public void GetLCChromatogramTest3()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 1280;
const int startScan = 163;
const double targetMZ = 464.25486;
const double toleranceInPPM = 25;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
using (mReader = new DataReader(FileRefs.LegacyFile1))
{
// int[] scanVals = null;
var sw = new Stopwatch();
sw.Start();
mReader.GetLCProfile(
startFrame - 200,
startFrame + 200,
UIMFData.FrameType.MS1,
startScan - 2,
startScan + 2,
targetMZ,
toleranceInMZ,
out var frameVals,
out var intensityVals);
sw.Stop();
Console.WriteLine("Time (ms) = " + sw.ElapsedMilliseconds);
// TestUtilities.display2DChromatogram(frameVals, intensityVals);
}
}
public void GetMSMSTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.MSMSData1))
{
const int testFrame = 2;
const int startScan = 1;
const int stopScan = 300;
reader.GetSpectrum(
testFrame,
testFrame,
UIMFData.FrameType.MS2,
startScan,
stopScan,
out var mzArray,
out var intensityArray);
var sb = new StringBuilder();
for (var i = 0; i < mzArray.Length; i++)
{
sb.Append(mzArray[i] + "\t" + intensityArray[i] + "\n");
}
Assert.IsNotNull(mzArray);
Assert.IsTrue(mzArray.Length > 0);
}
}
public void ContainsMSMSData_test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyFile1))
{
Assert.AreEqual(false, reader.HasMSMSData());
}
}
public void GetGlobalParams_test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyDemultiplexedFile1))
{
var gp = reader.GetGlobalParams();
var dt = DateTime.Parse(gp.GetValue(GlobalParamKeyType.DateStarted));
Assert.AreEqual("04/07/2011 06:40:30", dt.ToString(CultureInfo.InvariantCulture));
}
}
public void GetAvgTOFLengthTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyFile1))
{
var fp = reader.GetFrameParams(1);
var avgTOFLength = fp.GetValueDouble(FrameParamKeyType.AverageTOFLength, 0);
Assert.AreEqual(162555.56m, (decimal)avgTOFLength);
}
}
public void GetNumberOfFramesTest()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyFile1))
{
var numFrames = reader.GetGlobalParams().NumFrames;
// Console.WriteLine("Number of frames = " + numFrames);
Assert.AreEqual(3220, numFrames);
}
}
public void Get3DElutionProfile_test3()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 400;
const int stopFrame = 600;
const int startScan = 110;
const int stopScan = 210;
const double targetMZ = 475.7499;
const double toleranceInPPM = 25;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
const string filePath = @"\\proto-2\UnitTest_Files\DeconTools_TestFiles\UIMF\Sarc_MS_90_21Aug10_Cheetah_10-08-02_0000.uimf";
int[] frameVals;
int[] scanVals;
int[] intensityVals;
var sw = new Stopwatch();
sw.Start();
using (mReader = new DataReader(filePath))
{
mReader.Get3DElutionProfile(
startFrame,
stopFrame,
0,
startScan,
stopScan,
targetMZ,
toleranceInMZ,
out frameVals,
out scanVals,
out intensityVals);
}
sw.Stop();
Console.WriteLine("Time in millisec for extracting 3D profile = " + sw.ElapsedMilliseconds);
var sb = new StringBuilder();
for (var i = 0; i < frameVals.Length; i++)
{
sb.Append(frameVals[i] + "\t" + scanVals[i] + "\t" + intensityVals[i] + Environment.NewLine);
}
// Console.WriteLine(sb.ToString());
}
public void GetLCChromatogramTest2()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 600;
const int endFrame = 800;
const int startScan = 100;
const int stopScan = 350;
using (mReader = new DataReader(FileRefs.LegacyFile1))
{
const double targetMZ = 636.8466; // see frame 1000, scan 170
const double toleranceInPPM = 20;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
// mReader.GetDriftTimeProfile(testFrame, frameType, startScan, stopScan, targetMZ, toleranceInMZ, ref scanVals, ref intensityVals);
var sw = new Stopwatch();
sw.Start();
mReader.GetLCProfile(
startFrame,
endFrame,
UIMFData.FrameType.MS1,
startScan,
stopScan,
targetMZ,
toleranceInMZ,
out var frameVals,
out var intensityVals);
sw.Stop();
var sb = new StringBuilder();
for (var i = 0; i < frameVals.Length; i++)
{
sb.Append(frameVals[i]);
sb.Append('\t');
sb.Append(intensityVals[i]);
sb.Append(Environment.NewLine);
}
// Assert.AreEqual(171, frameVals[71]);
// Assert.AreEqual(6770, intensityVals[71]);
Assert.AreEqual(endFrame - startFrame + 1, frameVals.Length);
// Console.Write(sb.ToString());
Console.WriteLine("Time (ms) = " + sw.ElapsedMilliseconds);
}
}
public void Get3DElutionProfile_test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 1280;
const int startScan = 163;
const double targetMZ = 464.25486;
const double toleranceInPPM = 25;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
int[] intensityVals;
var sw = new Stopwatch();
sw.Start();
using (mReader = new DataReader(FileRefs.LegacyFile1))
{
mReader.Get3DElutionProfile(
startFrame - 20,
startFrame + 20,
0,
startScan - 20,
startScan + 20,
targetMZ,
toleranceInMZ,
out var frameVals,
out var scanVals,
out intensityVals);
}
sw.Stop();
var max = TestUtilities.GetMax(intensityVals);
var normInten = new float[intensityVals.Length];
for (var i = 0; i < intensityVals.Length; i++)
{
normInten[i] = (float)intensityVals[i] / max;
}
Assert.AreEqual(1913, max);
Assert.AreEqual((float)0.0172503926, normInten[16]);
Console.WriteLine("Time (ms) = " + sw.ElapsedMilliseconds);
}
public void Get3DElutionProfile_test2()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 524;
const int startScan = 128;
const double targetMZ = 295.9019; // see frame 2130, scan 153
const double toleranceInPPM = 25;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
using (mReader = new DataReader(FileRefs.LegacyFile1))
{
var values = mReader.GetFramesAndScanIntensitiesForAGivenMz(
startFrame - 40,
startFrame + 40,
0,
startScan - 60,
startScan + 60,
targetMZ,
toleranceInMZ);
var sb = new StringBuilder();
foreach (var frameIntensities in values)
{
foreach (var scanIntensityValue in frameIntensities)
{
if (scanIntensityValue > 0)
{
sb.Append(scanIntensityValue + ",");
}
}
sb.Append(Environment.NewLine);
}
Assert.AreEqual(293, values[0][64]);
Assert.AreEqual(510, values[2][66]);
Assert.AreEqual(663, values[3][64]);
Assert.AreEqual(436, values[4][57]);
// Console.WriteLine(sb.ToString());
}
}
public void GetFrameTypeTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.MSMSData1))
{
var gp = reader.GetGlobalParams();
var checkSum = 0;
for (var frame = 1; frame <= gp.NumFrames; frame++)
{
checkSum += frame * (int)reader.GetFrameTypeForFrame(frame);
}
Assert.AreEqual(222, checkSum);
}
}
public void GetFrameInfo_demultiplexed_firstFrame_Test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyDemultiplexedFile1))
{
const int firstFrame = 1;
var fp = reader.GetFrameParams(firstFrame);
Assert.AreEqual(UIMFData.FrameType.MS1, fp.FrameType);
Assert.AreEqual(0.03313236, fp.CalibrationIntercept);
Assert.AreEqual(0.3476655, fp.CalibrationSlope);
Assert.AreEqual(360, fp.Scans);
// TestUtilities.DisplayFrameParameters(fp);
}
}
public void GetMultipleSummedMassSpectrumsTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var dr = new DataReader(FileRefs.LegacyFile1))
{
var testFrameScanInfo2 = new FrameAndScanInfo(500, 550, 250, 256);
for (var frame = testFrameScanInfo2.startFrame; frame <= testFrameScanInfo2.stopFrame; frame++)
{
var gp = dr.GetGlobalParams();
var nonZeros = dr.GetSpectrum(
frame,
frame,
UIMFData.FrameType.MS1,
testFrameScanInfo2.startScan,
testFrameScanInfo2.stopScan,
out var mzValues,
out var intensities);
// jump back
nonZeros = dr.GetSpectrum(
frame - 1,
frame - 1,
UIMFData.FrameType.MS1,
testFrameScanInfo2.startScan,
testFrameScanInfo2.stopScan,
out mzValues,
out intensities);
// and ahead... just testing it's ability to jump around
nonZeros = dr.GetSpectrum(
frame + 2,
frame + 2,
UIMFData.FrameType.MS1,
testFrameScanInfo2.startScan,
testFrameScanInfo2.stopScan,
out mzValues,
out intensities);
}
}
}
public void GetFramePressure_lastFrame()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyFile1))
{
const int lastFrame = 3219;
const int secondToLastFrame = lastFrame - 1;
var pressureBackLastFrame = reader.GetFrameParams(lastFrame).GetValueDouble(FrameParamKeyType.PressureBack);
var pressureBackSecondToLastFrame = reader.GetFrameParams(secondToLastFrame).GetValueDouble(FrameParamKeyType.PressureBack);
// Console.WriteLine("Pressure for frame " + secondToLastFrame + " = " + pressureBackSecondToLastFrame);
// Console.WriteLine("Pressure for frame "+lastFrame + " = " + pressureBackLastFrame);
Assert.AreEqual(4.127, (decimal)pressureBackLastFrame);
Assert.AreEqual(4.136, (decimal)pressureBackSecondToLastFrame);
}
}
public void GetFrame0_MS_Test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var dr = new DataReader(FileRefs.LegacyFile1))
{
var gp = dr.GetGlobalParams();
var nonZeros = dr.GetSpectrum(
testFrameScanInfo1.startFrame,
testFrameScanInfo1.stopFrame,
UIMFData.FrameType.MS1,
testFrameScanInfo1.startScan,
testFrameScanInfo1.stopScan,
out var mzValues,
out var intensities);
TestUtilities.DisplayRawMassSpectrum(mzValues, intensities);
}
}
public void GetFrameInfo_demultiplexed_lastFrame_Test1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var reader = new DataReader(FileRefs.LegacyDemultiplexedFile1))
{
var numFrames = reader.GetGlobalParams().NumFrames;
var lastFrame = numFrames - 1;
Console.WriteLine("Last frame = " + lastFrame);
var fp = reader.GetFrameParams(lastFrame);
Assert.AreEqual(UIMFData.FrameType.MS1, fp.FrameType);
Assert.AreEqual(0.03313236, fp.CalibrationIntercept);
Assert.AreEqual(0.3476655, fp.CalibrationSlope);
Assert.AreEqual(360, fp.Scans);
// TestUtilities.DisplayFrameParameters(fp);
}
}
public void GetSingleSummedMassSpectrumTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
using (var dr = new DataReader(FileRefs.LegacyFile1))
{
var gp = dr.GetGlobalParams();
var nonZeros = dr.GetSpectrum(
testFrameScanInfo1.startFrame,
testFrameScanInfo1.stopFrame,
UIMFData.FrameType.MS1,
testFrameScanInfo1.startScan,
testFrameScanInfo1.stopScan,
out var mzValues,
out var intensities);
var nonZeroCount = (from n in mzValues where Math.Abs(n) > Single.Epsilon select n).Count();
Console.WriteLine("Num xy datapoints = " + nonZeroCount);
Assert.AreEqual(1137, nonZeros);
}
}
public void GetDriftTimeProfileTest1()
{
DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
const int startFrame = 1280;
const int startScan = 150;
const double targetMZ = 451.55;
const double toleranceInPPM = 10;
const double toleranceInMZ = toleranceInPPM / 1e6 * targetMZ;
int[] scanVals = null;
int[] intensityVals = null;
using (mReader = new DataReader(FileRefs.LegacyFile1))
{
mReader.GetDriftTimeProfile(
startFrame - 2,
startFrame + 2,
UIMFData.FrameType.MS1,
startScan - 100,
startScan + 100,
targetMZ,
toleranceInMZ,
ref scanVals,
ref intensityVals);
TestUtilities.Display2DChromatogram(scanVals, intensityVals);
Assert.AreEqual(50, scanVals[0]);
Assert.AreEqual(250, scanVals[200]);
Assert.AreEqual(6525, intensityVals[100]);
Assert.AreEqual(3199, intensityVals[105]);
Assert.AreEqual(255, intensityVals[111]);
}
}
