/// <summary>
/// Initializes a new instance of the <see cref="SimpleCurve" /> class.
/// </summary>
/// <param name="curve">The Curve.</param>
/// <exception cref="System.ArgumentNullException">Cannot create an instance of SimpleCurve when curve is null</exception>
public SimpleCurve(Curve curve, SimpleMeasurement simpleMeasurement)
{
if (curve == null)
{
throw new ArgumentNullException("Cannot create an instance of SimpleCurve when the specified Curve is null");
}
Curve = curve;
if (!Curve.IsFinished)
{
Curve.Finished += Curve_Finished;
Curve.NewDataAdded += Curve_NewDataAdded;
}
_simpleMeasurement = simpleMeasurement;
}
public SimpleMeasurement HackDPV(SimpleMeasurement unHackedMeasurement)
{
List <SimpleMeasurement> hackedMeasurements;
SimpleMeasurement hackedMeasurement;
String unHackedMeasurementString;
String hackedMeasurementString = "";
List <int> locations = new List <int>();
List <string> stringLocations = new List <string>();
int startSubstring = 0;
String file = Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "dpv.pssession");
SimpleLoadSaveFunctions.SaveMeasurement(unHackedMeasurement, file);
//Code here for manipulation the file
using (StreamReader sr = new StreamReader(file))
unHackedMeasurementString = sr.ReadToEnd();
locations = AddLocationsDPV(locations, unHackedMeasurementString);
stringLocations = AddStringLocationsDPV(stringLocations);
for (int i = 0; i < locations.Count; i++)
{
hackedMeasurementString += unHackedMeasurementString.Substring(startSubstring, locations[i]) + stringLocations[i];
startSubstring += locations[i] + stringLocations[i].Length;
}
hackedMeasurementString += unHackedMeasurementString.Substring(startSubstring);
using (StreamWriter writer = File.CreateText(file))
writer.Write(hackedMeasurementString);
hackedMeasurements = SimpleLoadSaveFunctions.LoadMeasurements(file);
hackedMeasurement = hackedMeasurements[0];
return(hackedMeasurement);
}
/// <summary>
/// Saves a simplemeasurement to a *.pssession file.
/// </summary>
/// <param name="simpleMeasurement">The simple measurement.</param>
/// <param name="filepath">The filepath of the *.pssession file.</param>
/// <exception cref="System.ArgumentException">File path must be specified</exception>
/// <exception cref="System.ArgumentNullException">SimpleMeasurement cannot be null</exception>
/// <exception cref="System.Exception">An error occured while saving, please make sure the file path is correct</exception>
public static void SaveMeasurement(SimpleMeasurement simpleMeasurement, string filepath)
{
if (string.IsNullOrEmpty(filepath))
{
throw new ArgumentException("File path must be specified");
}
if (simpleMeasurement == null)
{
throw new ArgumentNullException("SimpleMeasurement cannot be null");
}
SessionManager session = new SessionManager();
session.AddMeasurement(simpleMeasurement.Measurement);
session.MethodForEditor = simpleMeasurement.Measurement.Method;
try { LoadSaveHelperFunctions.SaveSessionFile(filepath, session); }
catch (Exception ex)
{
Crashes.TrackError(ex);
throw new Exception("An error occured while saving, please make sure the file path is correct");
}
}
//Simple connection to the palmsens, currently the only one used
public async void SimpleConnect(int fileNum, bool RunningPC, bool RunningNC, bool RunningReal, bool RunningDPV)
{
bool RunningBL = true;
string testRun = "5";
//Below sets which option the code will execute
SimpleMeasurement baseline;
AssetManager assetManager = Application.Context.Assets;
using (StreamReader sr = new StreamReader(assetManager.Open(testRun + "_2525AfterMch" + fileNum + ".pssession"))) //Loads a blank baseline curve to subtract from the scanned/loaded curve
baseline = SimpleLoadSaveFunctions.LoadMeasurements(sr)[0];
baselineCurves = baseline.SimpleCurveCollection;
//Runs a real scan depending on whatever parameters the person has set
if (RunningReal)
{
Context context = Application.Context; //Loads the current android context
IAttributeSet attributeSet = null;
psCommSimpleAndroid = new PSCommSimpleAndroid(context, attributeSet);
//Uses a simple comm with the palmsens
Device[] devices = await psCommSimpleAndroid.GetConnectedDevices();
try
{
await psCommSimpleAndroid.Connect(devices[0]); //Connect to the first palmsens found
}
catch (Exception ex)
{
Crashes.TrackError(ex);
}
psCommSimpleAndroid.MeasurementStarted += PsCommSimpleAndroid_MeasurementStarted; //Loads the necessary flags
psCommSimpleAndroid.MeasurementEnded += PsCommSimpleAndroid_MeasurementEnded;
psCommSimpleAndroid.SimpleCurveStartReceivingData += PsCommSimpleAndroid_SimpleCurveStartReceivingData;
Method runScan = await RunScan(); //Sets the scan parameters
activeSimpleMeasurement = await psCommSimpleAndroid.Measure(runScan); //Runs the scan on the potentiostat
psCommSimpleAndroid.Wait(11000);
psCommSimpleAndroid.Dispose();
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync(); //Loads the current database
//Add in processing stuff here
SimpleLoadSaveFunctions.SaveMeasurement(activeSimpleMeasurement, Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "dpv" + allDb.Count + ".pssession"));
//FileHack instance = new FileHack();
//activeSimpleMeasurement = instance.HackDPV(activeSimpleMeasurement);
List <SimpleCurve> simpleCurves = activeSimpleMeasurement.NewSimpleCurve(DataArrayType.Current, DataArrayType.Potential);
SimpleCurve subtractedCurve = simpleCurves[0].Subtract(baselineCurves[0]); //Note, replace simpleCurves[1] w/ the standard blank curve
SimpleCurve movingAverageBaseline = subtractedCurve.MovingAverageBaseline(); //Subtracts the baseline from the subtracted curve
SimpleCurve baselineCurve = subtractedCurve.Subtract(movingAverageBaseline);
subtractedCurve.Dispose(); //Disposes of the subtracted curve
SimpleCurve smoothedCurve = baselineCurve.Smooth(SmoothLevel.VeryHigh);
smoothedCurve.DetectPeaks(0.1, 0, true, false, false);
double peakLocation = smoothedCurve.Peaks[smoothedCurve.Peaks.nPeaks - 1].PeakX;
double peakHeight = smoothedCurve.Peaks[smoothedCurve.Peaks.nPeaks - 1].PeakValue;
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
if (peakLocation <= -0.3 && peakLocation >= -0.4) //If the peak is between a certain range, the sample is infected, add in a minimum value once one is determined
{
_database.IsInfected = true;
}
else
{
_database.IsInfected = false;
}
_database.PeakVoltage = peakHeight;
await App.Database.SaveScanAsync(_database); //Saves the current database
subtractedCurve.Dispose();
baselineCurve.Dispose(); //Disposes of the baseline curve
smoothedCurve.Dispose();
}
//Runs a differential pulse voltammetric scan for testing
else if (RunningDPV)
{
using (StreamReader sr = new StreamReader(assetManager.Open("blank.pssession"))) //Loads a blank curve as a baseline to be subtracted
baseline = SimpleLoadSaveFunctions.LoadMeasurements(sr)[0];
Context context = Application.Context; //Loads the current android context
IAttributeSet attributeSet = null;
psCommSimpleAndroid = new PSCommSimpleAndroid(context, attributeSet); //Initializes the palmsens comm
Device[] devices = await psCommSimpleAndroid.GetConnectedDevices();
try
{
await psCommSimpleAndroid.Connect(devices[0]); //Connects to the first palmsens found
}
catch (Exception ex)
{
psCommSimpleAndroid.Dispose();
Crashes.TrackError(ex);
return;
}
psCommSimpleAndroid.MeasurementStarted += PsCommSimpleAndroid_MeasurementStarted; //Loads the necessary flags
psCommSimpleAndroid.MeasurementEnded += PsCommSimpleAndroid_MeasurementEnded;
psCommSimpleAndroid.SimpleCurveStartReceivingData += PsCommSimpleAndroid_SimpleCurveStartReceivingData;
Method runScan = await RunScan(); //Sets the scan parameters
activeSimpleMeasurement = await psCommSimpleAndroid.Measure(runScan); //Runs the scan on the potentiostat
Thread.Sleep(50000);
psCommSimpleAndroid.Dispose(); //Disposes of the comm when it is done being used
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync(); //Loads the current database
//Add in processing stuff here
SimpleLoadSaveFunctions.SaveMeasurement(activeSimpleMeasurement, Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData), "dpv" + allDb.Count + ".pssession"));
//FileHack instance = new FileHack();
//activeSimpleMeasurement = instance.HackDPV(activeSimpleMeasurement);
List <SimpleCurve> simpleCurves = activeSimpleMeasurement.NewSimpleCurve(DataArrayType.Current, DataArrayType.Potential);
//SimpleCurve subtractedCurve = simpleCurves[0].Subtract(baselineCurves[0]); //Note, replace simpleCurves[1] w/ the standard blank curve
SimpleCurve movingAverageBaseline = simpleCurves[0].MovingAverageBaseline(); //Subtracts the baseline from the subtracted curve
SimpleCurve baselineCurve = simpleCurves[0].Subtract(movingAverageBaseline);
//subtractedCurve.Dispose(); //Disposes of the subtracted curve
SimpleCurve smoothedCurve = baselineCurve.Smooth(SmoothLevel.VeryHigh);
smoothedCurve.DetectPeaks(0.1, 0, true, false, false);
PeakList peakList = smoothedCurve.Peaks; //Detects the peaks on the subtracted curve
baselineCurve.Dispose(); //Disposes of the baseline curve
smoothedCurve.Dispose();
Peak mainPeak = peakList[peakList.nPeaks - 1]; //Note, the proper peak is the last peak, not the first peak
double peakLocation = mainPeak.PeakX;
double peakHeight = mainPeak.PeakValue;
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
if (peakLocation <= -0.3 && peakLocation >= -0.4) //If the peak is between a certain range, the sample is infected, add in a minimum value once one is determined
{
_database.IsInfected = true;
}
else
{
_database.IsInfected = false;
}
_database.PeakVoltage = peakHeight;
await App.Database.SaveScanAsync(_database); //Saves the current database
}
else if (RunningNC || RunningPC || RunningBL) //If a test scan is being run
{
if (RunningBL) //If a simple baseline test is run with no subtraction or curve manipulation
{
SimpleMeasurement baselineMeasurement;
using (StreamReader sr = new StreamReader(assetManager.Open(testRun + "_baselineOnly" + fileNum + ".pssession")))
baselineMeasurement = SimpleLoadSaveFunctions.LoadMeasurements(sr)[0];
List <SimpleCurve> avgBaselineCurves = baselineMeasurement.SimpleCurveCollection;
SimpleCurve avgBaselineCurve = avgBaselineCurves[0];
avgBaselineCurve.DetectPeaks(0.05, 0, true, false); //Detect peaks only if they are wider than 0.05 V
PeakList avgBaselinePeakList = avgBaselineCurve.Peaks;
if (avgBaselinePeakList.nPeaks != 0) //If it detects a peak run below code
{
Peak avgBaselinePeak = avgBaselinePeakList[avgBaselinePeakList.nPeaks - 1]; //Use the last peak detected which should be the wanted peak
double avgBaselinePeakLocation = avgBaselinePeak.PeakX;
double avgBaselinePeakValue = avgBaselinePeak.PeakValue;
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
if (avgBaselinePeakLocation <= -0.3 && avgBaselinePeakLocation >= -0.4) //If a peak is between a certain range, the sample is infected, add in a minimal value once determined
{
_database.IsInfected = true;
}
else
{
_database.IsInfected = false;
}
_database.PeakVoltage = avgBaselinePeakValue;
await App.Database.SaveScanAsync(_database);
}
else //If no peak is detected
{
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
_database.IsInfected = false;
_database.PeakVoltage = 0.0;
_database.VoltamType = "Failed PC";
await App.Database.SaveScanAsync(_database);
}
}
else if (RunningPC) //If a postitive control test is being run with known values
{
SimpleMeasurement positiveControl;
using (StreamReader sr = new StreamReader(assetManager.Open(testRun + "_2525AfterTarget" + fileNum + ".pssession")))
positiveControl = SimpleLoadSaveFunctions.LoadMeasurements(sr)[0];
List <SimpleCurve> positiveCurves = positiveControl.SimpleCurveCollection;
SimpleCurve baselineCurve;
SimpleCurve subtractedCurve = positiveCurves[0].Subtract(baselineCurves[0]);
baselineCurve = subtractedCurve.MovingAverageBaseline();
subtractedCurve.Dispose();
baselineCurve.DetectPeaks(0.05, 0, true, false); //Detect all peaks with width greater than 0.05 V
PeakList positivePeakList = baselineCurve.Peaks;
baselineCurve.Dispose();
if (positivePeakList.nPeaks != 0) //If a peak is detected, execute the code below
{
Peak positivePeak = positivePeakList[positivePeakList.nPeaks - 1];
double positivePeakLocation = positivePeak.PeakX;
double positivePeakValue = positivePeak.PeakValue;
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
if (positivePeakLocation <= -0.3 && positivePeakLocation >= -0.4) //If a peak is between a certain range, the sample is infected, add in minimum value once determined
{
_database.IsInfected = true;
}
else
{
_database.IsInfected = false;
}
_database.PeakVoltage = positivePeakValue;
await App.Database.SaveScanAsync(_database);
}
else //If no peak is detected, execute the code below
{
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
_database.IsInfected = false;
_database.PeakVoltage = 0.0;
_database.VoltamType = "Failed PC";
await App.Database.SaveScanAsync(_database);
}
}
else if (RunningNC) //If a negative control test is being run
{
SimpleMeasurement negativeControl;
using (StreamReader sr = new StreamReader(assetManager.Open(testRun + "_2525AfterMch" + fileNum + ".pssession")))
negativeControl = SimpleLoadSaveFunctions.LoadMeasurements(sr)[0];
List <SimpleCurve> negativeCurves = negativeControl.SimpleCurveCollection;
SimpleCurve baselineCurve;
SimpleCurve subtractedCurve = negativeCurves[0].Subtract(baselineCurves[0]);
baselineCurve = subtractedCurve.MovingAverageBaseline();
subtractedCurve.Dispose();
baselineCurve.DetectPeaks(0.05, 0, true, false); //Detect all peaks with a width greater than 0.05 V
PeakList negativePeakList = baselineCurve.Peaks;
baselineCurve.Dispose();
if (negativePeakList.nPeaks != 0) //If a peak is detected, execute the code below
{
Peak negativePeak = negativePeakList[negativePeakList.nPeaks - 1];
double negativePeakLocation = negativePeak.PeakX;
double negativePeakValue = negativePeak.PeakValue;
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
if (negativePeakLocation <= -0.3 && negativePeakLocation >= -0.4) //If a peak is in a certain range, the sample is infected, add a minimum value once determined
{
_database.IsInfected = true;
}
else
{
_database.IsInfected = false;
}
_database.PeakVoltage = negativePeakValue;
await App.Database.SaveScanAsync(_database);
}
else //If a peak is not detected
{
List <ScanDatabase> allDb = await App.Database.GetScanDatabasesAsync();
ScanDatabase _database = await App.Database.GetScanAsync(allDb.Count);
_database.IsInfected = false;
_database.PeakVoltage = 0.0;
_database.VoltamType = "Failed NC";
await App.Database.SaveScanAsync(_database);
}
}
}
}