org.jcamp.parser.ChromatogramJCAMPReader Maven / Gradle / Ivy

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package org.jcamp.parser;

import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.jcamp.spectrum.ArrayData;
import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.Chromatogram;
import org.jcamp.spectrum.EquidistantData;
import org.jcamp.spectrum.IDataArray1D;
import org.jcamp.spectrum.IOrderedDataArray1D;
import org.jcamp.spectrum.ISpectrumIdentifier;
import org.jcamp.spectrum.OrderedArrayData;
import org.jcamp.spectrum.Pattern;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;
/**
 * adapter between chromatography class and JCAMPReader.
 * @author Thomas Weber
 */
public class ChromatogramJCAMPReader extends CommonSpectrumJCAMPReader implements ISpectrumJCAMPReader {
    private final static String CRLF = "\r\n";
    private static Log log = LogFactory.getLog(ChromatogramJCAMPReader.class);

    protected ChromatogramJCAMPReader() {
        super();
    }
    /**
     * read chromatogram full spectrum.
     * 
     * @return Chromatogram
     * @param block JCAMPBlock
     */
    private Chromatogram createFS(JCAMPBlock block) throws JCAMPException {
        Chromatogram spectrum;
        Unit xUnit = getXUnits(block);
        if (xUnit == null)
            xUnit = CommonUnit.second;
        Unit yUnit = getYUnits(block);
        if (yUnit == null)
            yUnit = CommonUnit.intensity;
        double xFactor = getXFactor(block);
        double yFactor = getYFactor(block);
        double firstX = getFirstX(block);
        double lastX = getLastX(block);
        int nPoints = getNPoints(block);
        double[] intensities = getXYData(block, firstX, lastX, nPoints, xFactor, yFactor);
        if (intensities.length != nPoints) {
            block.getErrorHandler().error(
                "incorrect ##NPOINTS=: expected "
                    + Integer.toString(nPoints)
                    + " but got "
                    + Integer.toString(intensities.length));
            nPoints = intensities.length;
        }
        IOrderedDataArray1D x = new EquidistantData(firstX, lastX, nPoints, xUnit);
        IDataArray1D y = new ArrayData(intensities, yUnit);
        spectrum = new Chromatogram(x, y, true);
        return spectrum;
    }
    /**
     * create chromatogram peak table (peak spectrum) from JCAMPBlock.
     * 
     * @return chromatogram
     * @param block JCAMPBlock
     * @exception JCAMPException exception thrown if parsing fails.
     */
    private Chromatogram createPeakTable(JCAMPBlock block) throws JCAMPException {
        Chromatogram spectrum = null;
        Unit xUnit = getXUnits(block);
        if (xUnit == null)
            xUnit = CommonUnit.second;
        Unit yUnit = getYUnits(block);
        if (yUnit == null)
            yUnit = CommonUnit.intensity;
        double xFactor = getXFactor(block);
        double yFactor = getYFactor(block);
        int nPoints = getNPoints(block);
        Object[] tables = getPeaktable(block, nPoints, xFactor, yFactor);
        Peak1D[] peaks = (Peak1D[]) tables[0];
        if (peaks.length != nPoints) {
            block.getErrorHandler().error(
                "incorrect ##NPOINTS=: expected "
                    + Integer.toString(nPoints)
                    + " but got "
                    + Integer.toString(peaks.length));
            nPoints = peaks.length;
        }
        double[][] xy = peakTableToPeakSpectrum(peaks);
        IOrderedDataArray1D x = new OrderedArrayData(xy[0], xUnit);
        IDataArray1D y = new ArrayData(xy[1], yUnit);
        spectrum = new Chromatogram(x, y, false);
        spectrum.setPeakTable(peaks);
        if (tables.length > 1) {
            spectrum.setPatternTable((Pattern[]) tables[1]);
            if (tables.length > 2)
                spectrum.setAssignments((Assignment[]) tables[2]);
        }
        return spectrum;
    }
    /**
     * createSpectrum method comment.
     */
    public Spectrum createSpectrum(JCAMPBlock block) throws JCAMPException {
        if (block.getSpectrumID() != ISpectrumIdentifier.CHROMATOGRAM)
            block.getErrorHandler().fatal("JCAMP reader adapter missmatch");
        boolean isFID = false;
        Chromatogram spectrum = null;
        JCAMPDataRecord ldrDataType = block.getDataRecord("DATATYPE");
        String dataType = ldrDataType.getContent().toUpperCase();
        JCAMPBlock.Type type = block.getType();
        if (type.equals(JCAMPBlock.Type.FULLSPECTRUM))
            spectrum = createFS(block);
        else if (type.equals(JCAMPBlock.Type.PEAKTABLE))
            spectrum = createPeakTable(block);
        else if (type.equals(JCAMPBlock.Type.ASSIGNMENT))
            spectrum = createPeakTable(block);
        else // never reached
            block.getErrorHandler().fatal("illegal block type");
        setNotes(block, spectrum);
        return spectrum;
    }
}