V4.2.1a - added standard deviation threshold to ML Algorithm

app/build.gradle

@@ -29,6 +29,9 @@ android {
         targetCompatibility JavaVersion.VERSION_1_8
     }
     namespace 'uk.org.openseizuredetector'
+    buildFeatures {
+        viewBinding true
+    }
 }
 
 dependencies {
@@ -61,6 +64,8 @@ dependencies {
     implementation 'com.google.firebase:firebase-analytics'
     implementation 'com.firebaseui:firebase-ui-auth:7.2.0'
     implementation 'com.google.firebase:firebase-firestore'
+    implementation 'androidx.navigation:navigation-fragment:2.5.2'
+    implementation 'androidx.navigation:navigation-ui:2.5.2'
 
     testImplementation 'junit:junit:4.13.2'
     testImplementation "androidx.test:core"

app/src/main/AndroidManifest.xml

@@ -2,7 +2,7 @@
 <manifest xmlns:android="http://schemas.android.com/apk/res/android"
     xmlns:tools="http://schemas.android.com/tools"
     android:versionCode="125"
-    android:versionName="4.1.11a">
+    android:versionName="4.2.1a">
     <!-- android:allowBackup="false" -->
     <uses-permission android:name="android.permission.BLUETOOTH" />
     <uses-permission android:name="android.permission.BLUETOOTH_ADMIN" />
@@ -34,8 +34,12 @@
         android:label="@string/app_name"
         android:networkSecurityConfig="@xml/network_security_config"
         android:theme="@style/AppTheme">
-        <activity android:name=".AuthenticateActivity"/>
+        <activity
-        <!-- @android:style/Theme.Holo.Light" -->
+            android:name=".MlModelManager"
+            android:exported="false"
+            android:label="@string/title_activity_ml_model_manager"
+            android:theme="@style/AppTheme" />
+        <activity android:name=".AuthenticateActivity" /> <!-- @android:style/Theme.Holo.Light" -->
         <activity android:name=".BLEScanActivity" />
         <activity android:name=".ExportDataActivity" /> <!-- android:usesCleartextTraffic="true" -->
         <activity
@@ -70,9 +74,8 @@
 
         <receiver
             android:name=".BootBroadcastReceiver"
-            android:label="BootBroadcastReceiver"
             android:exported="true"
-            >
+            android:label="BootBroadcastReceiver">
             <intent-filter>
                 <action android:name="android.intent.action.BOOT_COMPLETED" />
             </intent-filter>

app/src/main/java/uk/org/openseizuredetector/SdAlgNn.java

@@ -1,7 +1,10 @@
 package uk.org.openseizuredetector;
 
 import android.content.Context;
+import android.content.SharedPreferences;
+import android.preference.PreferenceManager;
 import android.util.Log;
+import android.widget.Toast;
 
 import com.android.volley.AuthFailureError;
 import com.android.volley.Request;
@@ -31,10 +34,32 @@ public class SdAlgNn {
     private Context mContext;
     RequestQueue mQueue;
 
+    private double mSdThresh;  // Acceleration Standard Deviation Threshold required to activate analysis (%)
+    private int mModelId;   // ID of ML Model to be used (refers to information in MlModels.json for details).
+    private int mInputFormat; // ID of input format required for model (populated from MlModels.json).
+
 
     public SdAlgNn(Context context) {
         Log.d(TAG, "SdAlgNn Constructor");
         mContext = context;
+
+        SharedPreferences SP = PreferenceManager
+                .getDefaultSharedPreferences(mContext);
+        try {
+            String threshStr = SP.getString("CnnAlarmThreshold", "5");
+            mSdThresh = Double.parseDouble(threshStr);
+            Log.v(TAG, "SdAlgNn Constructor mSdThresh = " + mSdThresh);
+            threshStr = SP.getString("CnnModelId", "1");
+            mModelId = Integer.parseInt(threshStr);
+            Log.v(TAG, "SdAlgNn Constructor mModelId = " + mModelId);
+        } catch (Exception ex) {
+            Log.v(TAG, "SdAlgNn Constructor - problem parsing preferences. " + ex.toString());
+            Toast toast = Toast.makeText(mContext, "Problem Parsing ML Algorithm Preferences", Toast.LENGTH_SHORT);
+            toast.show();
+        }
+
+        mInputFormat = 1; // FIXME - this needs to be determined from the model ID specified by retrieving a configuration file.
+
         Task<Void> initializeTask = TfLite.initialize(mContext);
 
         initializeTask.addOnSuccessListener(a -> {
@@ -68,7 +93,14 @@ public class SdAlgNn {
         }
     }
 
-    public float getPseizure(SdData sdData) {
+    /**
+     * getPseizureFmt1 - calculate probability of sdData representing seizure-like movement
+     * using a model with input format #1, which is a simple vector of 125 accelerometer vector
+     * magnitude readings.
+     * @param sdData - seizure detector data as input to the model
+     * @return probability of data representing seizure-like movement.
+     */
+    private float getPseizureFmt1(SdData sdData) {
         int i;
         float[][][] modelInput = new float[1][125][1];
         float[][] modelOutput = new float[1][2];
@@ -83,4 +115,53 @@ public class SdAlgNn {
         Log.d(TAG, "run - pSeizure=" + modelOutput[0][1]);
         return (modelOutput[0][1]);
     }
+
+    public float getPseizure(SdData sdData) {
+        int i;
+
+        // First check that we have enough movement to analyse by comparing the acceleration standard deviation to a threshold.
+        double stdDev;
+        stdDev = calcRawDataStd(sdData);
+        if (stdDev < mSdThresh) {
+            Log.d(TAG, "getPseizure - acceleration stdev below movement threshold: std="+stdDev+", thresh="+mSdThresh);
+            return (0);
+        }
+
+        float pSeizure;
+        switch (mModelId) {
+            case 1:
+                pSeizure = getPseizureFmt1(sdData);
+                break;
+            default:
+                Log.e(TAG,"getPSeizure - invalid model ID "+mModelId);
+                pSeizure = 0;
+        }
+
+        return(pSeizure);
+    }
+
+    private double calcRawDataStd(SdData sdData) {
+        /**
+         * Calculate the standard deviation in % of the rawData array in the SdData instance provided.
+         * It assumes that rawdata will contain 125 samples.
+         * Returns the standard deviation in %.
+         */
+        // FIXME - assumes length of rawdata array is 125 data points
+        int j;
+        double sum = 0.0;
+        for (j = 0; j < 125; j++) { // FIXME - assumed length!
+            sum += sdData.rawData[j];
+        }
+        double mean = sum / 125;
+
+        double standardDeviation = 0.0;
+        for (j = 0; j < 125; j++) { // FIXME - assumed length!
+            standardDeviation += Math.pow(sdData.rawData[j] - mean, 2);
+        }
+        standardDeviation = Math.sqrt(standardDeviation / 125);  // FIXME - assumed length!
+
+        // Convert standard deviation from milli-g to %
+        standardDeviation = 100. * standardDeviation / mean;
+        return (standardDeviation);
+    }
 }

app/src/main/res/values/dimens.xml

@@ -2,5 +2,6 @@
     <!-- Default screen margins, per the Android Design guidelines. -->
     <dimen name="activity_horizontal_margin">16dp</dimen>
     <dimen name="activity_vertical_margin">16dp</dimen>
+    <dimen name="fab_margin">16dp</dimen>
     <!-- Default screen margins, per the Android Design guidelines. -->
 </resources>

app/src/main/res/values/strings.xml

@@ -3,7 +3,7 @@
     <string name="app_name">OpenSeizureDetector</string>
     <string name="changelog">
         "\n
-        \mV4.1.11 - Changed target Android Version to 13 (SDK33) (Play Store policy).
+        \mV4.2.1 - Changed target Android Version to 13 (SDK33) (Play Store policy).
         \nV4.1.10 - Added warning if heart rate readings freeze and do not change for more than 1 minute.
         \nV4.1.9 - Fixed problem with average heart rate alarm
         Fixed issue with phone data source generating continuous alarms for Heart Rate or O2Sat
@@ -100,7 +100,7 @@
     <string name="AlarmThreshTitle">Alarm Threshold</string>
     <string name="AlarmThreshSummary">Alarm Threshold (Default = 100)</string>
     <string name="AlarmRatioThreshTitle">Alarm Ratio Threshold</string>
-    <string name="AlarmRatioThreshSummary">Alarm Ratio Threshold (Default = 50). Increase to reduce sensitivity.</string>
+    <string name="AlarmRatioThreshSummary">Alarm Ratio Threshold (Default = 57). Increase to reduce sensitivity.</string>
     <string name="AlarmFreqMaxTitle">AlarmFreqMax (Hz)</string>
     <string name="AlarmFreqMaxSummary">Maximum Frequency of ROI (Hz) (Default = 8 Hz)</string>
     <string name="AlarmFreqMinTitle">AlarmFreqMin (Hz)</string>
@@ -503,4 +503,52 @@
     <string name="error_exporting_data">*** ERROR Exporting Data ***</string>
     <string name="HrFrozenTitle">Heart Rate measurement Frozen Warning</string>
     <string name="HrFrozenSummary">Produce a fault warning if the heart rate measurement freezes and does not change for more than 1 minute.</string>
+    <string name="ml_sd_settings_title">Machine Learning Seizure Detector Settings</string>
+    <string name="ml_sd_threshold_summary">Movement Threshold (% standard deviation) to activate the Machine Learning Algorithm</string>
+    <string name="ml_sd_threshold_title">Movement Threshold (%std)</string>
+    <string name="ml_sd_modelid_title">AI Model ID</string>
+    <string name="ml_sd_modelid_summary">ID number of machine learning (AI) model to be used - users should not edit this, but use the model Manager page instead.</string>
+    <string name="title_activity_ml_model_manager">MlModelManager</string>
+    <!-- Strings used for fragments for navigation -->
+    <string name="first_fragment_label">First Fragment</string>
+    <string name="second_fragment_label">Second Fragment</string>
+    <string name="next">Next</string>
+    <string name="previous">Previous</string>
+
+    <string name="lorem_ipsum">
+        Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam in scelerisque sem. Mauris
+        volutpat, dolor id interdum ullamcorper, risus dolor egestas lectus, sit amet mattis purus
+        dui nec risus. Maecenas non sodales nisi, vel dictum dolor. Class aptent taciti sociosqu ad
+        litora torquent per conubia nostra, per inceptos himenaeos. Suspendisse blandit eleifend
+        diam, vel rutrum tellus vulputate quis. Aliquam eget libero aliquet, imperdiet nisl a,
+        ornare ex. Sed rhoncus est ut libero porta lobortis. Fusce in dictum tellus.\n\n
+        Suspendisse interdum ornare ante. Aliquam nec cursus lorem. Morbi id magna felis. Vivamus
+        egestas, est a condimentum egestas, turpis nisl iaculis ipsum, in dictum tellus dolor sed
+        neque. Morbi tellus erat, dapibus ut sem a, iaculis tincidunt dui. Interdum et malesuada
+        fames ac ante ipsum primis in faucibus. Curabitur et eros porttitor, ultricies urna vitae,
+        molestie nibh. Phasellus at commodo eros, non aliquet metus. Sed maximus nisl nec dolor
+        bibendum, vel congue leo egestas.\n\n
+        Sed interdum tortor nibh, in sagittis risus mollis quis. Curabitur mi odio, condimentum sit
+        amet auctor at, mollis non turpis. Nullam pretium libero vestibulum, finibus orci vel,
+        molestie quam. Fusce blandit tincidunt nulla, quis sollicitudin libero facilisis et. Integer
+        interdum nunc ligula, et fermentum metus hendrerit id. Vestibulum lectus felis, dictum at
+        lacinia sit amet, tristique id quam. Cras eu consequat dui. Suspendisse sodales nunc ligula,
+        in lobortis sem porta sed. Integer id ultrices magna, in luctus elit. Sed a pellentesque
+        est.\n\n
+        Aenean nunc velit, lacinia sed dolor sed, ultrices viverra nulla. Etiam a venenatis nibh.
+        Morbi laoreet, tortor sed facilisis varius, nibh orci rhoncus nulla, id elementum leo dui
+        non lorem. Nam mollis ipsum quis auctor varius. Quisque elementum eu libero sed commodo. In
+        eros nisl, imperdiet vel imperdiet et, scelerisque a mauris. Pellentesque varius ex nunc,
+        quis imperdiet eros placerat ac. Duis finibus orci et est auctor tincidunt. Sed non viverra
+        ipsum. Nunc quis augue egestas, cursus lorem at, molestie sem. Morbi a consectetur ipsum, a
+        placerat diam. Etiam vulputate dignissim convallis. Integer faucibus mauris sit amet finibus
+        convallis.\n\n
+        Phasellus in aliquet mi. Pellentesque habitant morbi tristique senectus et netus et
+        malesuada fames ac turpis egestas. In volutpat arcu ut felis sagittis, in finibus massa
+        gravida. Pellentesque id tellus orci. Integer dictum, lorem sed efficitur ullamcorper,
+        libero justo consectetur ipsum, in mollis nisl ex sed nisl. Donec maximus ullamcorper
+        sodales. Praesent bibendum rhoncus tellus nec feugiat. In a ornare nulla. Donec rhoncus
+        libero vel nunc consequat, quis tincidunt nisl eleifend. Cras bibendum enim a justo luctus
+        vestibulum. Fusce dictum libero quis erat maximus, vitae volutpat diam dignissim.
+    </string>
 </resources>

app/src/main/res/xml/seizure_detector_prefs.xml

@@ -38,6 +38,11 @@
             android:title="@string/fall_detect_active_title" />
     </PreferenceCategory>
     <PreferenceCategory android:title="@string/SeizureDetectorSettingsTitle">
+        <CheckBoxPreference
+            android:defaultValue="true"
+            android:key="OsdAlarmActive"
+            android:summary="@string/OsdAlarmEnabledSummary"
+            android:title="@string/OsdAlarmEnabledTitle" />
         <EditTextPreference
             android:defaultValue="5"
             android:key="WarnTime"
@@ -72,11 +77,31 @@
 
         <EditTextPreference
             android:defaultValue="5"
+            android:enabled="false"
             android:key="SamplePeriod"
             android:summary="@string/sample_period_summary"
             android:title="@string/sample_period_title" />
     </PreferenceCategory>
 
+    <PreferenceCategory android:title="@string/ml_sd_settings_title">
+        <CheckBoxPreference
+            android:defaultValue="true"
+            android:key="CnnAlarmActive"
+            android:summary="@string/CnnAlarmEnabledSummary"
+            android:title="@string/CnnAlarmEnabledTitle" />
+        <EditTextPreference
+            android:defaultValue="5"
+            android:key="CnnAlarmThreshold"
+            android:summary="@string/ml_sd_threshold_summary"
+            android:title="@string/ml_sd_threshold_title" />
+        <EditTextPreference
+            android:defaultValue="1"
+            android:key="CnnModelId"
+            android:enabled="false"
+            android:summary="@string/ml_sd_modelid_summary"
+            android:title="@string/ml_sd_modelid_title" />
+
+    </PreferenceCategory>
     <PreferenceCategory android:title="@string/HeartRateAlarmSettingsTitle">
         <CheckBoxPreference
             android:defaultValue="false"