V3.1.9 - quite a few changes - see Changelog.md

CHANGELOG.md

@@ -4,6 +4,11 @@
     V3.2.0 - (NEXT VERSION!)
         - Added neural network based data analysis.
 
+    V3.1.9 - 14jun2019
+        - Now requests READ_PHONE_STATE along with SMS permissions (required for some phones to send SMS messages)
+        - Fixed issue with Garmin Seizure Detector not producing warnings.
+        - Added faut pips for missing heart rate data if heart rate alarm active
+
     V3.1.8 - 06jun2019
         - Added READ_PHONE_STATE permission which seems to be needed for some phones to send SMS (but not many).
 

app/src/main/AndroidManifest.xml

@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android"
     package="uk.org.openseizuredetector"
-    android:versionCode="62"
+    android:versionCode="63"
-    android:versionName="3.1.8"
+    android:versionName="3.1.9"
     >
     <!--android:allowBackup="false"-->
 

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

@@ -63,8 +63,6 @@ import com.github.mikephil.charting.data.BarEntry;
 import com.github.mikephil.charting.utils.ValueFormatter;
 import com.rohitss.uceh.UCEHandler;
 
-import static java.util.Objects.isNull;
-
 public class MainActivity extends AppCompatActivity {
     static final String TAG = "MainActivity";
     private int okColour = Color.BLUE;
@@ -435,15 +433,18 @@ public class MainActivity extends AppCompatActivity {
                     tv = (TextView) findViewById(R.id.pebbleTv);
                     if (mConnection.mSdServer.mSdData.mHRAlarmActive) {
                         tv.setText("HR = " + mConnection.mSdServer.mSdData.mHR);
-                        if (!mConnection.mSdServer.mSdData.mHRAlarmStanding) {
+                        if (mConnection.mSdServer.mSdData.mHRAlarmStanding) {
-                            tv.setBackgroundColor(okColour);
-                            tv.setTextColor(okTextColour);
-                        } else {
                             tv.setBackgroundColor(alarmColour);
                             tv.setTextColor(alarmTextColour);
+                        } else if (mConnection.mSdServer.mSdData.mHRFaultStanding) {
+                            tv.setBackgroundColor(warnColour);
+                            tv.setTextColor(warnTextColour);
+                        } else {
+                            tv.setBackgroundColor(okColour);
+                            tv.setTextColor(okTextColour);
                         }
                     } else {
-                        if (mConnection.mSdServer.mSdData.pebbleConnected) {
+                        if (mConnection.mSdServer.mSdData.watchConnected) {
                             tv.setText("HR Alarm OFF");
                             tv.setBackgroundColor(okColour);
                             tv.setTextColor(okTextColour);
@@ -455,7 +456,7 @@ public class MainActivity extends AppCompatActivity {
                         }
                     }
                     tv = (TextView) findViewById(R.id.appTv);
-                    if (mConnection.mSdServer.mSdData.pebbleAppRunning) {
+                    if (mConnection.mSdServer.mSdData.watchAppRunning) {
                         tv.setText("Watch App OK");
                         tv.setBackgroundColor(okColour);
                         tv.setTextColor(okTextColour);

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

@@ -96,6 +96,7 @@ public class OsdUtil implements ActivityCompat.OnRequestPermissionsResultCallbac
     private final String[] SMS_PERMISSIONS = {
             Manifest.permission.SEND_SMS,
             Manifest.permission.ACCESS_FINE_LOCATION,
+            Manifest.permission.READ_PHONE_STATE,
     };
 
 

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

@@ -0,0 +1,195 @@
+/*
+  Android_Pebble_SD - a simple accelerometer based seizure detector that runs on a
+  Pebble smart watch (http://getpebble.com).
+
+  See http://openseizuredetector.org for more information.
+
+  Copyright Graham Jones, 2015, 2016, 2017, 2018, 2019.
+
+  This file is part of android_pebble_sd.
+
+  Android_pebble_sd is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+
+  Android_pebble_sd is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with android_pebble_sd.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+package uk.org.openseizuredetector;
+
+import android.util.Log;
+
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
+import org.jtransforms.fft.DoubleFFT_1D;
+
+/**
+ * SdAnalyser implements the seizure detection algorithm on an Android Phone - it is used by SdDatasourceGarmin
+ */
+public class SdAnalyser {
+    private String TAG = "SdAnalyser";
+    private double mSampleFreq;
+    private double mAlarmFreqMin;
+    private double mAlarmFreqMax;
+    private double mSamplePeriod;
+    private double mWarnTime;
+    private double mAlarmTime;
+    private double mAlarmThresh;
+    private double mAlarmRatioThresh;
+    private double mFreqRes;
+    private int mAlarmCount;
+    private double mFreqCutoff;
+    private int mNSamp;
+
+    double roiPower;
+    double specPower;
+    double roiRatio;
+
+    SdAnalyser(double sampleFreq,
+               double alarmFreqMin,
+               double alarmFreqMax,
+               double samplePeriod,
+               double warnTime,
+               double alarmThresh,
+               double alarmRatioThresh) {
+        mSampleFreq = sampleFreq;
+        mAlarmFreqMin = alarmFreqMin;
+        mAlarmFreqMax = alarmFreqMax;
+        mSamplePeriod = samplePeriod;
+        mWarnTime = warnTime;
+        mAlarmThresh = alarmThresh;
+        mAlarmRatioThresh = alarmRatioThresh;
+
+        mFreqRes = 1.0 / mSamplePeriod;
+        mFreqCutoff = mSampleFreq / 2.0;
+        mNSamp = (int)(mSamplePeriod * mSampleFreq);
+    }
+
+    int freq2fftBin(double freq) {
+        int n = (int)(freq/mFreqRes);
+        return(n);
+    }
+
+    /**
+     * doAnalysis() - analyse the data if the accelerometer data array mAccData
+     * and populate the output data structure mSdData
+     */
+    void calculateSpectralPowers(double[] rawData) {
+        // Set the frequency bounds for the analysis in fft output bin numbers.
+        int nMin = freq2fftBin(mAlarmFreqMin);
+        int nMax = freq2fftBin(mAlarmFreqMax);
+        int nFreqCutoff = freq2fftBin(mFreqCutoff);
+
+        DoubleFFT_1D fftDo = new DoubleFFT_1D(mNSamp);
+        double[] fft = new double[mNSamp * 2];
+        System.arraycopy(rawData, 0, fft, 0, mNSamp);
+        fftDo.realForward(fft);
+
+        // Calculate the whole spectrum power (well a value equivalent to it that avoids square root calculations
+        // and zero any readings that are above the frequency cutoff.
+        double specPower = 0;
+        for (int i = 1; i < mNSamp / 2; i++) {
+            if (i <= nFreqCutoff) {
+                specPower = specPower + getMagnitude(fft, i);
+            } else {
+                fft[2 * i] = 0.;
+                fft[2 * i + 1] = 0.;
+            }
+        }
+        specPower = specPower / (mNSamp / 2);
+
+        // Calculate the Region of Interest power and power ratio.
+        double roiPower = 0;
+        for (int i = nMin; i < nMax; i++) {
+            roiPower = roiPower + getMagnitude(fft, i);
+        }
+        roiPower = roiPower / (nMax - nMin);
+        double roiRatio = 10 * roiPower / specPower;
+
+    }
+
+    /**
+     * Calculate the magnitude of entry i in the fft array fft
+     *
+     * @param fft
+     * @param i
+     * @return magnitude ( Re*Re + Im*Im )
+     */
+    double getMagnitude(double[] fft, int i) {
+        double mag;
+        mag = (fft[2 * i] * fft[2 * i] + fft[2 * i + 1] * fft[2 * i + 1]);
+        return mag;
+    }
+
+    // Force the data stored in this datasource to update in line with the JSON string encoded data provided.
+    // Used by webServer to update the GarminDatasource.
+    // Returns a message string that is passed back to the watch.
+    public String updateFromJSON(String jsonStr) {
+        String retVal = "undefined";
+        Log.v(TAG,"updateFromJSON - "+jsonStr);
+
+        try {
+            JSONObject mainObject = new JSONObject(jsonStr);
+            //JSONObject dataObject = mainObject.getJSONObject("dataObj");
+            JSONObject dataObject = mainObject;
+            String dataTypeStr = dataObject.getString("dataType");
+            Log.v(TAG,"updateFromJSON - dataType="+dataTypeStr);
+            if (dataTypeStr.equals("raw")) {
+                Log.v(TAG,"updateFromJSON - processing raw data");
+                try {
+                    mSdData.mHR = dataObject.getDouble("HR");
+                } catch (JSONException e) {
+                    // if we get 'null' HR (For example if the heart rate is not working)
+                    mSdData.mHR = -1;
+                }
+                try {
+                    mMute = dataObject.getInt("Mute");
+                } catch (JSONException e) {
+                    // if we get 'null' HR (For example if the heart rate is not working)
+                    mMute = 0;
+                }
+                JSONArray accelVals = dataObject.getJSONArray("data");
+                Log.v(TAG, "Received " + accelVals.length() + " acceleration values");
+                int i;
+                for (i = 0; i < accelVals.length(); i++) {
+                    mSdData.rawData[i] = accelVals.getInt(i);
+                }
+                mSdData.mNsamp = accelVals.length();
+                //mNSamp = accelVals.length();
+                mWatchAppRunningCheck = true;
+                doAnalysis();
+                if (mSdData.haveSettings == false) {
+                    retVal = "sendSettings";
+                } else {
+                    retVal = "OK";
+                }
+            } else if (dataTypeStr.equals("settings")){
+                Log.v(TAG,"updateFromJSON - processing settings");
+                mSamplePeriod = (short)dataObject.getInt("analysisPeriod");
+                mSampleFreq = (short)dataObject.getInt("sampleFreq");
+                mSdData.batteryPc = (short)dataObject.getInt("battery");
+                Log.v(TAG,"updateFromJSON - mSamplePeriod="+mSamplePeriod+" mSampleFreq="+mSampleFreq);
+                mSdData.haveSettings = true;
+                mSdData.mSampleFreq = mSampleFreq;
+                mWatchAppRunningCheck = true;
+                retVal = "OK";
+            } else {
+                Log.e(TAG,"updateFromJSON - unrecognised dataType "+dataTypeStr);
+                retVal = "ERROR";
+            }
+        } catch (Exception e) {
+            Log.e(TAG,"updateFromJSON - Error Parsing JSON String - "+e.toString());
+            e.printStackTrace();
+            retVal = "ERROR";
+        }
+        return(retVal);
+    }
+}

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

@@ -29,10 +29,6 @@ import android.os.Parcel;
 import android.text.format.Time;
 import android.util.Log;
 
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-import java.util.Locale;
-
 import org.json.JSONObject;
 import org.json.JSONArray;
 
@@ -82,11 +78,12 @@ public class SdData implements Parcelable {
     public long roiPower;
     public String alarmPhrase;
     public int simpleSpec[];
-    public boolean pebbleConnected = false;
+    public boolean watchConnected = false;
-    public boolean pebbleAppRunning = false;
+    public boolean watchAppRunning = false;
     public boolean serverOK = false;
 
     public boolean mHRAlarmStanding = false;
+    public boolean mHRFaultStanding = false;
     public double mHR = 0;
 
     public SdData() {
@@ -116,8 +113,8 @@ public class SdData implements Parcelable {
             specPower = jo.optInt("specPower");
             roiPower = jo.optInt("roiPower");
             batteryPc = jo.optInt("batteryPc");
-            pebbleConnected = jo.optBoolean("pebbleConnected");
+            watchConnected = jo.optBoolean("watchConnected");
-            pebbleAppRunning = jo.optBoolean("pebbleAppRunning");
+            watchAppRunning = jo.optBoolean("watchAppRunning");
             alarmState = jo.optInt("alarmState");
             alarmPhrase = jo.optString("alarmPhrase");
             alarmThresh = jo.optInt("alarmThresh");
@@ -159,8 +156,8 @@ public class SdData implements Parcelable {
             jsonObj.put("specPower", specPower);
             jsonObj.put("roiPower", roiPower);
             jsonObj.put("batteryPc", batteryPc);
-            jsonObj.put("pebbleConnected", pebbleConnected);
+            jsonObj.put("watchConnected", watchConnected);
-            jsonObj.put("pebbleAppRunning", pebbleAppRunning);
+            jsonObj.put("watchAppRunning", watchAppRunning);
             jsonObj.put("haveSettings", haveSettings);
             jsonObj.put("alarmState", alarmState);
             jsonObj.put("alarmPhrase", alarmPhrase);

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

@@ -683,8 +683,8 @@ public class SdDataSourceAw extends SdDataSource {
         tdiff = (tnow.toMillis(false) - mStatusTime.toMillis(false));
         Log.v(TAG, "getStatus() - mWatchAppRunningCheck=" + mWatchAppRunningCheck + " tdiff=" + tdiff);
         // Check we are actually connected to the pebble.
-        mSdData.pebbleConnected = PebbleKit.isWatchConnected(mContext);
+        mSdData.watchConnected = PebbleKit.isWatchConnected(mContext);
-        if (!mSdData.pebbleConnected) mWatchAppRunningCheck = false;
+        if (!mSdData.watchConnected) mWatchAppRunningCheck = false;
         // And is the pebble_sd app running?
         // set mWatchAppRunningCheck has been false for more than 10 seconds
         // the app is not talking to us
@@ -692,7 +692,7 @@ public class SdDataSourceAw extends SdDataSource {
         if (!mWatchAppRunningCheck &&
                 (tdiff > (mDataUpdatePeriod + mAppRestartTimeout) * 1000)) {
             Log.v(TAG, "getStatus() - tdiff = " + tdiff);
-            mSdData.pebbleAppRunning = false;
+            mSdData.watchAppRunning = false;
             //Log.v(TAG, "getStatus() - Pebble App Not Running - Attempting to Re-Start");
             //mUtil.writeToSysLogFile("SdDataSourceAw.getStatus() - Pebble App not Running - Attempting to Re-Start");
             //startWatchApp();
@@ -709,7 +709,7 @@ public class SdDataSourceAw extends SdDataSource {
                 Log.v(TAG, "getStatus() - Waiting for mFaultTimerPeriod before issuing audible warning...");
             }
         } else {
-            mSdData.pebbleAppRunning = true;
+            mSdData.watchAppRunning = true;
         }
 
         // if we have confirmation that the app is running, reset the

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

@@ -28,32 +28,22 @@ import android.content.Context;
 import android.content.Intent;
 import android.content.IntentFilter;
 import android.content.SharedPreferences;
-import android.net.ConnectivityManager;
-import android.os.BatteryManager;
 import android.os.Handler;
 import android.preference.PreferenceManager;
 import android.text.format.Time;
 import android.util.Log;
 import android.widget.Toast;
 
-import com.getpebble.android.kit.PebbleKit;
-import com.getpebble.android.kit.util.PebbleDictionary;
-
 import org.json.JSONArray;
 import org.json.JSONException;
 import org.json.JSONObject;
 import org.jtransforms.fft.DoubleFFT_1D;
 
-import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
-import java.nio.IntBuffer;
 import java.util.Arrays;
 import java.util.Timer;
 import java.util.TimerTask;
-import java.util.UUID;
 
 import static java.lang.Long.parseLong;
-import static java.lang.Math.sqrt;
 
 
 /**
@@ -66,7 +56,7 @@ public class SdDataSourceGarmin extends SdDataSource {
     private Handler mHandler = new Handler();
     private Timer mStatusTimer;
     private Timer mSettingsTimer;
-    private Timer mAlarmCheckTimer;
+    private Timer mFaultCheckTimer;
     private Time mDataStatusTime;
     private boolean mWatchAppRunningCheck = false;
     private int mAppRestartTimeout = 10;  // Timeout before re-starting watch app (sec) if we have not received
@@ -145,14 +135,14 @@ public class SdDataSourceGarmin extends SdDataSource {
             Log.v(TAG, "start(): status timer already running.");
             mUtil.writeToSysLogFile("SdDataSourceGarmin.start() - status timer already running??");
         }
-        if (mAlarmCheckTimer == null) {
+        if (mFaultCheckTimer == null) {
             Log.v(TAG, "start(): starting alarm check timer");
             mUtil.writeToSysLogFile("SdDataSourceGarmin.start() - starting alarm check timer");
-            mAlarmCheckTimer = new Timer();
+            mFaultCheckTimer = new Timer();
-            mAlarmCheckTimer.schedule(new TimerTask() {
+            mFaultCheckTimer.schedule(new TimerTask() {
                 @Override
                 public void run() {
-                    alarmCheck();
+                    faultCheck();
                 }
             }, 0, 1000);
         } else {
@@ -206,12 +196,12 @@ public class SdDataSourceGarmin extends SdDataSource {
                 mSettingsTimer = null;
             }
             // Stop the alarm check timer
-            if (mAlarmCheckTimer != null) {
+            if (mFaultCheckTimer != null) {
                 Log.v(TAG, "stop(): cancelling alarm check timer");
                 mUtil.writeToSysLogFile("SdDataSourceGarmin.stop() - cancelling alarm check timer");
-                mAlarmCheckTimer.cancel();
+                mFaultCheckTimer.cancel();
-                mAlarmCheckTimer.purge();
+                mFaultCheckTimer.purge();
-                mAlarmCheckTimer = null;
+                mFaultCheckTimer = null;
             }
 
         } catch (Exception e) {
@@ -467,7 +457,10 @@ public class SdDataSourceGarmin extends SdDataSource {
                 fft[2*i+1] = 0.;
             }
         }
+        //Log.v(TAG,"specPower = "+specPower);
+        //specPower = specPower/(mSdData.mNsamp/2);
         specPower = specPower/mSdData.mNsamp/2;
+        //Log.v(TAG,"specPower = "+specPower);
 
         // Calculate the Region of Interest power and power ratio.
         double roiPower = 0;
@@ -489,8 +482,6 @@ public class SdDataSourceGarmin extends SdDataSource {
             simpleSpec[ifreq] = simpleSpec[ifreq] / (binMax-binMin);
         }
 
-        checkFall();
-
         // Populate the mSdData structure to communicate with the main SdServer service.
         mDataStatusTime.setToNow();
         mSdData.specPower = (long)specPower / ACCEL_SCALE_FACTOR;
@@ -512,15 +503,102 @@ public class SdDataSourceGarmin extends SdDataSource {
 
         // Because we have received data, set flag to show watch app running.
         mWatchAppRunningCheck = true;
+
+        // Check this data to see if it represents an alarm state.
+        alarmCheck();
+        hrCheck();
+        fallCheck();
+        muteCheck();
+
         mSdDataReceiver.onSdDataReceived(mSdData);  // and tell SdServer we have received data.
     }
 
 
+    /****************************************************************
+     * checkAlarm() - checks the current accelerometer data and uses
+     * historical data to determine if we are in a fault, warning or ok
+     * state.
+     * Sets mSdData.alarmState and mSdData.hrAlarmStanding
+     */
+    private void alarmCheck() {
+        boolean inAlarm;
+        Log.v(TAG, "alarmCheck()");
+        // Is the current set of data representing an alarm state?
+        if ((mSdData.roiPower > mAlarmThresh) && (10 * (mSdData.roiPower / mSdData.specPower) > mAlarmRatioThresh)) {
+            inAlarm = true;
+        } else {
+            inAlarm = false;
+        }
+
+        // set the alarmState to Alarm, Warning or OK, depending on the current state and previous ones.
+        if (inAlarm) {
+            mAlarmCount += mSamplePeriod;
+            if (mAlarmCount > mAlarmTime) {
+                // full alarm
+                mSdData.alarmState = 2;
+            } else if (mAlarmCount > mWarnTime) {
+                // warning
+                mSdData.alarmState = 1;
+            }
+        } else {
+            // If we are not in an ALARM state, revert back to WARNING, otherwise
+            // revert back to OK.
+            if (mSdData.alarmState == 2) {
+                // revert to warning
+                mSdData.alarmState = 1;
+                mAlarmCount = mWarnTime + 1;  // pretend we have only just entered warning state.
+            } else {
+                // revert to OK
+                mSdData.alarmState = 0;
+                mAlarmCount = 0;
+            }
+        }
+
+        Log.v(TAG, "alarmCheck(): inAlarm=" + inAlarm + ", alarmState = " + mSdData.alarmState + " alarmCount=" + mAlarmCount + " mAlarmTime=" + mAlarmTime);
+
+    }
+
+    public void muteCheck() {
+        if (mMute != 0) {
+            Log.v(TAG, "Mute Active - setting alarms to mute");
+            mSdData.alarmState = 6;
+            mSdData.alarmPhrase = "MUTE";
+            mSdData.mHRAlarmStanding = false;
+        }
+
+    }
+
+    /**
+     * hrCheck - check the Heart rate data in mSdData to see if it represents an alarm condition.
+     * Sets mSdData.mHRAlarmStanding
+     */
+    public void hrCheck() {
+        Log.v(TAG, "hrCheck()");
+        /* Check Heart Rate against alarm settings */
+        if (mSdData.mHRAlarmActive) {
+            if (mSdData.mHR < 0) {
+                Log.i(TAG,"Heart Rate Fault (HR<0)");
+                mSdData.mHRFaultStanding = true;
+                mSdData.mHRAlarmStanding = false;
+            }
+            else if ((mSdData.mHR > mSdData.mHRTreshMax) || (mSdData.mHR < mSdData.mHRThreshMin)) {
+                Log.i(TAG, "Heart Rate Abnormal - " + mSdData.mHR + " bpm");
+                mSdData.mHRFaultStanding = false;
+                mSdData.mHRAlarmStanding = true;
+            }
+            else {
+                mSdData.mHRFaultStanding = false;
+                mSdData.mHRAlarmStanding = false;
+            }
+        }
+
+    }
+
     /****************************************************************
      * Simple threshold analysis to chech for fall.
      * Called from clock_tick_handler()
      */
-    public void checkFall() {
+    public void fallCheck() {
         int i,j;
         double minAcc, maxAcc;
 
@@ -575,7 +653,7 @@ public class SdDataSourceGarmin extends SdDataSource {
         Log.v(TAG, "getStatus() - mWatchAppRunningCheck=" + mWatchAppRunningCheck + " tdiff=" + tdiff);
         Log.v(TAG,"getStatus() - tdiff="+tdiff+", mDataUpatePeriod="+mDataUpdatePeriod+", mAppRestartTimeout="+mAppRestartTimeout);
 
-        mSdData.pebbleConnected = true;  // We can't check connection for passive network connection, so set it to true to avoid errors.
+        mSdData.watchConnected = true;  // We can't check connection for passive network connection, so set it to true to avoid errors.
         // And is the watch app running?
         // set mWatchAppRunningCheck has been false for more than 10 seconds
         // the app is not talking to us
@@ -583,7 +661,7 @@ public class SdDataSourceGarmin extends SdDataSource {
         if (!mWatchAppRunningCheck &&
                 (tdiff > (mDataUpdatePeriod + mAppRestartTimeout) * 1000)) {
             Log.v(TAG, "getStatus() - tdiff = " + tdiff);
-            mSdData.pebbleAppRunning = false;
+            mSdData.watchAppRunning = false;
             // Only make audible warning beep if we have not received data for more than mFaultTimerPeriod seconds.
             if (tdiff > (mDataUpdatePeriod + mFaultTimerPeriod) * 1000) {
                 Log.v(TAG, "getStatus() - Watch App Not Running");
@@ -596,7 +674,7 @@ public class SdDataSourceGarmin extends SdDataSource {
                 Log.v(TAG, "getStatus() - Waiting for mFaultTimerPeriod before issuing audible warning...");
             }
         } else {
-            mSdData.pebbleAppRunning = true;
+            mSdData.watchAppRunning = true;
         }
 
         // if we have confirmation that the app is running, reset the
@@ -612,71 +690,21 @@ public class SdDataSourceGarmin extends SdDataSource {
     }
 
     /**
-     * alarmCheck - determines alarm state based on seizure detector data SdData.   Called every second.
+     * faultCheck - determines alarm state based on seizure detector data SdData.   Called every second.
      */
-    private void alarmCheck() {
+    private void faultCheck() {
-        boolean inAlarm;
         Time tnow = new Time(Time.getCurrentTimezone());
         long tdiff;
         tnow.setToNow();
 
         // get time since the last data was received from the watch.
         tdiff = (tnow.toMillis(false) - mDataStatusTime.toMillis(false));
-        Log.v(TAG, "alarmCheck() - tdiff=" + tdiff + ", mDataUpatePeriod=" + mDataUpdatePeriod + ", mAppRestartTimeout=" + mAppRestartTimeout
+        Log.v(TAG, "faultCheck() - tdiff=" + tdiff + ", mDataUpatePeriod=" + mDataUpdatePeriod + ", mAppRestartTimeout=" + mAppRestartTimeout
                 + ", combined = " + (mDataUpdatePeriod + mAppRestartTimeout) * 1000);
         if (!mWatchAppRunningCheck &&
                 (tdiff > (mDataUpdatePeriod + mAppRestartTimeout) * 1000)) {
-            Log.v(TAG, "alarmCheck() - watch app not running so not doing anything");
+            Log.v(TAG, "faultCheck() - watch app not running so not doing anything");
             mAlarmCount = 0;
-        } else {
-            Log.v(TAG, "alarmCheck()");
-            if ((mSdData.roiPower > mAlarmThresh) && (10 * (mSdData.roiPower / mSdData.specPower) > mAlarmRatioThresh)) {
-                inAlarm = true;
-            } else {
-                inAlarm = false;
-            }
-
-            if (inAlarm) {
-                mAlarmCount += mSamplePeriod;
-                if (mAlarmCount > mAlarmTime) {
-                    // full alarm
-                    mSdData.alarmState = 2;
-                } else if (mAlarmCount > mWarnTime) {
-                    // warning
-                    mSdData.alarmState = 1;
-                }
-            } else {
-                // If we are not in an ALARM state, revert back to WARNING, otherwise
-                // revert back to OK.
-                if (mSdData.alarmState == 2) {
-                    // revert to warning
-                    mSdData.alarmState = 1;
-                    mAlarmCount = mWarnTime + 1;  // pretend we have only just entered warning state.
-                } else {
-                    // revert to OK
-                    mSdData.alarmState = 0;
-                    mAlarmCount = 0;
-                }
-            }
-
-            Log.v(TAG, "inAlarm=" + inAlarm + ", alarmState = " + mSdData.alarmState + " alarmCount=" + mAlarmCount + " mAlarmTime=" + mAlarmTime);
-
-            /* Check Heart Rate against alarm settings */
-            if (mSdData.mHRAlarmActive) {
-                Log.v(TAG,"Checking HR Alarm");
-                if ((mSdData.mHR > mSdData.mHRTreshMax) || (mSdData.mHR < mSdData.mHRThreshMin)) {
-                    Log.i(TAG, "Heart Rate Abnormal - " + mSdData.mHR + " bpm");
-                    mSdData.mHRAlarmStanding = true;
-                } else {
-                    mSdData.mHRAlarmStanding = false;
-                }
-            }
-            if (mMute != 0) {
-                Log.v(TAG,"Mute Active - setting alarms to mute");
-                mSdData.alarmState = 6;
-                mSdData.alarmPhrase = "MUTE";
-                mSdData.mHRAlarmStanding = false;
-            }
         }
     }
 

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

@@ -2,8 +2,6 @@ package uk.org.openseizuredetector;
 
 import android.content.Context;
 import android.content.SharedPreferences;
-import android.net.ConnectivityManager;
-import android.net.NetworkInfo;
 import android.os.AsyncTask;
 import android.os.Handler;
 import android.preference.PreferenceManager;
@@ -128,8 +126,8 @@ public class SdDataSourceNetwork extends SdDataSource {
                 if (result.startsWith("Unable to retrieve web page")) {
                     Log.v(TAG,"doInBackground() - Unable to retrieve data");
                     sdData.serverOK = false;
-                    sdData.pebbleConnected = false;
+                    sdData.watchConnected = false;
-                    sdData.pebbleAppRunning = false;
+                    sdData.watchAppRunning = false;
                     sdData.alarmState = ALARM_STATE_NETFAULT;
                     sdData.alarmPhrase = "Warning - No Connection to Server";
                     Log.v(TAG,"doInBackground(): No Connection to Server - sdData = "+sdData.toString());
@@ -147,8 +145,8 @@ public class SdDataSourceNetwork extends SdDataSource {
 
             } catch (IOException e) {
                 sdData.serverOK = false;
-                sdData.pebbleConnected = false;
+                sdData.watchConnected = false;
-                sdData.pebbleAppRunning = false;
+                sdData.watchAppRunning = false;
                 sdData.alarmState = ALARM_STATE_NETFAULT;
                 sdData.alarmPhrase = "Warning - No Connection to Server";
                 Log.v(TAG,"doInBackground(): IOException - "+e.toString());

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

@@ -37,11 +37,6 @@ import android.widget.Toast;
 import com.getpebble.android.kit.PebbleKit;
 import com.getpebble.android.kit.util.PebbleDictionary;
 
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.IntBuffer;
@@ -679,8 +674,8 @@ public class SdDataSourcePebble extends SdDataSource {
         tdiff = (tnow.toMillis(false) - mPebbleStatusTime.toMillis(false));
         Log.v(TAG, "getStatus() - mPebbleAppRunningCheck=" + mPebbleAppRunningCheck + " tdiff=" + tdiff);
         // Check we are actually connected to the pebble.
-        mSdData.pebbleConnected = PebbleKit.isWatchConnected(mContext);
+        mSdData.watchConnected = PebbleKit.isWatchConnected(mContext);
-        if (!mSdData.pebbleConnected) mPebbleAppRunningCheck = false;
+        if (!mSdData.watchConnected) mPebbleAppRunningCheck = false;
         // And is the pebble_sd app running?
         // set mPebbleAppRunningCheck has been false for more than 10 seconds
         // the app is not talking to us
@@ -688,7 +683,7 @@ public class SdDataSourcePebble extends SdDataSource {
         if (!mPebbleAppRunningCheck &&
                 (tdiff > (mDataUpdatePeriod + mAppRestartTimeout) * 1000)) {
             Log.v(TAG, "getStatus() - tdiff = " + tdiff);
-            mSdData.pebbleAppRunning = false;
+            mSdData.watchAppRunning = false;
             //Log.v(TAG, "getStatus() - Pebble App Not Running - Attempting to Re-Start");
             //mUtil.writeToSysLogFile("SdDataSourcePebble.getStatus() - Pebble App not Running - Attempting to Re-Start");
             //startWatchApp();
@@ -705,7 +700,7 @@ public class SdDataSourcePebble extends SdDataSource {
                 Log.v(TAG, "getStatus() - Waiting for mFaultTimerPeriod before issuing audible warning...");
             }
         } else {
-            mSdData.pebbleAppRunning = true;
+            mSdData.watchAppRunning = true;
         }
 
         // if we have confirmation that the app is running, reset the

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

@@ -629,7 +629,7 @@ public class SdServer extends Service implements SdDataReceiver {
         }
 
         // Fault
-        if ((sdData.alarmState) == 4 || (sdData.alarmState == 7)) {
+        if ((sdData.alarmState) == 4 || (sdData.alarmState == 7) || (sdData.mHRFaultStanding)) {
             sdData.alarmPhrase = "FAULT";
             writeAlarmToSD();
             faultWarningBeep();

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

@@ -101,7 +101,7 @@ public class SdServiceConnection implements ServiceConnection {
     public boolean pebbleConnected() {
         if (mSdServer!=null) {
             if (mSdServer.mSdData!=null) {
-                if (mSdServer.mSdData.pebbleConnected) {
+                if (mSdServer.mSdData.watchConnected) {
                     return true;
                 }
             }
@@ -116,7 +116,7 @@ public class SdServiceConnection implements ServiceConnection {
     public boolean pebbleAppRunning() {
         if (mSdServer!=null) {
             if (mSdServer.mSdData!=null) {
-                if (mSdServer.mSdData.pebbleAppRunning) {
+                if (mSdServer.mSdData.watchAppRunning) {
                     return true;
                 }
             }

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

@@ -340,7 +340,7 @@ public class StartupActivity extends Activity {
             // Is Pebble Watch App Running?
             tv = (TextView) findViewById(R.id.textItem4);
             pb = (ProgressBar) findViewById(R.id.progressBar4);
-            if (mConnection.pebbleAppRunning()) {
+            if (mConnection.watchAppRunning()) {
                 tv.setText("Watch App Running OK");
                 tv.setBackgroundColor(okColour);
                 tv.setTextColor(okTextColour);
@@ -506,6 +506,7 @@ public class StartupActivity extends Activity {
                             + "\n  V3.1.5 - Added repeat alarm beeps during SMS delay to alert user.."
                             + "\n  V3.1.6 - Made Cancel Audible button inhibit sending SMS alarms as well as audible beeps"
                             + "\n  V3.1.8 - Added READ_PHONE_STATE permission, which seems to be needed for some phones"
+                            + "\n  V3.1.9 - Fixed issue with Garmin Seizure Detector not producing warnings.  Added faut pips for missing heart rate data if heart rate alarm active"
                 );
             // This makes the links display as links, but they do not respond to clicks for some reason...
             Linkify.addLinks(s, Linkify.ALL);
@@ -540,6 +541,7 @@ public class StartupActivity extends Activity {
                             + "\n  V3.1.5 - Added repeat alarm beeps during SMS delay to alert user.."
                             + "\n  V3.1.6 - Made Cancel Audible button inhibit sending SMS alarms as well as audible beeps"
                             + "\n  V3.1.8 - Added READ_PHONE_STATE permission, which seems to be needed for some phones"
+                            + "\n  V3.1.9 - Fixed issue with Garmin Seizure Detector not producing warnings.  Added faut pips for missing heart rate data if heart rate alarm active"
                             + "\n "
             );
             // This makes the links display as links, but they do not respond to clicks for some reason...

app/src/test/java/uk/org/openseizuredetector/EventLogManagerTest.java

@@ -1,46 +0,0 @@
-package uk.org.openseizuredetector;
-
-import android.content.Context;
-import android.util.EventLog;
-import android.util.Log;
-
-import junit.framework.TestCase;
-import android.test.mock.MockContext;
-
-import org.junit.Test;
-import org.mockito.internal.exceptions.ExceptionIncludingMockitoWarnings;
-
-import uk.org.openseizuredetector.EventLogManager.EventLogManager;
-import uk.org.openseizuredetector.EventLogManager.LogEntryModel;
-
-/**
- * Created by graham on 12/05/16.
- */
-public class EventLogManagerTest extends TestCase {
-    private final static String TAG = "EventLogManagerTest";
-    Context mContext;
-
-    protected void setUp() throws Exception {
-        super.setUp();
-        Log.v(TAG,"setUp()");
-        mContext = new MockContext();
-}
-
-    @Test
-    public void testOpenDb() throws Exception {
-        Log.v(TAG,"testOpenDb()");
-        EventLogManager em = new EventLogManager(mContext);
-        assertNotNull(em);
-
-
-        LogEntryModel lem = new LogEntryModel();
-        //lem.setDate(new Date());
-        lem.setNote("Test Entry");
-        lem.setDataJSON("[]");
-        lem.setAlarmState(1);
-
-        em.addRow(lem);
-
-    }
-
-}

app/src/test/java/uk/org/openseizuredetector/SdAnalyserTest.java

@@ -0,0 +1,90 @@
+package uk.org.openseizuredetector;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class SdAnalyserTest {
+    public SdAnalyser sda;
+
+    public String alarmJSON = "{ dataType: 'raw', " +
+            "data: [" +
+            "1644, 1316, 1144, 1332, 1716, 1716, 1392, 1148, 1276, 1660, " +
+            "1716, 1496, 1196, 1232, 1572, 1684, 1552, 1236, 1228, 1528, " +
+            "1648, 1572, 1268, 1208, 1492, 1680, 1596, 1272, 1192, 1424, " +
+            "1668, 1636, 1300, 1200, 1356, 1652, 1684, 1420, 1208, 1304, " +
+            "1620, 1672, 1448, 1232, 1248, 1536, 1676, 1540, 1256, 1244, " +
+            "1544, 1644, 1512, 1252, 1236, 1504, 1684, 1540, 1252, 1200, " +
+            "1436, 1664, 1624, 1344, 1204, 1396, 1616, 1596, 1344, 1216, " +
+            "1368, 1648, 1660, 1388, 1220, 1316, 1588, 1672, 1460, 1232, " +
+            "1256, 1580, 1672, 1500, 1256, 1288, 1540, 1688, 1516, 1252, " +
+            "1212, 1464, 1684, 1584, 1288, 1224, 1468, 1692, 1616, 1316, " +
+            "1188, 1360, 1680, 1724, 1424, 1192, 1224, 1556, 1744, 1588, " +
+            "1260, 1220, 1472, 1692, 1608, 1328, 1192, 1412, 1668, 1656, " +
+            "1356, 1216, 1304, 1636, 1712], " +
+            "HR:54, " +
+            "Mute:0 " +
+            "}";
+
+    private String okJSON = "{ " +
+            "dataType: 'raw', " +
+            "data: [" +
+            "1140, 1188, 1144, 1172, 1228, 1212, 1236, 1236, 1256, 1320, " +
+            "1316, 1280, 1240, 1280, 1324, 1284, 1292, 1268, 1284, 1276, " +
+            "1296, 1324, 1308, 1288, 1304, 1276, 1304, 1304, 1276, 1296, " +
+            "1280, 1284, 1296, 1300, 1284, 1288, 1296, 1284, 1300, 1280, " +
+            "1300, 1292, 1276, 1304, 1276, 1316, 1280, 1288, 1296, 1280, " +
+            "1284, 1272, 1300, 1284, 1288, 1292, 1276, 1296, 1276, 1292, " +
+            "1280, 1284, 1284, 1284, 1284, 1284, 1288, 1284, 1304, 1284, " +
+            "1288, 1280, 1296, 1284, 1292, 1296, 1280, 1276, 1288, 1296, " +
+            "1276, 1292, 1288, 1276, 1288, 1276, 1272, 1272, 1292, 1284, " +
+            "1292, 1288, 1280, 1284, 1284, 1268, 1288, 1268, 1276, 1300, " +
+            "1268, 1292, 1292, 1304, 1288, 1284, 1280, 1276, 1288, 1280, " +
+            "1300, 1288, 1320, 1268, 1288, 1280, 1304, 1280, 1280, 1288, " +
+            "1292, 1308, 1268, 1292, 1280], " +
+            "HR:57, " +
+            "Mute:0 " +
+            "}";
+
+    @Before
+    public void setUp() throws Exception {
+        sda = new SdAnalyser(25.0,
+                3.0,
+                8.0,
+                5.0,
+                5.0,
+                100.0,
+                54.0
+        );
+    }
+
+    @After
+    public void tearDown() throws Exception {
+    }
+
+    @Test
+    public void freq2fftBin() {
+        int n;
+        n = sda.freq2fftBin(0.0);
+        assertEquals(0,n);
+        n = sda.freq2fftBin(5.0);
+        assertEquals(25,n);
+    }
+
+    @Test
+    public void getMagnitude() {
+        double[] fft = {1, 1,
+                        2, 1,
+                        2, 2};
+        double m;
+        m = sda.getMagnitude(fft,0);
+        assertEquals(2.0, m, m * 1e-4);
+        m = sda.getMagnitude(fft,1);
+        assertEquals(5.0, m, m * 1e-4);
+        m = sda.getMagnitude(fft,2);
+        assertEquals(8.0, m, m * 1e-4);
+    }
+
+}

build.gradle

@@ -9,7 +9,7 @@ buildscript {
         google()
     }
     dependencies {
-        classpath 'com.android.tools.build:gradle:3.4.0'
+        classpath 'com.android.tools.build:gradle:3.4.1'
     }
 }
 allprojects {