mapping(mapping_file: str | Path = "mapping.txt") -> Dict[int, Di
         mappings = load_label_mapping("mapping.txt")
         fig, ax = plt.subplots()
         ax.plot(time, signal)
-
         for _, row in intervals_df.iterrows():
-            color = mappings[int(row["labels"])]["color"]  # (3,) RGB in [0, 1]
+            color = mappings[int(row["labels"])]["color"]
             ax.axvspan(row["onset_s"], row["offset_s"], alpha=0.5, color=color)
-
-        # Build a legend from the mapping
         handles = [mpatches.Patch(color=m["color"], label=m["name"]) for m in mappings.values()]
         ax.legend(handles=handles)
         plt.show()
@@ -263,11 +269,9 @@ def load_label_mapping(mapping_file: str | Path = "mapping.txt") -> Dict[int, Di
             if parts[0].startswith("("):
                 nums = parts[0].strip("()").split(",")
                 label_id = (int(nums[0]), int(nums[1]))
-                order = int(parts[-1])
                 label_mappings[label_id] = {
                     "name": parts[1],
                     "color": _GAP_COLOR,
-                    "order": order,
                     "branch": 0,
                     "event_type": EVENT_TYPE_STATE,
                 }
@@ -280,11 +284,13 @@ def load_label_mapping(mapping_file: str | Path = "mapping.txt") -> Dict[int, Di
                 label_mappings[label_id] = {
                     "name": parts[1],
                     "color": np.array(_LABEL_COLORS[label_id % len(_LABEL_COLORS)]) / 255.0,
-                    "order": label_id,
                     "branch": branch,
                     "event_type": event_type,
                 }
 
+    if order is not None:
+        label_mappings = {k: label_mappings[k] for k in order if k in label_mappings}
+
     return label_mappings
 
 

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ethograph
-Version: 0.2.3
+Version: 0.2.4
 Summary: A multimodal timeseries GUI for neuroethology
 Author-email: Akseli Ilmanen <akseli.ilmanen@gmail.com>
 License-Expression: BSD-3-Clause
@@ -26,6 +26,7 @@ Requires-Dist: pandas
 Requires-Dist: xarray
 Requires-Dist: netcdf4
 Requires-Dist: scipy
+Requires-Dist: scikit-learn
 Requires-Dist: matplotlib
 Requires-Dist: pynapple
 Requires-Dist: pyyaml

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph.egg-info/SOURCES.txt

@@ -68,6 +68,7 @@ ethograph/gui/dialog_pose_video_matcher.py
 ethograph/gui/dialog_screen_recorder.py
 ethograph/gui/dialog_select_template.py
 ethograph/gui/dialog_video_downsample.py
+ethograph/gui/grid_section_container.py
 ethograph/gui/label_drawing_mixin.py
 ethograph/gui/make_pretty.py
 ethograph/gui/napari.yaml

{ethograph-0.2.3 → ethograph-0.2.4}/ethograph.egg-info/requires.txt

@@ -3,6 +3,7 @@ pandas
 xarray
 netcdf4
 scipy
+scikit-learn
 matplotlib
 pynapple
 pyyaml

{ethograph-0.2.3 → ethograph-0.2.4}/pyproject.toml

@@ -28,6 +28,7 @@ dependencies = [
     "xarray",
     "netcdf4",
     "scipy",
+    "scikit-learn",
     "matplotlib",
     "pynapple",
     "pyyaml",