public void TestGetScanDataSumScans(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, Dictionary<string, string>>>();
// Keys in this dictionary are the start scan for summing
var file1Data = new Dictionary<int, Dictionary<string, string>>
{
{1513, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file1Data[1513].Add("0_False", "1390 409.769 2.7E+5 1241.231 4.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("0_True", "1390 409.769 2.7E+5 1241.231 4.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_False", " 50 883.357 5.5E+6 1213.223 2.0E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_True", " 50 883.357 5.5E+6 1213.223 2.0E+6 + c ESI Full ms [400.00-2000.00]");
expectedData.Add("Shew_246a_LCQa_15Oct04_Andro_0904-2_4-20", file1Data);
var file2Data = new Dictionary<int, Dictionary<string, string>>
{
{16121, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file2Data[16121].Add("0_False", "26057 346.518 0.0E+0 753.312 8.7E+0 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("0_True", " 818 351.230 3.2E+5 820.778 2.3E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("50_False", " 50 503.553 1.2E+7 521.201 1.6E+7 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16121].Add("50_True", " 50 371.885 2.6E+7 650.717 9.8E+6 FTMS + p NSI Full ms [350.0000-1550.0000]");
expectedData.Add("HCC-38_ETciD_EThcD_4xdil_20uL_3hr_3_08Jan16_Pippin_15-08-53", file2Data);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Scan data for {0}", dataFile.Name);
Console.WriteLine("{0} {1,3} {2,8} {3,-8} {4,-8} {5,-8} {6,-8} {7,-8} {8}",
"Scan", "Max#", "Centroid", "DataCount",
"FirstMz", "FirstInt", "MidMz", "MidInt", "ScanFilter");
for (var iteration = 1; iteration <= 4; iteration++)
{
int maxNumberOfPeaks;
bool centroidData;
switch (iteration)
{
case 1:
maxNumberOfPeaks = 0;
centroidData = false;
break;
case 2:
maxNumberOfPeaks = 0;
centroidData = true;
break;
case 3:
maxNumberOfPeaks = 50;
centroidData = false;
break;
default:
maxNumberOfPeaks = 50;
centroidData = true;
break;
}
double[,] massIntensityPairs;
var dataPointsRead = reader.GetScanDataSumScans(scanStart, scanEnd, out massIntensityPairs, maxNumberOfPeaks, centroidData);
Assert.IsTrue(dataPointsRead > 0, string.Format("GetScanDataSumScans returned 0 summing scans {0} to {1}", scanStart, scanEnd));
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanStart, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanStart);
var lastIndex = massIntensityPairs.GetUpperBound(1);
int dataCount;
if (maxNumberOfPeaks > 0)
{
dataCount = maxNumberOfPeaks;
// Make sure the 2D array has values of 0 for mass and intensity beyond index maxNumberOfPeaks
for (var dataIndex = maxNumberOfPeaks; dataIndex < lastIndex; dataIndex++)
{
if (massIntensityPairs[0, dataIndex] > 0)
{
Console.WriteLine("Non-zero m/z value found at index {0} for scan {1}", dataIndex, scanStart);
Assert.AreEqual(0, massIntensityPairs[0, dataIndex], "Non-zero m/z value found in 2D array beyond expected index");
}
if (massIntensityPairs[1, dataIndex] > 0)
{
Console.WriteLine("Non-zero intensity value found at index {0} for scan {1}", dataIndex, scanStart);
Assert.AreEqual(0, massIntensityPairs[1, dataIndex], "Non-zero intensity value found in 2D array beyond expected index");
}
}
}
else
{
dataCount = lastIndex + 1;
}
Assert.AreEqual(dataPointsRead, dataCount, "Data count mismatch vs. function return value");
var midPoint = (int)(dataCount / 2f);
var scanSummary =
string.Format(
"{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7,8} {8}",
scanStart, maxNumberOfPeaks, centroidData,
dataCount,
massIntensityPairs[0, 0].ToString("0.000"), massIntensityPairs[1, 0].ToString("0.0E+0"),
massIntensityPairs[0, midPoint].ToString("0.000"), massIntensityPairs[1, midPoint].ToString("0.0E+0"),
scanInfo.FilterText);
Dictionary<int, Dictionary<string, string>> expectedDataThisFile;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedDataThisFile))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Dictionary<string, string> expectedDataByType;
if (expectedDataThisFile.TryGetValue(scanStart, out expectedDataByType))
{
var keySpec = maxNumberOfPeaks + "_" + centroidData;
string expectedDataDetails;
if (expectedDataByType.TryGetValue(keySpec, out expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary.Substring(22),
"Scan details mismatch, scan " + scanStart + ", keySpec " + keySpec);
}
}
Console.WriteLine(scanSummary);
}
}
}
private static void TestReader(string rawFilePath, bool centroid = false, bool testSumming = false, int scanStart = 0, int scanEnd = 0)
{
try {
if (!File.Exists(rawFilePath)) {
Console.WriteLine("File not found, skipping: " + rawFilePath);
return;
}
using (var oReader = new XRawFileIO(rawFilePath))
{
foreach(var method in oReader.FileInfo.InstMethods) {
Console.WriteLine(method);
}
var iNumScans = oReader.GetNumScans();
var strCollisionEnergies = string.Empty;
ShowMethod(oReader);
var scanStep = 1;
if (scanStart < 1)
scanStart = 1;
if (scanEnd < 1) {
scanEnd = iNumScans;
scanStep = 21;
} else {
if (scanEnd < scanStart) {
scanEnd = scanStart;
}
}
for (var iScanNum = scanStart; iScanNum <= scanEnd; iScanNum += scanStep) {
clsScanInfo oScanInfo;
var bSuccess = oReader.GetScanInfo(iScanNum, out oScanInfo);
if (bSuccess) {
Console.Write("Scan " + iScanNum + " at " + oScanInfo.RetentionTime.ToString("0.00") + " minutes: " + oScanInfo.FilterText);
var lstCollisionEnergies = oReader.GetCollisionEnergy(iScanNum);
if (lstCollisionEnergies.Count == 0) {
strCollisionEnergies = string.Empty;
} else if (lstCollisionEnergies.Count >= 1) {
strCollisionEnergies = lstCollisionEnergies[0].ToString("0.0");
if (lstCollisionEnergies.Count > 1) {
for (var intIndex = 1; intIndex <= lstCollisionEnergies.Count - 1; intIndex++) {
strCollisionEnergies += ", " + lstCollisionEnergies[intIndex].ToString("0.0");
}
}
}
if (string.IsNullOrEmpty(strCollisionEnergies)) {
Console.WriteLine();
} else {
Console.WriteLine("; CE " + strCollisionEnergies);
}
string monoMZ;
string chargeState;
string isolationWidth;
if (oScanInfo.TryGetScanEvent("Monoisotopic M/Z:", out monoMZ, false)) {
Console.WriteLine("Monoisotopic M/Z: " + monoMZ);
}
if (oScanInfo.TryGetScanEvent("Charge State", out chargeState, true))
{
Console.WriteLine("Charge State: " + chargeState);
}
if (oScanInfo.TryGetScanEvent("MS2 Isolation Width", out isolationWidth, true))
{
Console.WriteLine("MS2 Isolation Width: " + isolationWidth);
}
if (iScanNum % 50 == 0 || scanEnd - scanStart <= 50) {
// Get the data for scan iScanNum
Console.WriteLine();
Console.WriteLine("Spectrum for scan " + iScanNum);
double[] dblMzList;
double[] dblIntensityList;
var intDataCount = oReader.GetScanData(iScanNum, out dblMzList, out dblIntensityList, 0, centroid);
var mzDisplayStepSize = 50;
if (centroid) {
mzDisplayStepSize = 1;
}
for (var iDataPoint = 0; iDataPoint <= dblMzList.Length - 1; iDataPoint += mzDisplayStepSize) {
Console.WriteLine(" " + dblMzList[iDataPoint].ToString("0.000") + " mz " + dblIntensityList[iDataPoint].ToString("0"));
}
Console.WriteLine();
const int scansToSum = 15;
if (iScanNum + scansToSum < iNumScans & testSumming) {
// Get the data for scan iScanNum through iScanNum + 15
double[,] dblMassIntensityPairs;
var dataCount = oReader.GetScanDataSumScans(iScanNum, iScanNum + scansToSum, out dblMassIntensityPairs, 0, centroid);
Console.WriteLine("Summed spectrum, scans " + iScanNum + " through " + (iScanNum + scansToSum));
for (var iDataPoint = 0; iDataPoint <= dblMassIntensityPairs.GetLength(1) - 1; iDataPoint += 50) {
Console.WriteLine(" " + dblMassIntensityPairs[0, iDataPoint].ToString("0.000") + " mz " + dblMassIntensityPairs[1, iDataPoint].ToString("0"));
}
Console.WriteLine();
}
if (oScanInfo.IsFTMS) {
udtFTLabelInfoType[] ftLabelData;
var dataCount = oReader.GetScanLabelData(iScanNum, out ftLabelData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", "Mass", "Intensity", "Resolution", "Baseline", "Noise", "Charge");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", ftLabelData[iDataPoint].Mass.ToString("0.000"), ftLabelData[iDataPoint].Intensity.ToString("0"), ftLabelData[iDataPoint].Resolution.ToString("0"), ftLabelData[iDataPoint].Baseline.ToString("0.0"), ftLabelData[iDataPoint].Noise.ToString("0"), ftLabelData[iDataPoint].Charge.ToString("0"));
}
udtMassPrecisionInfoType[] ftPrecisionData;
dataCount = oReader.GetScanPrecisionData(iScanNum, out ftPrecisionData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", "Mass", "Intensity", "AccuracyMMU", "AccuracyPPM", "Resolution");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", ftPrecisionData[iDataPoint].Mass.ToString("0.000"), ftPrecisionData[iDataPoint].Intensity.ToString("0"), ftPrecisionData[iDataPoint].AccuracyMMU.ToString("0.000"), ftPrecisionData[iDataPoint].AccuracyPPM.ToString("0.000"), ftPrecisionData[iDataPoint].Resolution.ToString("0"));
}
}
}
}
}
}
} catch (Exception ex) {
Console.WriteLine("Error in sub TestReader: " + ex.Message);
}
}