public LiveWifiAndBluetoothShellDataViewModel(IBluetoothFinder bluetoothFinder,
IShellTemperatureRepository <ShellTemp> shellTemperatureRepository,
IShellTemperatureRepository <SdCardShellTemp> sdCardShellTemperatureRepository,
IDeviceRepository <DeviceInfo> deviceRepository,
IConfiguration configuration,
BluetoothConnectionSubject subject,
TemperatureSubject temperatureSubject,
ILogger <LiveBluetoothOnlyShellDataViewModel> logger,
OutlierDetector outlierDetector,
ClearList clear,
IRepository <ShellTemperatureComment> commentRepository,
IReadingCommentRepository <ReadingComment> readingCommentRepository,
IRepository <Positions> positionRepository,
IRepository <ShellTemperaturePosition> shellTempPositionRepository,
IRepository <SdCardShellTemperatureComment> sdCardCommentRepository)
: base(bluetoothFinder, shellTemperatureRepository, sdCardShellTemperatureRepository, deviceRepository, configuration, subject,
temperatureSubject, logger, outlierDetector, clear, commentRepository, readingCommentRepository,
positionRepository, shellTempPositionRepository, sdCardCommentRepository)
{
_shellTemperatureRepository = shellTemperatureRepository;
IList <DeviceInfo> potentialWifiDevices = FindPotentialWifiDevices();
foreach (DeviceInfo device in potentialWifiDevices.ToList())
{
DateTime start = DateTime.Now.AddMinutes(-2);
DateTime end = DateTime.Now;
WifiDevice wifiDevice = new WifiDevice(device.DeviceName, device.DeviceAddress, start);
IEnumerable <ShellTemp> shellTemps = _shellTemperatureRepository.GetShellTemperatureData(start, end,
device.DeviceName, device.DeviceAddress);
ShellTemp[] dataReadings = shellTemps as ShellTemp[] ?? shellTemps.ToArray();
if (dataReadings.Length == 0)
{
potentialWifiDevices.Remove(device);
}
else
{
SetWifiDeviceDataReadings(wifiDevice, dataReadings);
SetWifiDeviceDataPoints(wifiDevice);
InstantiateNewDevice(wifiDevice);
wifiDevice.State.Message = "Connected To - " + wifiDevice.DeviceName;
}
}
SetSelectedDeviceWhenNull();
if (Devices.Count == 1) // only one in devices so, must be selected
{
SetConnectionStatus(SelectedDevice, DeviceConnectionStatus.CONNECTED);
}
SetCanRemoveDevices();
}
public void TestDetect()
{
var values = new double[] { 6.0039, 6.4048, 6.7865, 6.6615, 13.9451 };
var loged = (from v in values select Math.Log(v)).ToList();
Assert.AreEqual(4, OutlierDetector.Detect(loged, 0.0001));
loged.RemoveAt(4);
Assert.AreEqual(-1, OutlierDetector.Detect(loged, 0.0001));
}
public void CheckEnabled(double outlierEvalue, int minValidTransitionPair)
{
var pips = (from p in this.ProductIonPairs
where p.Enabled && p.IsPaired
select p).ToList();
if (pips.Count > 0)
{
var values = (from p in pips
select Math.Log(p.Ratio)).ToList();
var outlier = OutlierDetector.Detect(values, outlierEvalue);
if (outlier != -1)
{
pips[outlier].Enabled = false;
}
}
this.Enabled = this.ProductIonPairs.Count(n => n.Enabled) >= minValidTransitionPair;
}
public LiveBluetoothOnlyShellDataViewModel(IBluetoothFinder bluetoothFinder,
IShellTemperatureRepository <ShellTemp> shellTemperatureRepository,
IShellTemperatureRepository <SdCardShellTemp> sdCardShellTemperatureRepository,
IDeviceRepository <DeviceInfo> deviceRepository,
IConfiguration configuration,
BluetoothConnectionSubject subject,
TemperatureSubject temperatureSubject,
ILogger <LiveBluetoothOnlyShellDataViewModel> logger,
OutlierDetector outlierDetector,
ClearList clear,
IRepository <ShellTemperatureComment> commentRepository,
IReadingCommentRepository <ReadingComment> readingCommentRepository,
IRepository <Positions> positionRepository,
IRepository <ShellTemperaturePosition> shellTempPositionRepository,
IRepository <SdCardShellTemperatureComment> sdCardCommentRepository)
: base(bluetoothFinder, shellTemperatureRepository, sdCardShellTemperatureRepository, deviceRepository,
configuration, subject,
temperatureSubject, logger, outlierDetector, clear, commentRepository, readingCommentRepository,
positionRepository, shellTempPositionRepository, sdCardCommentRepository)
{
}
public Statistics(IEnumerable <double> values)
{
OriginalValues = values.Where(d => !double.IsNaN(d)).ToArray();
SortedValues = OriginalValues.OrderBy(value => value).ToArray();
N = SortedValues.Count;
if (N == 0)
{
throw new InvalidOperationException("Sequence of values contains no elements, Statistics can't be calculated");
}
var quartiles = Quartiles.FromSorted(SortedValues);
Min = quartiles.Min;
Q1 = quartiles.Q1;
Median = quartiles.Median;
Q3 = quartiles.Q3;
Max = quartiles.Max;
InterquartileRange = quartiles.InterquartileRange;
var moments = Moments.Create(SortedValues);
Mean = moments.Mean;
StandardDeviation = moments.StandardDeviation;
Variance = moments.Variance;
Skewness = moments.Skewness;
Kurtosis = moments.Kurtosis;
var tukey = TukeyOutlierDetector.FromQuartiles(quartiles);
LowerFence = tukey.LowerFence;
UpperFence = tukey.UpperFence;
AllOutliers = SortedValues.Where(tukey.IsOutlier).ToArray();
LowerOutliers = SortedValues.Where(tukey.IsLowerOutlier).ToArray();
UpperOutliers = SortedValues.Where(tukey.IsUpperOutlier).ToArray();
outlierDetector = tukey;
StandardError = StandardDeviation / Math.Sqrt(N);
ConfidenceInterval = new ConfidenceInterval(Mean, StandardError, N);
Percentiles = new PercentileValues(SortedValues);
}
public List <ITraqPeptideRatioItem> Calculate(IIdentifiedProteinGroup protein)
{
var result = (from s in protein.GetPeptides()
where Filter(s)
let i = s.FindIsobaricItem()
where i != null && i.Valid
let si = GetSample(i)
let ri = GetReference(i)
where !double.IsNaN(si) && !double.IsInfinity(si) && !double.IsNaN(ri) && !double.IsInfinity(ri) && (ri != 0)
select new ITraqPeptideRatioItem()
{
Sample = si, Reference = ri, Ratio = si / ri, IonInjectTime = i.Scan.IonInjectionTime
}).ToList();
if (result.Count == 0)
{
foreach (var p in protein)
{
p.FindOrCreateITraqChannelItem(DatasetName, ChannelName).RatioStr = "#N/A";
}
}
else
{
var ratios = (from l in result
select Math.Log(l.Ratio)).ToList();
var outliers = OutlierDetector.Detect(ratios);
if (outliers.Count > 0)
{
// using (StreamWriter sw = new StreamWriter("e:/temp.txt", true))
// {
// sw.WriteLine("{0} outliers detected in {1} ratios", outliers.Count, ratios.Count);
// sw.Write("Outlier");
// foreach (var outlier in outliers)
// {
// sw.Write(",{0:0.0000}", ratios[outlier]);
// }
// sw.WriteLine();
// for (int i = outliers.Count - 1; i >= 0; i--)
// {
// ratios.RemoveAt(outliers[i]);
// }
// sw.Write("Other");
// foreach (var r in ratios)
// {
// sw.Write(",{0:0.0000}", r);
// }
// sw.WriteLine();
// sw.WriteLine();
// }
for (int i = outliers.Count - 1; i >= 0; i--)
{
result[outliers[i]].IsOutlier = true;
//result.RemoveAt(outliers[i]);
}
}
var validItems = (from r in result where !r.IsOutlier select r).ToList();
var ratio = RatioBuilder.Calculate(validItems);
foreach (var p in protein)
{
p.FindOrCreateITraqChannelItem(DatasetName, ChannelName).Ratio = ratio.Ratio;
}
}
return(result);
}