public void TestDemultiplexUIMFSingleFrame()
{
// Old: const int numSegments = 24;
const int numberOfBits = 4;
const int lcFramesToSum = 1;
const string matrixString = "100110101111000";
var multiplierMatrix = MatrixCreator.CreateMatrixForDemultiplexing(matrixString);
var scaledMatrix = (DenseMatrix)multiplierMatrix.Multiply(2.0 / 16.0);
var inversedScaledMatrix = (DenseMatrix)scaledMatrix.Inverse();
Assert.AreEqual(15, inversedScaledMatrix.ColumnCount);
Assert.AreEqual(15, inversedScaledMatrix.RowCount);
var expectMatrixVals = new List <int>
{
1,
-1,
-1,
1,
1,
-1,
1,
-1,
1,
1,
1,
1,
-1
};
for (var i = 0; i < expectMatrixVals.Count; i++)
{
Assert.AreEqual(expectMatrixVals[i], inversedScaledMatrix.Values[i], 0.01, "inversedScaledMatrix has unexpected values");
}
var uimfFile = VerifyLocalUimfFile(@"Test_Data\9pep_mix_1uM_4bit_50_12Dec11_encoded.uimf");
if (uimfFile == null)
{
var currentDirectory = new DirectoryInfo(".");
Assert.Fail("UIMF file not found; Current working directory is " + currentDirectory.FullName);
}
Console.WriteLine("Opening " + uimfFile.FullName);
var uimfReader = new DataReader(uimfFile.FullName);
var globalParams = uimfReader.GetGlobalParams();
var binWidth = globalParams.BinWidth;
var frameNumbers = new List <int>(uimfReader.GetFrameNumbers(UIMFData.FrameType.MS1));
frameNumbers.AddRange(uimfReader.GetFrameNumbers(UIMFData.FrameType.Calibration));
frameNumbers.AddRange(uimfReader.GetFrameNumbers(UIMFData.FrameType.MS2));
frameNumbers.Sort();
var numFrames = frameNumbers.Count;
Console.WriteLine("Total Data Frames = " + numFrames);
var baseFileName = Path.GetFileNameWithoutExtension(uimfFile.Name);
string newFileName;
if (baseFileName.Contains("encoded"))
{
newFileName = baseFileName.Replace("encoded", "decoded") + ".uimf";
}
else
{
newFileName = baseFileName + "_decoded.uimf";
}
if (uimfFile.DirectoryName == null)
{
Assert.Fail("Unable to determine the parent directory of " + uimfFile.FullName);
}
var newFile = new FileInfo(Path.Combine(uimfFile.DirectoryName, newFileName));
var bitSequence = DemultiplexerOptions.GetBitSequence(numberOfBits);
Assert.AreEqual(matrixString, bitSequence, "Unexpected bit sequence: " + bitSequence + "; expecting " + matrixString);
if (newFile.Exists)
{
Console.WriteLine("Deleting existing decoded UIMF file: " + newFile.FullName);
try
{
newFile.Delete();
}
catch (Exception ex)
{
Assert.Fail("Error deleting file: " + ex.Message);
}
}
Console.WriteLine("Demultiplexing to create " + newFile.FullName);
var executingAssembly = System.Reflection.Assembly.GetExecutingAssembly();
using (var uimfWriter = new DataWriter(newFile.FullName, executingAssembly))
{
uimfWriter.CreateTables(globalParams.GetValue(GlobalParamKeyType.DatasetType));
uimfWriter.InsertGlobal(globalParams);
// Old method of instantiating the Demultiplexer:
// var firstFrameParams = uimfReader.GetFrameParams(1);
// var averageTOFLength = firstFrameParams.GetValueDouble(FrameParamKeyType.AverageTOFLength);
// Demultiplexer demultiplexer = new Demultiplexer(inversedScaledMatrix, numSegments, binWidth, averageTOFLength);
var demultiplexerOptions = new DemultiplexerOptions();
var demultiplexer = new Demultiplexer(demultiplexerOptions);
var scanToIndexMap = demultiplexerOptions.ScanToIndexMap;
var segmentLength = demultiplexer.NumberOfSegments;
foreach (var currentFrameNumber in frameNumbers)
{
Console.WriteLine("Processing Frame " + currentFrameNumber);
// Setup the frame in the UIMFWriter
var frameParams = uimfReader.GetFrameParams(currentFrameNumber);
uimfWriter.InsertFrame(currentFrameNumber, frameParams);
// If we are dealing with a calibration frame, we just want to write the data to the new UIMF file as is
if (frameParams.FrameType == UIMFData.FrameType.Calibration)
{
for (var i = 0; i < frameParams.Scans; i++)
{
var intensities = uimfReader.GetSpectrumAsBins(
currentFrameNumber,
currentFrameNumber,
frameParams.FrameType,
startScanNumber: i,
endScanNumber: i);
var nonZeroCount = intensities.Count(x => x > 0);
uimfWriter.InsertScan(currentFrameNumber, frameParams, i, intensities, binWidth);
}
continue;
}
// Data pulled from the UIMF file will not be re-ordered
const bool isReordered = false;
// Get the data of the frame from the UIMF File
var arrayOfIntensityArrays = UIMFDemultiplexer.UIMFDemultiplexer.GetIntensityBlockForDemultiplexing(
uimfReader,
currentFrameNumber,
frameParams.FrameType,
segmentLength,
scanToIndexMap,
isReordered,
lcFramesToSum);
// Demultiplex the frame, which updates the array
var scanDataEnumerable = demultiplexer.DemultiplexFrame(arrayOfIntensityArrays, isReordered);
var sortByScanNumberQuery = (from scanData in scanDataEnumerable
orderby scanData.ScanNumber
select scanData).ToList();
Assert.AreEqual(93, sortByScanNumberQuery.Count);
foreach (var scanData in sortByScanNumberQuery)
{
var dataPoints = new List <Tuple <int, int> >(scanData.BinsToIntensitiesMap.Count);
dataPoints.AddRange(from dataPoint in scanData.BinsToIntensitiesMap
where dataPoint.Value != 0
orderby dataPoint.Key
select new Tuple <int, int>(dataPoint.Key, dataPoint.Value));
uimfWriter.InsertScan(
currentFrameNumber,
frameParams,
scanData.ScanNumber,
dataPoints,
binWidth,
0);
}
uimfWriter.FlushUimf();
}
}
}
public void CreateDB_test1(int frameCountToWrite)
{
DataReaderTests.DataReaderTests.PrintMethodName(System.Reflection.MethodBase.GetCurrentMethod());
var fiTarget = new FileInfo(FileRefs.WriterTest10Frames);
if (fiTarget.Exists)
{
fiTarget.Delete();
}
var executingAssembly = System.Reflection.Assembly.GetExecutingAssembly();
using (var writer = new DataWriter(fiTarget.FullName, executingAssembly))
{
writer.CreateTables("int");
var globalParameters = new GlobalParams();
globalParameters.AddUpdateValue(GlobalParamKeyType.Bins, 400000)
.AddUpdateValue(GlobalParamKeyType.BinWidth, 0.25)
.AddUpdateValue(GlobalParamKeyType.DateStarted, DateTime.Now)
.AddUpdateValue(GlobalParamKeyType.NumFrames, frameCountToWrite)
.AddUpdateValue(GlobalParamKeyType.TOFIntensityType, "ADC");
writer.InsertGlobal(globalParameters)
.AddUpdateGlobalParameter(GlobalParamKeyType.TimeOffset, 1)
.AddUpdateGlobalParameter(GlobalParamKeyType.InstrumentName, "IMS_Test");
Console.WriteLine("Adding frame 1");
const float SECONDS_PER_FRAME = 1.25f;
var randGenerator = new Random();
for (var frameNum = 1; frameNum <= frameCountToWrite; frameNum++)
{
var fp = new FrameParams();
fp.AddUpdateValue(FrameParamKeyType.FrameType, (int)UIMFData.FrameType.MS1)
.AddUpdateValue(FrameParamKeyType.CalibrationSlope, 0.3476349957054481)
.AddUpdateValue(FrameParamKeyType.CalibrationIntercept, 0.03434148864746093)
.AddUpdateValue(FrameParamKeyType.AverageTOFLength, 163366.6666666667)
.AddUpdateValue(FrameParamKeyType.StartTimeMinutes, frameNum * SECONDS_PER_FRAME)
.AddUpdateValue(FrameParamKeyType.Scans, 600);
writer.InsertFrame(frameNum, fp);
for (var scanNumber = 1; scanNumber <= 600; scanNumber++)
{
if (scanNumber == 1 | scanNumber % 100 == 0)
{
Console.WriteLine("Adding frame " + frameNum + ", scan " + scanNumber);
}
var intensities = new int[148000];
for (var i = 0; i < intensities.Length; i++)
{
var nextRandom = randGenerator.Next(0, 255);
if (nextRandom < 250)
{
intensities[i] = 0;
}
else
{
intensities[i] = nextRandom;
}
}
writer.InsertScan(frameNum, fp, scanNumber, intensities, globalParameters.BinWidth);
}
}
writer.UpdateGlobalStats();
Console.WriteLine("Wrote 10 frames of data to " + fiTarget.FullName);
}
}
private static void WriterTest()
{
var fiTestFile = new FileInfo("TestOutput.uimf");
try
{
if (fiTestFile.Exists)
{
fiTestFile.Delete();
}
}
catch (IOException)
{
Console.WriteLine("Existing " + fiTestFile.Name + " file exists and cannot be deleted (locked)");
return;
}
catch (Exception ex)
{
Console.WriteLine("Existing " + fiTestFile.Name + " file exists and cannot be deleted: " + ex.Message);
return;
}
try
{
Console.WriteLine("Creating " + fiTestFile.FullName);
using (var writer = new DataWriter(fiTestFile.FullName))
{
writer.CreateTables();
var globalParameters = new GlobalParams();
globalParameters.AddUpdateValue(GlobalParamKeyType.Bins, 400000)
.AddUpdateValue(GlobalParamKeyType.BinWidth, 0.25)
.AddUpdateValue(GlobalParamKeyType.DateStarted, DateTime.Now)
.AddUpdateValue(GlobalParamKeyType.TOFIntensityType, "ADC")
.AddUpdateValue(GlobalParamKeyType.TOFCorrectionTime, 0.0);
writer.InsertGlobal(globalParameters);
globalParameters = writer.GetGlobalParams();
writer.AddUpdateGlobalParameter(GlobalParamKeyType.TimeOffset, 1)
.AddUpdateGlobalParameter(GlobalParamKeyType.InstrumentName, "IMS_Test")
.FlushUimf();
const float SECONDS_PER_FRAME = 1.25f;
var randGenerator = new Random();
for (var frameNum = 1; frameNum <= 5; frameNum++)
{
var fp = new FrameParams();
fp.AddUpdateValue(FrameParamKeyType.FrameType, (int)UIMFLibrary.DataReader.FrameType.MS1)
.AddUpdateValue(FrameParamKeyType.CalibrationSlope, 0.3476349957054481)
.AddUpdateValue(FrameParamKeyType.CalibrationIntercept, 0.03434148864746093)
.AddUpdateValue(FrameParamKeyType.AverageTOFLength, 163366.6666666667)
.AddUpdateValue(FrameParamKeyType.StartTimeMinutes, frameNum * SECONDS_PER_FRAME);
writer.InsertFrame(frameNum, fp)
.AddUpdateFrameParameter(frameNum, FrameParamKeyType.Accumulations, "18")
.AddUpdateFrameParameter(frameNum, FrameParamKeyType.TOFLosses, randGenerator.Next(0, 150).ToString());
for (var scanNumber = 1; scanNumber < 600; scanNumber++)
{
if (scanNumber == 1 | scanNumber % 100 == 0)
{
Console.WriteLine("Adding frame " + frameNum + ", scan " + scanNumber);
}
var intensities = new int[148000];
for (var i = 0; i < intensities.Length; i++)
{
var nextRandom = randGenerator.Next(0, 255);
if (nextRandom < 250)
{
intensities[i] = 0;
}
else
{
intensities[i] = nextRandom;
}
}
writer.InsertScan(frameNum, fp, scanNumber, intensities, globalParameters.BinWidth);
}
}
}
Console.WriteLine("Wrote 5 frames of data to \n" + fiTestFile.FullName);
}
catch (Exception ex)
{
Console.WriteLine("Error testing the writer: " + ex.Message);
}
}
