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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
package org.jcamp.parser;
import java.util.StringTokenizer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.jcamp.math.IArray1D;
import org.jcamp.spectrum.ArrayData;
import org.jcamp.spectrum.Assignment;
import org.jcamp.spectrum.EquidistantData;
import org.jcamp.spectrum.IDataArray1D;
import org.jcamp.spectrum.IOrderedDataArray1D;
import org.jcamp.spectrum.ISpectrumIdentifier;
import org.jcamp.spectrum.NMRFIDSpectrum;
import org.jcamp.spectrum.NMRSpectrum;
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 NMR spectrum class and JCAMPReader.
* @author Thomas Weber
*/
public class NMRJCAMPReader extends CommonSpectrumJCAMPReader implements ISpectrumJCAMPReader {
private final static String CRLF = "\r\n";
private static Log log = LogFactory.getLog(NMRJCAMPReader.class);
/**
* NMRJCAMPAdapter constructor comment.
*/
protected NMRJCAMPReader() {
super();
}
/**
* create NMR FID spectrum from JCAMPBlock.
*
* @return NMRSpectrum
* @param block JCAMPBlock
* @exception JCAMPException exception thrown if parsing fails.
*/
private NMRSpectrum createFID(JCAMPBlock block) throws JCAMPException {
NMRSpectrum spectrum = null;
String nucleus = getNucleus(block);
double reference = getShiftReference(block);
double freq = getFrequency(block);
if (!block.isNTupleBlock()) {
block.getErrorHandler().warn("illegal FID, assuming y values are real FID part");
// this should never be happen, let's assume we have only real part of FID
Unit xUnit = getXUnits(block);
if (xUnit == null)
xUnit = CommonUnit.hertz;
Unit yUnit = getYUnits(block);
if (yUnit == null)
yUnit = CommonUnit.intensity;
double xFactor = getXFactor(block);
double yFactor = getYFactor(block);
int nPoints = getNPoints(block);
IOrderedDataArray1D x;
IDataArray1D y;
if (block.getDataRecord("XYDATA") != null) {
double firstX = getFirstX(block);
double lastX = getLastX(block);
double[] intensities = getXYData(block, firstX, lastX, nPoints, xFactor, yFactor);
if (intensities.length != nPoints)
throw new JCAMPException("incorrect ##NPOINTS= or bad ##XYDATA=");
x = new EquidistantData(firstX, lastX, nPoints, xUnit);
y = new ArrayData(intensities, yUnit);
} else if (block.getDataRecord("XYPOINTS") != null) {
double xy[][] = getXYPoints(block, nPoints, xFactor, yFactor);
x = new OrderedArrayData(xy[0], xUnit);
y = new ArrayData(xy[1], yUnit);
} else
throw new JCAMPException("missing data: ##XYDATA= or ##XYPOINTS= required.");
spectrum = new NMRFIDSpectrum(x, y, nucleus, freq, reference);
} else {
JCAMPNTuple ntuple = block.getNTuple();
JCAMPVariable x = block.getVariable("X");
JCAMPVariable r = block.getVariable("R");
JCAMPVariable i = block.getVariable("I");
if (x == null)
block.getErrorHandler().fatal("missing X variable");
if (r == null)
block.getErrorHandler().fatal("missing real fid");
if (i == null)
block.getErrorHandler().fatal("missing imaginary fid");
Double firstX = x.getFirst();
if (firstX == null)
block.getErrorHandler().fatal("missing required ##FIRST= for X");
Double lastX = x.getLast();
if (lastX == null)
block.getErrorHandler().fatal("missing required ##LAST= for X");
Double xFactor = x.getFactor();
if (xFactor == null) {
block.getErrorHandler().error("missing required ##FACTOR= for X");
xFactor = new Double(1.0);
}
Double rFactor = r.getFactor();
if (rFactor == null) {
block.getErrorHandler().error("missing required ##FACTOR= for R");
rFactor = new Double(1.0);
}
Double iFactor = i.getFactor();
if (iFactor == null) {
block.getErrorHandler().error("missing required ##FACTOR= for I");
iFactor = new Double(1.0);
}
Integer dim = x.getDimension();
if (dim == null)
block.getErrorHandler().fatal("missing required ##VARDIM= for X");
int nPoints = dim.intValue();
Unit xUnit = x.getUnit();
Unit rUnit = r.getUnit();
Unit iUnit = i.getUnit();
JCAMPNTuplePage page0 = block.getNTuple().getPage(0);
JCAMPNTuplePage page1 = block.getNTuple().getPage(1);
if (page0.getDatatableVariableSymbols()[1].equalsIgnoreCase("I")) { // swap pages, imaginary is first
JCAMPNTuplePage tmp = page0;
page0 = page1;
page1 = tmp;
}
IArray1D reals = page0.getXYData().getYArray();
IArray1D imags = page1.getXYData().getYArray();
IOrderedDataArray1D xData = new EquidistantData(firstX.doubleValue(), lastX.doubleValue(), nPoints, xUnit);
IDataArray1D rData = new ArrayData(reals, rUnit);
IDataArray1D iData = new ArrayData(imags, rUnit);
spectrum = new NMRFIDSpectrum(xData, rData, iData, nucleus, freq, reference);
}
return spectrum;
}
/**
* create NMR full spectrum from JCAMPBlock.
*
* @return NMRSpectrum
* @param block JCAMPBlock
* @exception JCAMPException exception thrown if parsing fails.
*/
private NMRSpectrum createFS(JCAMPBlock block) throws JCAMPException {
NMRSpectrum spectrum = null;
String nucleus = getNucleus(block);
if (!block.isNTupleBlock()) { // standard JCAMP
Unit xUnit = getXUnits(block);
if (xUnit == null)
xUnit = CommonUnit.hertz;
Unit yUnit = getYUnits(block);
if (yUnit == null)
yUnit = CommonUnit.intensity;
double xFactor = getXFactor(block);
double yFactor = getYFactor(block);
int nPoints = getNPoints(block);
IOrderedDataArray1D x = null;
IDataArray1D y = null;
if (block.getDataRecord("XYDATA") != null) {
double firstX = getFirstX(block);
double lastX = getLastX(block);
double[] intensities = getXYData(block, firstX, lastX, nPoints, xFactor, yFactor);
if (intensities.length != nPoints){
/*throw new JCAMPException(
"incorrect ##NPOINTS= or bad ##XYDATA=\n"
+ "found "
+ intensities.length
+ ", but ##NPOINTS= "
+ nPoints);*/
log.warn(
"incorrect ##NPOINTS= or bad ##XYDATA=\n"
+ "found "
+ intensities.length
+ ", but ##NPOINTS= "
+ nPoints+", setting NPOINTS to "+intensities.length);
nPoints=intensities.length;
}
x = new EquidistantData(firstX, lastX, nPoints, xUnit);
y = new ArrayData(intensities, yUnit);
} else if (block.getDataRecord("XYPOINTS") != null) {
double xy[][] = getXYPoints(block, nPoints, xFactor, yFactor);
x = new OrderedArrayData(xy[0], xUnit);
y = new ArrayData(xy[1], yUnit);
} else
block.getErrorHandler().fatal("missing data: ##XYDATA= or ##XYPOINTS= required.");
double reference = Double.NaN;
try {
int refPoint = getShiftReferencePoint(block);
reference = x.pointAt(refPoint);
} catch (JCAMPException e) {
reference = getShiftReference(block);
}
double freq = getFrequency(block);
spectrum = new NMRSpectrum(x, y, nucleus, freq, reference, true);
return spectrum;
} else {
// workaround for Bruker WinNMR real+imag 1D NMR spectra
JCAMPNTuple ntuple = block.getNTuple();
JCAMPVariable x = block.getVariable("X");
JCAMPVariable r = block.getVariable("R");
if (x == null)
block.getErrorHandler().fatal("missing X variable");
if (r == null)
block.getErrorHandler().fatal("missing real part");
Double firstX = x.getFirst();
if (firstX == null)
block.getErrorHandler().fatal("missing required ##FIRST= for X");
Double lastX = x.getLast();
if (lastX == null)
block.getErrorHandler().fatal("missing required ##LAST= for X");
Double xFactor = x.getFactor();
if (xFactor == null) {
block.getErrorHandler().error("missing required ##FACTOR= for X");
xFactor = new Double(1.0);
}
Double rFactor = r.getFactor();
if (rFactor == null) {
block.getErrorHandler().error("missing required ##FACTOR= for R");
rFactor = new Double(1.0);
}
Integer dim = x.getDimension();
if (dim == null)
block.getErrorHandler().fatal("missing required ##VARDIM= for X");
int nPoints = dim.intValue();
Unit xUnit = x.getUnit();
Unit rUnit = r.getUnit();
// first page are reals (TODO: check)
JCAMPNTuplePage page = block.getNTuple().getPage(0);
if (page.getDatatableVariableSymbols()[1].equalsIgnoreCase("I"))
page = block.getNTuple().getPage(1);
IArray1D reals = page.getXYData().getYArray();
IOrderedDataArray1D xData = new EquidistantData(firstX.doubleValue(), lastX.doubleValue(), nPoints, xUnit);
IDataArray1D rData = new ArrayData(reals, rUnit);
double reference = Double.NaN;
try {
int refPoint = getShiftReferencePoint(block);
reference = xData.pointAt(refPoint);
} catch (JCAMPException e) {
reference = getShiftReference(block);
}
double freq = getFrequency(block);
spectrum = new NMRSpectrum(xData, rData, nucleus, freq, reference, true);
return spectrum;
}
}
/**
* create NMR peak table (peak spectrum) from JCAMPBlock.
*
* @return NMRSpectrum
* @param block JCAMPBlock
* @exception JCAMPException exception thrown if parsing fails.
*/
private NMRSpectrum createPeakTable(JCAMPBlock block) throws JCAMPException {
NMRSpectrum spectrum = null;
String nucleus = getNucleus(block);
Unit xUnit = getXUnits(block);
if (xUnit == null)
xUnit = CommonUnit.hertz;
Unit yUnit = getYUnits(block);
if (yUnit == null)
yUnit = CommonUnit.intensity;
double xFactor = getXFactor(block);
double yFactor = getYFactor(block);
int refPoint;
double reference = Double.NaN;
double freq = Double.NaN;
int nPoints = getNPoints(block);
Object[] tables = getPeaktable(block, nPoints, xFactor, yFactor);
Peak1D[] peaks = (Peak1D[]) tables[0];
double[][] xy = peakTableToPeakSpectrum(peaks);
IOrderedDataArray1D x = new OrderedArrayData(xy[0], xUnit);
IDataArray1D y = new ArrayData(xy[1], yUnit);
try {
refPoint = getShiftReferencePoint(block);
reference = x.pointAt(refPoint);
} catch (JCAMPException e) {
// often solventreference is missing in peak tables
reference = getShiftReference(block);
}
try {
freq = getFrequency(block);
} catch (JCAMPException e) {
// often observe frequency is missing in peak tables
block.getErrorHandler().warn(e.getMessage());
}
spectrum = new NMRSpectrum(x, y, nucleus, freq, reference, 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.NMR)
block.getErrorHandler().fatal("adapter missmatch");
boolean isFID = false;
NMRSpectrum spectrum = null;
JCAMPDataRecord ldrDataType = block.getDataRecord("DATATYPE");
String dataType = ldrDataType.getContent().toUpperCase();
if (dataType.indexOf("FID") >= 0)
isFID = true;
// currently many NMR with NTUPLES are FIDs, should generate an error when 2D NMR is available
//
// Bruker writes X->R/I NMR spectra with WinNMR
//
if (!isFID && block.isNTupleBlock()) {
JCAMPVariable x = block.getNTuple().getVariable("X");
if (x.getUnit().equals(CommonUnit.second)) {
block.getErrorHandler().warn("NMR FID without NMR FID data type");
isFID = true;
}
block.getErrorHandler().warn("nD NMR or NMR spectra with real and imaginary part");
}
if (isFID) {
spectrum = createFID(block);
} else {
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");
}
String solvent = getSolvent(block);
spectrum.setSolvent(solvent);
spectrum.setSolventReference(getSolventReference(block, solvent));
setNotes(block, spectrum);
getLinkedAssignments(block, spectrum);
return spectrum;
}
/**
* gets ##$OFFSET= content (Bruker specific)
*
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private double getBrukerOffset(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldrOffset = block.getDataRecord("$OFFSET");
if (ldrOffset == null)
throw new JCAMPException();
String os = ldrOffset.getContent();
return Double.valueOf(os).doubleValue();
}
/**
* gets ##$SF= content (Bruker specific)
*
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private double getBrukerSF(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldrSF = block.getDataRecord("$SF");
if (ldrSF == null)
throw new JCAMPException();
String sf = ldrSF.getContent();
return Double.valueOf(sf).doubleValue();
}
/**
* gets ##$SW= content (Bruker specific)
*
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private double getBrukerSW(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldrSW = block.getDataRecord("$SW");
if (ldrSW == null)
throw new JCAMPException();
String sw = ldrSW.getContent();
return Double.valueOf(sw).doubleValue();
}
/**
* gets ##.OBSERVEFREQUENCY= content
*
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private double getFrequency(JCAMPBlock block) throws JCAMPException {
double freq = Double.NaN;
JCAMPDataRecord ldrFrequency = block.getDataRecord(".OBSERVEFREQUENCY");
if (ldrFrequency == null) {
// first try Bruker labels before quitting
try {
freq = getBrukerSF(block);
} catch (JCAMPException n) {
// again an error, throw original exception
block.getErrorHandler().fatal("missing required label ##.OBSERVEFREQUENCY=");
return 0;
}
block.getErrorHandler().warn("missing required label ##.OBSERVEFREQUENCY=, using Bruker custom labels");
return freq;
} else {
freq = Double.valueOf(ldrFrequency.getContent()).doubleValue();
return freq;
}
}
/**
* find linked peak tables and assignments.
*
* NOTE: works only with SpecInfo convention
*
* @param block com.creon.chem.jcamp.JCAMPBlock
* @param spectrum com.creon.chem.spectrum.NMRSpectrum
*/
private void getLinkedAssignments(JCAMPBlock block, NMRSpectrum spectrum) throws JCAMPException {
JCAMPBlock[] linked = block.getReferences();
for (int i = 0; i < linked.length; i++) {
if (linked[i].isStructureBlock() || linked[i].isLinkBlock())
continue;
JCAMPBlock.Type type = linked[i].getType();
if (linked[i].getSpectrumID() != ISpectrumIdentifier.NMR)
continue;
if (type.equals(JCAMPBlock.Type.PEAKTABLE) || type.equals(JCAMPBlock.Type.ASSIGNMENT)) {
NMRSpectrum linkSpectrum = createPeakTable(linked[i]);
// check if nucleus, frequency, and solvent reference are equal
if (!linkSpectrum.getNucleus().equals(spectrum.getNucleus()))
continue;
if (linkSpectrum.getFrequency() != linkSpectrum.getFrequency()) // Double.NaN
linkSpectrum.setFrequency(spectrum.getFrequency());
if (linkSpectrum.getReference() != linkSpectrum.getReference()) // Double.NaN
linkSpectrum.setReference(spectrum.getReference());
if (linkSpectrum.hasPeakTable())
spectrum.setPeakTable(linkSpectrum.getPeakTable());
if (linkSpectrum.hasPatternTable())
spectrum.setPatternTable(linkSpectrum.getPatternTable());
if (linkSpectrum.hasAssignments())
spectrum.setAssignments(linkSpectrum.getAssignments());
}
}
}
/**
* gets ##.OBSERVENUCLEUS= content
*
* @return java.lang.String
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private String getNucleus(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldrNucleus = block.getDataRecord(".OBSERVENUCLEUS");
if (ldrNucleus == null)
throw new JCAMPException("missing required label: ##.OBSERVENUCLEUS=");
return ldrNucleus.getContent();
}
/**
* gets ##.SHIFTREFERENCE= content
* NOTE: this is a open issue in the JCAMP spec. With standard JCAMP 5.00 it is not possible
* to specify a reference point, with 5.01 it is possible, but the resp. label ##.SHIFTREFERENCE0
* is marked as optional instead of required.
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private double getShiftReference(JCAMPBlock block) throws JCAMPException {
double reference = Double.NaN;
// first try Bruker custom labels
try {
double freq = getBrukerSF(block);
reference = freq * (getBrukerSW(block) - getBrukerOffset(block));
block.getErrorHandler().warn("missing ##.SHIFTREFERENCE=, using Bruker custom labels");
return reference;
} catch (JCAMPException e) {
JCAMPDataRecord ldrReferencePoint = block.getDataRecord("$REFERENCEPOINT");
if (ldrReferencePoint == null) {
block.getErrorHandler().warn("missing shift reference: assuming 0.0 Hz");
return 0.0;
} else {
block.getErrorHandler().warn("missing ##.SHIFTREFERENCE=, using SpecInfo ##$REFERENCEPOINT=");
return Double.valueOf(ldrReferencePoint.getContent()).doubleValue();
}
}
}
/**
* gets ##.SHIFTREFERENCE= content
* NOTE: this is a open issue in the JCAMP spec. With standard JCAMP 5.00 it is not possible
* to specify a reference point, with 5.01 it is possible, but the resp. label ##.SHIFTREFERENCE0
* is marked as optional instead of required.
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private int getShiftReferencePoint(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldrShiftReference = block.getDataRecord(".SHIFTREFERENCE");
if (ldrShiftReference == null) {
// block.getErrorHandler().warn("missing ##.SHIFTREFERENCE=");
throw new JCAMPException();
} else {
String shiftRef = ldrShiftReference.getContent();
StringTokenizer commaTokenizer = new java.util.StringTokenizer(shiftRef, ",");
commaTokenizer.nextToken(); // skip INTERNAL/EXTERNAL
commaTokenizer.nextToken(); // skip solvent
try{
int shiftPoint = Integer.parseInt(commaTokenizer.nextToken().trim());
return shiftPoint;
}catch(NumberFormatException ex){
//shk3: looking at the code where the method is used, it looks like
//there is a fallback, but the fallback only works if
throw new JCAMPException(ex.getMessage());
}
}
}
/**
* gets ##.SHIFTREFERENCE= content
* NOTE: this is a open issue in the JCAMP spec. With standard JCAMP 5.00 it is not possible
* to specify a reference point, with 5.01 it is possible, but the resp. label ##.SHIFTREFERENCE0
* is marked as optional instead of required.
* @return double
* @param block JCAMPBlock
* @exception JCAMPException The exception description.
*/
private String getSolvent(JCAMPBlock block) throws JCAMPException {
JCAMPDataRecord ldr = block.getDataRecord(".SHIFTREFERENCE");
if (ldr == null) {
ldr = block.getDataRecord("$SOLVENT"); // Bruker??? or SpecInfo???
if (ldr == null)
return "TMS";
else
return ldr.getContent();
} else {
String shiftRef = ldr.getContent();
StringTokenizer commaTokenizer = new java.util.StringTokenizer(shiftRef, ",");
commaTokenizer.nextToken(); // skip INTERNAL/EXTERNAL
return commaTokenizer.nextToken();
}
}
/**
* gets solvent reference in ppm from either ##.SHIFTREFERENCE= or ##.SOLVENTREFERENCE= content
* NOTE: this is a open issue in the JCAMP spec. With standard JCAMP 5.00 it is not possible
* to specify a reference point, with 5.01 it is possible, but the resp. label ##.SHIFTREFERENCE=
* is marked as optional instead of required.
* @return double
* @param block JCAMPBlock
* @param solvent the solvent
* @exception JCAMPException The exception description.
*/
private double getSolventReference(JCAMPBlock block, String solvent) throws JCAMPException {
JCAMPDataRecord ldr = block.getDataRecord(".SHIFTREFERENCE");
if (ldr == null) {
ldr = block.getDataRecord(".SOLVENTREFERENCE");
if (ldr == null) {
if (solvent.equals("TMS"))
return 0.0;
else {
block.getErrorHandler().warn(
"missing required label for non-TMS solvent: ##.SOLVENTREFERENCE=, setting reference to 0.0");
return 0.0;
}
} else
return Double.parseDouble(ldr.getContent());
} else {
String shiftRef = ldr.getContent();
String[] tokens = shiftRef.split(",", -1);
//shk3 changed this to using split since the StringTokenizer ignores empty fields
//and the .SHIFTREFERENCE may look like ,TMS,0,0.0
// StringTokenizer commaTokenizer = new java.util.StringTokenizer(shiftRef, ",");
// commaTokenizer.nextToken(); // skip INTERNAL/EXTERNAL
// commaTokenizer.nextToken(); // skip solvent
// commaTokenizer.nextToken(); // skip shiftPoint
// double solvRef = Double.parseDouble(commaTokenizer.nextToken().trim());
double solvRef = Double.parseDouble(tokens[3]);
return solvRef;
}
}
}
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