Adds support for visual oddball ERP analysis after a recording comple…

…tes (#239)

* add: reload experiment button + end screen for visual oddball

* add: support for visual oddball analysis

analysis_api/app.py

@@ -9,6 +9,9 @@
 from flask_cors import CORS
 import base64
 import re
+import functools
+import numpy as np
+from scipy import stats
 
 import eeg
 import cocoa_pad
@@ -22,6 +25,24 @@ def encode_image_to_base64(image_path):
         encoded_string = base64.b64encode(image_file.read()).decode('utf-8')
     return encoded_string
 
+def compute_confidence_interval(data, confidence=0.95):
+    """
+    Compute the confidence interval for the provided data.
+
+    Parameters:
+    - data (np.array): Array of data points.
+    - confidence (float): Confidence level (default is 0.95).
+
+    Returns:
+    - ci_lower (np.array): Lower bound of the confidence interval.
+    - ci_upper (np.array): Upper bound of the confidence interval.
+    """
+    n = data.shape[0]
+    m = np.mean(data, axis=0)
+    se = stats.sem(data, axis=0)
+    h = se * stats.t.ppf((1 + confidence) / 2., n - 1)
+    return m - h, m + h
+
 # TODO: handle multiple files
 @app.route('/api/v1/process_eeg', methods=['POST'])
 def process_eeg():
@@ -94,11 +115,131 @@ def process_eeg():
         print("error", e)
         return jsonify({'error': str(e)}), 500
 
-# TODO: endpoint for ERP analysis
-@app.route('/api/v1/process_eeg_erp', methods=['POST'])
-def process_eeg_erp():
+def validate_eeg_file(func):
+    @functools.wraps(func)
+    def wrapper(*args, **kwargs):
+        if 'eegFile' not in request.files:
+            return jsonify({'error': 'No EEG file submitted for processing'}), 400
+        return func(*args, **kwargs)
+    return wrapper
+
+@app.route('/api/v1/process_visual_oddball', methods=['POST'])
+@validate_eeg_file
+def process_visual_oddball():
+    import matplotlib
+    matplotlib.use('Agg')
+    import matplotlib.pyplot as plt
+    import mne
+    import json
+    import io
     try:
-        return jsonify({'response': "works perfect"}), 200
+        eegFile = request.files['eegFile']
+        samplingFrequency = int(request.form['samplingFrequency'])
+        stimulusFile = request.files['stimulusFile']
+
+        # assumptions, eeg file is csv.. situmuls file is .json
+        eeg_df = pd.read_csv(eegFile)
+        eeg_df.drop(columns=['index'], inplace=True)
+        sfreq = samplingFrequency
+
+        # Find periods of interest that overlap both eeg and stimulus
+        eeg_timestamps = eeg_df['unixTimestamp'].tolist()
+        eeg_timestamps_range = (min(eeg_timestamps), max(eeg_timestamps))
+        stimulus_json = json.loads(stimulusFile.read().decode('utf-8'))
+        filtered_json_events = [trial for trial in stimulus_json['trials'] if 'unixTimestamp' in trial and 
+                            eeg_timestamps_range[0] <= trial['unixTimestamp'] <= eeg_timestamps_range[1]]
+        if len(filtered_json_events) == 0:
+            raise ValueError("No valid events found after filtering with the CSV timestamps range.")
+
+        # Create MNE events array from filtered JSON events
+        event_id = {'standard': 1, 'oddball': 2}
+        events = []
+        start_time = eeg_timestamps[0] / 1e3  # Convert to seconds #TODO: check if it's in milliseconds first
+        for trial in filtered_json_events:
+            if 'value' in trial:
+                if 'oddball' in trial['value']:
+                    event_type = event_id['oddball']
+                elif 'standard' in trial['value']:
+                    event_type = event_id['standard']
+                else:
+                    continue
+                event_time = trial['unixTimestamp'] / 1e3  # Convert to seconds
+                event_sample = int((event_time - start_time) * sfreq)
+                events.append([event_sample, 0, event_type])
+
+        events = np.array(events)
+        if len(events) == 0:
+            raise ValueError("No valid events found for creating epochs.")
+
+        # Create MNE Raw object
+        info = mne.create_info(ch_names=list(eeg_df.columns[1:]), sfreq=sfreq, ch_types='eeg')
+        eeg_df = eeg_df.values[:, 1:].T
+        eeg_df *= 1e-6 # convert from uV to V
+        raw = mne.io.RawArray(eeg_df, info)
+        raw.set_montage('standard_1020')
+
+        lfreq = 1
+        ufreq = 40
+
+        # Filter the data
+        raw.filter(lfreq, ufreq, fir_design='firwin')
+
+        # Create epochs
+        epochs = mne.Epochs(raw, events, event_id, tmin=-0.2, tmax=0.8, baseline=(None, 0), preload=True)
+
+        # Compute the average ERP for each condition
+        evoked_standard = epochs['standard'].average()
+        evoked_oddball = epochs['oddball'].average()
+
+        print("ERP data computed.")
+
+        # Plot the ERP for the standard and oddball stimulus
+        print("Plotting ERP for standard and oddball stimulus...")
+        fig, axes = plt.subplots(2, 2, figsize=(15, 10))
+        fig.suptitle('ERP for Standard and Oddball Stimulus')
+
+        for idx, ch_name in enumerate(evoked_standard.ch_names):
+            ax = axes[idx // 2, idx % 2]
+
+            # Plot standard ERP
+            ax.plot(evoked_standard.times, evoked_standard.data[idx], 
+                    label='Standard', color='blue')
+
+            # Plot oddball ERP
+            ax.plot(evoked_oddball.times, evoked_oddball.data[idx], 
+                    label='Oddball', color='red')
+
+            # Calculate and plot the difference waveform (Oddball - Standard)
+            # difference_wave = evoked_oddball.data[idx] - evoked_standard.data[idx]
+            # ax.plot(evoked_standard.times, difference_wave, 
+            #         label='Difference (Oddball - Standard)', color='green')
+
+            ax.axvline(0, color='k', linestyle='--', label='Stimulus Onset')
+            ax.set_title(f'Channel: {ch_name}')
+            ax.set_xlabel('Time (s)')
+            ax.set_ylabel('Amplitude (µV)')
+            ax.legend()
+            ax.grid(True)
+
+        plt.tight_layout()
+
+        # Save the plot to a BytesIO object
+        img_buffer = io.BytesIO()
+        plt.savefig(img_buffer, format='png')
+        img_buffer.seek(0)
+
+        # Encode the image to base64
+        img_str = base64.b64encode(img_buffer.getvalue()).decode()
+
+        # Create a dictionary with the image data
+        erp_plot = {
+            "key": "ERP Standard vs Oddball (All Channels)",
+            "value": f"data:image/png;base64,{img_str}",
+            "summary": "ERP plot for standard and oddball stimulus across all channels.\n Filtered between 1 and 40 Hz. Using MNE firwin"
+        }
+        plt.close() 
+
+        return jsonify({'images': [erp_plot], 'summary': "ERP Standard vs Oddball (All Channels)"}), 200
     except Exception as e:
         return jsonify({'error': 'error processing', 'message': e}), 500
 
@@ -124,8 +265,6 @@ def process_eeg_fooof():
         eegFile = request.files['eegFile']
         samplingFrequency = int(request.form['samplingFrequency'])
 
-        print("eegFile", eegFile)
-
         # Check if the file has a filename
         if eegFile.filename == '':
             return jsonify({'error': 'No selected EEG file'}), 400

frontend/public/experiments/visual_oddball.html

@@ -280,6 +280,12 @@
       trials.push(...relaxSequenceGenerator());
       trials.push(...oddballSequenceGenerator(40));
 
+      trials.push({
+        type: jsPsychHtmlButtonResponse,
+        stimulus: "Thank you for your time! We'll download and analyze your data.",
+        choices: [],
+      });
+
       jsPsych.run(trials);
     </script>
   </body>

frontend/src/components/lab/experiment.tsx

@@ -7,13 +7,12 @@ import { Button } from "../ui/button/button";
 
 import { connectToNeurosityDevice, useNeurosityState } from "~/hooks";
 import { neurosityService, neurosity } from "~/services";
-import { PlugZap } from "lucide-react";
+import { PlugZap, RotateCw } from "lucide-react";
 import { appInsights } from "~/utils/appInsights";
 import { IExperiment, EventData } from "~/@types";
 import SignalQuality from "./signalquality";
 import { Input } from "../ui";
 import dayjs from "dayjs";
-import exp from "constants";
 import { MuseContext } from "~/hooks/muse.context";
 import { MuseEEGService, NeuroFusionParsedEEG } from "~/services/integrations/muse.service";
 import { SignalViewer } from "./signalviewer";
@@ -273,6 +272,23 @@ export const Experiment: FC<IExperiment> = (experiment) => {
               allow="accelerometer; ambient-light-sensor; camera; encrypted-media; geolocation; gyroscope; hid; microphone; midi; payment; usb; vr; xr-spatial-tracking; download; fullscreen;"
               sandbox="allow-forms allow-downloads allow-modals allow-popups allow-presentation allow-same-origin allow-scripts"
             ></iframe>
+            <div className="mt-3 flex justify-end">
+              <Button
+                onClick={() => {
+                  if (experiment.url) {
+                    const iframe = document.querySelector("iframe") as HTMLIFrameElement;
+                    if (iframe) {
+                      iframe.src = iframe.src;
+                    }
+                  }
+                }}
+                size="sm"
+                intent="dark"
+                leftIcon={<RotateCw />}
+              >
+                Restart Experiment
+              </Button>
+            </div>
           </div>
         )}
         <>

frontend/src/pages/analysis.tsx

@@ -60,7 +60,8 @@ const AnalysisPage: NextPage = () => {
 
       try {
         setLoading(true);
-        const response = await fetch(`${process.env["NEXT_PUBLIC_ANALYSIS_SERVER_URL"]}/api/v1/process_eeg_fooof`, {
+        const urlEndpoint = stimulusFile ? "process_visual_oddball" : "process_eeg_fooof";
+        const response = await fetch(`${process.env["NEXT_PUBLIC_ANALYSIS_SERVER_URL"]}/api/v1/${urlEndpoint}`, {
           method: "POST",
           body: formData,
         });
@@ -233,9 +234,11 @@ export const getServerSideProps: GetServerSideProps = async ({ req, res }) => {
   const session = await getServerSession(req, res, authOptions);
 
   if (!session) {
+    // login the user
+    const currentUrl = `${req.url}`;
     return {
       redirect: {
-        destination: "/auth/login",
+        destination: `/auth/login?callbackUrl=${encodeURIComponent(currentUrl)}`,
         permanent: false,
       },
     };

frontend/src/pages/recordings.tsx

@@ -74,9 +74,11 @@ export const getServerSideProps: GetServerSideProps = async ({ req, res }) => {
   const session = await getServerSession(req, res, authOptions);
 
   if (!session) {
+    // login the user
+    const currentUrl = `${req.url}`;
     return {
       redirect: {
-        destination: "/auth/login",
+        destination: `/auth/login?callbackUrl=${encodeURIComponent(currentUrl)}`,
         permanent: false,
       },
     };