Analysis Page: Display fft and 1/f summaries after a recording comple…

…tes (#236)


* add: display fooof results after dataset upload

.github/workflows/staging_fusion-staging.yml

@@ -31,6 +31,8 @@ jobs:
           echo "NEXT_PUBLIC_FUSION_RELAY_URL=${{ secrets.NEXT_PUBLIC_FUSION_RELAY_URL }}" >> .env.production
           echo "NEXT_PUBLIC_FUSION_NOSTR_PUBLIC_KEY=${{ secrets.NEXT_PUBLIC_FUSION_NOSTR_PUBLIC_KEY }}" >> .env.production
           echo "NEXT_PUBLIC_NEUROFUSION_BACKEND_URL=${{ secrets.NEXT_PUBLIC_NEUROFUSION_BACKEND_URL }}" >> .env.production
+          echo "NEXT_PUBLIC_ANALYSIS_SERVER_URL=${{ secrets.NEXT_PUBLIC_ANALYSIS_SERVER_URL }}" >> .env.production
+          echo "NEXT_PUBLIC_APP_INSIGHTS_KEY=${{ secrets.NEXT_PUBLIC_APP_INSIGHTS_KEY }}" >> .env.production
           npm run build --if-present
           npm run test --if-present
 

README.md

@@ -15,22 +15,21 @@ We build tools to accelerate the adoption of neurotechnology and behavior resear
   - [x] Resting state (Eyes Closed/Eyes Open)
   - [x] Stroop Task
   - [x] Auditory Oddball
+  - [x] Visual Oddball
   - [x] Flappy Bird game (Detecting intent & frustration)
 
 - [ ] Analysis of collected data https://usefusion.ai/analysis
 
   - [x] Chart of steady state frequency power across recordings
-  - [ ] Periodic vs. aperiodic frequency evaluation using [fooof package](https://fooof-tools.github.io/fooof/)
+  - [x] Periodic vs. aperiodic frequency evaluation using [fooof package](https://fooof-tools.github.io/fooof/)
   - [ ] If applicable event related potential analysis
 
 - [ ] Running Distributed Studies with people (Quests) https://usefusion.ai/blog/quests
 
   - [x] A set of prompts people respond to at intervals on a topic related to you
   - [x] Connecting Apple Health - steps, sleep, heart-rate
-  - [ ] Support for cognitive experiments
-  - [ ] Quest Dashboard - view submissions, analyze and publish results
-
-- [ ] Design and upload custom EEG experiment protocols to participants' devices
+  - [x] Quest Dashboard - view submissions, analyze and publish results
+  - [ ] Design and upload custom EEG experiment protocols to participants' devices
 
 - [ ] Connecting Other Sources
   - [ ] Connect your screentime events & productivity metrics using [ActivityWatch](https://activitywatch.net)

analysis_api/.gitignore

@@ -1,4 +1,5 @@
 temp_unzip
 powerComparisons.png
 powerDistributions.png
-.env
+.env
+fooof_outputs

analysis_api/app.py

@@ -95,40 +95,117 @@ def process_eeg():
         return jsonify({'error': str(e)}), 500
 
 # TODO: endpoint for ERP analysis
+@app.route('/api/v1/process_eeg_erp', methods=['POST'])
+def process_eeg_erp():
+    try:
+        return jsonify({'response': "works perfect"}), 200
+    except Exception as e:
+        return jsonify({'error': 'error processing', 'message': e}), 500
 
 @app.route('/api/v1/process_eeg_fooof', methods=['POST'])
 def process_eeg_fooof():
+    """
+    When a person uploads an EEG file, we need to process it and return the FOOOF results
+    as images"""
     try:
-        # Check if the POST request contains a file with the key 'file'
-        if 'file' not in request.files:
-            return jsonify({'error': 'No file part'}), 400
+        import matplotlib
+        matplotlib.use('Agg')
+        import matplotlib.pyplot as plt
+        from fooof import FOOOFGroup
+        import mne
+        import io
+        import base64
+        import time
 
-        if 'fileTimestamp' not in request.form:
-            return jsonify({'error': 'No file timestamp'}), 400
+        # Check if the POST request contains a file with the key 'file'
+        if 'eegFile' not in request.files:
+            return jsonify({'error': 'No EEG file submitted for processing'}), 400
 
-        file = request.files['file']
+        eegFile = request.files['eegFile']
+        samplingFrequency = int(request.form['samplingFrequency'])
 
-        fileTimestamp = request.form['fileTimestamp']
+        print("eegFile", eegFile)
 
         # Check if the file has a filename
-        if file.filename == '':
-            return jsonify({'error': 'No selected file'}), 400
+        if eegFile.filename == '':
+            return jsonify({'error': 'No selected EEG file'}), 400
+
+        if eegFile.filename.endswith('.csv'):
+            # Read the CSV file into a pandas DataFrame
+            df = pd.read_csv(eegFile)
+            df.drop(columns=['index'], inplace=True)
+            sfreq = samplingFrequency
+            info = mne.create_info(ch_names=list(df.columns[1:]), sfreq=sfreq, ch_types='eeg')
+
+            # transpose data
+            df = df.values[:, 1:].T
+            df *= 1e-6 # convert from uV to V
+            raw = mne.io.RawArray(df, info)
+            raw.set_montage('standard_1020')
 
-        # Check if the file is a ZIP file
-        if file.filename.endswith('.zip'):
-            # Create a temporary directory to store the unzipped files
-            temp_dir = 'temp_unzip' # +`` "_" + str(int(time.time()))
-            os.makedirs(temp_dir, exist_ok=True)
+            events = mne.make_fixed_length_events(raw, duration=5)
+            epochs = mne.Epochs(raw, events, tmin=0, tmax=0.5, baseline=None)
 
-            # Save the ZIP file to the temporary directory
-            zip_file_path = os.path.join(temp_dir, file.filename)
-            file.save(zip_file_path)
+            epochsSpectrum = epochs.compute_psd(fmin=1, fmax=40, method='welch', verbose=False)
+
+            fg = FOOOFGroup(peak_width_limits=[1.0, 8.0], min_peak_height=0.1, peak_threshold=2.)
+            fg.fit(epochsSpectrum.freqs, epochsSpectrum.average().get_data(), freq_range=[1, 40])
 
-            # Unzip the file
-            with zipfile.ZipFile(zip_file_path, 'r') as zip_ref:
-                zip_ref.extractall(temp_dir + "/raw_files")
+            temp_dir = 'fooof_outputs'
+            os.makedirs(temp_dir, exist_ok=True)
+            file_name = f"fooof_results_{int(time.time())}.png"
+            fg.save_report(file_name, file_path=temp_dir)
+
+            images = [{
+                "key": "FOOOF - Group Results",
+                "value": "data:image/png;base64," + encode_image_to_base64(temp_dir + "/" + file_name)
+            }]
+
+            # Get the FOOOF results for each channel
+            ch_names = raw.info['ch_names']
+            for i in range(len(ch_names)):
+                result = fg.get_fooof(i)
+
+                # Print the result
+                results = result.get_results()
+                results_str = (
+                    f" FOOOF - POWER SPECTRUM MODEL\n\n"
+                    f"The model was run on the frequency range {result.freq_range[0]:.2f} - {result.freq_range[1]:.2f} Hz\n"
+                    f"Frequency Resolution is {result.freq_res:.2f} Hz\n\n"
+                    f"Aperiodic Parameters (offset, exponent):\n"
+                    f"{results.aperiodic_params[0]:.4f}, {results.aperiodic_params[1]:.4f}\n\n"
+                    f"{len(results.peak_params)} peaks were found:\n"
+                )
+                for peak in results.peak_params:
+                    results_str += f"CF: {peak[0]:6.2f}, PW: {peak[1]:6.3f}, BW: {peak[2]:6.2f}\n"
+                results_str += (
+                    f"\nGoodness of fit metrics:\n"
+                    f"R^2 of model fit is {results.r_squared:.4f}\n"
+                    f"Error of the fit is {results.error:.4f}"
+                )
+                fig, ax = plt.subplots()
+
+                # Plot the result
+                result.plot(ax=ax, show=False)
+
+                # Save the plot to a BytesIO object
+                img_buffer = io.BytesIO()
+                fig.savefig(img_buffer, format='png')
+                img_buffer.seek(0)
+                plt.close(fig)
+
+                # Encode the image to base64
+                img_str = base64.b64encode(img_buffer.getvalue()).decode()
+
+                # Add the image to the list
+                images.append({
+                    "key": f"FOOOF Results for {ch_names[i]}",
+                    "value": f"data:image/png;base64,{img_str}",
+                    "summary": results_str
+                })
 
-            print("file directory", temp_dir)
+            return jsonify({"images": images, "summary": "FOOOF Results"}), 200
+
     except Exception as e:
         print("error", e)
         return jsonify({'error': str(e)}), 500

analysis_api/requirements.txt

@@ -8,4 +8,5 @@ scipy
 fooof
 nltk
 python-dotenv
-requests
+requests
+mne

frontend/next.config.js

@@ -13,5 +13,7 @@ module.exports = {
     NEXT_PUBLIC_FUSION_RELAY_URL: process.env.NEXT_PUBLIC_FUSION_RELAY_URL,
     NEXT_PUBLIC_FUSION_NOSTR_PUBLIC_KEY: process.env.NEXT_PUBLIC_FUSION_NOSTR_PUBLIC_KEY,
     NEXT_PUBLIC_NEUROFUSION_BACKEND_URL: process.env.NEXT_PUBLIC_NEUROFUSION_BACKEND_URL,
+    NEXT_PUBLIC_ANALYSIS_SERVER_URL: process.env.NEXT_PUBLIC_ANALYSIS_SERVER_URL,
+    NEXT_PUBLIC_APP_INSIGHTS_KEY: process.env.NEXT_PUBLIC_APP_INSIGHTS_KEY,
   },
 };