fix to boris events

flares.py

@@ -50,8 +50,8 @@ from scipy.spatial.distance import cdist
 
 # Backen visualization needed to be defined for pyinstaller
 import pyvistaqt # type: ignore
-import vtkmodules.util.data_model
-import vtkmodules.util.execution_model
+# import vtkmodules.util.data_model
+# import vtkmodules.util.execution_model
 
 # External library imports for mne
 from mne import (
@@ -1108,7 +1108,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
     evokeds3 = []
     colors = []
     conditions = list(epochs.event_id.keys())
-    cmap = plt.cm.get_cmap("tab10", len(conditions))
+    cmap = plt.get_cmap("tab10", len(conditions))
 
     for idx, cond in enumerate(conditions):
         evoked = epochs[cond].average(picks="hbo")

main.py

@@ -10,6 +10,7 @@ License: GPL-3.0
 import os
 import re
 import sys
+import json
 import time
 import shlex
 import pickle
@@ -33,6 +34,7 @@ from mne.io import read_raw_snirf
 from mne.preprocessing.nirs import source_detector_distances
 from mne_nirs.io import write_raw_snirf
 from mne.channels import make_dig_montage
+from mne import Annotations
 
 from PySide6.QtWidgets import (
     QApplication, QWidget, QMessageBox, QVBoxLayout, QHBoxLayout, QTextEdit, QScrollArea, QComboBox, QGridLayout,
@@ -624,6 +626,430 @@ class UpdateOptodesWindow(QWidget):
 
 
 
+class UpdateEventsWindow(QWidget):
+
+    def __init__(self, parent=None):
+        super().__init__(parent, Qt.WindowType.Window)
+        self.setWindowTitle("Update event markers")
+        self.resize(760, 200)
+
+        self.label_file_a = QLabel("SNIRF file:")
+        self.line_edit_file_a = QLineEdit()
+        self.line_edit_file_a.setReadOnly(True)
+        self.btn_browse_a = QPushButton("Browse .snirf")
+        self.btn_browse_a.clicked.connect(self.browse_file_a)
+
+        self.label_file_b = QLabel("BORIS file:")
+        self.line_edit_file_b = QLineEdit()
+        self.line_edit_file_b.setReadOnly(True)
+        self.btn_browse_b = QPushButton("Browse .boris")
+        self.btn_browse_b.clicked.connect(self.browse_file_b)
+
+        self.label_suffix = QLabel("Filename in BORIS project file:")
+        self.combo_suffix = QComboBox()
+        self.combo_suffix.setEditable(False)
+        self.combo_suffix.currentIndexChanged.connect(self.on_observation_selected)
+
+        self.label_events = QLabel("Events in selected observation:")
+        self.combo_events = QComboBox()
+        self.combo_events.setEnabled(False)
+        
+        self.label_snirf_events = QLabel("Events in SNIRF file:")
+        self.combo_snirf_events = QComboBox()
+        self.combo_snirf_events.setEnabled(False)
+
+        self.btn_clear = QPushButton("Clear")
+        self.btn_go = QPushButton("Go")
+        self.btn_clear.clicked.connect(self.clear_files)
+        self.btn_go.clicked.connect(self.go_action)
+
+        # --- 
+        layout = QVBoxLayout()
+        self.description = QLabel()
+        self.description.setTextFormat(Qt.TextFormat.RichText)
+        self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
+        self.description.setOpenExternalLinks(False) # Handle the click internally
+            
+        self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
+        "This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
+        "Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
+        "The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
+        "An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
+
+        layout.addWidget(self.description)
+
+        help_text_a = "Select the SNIRF (.snirf) file to update with new event markers."
+
+        file_a_layout = QHBoxLayout()
+
+        # Help button on the left
+        help_btn_a = QPushButton("?")
+        help_btn_a.setFixedWidth(25)
+        help_btn_a.setToolTip(help_text_a)
+        help_btn_a.clicked.connect(lambda _, text=help_text_a: self.show_help_popup(text))
+        file_a_layout.addWidget(help_btn_a)
+
+        # Container for label + line_edit + browse button with tooltip
+        file_a_container = QWidget()
+        file_a_container_layout = QHBoxLayout()
+        file_a_container_layout.setContentsMargins(0, 0, 0, 0)
+        file_a_container_layout.addWidget(self.label_file_a)
+        file_a_container_layout.addWidget(self.line_edit_file_a)
+        file_a_container_layout.addWidget(self.btn_browse_a)
+        file_a_container.setLayout(file_a_container_layout)
+        file_a_container.setToolTip(help_text_a)
+
+        file_a_layout.addWidget(file_a_container)
+        layout.addLayout(file_a_layout)
+
+
+        help_text_b = "Provide a .boris project file that contains events for this participant."
+
+        file_b_layout = QHBoxLayout()
+
+        help_btn_b = QPushButton("?")
+        help_btn_b.setFixedWidth(25)
+        help_btn_b.setToolTip(help_text_b)
+        help_btn_b.clicked.connect(lambda _, text=help_text_b: self.show_help_popup(text))
+        file_b_layout.addWidget(help_btn_b)
+
+        file_b_container = QWidget()
+        file_b_container_layout = QHBoxLayout()
+        file_b_container_layout.setContentsMargins(0, 0, 0, 0)
+        file_b_container_layout.addWidget(self.label_file_b)
+        file_b_container_layout.addWidget(self.line_edit_file_b)
+        file_b_container_layout.addWidget(self.btn_browse_b)
+        file_b_container.setLayout(file_b_container_layout)
+        file_b_container.setToolTip(help_text_b)
+
+        file_b_layout.addWidget(file_b_container)
+        layout.addLayout(file_b_layout)
+
+
+        help_text_suffix = "This participant from the .boris project file matches the .snirf file."
+
+        suffix_layout = QHBoxLayout()
+
+        help_btn_suffix = QPushButton("?")
+        help_btn_suffix.setFixedWidth(25)
+        help_btn_suffix.setToolTip(help_text_suffix)
+        help_btn_suffix.clicked.connect(lambda _, text=help_text_suffix: self.show_help_popup(text))
+        suffix_layout.addWidget(help_btn_suffix)
+
+        suffix_container = QWidget()
+        suffix_container_layout = QHBoxLayout()
+        suffix_container_layout.setContentsMargins(0, 0, 0, 0)
+        suffix_container_layout.addWidget(self.label_suffix)
+        suffix_container_layout.addWidget(self.combo_suffix)
+        suffix_container.setLayout(suffix_container_layout)
+        suffix_container.setToolTip(help_text_suffix)
+
+        suffix_layout.addWidget(suffix_container)
+        layout.addLayout(suffix_layout)
+
+
+        help_text_suffix = "The events extracted from the BORIS project file for the selected observation."
+
+        suffix2_layout = QHBoxLayout()
+
+        help_btn_suffix = QPushButton("?")
+        help_btn_suffix.setFixedWidth(25)
+        help_btn_suffix.setToolTip(help_text_suffix)
+        help_btn_suffix.clicked.connect(lambda _, text=help_text_suffix: self.show_help_popup(text))
+        suffix2_layout.addWidget(help_btn_suffix)
+        
+        suffix2_container = QWidget()
+        suffix2_container_layout = QHBoxLayout()
+        suffix2_container_layout.setContentsMargins(0, 0, 0, 0)
+        suffix2_container_layout.addWidget(self.label_events)
+        suffix2_container_layout.addWidget(self.combo_events)
+        suffix2_container.setLayout(suffix2_container_layout)
+        suffix2_container.setToolTip(help_text_suffix)
+
+        suffix2_layout.addWidget(suffix2_container)
+        layout.addLayout(suffix2_layout)
+        
+        snirf_events_layout = QHBoxLayout()
+
+        help_text_snirf_events = "The event markers extracted from the SNIRF file."
+        help_btn_snirf_events = QPushButton("?")
+        help_btn_snirf_events.setFixedWidth(25)
+        help_btn_snirf_events.setToolTip(help_text_snirf_events)
+        help_btn_snirf_events.clicked.connect(lambda _, text=help_text_snirf_events: self.show_help_popup(text))
+        snirf_events_layout.addWidget(help_btn_snirf_events)
+
+        snirf_events_container = QWidget()
+        snirf_events_container_layout = QHBoxLayout()
+        snirf_events_container_layout.setContentsMargins(0, 0, 0, 0)
+        snirf_events_container_layout.addWidget(self.label_snirf_events)
+        snirf_events_container_layout.addWidget(self.combo_snirf_events)
+        snirf_events_container.setLayout(snirf_events_container_layout)
+        snirf_events_container.setToolTip(help_text_snirf_events)
+
+        snirf_events_layout.addWidget(snirf_events_container)
+        layout.addLayout(snirf_events_layout)
+
+        buttons_layout = QHBoxLayout()
+        buttons_layout.addStretch()
+        buttons_layout.addWidget(self.btn_clear)
+        buttons_layout.addWidget(self.btn_go)
+        layout.addLayout(buttons_layout)
+
+        self.setLayout(layout)
+
+
+    def show_help_popup(self, text):
+        msg = QMessageBox(self)
+        msg.setWindowTitle("Parameter Info")
+        msg.setText(text)
+        msg.exec()
+
+    def browse_file_a(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, "Select SNIRF File", "", "SNIRF Files (*.snirf)")
+        if file_path:
+            self.line_edit_file_a.setText(file_path)
+            try:
+                raw = read_raw_snirf(file_path, preload=False)
+                annotations = raw.annotations
+
+                # Build individual event entries
+                event_entries = []
+                for onset, description in zip(annotations.onset, annotations.description):
+                    event_str = f"{description} @ {onset:.3f}s"
+                    event_entries.append(event_str)
+
+                if not event_entries:
+                    QMessageBox.information(self, "No Events", "No events found in SNIRF file.")
+                    self.combo_snirf_events.clear()
+                    self.combo_snirf_events.setEnabled(False)
+                    return
+
+                self.combo_snirf_events.clear()
+                self.combo_snirf_events.addItems(event_entries)
+                self.combo_snirf_events.setEnabled(True)
+
+            except Exception as e:
+                QMessageBox.warning(self, "Error", f"Could not read SNIRF file with MNE:\n{str(e)}")
+                self.combo_snirf_events.clear()
+                self.combo_snirf_events.setEnabled(False)
+
+    def browse_file_b(self):
+        file_path, _ = QFileDialog.getOpenFileName(self, "Select BORIS File", "", "BORIS project Files (*.boris)")
+        if file_path:
+            self.line_edit_file_b.setText(file_path)
+            
+            try:
+                with open(file_path, 'r', encoding='utf-8') as f:
+                    data = json.load(f)
+                self.boris_data = data
+
+                observation_keys = self.extract_boris_observation_keys(data)
+                self.combo_suffix.clear()
+                self.combo_suffix.addItems(observation_keys)
+
+            except (json.JSONDecodeError, FileNotFoundError, KeyError) as e:
+                QMessageBox.warning(self, "Error", f"Failed to parse BORIS file:\n{e}")
+                
+    def extract_boris_observation_keys(self, data):
+        if "observations" not in data:
+            raise KeyError("Missing 'observations' key in BORIS file.")
+
+        observations = data["observations"]
+        if not isinstance(observations, dict):
+            raise TypeError("'observations' must be a dictionary.")
+
+        return list(observations.keys())
+    
+    def on_observation_selected(self):
+        selected_obs = self.combo_suffix.currentText()
+        if not selected_obs or not hasattr(self, 'boris_data'):
+            self.combo_events.clear()
+            self.combo_events.setEnabled(False)
+            return
+
+        try:
+            events = self.boris_data["observations"][selected_obs]["events"]
+        except (KeyError, TypeError):
+            self.combo_events.clear()
+            self.combo_events.setEnabled(False)
+            return
+
+        event_entries = []
+        for event in events:
+            if isinstance(event, list) and len(event) >= 3:
+                timestamp = event[0]
+                label = event[2]
+                display = f"{label} @ {timestamp:.3f}"
+                event_entries.append(display)
+
+        self.combo_events.clear()
+        self.combo_events.addItems(event_entries)
+        self.combo_events.setEnabled(bool(event_entries))
+
+    def clear_files(self):
+        self.line_edit_file_a.clear()
+        self.line_edit_file_b.clear()
+    
+    
+    def go_action(self):
+        
+        file_a = self.line_edit_file_a.text()
+        file_b = self.line_edit_file_b.text()
+        suffix = "flare" 
+    
+        if not hasattr(self, "boris_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
+            QMessageBox.warning(self, "Missing data", "Please make sure a BORIS and SNIRF event are selected.")
+            return
+
+        # Extract BORIS anchor
+        try:
+            boris_label, boris_time_str = self.combo_events.currentText().split(" @ ")
+            boris_anchor_time = float(boris_time_str.replace("s", "").strip())
+        except Exception as e:
+            QMessageBox.critical(self, "BORIS Event Error", f"Could not parse BORIS anchor event:\n{e}")
+            return
+
+        # Extract SNIRF anchor
+        try:
+            snirf_label, snirf_time_str = self.combo_snirf_events.currentText().split(" @ ")
+            snirf_anchor_time = float(snirf_time_str.replace("s", "").strip())
+        except Exception as e:
+            QMessageBox.critical(self, "SNIRF Event Error", f"Could not parse SNIRF anchor event:\n{e}")
+            return
+
+        time_shift = snirf_anchor_time - boris_anchor_time
+
+        selected_obs = self.combo_suffix.currentText()
+        if not selected_obs or selected_obs not in self.boris_data["observations"]:
+            QMessageBox.warning(self, "Invalid selection", "Selected observation not found in BORIS file.")
+            return
+
+        boris_events = self.boris_data["observations"][selected_obs].get("events", [])
+        if not boris_events:
+            QMessageBox.warning(self, "No BORIS events", "No events found in selected BORIS observation.")
+            return
+
+        snirf_path = self.line_edit_file_a.text()
+        if not snirf_path:
+            QMessageBox.warning(self, "No SNIRF file", "Please select a SNIRF file.")
+            return
+
+        base_name = os.path.splitext(os.path.basename(file_a))[0]
+        suggested_name = f"{base_name}_{suffix}.snirf"
+
+        # Open save dialog
+        save_path, _ = QFileDialog.getSaveFileName(
+            self,
+            "Save SNIRF File As",
+            suggested_name,
+            "SNIRF Files (*.snirf)"
+        )
+
+        if not save_path:
+            print("Save cancelled.")
+            return
+
+        if not save_path.lower().endswith(".snirf"):
+            save_path += ".snirf"
+
+        try:
+            raw = read_raw_snirf(snirf_path, preload=True)
+
+            # Build new Annotations from shifted BORIS events
+            onsets = []
+            durations = []
+            descriptions = []
+
+            label_counts = {}
+
+            used_times = set()
+            
+            sfreq = raw.info['sfreq']  # sampling frequency in Hz
+            min_shift = 1.0 / sfreq
+            
+            max_attempts = 10
+            
+            for event in boris_events:
+                if not isinstance(event, list) or len(event) < 3:
+                    continue
+
+                orig_time = event[0]
+                desc = event[2]
+
+                # Count occurrences per event label
+                count = label_counts.get(desc, 0)
+                label_counts[desc] = count + 1
+
+                # Only use 1st, 3rd, 5th... (odd occurrences)
+                if (count % 2) == 0:
+                    shifted_time = orig_time + time_shift
+
+                    # Ensure unique timestamp by checking and adjusting slightly
+                    adjusted_time = shifted_time
+
+                    # Try to find a unique timestamp
+                    attempts = 0
+                    while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                        adjusted_time += min_shift
+                        attempts += 1
+
+                    if attempts == max_attempts:
+                        print(f"Warning: Could not find unique timestamp for event '{desc}' at original time {orig_time:.3f}s. Skipping.")
+                        continue  # Skip problematic event
+
+                    adjusted_time = round(adjusted_time, 6)
+                    used_times.add(adjusted_time)
+
+                    print(f"Applying event: {desc} @ {adjusted_time:.3f}s (original: {orig_time:.3f}s)")
+
+                    onsets.append(adjusted_time)
+                    durations.append(0.0)
+                    descriptions.append(desc)
+
+            new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
+
+            # Replace annotations in raw object
+            raw.set_annotations(new_annotations)
+
+            # Write a new SNIRF file
+            write_raw_snirf(raw, suggested_name)
+
+            QMessageBox.information(self, "Success", "SNIRF file updated with aligned BORIS events.")
+
+        except Exception as e:
+            QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
+
+
+    def update_optode_positions(self, file_a, file_b, save_path):
+                
+        fiducials = {}
+        ch_positions = {}
+
+        # Read the lines from the optode file
+        with open(file_b, 'r') as f:
+            for line in f:
+                if line.strip():
+                    # Split by the semicolon and convert to meters
+                    ch_name, coords_str = line.split(":")
+                    coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
+
+                    # The key we have is a fiducial
+                    if ch_name.lower() in ['lpa', 'nz', 'rpa']:
+                        fiducials[ch_name.lower()] = coords
+
+                    # The key we have is a source or detector
+                    else:
+                        ch_positions[ch_name.upper()] = coords
+
+        # Create montage with updated coords in head space
+        initial_montage = make_dig_montage(ch_pos=ch_positions, nasion=fiducials.get('nz'), lpa=fiducials.get('lpa'), rpa=fiducials.get('rpa'), coord_frame='head') # type: ignore
+
+        # Read the SNIRF file, set the montage, and write it back
+        raw = read_raw_snirf(file_a, preload=True)
+        raw.set_montage(initial_montage)
+        write_raw_snirf(raw, save_path)
+
+
 class ProgressBubble(QWidget):
     """
     A clickable widget displaying a progress bar made of colored rectangles and a label.
@@ -2636,6 +3062,7 @@ class MainApplication(QMainWindow):
         self.about = None
         self.help = None
         self.optodes = None
+        self.events = None
         self.bubble_widgets = {}
         self.param_sections = []
         self.folder_paths = []
@@ -2868,12 +3295,13 @@ class MainApplication(QMainWindow):
             ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
             ("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
             ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
             ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
 
         for i, (name, shortcut, slot, icon) in enumerate(options_actions):
             options_menu.addAction(make_action(name, shortcut, slot, icon=icon))
-            if i == 1 or i == 2:  # after the first 2 actions (0,1)
+            if i == 1 or i == 3:  # after the first 2 actions (0,1)
                 options_menu.addSeparator()
 
         self.statusbar = self.statusBar()
@@ -2964,6 +3392,11 @@ class MainApplication(QMainWindow):
             self.optodes.show()
 
 
+    def update_event_markers(self):
+        if self.events is None or not self.events.isVisible():
+            self.events = UpdateEventsWindow(self)
+            self.events.show()
+
     def open_file_dialog(self):
         file_path, _ = QFileDialog.getOpenFileName(
             self, "Open File", "", "All Files (*);;Text Files (*.txt)"