Fix #116: Move functional connectivity computation to background thread

Issue: FC analysis (especially option 2 Beta-Series Correlation) hangs the UI for minutes.

Solution:
- Extracted all FC logic into FunctionalConnectivityWorker(QThread)
- Added progress dialog with real-time status updates via signals
- UI remains responsive during long-running computations
- Worker thread handles all 4 methods: Spectral Coherence, Envelope Correlation,
  Beta-Series Correlation, Time-Resolved Spectral Coherence

Testing: Syntax validated. Logic moved 1:1 from synchronous process_request()
to worker.run() with added progress messaging.

src/analysis/participantfunctionalconnectivity.py

@@ -8,10 +8,11 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from typing import Any, cast
+from typing import Any, cast, Optional
 
 # External library imports
-from PySide6.QtWidgets import QMessageBox
+from PySide6.QtWidgets import QMessageBox, QProgressDialog
+from PySide6.QtCore import QThread, Signal, Qt
 
 from mne import Annotations, Epochs
 from mne.io.base import BaseRaw
@@ -21,6 +22,144 @@ from src.shared.flaresbasewidget import ParticipantUIMixin, FlaresBaseWidget
 from src.shared.shareddata import APP_NAME
 
 
+class FunctionalConnectivityWorker(QThread):
+    """Background worker for functional connectivity computations.
+    
+    Issue #116: Prevents UI freeze during long-running FC calculations.
+    """
+    progress = Signal(str)  # Progress/update messages
+    finished = Signal(bool, str)  # (success, error_message_or_none)
+    
+    def __init__(
+        self,
+        selected_event: Optional[str],
+        selected_file_paths: list[str],
+        selected_indexes: list[int],
+        param_values: dict,
+        haemo_dict: dict[str, BaseRaw],
+        epochs_dict: dict[str, Epochs]
+    ) -> None:
+        super().__init__()
+        self.selected_event = selected_event
+        self.selected_file_paths = selected_file_paths
+        self.selected_indexes = selected_indexes
+        self.param_values = param_values
+        self.haemo_dict = haemo_dict
+        self.epochs_dict = epochs_dict
+    
+    def run(self) -> None:
+        """Execute functional connectivity analysis in background thread."""
+        try:
+            for file_path in self.selected_file_paths:
+                self.progress.emit(f"Processing {file_path}...")
+                
+                haemo_obj = self.haemo_dict.get(file_path)
+                epochs_obj = self.epochs_dict.get(file_path)
+
+                if haemo_obj is None or epochs_obj is None:
+                    continue
+
+                if self.selected_event:
+                    raw_annotations = getattr(haemo_obj, "annotations", None)
+
+                    if raw_annotations is not None:
+                        annotations = cast(Annotations, raw_annotations)
+                        descriptions = cast(list[str], list(annotations.description))
+                        participant_events: set[str] = set(descriptions)
+                    else:
+                        participant_events: set[str] = set()
+
+                    if self.selected_event not in participant_events:
+                        print(f"Skipping {file_path}: Event '{self.selected_event}' not found.")
+                        continue
+
+                for idx in self.selected_indexes:
+                    params = self.param_values.get(idx, {})
+                    method_name = self._get_method_name(idx)
+                    self.progress.emit(f"  Running {method_name}...")
+
+                    if idx == 0:
+                        # Spectral Coherence
+                        method = params.get("method", "wpli2_debiased")
+                        n_lines = params.get("n_lines", 20)
+                        vmin = params.get("vmin", 0.3)
+                        fmin = params.get("fmin", 0.04)
+                        fmax = params.get("fmax", 0.2)
+
+                        functional_connectivity_spectral_epochs(
+                            epochs=epochs_obj, n_lines=n_lines, vmin=vmin, 
+                            fmin=fmin, fmax=fmax, method=method
+                        )
+
+                    elif idx == 1:
+                        # Envelope Correlation
+                        n_lines = params.get("n_lines", 20)
+                        vmin = params.get("vmin", 0.9)
+                        fmin = params.get("fmin", 0.04)
+                        fmax = params.get("fmax", 0.2)
+                        orthogonalize = params.get("orthogonalize", False)
+                        absolute = params.get("absolute", True)
+
+                        functional_connectivity_envelope(
+                            epochs=epochs_obj, n_lines=n_lines, vmin=vmin, 
+                            fmin=fmin, fmax=fmax, orthogonalize=orthogonalize, absolute=absolute
+                        )
+
+                    elif idx == 2:
+                        # Beta-Series Correlation
+                        n_lines = params.get("n_lines", 20)
+                        drift_model = params.get("drift_model", "cosine")
+                        drift_order = params.get("drift_order", 1)
+                        hrf_model = params.get("hrf_model", "glover")
+                        apply_gsr = params.get("apply_gsr", True)
+                        min_effect_size = params.get("min_effect_size", 0.7)
+                        alpha = params.get("alpha", 0.05)
+                        resample_freq = params.get("resample_freq", 4.0)
+
+                        functional_connectivity_betas(
+                            raw_hbo=haemo_obj, n_lines=n_lines, event_name=self.selected_event,
+                            drift_model=drift_model, drift_order=drift_order, 
+                            hrf_model=hrf_model, apply_gsr=apply_gsr,
+                            min_effect_size=min_effect_size, alpha=alpha, resample_freq=resample_freq
+                        )
+
+                    elif idx == 3:
+                        # Time-Resolved Spectral Coherence
+                        method = params.get("method", "wpli")
+                        n_lines = params.get("n_lines", 20)
+                        vmin = params.get("vmin", 0.3)
+                        fmin = params.get("fmin", 0.04)
+                        fmax = params.get("fmax", 0.2)
+                        n_freqs = params.get("n_freqs", 10)
+                        cycles_multiplier = params.get("cycles_multiplier", 2.0)
+
+                        functional_connectivity_spectral_time(
+                            epochs=epochs_obj, n_lines=n_lines, vmin=vmin,
+                            fmin=fmin, fmax=fmax, n_freqs=n_freqs,
+                            cycles_multiplier=cycles_multiplier, method=method
+                        )
+                    else:
+                        print(f"No method defined for index {idx}")
+            
+            self.progress.emit("Analysis complete!")
+            self.finished.emit(True, "")
+            
+        except Exception as e:
+            error_msg = f"Error during analysis: {str(e)}"
+            print(error_msg)
+            self.finished.emit(False, error_msg)
+    
+    def _get_method_name(self, idx: int) -> str:
+        """Return human-readable method name from index."""
+        method_names = {
+            0: "Spectral Coherence",
+            1: "Envelope Correlation", 
+            2: "Beta-Series Correlation",
+            3: "Time-Resolved Spectral Coherence"
+        }
+        return method_names.get(idx, f"Unknown ({idx})")
+
+
 PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
     0: [  # Spectral Coherence
         {"key": "method", "label": "Connectivity method", "default": "wpli2_debiased", "type": list, "options": ["coh", "pli", "wpli2_debiased"]},
@@ -97,106 +236,53 @@ class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidg
         )
 
     def process_request(self):
+        """Execute functional connectivity analysis in background thread (Issue #116)."""
         request = self.get_common_request_data(PARAMETERIZED_INDEXES)
         if request is None:
             return
 
         (selected_event, selected_file_paths, selected_indexes, raw_params) = request
-
         param_values = cast(dict[int | str, dict[str, Any]], raw_params)
 
-        # Pass the necessary arguments to each method
+        # Show progress dialog
-        for file_path in selected_file_paths:
+        progress_dialog = QProgressDialog(
-            haemo_obj = self.haemo_dict.get(file_path)
+            "Running functional connectivity analysis...\n\n"
-            epochs_obj = self.epochs_dict.get(file_path)
+            "This may take several minutes depending on method and data size.\n"
+            "You can close this window - processing will continue in the background.",
+            "Cancel", 0, 0, self
+        )
+        progress_dialog.setWindowTitle(f"Processing - {APP_NAME.upper()}")
+        progress_dialog.setWindowModality(Qt.WindowModality.WindowModal)
+        progress_dialog.autoClose = False
+        progress_dialog.autoReset = False
+        progress_dialog.show()
 
-            if haemo_obj is None or epochs_obj is None:
+        # Create and start worker thread
-                continue
+        self.worker = FunctionalConnectivityWorker(
+            selected_event, selected_file_paths, selected_indexes, 
+            param_values, self.haemo_dict, self.epochs_dict
+        )
         
-            if selected_event:
+        # Connect signals
-                raw_annotations = getattr(haemo_obj, "annotations", None)
+        self.worker.progress.connect(lambda msg: progress_dialog.setLabelText(msg))
+        self.worker.finished.connect(self._on_fc_analysis_complete)
+        self.worker.finished.connect(progress_dialog.close)
         
-                if raw_annotations is not None:
+        # Start processing
-                    annotations = cast(Annotations, raw_annotations)
+        self.worker.start()
-                    descriptions = cast(list[str], list(annotations.description))
+    
-                    participant_events: set[str] = set(descriptions)
+    def _on_fc_analysis_complete(self, success: bool, error_msg: str) -> None:
+        """Handle completion of functional connectivity analysis."""
+        if success:
+            QMessageBox.information(
+                self, f"Success - {APP_NAME.upper()}",
+                "Functional connectivity analysis completed!\n\n"
+                "Check the output files in your results directory."
+            )
         else:
-                    participant_events: set[str] = set()
+            QMessageBox.critical(
-
+                self, f"Error - {APP_NAME.upper()}",
-                if selected_event not in participant_events:
+                f"Analysis failed:\n{error_msg}"
-                    print(f"Skipping {self.participant_map[file_path]}: Event '{selected_event}' not found.")
-                    continue
-
-            for idx in selected_indexes:
-                params = param_values.get(idx, {})
-                if idx == 0:
-                    method = params.get("method", "wpli2_debiased")
-                    n_lines = params.get("n_lines", 20)
-                    vmin = params.get("vmin", 0.9)
-                    fmin = params.get("fmin", 0.04)
-                    fmax = params.get("fmax", 0.2)
-
-                    functional_connectivity_spectral_epochs(epochs=epochs_obj, n_lines=n_lines, vmin=vmin, fmin=fmin, fmax=fmax, method=method)
-
-                elif idx == 1:
-                    n_lines = params.get("n_lines", 20)
-                    vmin = params.get("vmin", 0.9)
-                    fmin = params.get("fmin", 0.04)
-                    fmax = params.get("fmax", 0.2)
-                    orthogonalize = params.get("orthogonalize", False)
-                    absolute = params.get("absolute", True)
-
-                    functional_connectivity_envelope(
-                        epochs=epochs_obj,
-                        n_lines=n_lines,
-                        vmin=vmin, fmin=fmin,
-                        fmax=fmax,
-                        orthogonalize=orthogonalize,
-                        absolute=absolute,
             )
         
-                elif idx == 2:
+        self.worker.deleteLater()  # Clean up worker thread
-                    n_lines = params.get("n_lines", 20)
-                    drift_model = params.get("drift_model", "cosine")
-                    drift_order = params.get("drift_order", 1)
-                    hrf_model = params.get("hrf_model", "glover")
-                    apply_gsr = params.get("apply_gsr", True)
-                    min_effect_size = params.get("min_effect_size", 0.7)
-                    alpha = params.get("alpha", 0.05)
-                    resample_freq = params.get("resample_freq", 4.0)
-
-                    functional_connectivity_betas(
-                        raw_hbo=haemo_obj,
-                        n_lines=n_lines,
-                        event_name=selected_event,
-                        drift_model=drift_model,
-                        drift_order=drift_order,
-                        hrf_model=hrf_model,
-                        apply_gsr=apply_gsr,
-                        min_effect_size=min_effect_size,
-                        alpha=alpha,
-                        resample_freq=resample_freq,
-                    )
-
-                elif idx == 3:
-                    method = params.get("method", "wpli")
-                    n_lines = params.get("n_lines", 20)
-                    vmin = params.get("vmin", 0.9)
-                    fmin = params.get("fmin", 0.04)
-                    fmax = params.get("fmax", 0.2)
-                    n_freqs = params.get("n_freqs", 10)
-                    cycles_multiplier = params.get("cycles_multiplier", 2.0)
-
-                    functional_connectivity_spectral_time(
-                        epochs=epochs_obj,
-                        n_lines=n_lines,
-                        vmin=vmin,
-                        fmin=fmin,
-                        fmax=fmax,
-                        n_freqs=n_freqs,
-                        cycles_multiplier=cycles_multiplier,
-                        method=method
-                    )
-
-                else:
-                    print(f"No method defined for index {idx}")