Show channel stats

CHANGELOG.md

@@ -5,6 +5,7 @@
 - XDF reader now parses measurement date ([#470](https://github.com/cbrnr/mnelab/pull/470) by [Stefan Appelhoff](https://stefanappelhoff.com))
 - Add support for loading custom montage files ([#468](https://github.com/cbrnr/mnelab/pull/468) by [Benedikt Klöckl](https://github.com/bkloeckl) and [Clemens Brunner](https://github.com/cbrnr))
 - Add new filter dialog option for notch filter and improve UI ([#469](https://github.com/cbrnr/mnelab/pull/469) by [Benedikt Klöckl](https://github.com/bkloeckl))
+- Add functionality to display channel stats ([#462](https://github.com/cbrnr/mnelab/pull/462) by [Benedikt Klöckl](https://github.com/bkloeckl))
 
 ### 🌀 Changed
 - Change the append dialog appearance to include original indices used for identifying the data ([#449](https://github.com/cbrnr/mnelab/pull/449) by [Benedikt Klöckl](https://github.com/bkloeckl))

pyproject.toml

@@ -22,16 +22,17 @@ classifiers = [
 ]
 keywords = ["EEG", "MEG", "MNE", "GUI", "electrophysiology"]
 dependencies = [
-    "mne >= 1.7.0",
-    "PySide6 >= 6.7.1",
     "edfio >= 0.4.2",
     "matplotlib >= 3.8.0",
+    "mne >= 1.7.0",
     "numpy >= 2.0.0",
-    "scipy >= 1.14.1",
     "pybv >= 0.7.4",
+    "pyobjc-framework-cocoa >= 10.0; platform_system=='Darwin'",
     "pyxdf >= 1.16.4",
-    "pyobjc-framework-Cocoa >= 10.0; platform_system=='Darwin'",
+    "pyside6 >= 6.7.1",
+    "scipy >= 1.14.1",
 ]
+
 dynamic = ["version"]
 
 [project.optional-dependencies]

src/mnelab/dialogs/channel_stats.py

@@ -0,0 +1,102 @@
+# © MNELAB developers
+#
+# License: BSD (3-clause)
+
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import (
+    QDialog,
+    QPushButton,
+    QTableWidget,
+    QTableWidgetItem,
+    QVBoxLayout,
+)
+
+from mnelab.utils import calculate_channel_stats
+
+
+class SortableTableWidgetItem(QTableWidgetItem):
+    def __init__(self, value):
+        super().__init__(str(value))
+        self.value = value
+
+    def __lt__(self, other):
+        try:
+            return float(self.value) < float(other.value)
+        except ValueError:
+            return str(self.value) < str(other.value)
+
+
+class ChannelStats(QDialog):
+    def __init__(self, parent, raw):
+        super().__init__(parent=parent)
+
+        # window
+        self.setWindowTitle("Channel Stats")
+        self.setMinimumSize(400, 300)
+        layout = QVBoxLayout(self)
+
+        # create table
+        self.table = QTableWidget(self)
+        self.table.setSortingEnabled(True)
+        layout.addWidget(self.table)
+
+        # populate table
+        self.populate_table(raw)
+        self.table.resizeColumnsToContents()
+
+        # add close button
+        close_button = QPushButton("Close")
+        close_button.clicked.connect(self.close)
+        layout.addWidget(close_button)
+
+        # calculate table width
+        table_width = self.table.verticalHeader().width()
+        table_width += sum(
+            self.table.columnWidth(i) for i in range(self.table.columnCount())
+        )
+        table_width += self.table.verticalScrollBar().width()
+        self.resize(table_width - 30, 550)
+        self.setLayout(layout)
+
+    def populate_table(self, raw):
+        cols, nchan = calculate_channel_stats(raw)
+        self.table.setColumnCount(9)
+        self.table.setRowCount(nchan)
+        self.table.setHorizontalHeaderLabels(
+            [
+                "Channel",
+                "Name",
+                "Type",
+                "Unit",
+                "Min",
+                "Q1",
+                "Mean",
+                "Median",
+                "Q3",
+                "Max",
+            ]
+        )
+
+        for i in range(nchan):
+            item = QTableWidgetItem(str(i))
+            item.setFlags(item.flags() & ~Qt.ItemIsEditable)
+            self.table.setItem(i, 0, item)
+
+            item = QTableWidgetItem(cols["name"][i])
+            item.setFlags(item.flags() & ~Qt.ItemIsEditable)
+            self.table.setItem(i, 1, item)
+
+            item = QTableWidgetItem(cols["type"][i].upper())
+            item.setFlags(item.flags() & ~Qt.ItemIsEditable)
+            self.table.setItem(i, 2, item)
+
+            item = QTableWidgetItem(cols["unit"][i])
+            item.setFlags(item.flags() & ~Qt.ItemIsEditable)
+            self.table.setItem(i, 3, item)
+
+            for j, key in enumerate(["min", "Q1", "median", "Q3", "max"], start=4):
+                formatted_value = f"{cols[key][i]:.2f}"
+                item = QTableWidgetItem(formatted_value)
+                item.setFlags(item.flags() & ~Qt.ItemIsEditable)
+                item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
+                self.table.setItem(i, j, item)

src/mnelab/mainwindow.py

@@ -29,6 +29,7 @@
 from pyxdf import resolve_streams
 
 from mnelab.dialogs import *  # noqa: F403
+from mnelab.dialogs.channel_stats import ChannelStats
 from mnelab.io import writers
 from mnelab.io.mat import parse_mat
 from mnelab.io.npy import parse_npy
@@ -315,6 +316,10 @@ def __init__(self, model: Model):
             self.show_history,
             QKeySequence(Qt.CTRL | Qt.Key_Y),
         )
+        self.actions["channel_stats"] = view_menu.addAction(
+            "&Channel Stats",
+            self.show_channel_stats,
+        )
         self.actions["toolbar"] = view_menu.addAction("&Toolbar", self._toggle_toolbar)
         self.actions["toolbar"].setCheckable(True)
         self.actions["statusbar"] = view_menu.addAction(
@@ -542,6 +547,9 @@ def data_changed(self):
             self.actions["epoch_data"].setEnabled(
                 enabled and events and self.model.current["dtype"] == "raw"
             )
+            self.actions["channel_stats"].setEnabled(
+                enabled and self.model.current["dtype"] == "raw"
+            )
             self.actions["drop_bad_epochs"].setEnabled(
                 enabled and events and self.model.current["dtype"] == "epochs"
             )
@@ -1248,6 +1256,11 @@ def show_history(self):
         dialog = HistoryDialog(self, "\n".join(self.model.history))
         dialog.exec()
 
+    def show_channel_stats(self):
+        """Show channel stats."""
+        dialog = ChannelStats(self, self.model.current["data"])
+        dialog.exec_()
+
     def show_about(self):
         """Show About dialog."""
         from . import __version__

src/mnelab/utils/__init__.py

@@ -4,4 +4,10 @@
 
 from mnelab.utils.dependencies import have
 from mnelab.utils.syntax import PythonHighlighter
-from mnelab.utils.utils import Montage, count_locations, image_path, natural_sort
+from mnelab.utils.utils import (
+    Montage,
+    calculate_channel_stats,
+    count_locations,
+    image_path,
+    natural_sort,
+)

src/mnelab/utils/utils.py

@@ -3,11 +3,14 @@
 # License: BSD (3-clause)
 
 import re
+from collections import defaultdict
 from dataclasses import dataclass
 from pathlib import Path
 
 import numpy as np
+from mne import channel_type
 from mne.channels import DigMontage
+from mne.defaults import _handle_default
 
 
 def count_locations(info):
@@ -33,6 +36,35 @@ def key(s):
     return sorted(lst, key=key)
 
 
+def calculate_channel_stats(raw):
+    # extract channel info
+    nchan = raw.info["nchan"]
+    data = raw.get_data()
+    cols = defaultdict(list)
+    cols["name"] = raw.ch_names
+    cols["type"] = [channel_type(raw.info, i) for i in range(nchan)]
+
+    # vectorized calculations
+    cols["min"], cols["Q1"], cols["median"], cols["Q3"], cols["max"] = np.percentile(
+        data, [0, 25, 50, 75, 100], axis=1
+    )
+    cols["mean"] = np.mean(data, axis=1)
+
+    # scaling and units
+    scalings = _handle_default("scalings")
+    units = _handle_default("units")
+    cols["unit"] = []
+    for i in range(nchan):
+        unit = units.get(cols["type"][i])
+        scaling = scalings.get(cols["type"][i], 1)
+        cols["unit"].append(unit if scaling != 1 else "")
+        if scaling != 1:
+            for col in ["min", "Q1", "mean", "median", "Q3", "max"]:
+                cols[col][i] *= scaling
+
+    return cols, nchan
+
+
 @dataclass
 class Montage:
     montage: DigMontage