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The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.
package org.jcamp.spectrum;
import org.jcamp.math.AxisMap;
import org.jcamp.math.DataException;
import org.jcamp.math.LinearAxisMap;
import org.jcamp.math.LinearGrid2D;
import org.jcamp.math.Range1D;
import org.jcamp.math.Range3D;
import org.jcamp.math.RectangularGrid2D;
/**
* 2D spectra.
* @author Thomas Weber
*/
abstract public class Spectrum2D extends Spectrum {
protected IOrderedDataArray1D yData;
protected IOrderedDataArray1D xData;
protected IDataArray1D zData;
protected AxisMap xAxisMap;
protected AxisMap yAxisMap;
protected AxisMap zAxisMap;
protected boolean fullSpectrum = true;
private LinearGrid2D xyGrid = null;
/**
* standard Spectrum2D ctor.
*/
protected Spectrum2D(IOrderedDataArray1D x, IOrderedDataArray1D y, IDataArray1D z) {
super();
this.xData = x;
this.yData = y;
this.zData = z;
this.fullSpectrum = true;
if (x instanceof IEquidistant && y instanceof IEquidistant)
xyGrid = new LinearGrid2D(((IEquidistant) x).getDataGrid(), ((IEquidistant) y).getDataGrid());
}
/**
* cloning.
*
* @return java.lang.Object
*/
public Object clone() {
return (Spectrum2D) super.clone();
}
/**
* gets data range.
*/
public Range3D.Double getDataRange() {
return new Range3D.Double(xAxisMap.getDataRange(), yAxisMap.getDataRange(), zAxisMap.getDataRange());
}
/**
* gets label on x-axis.
*
* @return java.lang.String
*/
public String getXAxisLabel() {
if (xData != null)
return xData.getLabel();
else
return "";
}
/**
* gets mapping to x axis.
* @return AxisMap
*/
public AxisMap getXAxisMap() {
return xAxisMap;
}
/**
* gets x data.
*
* @return com.creon.chem.spectrum.IOrderedDataArray1D
*/
public IOrderedDataArray1D getXData() {
return xData;
}
/**
* gets full view range on x axis.
*/
public Range1D.Double getXFullViewRange() {
return new Range1D.Double(xAxisMap.getFullViewRange());
}
/**
* gets label on y-axis.
*
* @return java.lang.String
*/
public String getYAxisLabel() {
if (yData != null)
return yData.getLabel();
else
return "";
}
/**
* gets mapping to y axis.
* @return AxisMap
*/
public AxisMap getYAxisMap() {
return yAxisMap;
}
/**
* gets y data.
*
* @return com.creon.chem.spectrum.IOrderedDataArray1D
*/
public IOrderedDataArray1D getYData() {
return yData;
}
/**
* gets full view range on y axis.
*/
public Range1D.Double getYFullViewRange() {
return new Range1D.Double(yAxisMap.getFullViewRange());
}
/**
* gets label on z-axis.
*
* @return java.lang.String
*/
public String getZAxisLabel() {
if (zData != null)
return zData.getLabel();
else
return "";
}
/**
* gets mapping to z axis.
* @return AxisMap
*/
public AxisMap getZAxisMap() {
return zAxisMap;
}
/**
* gets z data.
*
* @return com.creon.chem.spectrum.IDataArray1D
*/
public IDataArray1D getZData() {
return zData;
}
/**
* gets full view range on z axis.
*/
public Range1D.Double getZFullViewRange() {
return new Range1D.Double(zAxisMap.getFullViewRange());
}
/**
* interpolate spectrum z-value for given spectrum xy coordinate.
* @param x double
* @param y double
* @return double interpolated height
*/
public double interpolateZ(double xvalue, double yvalue) {
if (xyGrid != null)
return interpolateZGrid(xvalue, yvalue);
else
return interpolateZArray(xvalue, yvalue);
}
/**
* interpolate spectrum z-value for given spectrum xy coordinate.
* @param x double
* @param y double
* @return double interpolated height
*/
private double interpolateZArray(double xvalue, double yvalue) {
// slow algo for xy arrays
final double EPS = 1E-10;
int lengthX = xData.getLength();
int lengthY = yData.getLength();
int[] bx;
int[] by;
try {
bx = xData.boundIndices(xvalue);
by = yData.boundIndices(yvalue);
} catch (DataException e) {
return 0.0;
};
double x0, x1, y0, y1, dx, dy;
if (bx[0] == bx[1]) {
if (by[0] == by[1]) // on grid!
return zData.pointAt(by[0] * lengthX + bx[0]);
// calculate interpolation weights
x0 = xData.pointAt(bx[0]);
x1 = x0;
dx = 0.;
y1 = yData.pointAt(by[1]);
y0 = yData.pointAt(by[0]);
if (yvalue - y0 > EPS)
if (y1 - yvalue > EPS)
dy = Math.max(0., Math.min(1., (yvalue - y0) / (y1 - y0)));
else
dy = 1.0;
else
dy = 0.;
} else {
x0 = xData.pointAt(bx[0]);
x1 = xData.pointAt(bx[1]);
if (xvalue - x0 > EPS)
if (x1 - xvalue > EPS)
dx = Math.max(0., Math.min(1., (xvalue - x0) / (x1 - x0)));
else
dx = 1.0;
// min max to avoid rounding errors
else
dx = 0.;
if (by[0] == by[1]) {
y0 = yData.pointAt(by[0]);
y1 = y0;
dy = 0;
} else {
y0 = yData.pointAt(by[0]);
y1 = yData.pointAt(by[1]);
if (yvalue - y0 > EPS)
if (y1 - yvalue > EPS)
dy = Math.max(0., Math.min(1., (yvalue - y0) / (y1 - y0)));
else
dy = 1.0;
else
dy = 0.;
}
}
if (dx == 0) {
if (dy == 0)
return zData.pointAt(by[0] * lengthX + bx[0]);
else if (dy == 1)
return zData.pointAt(by[1] * lengthX + bx[0]);
} else if (dx == 1) {
if (dy == 0)
return zData.pointAt(by[0] * lengthX + bx[1]);
else if (dy == 1)
return zData.pointAt(by[1] * lengthX + bx[1]);
}
// bounding rectangle:
int lb = by[0] * lengthX + bx[0];
int rb = by[0] * lengthX + bx[1];
int lt = by[1] * lengthX + bx[0];
int rt = by[1] * lengthX + bx[1];
double zlb = zData.pointAt(lb);
double zrb = zData.pointAt(rb);
double zlt = zData.pointAt(lt);
double zrt = zData.pointAt(rt);
double zvalue;
if (dx + dy - 1 < 0) {
zvalue = zlb + dx * (zrb - zlb) + dy * (zlt - zlb);
} else {
dx = 1.0 - dx;
dy = 1.0 - dy;
zvalue = zrt + dx * (zlt - zrt) + dy * (zrb - zrt);
}
return zvalue;
}
/**
* interpolate spectrum z-value for given spectrum xy coordinate.
* @param x double
* @param y double
* @return double interpolated height
*/
private double interpolateZGrid(double xvalue, double yvalue) {
// faster algo for xy grids
int lengthX = xyGrid.getXGrid().getLength();
int lengthY = xyGrid.getYGrid().getLength();
double gx = xyGrid.getXGrid().coordinateAt(xvalue);
double gy = xyGrid.getYGrid().coordinateAt(yvalue);
if (gx < -0.5 || gx > lengthX - 0.5 || gy < -0.5 || gy > lengthY - 0.5) { // out of bounds
return Double.NaN;
}
// find nearest integer lesser than g
int gx0 = (int) Math.floor(gx + 0.5);
if (gx0 < 0)
gx0 = 0;
if (gx0 > lengthX - 2)
gx0 = lengthX - 2;
int gy0 = (int) Math.floor(gy + 0.5);
if (gy0 < 0)
gy0 = 0;
if (gy0 > lengthY - 2)
gy0 = lengthY - 2;
// bounding rectangle:
int lb = gy0 * lengthX + gx0;
int rb = gy0 * lengthX + gx0 + 1;
int lt = (gy0 + 1) * lengthX + gx0;
int rt = (gy0 + 1) * lengthX + gx0 + 1;
double dx = Math.max(0.0, Math.min(1.0, gx - gx0));
double dy = Math.max(0.0, Math.min(1.0, gy - gy0));
double zlb = zData.pointAt(lb);
double zrb = zData.pointAt(rb);
double zlt = zData.pointAt(lt);
double zrt = zData.pointAt(rt);
if (dx + dy - 1 < 0) {
return zlb + dx * (zrb - zlb) + dy * (zlt - zlb);
} else {
dx = Math.max(0.0, Math.min(1.0, gx0 + 1 - gx));
dy = Math.max(0.0, Math.min(1.0, gy0 + 1 - gy));
dx = gx0 + 1 - gx;
dy = gy0 + 1 - gy;
return zrt + dx * (zlt - zrt) + dy * (zrb - zrt);
}
}
/**
* isFullSpectrum method comment.
*/
public boolean isFullSpectrum() {
return fullSpectrum;
}
/**
* isSameType method comment.
*/
public boolean isSameType(Spectrum otherSpectrum) {
return false;
}
/**
* faster complete interpolation
*
* @return double[]
* @param newGrid com.creon.math.RectangularGrid2D
*/
public double[] resample(RectangularGrid2D newGrid) {
if (xyGrid != null)
return xyGrid.interpolate(newGrid, zData.toArray());
else {
int n = newGrid.getLength();
double[] sampled = new double[n];
for (int i = 0; i < n; i++) {
double[] xy = newGrid.gridPointAt(i);
sampled[i] = interpolateZArray(xy[0], xy[1]);
}
return sampled;
}
}
/**
* sets full spectrum status.
*
* @param newFullSpectrum boolean
*/
public void setFullSpectrum(boolean newFullSpectrum) {
fullSpectrum = newFullSpectrum;
}
/**
* set ful view data range in mapping
* should be overloaded
* @param range Range3D
*/
public void setFullViewRange(Range3D.Double range) {
setXFullViewRange(range.getRange(0));
setYFullViewRange(range.getRange(1));
setZFullViewRange(range.getRange(2));
}
/**
* Insert the method's description here.
*
* @param newXData com.creon.chem.spectrum.IOrderedDataArray1D
*/
private void setXData(IOrderedDataArray1D newXData) {
xData = newXData;
}
/**
* sets full view range on x axis
*/
public void setXFullViewRange(Range1D.Double dataRange) {
xAxisMap = new LinearAxisMap(xData, dataRange);
}
/**
* Insert the method's description here.
*
* @param newYData com.creon.chem.spectrum.IOrderedDataArray1D
*/
private void setYData(IOrderedDataArray1D newYData) {
yData = newYData;
}
/**
* sets full view range on y axis.
*/
public void setYFullViewRange(Range1D.Double dataRange) {
yAxisMap = new LinearAxisMap(yData, dataRange);
}
/**
* Insert the method's description here.
*
* @param newZData com.creon.chem.spectrum.IDataArray1D
*/
private void setZData(IDataArray1D newZData) {
zData = newZData;
}
/**
* sets full view range on z axis
*/
public void setZFullViewRange(Range1D.Double dataRange) {
zAxisMap = new LinearAxisMap(zData, dataRange);
}
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