org.jcamp.parser.NMRJCAMPWriter Maven / Gradle / Ivy
package org.jcamp.parser;
import java.util.Iterator;
import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.NMRFIDSpectrum;
import org.jcamp.spectrum.NMRSpectrum;
import org.jcamp.spectrum.Pattern;
import org.jcamp.spectrum.Peak1D;
import org.jcamp.spectrum.Spectrum;
import org.jcamp.spectrum.notes.Note;
import org.jcamp.spectrum.notes.NoteDescriptor;
import org.jcamp.units.CommonUnit;
/**
* adapter between NMR spectrum class and JCAMPWriter.
*
* @author Thomas Weber
*/
public class NMRJCAMPWriter
implements ISpectrumJCAMPWriter {
private final static String CRLF = "\r\n";
/**
* NMRJCAMPAdapter constructor comment.
*/
protected NMRJCAMPWriter() {
super();
}
/**
* build assignment table
*
* @return java.lang.String
* @param block int block number (0: no xref, main block)
* @param nmr NMRSpectrum
*/
private String buildAssignmentTable(int block, NMRSpectrum nmr) {
StringBuilder jcamp = new StringBuilder();
Assignment[] assigns = nmr.getAssignments();
String title = nmr.getTitle();
String origin = nmr.getOrigin();
String owner = nmr.getOwner();
int n = assigns.length;
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=NMR PEAK ASSIGNMENTS").append(CRLF);
jcamp.append("##DATACLASS=ASSIGNMENTS").append(CRLF);
jcamp.append("##ORIGIN=").append(origin != null ? origin : "").append(CRLF);
jcamp.append("##OWNER=").append(owner != null ? owner : "COPYRIGHT ??? BY UNKNOWN").append(CRLF);
if (block != 0) {
jcamp.append("##BLOCKID=").append(block).append(CRLF);
}
jcamp.append("##.OBSERVENUCLEUS=").append(nmr.getNucleus()).append(CRLF);
jcamp.append("##.OBSERVEFREQUENCY=").append(nmr.getFrequency()).append(CRLF);
if (!nmr.getSolvent().equals("TMS")) {
jcamp.append("##.SOLVENTREFERENCE=").append(nmr.getSolventReference()).append(CRLF);
}
jcamp.append("##XUNITS=PPM").append(CRLF);
jcamp.append("##YUNITS=ARBITRARY UNITS").append(CRLF);
jcamp.append("##NPOINTS=").append(n).append(CRLF);
jcamp.append("##PEAKASSIGNMENTS=(XYMA)").append(CRLF);
for (int i = 0; i < n; i++) {
double x = assigns[i].getPosition()[0];
jcamp
.append('(')
.append(x)
.append(",1,")
.append(assigns[i].getPattern().getLabel())
.append(",<")
.append(assigns[i].getLabel())
.append(">)")
.append(CRLF);
}
jcamp.append("##END=").append(CRLF);
return jcamp.toString();
}
/**
* build FID data block.
*
* @return java.lang.String
* @param nmr NMRFIDSpectrum
*/
private String buildFIDData(int block, NMRFIDSpectrum nmr) {
StringBuilder jcamp = new StringBuilder();
int n = nmr.getXData().getLength();
double x0 = nmr.getXData().pointAt(0);
double x1 = nmr.getXData().pointAt(n - 1);
double xf = (x1 - x0) / (n - 1);
nmr.mapRealFID();
double r0 = nmr.getYData().pointAt(0);
double r1 = nmr.getYData().pointAt(n - 1);
int[] r = new int[n];
double rf = nmr.getYDataAs16BitIntArray(r);
nmr.mapImaginaryFID();
double im0 = nmr.getYData().pointAt(0);
double im1 = nmr.getYData().pointAt(n - 1);
int[] im = new int[n];
double imf = nmr.getYDataAs16BitIntArray(im);
String title = nmr.getTitle();
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=NMR FID").append(CRLF);
jcamp.append("##DATACLASS=NTUPLES").append(CRLF);
jcamp.append(getJCAMPNotes(nmr));
if (block != 0) {
jcamp.append("##BLOCKID=").append(block).append(CRLF);
}
jcamp.append("##.OBSERVENUCLEUS=").append(nmr.getNucleus()).append(CRLF);
jcamp.append("##.OBSERVEFREQUENCY=").append(nmr.getFrequency()).append(CRLF);
jcamp.append("##.DELAY=").append(CRLF); // TODO
jcamp.append("##.ACQUISITIONMODE=").append(CRLF);
jcamp.append("##NTUPLES=NMR FID").append(CRLF);
jcamp.append("##VAR_NAME=TIME, FID/REAL, FID/IMAG, PAGE NUMBER").append(CRLF);
jcamp.append("##SYMBOL= X, R, I, N").append(CRLF);
jcamp.append("##VAR_TYPE=INDEPENDENT, DEPENDENT, DEPENDENT, PAGE").append(CRLF);
jcamp.append("##VAR_FORM=AFFN, ASDF, ASDF, AFFN").append(CRLF);
jcamp.append("##VAR_DIM=").append(n).append(',').append(n).append(',').append(n).append(",2").append(CRLF);
jcamp.append("##UNITS= SECONDS, ARBITRARY UNITS, ARBITRARY UNITS,").append(CRLF);
jcamp.append("##FIRST=").append(x0).append(',').append(r0).append(',').append(im0).append(",1").append(CRLF);
jcamp.append("##LAST=").append(x1).append(',').append(r1).append(',').append(im1).append(",2").append(CRLF);
jcamp.append("##FACTOR=").append(xf).append(',').append(rf).append(',').append(imf).append(",1").append(CRLF);
jcamp.append("##PAGE= N=1").append(CRLF);
jcamp.append("##DATATABLE=(X++(R..R)), XYDATA").append(CRLF);
jcamp.append(ASDFEncoder.encode(x0 * xf, x1 * xf, r));
jcamp.append("##PAGE= N=2").append(CRLF);
jcamp.append("##DATATABLE=(X++(I..I)), XYDATA").append(CRLF);
jcamp.append(ASDFEncoder.encode(x0 * xf, x1 * xf, im));
jcamp.append("##ENDNTUPLES=NMR FID").append(CRLF);
jcamp.append("##END=").append(CRLF);
return jcamp.toString();
}
/**
* build full spectrum data block.
*
* @return java.lang.String
* @param nmr NMRSpectrum
*/
private String buildFSData(int block, NMRSpectrum nmr) {
StringBuilder jcamp = new StringBuilder();
int n = nmr.getXData().getLength();
double x0 = nmr.getXData().pointAt(0);
double x1 = nmr.getXData().pointAt(n - 1);
double freq = nmr.getFrequency();
double ref = nmr.getReference();
if (nmr.getXData().getUnit().equals(CommonUnit.ppm)) {
x0 = NMRSpectrum.convertToHertz(x0, freq, ref);
x1 = NMRSpectrum.convertToHertz(x1, freq, ref);
}
double y0 = nmr.getYData().pointAt(0);
double y1 = nmr.getYData().pointAt(n - 1);
double xf = (n - 1) / (x0 - x1);
int[] y = new int[n];
double yf = nmr.getYDataAs16BitIntArray(y);
String title = nmr.getTitle();
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=NMR SPECTRUM").append(CRLF);
jcamp.append("##DATACLASS=XYDATA").append(CRLF);
if (block != 0) {
jcamp.append("##BLOCKID=").append(block).append(CRLF);
}
jcamp.append(getJCAMPNotes(nmr));
jcamp.append("##.OBSERVENUCLEUS=").append(nmr.getNucleus()).append(CRLF);
jcamp.append("##.OBSERVEFREQUENCY=").append(nmr.getFrequency()).append(CRLF);
String solvent = nmr.getSolvent();
if (ref == ref) {
// ensure we have a reference frequency (possibly a peak table)
int shiftPoint = (int) ((ref - x0) / xf);
jcamp
.append("##.SHIFTREFERENCE=,")
.append(nmr.getSolvent())
.append(",")
.append(shiftPoint)
.append(",")
.append(nmr.getSolventReference())
.append(CRLF);
}
if (!solvent.equals("TMS")) {
jcamp.append("##.SOLVENTREFERENCE=").append(nmr.getSolventReference()).append(CRLF);
}
jcamp.append("##XUNITS=HZ").append(CRLF);
jcamp.append("##YUNITS=ARBITRARY UNITS").append(CRLF);
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 pattern table
*
* @return java.lang.String
* @param block int block number (0: no xref, main block)
* @param nmr NMRSpectrum
*/
private String buildPatternTable(int block, NMRSpectrum nmr) {
StringBuilder jcamp = new StringBuilder();
Pattern[] pattern = nmr.getPatternTable();
String title = nmr.getTitle();
int n = pattern.length;
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=NMR PEAK TABLE").append(CRLF);
jcamp.append("##DATACLASS=PEAK TABLE").append(CRLF);
if (block != 0) {
jcamp.append("##BLOCKID=").append(block).append(CRLF);
}
jcamp.append(getJCAMPNotes(nmr));
jcamp.append("##.OBSERVENUCLEUS=").append(nmr.getNucleus()).append(CRLF);
jcamp.append("##.OBSERVEFREQUENCY=").append(nmr.getFrequency()).append(CRLF);
if (!nmr.getSolvent().equals("TMS")) {
jcamp.append("##.SOLVENTREFERENCE=").append(nmr.getSolventReference()).append(CRLF);
}
jcamp.append("##XUNITS=PPM").append(CRLF);
jcamp.append("##YUNITS=ARBITRARY UNITS").append(CRLF);
jcamp.append("##NPOINTS=").append(n).append(CRLF);
jcamp.append("##PEAKTABLE=(XYM..XYM)").append(CRLF);
for (int i = 0; i < n; i++) {
double x = pattern[i].getPosition()[0];
double y = pattern[i].getPosition()[1];
jcamp.append(x).append(',').append(y).append(',').append(pattern[i].getLabel()).append(CRLF);
}
jcamp.append("##END=").append(CRLF);
return jcamp.toString();
}
/**
* build a peak table.
*
* @return java.lang.String
* @param nmr NMRSpectrum
*/
private String buildPeakTable(int block, NMRSpectrum nmr) {
StringBuilder jcamp = new StringBuilder();
Peak1D[] peaks = nmr.getPeakTable();
int n = peaks.length;
String title = nmr.getTitle();
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=NMR PEAK TABLE").append(CRLF);
jcamp.append("##DATACLASS=PEAK TABLE").append(CRLF);
jcamp.append(getJCAMPNotes(nmr));
if (block != 0) {
jcamp.append("##BLOCKID=").append(block).append(CRLF);
}
jcamp.append("##.OBSERVENUCLEUS=").append(nmr.getNucleus()).append(CRLF);
jcamp.append("##.OBSERVEFREQUENCY=").append(nmr.getFrequency()).append(CRLF);
if (!nmr.getSolvent().equals("TMS")) {
jcamp.append("##.SOLVENTREFERENCE=").append(nmr.getSolventReference()).append(CRLF);
}
jcamp.append("##XUNITS=PPM").append(CRLF);
jcamp.append("##YUNITS=ARBITRARY UNITS").append(CRLF);
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);
}
jcamp.append("##END=").append(CRLF);
return jcamp.toString();
}
/**
* gets spectrum notes in JCAMP form.
* title note is ignored, it is handled directly
* shk3: BLOCKID is also ignored, this caused multiply block elements in a block
* when writing a link spectrum.
* @return java.lang.String
*/
protected String getJCAMPNotes(Spectrum spectrum) {
StringBuilder notesStr = new StringBuilder();
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.isAllowedForSpectrum(spectrum))
continue;
if ("BLOCKID".equals(descr.getKey()))
continue;
Object value = note.getValue();
IJCAMPNoteMarshaller marshaller = NoteMarshallerFactory.getInstance().findByDescriptor(descr);
notesStr.append(marshaller.toJCAMP(value));
}
return notesStr.toString();
}
/**
* writes spectrum as compound JCAMP.
*/
public String toJCAMP(Spectrum spectrum) throws JCAMPException {
if (!(spectrum instanceof NMRSpectrum))
throw new JCAMPException("JCAMP adapter missmatch");
NMRSpectrum nmr = (NMRSpectrum) spectrum;
StringBuilder jcamp = new StringBuilder();
String title = nmr.getTitle();
// main data
int nDataBlocks = 1;
int block = 1;
boolean linked = false;
if (nmr.hasAssignments())
nDataBlocks++;
else { // pattern are only included pattern if no assignment table is present
if (nmr.hasPatternTable())
nDataBlocks++;
}
if (nmr.hasPeakTable() && nmr.isFullSpectrum())
nDataBlocks++;
if (nDataBlocks > 1) {
jcamp.append("##TITLE=").append(title != null ? title : "").append(CRLF);
jcamp.append("##JCAMP-DX=5.01").append(CRLF);
jcamp.append("##DATATYPE=LINK").append(CRLF);
jcamp.append("##NBLOCKS=").append(nDataBlocks + 1).append(CRLF);
jcamp.append("##BLOCKID=").append(block).append(CRLF);
block++;
linked = true;
}
if (nmr.isFullSpectrum()) {
if (nmr.isFID()) {
jcamp.append(buildFIDData(linked ? block : 0, (NMRFIDSpectrum) nmr));
block++;
} else {
jcamp.append(buildFSData(linked ? block : 0, nmr));
block++;
}
if (nmr.hasAssignments()) {
jcamp.append(buildAssignmentTable(linked ? block : 0, nmr));
block++;
} else {
if (nmr.hasPatternTable()) {
jcamp.append(buildPatternTable(linked ? block : 0, nmr));
block++;
}
}
if (nmr.hasPeakTable()) {
jcamp.append(buildPeakTable(linked ? block : 0, nmr));
block++;
}
} else { // peak spectrum
jcamp.append(buildPeakTable(linked ? block : 0, nmr));
block++;
if (nmr.hasAssignments()) {
jcamp.append(buildAssignmentTable(linked ? block : 0, nmr));
block++;
} else {
if (nmr.hasPatternTable()) {
jcamp.append(buildPatternTable(linked ? block : 0, nmr));
block++;
}
}
}
if (linked)
jcamp.append("##END=").append(CRLF);
return jcamp.toString();
}
/**
* writes spectrum as simple JCAMP with possible information loss.
*/
public String toSimpleJCAMP(Spectrum spectrum) throws JCAMPException {
if (!(spectrum instanceof NMRSpectrum))
throw new JCAMPException("JCAMP adapter missmatch");
NMRSpectrum nmr = (NMRSpectrum) spectrum;
StringBuilder jcamp = new StringBuilder();
// main data
if (nmr.isFullSpectrum()) {
if (nmr.isFID()) {
jcamp.append(buildFIDData(0, (NMRFIDSpectrum) nmr));
} else {
jcamp.append(buildFSData(0, nmr));
}
} else {
if (nmr.hasAssignments()) {
jcamp.append(buildAssignmentTable(0, nmr));
} else if (nmr.hasPatternTable()) {
jcamp.append(buildPatternTable(0, nmr));
} else if (nmr.hasPeakTable()) {
jcamp.append(buildPeakTable(0, nmr));
}
}
return jcamp.toString();
}
}
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