imptovements for blazes and fix fold again

flares.py

@@ -1743,7 +1743,7 @@ def fold_channels(raw: BaseRaw) -> None:
 
     # Locate the fOLD excel files
     if getattr(sys, 'frozen', False):
-        set_config('MNE_NIRS_FOLD_PATH', resource_path("/mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
+        set_config('MNE_NIRS_FOLD_PATH', resource_path("./mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
     else:
         path = os.path.expanduser("~") + "/mne_data/fOLD/fOLD-public-master/Supplementary"
         set_config('MNE_NIRS_FOLD_PATH', resource_path(path)) # type: ignore

main.py

@@ -46,7 +46,7 @@ from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleVa
 from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
-CURRENT_VERSION = "1.4.1"
+CURRENT_VERSION = "1.4.3"
 APP_NAME = "flares"
 API_URL = f"https://git.research.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
 API_URL_SECONDARY = f"https://git.research2.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
@@ -1413,44 +1413,44 @@ class UpdateEventsBlazesWindow(QWidget):
                 self.combo_snirf_events.setEnabled(False)
 
     def browse_file_b(self):
-        file_path, _ = QFileDialog.getOpenFileName(self, "Select BLAZES File", "", "BLAZES project Files (*.blaze)")
+        file_path, _ = QFileDialog.getOpenFileName(self, "Select JSON Timeline File", "", "JSON Files (*.json)")
         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.blazes_data = data
+                self.json_data = data
 
-                obs_keys = self.extract_blazes_observation_strings(data)
+                obs_keys = self.extract_json_observation_strings(data)
                 self.combo_events.clear()
                 if obs_keys:
                     self.combo_events.addItems(obs_keys)
                     self.combo_events.setEnabled(True)
                 else:
-                    QMessageBox.information(self, "No Events", "No observation keys found in BLAZES file.")
+                    QMessageBox.information(self, "No Events", "No events found in JSON file.")
                     self.combo_events.setEnabled(False)
 
             except (json.JSONDecodeError, FileNotFoundError, KeyError, TypeError) as e:
-                QMessageBox.warning(self, "Error", f"Failed to parse BLAZES file:\n{e}")
+                QMessageBox.warning(self, "Error", f"Failed to parse JSON file:\n{e}")
                 self.combo_events.clear()
                 self.combo_events.setEnabled(False)
                 
 
-    def extract_blazes_observation_strings(self, data):
+    def extract_json_observation_strings(self, data):
-        if "obs" not in data:
+        if "events" not in data:
-            raise KeyError("Missing 'obs' key in BLAZES file.")
+            raise KeyError("Missing 'events' key in JSON file.")
 
-        obs = data["obs"]
         event_strings = []
 
-        for event_name, occurrences in obs.items():
+        # The new format is a flat list chronologically ordered
-            # occurrences is a list of dicts: [{"start_frame": 642, "start_time_sec": 26.777, ...}]
+        for event in data["events"]:
-            for entry in occurrences:
+            track_name = event.get("track_name", "Unknown")
-                onset = entry.get("start_time_sec", 0.0)
+            onset = event.get("start_sec", 0.0)
-                # Formatting to match your SNIRF style: "Event Name @ 0.000s"
+            
-                display_str = f"{event_name} @ {onset:.3f}s"
+            # Formatting to match your SNIRF style: "Event Name @ 0.000s"
-                event_strings.append(display_str)
+            display_str = f"{track_name} @ {onset:.3f}s"
+            event_strings.append(display_str)
 
         return event_strings
     
@@ -1465,16 +1465,16 @@ class UpdateEventsBlazesWindow(QWidget):
         file_b = self.line_edit_file_b.text()
         suffix = APP_NAME
     
-        if not hasattr(self, "blazes_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
+        if not hasattr(self, "json_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
-            QMessageBox.warning(self, "Missing data", "Please make sure a BLAZES and SNIRF event are selected.")
+            QMessageBox.warning(self, "Missing data", "Please make sure a JSON and SNIRF event are selected.")
             return
 
         try:
-            blaze_text = self.combo_events.currentText()
+            json_text = self.combo_events.currentText()
-            _, blaze_time_str = blaze_text.split(" @ ")
+            _, json_time_str = json_text.split(" @ ")
-            blaze_anchor_time = float(blaze_time_str.replace("s", "").strip())
+            json_anchor_time = float(json_time_str.replace("s", "").strip())
         except Exception as e:
-            QMessageBox.critical(self, "BLAZE Event Error", f"Could not parse BLAZE anchor:\n{e}")
+            QMessageBox.critical(self, "JSON Event Error", f"Could not parse JSON anchor:\n{e}")
             return
 
         try:
@@ -1485,33 +1485,33 @@ class UpdateEventsBlazesWindow(QWidget):
             QMessageBox.critical(self, "SNIRF Event Error", f"Could not parse SNIRF anchor:\n{e}")
             return
 
-        time_shift = snirf_anchor_time - blaze_anchor_time
+        time_shift = snirf_anchor_time - json_anchor_time
 
         onsets, durations, descriptions = [], [], []
         skipped_count = 0
         
         try:
-            ai_data = self.blazes_data.get("ai_tracks", {})
+            events_list = self.json_data.get("events", [])
             
-            for track_name, events in ai_data.items():
+            for event in events_list:
+                track_name = event.get("track_name", "Unknown")
                 clean_name = track_name.replace("AI: ", "").strip()
                 
-                for event in events:
+                original_start = event.get("start_sec", 0.0)
-                    original_start = event.get("start_time_sec", 0.0)
+                original_end = event.get("end_sec", original_start)
-                    original_end = event.get("end_time_sec", original_start)
+                duration = original_end - original_start
-                    duration = original_end - original_start
 
-                    # FILTER: Minimum 0.1s duration
+                # FILTER: Minimum 0.1s duration
-                    if duration < 0.1:
+                if duration < 0.1:
-                        skipped_count += 1
+                    skipped_count += 1
-                        continue
+                    continue
 
-                    # Apply shift
+                # Apply shift
-                    adjusted_onset = original_start + time_shift
+                adjusted_onset = original_start + time_shift
 
-                    onsets.append(round(adjusted_onset, 6))
+                onsets.append(round(adjusted_onset, 6))
-                    durations.append(round(duration, 6))
+                durations.append(round(duration, 6))
-                    descriptions.append(clean_name) 
+                descriptions.append(clean_name) 
 
         except Exception as e:
             QMessageBox.critical(self, "Track Error", f"Failed to process tracks: {e}")
@@ -1538,7 +1538,7 @@ class UpdateEventsBlazesWindow(QWidget):
                     description=descriptions
                 )
                 
-                # Replace existing annotations with the new aligned AI tracks
+                # Replace existing annotations with the new aligned JSON tracks
                 raw.set_annotations(new_annotations)
                 
                 write_raw_snirf(raw, save_path)
@@ -1548,75 +1548,6 @@ class UpdateEventsBlazesWindow(QWidget):
                 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
-        # 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 ProgressBubble(QWidget):
     """