start of plugin support?

changelog.md

@@ -1,6 +1,8 @@
 # Version 1.7.1
 
-- Fixed an issue where the application could not automatically update between versions 1.5.1 to 1.7.1. Sorry!
+- Fixed an issue where the application could not automatically update between versions 1.5.1 to 1.7.1. Sorry! 1.7.1 upgrading onward should be fixed and more robust
+- Fixed an issue where some log files would not generate, or would generate in an incorrect location
+- Fixed an issue where updating events in a snirf file would not release memory properly
 
 
 # Version 1.7.0

flares.py

@@ -105,7 +105,7 @@ from mne_nirs.statistics._glm_level_first import RegressionResults  # type: igno
 from mne_connectivity.viz import plot_connectivity_circle # type: ignore
 from mne_connectivity import envelope_correlation, spectral_connectivity_epochs, spectral_connectivity_time # type: ignore
 
-from src.shared.shareddata import PLATFORM_NAME, resource_path
+from src.shared.shareddata import PLATFORM_NAME, resource_path, get_app_dir
 
 
 
@@ -162,42 +162,7 @@ QC_METRIC_LABELS = {
     "total_processing_seconds": "Processing Time (s)",
 }
 
-
+ROI_MAP = {} # TODO: Should be grabbed from the json file
-ROI_MAP = {
-    'ROI_OccipitoParietal_BA18_19_7': [
-        'S1_D1', 'S1_D2', 'S4_D3'
-    ],
-    'ROI_SuperiorParietal_BA7_5': [
-        'S2_D1', 'S3_D1', 'S2_D2', 'S2_D4', 'S4_D4'
-    ],
-    'ROI_TPJ_AngularGyrus_BA39_19_40': [
-        'S4_D2', 'S5_D3', 'S4_D5', 'S5_D5'
-    ],
-    # --- SPLIT BA40 REGIONS ---
-    'ROI_Posterior_BA40_Parietal': [
-        'S6_D4', 'S6_D5'
-    ],
-    'ROI_Anterior_BA40_Sensorimotor': [
-        'S10_D5', 'S8_D5'
-    ],
-    # --------------------------
-    'ROI_Supramarginal_Inferior_BA40_6': [
-        'S6_D6'
-    ],
-    'ROI_VentralSomatosensory_BA1_2_3_43_48': [
-        'S8_D6', 'S9_D6'
-    ],
-    'ROI_Sensorimotor_BA1_2_3_4_6': [
-        'S6_D8', 'S10_D8'
-    ],
-    'ROI_DLPFC_FEF_BA6_8_9': [
-        'S7_D7', 'S7_D8'
-    ],
-    'ROI_Broca_VLPFC_BA6_44_45_4': [
-        'S9_D7', 'S10_D7'
-    ]
-}
-
 
 DOWNSAMPLE: bool
 DOWNSAMPLE_FREQUENCY: int
@@ -345,24 +310,20 @@ FEATURE_2: bool = False
 script_dir = os.path.dirname(os.path.abspath(__file__))
 os.chdir(script_dir)
 
+
 # Configure logging to file with timestamps and realtime flush
 if PLATFORM_NAME == 'darwin':
-    logging.basicConfig(
+    log_path = os.path.abspath(os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"))
-        filename=os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"),  # Needed to get out of the bundled application
-        level=logging.INFO,
-        format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
-        datefmt='%Y-%m-%d %H:%M:%S',
-        filemode='a'
-    )
-
 else:
-    logging.basicConfig(
+    log_path = os.path.join(get_app_dir(), "fnirs_analysis.log")
-        filename='fnirs_analysis.log',
+
-        level=logging.INFO,
+logging.basicConfig(
-        format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
+    filename=log_path,
-        datefmt='%Y-%m-%d %H:%M:%S',
+    level=logging.INFO,
-        filemode='a'
+    format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
-    )
+    datefmt='%Y-%m-%d %H:%M:%S',
+    filemode='a'
+)
 
 logger = logging.getLogger()
 
@@ -514,7 +475,8 @@ def process_multiple_participants(file_paths, file_params, file_metadata,
     success_count = {"value": 0}
     failed_stages = {"value": []}
     qc_rows: list[dict[str, Any]] = []
-    qc_summary_path="qc_summary.xlsx"
+    if qc_summary_path is None:
+        qc_summary_path = os.path.join(get_app_dir(), "qc_summary.xlsx")
 
     def elapsed_heartbeat():
         # Ticks once a second so the GUI can show a live-updating timer,

main.py

@@ -36,6 +36,7 @@ from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is no
 from file_ext_registration import register_file_association, ELEVATION_FLAG
 from project_manager import ProjectManager
 from src.window.about import AboutWindow
+from src.window.plugins import PluginsWindow
 from src.window.terminal import TerminalWindow
 from src.window.updateevents import EventUpdateMode, UpdateEventsBlazesWindow, UpdateEventsWindow
 from src.window.updateoptodes import UpdateOptodesWindow
@@ -43,7 +44,7 @@ from src.window.userguide import UserGuideWindow
 from src.window.viewerlauncher import ViewerLauncherWidget
 from src.window.welcome import WelcomeDialog
 from src.shared.flaresbasewidget import FilePickerWidget, ParamSection, ProgressBubble
-from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA
+from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA, get_app_dir
 from startup_args import parse_startup_args
 from updater import finish_update_if_needed, UpdateManager, LocalPendingUpdateCheckThread
 
@@ -556,6 +557,7 @@ class MainApplication(QMainWindow):
         self.optodes = None
         self.events = None
         self.events_blazes = None
+        self.plugins = None
         self.terminal = None
         self.bubble_widgets = {}
         self.param_sections = []
@@ -910,6 +912,13 @@ class MainApplication(QMainWindow):
             preferences_menu.addAction(action)
             self.pref_actions[config_key] = action
 
+        plugins_menu = menu_bar.addMenu("Plugins")
+        plugins_actions = [
+            ("Plugin Manager", "Ctrl+Alt+P", self.plugins_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
+        ]
+        for name, shortcut, slot, icon in plugins_actions:
+            plugins_menu.addAction(make_action(name, shortcut, slot, icon=icon))
+
         terminal_menu = menu_bar.addMenu("Terminal")
         terminal_actions = [
             ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
@@ -1316,6 +1325,11 @@ class MainApplication(QMainWindow):
                     QMessageBox.Ok
                 )
 
+    def plugins_gui(self):
+        if self.plugins is None or not self.plugins.isVisible():
+            self.plugins = PluginsWindow(self)
+            self.plugins.show()
+
     def terminal_gui(self):
         if self.terminal is None or not self.terminal.isVisible():
             self.terminal = TerminalWindow(self)
@@ -2746,12 +2760,13 @@ if __name__ == "__main__":
         log_path = os.path.join(os.path.dirname(sys.executable), f"../../../{APP_NAME}.log")
         cfg_path = os.path.join(os.path.dirname(sys.executable), f"../../../{APP_NAME}.cfg")
     else:
-        log_path = os.path.join(os.getcwd(), f"{APP_NAME}.log")
+        log_path = os.path.join(get_app_dir(), f"{APP_NAME}.log")
-        cfg_path = os.path.join(os.getcwd(), f"{APP_NAME}.cfg")
+        cfg_path = os.path.join(get_app_dir(), f"{APP_NAME}.cfg")
     try:
-        os.remove(log_path)
+        if os.path.exists(log_path):
-    except:
+            os.remove(log_path)
-        pass
+    except Exception as e:
+        print(f"Warning: Could not remove old log file: {e}")
 
     sys.stdout = open(log_path, "a", buffering=1)
     sys.stderr = sys.stdout
@@ -2778,4 +2793,4 @@ if __name__ == "__main__":
         window.show()
         sys.exit(app.exec())
 
-# Not 2600 lines yay!
+# Not 2800 lines yay!

project_manager.py

@@ -15,6 +15,7 @@ import copy
 import pickle
 import concurrent
 import configparser
+import concurrent.futures
 from pathlib import Path, PurePosixPath
 from typing import TYPE_CHECKING, Any, List, Optional, Union
 
@@ -719,7 +720,7 @@ def _get_bids_demographics(snirf_path: str) -> dict[str, str]:
         return {}
 
     def _row_to_dict(row: pd.Series) -> dict[str, str]:
-        result = {}
+        result: dict[str, str] = {}
         for field in fields:
             if field not in row:
                 continue

pylance_progress

@@ -1,7 +1,6 @@
 src\analysis\participantfoldchannels.py  158
-src\shared\flaresbasewidget.py  1001+
+src\shared\flaresbasewidget.py  1155
-src\window\updateevents.py  83
+flares.py  2900
-flares.py  1001+
+main_unit_tests.py  152
-main_unit_tests.py  153
+main.py  732
-main.py  691
+project_manager.py 109
-project_manager.py 113

src/shared/shareddata.py

@@ -13,7 +13,7 @@ import sys
 import platform
 
 
-CURRENT_VERSION = "1.7.0"
+CURRENT_VERSION = "1.7.1"
 APP_NAME = "flares"
 APP_NAME_EXPANDED = "fNIRS Lightweight Analysis, Research, & Evaluation Suite"
 API_URL = f"https://git.research.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"

src/window/plugins.py

@@ -0,0 +1,224 @@
+"""
+Filename: plugins.py
+Description: Plugins window
+Note: Compliant with pylance strict type checking
+
+Author: Tyler de Zeeuw
+License: GPL-3.0
+"""
+
+# Built-in imports
+import json
+import sys
+import urllib.request
+from pathlib import Path
+from typing import Any, cast
+
+# External library imports
+from PySide6.QtCore import Qt
+from PySide6.QtWidgets import QHBoxLayout, QLabel, QLineEdit, QListWidget, QListWidgetItem, QPushButton, QTabWidget, QVBoxLayout, QWidget
+
+from src.shared.shareddata import APP_NAME, PLATFORM_NAME, PLUGINS_URL
+
+
+class PluginsWindow(QWidget):
+    """
+    Plugins window containing two tabs: Installed Plugins and Plugin Browser.
+
+    Args:
+        parent (QWidget | None, optional): Parent widget of this window. Defaults to None.
+    """
+
+    def __init__(self, parent: QWidget | None = None) -> None:
+        super().__init__(parent, Qt.WindowType.Window)
+        self.setWindowTitle(f"{APP_NAME.upper()} - Plugins")
+        self.resize(650, 500)
+
+        self.plugins_dir: Path = self._resolve_plugins_dir()
+        self.repository_urls: list[str] = [PLUGINS_URL]
+        self.remote_plugins_data: list[dict[str, Any]] = []
+        self._has_fetched_remote: bool = False
+
+        main_layout = QVBoxLayout(self)
+
+        self.tab_widget = QTabWidget(self)
+        self.installed_tab = self._create_installed_tab()
+        self.browser_tab = self._create_browser_tab()
+
+        self.tab_widget.addTab(self.installed_tab, "Installed Plugins")
+        self.tab_widget.addTab(self.browser_tab, "Plugin Browser")
+
+        self.tab_widget.setCurrentIndex(0)
+        self.tab_widget.currentChanged.connect(self._on_tab_changed)
+
+        main_layout.addWidget(self.tab_widget)
+        self.setLayout(main_layout)
+
+        self.refresh_installed_plugins()
+
+    def _resolve_plugins_dir(self) -> Path:
+        """Determines the local plugins directory based on execution context."""
+        if PLATFORM_NAME == "darwin":
+            base_dir = Path(sys.executable).parent / "../../.."
+        else:
+            base_dir = Path.cwd()
+
+        return (base_dir / "plugins").resolve()
+
+    def _on_tab_changed(self, index: int) -> None:
+        """Triggers remote fetch only when switching specifically to the Plugin Browser tab."""
+        if index == 1 and not self._has_fetched_remote:
+            self.fetch_remote_plugins()
+
+    def refresh_installed_plugins(self) -> None:
+        """Scans local plugins directory silently without UI popups."""
+        self.installed_list.clear()
+        self.plugins_dir.mkdir(parents=True, exist_ok=True)
+
+        installed_plugins: list[str] = []
+
+        for entry in self.plugins_dir.iterdir():
+            if entry.is_dir() and not entry.name.startswith((".", "__")):
+                installed_plugins.append(entry.name)
+            elif entry.is_file() and entry.suffix == ".py" and entry.stem != "__init__":
+                installed_plugins.append(entry.stem)
+
+        if installed_plugins:
+            self.installed_list.addItems(sorted(installed_plugins))
+        else:
+            self.installed_list.addItem("No plugins installed.")
+
+    def add_custom_repository(self) -> None:
+        """Adds a custom repository URL from the input field and refreshes the browser list."""
+        url = self.repo_input.text().strip()
+        if not url:
+            return
+
+        if not (url.startswith("http://") or url.startswith("https://")):
+            self._show_browser_error("Invalid URL format. Must start with http:// or https://")
+            return
+
+        if url not in self.repository_urls:
+            self.repository_urls.append(url)
+
+        self.repo_input.clear()
+        self.fetch_remote_plugins()
+
+    def fetch_remote_plugins(self) -> None:
+        """
+        Fetches plugins.json from all configured repository URLs directly into memory.
+        Aggregates results and handles network failures gracefully in-line.
+        """
+        self.browser_list.clear()
+        self.browser_list.addItem("Fetching remote repositories...")
+
+        aggregated_plugins: list[dict[str, Any]] = []
+        failed_count: int = 0
+
+        for url in self.repository_urls:
+            try:
+                req = urllib.request.Request(
+                    url,
+                    headers={"User-Agent": f"{APP_NAME}-PluginManager"},
+                )
+                with urllib.request.urlopen(req, timeout=5) as response:
+                    if response.status == 200:
+                        raw_data = response.read().decode("utf-8")
+                        plugins = json.loads(raw_data)
+                        if isinstance(plugins, list):
+                            aggregated_plugins.extend(cast(list[Any], plugins))
+                    else:
+                        failed_count += 1
+            except Exception:
+                failed_count += 1
+
+        self.remote_plugins_data = aggregated_plugins
+        self._has_fetched_remote = True
+
+        if aggregated_plugins:
+            self._populate_browser_list()
+        elif failed_count == len(self.repository_urls):
+            self._show_browser_error(
+                "Unable to load plugins from any repository. Check your connection or URLs."
+            )
+        else:
+            self._show_browser_error("No plugins found across configured repositories.")
+
+    def _show_browser_error(self, message: str) -> None:
+        """Renders error text directly in the list widget."""
+        self.browser_list.clear()
+        self.browser_list.addItem(message)
+
+    def _populate_browser_list(self) -> None:
+        """Populates list widget with parsed remote plugin data."""
+        self.browser_list.clear()
+
+        for plugin in self.remote_plugins_data:
+            name = plugin.get("name", "Unknown Plugin")
+            version = plugin.get("version", "v0.0")
+            desc = plugin.get("description", "No description provided.")
+
+            display_text = f"{name} ({version}) - {desc}"
+            item = QListWidgetItem(display_text, self.browser_list)
+            item.setData(Qt.ItemDataRole.UserRole, plugin)
+
+    def _create_installed_tab(self) -> QWidget:
+        """Creates 'Installed Plugins' tab UI."""
+        tab = QWidget()
+        layout = QVBoxLayout(tab)
+
+        path_label = QLabel(f"Directory: {self.plugins_dir}", tab)
+        self.installed_list = QListWidget(tab)
+
+        button_layout = QHBoxLayout()
+        self.btn_refresh_local = QPushButton("Refresh List", tab)
+        self.btn_enable_disable = QPushButton("Enable/Disable", tab)
+        self.btn_uninstall = QPushButton("Uninstall", tab)
+
+        self.btn_refresh_local.clicked.connect(self.refresh_installed_plugins)
+
+        button_layout.addWidget(self.btn_refresh_local)
+        button_layout.addStretch()
+        button_layout.addWidget(self.btn_enable_disable)
+        button_layout.addWidget(self.btn_uninstall)
+
+        layout.addWidget(path_label)
+        layout.addWidget(self.installed_list)
+        layout.addLayout(button_layout)
+
+        return tab
+
+    def _create_browser_tab(self) -> QWidget:
+        """Creates 'Plugin Browser' tab UI."""
+        tab = QWidget()
+        layout = QVBoxLayout(tab)
+
+        # Custom Repository Input Controls
+        repo_layout = QHBoxLayout()
+        self.repo_input = QLineEdit(tab)
+        self.repo_input.setPlaceholderText("Enter custom plugins.json URL...")
+        self.btn_add_repo = QPushButton("Add Repo", tab)
+        self.btn_add_repo.clicked.connect(self.add_custom_repository)
+
+        repo_layout.addWidget(self.repo_input)
+        repo_layout.addWidget(self.btn_add_repo)
+
+        label = QLabel("Available Plugins from Repositories:", tab)
+        self.browser_list = QListWidget(tab)
+
+        button_layout = QHBoxLayout()
+        self.btn_fetch_remote = QPushButton("Fetch Remote Lists", tab)
+        self.btn_install = QPushButton("Install Plugin", tab)
+
+        self.btn_fetch_remote.clicked.connect(self.fetch_remote_plugins)
+
+        button_layout.addWidget(self.btn_fetch_remote)
+        button_layout.addStretch()
+        button_layout.addWidget(self.btn_install)
+
+        layout.addLayout(repo_layout)
+        layout.addWidget(label)
+        layout.addWidget(self.browser_list)
+        layout.addLayout(button_layout)
+
+        return tab

src/window/updateevents.py

@@ -1,6 +1,7 @@
 """
 Filename: updateevents.py
-Description: Methods to update snirf events for FLARES
+Description: Methods to update snirf events
+Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
@@ -9,27 +10,184 @@ License: GPL-3.0
 # Built-in imports
 import os
 import json
+import concurrent.futures
 from enum import Enum, auto
-from typing import Any, List, Optional, cast
+from typing import Any, List, Optional, Sequence, Union, cast
 
 # External library imports
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QLineEdit, QPushButton, QComboBox, QHBoxLayout, QMessageBox, QFileDialog
 from PySide6.QtCore import Qt
 
 from mne import Annotations
-from mne.io import read_raw_snirf #type: ignore
+from mne.io import read_raw_snirf  #type: ignore
-from mne_nirs.io import write_raw_snirf #type: ignore
+from mne_nirs.io import write_raw_snirf  #type: ignore
 
+from mne.io.base import BaseRaw
 from src.shared.shareddata import APP_NAME
 
 
+def _load_annotations_worker(file_path: str) -> Annotations:
+    """Isolated worker process to load SNIRF annotations without leaving HDF5 memory leaks in main process."""
+    raw: BaseRaw = read_raw_snirf(file_path, preload=False, verbose=False)
+    return cast(Annotations, getattr(raw, "annotations"))
+
+
+def load_snirf_annotations_isolated(file_path: str) -> Annotations:
+    """Spawns a short-lived process to extract annotations and cleanly releases C-memory allocations."""
+    with concurrent.futures.ProcessPoolExecutor(max_workers=1) as executor:
+        future = executor.submit(_load_annotations_worker, file_path)
+        return future.result()
+
+
+def _write_snirf_worker(
+    file_path: str,
+    save_path: str,
+    onsets: list[float],
+    durations: list[float],
+    descriptions: list[str]
+) -> None:
+    """Isolated process worker to read, annotate, write, and immediately free memory/file handles."""
+    raw = read_raw_snirf(file_path, preload=True, verbose=False)
+    new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
+    raw.set_annotations(new_annotations)  #type: ignore
+    write_raw_snirf(raw, save_path)
+
+
+def write_snirf_with_annotations_isolated(
+    file_path: str,
+    save_path: str,
+    onsets: list[float],
+    durations: list[float],
+    descriptions: list[str]
+) -> None:
+    """Executes SNIRF writing in a dedicated worker process to ensure 100% memory/handle cleanup."""
+    with concurrent.futures.ProcessPoolExecutor(max_workers=1) as executor:
+        future = executor.submit(
+            _write_snirf_worker,
+            file_path,
+            save_path,
+            onsets,
+            durations,
+            descriptions
+        )
+        future.result()
+
+
+def _align_boris_and_write_snirf_worker(
+    file_path: str,
+    save_path: str,
+    boris_events: list[Any],
+    time_shift: float
+) -> int:
+    """
+    Isolated process worker to read SNIRF, align BORIS events, write updated file,
+    and cleanly exit releasing all HDF5 C-memory allocations and file locks.
+    """
+    raw = read_raw_snirf(file_path, preload=True, verbose=False)
+
+    # Type-safe extraction of sampling frequency from raw.info
+    info_dict = cast(dict[str, Any], raw.info)
+    sfreq = float(info_dict.get("sfreq", 10.0))
+    min_shift = 1.0 / sfreq if sfreq > 0 else 0.1
+    max_attempts = 10
+
+    onsets: list[float] = []
+    durations: list[float] = []
+    descriptions: list[str] = []
+
+    open_events: dict[str, list[float]] = {}
+    label_counts: dict[str, int] = {}
+    used_times: set[float] = set()
+
+    for raw_event in boris_events:
+        if not isinstance(raw_event, (list, tuple)):
+            continue
+        
+        event = cast(Sequence[Any], raw_event)
+
+        if len(event) < 3:
+            continue
+
+        event_time = float(event[0])
+        label = str(event[2])
+
+        count = label_counts.get(label, 0) + 1
+        label_counts[label] = count
+
+        if label not in open_events:
+            open_events[label] = []
+
+        if count % 2 == 1:
+            open_events[label].append(event_time)
+        else:
+            if open_events[label]:
+                start_time = open_events[label].pop(0)
+                duration = event_time - start_time
+                if duration <= 0:
+                    continue
+
+                adjusted_time = start_time + time_shift
+                attempts = 0
+                while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                    adjusted_time += min_shift
+                    attempts += 1
+                if attempts == max_attempts:
+                    continue
+
+                adjusted_time = round(adjusted_time, 6)
+                used_times.add(adjusted_time)
+                onsets.append(adjusted_time)
+                durations.append(round(duration, 6))
+                descriptions.append(label)
+
+    # Handle unmatched start markers
+    for label, starts in open_events.items():
+        for start_time in starts:
+            adjusted_time = start_time + time_shift
+            attempts = 0
+            while round(adjusted_time, 6) in used_times and attempts < max_attempts:
+                adjusted_time += min_shift
+                attempts += 1
+            if attempts == max_attempts:
+                continue
+            adjusted_time = round(adjusted_time, 6)
+            used_times.add(adjusted_time)
+            onsets.append(adjusted_time)
+            durations.append(0.0)
+            descriptions.append(label)
+
+    new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
+    raw.set_annotations(new_annotations)  #type: ignore
+    write_raw_snirf(raw, save_path)
+
+    return len(onsets)
+
+
+def align_boris_and_write_snirf_isolated(
+    file_path: str,
+    save_path: str,
+    boris_events: list[Any],
+    time_shift: float
+) -> int:
+    """Executes BORIS alignment and SNIRF writing in a dedicated worker process."""
+    with concurrent.futures.ProcessPoolExecutor(max_workers=1) as executor:
+        future = executor.submit(
+            _align_boris_and_write_snirf_worker,
+            file_path,
+            save_path,
+            boris_events,
+            time_shift
+        )
+        return future.result()
+    
+
 class EventUpdateMode(Enum):
     WRITE_SNIRF = auto()   # destructive
     WRITE_JSON = auto()    # non-destructive
 
 
 class UpdateEventsWindow(QWidget):
-    def __init__(self, parent: Optional[QWidget]=None, mode=EventUpdateMode.WRITE_SNIRF, caller=None):
+    def __init__(self, parent: Optional[QWidget]=None, mode: EventUpdateMode=EventUpdateMode.WRITE_SNIRF, caller: Optional[Union[str, object]] = None,):
         super().__init__(parent, Qt.WindowType.Window)
 
         self.mode = mode
@@ -210,12 +368,13 @@ class UpdateEventsWindow(QWidget):
         if file_path:
             self.line_edit_file_a.setText(file_path)
             try:
-                # TODO: Bad! read_raw_snirf doesnt release memory properly! Should be spawned in a seperate process and killed once completed
+                # Memory leak safe: Extracted in a separate process that terminates immediately
-                raw = read_raw_snirf(file_path, preload=False)
+                annotations: Annotations = load_snirf_annotations_isolated(file_path)
-                annotations = raw.annotations
+                
+                print(f"Loaded {len(annotations)} annotations from {file_path}")
 
                 # Build individual event entries
-                event_entries = []
+                event_entries: list[str] = []
                 for onset, description in zip(annotations.onset, annotations.description):
                     event_str = f"{description} @ {onset:.3f}s"
                     event_entries.append(event_str)
@@ -252,6 +411,7 @@ class UpdateEventsWindow(QWidget):
             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: dict[str, Any]) -> List[str]:
         if "observations" not in data:
             raise KeyError("Missing 'observations' key in BORIS file.")
@@ -274,11 +434,16 @@ class UpdateEventsWindow(QWidget):
             self.combo_events.setEnabled(False)
             return
 
-        event_entries = []
+        event_entries: list[str] = []
-        for event in events:
+        for raw_event in events:
-            if isinstance(event, list) and len(event) >= 3:
+            if not isinstance(raw_event, (list, tuple)):
-                timestamp = event[0]
+                continue
-                label = event[2]
+
+            event = cast(Sequence[Any], raw_event)
+
+            if len(event) >= 3:
+                timestamp = float(event[0])
+                label = str(event[2])
                 display = f"{label} @ {timestamp:.3f}"
                 event_entries.append(display)
 
@@ -363,71 +528,15 @@ class UpdateEventsWindow(QWidget):
                 save_path += ".snirf"
 
             try:
-                raw = read_raw_snirf(file_a, preload=True)
+                # Memory leak safe: Worker handles alignment calculation, read, write, and process termination
+                event_count = align_boris_and_write_snirf_isolated(
+                    file_a,
+                    save_path,
+                    boris_events,
+                    time_shift
+                )
 
-                # --- Align BORIS events to SNIRF ---
+                QMessageBox.information(self, "Success", f"SNIRF file updated with {event_count} aligned BORIS events.")
-                boris_events = boris_obs.get("events", [])
-                onsets, durations, descriptions = [], [], []
-                open_events = {}  # label -> list of start times
-                label_counts = {}
-                used_times = set()
-                sfreq = raw.info['sfreq']
-                min_shift = 1.0 / sfreq
-                max_attempts = 10
-
-                for event in boris_events:
-                    if not isinstance(event, list) or len(event) < 3:
-                        continue
-                    event_time = event[0]
-                    label = event[2]
-                    count = label_counts.get(label, 0) + 1
-                    label_counts[label] = count
-
-                    if label not in open_events:
-                        open_events[label] = []
-
-                    if count % 2 == 1:
-                        open_events[label].append(event_time)
-                    else:
-                        if open_events[label]:
-                            start_time = open_events[label].pop(0)
-                            duration = event_time - start_time
-                            if duration <= 0:
-                                continue
-
-                            adjusted_time = start_time + time_shift
-                            attempts = 0
-                            while round(adjusted_time, 6) in used_times and attempts < max_attempts:
-                                adjusted_time += min_shift
-                                attempts += 1
-                            if attempts == max_attempts:
-                                continue
-
-                            adjusted_time = round(adjusted_time, 6)
-                            used_times.add(adjusted_time)
-                            onsets.append(adjusted_time)
-                            durations.append(duration)
-                            descriptions.append(label)
-                # Handle unmatched starts
-                for label, starts in open_events.items():
-                    for start_time in starts:
-                        adjusted_time = start_time + time_shift
-                        attempts = 0
-                        while round(adjusted_time, 6) in used_times and attempts < max_attempts:
-                            adjusted_time += min_shift
-                            attempts += 1
-                        if attempts == max_attempts:
-                            continue
-                        adjusted_time = round(adjusted_time, 6)
-                        used_times.add(adjusted_time)
-                        onsets.append(adjusted_time)
-                        durations.append(0.0)
-                        descriptions.append(label)
-
-                new_annotations = Annotations(onset=onsets, duration=durations, description=descriptions)
-                raw.set_annotations(new_annotations)
-                write_raw_snirf(raw, save_path)
-                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}")
@@ -466,79 +575,9 @@ class UpdateEventsWindow(QWidget):
                 QMessageBox.critical(self, "Error", f"Failed to write JSON:\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
-    #     # TODO: Bad! read_raw_snirf doesnt release memory properly! Should be spawned in a seperate process and killed once completed
-    #     raw = read_raw_snirf(file_a, preload=True)
-    #     raw.set_montage(initial_montage)
-    #     write_raw_snirf(raw, save_path)
-
-
-    # def _apply_events_to_snirf(self, raw, new_annotations, save_path):
-    #     raw.set_annotations(new_annotations)
-    #     write_raw_snirf(raw, save_path)
-        
-    # def _write_event_mapping_json(
-    #     self,
-    #     file_a,
-    #     file_b,
-    #     selected_obs,
-    #     snirf_anchor,
-    #     boris_anchor,
-    #     time_shift,
-    #     mapped_events,
-    #     save_path
-    # ):
-
-    #     payload = {
-    #         "source": {
-    #             "called_from": self.caller,
-    #             "snirf_file": os.path.basename(file_a),
-    #             "boris_file": os.path.basename(file_b),
-    #             "observation": selected_obs
-    #         },
-    #         "alignment": {
-    #             "snirf_anchor": snirf_anchor,
-    #             "boris_anchor": boris_anchor,
-    #             "time_shift_seconds": time_shift
-    #         },
-    #         "events": mapped_events,
-    #         "created_at": datetime.utcnow().isoformat() + "Z"
-    #     }
-
-    #     with open(save_path, "w", encoding="utf-8") as f:
-    #         json.dump(payload, f, indent=2)
-
-    #     return save_path
-
-
-
 class UpdateEventsBlazesWindow(QWidget):
 
-    def __init__(self, parent: Optional[QWidget]=None, mode=EventUpdateMode.WRITE_SNIRF, caller=None):
+    def __init__(self, parent: Optional[QWidget]=None, mode: EventUpdateMode=EventUpdateMode.WRITE_SNIRF, caller: Optional[Union[str, object]] = None,):
         super().__init__(parent, Qt.WindowType.Window)
 
         self.mode = mode
@@ -692,12 +731,13 @@ class UpdateEventsBlazesWindow(QWidget):
         if file_path:
             self.line_edit_file_a.setText(file_path)
             try:
-                # TODO: Bad! read_raw_snirf doesnt release memory properly! Should be spawned in a seperate process and killed once completed
+                # Memory leak safe: Extracted in a separate process that terminates immediately
-                raw = read_raw_snirf(file_path, preload=False)
+                annotations: Annotations = load_snirf_annotations_isolated(file_path)
-                annotations = raw.annotations
+                
+                print(f"Loaded {len(annotations)} annotations from {file_path}")
 
                 # Build individual event entries
-                event_entries = []
+                event_entries: list[str] = []
                 for onset, description in zip(annotations.onset, annotations.description):
                     event_str = f"{description} @ {onset:.3f}s"
                     event_entries.append(event_str)
@@ -748,12 +788,11 @@ class UpdateEventsBlazesWindow(QWidget):
 
         event_strings: List[str] = []
 
-        # The new format is a flat list chronologically ordered
+        # Flat list chronologically ordered
         for event in data["events"]:
             track_name = event.get("track_name", "Unknown")
             onset = event.get("start_sec", 0.0)
             
-            # Formatting to match your SNIRF style: "Event Name @ 0.000s"
             display_str = f"{track_name} @ {onset:.3f}s"
             event_strings.append(display_str)
 
@@ -792,7 +831,9 @@ class UpdateEventsBlazesWindow(QWidget):
 
         time_shift = snirf_anchor_time - json_anchor_time
 
-        onsets, durations, descriptions = [], [], []
+        onsets: list[float] = []
+        durations: list[float] = []
+        descriptions: list[str] = []
         skipped_count = 0
         
         try:
@@ -806,7 +847,7 @@ class UpdateEventsBlazesWindow(QWidget):
                 original_end = event.get("end_sec", original_start)
                 duration = original_end - original_start
 
-                # FILTER: Minimum 0.1s duration
+                # Minimum 0.1s duration
                 if duration < 0.1:
                     skipped_count += 1
                     continue
@@ -834,19 +875,9 @@ class UpdateEventsBlazesWindow(QWidget):
             if not save_path.lower().endswith(".snirf"): save_path += ".snirf"
 
             try:
-                raw = read_raw_snirf(file_a, preload=True)
+                # Memory leak safe: Worker handles read, write, and complete memory reclamation upon exit
+                write_snirf_with_annotations_isolated(file_a, save_path, onsets, durations, descriptions)
 
-                # Create annotations
-                new_annotations = Annotations(
-                    onset=onsets, 
-                    duration=durations, 
-                    description=descriptions
-                )
-                
-                # Replace existing annotations with the new aligned JSON tracks
-                raw.set_annotations(new_annotations)
-                
-                write_raw_snirf(raw, save_path)
                 QMessageBox.information(self, "Success", 
                     f"Aligned {len(onsets)} events.\n(Filtered out {skipped_count} short events)")
             except Exception as e:

src/window/updateoptodes.py

@@ -1,6 +1,6 @@
 """
 Filename: updateoptodes.py
-Description: Methods to update optode locations for FLARES
+Description: Methods to update optode locations
 Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-import os
 from pathlib import Path
 from typing import Dict, Optional, Union