FIX: Connectivity saved to .nc and other fixes

mne_pipeline_hd/__main__.py

@@ -5,10 +5,11 @@
 Github: https://github.com/marsipu/mne-pipeline-hd
 """
 
-import logging
 import os
+import re
 import sys
 from importlib import resources
+from os.path import join
 
 import qtpy
 from qtpy.QtCore import QTimer, Qt
@@ -19,14 +20,27 @@
 from mne_pipeline_hd.gui.gui_utils import StdoutStderrStream, UncaughtHook
 from mne_pipeline_hd.gui.welcome_window import WelcomeWindow
 from mne_pipeline_hd.pipeline.legacy import legacy_import_check
-from mne_pipeline_hd.pipeline.pipeline_utils import ismac, islin, QS
+from mne_pipeline_hd.pipeline.pipeline_utils import (
+    ismac,
+    islin,
+    QS,
+    iswin,
+    init_logging,
+    logger,
+)
 
 # Check for changes in required packages
 legacy_import_check()
 
 import qdarktheme  # noqa: E402
 
 
+def init_streams():
+    # Redirect stdout and stderr to capture it later in GUI
+    sys.stdout = StdoutStderrStream("stdout")
+    sys.stderr = StdoutStderrStream("stderr")
+
+
 def main():
     app_name = "mne-pipeline-hd"
     organization_name = "marsipu"
@@ -40,6 +54,8 @@ def main():
     app.setApplicationName(app_name)
     app.setOrganizationName(organization_name)
     app.setOrganizationDomain(domain_name)
+    # For Spyder to make console accessible again
+    app.lastWindowClosed.connect(app.quit)
 
     # Avoid file-dialog-problems with custom file-managers in linux
     if islin:
@@ -54,37 +70,23 @@ def main():
     # # Set multiprocessing method to spawn
     # multiprocessing.set_start_method('spawn')
 
-    # Redirect stdout to capture it later in GUI
-    sys.stdout = StdoutStderrStream("stdout")
-    # Redirect stderr to capture it later in GUI
-    sys.stderr = StdoutStderrStream("stderr")
+    init_streams()
 
     debug_mode = os.environ.get("MNEPHD_DEBUG", False) == "true"
+    init_logging(debug_mode)
 
-    # Initialize Logger (root)
-    logger = logging.getLogger()
-    if debug_mode:
-        logger.setLevel(logging.DEBUG)
-    else:
-        logger.setLevel(QS().value("log_level", defaultValue=logging.INFO))
-    formatter = logging.Formatter(
-        "%(asctime)s: %(message)s", datefmt="%Y/%m/%d %H:%M:%S"
-    )
-    console_handler = logging.StreamHandler()
-    console_handler.setFormatter(formatter)
-    logger.addHandler(console_handler)
-    logger.info("Starting MNE-Pipeline HD")
+    logger().info("Starting MNE-Pipeline HD")
 
     # Show Qt-binding
     if any([qtpy.PYQT5, qtpy.PYQT6]):
         qt_version = qtpy.PYQT_VERSION
     else:
         qt_version = qtpy.PYSIDE_VERSION
-    logger.info(f"Using {qtpy.API_NAME} {qt_version}")
+    logger().info(f"Using {qtpy.API_NAME} {qt_version}")
 
     # Initialize Exception-Hook
     if debug_mode:
-        logger.info("Debug-Mode is activated")
+        logger().info("Debug-Mode is activated")
     else:
         qt_exception_hook = UncaughtHook()
         # this registers the exception_hook() function
@@ -103,40 +105,34 @@ def main():
     if app_style not in ["dark", "light", "auto"]:
         app_style = "auto"
 
-    if app_style == "dark":
-        qdarktheme.setup_theme("dark")
+    qdarktheme.setup_theme(app_style)
+    st = qdarktheme.load_stylesheet(app_style)
+    is_dark = "background:rgba(32, 33, 36, 1.000)" in st
+    if is_dark:
         icon_name = "mne_pipeline_icon_dark.png"
-    elif app_style == "light":
-        qdarktheme.setup_theme("light")
-        icon_name = "mne_pipeline_icon_light.png"
+        # Fix ToolTip-Problem on Windows
+        # https://github.com/5yutan5/PyQtDarkTheme/issues/239
+        if iswin:
+            match = re.search(r"QToolTip \{([^\{\}]+)\}", st)
+            if match is not None:
+                replace_str = "QToolTip {" + match.group(1) + ";border: 0px}"
+                st = st.replace(match.group(0), replace_str)
+                QApplication.instance().setStyleSheet(st)
     else:
-        qdarktheme.setup_theme("auto")
-        st = qdarktheme.load_stylesheet("auto")
-        if "background:rgba(32, 33, 36, 1.000)" in st:
-            icon_name = "mne_pipeline_icon_dark.png"
-        else:
-            icon_name = "mne_pipeline_icon_light.png"
-
-    icon_path = resources.files(mne_pipeline_hd.extra) / icon_name
+        icon_name = "mne_pipeline_icon_light.png"
+
+    icon_path = join(resources.files(mne_pipeline_hd.extra), icon_name)
     app_icon = QIcon(str(icon_path))
     app.setWindowIcon(app_icon)
 
     # Initiate WelcomeWindow
     WelcomeWindow()
 
-    # Redirect stdout to capture it later in GUI
-    sys.stdout = StdoutStderrStream("stdout")
-    # Redirect stderr to capture it later in GUI
-    sys.stderr = StdoutStderrStream("stderr")
-
     # Command-Line interrupt with Ctrl+C possible
     timer = QTimer()
     timer.timeout.connect(lambda: None)
     timer.start(500)
 
-    # For Spyder to make console accessible again
-    app.lastWindowClosed.connect(app.quit)
-
     sys.exit(app.exec())
 
 

mne_pipeline_hd/development/console_widget_speed.py

@@ -1,42 +1,75 @@
 # -*- coding: utf-8 -*-
 import sys
-from time import perf_counter
 
-import numpy as np
 from PyQt5.QtCore import QTimer
 from PyQt5.QtWidgets import QApplication, QWidget, QVBoxLayout, QPushButton
 
 from mne_pipeline_hd.gui.gui_utils import ConsoleWidget
 
-app = QApplication(sys.argv)
-widget = QWidget()
-layout = QVBoxLayout()
-cw = ConsoleWidget()
-layout.addWidget(cw)
-close_bt = QPushButton("Close")
-close_bt.clicked.connect(widget.close)
-layout.addWidget(close_bt)
-widget.setLayout(layout)
-widget.show()
-last_time = perf_counter()
-
-performance_buffer = list()
-
-
-def test_write():
-    global last_time
-    cw.write_progress("\r" + (f"Test {len(performance_buffer)}" * 1000))
-    diff = perf_counter() - last_time
-    performance_buffer.append(diff)
-    if len(performance_buffer) >= 100:
-        fps = 1 / np.mean(performance_buffer)
-        print(f"Performance is: {fps:.2f} FPS")
-        performance_buffer.clear()
-    last_time = perf_counter()
-
-
-timer = QTimer()
-timer.timeout.connect(test_write)
-timer.start(1)
-
-sys.exit(app.exec())
+test_text = """Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus.
+Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed,
+dolor. Cras elementum ultrices diam. Maecenas ligula massa, varius a, semper
+congue, euismod non, mi. Proin porttitor, orci nec nonummy molestie, enim est
+eleifend mi, non fermentum diam nisl sit amet erat. Duis semper. Duis arcu
+massa, scelerisque vitae, consequat in, pretium a, enim. Pellentesque congue.
+Ut in risus volutpat libero pharetra tempor. Cras vestibulum bibendum augue.
+Praesent egestas leo in pede. Praesent blandit odio eu enim. Pellentesque
+sed dui ut augue blandit sodales. Vestibulum ante ipsum primis in faucibus
+orci luctus et ultrices posuere cubilia Curae; Aliquam nibh. Mauris ac mauris
+sed pede pellentesque fermentum. Maecenas adipiscing ante non diam sodales
+hendrerit.
+\r Progress: 0%
+\r Progress: 10%
+\r Progress: 20%
+\r Progress: 30%
+\r Progress: 40%
+\r Progress: 50%
+\r Progress: 60%
+\r Progress: 70%
+\r Progress: 80%
+\r Progress: 90%
+\r Progress: 100%"""
+
+
+class SpeedWidget(QWidget):
+    def __init__(self):
+        super().__init__()
+
+        layout = QVBoxLayout(self)
+        self.cw = ConsoleWidget()
+        layout.addWidget(self.cw)
+        startbt = QPushButton("Start")
+        startbt.clicked.connect(self.start)
+        layout.addWidget(startbt)
+        stopbt = QPushButton("Stop")
+        stopbt.clicked.connect(self.stop)
+        layout.addWidget(stopbt)
+        close_bt = QPushButton("Close")
+        close_bt.clicked.connect(self.close)
+        layout.addWidget(close_bt)
+
+        self.test_text = test_text.split("\n")
+        self.line_idx = 0
+
+        self.timer = QTimer(self)
+        self.timer.timeout.connect(self.write)
+
+    def start(self):
+        self.timer.start(42)
+
+    def stop(self):
+        self.timer.stop()
+
+    def write(self):
+        if self.line_idx >= len(self.test_text):
+            self.line_idx = 0
+        text = self.test_text[self.line_idx]
+        self.cw.write_stdout(text)
+        self.line_idx += 1
+
+
+if __name__ == "__main__":
+    app = QApplication(sys.argv)
+    w = SpeedWidget()
+    w.show()
+    sys.exit(app.exec())

mne_pipeline_hd/extra/functions.csv

@@ -1,6 +1,8 @@
 ;alias;target;tab;group;matplotlib;mayavi;dependencies;module;pkg_name;func_args
 find_bads;Find Bad Channels;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,n_jobs
 filter_data;Filter;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,filter_target,highpass,lowpass,filter_length,l_trans_bandwidth,h_trans_bandwidth,filter_method,iir_params,fir_phase,fir_window,fir_design,skip_by_annotation,fir_pad,n_jobs,enable_cuda,erm_t_limit,bad_interpolation
+notch_filter;Notch Filter;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,notch_frequencies,n_jobs
+interpolate_bads;Interpolate Bads;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,bad_interpolation
 add_erm_ssp;Empty-Room SSP;MEEG;Compute;Preprocessing;True;False;;operations;basic;meeg,erm_ssp_duration,erm_n_grad,erm_n_mag,erm_n_eeg,n_jobs,show_plots
 eeg_reference_raw;Set EEG Reference;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,ref_channels
 find_events;Find events;MEEG;Compute;events;False;False;;operations;basic;meeg,stim_channels,min_duration,shortest_event,adjust_timeline_by_msec
@@ -10,7 +12,6 @@ estimate_noise_covariance;Noise-Covariance;MEEG;Compute;Preprocessing;False;Fals
 run_ica;Run ICA;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,ica_method,ica_fitto,n_components,ica_noise_cov,ica_remove_proj,ica_reject,ica_autoreject,overwrite_ar,ch_types,ch_names,reject_by_annotation,ica_eog,eog_channel,ica_ecg,ecg_channel
 apply_ica;Apply ICA;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,ica_apply_target,n_pca_components
 get_evokeds;Get Evokeds;MEEG;Compute;events;False;False;;operations;basic;meeg
-interpolate_bads;Interpolate Bads;MEEG;Compute;Preprocessing;False;False;;operations;basic;meeg,bad_interpolation
 compute_psd_raw;Compute PSD (Raw);MEEG;Compute;Time-Frequency;False;False;;operations;basic;meeg,psd_method,n_jobs
 compute_psd_epochs;Compute PSD (Epochs);MEEG;Compute;Time-Frequency;False;False;;operations;basic;meeg,psd_method,n_jobs
 tfr;Time-Frequency;MEEG;Compute;Time-Frequency;False;False;;operations;basic;meeg,tfr_freqs,tfr_n_cycles,tfr_average,tfr_use_fft,tfr_baseline,tfr_baseline_mode,tfr_method,multitaper_bandwidth,stockwell_width,n_jobs
@@ -26,9 +27,9 @@ morph_labels_from_fsaverage;;FSMRI;Compute;MRI-Preprocessing;False;False;;operat
 create_inverse_operator;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg
 source_estimate;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,inverse_method,pick_ori,lambda2
 apply_morph;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,morph_to
-label_time_course;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,target_labels,target_parcellation,extract_mode
+label_time_course;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,target_labels,extract_mode
 ecd_fit;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,ecd_times,ecd_positions,ecd_orientations,t_epoch
-src_connectivity;;MEEG;Compute;Inverse;False;False;;operations;basic;meeg,target_labels,target_parcellation,inverse_method,lambda2,con_methods,con_frequencies,con_time_window,n_jobs
+src_connectivity;;MEEG;Compute;Time-Frequency;False;False;;operations;basic;meeg,target_labels,inverse_method,lambda2,con_methods,con_fmin,con_fmax,con_time_window,n_jobs
 grand_avg_evokeds;;Group;Compute;Grand-Average;False;False;;operations;basic;group,ga_interpolate_bads,ga_drop_bads
 grand_avg_tfr;;Group;Compute;Grand-Average;False;False;;operations;basic;group
 grand_avg_morphed;;Group;Compute;Grand-Average;False;False;;operations;basic;group,morph_to
@@ -61,21 +62,21 @@ plot_evoked_white;;MEEG;Plot;Evoked;True;False;;plot;basic;meeg,show_plots
 plot_evoked_image;;MEEG;Plot;Evoked;True;False;;plot;basic;meeg,show_plots
 plot_compare_evokeds;;MEEG;Plot;Evoked;True;False;;plot;basic;meeg,show_plots
 plot_gfp;;MEEG;Plot;Evoked;True;False;;plot;basic;meeg,show_plots
-plot_stc;Plot Source-Estimate;MEEG;Plot;Inverse;True;True;;plot;basic;meeg,target_labels,target_parcellation,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
+plot_stc;Plot Source-Estimate;MEEG;Plot;Inverse;True;True;;plot;basic;meeg,target_labels,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
 plot_stc_interactive;;MEEG;Plot;Inverse;True;True;;plot;basic;meeg,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
-plot_labels;;FSMRI;Plot;Inverse;True;True;;plot;basic;fsmri,target_labels,target_parcellation,label_colors,stc_hemi,stc_surface,stc_views,backend_3d
-plot_animated_stc;Plot Source-Estimate Video;MEEG;Plot;Inverse;True;True;;plot;basic;meeg,target_labels,target_parcellation,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,stc_animation_span,stc_animation_dilat,backend_3d
+plot_labels;;FSMRI;Plot;Inverse;True;True;;plot;basic;fsmri,target_labels,label_colors,stc_hemi,stc_surface,stc_views,backend_3d
+plot_animated_stc;Plot Source-Estimate Video;MEEG;Plot;Inverse;True;True;;plot;basic;meeg,target_labels,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,stc_animation_span,stc_animation_dilat,backend_3d
 plot_snr;;MEEG;Plot;Inverse;True;False;;plot;basic;meeg,show_plots
-plot_label_time_course;;MEEG;Plot;Inverse;True;False;;plot;basic;meeg,show_plots
+plot_label_time_course;;MEEG;Plot;Inverse;True;False;;plot;basic;meeg,label_colors,show_plots
 plot_ecd;;MEEG;Plot;Inverse;True;True;;plot;basic;meeg
-plot_src_connectivity;;MEEG;Plot;Time-Frequency;True;False;;plot;basic;meeg,show_plots
+plot_src_connectivity;;MEEG;Plot;Time-Frequency;True;False;;plot;basic;meeg,label_colors,show_plots
 plot_grand_avg_evokeds;;Group;Plot;Grand-Average;True;False;;plot;basic;group,show_plots
 plot_grand_avg_tfr;;Group;Plot;Grand-Average;True;False;;plot;basic;group,show_plots
-plot_grand_avg_stc;;Group;Plot;Grand-Average;True;True;;plot;basic;group,target_labels,target_parcellation,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
-plot_grand_avg_stc_anim;;Group;Plot;Grand-Average;True;True;;plot;basic;group,target_labels,target_parcellation,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,stc_animation_span,stc_animation_dilat,backend_3d
+plot_grand_avg_stc;;Group;Plot;Grand-Average;True;True;;plot;basic;group,target_labels,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
+plot_grand_avg_stc_anim;;Group;Plot;Grand-Average;True;True;;plot;basic;group,target_labels,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,stc_animation_span,stc_animation_dilat,backend_3d
 plot_grand_average_stc_interactive;;Group;Plot;Grand-Average;True;True;;plot;basic;group,label_colors,stc_surface,stc_hemi,stc_views,stc_time,stc_clim,stc_roll,stc_azimuth,stc_elevation,backend_3d
-plot_grand_avg_ltc;;Group;Plot;Grand-Average;True;False;;plot;basic;group,show_plots
-plot_grand_avg_connect;;Group;Plot;Grand-Average;True;False;;plot;basic;group,morph_to,show_plots,connectivity_vmin,connectivity_vmax,con_group_boundaries
+plot_grand_avg_ltc;;Group;Plot;Grand-Average;True;False;;plot;basic;group,label_colors,show_plots
+plot_grand_avg_connect;;Group;Plot;Grand-Average;True;False;;plot;basic;group,label_colors,show_plots
 plot_ica_components;Plot ICA-Components;MEEG;Plot;ICA;True;False;;plot;basic;meeg,show_plots,close_func
 plot_ica_sources;Plot ICA-Sources;MEEG;Plot;ICA;True;False;;plot;basic;meeg,ica_source_data,show_plots,close_func
 plot_ica_overlay;Plot ICA-Overlay;MEEG;Plot;ICA;True;False;;plot;basic;meeg,ica_overlay_data,show_plots

mne_pipeline_hd/extra/parameters.csv

@@ -76,12 +76,12 @@ stc_azimuth;;Inverse;70;;Azimuth for view for Source Estimate Plots;IntGui;{'max
 stc_elevation;;Inverse;60;;Elevation for view for Source Estimate Plots;IntGui;{'max_val': 360}
 stc_animation_span;;Inverse;(0,0.5);s;time-span for stc-animation[s];TupleGui;
 stc_animation_dilat;;Inverse;20;;time-dilation for stc-animation;IntGui;
-target_parcellation;Target Parcellation;Inverse;aparc;;The parcellation to use.;StringGui;
 target_labels;Target Labels;Inverse;[];;;LabelGui;
 label_colors;;Inverse;{};;Set custom colors for labels.;ColorGui;{'keys': 'target_labels', 'none_select':True}
 extract_mode;Label-Extraction-Mode;Inverse;auto;;mode for extracting label-time-course from Source-Estimate;ComboGui;{'options': ['auto', 'max', 'mean', 'mean_flip', 'pca_flip']}
 con_methods;;Connectivity;['coh'];;methods for connectivity;CheckListGui;{'options': ['coh', 'cohy', 'imcoh', 'plv', 'ciplv', 'ppc', 'pli', 'pli2_unbiased', 'wpli', 'wpli2_debiased']}
-con_frequencies;;Connectivity;(30, 80);;frequencies for connectivity;TupleGui;{'none_select': True, 'step': 1}
+con_fmin;;Connectivity;30;;lower frequency/frequencies for connectivity;MultiTypeGui;{'type_selection': True, 'types': ['float', 'list']}
+con_fmax;;Connectivity;80;;upper frequency/frequencies for connectivity;MultiTypeGui;{'type_selection': True, 'types': ['float', 'list']}
 con_time_window;;Connectivity;(0, 0.5);;time-window for connectivity;TupleGui;{'none_select': True, 'step': 0.001}
 ecd_times;;Inverse;{};;;DictGui;
 ecd_positions;;Inverse;{};;;DictGui;
@@ -96,9 +96,8 @@ erm_n_mag;;Preprocessing;2;;The number of projections for Magnetometer;IntGui;
 erm_n_eeg;;Preprocessing;0;;The number of projections for EEG;IntGui;
 ga_interpolate_bads;;Grand-Average;True;;If to interpolate bad channels for the Grand-Average;BoolGui;
 ga_drop_bads;;Grand-Average;True;;If to drop bad channels for the Grand-Average;BoolGui;
-connectivity_vmin;;Connectivity;None;;Minimum value for colormap;FloatGui;{'step': 0.01, 'none_select':True}
-connectivity_vmax;;Connectivity;None;;Maximum value for colormap;FloatGui;{'step': 0.01, 'none_select':True}
 psd_method;;Time-Frequency;welch;;The method for spectral estimation;ComboGui;{'options': ['welch', 'multitaper']}
 psd_topomap_bands;;Time-Frequency;None;;The frequency bands for the topomap-plot;DictGui;{'none_select': True}
 backend_3d;3D-Backend;Plot;pyvistaqt;;Choose the 3D-Backend for Brain-plots.;ComboGui;{'options': ['pyvistaqt', 'notebook']}
 con_group_boundaries;;Connectivity;None;;Set group-boundaries for circular plot.;FuncGui;{'none_select': True}
+notch_frequencies;;Preprocessing;50;;Set frequencies for Notch filtering;FuncGui;""