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Merged
YukiMatsuzawa merged 3 commits into from
Aug 19, 2026
Merged

Expose a dedicated RT correction Console command #774

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46e3534
Clarify Console info and RT correction commands
Aug 19, 2026
d8e9d1f
Merge remote-tracking branch 'origin/master' into refactor/console-in…
Aug 19, 2026
8091c4d
Remove partial Console feature inventory
Aug 19, 2026
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275 changes: 0 additions & 275 deletions tests/MSDIAL5/MsdialCoreTestApp/Process/EicProcess.cs
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Original file line number Diff line number Diff line change
@@ -1,13 +1,10 @@
using CompMs.App.MsdialConsole.Parser;
using CompMs.Common.Components;
using CompMs.Common.DataObj;
using CompMs.Common.Enum;
using CompMs.Common.Extension;
using CompMs.Common.Parser;
using CompMs.MsdialCore.DataObj;
using CompMs.MsdialCore.Parameter;
using CompMs.MsdialCore.Parser;
using CompMs.MsdialLcmsApi.Parameter;
using CompMs.RawDataHandler.Core;
using System;
using System.Collections.Generic;
Expand All @@ -32,10 +29,6 @@ public int Run(string[] args) {
if (subcommand == "project") {
return RunProject(args);
}
if (subcommand == "rtcorrection") {
return RunRtCorrection(args);
}

Console.Error.WriteLine($"Invalid eic subcommand: {subcommand}");
return -1;
}
Expand Down Expand Up @@ -90,85 +83,6 @@ public int RunProject(FileInfo inputFile, FileInfo outputFile, string outputForm
return -1;
}

public int RunRtCorrection(
IReadOnlyList<FileSystemInfo> inputPaths,
FileInfo libraryFile,
FileInfo outputFile,
FileInfo? methodFile,
FileInfo? selectionFile,
IonMode ionMode,
AcquisitionType acquisitionType) {
if (inputPaths.Count == 0) {
return ArgsError();
}
if (!libraryFile.Exists) {
Console.Error.WriteLine($"RT correction standard library was not found: {libraryFile.FullName}");
return -1;
}

var standards = TextLibraryParser.StandardTextLibraryReader(libraryFile.FullName, out var error)
?.Where(standard => standard.IsTargetMolecule)
.OrderBy(standard => standard.ChromXs.RT.Value)
.ToList() ?? [];
if (!error.IsEmptyOrNull()) {
Console.Error.WriteLine(error);
}
if (standards.Count == 0) {
Console.Error.WriteLine("No enabled RT correction standards were found.");
return -1;
}

var rawFiles = ResolveRawFiles(inputPaths.Select(path => path.FullName));
if (rawFiles.Count == 0) {
Console.Error.WriteLine("No supported raw data files were found.");
return -1;
}

Directory.CreateDirectory(Path.GetDirectoryName(outputFile.FullName) ?? ".");
var parameter = methodFile is null
? new MsdialLcmsParameter()
: ConfigParser.ReadForLcmsParameter(methodFile.FullName);
parameter.IonMode = ionMode;
parameter.CompoundListForRtCorrectionPath = libraryFile.FullName;
parameter.RetentionTimeCorrectionCommon.RetentionTimeCorrectionParam.ExcuteRtCorrection = true;
parameter.ReferenceFileParam.RtCorrectionPeakSelectionFilePath = selectionFile?.FullName ?? string.Empty;
var analysisFiles = CreateRtCorrectionAnalysisFiles(rawFiles, acquisitionType, outputFile.FullName);
RetentionTimeCorrectionProcess.Prepare(
analysisFiles,
parameter,
Path.GetDirectoryName(outputFile.FullName) ?? ".");
var analysisFilesByPath = analysisFiles.ToDictionary(
file => Path.GetFullPath(file.AnalysisFilePath),
StringComparer.OrdinalIgnoreCase);
using var writer = new StreamWriter(outputFile.FullName, false, new UTF8Encoding(encoderShouldEmitUTF8Identifier: false));
writer.WriteLine("FileName,FilePath,StandardId,StandardName,ReferenceRT,RTTolerance,TargetMz,MzTolerance,MinimumHeight,ScanId,RT,CorrectedRT,Intensity,SmoothedIntensity");
var successfulFiles = 0;
foreach (var rawFile in rawFiles) {
Console.WriteLine($"Extracting RT correction EICs: {rawFile}");
var spectra = LoadMeasurement(rawFile);
if (spectra.Count == 0) {
Console.Error.WriteLine($"No raw spectra were found: {rawFile}");
continue;
}
WriteRtCorrectionEics(
writer,
rawFile,
standards,
spectra,
ionMode,
acquisitionType,
analysisFilesByPath[Path.GetFullPath(rawFile)]);
successfulFiles++;
}

if (successfulFiles == 0) {
Console.Error.WriteLine("RT correction EIC extraction failed for every input file.");
return -1;
}
Console.WriteLine($"RT correction EIC audit CSV: {outputFile.FullName}");
return 0;
}

private int RunRaw(string[] args)
{
var inputFile = string.Empty;
Expand Down Expand Up @@ -213,194 +127,6 @@ private int RunRaw(string[] args)
return RunRaw(new FileInfo(inputFile), new FileInfo(outputFile), targets, acquisitionType);
}

private int RunRtCorrection(string[] args) {
var inputPaths = new List<FileSystemInfo>();
FileInfo? libraryFile = null;
FileInfo? methodFile = null;
FileInfo? selectionFile = null;
FileInfo? outputFile = null;
var acquisitionType = AcquisitionType.DDA;
var ionMode = IonMode.Positive;

for (var i = 2; i < args.Length; i++) {
if (args[i] == "-i" && i + 1 < args.Length) {
inputPaths.Add(ToFileSystemInfo(args[++i]));
}
else if (args[i] == "-library" && i + 1 < args.Length) {
libraryFile = new FileInfo(args[++i]);
}
else if (args[i] == "-o" && i + 1 < args.Length) {
outputFile = new FileInfo(args[++i]);
}
else if (args[i] == "-m" && i + 1 < args.Length) {
methodFile = new FileInfo(args[++i]);
}
else if (args[i] == "-selection" && i + 1 < args.Length) {
selectionFile = new FileInfo(args[++i]);
}
else if (args[i] == "-acquisitiontype" && i + 1 < args.Length) {
if (!Enum.TryParse(args[++i], true, out acquisitionType)) {
return ArgsError();
}
}
else if (args[i] == "-ionmode" && i + 1 < args.Length) {
if (!Enum.TryParse(args[++i], true, out ionMode)) {
return ArgsError();
}
}
}

if (inputPaths.Count == 0 || libraryFile is null || outputFile is null) {
return ArgsError();
}
return RunRtCorrection(inputPaths, libraryFile, outputFile, methodFile, selectionFile, ionMode, acquisitionType);
}

private static List<AnalysisFileBean> CreateRtCorrectionAnalysisFiles(
IReadOnlyList<string> rawFiles,
AcquisitionType acquisitionType,
string outputFile) {
var outputDirectory = Path.GetDirectoryName(Path.GetFullPath(outputFile)) ?? ".";
var runId = DateTime.Now.ToString("yyyyMMddHHmmssfff", CultureInfo.InvariantCulture);
return rawFiles.Select((rawFile, index) => {
var name = Path.GetFileNameWithoutExtension(rawFile);
return new AnalysisFileBean {
AnalysisFileId = index,
AnalysisFileIncluded = true,
AnalysisFileName = name,
AnalysisFilePath = Path.GetFullPath(rawFile),
AnalysisFileAnalyticalOrder = index + 1,
AnalysisFileClass = "Sample",
AnalysisFileType = AnalysisFileType.Sample,
AcquisitionType = acquisitionType,
RetentionTimeCorrectionBean = new RetentionTimeCorrectionBean(
Path.Combine(outputDirectory, $"{name}_{runId}.rtc")),
};
}).ToList();
}

private static void WriteRtCorrectionEics(
StreamWriter writer,
string rawFile,
IReadOnlyList<MoleculeMsReference> standards,
IReadOnlyList<RawSpectrum> spectra,
IonMode ionMode,
AcquisitionType acquisitionType,
AnalysisFileBean analysisFile) {
var rawSpectra = new RawSpectra(spectra, ionMode, acquisitionType);
var originalRts = analysisFile.RetentionTimeCorrectionBean.OriginalRt;
var correctedRts = analysisFile.RetentionTimeCorrectionBean.PredictedRt;
foreach (var standard in standards) {
var referenceRt = standard.ChromXs.RT.Value;
var begin = Math.Max(0d, referenceRt - standard.RetentionTimeTolerance);
var end = referenceRt + standard.RetentionTimeTolerance;
var range = new ChromatogramRange(begin, end, ChromXType.RT, ChromXUnit.Min);
using var chromatogram = rawSpectra.GetMS1ExtractedChromatogram(
new MzRange(standard.PrecursorMz, standard.MassTolerance), range);
using var smoothed = chromatogram.ChromatogramSmoothing(SmoothingMethod.LinearWeightedMovingAverage, 3);
for (var i = 0; i < chromatogram.Length; i++) {
writer.WriteLine(string.Join(",",
CsvEscape(Path.GetFileNameWithoutExtension(rawFile)),
CsvEscape(Path.GetFullPath(rawFile)),
standard.ScanID,
CsvEscape(standard.Name),
referenceRt.ToString(CultureInfo.InvariantCulture),
standard.RetentionTimeTolerance.ToString(CultureInfo.InvariantCulture),
standard.PrecursorMz.ToString(CultureInfo.InvariantCulture),
standard.MassTolerance.ToString(CultureInfo.InvariantCulture),
standard.MinimumPeakHeight.ToString(CultureInfo.InvariantCulture),
chromatogram.Id(i),
chromatogram.Time(i).ToString(CultureInfo.InvariantCulture),
MapCorrectedRetentionTime(chromatogram.Time(i), originalRts, correctedRts)
.ToString(CultureInfo.InvariantCulture),
chromatogram.Intensity(i).ToString(CultureInfo.InvariantCulture),
smoothed.Intensity(i).ToString(CultureInfo.InvariantCulture)));
}
}
}

private static double MapCorrectedRetentionTime(
double retentionTime,
IReadOnlyList<double>? originalRts,
IReadOnlyList<double>? correctedRts) {
if (originalRts is null || correctedRts is null || originalRts.Count == 0
|| originalRts.Count != correctedRts.Count) {
return retentionTime;
}
if (retentionTime <= originalRts[0]) {
return correctedRts[0];
}
var last = originalRts.Count - 1;
if (retentionTime >= originalRts[last]) {
return correctedRts[last];
}
var low = 0;
var high = last;
while (low + 1 < high) {
var middle = low + (high - low) / 2;
if (originalRts[middle] < retentionTime) {
low = middle;
}
else {
high = middle;
}
}
var lower = low;
var upper = high;
var width = originalRts[upper] - originalRts[lower];
if (width <= 0d) {
return correctedRts[lower];
}
var ratio = (retentionTime - originalRts[lower]) / width;
return correctedRts[lower] + ratio * (correctedRts[upper] - correctedRts[lower]);
}

private static List<string> ResolveRawFiles(IEnumerable<string> inputPaths) {
var files = new List<string>();
foreach (var inputPath in inputPaths) {
if ((File.Exists(inputPath) && IsSupportedRawPath(inputPath)) || IsVendorDataDirectory(inputPath)) {
files.Add(Path.GetFullPath(inputPath));
continue;
}
if (File.Exists(inputPath)) {
Console.Error.WriteLine($"Unsupported raw data path: {inputPath}");
continue;
}
if (!Directory.Exists(inputPath)) {
Console.Error.WriteLine($"Input path was not found: {inputPath}");
continue;
}

files.AddRange(Directory.EnumerateFileSystemEntries(inputPath)
.Where(path => File.Exists(path) || IsVendorDataDirectory(path))
.Where(IsSupportedRawPath)
.Select(Path.GetFullPath));
}
return files.Distinct(StringComparer.OrdinalIgnoreCase).OrderBy(path => path).ToList();
}

private static bool IsVendorDataDirectory(string path) {
return Directory.Exists(path) && IsSupportedRawPath(path);
}

private static bool IsSupportedRawPath(string path) {
var extension = Path.GetExtension(path);
return extension.Equals(".abf", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".cdf", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".d", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".ibf", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".mzml", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".raw", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".wiff", StringComparison.OrdinalIgnoreCase)
|| extension.Equals(".wiff2", StringComparison.OrdinalIgnoreCase);
}

private static FileSystemInfo ToFileSystemInfo(string path) {
return Directory.Exists(path)
? new DirectoryInfo(path)
: new FileInfo(path);
}

private static void WriteRawCsv(string outputPath, IReadOnlyList<TargetQuery> targets, IReadOnlyList<RawSpectrum> spectra, AcquisitionType acquisitionType)
{
var ionMode = spectra.FirstOrDefault(s => s.MsLevel == 1)?.ScanPolarity == ScanPolarity.Negative ? IonMode.Negative : IonMode.Positive;
Expand Down Expand Up @@ -632,7 +358,6 @@ private static IReadOnlyList<RawSpectrum> LoadMeasurement(string inputFile) {
private static int ArgsError() {
Console.Error.WriteLine("MsdialConsoleApp.exe eic raw -i <input file> -o <output csv> -target <mz> <tolerance> [-target <mz> <tolerance> ...] [-acquisitiontype DDA|DIA]");
Console.Error.WriteLine("MsdialConsoleApp.exe eic project -i <project file> -o <output file> [-format csv|json]");
Console.Error.WriteLine("MsdialConsoleApp.exe eic rtcorrection -i <raw file or folder> [-i <raw file> ...] -library <standard txt> -o <output csv> [-m <method file>] [-selection <edited selections.tsv>] [-ionmode Positive|Negative] [-acquisitiontype DDA|SWATH|AIF]");
return -1;
}

Expand Down
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