use of net.sf.mzmine.util.R.RSessionWrapperException in project mzmine2 by mzmine.
the class HeatMapTask method run.
public void run() {
errorMsg = null;
setStatus(TaskStatus.PROCESSING);
logger.info("Heat map plot");
if (plegend) {
newPeakList = groupingDataset(selectedParameter, referenceGroup.toString());
} else {
newPeakList = modifySimpleDataset(selectedParameter, referenceGroup.toString());
}
if (newPeakList.length == 0 || newPeakList[0].length == 0) {
setStatus(TaskStatus.ERROR);
setErrorMessage("The data for heat map is empty.");
return;
}
try {
// Load gplots library
String[] reqPackages = { "gplots" };
rSession = new RSessionWrapper(this.rEngineType, "HeatMap analysis module", reqPackages, null);
rSession.open();
finishedPercentage = 0.3f;
if (outputType.contains("png")) {
if (height < 500 || width < 500) {
setStatus(TaskStatus.ERROR);
setErrorMessage("Figure height or width is too small. " + "Minimun height and width is 500.");
return;
}
}
rSession.eval("dataset<- matrix(\"\",nrow =" + newPeakList[0].length + ",ncol=" + newPeakList.length + ")");
if (plegend) {
rSession.eval("stars<- matrix(\"\",nrow =" + newPeakList[0].length + ",ncol=" + newPeakList.length + ")");
}
// assing the values to the matrix
for (int row = 0; row < newPeakList[0].length; row++) {
for (int column = 0; column < newPeakList.length; column++) {
int r = row + 1;
int c = column + 1;
double value = newPeakList[column][row];
if (plegend) {
String pValue = pValueMatrix[column][row];
rSession.eval("stars[" + r + "," + c + "] = \"" + pValue + "\"");
}
if (!Double.isInfinite(value) && !Double.isNaN(value)) {
rSession.eval("dataset[" + r + "," + c + "] = " + value);
} else {
rSession.eval("dataset[" + r + "," + c + "] = NA");
}
}
}
finishedPercentage = 0.4f;
rSession.eval("dataset <- apply(dataset, 2, as.numeric)");
// Assign row names to the data set
rSession.assign("rowNames", rowNames);
rSession.eval("rownames(dataset)<-rowNames");
// Assign column names to the data set
rSession.assign("colNames", colNames);
rSession.eval("colnames(dataset)<-colNames");
finishedPercentage = 0.5f;
// Remove the rows with too many NA's. The distances between
// rows can't be calculated if the rows don't have
// at least one sample in common.
rSession.eval("d <- as.matrix(dist(dataset))");
rSession.eval("d[upper.tri(d)] <- 0");
rSession.eval("naindices <- na.action(na.omit(d))");
rSession.eval("if (! is.null(naindices)) dataset <- dataset[-naindices,]");
finishedPercentage = 0.8f;
String marginParameter = "margins = c(" + columnMargin + "," + rowMargin + ")";
rSession.eval("br<-c(seq(from=min(dataset,na.rm=T),to=0,length.out=256)," + "seq(from=0.00001,to=max(dataset,na.rm=T),length.out=256))", false);
// Convert the path to R-compatible string
final String escapedOutputFileName = Rsession.toRpath(outputFile);
// Possible output file types
if (outputType.contains("pdf")) {
rSession.eval("pdf(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
} else if (outputType.contains("fig")) {
rSession.eval("xfig(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ", horizontal = FALSE, pointsize = 12)");
} else if (outputType.contains("svg")) {
// Load RSvgDevice library
rSession.loadPackage("RSvgDevice");
rSession.eval("devSVG(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
} else if (outputType.contains("png")) {
rSession.eval("png(\"" + escapedOutputFileName + "\", height=" + height + ", width=" + width + ")");
}
if (plegend) {
rSession.eval("heatmap.2(dataset," + marginParameter + ", trace=\"none\", col=bluered(length(br)-1)," + " breaks=br, cellnote=stars, notecol=\"black\"" + ", notecex=" + starSize + ", na.color=\"grey\")", false);
} else {
rSession.eval("heatmap.2(dataset," + marginParameter + ", trace=\"none\", col=bluered(length(br)-1)," + " breaks=br, na.color=\"grey\")", false);
}
rSession.eval("dev.off()", false);
// Stands for a (void) collect!
this.rSession.runOnlyOnline();
// Done: Refresh R code stack
this.rSession.clearCode();
finishedPercentage = 1.0;
// Turn off R instance, once task ended gracefully.
if (!isCanceled())
rSession.close(false);
} catch (RSessionWrapperException e) {
if (!isCanceled()) {
errorMsg = "'R computing error' during heatmap generation. \n" + e.getMessage();
}
} catch (Exception e) {
if (!isCanceled()) {
errorMsg = "'Unknown error' during heatmap generation. \n" + e.getMessage();
}
}
// Turn off R instance, once task ended UNgracefully.
try {
if (!isCanceled())
if (rSession != null)
rSession.close(isCanceled());
} catch (RSessionWrapperException e) {
if (!isCanceled()) {
// Do not override potential previous error message.
if (errorMsg == null) {
errorMsg = e.getMessage();
}
} else {
// User canceled: Silent.
}
}
// Report error.
if (errorMsg != null) {
setErrorMessage(errorMsg);
setStatus(TaskStatus.ERROR);
} else {
setStatus(TaskStatus.FINISHED);
}
}
use of net.sf.mzmine.util.R.RSessionWrapperException in project mzmine2 by mzmine.
the class DeconvolutionTask method run.
@Override
public void run() {
errorMsg = null;
if (!isCanceled()) {
setStatus(TaskStatus.PROCESSING);
LOG.info("Started peak deconvolution on " + originalPeakList);
// Check raw data files.
if (originalPeakList.getNumberOfRawDataFiles() > 1) {
setStatus(TaskStatus.ERROR);
setErrorMessage("Peak deconvolution can only be performed on feature lists with a single raw data file");
} else {
try {
// Peak resolver.
final MZmineProcessingStep<PeakResolver> resolver = parameters.getParameter(PEAK_RESOLVER).getValue();
if (resolver.getModule().getRequiresR()) {
// Check R availability, by trying to open the
// connection.
String[] reqPackages = resolver.getModule().getRequiredRPackages();
String[] reqPackagesVersions = resolver.getModule().getRequiredRPackagesVersions();
String callerFeatureName = resolver.getModule().getName();
REngineType rEngineType = resolver.getModule().getREngineType(resolver.getParameterSet());
this.rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, reqPackagesVersions);
this.rSession.open();
} else {
this.rSession = null;
}
// Deconvolve peaks.
newPeakList = resolvePeaks(originalPeakList, this.rSession);
if (!isCanceled()) {
// Add new peaklist to the project.
project.addPeakList(newPeakList);
// Add quality parameters to peaks
QualityParameters.calculateQualityParameters(newPeakList);
// Remove the original peaklist if requested.
if (parameters.getParameter(AUTO_REMOVE).getValue()) {
project.removePeakList(originalPeakList);
}
setStatus(TaskStatus.FINISHED);
LOG.info("Finished peak recognition on " + originalPeakList);
}
// Turn off R instance.
if (this.rSession != null)
this.rSession.close(false);
} catch (RSessionWrapperException e) {
errorMsg = "'R computing error' during CentWave detection. \n" + e.getMessage();
} catch (Exception e) {
errorMsg = "'Unknown error' during CentWave detection. \n" + e.getMessage();
} catch (Throwable t) {
setStatus(TaskStatus.ERROR);
setErrorMessage(t.getMessage());
LOG.log(Level.SEVERE, "Peak deconvolution error", t);
}
// Turn off R instance, once task ended UNgracefully.
try {
if (this.rSession != null && !isCanceled())
rSession.close(isCanceled());
} catch (RSessionWrapperException e) {
if (!isCanceled()) {
// Do not override potential previous error message.
if (errorMsg == null) {
errorMsg = e.getMessage();
}
} else {
// User canceled: Silent.
}
}
// Report error.
if (errorMsg != null) {
setErrorMessage(errorMsg);
setStatus(TaskStatus.ERROR);
}
}
}
}
use of net.sf.mzmine.util.R.RSessionWrapperException in project mzmine2 by mzmine.
the class CameraSearchTask method cameraSearch.
/**
* Perform CAMERA search.
*
* @param rawFile raw data file of feature list to process.
*/
private void cameraSearch(final RawDataFile rawFile) {
LOG.finest("Detecting peaks.");
errorMsg = null;
try {
String[] reqPackages = { "CAMERA" };
String[] reqPackagesVersions = { CAMERA_VERSION };
this.rSession = new RSessionWrapper(this.rEngineType, "Camera search feature", reqPackages, reqPackagesVersions);
this.rSession.open();
// Create empty peaks matrix.
this.rSession.eval("columnHeadings <- c('mz','mzmin','mzmax','rt','rtmin','rtmax','into','intb','maxo','sn')");
this.rSession.eval("peaks <- matrix(nrow=0, ncol=length(columnHeadings))");
this.rSession.eval("colnames(peaks) <- columnHeadings");
// Initialize.
final Feature[] peaks = peakList.getPeaks(rawFile);
progress = 0.0;
// Initialize scan map.
final Map<Scan, Set<DataPoint>> peakDataPointsByScan = new HashMap<Scan, Set<DataPoint>>(rawFile.getNumOfScans(MS_LEVEL));
int dataPointCount = 0;
for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {
// Create a set to hold data points (sorted by m/z).
final Set<DataPoint> dataPoints = new TreeSet<DataPoint>(ASCENDING_MASS_SORTER);
// Add a dummy data point.
dataPoints.add(new SimpleDataPoint(0.0, 0.0));
dataPointCount++;
// Map the set.
peakDataPointsByScan.put(rawFile.getScan(scanNumber), dataPoints);
}
// Add peaks.
// 80 percents for building peaks list.
double progressInc = 0.8 / (double) peaks.length;
for (final Feature peak : peaks) {
// Get peak data.
Range<Double> rtRange = null;
Range<Double> intRange = null;
final double mz = peak.getMZ();
// Get the peak's data points per scan.
for (final int scanNumber : peak.getScanNumbers()) {
final Scan scan = rawFile.getScan(scanNumber);
if (scan.getMSLevel() != MS_LEVEL) {
throw new IllegalStateException("CAMERA can only process feature lists from MS-level " + MS_LEVEL);
}
// Copy the data point.
final DataPoint dataPoint = peak.getDataPoint(scanNumber);
if (dataPoint != null) {
final double intensity = dataPoint.getIntensity();
peakDataPointsByScan.get(scan).add(new SimpleDataPoint(mz, intensity));
dataPointCount++;
// Update RT & intensity range.
final double rt = scan.getRetentionTime();
if (rtRange == null) {
rtRange = Range.singleton(rt);
intRange = Range.singleton(intensity);
} else {
rtRange = rtRange.span(Range.singleton(rt));
intRange = intRange.span(Range.singleton(intensity));
}
}
}
// Set peak values.
final double area = peak.getArea();
final double maxo = intRange == null ? peak.getHeight() : intRange.upperEndpoint();
final double rtMin = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).lowerEndpoint();
final double rtMax = (rtRange == null ? peak.getRawDataPointsRTRange() : rtRange).upperEndpoint();
// Add peak row.
this.rSession.eval(// mz
"peaks <- rbind(peaks, c(" + mz + ", " + mz + // mzmin: use the same as mz.
", " + mz + // mzmax: use the same as mz.
", " + peak.getRT() + // rt
", " + rtMin + // rtmin
", " + rtMax + // rtmax
", " + area + // into: peak area.
", " + area + // intb: doesn't affect result, use area.
", " + maxo + // maxo
", " + SIGNAL_TO_NOISE + "))", false);
progress += progressInc;
}
// 20 percents (5*4) for building pseudo-isotopes groups.
progressInc = 0.05;
// Create R vectors.
final int scanCount = peakDataPointsByScan.size();
final double[] scanTimes = new double[scanCount];
final int[] scanIndices = new int[scanCount];
final double[] masses = new double[dataPointCount];
final double[] intensities = new double[dataPointCount];
// Fill vectors.
int scanIndex = 0;
int pointIndex = 0;
for (final int scanNumber : rawFile.getScanNumbers(MS_LEVEL)) {
final Scan scan = rawFile.getScan(scanNumber);
scanTimes[scanIndex] = scan.getRetentionTime();
scanIndices[scanIndex] = pointIndex + 1;
scanIndex++;
for (final DataPoint dataPoint : peakDataPointsByScan.get(scan)) {
masses[pointIndex] = dataPoint.getMZ();
intensities[pointIndex] = dataPoint.getIntensity();
pointIndex++;
}
}
// Set vectors.
this.rSession.assign("scantime", scanTimes);
this.rSession.assign("scanindex", scanIndices);
this.rSession.assign("mass", masses);
this.rSession.assign("intensity", intensities);
// Construct xcmsRaw object
this.rSession.eval("xRaw <- new(\"xcmsRaw\")");
this.rSession.eval("xRaw@tic <- intensity");
this.rSession.eval("xRaw@scantime <- scantime * " + SECONDS_PER_MINUTE);
this.rSession.eval("xRaw@scanindex <- as.integer(scanindex)");
this.rSession.eval("xRaw@env$mz <- mass");
this.rSession.eval("xRaw@env$intensity <- intensity");
// Create the xcmsSet object.
this.rSession.eval("xs <- new(\"xcmsSet\")");
// Set peaks.
this.rSession.eval("xs@peaks <- peaks");
// Set file (dummy) file path.
this.rSession.eval("xs@filepaths <- ''");
// Set sample name.
this.rSession.assign("sampleName", peakList.getName());
this.rSession.eval("sampnames(xs) <- sampleName");
// Create an empty xsAnnotate.
this.rSession.eval("an <- xsAnnotate(xs, sample=1)");
// Group by RT.
this.rSession.eval("an <- groupFWHM(an, sigma=" + fwhmSigma + ", perfwhm=" + fwhmPercentage + ')');
progress += progressInc;
switch(parameters.getParameter(CameraSearchParameters.ORDER).getValue()) {
case CameraSearchParameters.GROUP_CORR_FIRST:
// Split groups by correlating peak shape (need to set xraw to raw
// data).
this.rSession.eval("an <- groupCorr(an, calcIso=FALSE, xraw=xRaw, cor_eic_th=" + corrThreshold + ", pval=" + corrPValue + ')');
progress += progressInc;
// Identify isotopes.
this.rSession.eval("an <- findIsotopes(an, maxcharge=" + isoMaxCharge + ", maxiso=" + isoMaxCount + ", ppm=" + isoMassTolerance.getPpmTolerance() + ", mzabs=" + isoMassTolerance.getMzTolerance() + ')');
progress += progressInc;
break;
default:
// case CameraSearchParameters.FIND_ISOTOPES_FIRST
// Identify isotopes.
this.rSession.eval("an <- findIsotopes(an, maxcharge=" + isoMaxCharge + ", maxiso=" + isoMaxCount + ", ppm=" + isoMassTolerance.getPpmTolerance() + ", mzabs=" + isoMassTolerance.getMzTolerance() + ')');
// this.rSession.eval("write.csv(getPeaklist(an),
// file='/Users/aleksandrsmirnov/test_camera.csv')");
progress += progressInc;
// Split groups by correlating peak shape (need to set xraw to raw
// data).
this.rSession.eval("an <- groupCorr(an, calcIso=" + String.valueOf(calcIso).toUpperCase() + ", xraw=xRaw, cor_eic_th=" + corrThreshold + ", pval=" + corrPValue + ')');
progress += progressInc;
}
this.rSession.eval("an <- findAdducts(an, polarity='" + polarity + "')");
// Get the feature list.
this.rSession.eval("peakList <- getPeaklist(an)");
// Extract the pseudo-spectra and isotope annotations from the peak
// list.
rSession.eval("pcgroup <- as.integer(peakList$pcgroup)");
rSession.eval("isotopes <- peakList$isotopes");
rSession.eval("adducts <- peakList$adduct");
final int[] spectra = (int[]) rSession.collect("pcgroup");
final String[] isotopes = (String[]) rSession.collect("isotopes");
final String[] adducts = (String[]) rSession.collect("adducts");
// Done: Refresh R code stack
this.rSession.clearCode();
// Add identities.
if (spectra != null) {
addPseudoSpectraIdentities(peaks, spectra, isotopes, adducts);
}
progress += progressInc;
// Turn off R instance, once task ended gracefully.
if (!this.userCanceled)
this.rSession.close(false);
} catch (RSessionWrapperException e) {
if (!this.userCanceled) {
errorMsg = "'R computing error' during CAMERA search. \n" + e.getMessage();
e.printStackTrace();
}
} catch (Exception e) {
if (!this.userCanceled) {
errorMsg = "'Unknown error' during CAMERA search. \n" + e.getMessage();
e.printStackTrace();
}
}
// Turn off R instance, once task ended UNgracefully.
try {
if (!this.userCanceled)
this.rSession.close(this.userCanceled);
} catch (RSessionWrapperException e) {
if (!this.userCanceled) {
// Do not override potential previous error message.
if (errorMsg == null) {
errorMsg = e.getMessage();
}
} else {
// User canceled: Silent.
}
}
// Report error.
if (errorMsg != null) {
setErrorMessage(errorMsg);
setStatus(TaskStatus.ERROR);
}
}
use of net.sf.mzmine.util.R.RSessionWrapperException in project mzmine2 by mzmine.
the class BaselineCorrectionTask method run.
@Override
public void run() {
errorMsg = null;
// Update the status of this task.
setStatus(TaskStatus.PROCESSING);
try {
// Check R availability, by trying to open the connection.
String[] reqPackages = this.baselineCorrectorProcStep.getModule().getRequiredRPackages();
String callerFeatureName = this.baselineCorrectorProcStep.getModule().getName();
this.rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, null);
this.rSession.open();
this.baselineCorrectorProcStep.getModule().initProgress(origDataFile);
final RawDataFile correctedDataFile = this.baselineCorrectorProcStep.getModule().correctDatafile(this.rSession, origDataFile, baselineCorrectorProcStep.getParameterSet(), this.commonParameters);
// If this task was canceled, stop processing.
if (!isCanceled() && correctedDataFile != null) {
this.correctedDataFile = correctedDataFile;
// Add the newly created file to the project
this.project.addFile(this.correctedDataFile);
// Remove the original data file if requested.
if (removeOriginal) {
project.removeFile(origDataFile);
}
// Set task status to FINISHED
setStatus(TaskStatus.FINISHED);
LOG.info("Baseline corrected " + origDataFile.getName());
}
// Turn off R instance, once task ended gracefully.
if (!isCanceled())
this.rSession.close(false);
} catch (IOException | RSessionWrapperException e) {
if (!isCanceled()) {
errorMsg = "'R computing error' during baseline correction. \n" + e.getMessage();
}
} catch (Exception e) {
if (!isCanceled()) {
errorMsg = "'Unknown error' during baseline correction. \n" + e.getMessage();
}
}
this.baselineCorrectorProcStep.getModule().setAbortProcessing(origDataFile, true);
// Turn off R instance, once task ended UNgracefully.
try {
if (!isCanceled())
this.rSession.close(isCanceled());
} catch (RSessionWrapperException e) {
if (!isCanceled()) {
// Do not override potential previous error message.
if (errorMsg == null) {
errorMsg = e.getMessage();
}
} else {
// User canceled: Silent.
}
}
// Report error.
if (errorMsg != null) {
setErrorMessage(errorMsg);
setStatus(TaskStatus.ERROR);
}
// ...
this.baselineCorrectorProcStep.getModule().clearProgress(origDataFile);
}
use of net.sf.mzmine.util.R.RSessionWrapperException in project mzmine2 by mzmine.
the class PeakResolverSetupDialog method parametersChanged.
@Override
public void parametersChanged() {
if (preview != null && preview.isSelected()) {
final PeakListRow previewRow = (PeakListRow) comboPeak.getSelectedItem();
if (previewRow != null) {
LOG.finest("Loading new preview peak " + previewRow);
ticPlot.removeAllTICDataSets();
ticPlot.addTICDataset(new ChromatogramTICDataSet(previewRow.getPeaks()[0]));
// Auto-range to axes.
ticPlot.getXYPlot().getDomainAxis().setAutoRange(true);
ticPlot.getXYPlot().getDomainAxis().setAutoTickUnitSelection(true);
ticPlot.getXYPlot().getRangeAxis().setAutoRange(true);
ticPlot.getXYPlot().getRangeAxis().setAutoTickUnitSelection(true);
updateParameterSetFromComponents();
// If there is some illegal value, do not load the preview but
// just exit.
ArrayList<String> errors = new ArrayList<String>();
if (!parameterSet.checkParameterValues(errors)) {
LOG.fine("Illegal parameter value: " + errors);
return;
}
// Load the intensities and RTs into array.
final Feature previewPeak = previewRow.getPeaks()[0];
// Resolve peaks.
Feature[] resolvedPeaks = {};
RSessionWrapper rSession;
try {
if (peakResolver.getRequiresR()) {
// Check R availability, by trying to open the
// connection.
String[] reqPackages = peakResolver.getRequiredRPackages();
String[] reqPackagesVersions = peakResolver.getRequiredRPackagesVersions();
String callerFeatureName = peakResolver.getName();
REngineType rEngineType = peakResolver.getREngineType(parameters);
rSession = new RSessionWrapper(rEngineType, callerFeatureName, reqPackages, reqPackagesVersions);
rSession.open();
} else {
rSession = null;
}
CenterFunction mzCenterFunction = new CenterFunction(CenterMeasure.MEDIAN);
// preview doesn't show msms scans
// set it to be default searching range
resolvedPeaks = peakResolver.resolvePeaks(previewPeak, parameters, rSession, mzCenterFunction, 0, 0);
// Turn off R instance.
if (rSession != null)
rSession.close(false);
} catch (RSessionWrapperException e) {
throw new IllegalStateException(e.getMessage());
} catch (Throwable t) {
LOG.log(Level.SEVERE, "Peak deconvolution error", t);
MZmineCore.getDesktop().displayErrorMessage(this, t.toString());
}
// Add resolved peaks to TIC plot.
final int peakCount = Math.min(MAX_PEAKS, resolvedPeaks.length);
for (int i = 0; i < peakCount; i++) {
final XYDataset peakDataSet = new PeakDataSet(resolvedPeaks[i]);
ticPlot.addPeakDataset(peakDataSet);
}
// Check peak count.
if (resolvedPeaks.length > MAX_PEAKS) {
// MZmineCore.getDesktop().displayMessage(this,
// "Too many peaks detected, please adjust parameter values");
MZmineCore.getDesktop().displayMessage(this, "Too many peaks detected. Not all of the peaks might be displayed");
}
}
}
}
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