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

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package org.jcamp.parser;

import java.util.Iterator;

import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.ISpectrumIdentifier;
import org.jcamp.spectrum.Pattern;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.RamanSpectrum;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.spectrum.notes.Note;
import org.jcamp.spectrum.notes.NoteDescriptor;
import org.jcamp.units.CommonUnit;
import org.jcamp.units.Unit;
/**
 * adapter between Raman spectrum class and JCAMPWriter.
 * @author Thomas Weber
 */
public class RamanJCAMPWriter extends CommonSpectrumJCAMPWriter implements ISpectrumJCAMPWriter {
    private final static String CRLF = "\r\n";
    /**
     * RamanJCAMPAdapter constructor comment.
     */
    protected RamanJCAMPWriter() {
        super();
    }
    /**
     * build assignment table
     * 
     * @return java.lang.String
     * @param block int  block number (0: no xref, main block)
     * @param raman RamanSpectrum
     */
    private String buildAssignmentTable(int block, RamanSpectrum raman) {
        StringBuffer jcamp = new StringBuffer();
        String origin = raman.getOrigin();
        String owner = raman.getOwner();
        Assignment[] assigns = raman.getAssignments();
        String title = raman.getTitle();
        int n = assigns.length;
        jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
        jcamp.append("##JCAMP-DX=4.24").append(CRLF);
        jcamp.append("##DATATYPE=RAMAN PEAK ASSIGNMENTS").append(CRLF);
        jcamp.append("##DATACLASS=ASSIGNMENTS").append(CRLF);
        if (block != 0) {
            jcamp.append("##BLOCKID=").append(block).append(CRLF);
        }
        jcamp.append(getJCAMPNotes(raman));
        jcamp.append(getXUnitLDR(raman));
        jcamp.append(getYUnitLDR(raman));
        jcamp.append("##NPOINTS=").append(n).append(CRLF);
        jcamp.append("##PEAKASSIGNMENTS=(XYA)").append(CRLF);
        for (int i = 0; i < n; i++) {
            Pattern pattern = assigns[i].getPattern();
            double x = assigns[i].getPosition()[0];
            jcamp.append('(').append(x).append(",1,").append(",<").append(assigns[i].getLabel()).append(">)").append(
                CRLF);
        }
        jcamp.append("##END=").append(CRLF);
        return jcamp.toString();
    }
    /**
     * build full spectrum data block.
     * 
     * @return java.lang.String
     * @param raman RamanSpectrum
     */
    private String buildFSData(int block, RamanSpectrum raman) {
        StringBuffer jcamp = new StringBuffer();
        String origin = raman.getOrigin();
        String owner = raman.getOwner();
        int n = raman.getXData().getLength();
        double x0 = raman.getXData().pointAt(0);
        double x1 = raman.getXData().pointAt(n - 1);
        double y0 = raman.getYData().pointAt(0);
        double y1 = raman.getYData().pointAt(n - 1);
        double xf = (n - 1) / (x0 - x1);
        int[] y = new int[n];
        double yf = raman.getYDataAs16BitIntArray(y);
        String title = raman.getTitle();
        jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
        jcamp.append("##JCAMP-DX=4.24").append(CRLF);
        jcamp.append("##DATATYPE=RAMAN SPECTRUM").append(CRLF);
        jcamp.append("##DATACLASS=XYDATA").append(CRLF);
        if (block != 0) {
            jcamp.append("##BLOCKID=").append(block).append(CRLF);
        }
        jcamp.append(getJCAMPNotes(raman));
        jcamp.append(getXUnitLDR(raman));
        jcamp.append(getYUnitLDR(raman));
        jcamp.append("##NPOINTS=").append(n).append(CRLF);
        jcamp.append("##FIRSTX=").append(x0).append(CRLF);
        jcamp.append("##LASTX=").append(x1).append(CRLF);
        jcamp.append("##DELTAX=").append((x1 - x0) / (n - 1)).append(CRLF);
        jcamp.append("##XFACTOR=").append(xf).append(CRLF);
        jcamp.append("##FIRSTY=").append(y0).append(CRLF);
        jcamp.append("##LASTY=").append(y1).append(CRLF);
        jcamp.append("##YFACTOR=").append(yf).append(CRLF);
        jcamp.append("##XYDATA=(X++(Y..Y))").append(CRLF);
        jcamp.append(ASDFEncoder.encode(Math.round(x0 * xf), Math.round(x1 * xf), y));
        jcamp.append("##END=").append(CRLF);
        return jcamp.toString();
    }
    /**
     * build a peak table.
     * 
     * @return java.lang.String
     * @param raman RamanSpectrum
     */
    private String buildPeakTable(int block, RamanSpectrum raman) {
        StringBuffer jcamp = new StringBuffer();
        String title = raman.getTitle();
        String origin = raman.getOrigin();
        String owner = raman.getOwner();
        jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
        jcamp.append("##JCAMP-DX=4.24").append(CRLF);
        jcamp.append("##DATATYPE=RAMAN PEAK TABLE").append(CRLF);
        jcamp.append("##DATACLASS=PEAK TABLE").append(CRLF);
        if (block != 0) {
            jcamp.append("##BLOCKID=").append(block).append(CRLF);
        }
        jcamp.append(getJCAMPNotes(raman));
        jcamp.append(getXUnitLDR(raman));
        jcamp.append(getYUnitLDR(raman));
        if (raman.hasPeakTable()) {
            Peak1D[] peaks = raman.getPeakTable();
            int n = peaks.length;
            jcamp.append("##NPOINTS=").append(n).append(CRLF);
            jcamp.append("##PEAKTABLE=(XY..XY)").append(CRLF);
            for (int i = 0; i < n; i++) {
                double x = peaks[i].getPosition()[0];
                double y = peaks[i].getPosition()[1];
                jcamp.append(x).append(',').append(y).append(CRLF);
            }
        } else {
            if (!raman.isFullSpectrum()) {
                int n = raman.getXData().getLength();
                jcamp.append("##NPOINTS=").append(n).append(CRLF);
                jcamp.append("##PEAKTABLE=(XY..XY)").append(CRLF);
                for (int i = 0; i < n; i++) {
                    double x = raman.getXData().pointAt(i);
                    double y = raman.getYData().pointAt(i);
                    jcamp.append(x).append(',').append(y).append(CRLF);
                }
            }
        }
        jcamp.append("##END=").append(CRLF);
        return jcamp.toString();
    }
    /**
     * gets spectrum notes in JCAMP form.
     * title note is ignored, it is handled directly
     * @return java.lang.String
     */
    protected String getJCAMPNotes(Spectrum spectrum) {
        StringBuffer notesStr = new StringBuffer();
        Iterator notesIt = spectrum.getNotes().iterator();
        while (notesIt.hasNext()) {
            Note note = (Note) notesIt.next();
            NoteDescriptor descr = note.getDescriptor();
            if ("title".equals(descr.getKey()))
                continue;
            if (!descr.isAllowedForSpectrumID(ISpectrumIdentifier.RAMAN))
                continue;
            Object value = note.getValue();
            IJCAMPNoteMarshaller marshaller = NoteMarshallerFactory.getInstance().findByDescriptor(descr);
            notesStr.append(marshaller.toJCAMP(value));
        }
        return notesStr.toString();
    }
    /**
     * returns  standard JCAMP unit name.
     * 
     * @return java.lang.String
     * @param raman RamanSpectrum
     */
    private static String getXUnitLDR(RamanSpectrum raman) {
        String name;
        Unit unit = raman.getXData().getUnit();
        if (unit.equals(CommonUnit.perCM))
            name = "##XUNITS=1/CM" + CRLF;
        else if (unit.equals(CommonUnit.micrometerWavelength))
            name = "##XUNITS=MICROMETERS" + CRLF;
        else if (unit.equals(CommonUnit.nanometerWavelength))
            name = "##XUNITS=NANOMETERS" + CRLF;
        else if (unit.equals(CommonUnit.second))
            name = "##XUNITS=SECONDS" + CRLF;
        else
            name = "##XUNITS=ARBITRARY UNITS" + CRLF;
        return name;
    }
    /**
     * return standard JCAMP unit name.
     * 
     * @return java.lang.String
     * @param raman RamanSpectrum
     */
    private static String getYUnitLDR(RamanSpectrum raman) {
        String name;
        Unit unit = raman.getYData().getUnit();
        if (unit.equals(CommonUnit.transmittance) || unit.equals(CommonUnit.percentTransmittance))
            name = "##YUNITS=TRANSMITTANCE" + CRLF;
        else if (unit.equals(CommonUnit.reflectance) || unit.equals(CommonUnit.percentReflectance))
            name = "##YUNITS=REFLECTANCE" + CRLF;
        else if (unit.equals(CommonUnit.absorbance))
            name = "##YUNITS=ABSORBANCE" + CRLF;
        else if (unit.equals(CommonUnit.kubelka))
            name = "##YUNITS=KUBELKA-MUNK" + CRLF;
        else
            name = "##YUNITS=ARBITRARY UNITS" + CRLF;
        return name;
    }
    /**
     * writes spectrum as compound JCAMP.
     */
    public String toJCAMP(Spectrum spectrum) throws JCAMPException {
        if (!(spectrum instanceof RamanSpectrum))
            throw new JCAMPException("JCAMP adapter missmatch");
        RamanSpectrum raman = (RamanSpectrum) spectrum;
        StringBuffer jcamp = new StringBuffer();
        String title = raman.getTitle();
        // main data
        int nDataBlocks = 1;
        int block = 1;
        boolean linked = false;
        if (raman.hasAssignments())
            nDataBlocks++;
        if (raman.hasPeakTable() && raman.isFullSpectrum())
            nDataBlocks++;
        if (nDataBlocks > 1) {
            jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
            jcamp.append("##JCAMP-DX=4.24").append(CRLF);
            jcamp.append("##DATATYPE=LINK").append(CRLF);
            jcamp.append("##NBLOCKS=").append(nDataBlocks + 1).append(CRLF);
            jcamp.append("##BLOCKID=").append(block).append(CRLF);
            jcamp.append(super.getJCAMPNotes(spectrum));
            block++;
            linked = true;
        }
        if (raman.isFullSpectrum()) {
            jcamp.append(buildFSData(linked ? block : 0, raman));
            block++;
            if (raman.hasAssignments()) {
                jcamp.append(buildAssignmentTable(linked ? block : 0, raman));
                block++;
            }
            if (raman.hasPeakTable()) {
                jcamp.append(buildPeakTable(linked ? block : 0, raman));
                block++;
            }
        } else { // peak spectrum
            jcamp.append(buildPeakTable(linked ? block : 0, raman));
            block++;
            if (raman.hasAssignments()) {
                jcamp.append(buildAssignmentTable(linked ? block : 0, raman));
                block++;
            }
        }
        if (linked)
            jcamp.append("##END=").append(CRLF);
        return jcamp.toString();
    }
    /**
     * writes spectrum as simple JCAMP.
     */
    public String toSimpleJCAMP(Spectrum spectrum) throws JCAMPException {
        if (!(spectrum instanceof RamanSpectrum))
            throw new JCAMPException("JCAMP adapter missmatch");
        RamanSpectrum raman = (RamanSpectrum) spectrum;
        StringBuffer jcamp = new StringBuffer();
        String title = raman.getTitle();
        // main data
        if (raman.isFullSpectrum()) {
            jcamp.append(buildFSData(0, raman));
        } else { // peak spectrum
            if (raman.hasAssignments()) {
                jcamp.append(buildAssignmentTable(0, raman));
            } else {
                jcamp.append(buildPeakTable(0, raman));
            }
        }
        return jcamp.toString();
    }
}