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Merge branch 'v2.0.x' of https://github.com/OpenSeizureDetector/Android_Pebble_SD into v2.0.x

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This commit is contained in:
Graham Jones
2016-06-30 19:37:14 +01:00
parent 9612b7c639 994655d55a
commit 5bf50d8c7c
12 changed files with 344 additions and 31 deletions
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5
app/build.gradle
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@@ -24,17 +24,16 @@ android {
dependencies {
compile files('libs/mpandroidchartlibrary-2-0-7.jar')
compile 'com.getpebble:pebblekit:3.0.0@aar'
compile 'com.getpebble:pebblekit:3.1.0@aar'
// Unit testing dependencies
testCompile 'junit:junit:4.12'
// Set this dependency if you want to use Mockito
testCompile 'org.mockito:mockito-core:1.10.19'
// Set this dependency if you want to use Hamcrest matching
testCompile 'org.hamcrest:hamcrest-library:1.1'
compile 'com.android.support:appcompat-v7:22.2.1'
compile 'com.android.support:support-v4:22.2.1'
compile files('libs/JTransforms-3.1-with-dependencies.jar')
}
repositories {

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app/libs/JTransforms-3.1-with-dependencies.jar Normal file
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app/src/main/assets/pebble_sd.pbw
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85
app/src/main/java/uk/org/openseizuredetector/AccelData.java Normal file
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@@ -0,0 +1,85 @@
package uk.org.openseizuredetector;
import android.util.Log;
import org.json.JSONException;
import org.json.JSONObject;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.TimeZone;
/**
* Created by graham on 27/06/16.
*/
/* From https://github.com/kramimus/pebble-accel-analyzer */
public class AccelData {
private final String TAG = AccelData.class.getSimpleName();
final private int x;
final private int y;
final private int z;
private long timestamp = 0;
final private boolean didVibrate;
public AccelData(byte[] data) {
x = (data[0] & 0xff) | (data[1] << 8);
y = (data[2] & 0xff) | (data[3] << 8);
z = (data[4] & 0xff) | (data[5] << 8);
didVibrate = data[6] != 0;
for (int i = 0; i < 8; i++) {
timestamp |= ((long)(data[i+7] & 0xff)) << (i * 8);
}
}
public JSONObject toJson() {
JSONObject json = new JSONObject();
try {
json.put("x", x);
json.put("y", y);
json.put("z", z);
json.put("ts", timestamp);
json.put("v", didVibrate);
return json;
} catch (JSONException e) {
Log.w(TAG, "problem constructing accel data, skipping " + e);
}
return null;
}
public static List<AccelData> fromDataArray(byte[] data) {
List<AccelData> accels = new ArrayList<AccelData>();
for (int i = 0; i < data.length; i += 15) {
accels.add(new AccelData(Arrays.copyOfRange(data, i, i + 15)));
}
return accels;
}
public long getTimestamp() {
return timestamp;
}
public int getX() {
return x;
}
public int getY() {
return y;
}
public int getZ() {
return z;
}
public int getMagnitude() {
return (int)Math.sqrt(x*x + y*y + z*z);
}
public void applyTimezone(TimeZone tz) {
timestamp -= tz.getOffset(timestamp);
}
}

107
app/src/main/java/uk/org/openseizuredetector/CircularArrayList.java Normal file
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@@ -0,0 +1,107 @@
package uk.org.openseizuredetector;
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.RandomAccess;
/**
* Created by graham on 28/06/16.
*/
public class CircularArrayList<E>
extends AbstractList<E> implements RandomAccess {
/**
* If you use this code, please consider notifying isak at du-preez dot com
* with a brief description of your application.
*
* This is free and unencumbered software released into the public domain.
* Anyone is free to copy, modify, publish, use, compile, sell, or
* distribute this software, either in source code form or as a compiled
* binary, for any purpose, commercial or non-commercial, and by any
* means.
*/
private final int n; // buffer length
private final List<E> buf; // a List implementing RandomAccess
private int head = 0;
private int tail = 0;
public CircularArrayList(int capacity) {
n = capacity + 1;
buf = new ArrayList<E>(Collections.nCopies(n, (E) null));
}
public int capacity() {
return n - 1;
}
private int wrapIndex(int i) {
int m = i % n;
if (m < 0) { // java modulus can be negative
m += n;
}
return m;
}
// This method is O(n) but will never be called if the
// CircularArrayList is used in its typical/intended role.
private void shiftBlock(int startIndex, int endIndex) {
assert (endIndex > startIndex);
for (int i = endIndex - 1; i >= startIndex; i--) {
set(i + 1, get(i));
}
}
@Override
public int size() {
return tail - head + (tail < head ? n : 0);
}
@Override
public E get(int i) {
if (i < 0 || i >= size()) {
throw new IndexOutOfBoundsException();
}
return buf.get(wrapIndex(head + i));
}
@Override
public E set(int i, E e) {
if (i < 0 || i >= size()) {
throw new IndexOutOfBoundsException();
}
return buf.set(wrapIndex(head + i), e);
}
@Override
public void add(int i, E e) {
int s = size();
if (s == n - 1) {
throw new IllegalStateException("Cannot add element."
+ " CircularArrayList is filled to capacity.");
}
if (i < 0 || i > s) {
throw new IndexOutOfBoundsException();
}
tail = wrapIndex(tail + 1);
if (i < s) {
shiftBlock(i, s);
}
set(i, e);
}
@Override
public E remove(int i) {
int s = size();
if (i < 0 || i >= s) {
throw new IndexOutOfBoundsException();
}
E e = get(i);
if (i > 0) {
shiftBlock(0, i);
}
head = wrapIndex(head + 1);
return e;
}
}

5
app/src/main/java/uk/org/openseizuredetector/OsdUtil.java
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@@ -42,7 +42,12 @@ import org.apache.http.conn.util.InetAddressUtils;
import java.net.InetAddress;
import java.net.NetworkInterface;
import java.util.AbstractList;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
import java.util.RandomAccess;
/**
* OsdUtil - OpenSeizureDetector Utilities

4
app/src/main/java/uk/org/openseizuredetector/SdData.java
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@@ -50,6 +50,8 @@ public class SdData implements Parcelable {
public short mFallThreshMin;
public short mFallThreshMax;
public short mFallWindow;
public long mSdMode;
public long mSampleFreq;
public long alarmFreqMin;
public long alarmFreqMax;
public long nMin;
@@ -148,6 +150,8 @@ public class SdData implements Parcelable {
jsonObj.put("haveSettings", haveSettings);
jsonObj.put("alarmState", alarmState);
jsonObj.put("alarmPhrase", alarmPhrase);
jsonObj.put("sdMode",mSdMode);
jsonObj.put("sampleFreq",mSampleFreq);
jsonObj.put("alarmFreqMin",alarmFreqMin);
jsonObj.put("alarmFreqMax",alarmFreqMax);
jsonObj.put("alarmThresh", alarmThresh);

115
app/src/main/java/uk/org/openseizuredetector/SdDataSourcePebble.java
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@@ -38,6 +38,10 @@ import com.getpebble.android.kit.Constants;
import com.getpebble.android.kit.PebbleKit;
import com.getpebble.android.kit.util.PebbleDictionary;
import org.json.JSONException;
import org.json.JSONObject;
import org.jtransforms.fft.DoubleFFT_1D;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
@@ -46,6 +50,10 @@ import java.io.OutputStream;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.nio.IntBuffer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.TimeZone;
import java.util.Timer;
import java.util.TimerTask;
import java.util.UUID;
@@ -101,14 +109,27 @@ public class SdDataSourcePebble extends SdDataSource {
private int KEY_DATA_UPDATE_PERIOD = 25;
private int KEY_MUTE_PERIOD = 26;
private int KEY_MAN_ALARM_PERIOD = 27;
private int KEY_SD_MODE = 28;
private int KEY_SAMPLE_FREQ = 29;
private int KEY_RAW_DATA = 30;
private int KEY_NUM_RAW_DATA = 31;
// Values of the KEY_DATA_TYPE entry in a message
private int DATA_TYPE_RESULTS = 1; // Analysis Results
private int DATA_TYPE_SETTINGS = 2; // Settings
private int DATA_TYPE_SPEC = 3; // FFT Spectrum (or part of a spectrum)
private int DATA_TYPE_RAW = 4; // raw accelerometer data.
// Values for SD_MODE
private int SD_MODE_FFT = 0; // The original OpenSeizureDetector mode (FFT based)
private int SD_MODE_RAW = 1; // Send raw, unprocessed data to the phone.
private int SD_MODE_FILTER = 2; // Use digital filter rather than FFT.
private short mDataUpdatePeriod;
private short mMutePeriod;
private short mManAlarmPeriod;
private short mPebbleSdMode;
private short mSampleFreq;
private short mAlarmFreqMin;
private short mAlarmFreqMax;
private short mWarnTime;
@@ -120,8 +141,13 @@ public class SdDataSourcePebble extends SdDataSource {
private short mFallThreshMax;
private short mFallWindow;
// raw data storage for SD_MODE_RAW
private int MAX_RAW_DATA = 500;
private double[] rawData = new double[MAX_RAW_DATA];
private int nRawData = 0;
public SdDataSourcePebble(Context context, SdDataReceiver sdDataReceiver) {
super(context,sdDataReceiver);
super(context, sdDataReceiver);
mName = "Pebble";
// Set default settings from XML files (mContext is set by super().
PreferenceManager.setDefaultValues(mContext,
@@ -251,7 +277,15 @@ public class SdDataSourcePebble extends SdDataSource {
mManAlarmPeriod = (short) Integer.parseInt(prefStr);
Log.v(TAG, "updatePrefs() ManAlarmPeriod = " + mManAlarmPeriod);
prefStr = SP.getString("AlarmFreqMin","SET_FROM_XML");
prefStr = SP.getString("PebbleSdMode", "SET_FROM_XML");
mPebbleSdMode = (short) Integer.parseInt(prefStr);
Log.v(TAG, "updatePrefs() PebbleSdMode = " + mPebbleSdMode);
prefStr = SP.getString("SampleFreq", "SET_FROM_XML");
mSampleFreq = (short) Integer.parseInt(prefStr);
Log.v(TAG, "updatePrefs() SampleFreq = " + mSampleFreq);
prefStr = SP.getString("AlarmFreqMin", "SET_FROM_XML");
mAlarmFreqMin = (short) Integer.parseInt(prefStr);
Log.v(TAG, "updatePrefs() AlarmFreqMin = " + mAlarmFreqMin);
@@ -313,7 +347,7 @@ public class SdDataSourcePebble extends SdDataSource {
Log.v(TAG, "Received message from Pebble - data type="
+ data.getUnsignedIntegerAsLong(KEY_DATA_TYPE));
// If we have a message, the app must be running
Log.v(TAG,"Setting mPebbleAppRunningCheck to true");
Log.v(TAG, "Setting mPebbleAppRunningCheck to true");
mPebbleAppRunningCheck = true;
PebbleKit.sendAckToPebble(context, transactionId);
//Log.v(TAG,"Message is: "+data.toJsonString());
@@ -365,6 +399,23 @@ public class SdDataSourcePebble extends SdDataSource {
mSdData.batteryPc = data.getUnsignedIntegerAsLong(KEY_BATTERY_PC);
mSdData.haveSettings = true;
}
if (data.getUnsignedIntegerAsLong(KEY_DATA_TYPE)
== DATA_TYPE_RAW) {
Log.v(TAG, "DATA_TYPE = Raw");
long numSamples;
numSamples = data.getUnsignedIntegerAsLong(KEY_NUM_RAW_DATA);
Log.v(TAG, "numSamples = " + numSamples);
byte[] rawDataBytes = data.getBytes(KEY_RAW_DATA);
for (AccelData reading : AccelData.fromDataArray(rawDataBytes)) {
if (nRawData < MAX_RAW_DATA) {
rawData[nRawData] = reading.getMagnitude();
nRawData++;
} else {
Log.i(TAG, "WARNING - rawData Buffer Full");
}
}
}
}
};
PebbleKit.registerReceivedDataHandler(mContext, msgDataHandler);
@@ -427,12 +478,14 @@ public class SdDataSourcePebble extends SdDataSource {
* variables to the watch.
*/
public void sendPebbleSdSettings() {
Log.v(TAG, "sendPebblSdSettings() - preparing settings dictionary..");
Log.v(TAG, "sendPebblSdSettings() - preparing settings dictionary.. mSampleFreq=" + mSampleFreq);
// Watch Settings
final PebbleDictionary setDict = new PebbleDictionary();
setDict.addInt16(KEY_DATA_UPDATE_PERIOD, mDataUpdatePeriod);
setDict.addInt16(KEY_MUTE_PERIOD, mMutePeriod);
setDict.addInt16(KEY_MAN_ALARM_PERIOD, mManAlarmPeriod);
setDict.addInt16(KEY_SD_MODE, mPebbleSdMode);
setDict.addInt16(KEY_SAMPLE_FREQ, mSampleFreq);
setDict.addInt16(KEY_ALARM_FREQ_MIN, mAlarmFreqMin);
setDict.addInt16(KEY_ALARM_FREQ_MAX, mAlarmFreqMax);
setDict.addUint16(KEY_WARN_TIME, mWarnTime);
@@ -462,55 +515,55 @@ public class SdDataSourcePebble extends SdDataSource {
public boolean checkWatchSettings() {
boolean settingsOk = true;
if (mDataUpdatePeriod != mSdData.mDataUpdatePeriod) {
Log.v(TAG,"checkWatchSettings - mDataUpdatePeriod Wrong");
Log.v(TAG, "checkWatchSettings - mDataUpdatePeriod Wrong");
settingsOk = false;
}
if (mMutePeriod != mSdData.mMutePeriod) {
Log.v(TAG,"checkWatchSettings - mMutePeriod Wrong");
Log.v(TAG, "checkWatchSettings - mMutePeriod Wrong");
settingsOk = false;
}
if (mManAlarmPeriod != mSdData.mManAlarmPeriod) {
Log.v(TAG,"checkWatchSettings - mManAlarmPeriod Wrong");
Log.v(TAG, "checkWatchSettings - mManAlarmPeriod Wrong");
settingsOk = false;
}
if (mAlarmFreqMin != mSdData.alarmFreqMin) {
Log.v(TAG,"checkWatchSettings - mAlarmFreqMin Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmFreqMin Wrong");
settingsOk = false;
}
if (mAlarmFreqMax != mSdData.alarmFreqMax) {
Log.v(TAG,"checkWatchSettings - mAlarmFreqMax Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmFreqMax Wrong");
settingsOk = false;
}
if (mWarnTime != mSdData.warnTime) {
Log.v(TAG,"checkWatchSettings - mWarnTime Wrong");
Log.v(TAG, "checkWatchSettings - mWarnTime Wrong");
settingsOk = false;
}
if (mAlarmTime != mSdData.alarmTime) {
Log.v(TAG,"checkWatchSettings - mAlarmTime Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmTime Wrong");
settingsOk = false;
}
if (mAlarmThresh != mSdData.alarmThresh) {
Log.v(TAG,"checkWatchSettings - mAlarmThresh Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmThresh Wrong");
settingsOk = false;
}
if (mAlarmRatioThresh != mSdData.alarmRatioThresh) {
Log.v(TAG,"checkWatchSettings - mAlarmRatioThresh Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmRatioThresh Wrong");
settingsOk = false;
}
if (mFallActive != mSdData.mFallActive) {
Log.v(TAG,"checkWatchSettings - mAlarmFreqMin Wrong");
Log.v(TAG, "checkWatchSettings - mAlarmFreqMin Wrong");
settingsOk = false;
}
if (mFallThreshMin != mSdData.mFallThreshMin) {
Log.v(TAG,"checkWatchSettings - mFallThreshMin Wrong");
Log.v(TAG, "checkWatchSettings - mFallThreshMin Wrong");
settingsOk = false;
}
if (mFallThreshMax != mSdData.mFallThreshMax) {
Log.v(TAG,"checkWatchSettings - mFallThreshMax Wrong");
Log.v(TAG, "checkWatchSettings - mFallThreshMax Wrong");
settingsOk = false;
}
if (mFallWindow != mSdData.mFallWindow) {
Log.v(TAG,"checkWatchSettings - mFallWindow Wrong");
Log.v(TAG, "checkWatchSettings - mFallWindow Wrong");
settingsOk = false;
}
@@ -543,7 +596,7 @@ public class SdDataSourcePebble extends SdDataSource {
tnow.setToNow();
// get time since the last data was received from the Pebble watch.
tdiff = (tnow.toMillis(false) - mPebbleStatusTime.toMillis(false));
Log.v(TAG, "getPebbleStatus() - mPebbleAppRunningCheck="+mPebbleAppRunningCheck+" tdiff="+tdiff);
Log.v(TAG, "getPebbleStatus() - mPebbleAppRunningCheck=" + mPebbleAppRunningCheck + " tdiff=" + tdiff);
// Check we are actually connected to the pebble.
mSdData.pebbleConnected = PebbleKit.isWatchConnected(mContext);
if (!mSdData.pebbleConnected) mPebbleAppRunningCheck = false;
@@ -552,7 +605,7 @@ public class SdDataSourcePebble extends SdDataSource {
// the app is not talking to us
// mPebbleAppRunningCheck is set to true in the receiveData handler.
if (!mPebbleAppRunningCheck &&
(tdiff > (mDataUpdatePeriod+mAppRestartTimeout) * 1000)) {
(tdiff > (mDataUpdatePeriod + mAppRestartTimeout) * 1000)) {
Log.v(TAG, "getPebbleStatus() - tdiff = " + tdiff);
mSdData.pebbleAppRunning = false;
Log.v(TAG, "getPebbleStatus() - Pebble App Not Running - Attempting to Re-Start");
@@ -560,7 +613,7 @@ public class SdDataSourcePebble extends SdDataSource {
//mPebbleStatusTime = tnow; // set status time to now so we do not re-start app repeatedly.
getPebbleSdSettings();
// Only make audible warning beep if we have not received data for more than mFaultTimerPeriod seconds.
if (tdiff > (mDataUpdatePeriod+mFaultTimerPeriod) * 1000) {
if (tdiff > (mDataUpdatePeriod + mFaultTimerPeriod) * 1000) {
mSdDataReceiver.onSdDataFault(mSdData);
} else {
Log.v(TAG, "getPebbleStatus() - Waiting for mFaultTimerPeriod before issuing audible warning...");
@@ -581,6 +634,19 @@ public class SdDataSourcePebble extends SdDataSource {
getPebbleSdSettings();
getPebbleData();
}
if (mPebbleSdMode == SD_MODE_RAW) {
analyseRawData();
}
}
private void analyseRawData() {
Log.v(TAG,"analyserawData()");
DoubleFFT_1D fft = new DoubleFFT_1D(MAX_RAW_DATA);
fft.realForward(rawData);
// FIXME - rawData should really be a circular buffer.
nRawData = 0;
}
/**
@@ -614,10 +680,9 @@ public class SdDataSourcePebble extends SdDataSource {
}
}
}

16
app/src/main/res/values/pebble_sample_freq_list.xml Normal file
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@@ -0,0 +1,16 @@
<?xml version="1.0" encoding="utf-8"?>
<resources>
<string-array name="pebble_sample_freq_list">
<item>"100 Hz"</item>
<item>"50 Hz"</item>
<item>"25 Hz"</item>
<item>"10 Hz"</item>
</string-array>
<string-array name="pebble_sample_freq_list_values">
<item>"100"</item>
<item>"50"</item>
<item>"25"</item>
<item>"10"</item>
</string-array>
</resources>

14
app/src/main/res/values/pebble_sd_mode_list.xml Normal file
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@@ -0,0 +1,14 @@
<?xml version="1.0" encoding="utf-8"?>
<resources>
<string-array name="pebble_sd_mode_list">
<item>"Normal - OpenSeizureDetector FFT"</item>
<item>"Raw"</item>
<item>"Digital Filter"</item>
</string-array>
<string-array name="pebble_sd_mode_list_values">
<item>"0"</item>
<item>"1"</item>
<item>"2"</item>
</string-array>
</resources>

1
app/src/main/res/xml/general_prefs.xml
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@@ -6,6 +6,7 @@
android:summary="Select whether to use a Pebble Watch or network connection as the seizure detector data source."
android:entries="@array/datasource_list"
android:entryValues="@array/datasource_list_values"
android:defaultValue="Pebble"
android:dialogTitle="Select Data Source" />
<CheckBoxPreference
android:defaultValue="true"

17
app/src/main/res/xml/pebble_datasource_prefs.xml
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@@ -19,6 +19,23 @@
android:title="Manual Alarm Period (sec)" />
</PreferenceCategory>
<PreferenceCategory android:title="Seizure Detector Settings">
<ListPreference
android:key="PebbleSdMode"
android:title="Seizure Detector Mode"
android:summary="Select one of the three available modes of operation."
android:entries="@array/pebble_sd_mode_list"
android:entryValues="@array/pebble_sd_mode_list_values"
android:defaultValue="0"
android:dialogTitle="Select Seizure Detector Mode" />
<ListPreference
android:key="SampleFreq"
android:title="Select Sample Frequency"
android:summary="Higher Frequency is more Accurate, but uses more battery power."
android:entries="@array/pebble_sample_freq_list"
android:entryValues="@array/pebble_sample_freq_list_values"
android:defaultValue="100"
android:dialogTitle="Select Sample Frequency" />
<EditTextPreference
android:defaultValue="3"
android:key="AlarmFreqMin"