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General chromatograms
1 parent c4b5018 commit 89ad1c5

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2 files changed

+238
-152
lines changed

2 files changed

+238
-152
lines changed

‎Writer/MzMlSpectrumWriter.cs‎

Lines changed: 45 additions & 152 deletions
Original file line numberDiff line numberDiff line change
@@ -196,7 +196,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
196196
value = ""
197197
});
198198
}
199-
//TODO FID chromatogram as ion current
199+
//TODO non-standard chromatograms pressure, flow, FID, etc
200200
}
201201

202202
_writer.WriteEndElement(); // fileContent
@@ -283,7 +283,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
283283
{
284284
PopulateInstrumentConfigurationList(firstScanNumber, lastScanNumber, instrumentModel);
285285
}
286-
else //TODO Fake instrument configuration
286+
else
287287
{
288288
_writer.WriteStartElement("instrumentConfigurationList");
289289
_writer.WriteAttributeString("count", "1");
@@ -952,24 +952,9 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
952952
for (var i = 0; i < trace.Length; i++)
953953
{
954954
// CV Data for Total Absorbance Chromatogram
955-
var chroType = new CVParamType
956-
{
957-
accession = "MS:1000812",
958-
name = "absorption chromatogram",
959-
cvRef = "MS",
960-
value = ""
961-
};
962-
963-
var intensType = new CVParamType
964-
{
965-
accession = "MS:1000515",
966-
name = "intensity array",
967-
cvRef = "MS",
968-
unitName = "absorbance unit",
969-
value = instData.Units.ToString(),
970-
unitCvRef = "UO",
971-
unitAccession = "UO:0000269"
972-
};
955+
var chroType = OntologyMapping.chromatogramTypes["absoption"];
956+
var intensType = OntologyMapping.dataArrayTypes["absoption"];
957+
intensType.value = instData.Units.ToString();
973958

974959
var chromatogram = TraceToChromatogram(trace[i],
975960
String.Format("PDA#{0}_TotalAbsorbance_{1}", nrI, i),
@@ -998,25 +983,10 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
998983
for (var i = 0; i < trace.Length; i++)
999984
{
1000985
// CV Data for Absorbance Chromatogram
1001-
var chroType = new CVParamType
1002-
{
1003-
accession = "MS:1000812",
1004-
name = "absorption chromatogram",
1005-
cvRef = "MS",
1006-
value = ""
1007-
};
1008-
1009-
var intensType = new CVParamType
1010-
{
1011-
accession = "MS:1000515",
1012-
name = "intensity array",
1013-
cvRef = "MS",
1014-
unitName = "absorbance unit",
1015-
value = instData.Units.ToString(),
1016-
unitCvRef = "UO",
1017-
unitAccession = "UO:0000269"
1018-
};
1019-
986+
var chroType = OntologyMapping.chromatogramTypes["absorbtion"];
987+
var intensType = OntologyMapping.dataArrayTypes["absoption"];
988+
intensType.value = instData.Units.ToString();
989+
1020990
var chromatogram = TraceToChromatogram(trace[i],
1021991
String.Format("UV#{0}_{1}_{2}", nrI, channelName, i),
1022992
chroType, intensType);
@@ -1026,129 +996,61 @@ private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int l
1026996
}
1027997
}
1028998

1029-
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.Analog) + 1; nrI++)
999+
//Chromatograms from (MS)Analog devices: Pressure, FID, etc
1000+
foreach (var deviceType in new Device[2] { Device.Analog, Device.MSAnalog })
10301001
{
1031-
_rawFile.SelectInstrument(Device.Analog, nrI);
1032-
1033-
var instData = _rawFile.GetInstrumentData();
1034-
1035-
for (int channel = 0; channel < instData.ChannelLabels.Length; channel++)
1002+
var channelNameIndex = 0;
1003+
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(deviceType) + 1; nrI++)
10361004
{
1037-
var channelName = instData.ChannelLabels[channel];
1005+
_rawFile.SelectInstrument(deviceType, nrI);
10381006

1039-
if (channelName.ToLower().Contains("pressure"))
1040-
{
1041-
settings = new ChromatogramTraceSettings(TraceType.StartAnalogChromatogramTraces + channel + 1);
1007+
var instData = _rawFile.GetInstrumentData();
10421008

1043-
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] {settings}, -1, -1);
1009+
for (int channel = 0; channel < instData.ChannelLabels.Length; channel++)
1010+
{
1011+
var channelName = instData.ChannelLabels[channel];
1012+
if (channelName.IsNullOrEmpty())
1013+
{
1014+
channelName = $"Channel{channelNameIndex++}";
1015+
}
10441016

1017+
settings = new ChromatogramTraceSettings(TraceType.StartAnalogChromatogramTraces + channel + 1);
1018+
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, -1, -1);
10451019
trace = ChromatogramSignal.FromChromatogramData(data);
10461020

10471021
for (var i = 0; i < trace.Length; i++)
10481022
{
1049-
// CV Data for Absorbance Chromatogram
1050-
var chroType = new CVParamType
1023+
//Default data type
1024+
var chroType = OntologyMapping.chromatogramTypes["unknown"];
1025+
var intensType = OntologyMapping.dataArrayTypes["unknown"];
1026+
1027+
if (channelName.ToLower().Contains("pressure"))
10511028
{
1052-
accession = "MS:1003019",
1053-
name = "pressure chromatogram",
1054-
cvRef = "MS",
1055-
value = ""
1056-
};
1057-
1058-
var intensType = new CVParamType
1029+
chroType = OntologyMapping.chromatogramTypes["pressure"];
1030+
intensType = OntologyMapping.dataArrayTypes["pressure"];
1031+
}
1032+
else if (channelName.ToLower().Contains("flow"))
10591033
{
1060-
accession = "MS:1000821",
1061-
name = "pressure array",
1062-
cvRef = "MS",
1063-
unitName = "pressure unit",
1064-
value = "",
1065-
unitCvRef = "UO",
1066-
unitAccession = "UO:0000109"
1067-
};
1034+
chroType = OntologyMapping.chromatogramTypes["flow"];
1035+
intensType = OntologyMapping.dataArrayTypes["flow"];
1036+
}
1037+
else if (channelName.ToLower().Contains("fid"))
1038+
{
1039+
//FID is ion current type
1040+
chroType = OntologyMapping.chromatogramTypes["current"];
1041+
intensType = OntologyMapping.dataArrayTypes["intensity"];
1042+
}
10681043

10691044
var chromatogram = TraceToChromatogram(trace[i],
1070-
String.Format("AD#{0}_{1}_{2}", nrI, channelName, i),
1045+
String.Format("{0}#{1}_{2}_{3}", deviceType.ToString(), nrI, channelName.Replace(" ", "_"), i),
10711046
chroType, intensType);
10721047

10731048
chromatograms.Add(chromatogram);
10741049
}
10751050
}
10761051
}
10771052
}
1078-
1079-
var channelNameIndex = 0;
1080-
1081-
for (int nrI = 1; nrI < _rawFile.GetInstrumentCountOfType(Device.MSAnalog) + 1; nrI++)
1082-
{
1083-
_rawFile.SelectInstrument(Device.MSAnalog, nrI);
1084-
1085-
var instData = _rawFile.GetInstrumentData();
1086-
1087-
for (int channel = 0; channel < instData.ChannelLabels.Length; channel++)
1088-
{
1089-
var channelName = instData.ChannelLabels[channel];
1090-
1091-
if (channelName.IsNullOrEmpty())
1092-
{
1093-
channelName = $"Channel{channelNameIndex++}";
1094-
}
1095-
1096-
settings = new ChromatogramTraceSettings(TraceType.StartAnalogChromatogramTraces + channel + 1);
1097-
data = _rawFile.GetChromatogramData(new IChromatogramSettings[] { settings }, -1, -1);
1098-
trace = ChromatogramSignal.FromChromatogramData(data);
1099-
1100-
for (var i = 0; i < trace.Length; i++)
1101-
{
1102-
// CV Data for Chromatogram
1103-
var chroType = new CVParamType
1104-
{
1105-
accession = "MS:1000626",
1106-
name = "chromatogram type",
1107-
cvRef = "MS",
1108-
value = $"{channelName} chromatogram"
1109-
};
1110-
1111-
var intensType = new CVParamType
1112-
{
1113-
accession = "MS:1000786",
1114-
name = "non-standard data array",
1115-
cvRef = "MS",
1116-
unitName = "unit",
1117-
value = instData.Units.ToString(),
1118-
unitCvRef = "UO",
1119-
unitAccession = "UO:0000000"
1120-
};
1121-
1122-
if (instData.Units.ToString().ToLower().Contains("absorbance"))
1123-
{
1124-
chroType = new CVParamType
1125-
{
1126-
accession = "MS:1000812",
1127-
name = "absorption chromatogram",
1128-
cvRef = "MS",
1129-
value = $"{channelName} chromatogram"
1130-
};
1131-
1132-
intensType = new CVParamType
1133-
{
1134-
accession = "MS:1000515",
1135-
name = "intensity array",
1136-
cvRef = "MS",
1137-
unitName = "absorbance unit",
1138-
value = instData.Units.ToString(),
1139-
unitCvRef = "UO",
1140-
unitAccession = "UO:0000269"
1141-
};
1142-
}
1143-
1144-
var chromatogram = TraceToChromatogram(trace[i],
1145-
String.Format("MSAD#{0}_{1}_{2}", nrI, channelName.Replace(" ", "_"), i),
1146-
chroType, intensType);
1147-
1148-
chromatograms.Add(chromatogram);
1149-
}
1150-
}
1151-
}
1053+
11521054
}
11531055

11541056
return chromatograms;
@@ -1192,16 +1094,7 @@ private ChromatogramType TraceToChromatogram(ChromatogramSignal trace, string ch
11921094
.binary.Length / 3)).ToString(CultureInfo.InvariantCulture);
11931095
var timesBinaryDataCvParams = new List<CVParamType>
11941096
{
1195-
new CVParamType
1196-
{
1197-
accession = "MS:1000595",
1198-
name = "time array",
1199-
cvRef = "MS",
1200-
unitName = "minute",
1201-
value = "",
1202-
unitCvRef = "UO",
1203-
unitAccession = "UO:0000031"
1204-
},
1097+
OntologyMapping.dataArrayTypes["time"],
12051098
new CVParamType
12061099
{
12071100
accession = "MS:1000523", name = "64-bit float", cvRef = "MS", value = ""

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