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caeteracaetera
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UV and pressure chromatograms
1 parent 3102c48 commit ec418d5

3 files changed

Lines changed: 205 additions & 37 deletions

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‎.gitignore‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,6 @@
22
bin/
33
obj/
44
*.log
5-
ThermoRawFileParser.sln.DotSettings.user
5+
*.sln.DotSettings.user
66
.vs/
7-
7+
*.csproj.user

‎ThermoRawFileParser.csproj.user‎

Lines changed: 0 additions & 6 deletions
This file was deleted.

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 203 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -151,6 +151,42 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
151151
cvRef = "MS",
152152
value = ""
153153
});
154+
//ion current chromatogram
155+
SerializeCvParam(new CVParamType
156+
{
157+
accession = "MS:1000810",
158+
name = "ion current chromatogram",
159+
cvRef = "MS",
160+
value = ""
161+
});
162+
163+
//other detector data
164+
if(ParseInput.AllDetectors)
165+
{
166+
//PDA spectrum
167+
if(_rawFile.GetInstrumentCountOfType(Device.Pda) > 0)
168+
{
169+
SerializeCvParam(new CVParamType
170+
{
171+
accession = "MS:1000806",
172+
name = "absorption spectrum",
173+
cvRef = "MS",
174+
value = ""
175+
});
176+
}
177+
178+
//absorption chromatogram
179+
if (_rawFile.GetInstrumentCountOfType(Device.Pda) > 0 || _rawFile.GetInstrumentCountOfType(Device.UV) > 0)
180+
{
181+
SerializeCvParam(new CVParamType
182+
{
183+
accession = "MS:1000812",
184+
name = "absorption chromatogram",
185+
cvRef = "MS",
186+
value = ""
187+
});
188+
}
189+
}
154190
_writer.WriteEndElement(); // fileContent
155191

156192
// sourceFileList
@@ -244,6 +280,19 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
244280
name = "Conversion to mzML",
245281
value = ""
246282
});
283+
if (!ParseInput.NoPeakPicking)
284+
{
285+
_writer.WriteStartElement("processingMethod");
286+
_writer.WriteAttributeString("order", "1");
287+
_writer.WriteAttributeString("softwareRef", "ThermoRawFileParser");
288+
SerializeCvParam(new CVParamType
289+
{
290+
accession = "MS:1000035",
291+
cvRef = "MS",
292+
name = "peak picking",
293+
value = ""
294+
});
295+
}
247296
_writer.WriteEndElement(); // processingMethod
248297
_writer.WriteEndElement(); // dataProcessing
249298
_writer.WriteEndElement(); // dataProcessingList
@@ -257,7 +306,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
257306
_writer.WriteAttributeString("defaultSourceFileRef", SourceFileId);
258307
// spectrumList
259308
_writer.WriteStartElement("spectrumList");
260-
_writer.WriteAttributeString("count", _rawFile.RunHeaderEx.SpectraCount.ToString());
309+
_writer.WriteAttributeString("count", GetTotalScanNumber());
261310
_writer.WriteAttributeString("defaultDataProcessingRef", "ThermoRawFileParserProcessing");
262311

263312
serializer = _factory.CreateSerializer(typeof(SpectrumType));
@@ -266,7 +315,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
266315
var index = 0;
267316
var lastScanProgress = 0;
268317

269-
Log.Info("Processing " + (lastScanNumber - firstScanNumber) + " MS scans");
318+
Log.Info(String.Format("Processing {0} MS scans", + (1 + lastScanNumber - firstScanNumber)));
270319

271320
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
272321
{
@@ -318,14 +367,14 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
318367
// PDA spectra
319368
if (ParseInput.AllDetectors && _rawFile.GetInstrumentCountOfType(Device.Pda) > 0)
320369
{
321-
for (int nrI = 0; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda); nrI++)
370+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda) + 1; nrI++)
322371
{
323-
_rawFile.SelectInstrument(Device.Pda, nrI + 1);
372+
_rawFile.SelectInstrument(Device.Pda, nrI);
324373
firstScanNumber = _rawFile.RunHeader.FirstSpectrum;
325374
lastScanNumber = _rawFile.RunHeader.LastSpectrum;
326375
lastScanProgress = 0;
327376

328-
Log.Info("Processing " + (lastScanNumber - firstScanNumber) + " PDA scans from Device #" + (nrI + 1));
377+
Log.Info(String.Format("Processing {0} PDA scans from Device #{1}", (1 + lastScanNumber - firstScanNumber), nrI));
329378

330379
for (var scanNumber = firstScanNumber; scanNumber <= lastScanNumber; scanNumber++)
331380
{
@@ -342,7 +391,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
342391
}
343392
}
344393

345-
var spectrum = ConstructPDASpectrum(scanNumber, nrI + 1);
394+
var spectrum = ConstructPDASpectrum(scanNumber, nrI);
346395
if (spectrum != null)
347396
{
348397
spectrum.index = index.ToString();
@@ -532,6 +581,32 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
532581
}
533582
}
534583

584+
private string GetTotalScanNumber()
585+
{
586+
//save instrument that was selected last time
587+
var lastSelectedInstrument =_rawFile.SelectedInstrument;
588+
var numScans = 0;
589+
590+
_rawFile.SelectInstrument(Device.MS, 1);
591+
592+
numScans += 1 + _rawFile.RunHeader.LastSpectrum - _rawFile.RunHeader.FirstSpectrum;
593+
594+
if (ParseInput.AllDetectors)
595+
{
596+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda) + 1; nrI++)
597+
{
598+
_rawFile.SelectInstrument(Device.Pda, nrI);
599+
numScans += 1 + _rawFile.RunHeader.LastSpectrum - _rawFile.RunHeader.FirstSpectrum;
600+
}
601+
}
602+
603+
//return instrument to last selected one
604+
if (lastSelectedInstrument != null)
605+
_rawFile.SelectInstrument(lastSelectedInstrument.DeviceType, lastSelectedInstrument.InstrumentIndex);
606+
607+
return numScans.ToString();
608+
}
609+
535610
/// <summary>
536611
/// Populate the instrument configuration list
537612
/// </summary>
@@ -704,6 +779,8 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
704779
var chromatograms = new List<ChromatogramType>();
705780

706781
//MS chromatograms
782+
//Reselect MS device
783+
_rawFile.SelectInstrument(Device.MS, 1);
707784
// Define the settings for getting the Base Peak chromatogram
708785
var settings = new ChromatogramTraceSettings(TraceType.BasePeak);
709786

@@ -744,21 +821,22 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
744821

745822
}
746823

747-
//UV chromatograms
824+
//Chromatograms from other devices: UV, PDA
748825
if (ParseInput.AllDetectors)
749826
{
750-
for (int nrI = 0; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda); nrI++)
827+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.Pda) + 1; nrI++)
751828
{
752-
_rawFile.SelectInstrument(Device.Pda, nrI + 1);
829+
_rawFile.SelectInstrument(Device.Pda, nrI);
753830

754-
var settingsPDA = new ChromatogramTraceSettings(TraceType.TotalAbsorbance);
831+
var instData = _rawFile.GetInstrumentData();
755832

756-
var dataPDA = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settingsPDA },
757-
-1, -1);
833+
settings = new ChromatogramTraceSettings(TraceType.TotalAbsorbance);
758834

759-
var tracePDA = ChromatogramSignal.FromChromatogramData(dataPDA);
835+
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, -1, -1);
760836

761-
for (var i = 0; i < tracePDA.Length; i++)
837+
trace = ChromatogramSignal.FromChromatogramData(data);
838+
839+
for (var i = 0; i < trace.Length; i++)
762840
{
763841
// CV Data for Total Absorbance Chromatogram
764842
var chroType = new CVParamType
@@ -775,17 +853,115 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
775853
name = "intensity array",
776854
cvRef = "MS",
777855
unitName = "absorbance unit",
778-
value = "",
856+
value = instData.Units.ToString(),
779857
unitCvRef = "UO",
780858
unitAccession = "UO:0000269"
781859
};
782860

783-
var chromatogram = TraceToChromatogram(tracePDA[i], String.Format("PDA{0}_{1}", nrI, i.ToString()),
784-
chroType, intensType);
861+
var chromatogram = TraceToChromatogram(trace[i],
862+
String.Format("PDA#{0}_TotalAbsorbance_{1}", nrI, i),
863+
chroType, intensType);
785864

786865
chromatograms.Add(chromatogram);
787866
}
788867
}
868+
869+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.UV) + 1; nrI++)
870+
{
871+
_rawFile.SelectInstrument(Device.UV, nrI);
872+
873+
var instData = _rawFile.GetInstrumentData();
874+
875+
for (int channel = 0; channel < instData.ChannelLabels.Length; channel++)
876+
{
877+
var channelName = instData.ChannelLabels[channel];
878+
879+
settings = new ChromatogramTraceSettings(TraceType.StartUVChromatogramTraces + channel + 1);
880+
881+
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, -1, -1);
882+
883+
trace = ChromatogramSignal.FromChromatogramData(data);
884+
885+
for (var i = 0; i < trace.Length; i++)
886+
{
887+
// CV Data for Absorbance Chromatogram
888+
var chroType = new CVParamType
889+
{
890+
accession = "MS:1000812",
891+
name = "absorption chromatogram",
892+
cvRef = "MS",
893+
value = ""
894+
};
895+
896+
var intensType = new CVParamType
897+
{
898+
accession = "MS:1000515",
899+
name = "intensity array",
900+
cvRef = "MS",
901+
unitName = "absorbance unit",
902+
value = instData.Units.ToString(),
903+
unitCvRef = "UO",
904+
unitAccession = "UO:0000269"
905+
};
906+
907+
var chromatogram = TraceToChromatogram(trace[i],
908+
String.Format("UV#{0}_{1}_{2}", nrI, channelName, i),
909+
chroType, intensType);
910+
911+
chromatograms.Add(chromatogram);
912+
}
913+
}
914+
}
915+
916+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.Analog) + 1; nrI++)
917+
{
918+
_rawFile.SelectInstrument(Device.Analog, nrI);
919+
920+
var instData = _rawFile.GetInstrumentData();
921+
922+
for (int channel = 0; channel < instData.ChannelLabels.Length; channel++)
923+
{
924+
var channelName = instData.ChannelLabels[channel];
925+
926+
if (channelName.ToLower().Contains("pressure"))
927+
{
928+
settings = new ChromatogramTraceSettings(TraceType.StartPCA2DChromatogramTraces + channel + 1);
929+
930+
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, -1, -1);
931+
932+
trace = ChromatogramSignal.FromChromatogramData(data);
933+
934+
for (var i = 0; i < trace.Length; i++)
935+
{
936+
// CV Data for Absorbance Chromatogram
937+
var chroType = new CVParamType
938+
{
939+
accession = "MS:1003019",
940+
name = "pressure chromatogram",
941+
cvRef = "MS",
942+
value = ""
943+
};
944+
945+
var intensType = new CVParamType
946+
{
947+
accession = "MS:1000821",
948+
name = "pressure array",
949+
cvRef = "MS",
950+
unitName = "pressure unit",
951+
value = "",
952+
unitCvRef = "UO",
953+
unitAccession = "UO:0000109"
954+
};
955+
956+
var chromatogram = TraceToChromatogram(trace[i],
957+
String.Format("AD#{0}_{1}_{2}", nrI, channelName, i),
958+
chroType, intensType);
959+
960+
chromatograms.Add(chromatogram);
961+
}
962+
}
963+
}
964+
}
789965
}
790966

791967
return chromatograms;
@@ -1295,7 +1471,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
12951471
// Set the spectrum default array length if necessary
12961472
if (spectrum.defaultArrayLength == 0)
12971473
{
1298-
spectrum.defaultArrayLength = masses.Length;
1474+
spectrum.defaultArrayLength = intensities.Length;
12991475
}
13001476

13011477
var intensitiesBinaryData =
@@ -1377,17 +1553,7 @@ private SpectrumType ConstructPDASpectrum(int scanNumber, int instrumentNumber)
13771553
// Construct and set the scan list element of the spectrum
13781554
var scanListType = ConstructScanList(scanNumber, scan);
13791555
spectrum.scanList = scanListType;
1380-
13811556

1382-
// Total ion current
1383-
spectrumCvParams.Add(new CVParamType
1384-
{
1385-
name = "total ion current",
1386-
accession = "MS:1000285",
1387-
value = scan.ScanStatistics.TIC.ToString(CultureInfo.InvariantCulture),
1388-
cvRef = "MS"
1389-
});
1390-
13911557
//Scan data
13921558
double? basePeakPosition = null;
13931559
double? basePeakIntensity = null;
@@ -1845,7 +2011,8 @@ private PrecursorListType ConstructPrecursorList(IScanEventBase scanEvent, int?
18452011
}
18462012

18472013
/// <summary>
1848-
/// Populate the scan list element
2014+
/// Populate the scan list element. Full version used for mass spectra,
2015+
/// having Scan Event, scan Filter etc
18492016
/// </summary>
18502017
/// <param name="scanNumber">the scan number</param>
18512018
/// <param name="scan">the scan object</param>
@@ -1973,6 +2140,13 @@ private ScanListType ConstructScanList(int scanNumber, Scan scan, IScanFilter sc
19732140
return scanList;
19742141
}
19752142

2143+
/// <summary>
2144+
/// Populate the scan list element. Simple version used for PDA spectra,
2145+
/// without Scan Event and other parameters
2146+
/// </summary>
2147+
/// <param name="scanNumber">the scan number</param>
2148+
/// <param name="scan">the scan object</param>
2149+
/// <returns></returns>
19762150
private ScanListType ConstructScanList(int scanNumber, Scan scan)
19772151
{
19782152
// Scan list

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