Merge pull request #38 from cibr-jyu/update-mne

Update mne and docs

Makefile

@@ -15,7 +15,7 @@ test:
 update_docs:
 	rm -fr docs_updated
 	cp -fr docs docs_updated
-	python update_docs.py docs_updated
+	python scripts/update_docs.py docs_updated
 
 .PHONY: serve_docs
 serve_docs: update_docs

docs/user-guide/plugins.md

@@ -0,0 +1,32 @@
+# Plugins
+
+Meggie's capabilities can be extended through the use of plugins. These plugins are developed by the community and allow you to customize and enhance your experience with new features.
+
+## Why Use Plugins?
+
+Plugins let you tailor Meggie to your specific research needs. They can provide new analysis options, data handling capabilities, or help optimize your existing workflows.
+
+## Finding Plugins
+
+Below is a list of available meggie plugins found on PyPi.
+
+{{PLUGIN_INFO}}
+
+## Installing Plugins
+
+To install a plugin, first activate the Python environment in which Meggie is installed. Then, you can simply use pip to install the plugin of your choice:
+
+```bash
+$ pip install <plugin_name>
+```
+
+For example, if you wanted to install the "meggie_example" plugin, you would run:
+
+```bash
+$ pip install meggie_example
+```
+
+## Need Help?
+
+If you have questions about selecting or installing plugins, the Meggie community is ready to help. We're all part of making Meggie a versatile and user-friendly tool for everyone.
+

meggie/actions/raw_ica/controller/ica.py

@@ -25,21 +25,20 @@ def plot_topographies(ica, n_components):
     """Plots topographies from the ICA solution."""
 
     figs = ica.plot_components(title="")
+    if not isinstance(figs, list):
+        figs = [figs]
+
     for fig in figs:
         set_figure_title(fig, "ICA topographic maps")
 
-    def update_topography_texts():
-        """Change texts in the axes to match names in the dialog"""
-        idx = 0
-        for fig in figs:
-            for ax in fig.get_axes():
-                if idx > n_components:
-                    return
-
-                ax.set_title("Component " + str(idx), fontsize=12)
-                idx += 1
+    idx = 0
+    for fig in figs:
+        for ax in fig.get_axes():
+            if idx > n_components:
+                return
 
-    update_topography_texts()
+            ax.set_title("Component " + str(idx), fontsize=12)
+            idx += 1
 
 
 def plot_sources(raw, ica):

meggie/datatypes/spectrum/spectrum.py

@@ -67,7 +67,7 @@ def _load_content(self):
     def _get_info(self):
         """Gets info from file system."""
         info_path = os.path.join(self._directory, self._name + "-info.fif")
-        info = mne.io.meas_info.read_info(info_path)
+        info = mne.io.read_info(info_path)
 
         return info
 
@@ -115,7 +115,7 @@ def save_content(self):
         try:
             # save info
             info_path = os.path.join(self._directory, self._name + "-info.fif")
-            mne.io.meas_info.write_info(info_path, self._info)
+            mne.io.write_info(info_path, self._info)
             self._params["info_set"] = True
 
             # save data

meggie/mainwindow/dialogs/addSubjectDialogMain.py

@@ -4,8 +4,6 @@
 import os
 import logging
 
-import mne
-
 from PyQt5 import QtWidgets
 from PyQt5 import QtCore
 
@@ -15,6 +13,7 @@
 from meggie.utilities.messaging import messagebox
 from meggie.utilities.threading import threaded
 from meggie.utilities.names import next_available_name
+from meggie.utilities.filemanager import get_supported_formats
 
 
 class AddSubjectDialog(QtWidgets.QDialog):
@@ -78,15 +77,14 @@ def on_pushButtonBrowse_clicked(self, checked=None):
         if checked is None:
             return
 
-        mne_supported = mne.io._read_raw.supported
+        mne_supported = get_supported_formats()
+
+        all_ext = [val[0] for val in mne_supported]
 
-        all_ext = []
         all_items = []
-        for row in mne_supported.items():
-            ext = row[0]
-            name = row[1].__name__.split("_")[-1]
-            all_ext.append(ext)
-            all_items.append(name + " files (*" + ext + ")")
+        for ext, names in mne_supported:
+            for name in names:
+                all_items.append(name + " files (*" + ext + ")")
 
         filter_string = "All supported (*" + " *".join(all_ext) + ");" ";"
         filter_string = filter_string + ";" ";".join(all_items)

meggie/utilities/filemanager.py

@@ -11,6 +11,8 @@
 import numpy as np
 import mne
 
+from mne.io._read_raw import _get_supported as mne_get_supported
+
 
 def open_raw(fname, preload=True, verbose="info"):
     """Reads a raw from file.
@@ -266,3 +268,15 @@ def homepath():
         return "."
 
     return home
+
+
+def get_supported_formats():
+    mne_supported = mne_get_supported()
+
+    items = []
+    for ext_item in mne_supported.items():
+        ext = ext_item[0]
+        names = [val[0] for val in ext_item[1].items()]
+        items.append((ext, names))
+
+    return items

meggie/utilities/testing.py

@@ -314,15 +314,6 @@ def setup_experiment(self):
 
     def run_action(self, action_name, handler, data={}, patch_paths=[]):
 
-        # patch mne's plt_show to not show plots
-        utils = importlib.import_module("mne.viz.utils")
-        epochs = importlib.import_module("mne.viz.epochs")
-
-        def patched_plt_show(*args, **kwargs):
-            utils.plt_show(show=False, fig=None, **kwargs)
-
-        self.monkeypatch.setattr(epochs, "plt_show", patched_plt_show)
-
         # patch logger to raise exceptions
         logger = logging.getLogger("ui_logger")
         self.monkeypatch.setattr(logger, "exception", patched_logger_exception)

meggie/utilities/tests/test_filemanager.py

@@ -9,6 +9,7 @@
 from meggie.utilities.filemanager import load_csv
 from meggie.utilities.filemanager import open_raw
 from meggie.utilities.filemanager import save_raw
+from meggie.utilities.filemanager import get_supported_formats
 
 
 def test_create_timestamped_folder():
@@ -63,3 +64,11 @@ def test_save_and_load_raw():
         raw = None
 
         open_raw(path)
+
+
+def test_supported_formats():
+    supported_formats = get_supported_formats()
+    assert isinstance(supported_formats, list)
+    assert isinstance(supported_formats[0], tuple)
+    assert isinstance(supported_formats[0][0], str)
+    assert isinstance(supported_formats[0][1], list)

mkdocs.yml

@@ -9,6 +9,7 @@ nav:
         - Getting Started: user-guide/getting-started.md
         - Experiments: user-guide/experiments.md
         - Actions: user-guide/actions.md
+        - Plugins: user-guide/plugins.md
     - Developer Guide:
         - Architecture: developer-guide/architecture.md
         - Development: developer-guide/development.md

requirements.txt

@@ -1,6 +1,6 @@
-mne==1.3.1
-numpy==1.23.5
-matplotlib==3.7.3
+mne==1.6.1
+numpy==1.26.4
+matplotlib==3.8.3
 scikit-learn
 python-json-logger
 h5io