further variable changes

changelog.md

@@ -1,6 +1,7 @@
 # Version 1.2.0
+
 - Added new parameters to the right side of the screen
-- These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, and BINS.
+- These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, BINS, and VERBOSITY.
 - All the new parameters have default values matching the underlying values in version 1.1.7
 - The order of the parameters have changed to match the order that the code runs when the Process button is clicked
 - Moved TIME_WINDOW_START and TIME_WINDOW_END to the 'Other' category
@@ -12,6 +13,8 @@
 - Fixed a crash when attempting to fOLD channels without the fOLD dataset installed
 - Lowered the number of rectangles in the progress bar to 24 after combining some actions
 - Fixed the User Guide window to properly display information about the 24 stages and added a link to the Git wiki page
+- MAX_WORKERS should now properly repect the value set
+- Added a new CSV export option to be used by other applications
 
 
 # Version 1.1.7

flares.py

@@ -90,7 +90,7 @@ from mne_nirs.io.fold import fold_channel_specificity  # type: ignore
 from mne_nirs.preprocessing import peak_power  # type: ignore
 from mne_nirs.statistics._glm_level_first import RegressionResults  # type: ignore
 
-# Needs to be set for men
+# Needs to be set for mne
 os.environ["SUBJECTS_DIR"] = str(data_path()) + "/subjects" # type: ignore
 
 # TODO: Tidy this up
@@ -167,6 +167,8 @@ H_FREQ: float
 L_TRANS_BANDWIDTH: float
 H_TRANS_BANDWIDTH: float
 
+RESAMPLE: bool
+RESAMPLE_FREQ: int
 STIM_DUR: float
 HRF_MODEL: str
 DRIFT_MODEL: str
@@ -184,8 +186,8 @@ N_JOBS: int
 
 TIME_WINDOW_START: int
 TIME_WINDOW_END: int
-
+MAX_WORKERS: int
-VERBOSITY = True
+VERBOSITY: bool
 
 AGE = 25    # Assume 25 if not set from the GUI. This will result in a reasonable PPF
 GENDER = ""
@@ -1252,7 +1254,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
                 continue
 
             data = evoked.data[picks_idx, :].mean(axis=0)
-            t_start, t_end = 0, 15
+            t_start, t_end = 0, 15 #TODO: Is this in seconds? or is it 1hz input that makes it 15s?
             times_mask = (evoked.times >= t_start) & (evoked.times <= t_end)
             data_segment = data[times_mask]
             times_segment = evoked.times[times_mask]
@@ -1314,11 +1316,16 @@ def make_design_matrix(raw_haemo, short_chans):
     # Set the new annotations
     raw_haemo.set_annotations(new_annot)
 
-    raw_haemo.resample(1, npad="auto")
+    if RESAMPLE:
+        raw_haemo.resample(RESAMPLE_FREQ, npad="auto")
         raw_haemo._data = raw_haemo._data * 1e6
+        try:
+            short_chans.resample(RESAMPLE_FREQ)
+        except:
+            pass
+
     # 2) Create design matrix
-    if SHORT_CHANNEL:
+    if SHORT_CHANNEL_REGRESSION:
-        short_chans.resample(1)
         design_matrix = make_first_level_design_matrix(
             raw=raw_haemo,
             stim_dur=STIM_DUR,

main.py

@@ -22,6 +22,7 @@ import subprocess
 from pathlib import Path, PurePosixPath
 from datetime import datetime
 from multiprocessing import Process, current_process, freeze_support, Manager
+from enum import Enum, auto
 
 # External library imports
 import numpy as np
@@ -215,9 +216,10 @@ SECTIONS = [
     {
         "title": "Other",
         "params": [
-            {"name": "TIME_WINDOW_START", "default": "0", "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "TIME_WINDOW_START", "default": 0, "type": int, "help": "Where to start averaging the fir model bins. Only affects the significance and contrast images."},
-            {"name": "TIME_WINDOW_END", "default": "15", "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
+            {"name": "TIME_WINDOW_END", "default": 15, "type": int, "help": "Where to end averaging the fir model bins. Only affects the significance and contrast images."},
-            {"name": "MAX_WORKERS", "default": 4, "type": int, "help": "Number of files to be processed at once. Lowering this value may help on underpowered systems."},
+            {"name": "MAX_WORKERS", "default": 4, "type": str, "help": "Number of files to be processed at once. Setting this to a small integer value may help on underpowered systems. Remove the value to use an automatic amount."},
+            {"name": "VERBOSITY", "default": False, "type": bool, "help": "True will log lots of debugging information to the log file. False will only log required data."},
         ]
     },
 ]
@@ -766,15 +768,23 @@ class UpdateOptodesWindow(QWidget):
         write_raw_snirf(raw, save_path)
 
 
+class EventUpdateMode(Enum):
+    WRITE_SNIRF = auto()   # destructive
+    WRITE_JSON = auto()    # non-destructive
 
 
 class UpdateEventsWindow(QWidget):
 
-    def __init__(self, parent=None):
+    def __init__(self, parent=None, mode=EventUpdateMode.WRITE_SNIRF, caller=None):
         super().__init__(parent, Qt.WindowType.Window)
+
+        self.mode = mode
+        self.caller = caller or self.__class__.__name__
         self.setWindowTitle("Update event markers")
         self.resize(760, 200)
 
+        print("INIT MODE:", mode)
+
         self.label_file_a = QLabel("SNIRF file:")
         self.line_edit_file_a = QLineEdit()
         self.line_edit_file_a.setReadOnly(True)
@@ -1075,46 +1085,55 @@ class UpdateEventsWindow(QWidget):
             QMessageBox.warning(self, "No SNIRF file", "Please select a SNIRF file.")
             return
 
+
+        boris_obs = self.boris_data["observations"][selected_obs]
+
+        # --- Extract videos + delays ---
+        files = boris_obs.get("file", {})
+        offsets = boris_obs.get("media_info", {}).get("offset", {})
+
+        videos = {}
+        for key, path in files.items():
+            if path:  # only include videos that exist
+                delay = offsets.get(key, 0.0)  # default 0 if missing
+                videos[key] = {"file": path, "delay": delay}
+
+        base_name = os.path.splitext(os.path.basename(file_a))[0]
+
+        if self.mode == EventUpdateMode.WRITE_SNIRF:
+            # Open save dialog for SNIRF
             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.")
+                print("SNIRF save cancelled.")
                 return
-
             if not save_path.lower().endswith(".snirf"):
                 save_path += ".snirf"
 
             try:
-            raw = read_raw_snirf(snirf_path, preload=True)
+                raw = read_raw_snirf(file_a, preload=True)
-
-            onsets = []
-            durations = []
-            descriptions = []
 
+                # --- Align BORIS events to SNIRF ---
+                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']  # sampling frequency in Hz
+                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
 
@@ -1122,74 +1141,84 @@ class UpdateEventsWindow(QWidget):
                         open_events[label] = []
 
                     if count % 2 == 1:
-                    # Odd occurrence = start event
                         open_events[label].append(event_time)
                     else:
-                    # Even occurrence = end event
                         if open_events[label]:
-                        matched_start = open_events[label].pop(0)
+                            start_time = open_events[label].pop(0)
-                        duration = event_time - matched_start
+                            duration = event_time - start_time
-
                             if duration <= 0:
-                            print(f"Warning: Duration for {label} is non-positive ({duration}). Skipping.")
                                 continue
 
-                        shifted_start = matched_start + time_shift
+                            adjusted_time = start_time + time_shift
-
-                        adjusted_time = shifted_start
                             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: Couldn't find unique time for {label} @ {matched_start}s. Skipping.")
                                 continue
 
                             adjusted_time = round(adjusted_time, 6)
                             used_times.add(adjusted_time)
-
-                        print(f"Adding event: {label} @ {adjusted_time:.3f}s for {duration:.3f}s")
-
                             onsets.append(adjusted_time)
                             durations.append(duration)
                             descriptions.append(label)
-                    else:
+                # Handle unmatched starts
-                        print(f"Warning: Unmatched end for label '{label}' at {event_time:.3f}s. Skipping.")
-
-            # Optionally warn about any unmatched starts left open
                 for label, starts in open_events.items():
                     for start_time in starts:
-                    shifted_start = start_time + time_shift
+                        adjusted_time = start_time + time_shift
-
-                    adjusted_time = shifted_start
                         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: Couldn't find unique time for unmatched start {label} @ {start_time}s. Skipping.")
                             continue
-
                         adjusted_time = round(adjusted_time, 6)
                         used_times.add(adjusted_time)
-
-                    print(f"Warning: Unmatched start for label '{label}' at {start_time:.3f}s. Adding with duration 0.")
                         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}")
 
+        elif self.mode == EventUpdateMode.WRITE_JSON:
+            # Open save dialog for JSON
+            base_name = os.path.splitext(os.path.basename(file_a))[0]
+            suggested_name = f"{base_name}_{suffix}_alignment.json"
+            save_path, _ = QFileDialog.getSaveFileName(
+                self,
+                "Save Event Alignment JSON As",
+                suggested_name,
+                "JSON Files (*.json)"
+            )
+            if not save_path:
+                print("JSON save cancelled.")
+                return
+            if not save_path.lower().endswith(".json"):
+                save_path += ".json"
+
+            # Build JSON dict
+            json_data = {
+                "observation": selected_obs,
+                "snirf_anchor": {"label": snirf_label, "time": snirf_anchor_time},
+                "boris_anchor": {"label": boris_label, "time": boris_anchor_time},
+                "time_shift": time_shift,
+                "videos": videos
+            }
+
+            # Write JSON
+            try:
+                with open(save_path, "w", encoding="utf-8") as f:
+                    json.dump(json_data, f, indent=4)
+                QMessageBox.information(self, "Success", f"Event alignment saved to:\n{save_path}")
+            except Exception as e:
+                QMessageBox.critical(self, "Error", f"Failed to write JSON:\n{e}")
+
 
     def update_optode_positions(self, file_a, file_b, save_path):
                 
@@ -1221,6 +1250,47 @@ class UpdateEventsWindow(QWidget):
         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
+    ):
+        import json
+        from datetime import datetime
+        import os
+
+        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):
     """
     A clickable widget displaying a progress bar made of colored rectangles and a label.
@@ -2506,7 +2576,7 @@ class ExportDataAsCSVViewerWidget(QWidget):
               
         self.index_texts = [
             "0 (Export Data to CSV)",
-            # "1 (second image)",
+            "1 (CSV for SPARKS)",
             # "2 (third image)",
             # "3 (fourth image)",
             ]
@@ -2658,7 +2728,6 @@ class ExportDataAsCSVViewerWidget(QWidget):
         # Pass the necessary arguments to each method
         for file_path in selected_file_paths:
             haemo_obj = self.haemo_dict.get(file_path)
-
             if haemo_obj is None:
                 continue
 
@@ -2692,10 +2761,63 @@ class ExportDataAsCSVViewerWidget(QWidget):
                         QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
 
 
+                elif idx == 1:
+                    try:
+                        suggested_name = f"{file_path}_sparks.csv"
+
+                        # Open save dialog
+                        save_path, _ = QFileDialog.getSaveFileName(
+                            self,
+                            "Save SNIRF File As",
+                            suggested_name,
+                            "CSV Files (*.csv)"
+                        )
+
+                        if not save_path:
+                            print("Save cancelled.")
+                            return
+
+                        if not save_path.lower().endswith(".csv"):
+                            save_path += ".csv"
+                        # Save the CSV here
+                        
+                        raw = haemo_obj
+
+                        data, times = raw.get_data(return_times=True)
+
+
+                        ann_col = np.full(times.shape, "", dtype=object)
+
+                        if raw.annotations is not None and len(raw.annotations) > 0:
+                            for onset, duration, desc in zip(
+                                raw.annotations.onset,
+                                raw.annotations.duration,
+                                raw.annotations.description
+                            ):
+                                mask = (times >= onset) & (times < onset + duration)
+                                ann_col[mask] = desc
+
+                        df = pd.DataFrame(data.T, columns=raw.ch_names)
+                        df.insert(0, "annotation", ann_col)
+
+                        df.insert(0, "time", times)
+                        df.to_csv(save_path, index=False)
+                        QMessageBox.information(self, "Success", "CSV file has been saved.")
+
+                        win = UpdateEventsWindow(
+                            parent=self,
+                            mode=EventUpdateMode.WRITE_JSON,
+                            caller="Video Alignment Tool"
+                        )
+                        win.show()
+
+                    except Exception as e:
+                        QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
+
+
                 else:
                     print(f"No method defined for index {idx}")
 
-
 class ClickableLabel(QLabel):
     def __init__(self, full_pixmap: QPixmap, thumbnail_pixmap: QPixmap):
         super().__init__()
@@ -4321,7 +4443,7 @@ class MainApplication(QMainWindow):
 
     def update_event_markers(self):
         if self.events is None or not self.events.isVisible():
-            self.events = UpdateEventsWindow(self)
+            self.events = UpdateEventsWindow(self, EventUpdateMode.WRITE_SNIRF, "Manual SNIRF Edit")
             self.events.show()
 
     def open_file_dialog(self):