public void TestCorruptDataHandling(
string rawFileName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int corruptScanStart,
int corruptScanEnd)
{
var dataFile = GetRawDataFile(rawFileName);
try
{
using (var reader = new XRawFileIO(dataFile.FullName))
{
var scanCount = reader.GetNumScans();
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(reader.FileInfo.CorruptFile, "CorruptFile is false while we expected it to be true");
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsFalse(reader.FileInfo.CorruptFile, "CorruptFile is true while we expected it to be false");
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanCountMS1 = 0;
var scanCountMS2 = 0;
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
try
{
clsScanInfo scanInfo;
reader.GetScanInfo(scanNumber, out scanInfo);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is not empty but should be since corrupt file");
}
else
{
Assert.IsFalse(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is empty but should not be");
if (scanInfo.MSLevel > 1)
scanCountMS2++;
else
scanCountMS1++;
}
double[] mzList;
double[] intensityList;
// Note: this function call will fail randomly with file Corrupt_Scans6920-7021_AID_STM_013_101104_06_LTQ_16Nov04_Earth_0904-8.raw
// Furthermore, we are unable to catch the exception that occurs (or no exception is thrown) and adding
// [System.Runtime.ExceptionServices.HandleProcessCorruptedStateExceptions] to the function does not help
var dataPointCount = reader.GetScanData(scanNumber, out mzList, out intensityList);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(dataPointCount == 0, "GetScanData unexpectedly reported a non-zero data count for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
if (dataPointCount == 0)
{
Console.WriteLine("Corrupt scan encountered: {0}", scanNumber);
Assert.IsTrue(scanNumber >= corruptScanStart && scanNumber <= corruptScanEnd, "Unexpected corrupt scan found, scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
Assert.IsTrue(dataPointCount > 0, "GetScanData reported a data point count of 0 for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length > 0, "GetScanData unexpectedly returned no m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length > 0, "GetScanData unexpectedly returned no intensity data for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == intensityList.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
Assert.IsTrue(dataPointCount == mzList.Length, "Array length does not agree with dataPointCount for scan {0}", scanNumber);
}
}
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
catch (Exception ex)
{
var msg = string.Format("Exception opening .raw file {0}:\n{1}", rawFileName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
public void TestGetScanData(string rawFileName, int scanStart, int scanEnd)
{
var expectedData = new Dictionary<string, Dictionary<int, Dictionary<string, string>>>();
// Keys in this dictionary are the scan number of data being retrieved
var file1Data = new Dictionary<int, Dictionary<string, string>>
{
{1513, new Dictionary<string, string>()},
{1514, new Dictionary<string, string>()},
{1515, new Dictionary<string, string>()},
{1516, new Dictionary<string, string>()},
{1517, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file1Data[1513].Add("0_False", " 851 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_False", " 109 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("0_False", " 290 290 335.798 3.8E+4 1034.194 1.6E+4 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("0_False", " 154 154 461.889 7.3E+3 1203.274 2.6E+3 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("0_False", " 887 887 420.016 9.7E+5 1232.206 8.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("0_True", " 851 851 409.615 4.8E+5 1227.956 1.6E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("0_True", " 109 109 281.601 2.4E+4 633.151 4.4E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("0_True", " 290 290 335.798 3.8E+4 1034.194 1.6E+4 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("0_True", " 154 154 461.889 7.3E+3 1203.274 2.6E+3 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("0_True", " 887 887 420.016 9.7E+5 1232.206 8.0E+5 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_False", " 50 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_False", " 50 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("50_False", " 50 50 353.590 9.7E+4 1157.949 3.6E+5 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("50_False", " 50 50 461.889 7.3E+3 1146.341 1.4E+4 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("50_False", " 50 50 883.347 8.9E+6 1206.792 5.5E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1513].Add("50_True", " 50 50 747.055 2.5E+6 1148.485 3.4E+6 + c ESI Full ms [400.00-2000.00]");
file1Data[1514].Add("50_True", " 50 50 281.601 2.4E+4 632.089 2.6E+4 + c d Full ms2 [email protected] [230.00-1780.00]");
file1Data[1515].Add("50_True", " 50 50 353.590 9.7E+4 1157.949 3.6E+5 + c d Full ms2 [email protected] [305.00-2000.00]");
file1Data[1516].Add("50_True", " 50 50 461.889 7.3E+3 1146.341 1.4E+4 + c d Full ms2 [email protected] [400.00-2000.00]");
file1Data[1517].Add("50_True", " 50 50 883.347 8.9E+6 1206.792 5.5E+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>()},
{16122, new Dictionary<string, string>()},
{16126, new Dictionary<string, string>()},
{16131, new Dictionary<string, string>()},
{16133, new Dictionary<string, string>()},
{16141, new Dictionary<string, string>()}
};
// The KeySpec for each dictionary entry is MaxDataCount_Centroid
file2Data[16121].Add("0_False", "11888 11888 346.518 0.0E+0 706.844 9.8E+4 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_False", " 490 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("0_False", " 753 753 231.045 1.1E+1 1004.586 2.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("0_False", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("0_False", " 280 280 260.118 2.3E+1 663.160 7.7E+0 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("0_False", " 240 240 304.425 1.3E+1 1447.649 3.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("0_True", " 833 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("0_True", " 490 490 116.232 7.0E+1 403.932 1.1E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("0_True", " 753 753 231.045 1.1E+1 1004.586 2.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("0_True", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("0_True", " 280 280 260.118 2.3E+1 663.160 7.7E+0 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("0_True", " 240 240 304.425 1.3E+1 1447.649 3.0E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("50_False", " 50 50 503.553 2.0E+7 504.571 2.1E+7 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_False", " 50 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("50_False", " 50 50 535.311 2.5E+3 798.982 1.3E+3 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("50_False", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("50_False", " 50 50 356.206 7.5E+1 795.543 1.3E+2 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("50_False", " 50 50 853.937 5.6E+1 1705.974 9.8E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
file2Data[16121].Add("50_True", " 833 833 351.231 2.9E+5 712.813 2.9E+5 FTMS + p NSI Full ms [350.0000-1550.0000]");
file2Data[16122].Add("50_True", " 50 50 157.049 2.0E+4 385.181 6.0E+3 ITMS + c NSI r d Full ms2 [email protected] [106.0000-817.0000]");
file2Data[16126].Add("50_True", " 50 50 535.311 2.5E+3 798.982 1.3E+3 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-1627.0000]");
file2Data[16131].Add("50_True", " 29 29 984.504 9.5E+3 1931.917 2.4E+1 ITMS + c NSI r d Full ms2 [email protected] [120.0000-1986.0000]");
file2Data[16133].Add("50_True", " 50 50 356.206 7.5E+1 795.543 1.3E+2 ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00 [120.0000-853.0000]");
file2Data[16141].Add("50_True", " 50 50 853.937 5.6E+1 1705.974 9.8E+1 ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00 [120.0000-1760.0000]");
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))
{
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;
}
if (iteration == 1)
{
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,-8} {9}",
"Scan", "Max#", "Centroid", "MzCount", "IntCount",
"FirstMz", "FirstInt", "MidMz", "MidInt", "ScanFilter");
}
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
double[] mzList;
double[] intensityList;
var dataPointsRead = reader.GetScanData(scanNumber, out mzList, out intensityList, maxNumberOfPeaks, centroidData);
Assert.IsTrue(dataPointsRead > 0, "GetScanData returned 0 for scan {0}", scanNumber);
Assert.AreEqual(dataPointsRead, mzList.Length, "Data count mismatch vs. function return value");
var midPoint = (int)(intensityList.Length / 2f);
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var scanSummary =
string.Format(
"{0} {1,3} {2,8} {3,8} {4,8} {5,8} {6,8} {7,8} {8,8} {9}",
scanNumber, maxNumberOfPeaks, centroidData,
mzList.Length, intensityList.Length,
mzList[0].ToString("0.000"), intensityList[0].ToString("0.0E+0"),
mzList[midPoint].ToString("0.000"), intensityList[midPoint].ToString("0.0E+0"),
scanInfo.FilterText);
Console.WriteLine(scanSummary);
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(scanNumber, out expectedDataByType))
{
var keySpec = maxNumberOfPeaks + "_" + centroidData;
string expectedDataDetails;
if (expectedDataByType.TryGetValue(keySpec, out expectedDataDetails))
{
Assert.AreEqual(expectedDataDetails, scanSummary.Substring(22),
"Scan details mismatch, scan " + scanNumber + ", keySpec " + keySpec);
}
}
}
}
}
}
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);
}
}