private synchronized void display(ExtSed sed) {
manageAssociatedManagerWindows(sed);
try {
SpectrumContainer container =
(SpectrumContainer) sed.getAttachment(IrisDisplayManager.FIT_MODEL);
// There is no Sed attachment, so build a model manager and attach it.
if (container == null) {
if (buildAttachment(sed)) {
return;
}
}
// VAOPD-879: spectrum name must be identical with Sed name.
if (container != null) {
container.getSpectrum().setName(sed.getId());
}
// Now display the Sed.
idm.display(sed, sed.getId());
// and add its frame to the workspace.
JInternalFrame frame = idm.getInternalFrame();
// VAOPD-863
frame.setTitle(sed.getId());
if (container != null) {
JFrame modelManagerFrame = container.getModelManager().getFrame();
if (modelManagerFrame != null) {
modelManagerFrame.setTitle(sed.getId());
}
}
if (frame != currentFrame) {
lastLocation = null;
disposeCurrentFrame();
currentFrame = frame;
currentFrame.setDefaultCloseOperation(JInternalFrame.HIDE_ON_CLOSE);
if (lastLocation != null) {
currentFrame.setLocation(lastLocation);
}
frame.setTitle("Iris Visualizer");
ws.addFrame(frame);
}
} catch (Exception ex) {
LogEvent.getInstance().fire(this, new LogEntry("Error: " + ex.getMessage(), sed));
Logger.getLogger("IrisVisualizer").log(Level.SEVERE, null, ex);
}
}
public ExtSed interpolate(ExtSed sed, InterpolationConfig interpConf) throws Exception {
if (sed.getNumberOfSegments() == 0) {
throw new SedNoDataException();
}
ExtSed newsed = ExtSed.flatten(sed, "Angstrom", "Jy");
String intervUnits = interpConf.getUnits();
Double xmin = interpConf.getXMin();
Double xmax = interpConf.getXMax();
if (xmin > Double.NEGATIVE_INFINITY)
xmin = um.convertX(new double[] {xmin}, intervUnits, "Angstrom")[0];
if (xmax < Double.POSITIVE_INFINITY)
xmax = um.convertX(new double[] {xmax}, intervUnits, "Angstrom")[0];
interpConf.setXMin(Math.min(xmin, xmax));
interpConf.setXMax(Math.max(xmin, xmax));
interpConf.setX(newsed.getSegment(0).getSpectralAxisValues());
interpConf.setY(newsed.getSegment(0).getFluxAxisValues());
SAMPMessage message =
SAMPFactory.createMessage(INTERPOLATE_MTYPE, interpConf, InterpolationPayload.class);
Response rspns = client.sendMessage(message);
InterpolationPayload response =
(InterpolationPayload) SAMPFactory.get(rspns.getResult(), InterpolationPayload.class);
if (xmin > Double.NEGATIVE_INFINITY)
xmin = um.convertX(new double[] {xmin}, "Angstrom", intervUnits)[0];
if (xmax < Double.POSITIVE_INFINITY)
xmax = um.convertX(new double[] {xmax}, "Angstrom", intervUnits)[0];
interpConf.setXMin(Math.min(xmin, xmax));
interpConf.setXMax(Math.max(xmin, xmax));
double[] x = um.convertX(response.getX(), "Angstrom", intervUnits);
Segment segment = new Segment();
segment.setSpectralAxisValues(x);
segment.setFluxAxisValues(response.getY());
segment.setTarget(sed.getSegment(0).getTarget());
segment.setSpectralAxisUnits(intervUnits);
segment.setFluxAxisUnits("Jy");
String ucd = "em.wl";
if (intervUnits.equals("Hz")) ucd = "em.freq";
else if (intervUnits.equals("keV")) ucd = "em.energy";
segment.createChar().createSpectralAxis().setUcd(ucd);
segment.createChar().createFluxAxis().setUcd("phot.flux.density;" + ucd);
ExtSed newSed = manager.newSed(sed.getId() + "_" + interpConf.getMethod().replaceAll(" ", ""));
newSed.addSegment(segment);
newSed.checkChar();
return newSed;
}
public void invalidateModel(ExtSed sed) {
if (sed != null) {
SpectrumContainer container =
(SpectrumContainer) sed.getAttachment(IrisDisplayManager.FIT_MODEL);
if (container != null) {
ModelManager2 mm = container.getModelManager();
if (mm != null && mm.isActive()) {
mm.dispose();
}
sed.removeAttachment(IrisDisplayManager.FIT_MODEL);
}
}
}
private void manageAssociatedManagerWindows(ExtSed sed) {
ExtSed displaying = idm.getDisplaying();
if (displaying != null) {
if (!sed.getId().equals(displaying.getId())) {
// displayed Sed is exiting: make its model manager and metadata windows invisible.
SpectrumContainer container =
(SpectrumContainer) displaying.getAttachment(IrisDisplayManager.FIT_MODEL);
if (container != null) {
ModelManager2 modelManager = container.getModelManager();
modelManager.setVisible(false);
SpectrumVisualEditor editor = idm.getVisualEditor();
if (editor != null) {
editor.getJFrame().setVisible(false);
}
}
// new Sed is entering display: make its model manager window visible if active.
if (sed != null) {
container = (SpectrumContainer) sed.getAttachment(IrisDisplayManager.FIT_MODEL);
if (container != null) {
ModelManager2 modelManager = container.getModelManager();
modelManager.setVisible(modelManager.isActive());
}
}
}
}
}
public boolean buildAttachment(ExtSed sed)
throws SedNoDataException, SedInconsistentException, SpectrumException {
Spectrum sp = factory.readAllSegments(null, sed);
if (sp == null) {
return true;
}
sp.setName(sed.getId());
JDesktopPane desktop = ws.getDesktop();
SherpaModelManager modelManager = new SherpaModelManager(sp, idm.getSAMPConnector(), desktop);
modelManager.setActive(false);
SpectrumContainer container = new SpectrumContainer(sp, modelManager);
sed.addAttachment(IrisDisplayManager.FIT_MODEL, container);
// This is needed to capture the 'Quit' button action
// that comes from the model manager GUI.
modelManager.setCallbackOnDispose(new OnDisposeCommand(sed));
return false;
}
@Test
public void testStacker() throws Exception {
ExtSed sed1 = new ExtSed("Sed1");
ExtSed sed2 = new ExtSed("Sed2");
ExtSed sed3 = new ExtSed("Sed3");
Segment seg1 = new Segment();
for (int k = 0; k < x1.length; k++) {
y1[k] = y1[k] * 1e23;
yerr1[k] = yerr1[k] * 1e23;
}
seg1.setFluxAxisValues(y1);
seg1.setSpectralAxisValues(x1);
seg1.setFluxAxisUnits("Jy");
seg1.setSpectralAxisUnits("Angstrom");
seg1.setDataValues(yerr1, UTYPE.FLUX_STAT_ERROR);
sed1.addSegment(seg1);
Segment seg2 = new Segment();
seg2.setFluxAxisValues(y2);
seg2.setSpectralAxisValues(x2);
seg2.setFluxAxisUnits("erg/s/cm2/Hz");
seg2.setSpectralAxisUnits("Angstrom");
seg2.setDataValues(yerr2, UTYPE.FLUX_STAT_ERROR);
sed2.addSegment(seg2);
Segment seg3 = new Segment();
seg3.setFluxAxisValues(y3);
// convert the values in x3 to nm so I can test the unit conversions
// too.
int k = 0;
for (double x : x3) {
x3[k] = x * 0.1;
k++;
}
seg3.setSpectralAxisValues(x3);
seg3.setFluxAxisUnits("erg/s/cm2/Hz");
seg3.setSpectralAxisUnits("nm");
seg3.setDataValues(yerr3, UTYPE.FLUX_STAT_ERROR);
sed3.addSegment(seg3);
SedStack stack = new SedStack("Stack");
stack.add(sed1);
stack.add(sed2);
stack.add(sed3);
// setup the stacking configuration
StackConfiguration config = new StackConfiguration();
config.setBinsize(2.0);
config.setBinsizeUnit("Angstrom");
config.setLogbin(false);
config.setSmooth(false);
config.setSmoothBinsize(20.);
config.setStatistic("avg");
config.setYUnits("erg/s/cm2/Hz");
// stack
stacker = new SedStackerStacker(client, (UnitsManager) null);
ExtSed result = stacker.stack(stack, config);
List<double[]> xs = new ArrayList<>();
List<double[]> ys = new ArrayList<>();
xs.add(x1);
xs.add(x2);
xs.add(x3);
ys.add(y1);
ys.add(y2);
ys.add(y3);
// stack.getOrigSeds() should return original seds
for (int j = 0; j < stack.getOrigSeds().size(); j++) {
ExtSed origSed = stack.getOrigSeds().get(j);
double[] x = xs.get(j);
double[] y = ys.get(j);
for (int i = 0; i < stack.getOrigSeds().get(j).getSegment(0).getLength(); i++) {
double xOrigValue = origSed.getSegment(0).getSpectralAxisValues()[i];
double yOrigValue = origSed.getSegment(0).getFluxAxisValues()[i];
assertEquals(xOrigValue, x[i], EPSILON);
assertEquals(yOrigValue, y[i], EPSILON);
}
}
double[] controlY =
new double[] {5.0, 5.36666667, 4.5, 2.66666667, 4.0, 6.5, 1.5, 10.5, 5.0, 10.0};
double[] controlX = new double[] {0., 2., 4., 6., 8., 10., 16., 22., 50., 100.};
// double[] controlYerr = new double[] {0.5, 0.501120965, 0.3640055,
// 0.18104634, 0.4, 0.48102899, 0.15, 1.05, 0.5, 1.0}; // calculated
// from errors [sqrt(sum(errors^2))/N]
double[] controlYerr =
new double[] {0, 6.82169741, 2.5, 1.64991582, 0., 5.21216526, 0., 0., 0., 0.}; // calculated
// from
// stddev(flux)
double[] controlCounts = new double[] {1, 3, 2, 3, 1, 3, 1, 1, 1, 1};
// test values of stacked Sed
double[] yerrValues = (double[]) result.getSegment(0).getDataValues(UTYPE.FLUX_STAT_ERROR);
double[] counts = (double[]) result.getAttachment(COUNTS);
for (int i = 0; i < result.getSegment(0).getLength(); i++) {
double xValue = result.getSegment(0).getSpectralAxisValues()[i];
double yValue = result.getSegment(0).getFluxAxisValues()[i];
assertEquals(controlX[i], xValue, EPSILON);
assertEquals(controlY[i], yValue, EPSILON);
assertEquals(controlYerr[i], yerrValues[i], EPSILON);
assertEquals(controlCounts[i], counts[i], EPSILON);
}
}
public void execute(Object o) {
sed.removeAttachment(IrisDisplayManager.FIT_MODEL);
idm.removeVisualEditor();
display(sed);
}
private void remove(ExtSed source) {
invalidateModel(source); // Might be needed in the future?
idm.remove(source.getId());
}
public void testWriteAscii() throws Exception {
URL fileURL = SaveSedDialog.class.getResource("/test_data/3c273.xml");
Sed s = Sed.read(fileURL.openStream(), SedFormat.VOT);
List<Segment> segList = new ArrayList<>();
// To assign the RA and DEC correctly, in case the pos.eq is in
// SpatialAxis.Coverage.Location rather than Target.Pos
for (int i = 0; i < s.getNumberOfSegments(); i++) {
Segment seg = s.getSegment(i);
if (s.getSegment(i).createTarget().getPos() == null) {
if (seg.createChar().createSpatialAxis().createCoverage().getLocation() != null) {
seg.createTarget()
.createPos()
.setValue(seg.getChar().getSpatialAxis().getCoverage().getLocation().getValue());
} else {
seg.createTarget()
.createPos()
.setValue(
new DoubleParam[] {new DoubleParam(Double.NaN), new DoubleParam(Double.NaN)});
}
}
segList.add(s.getSegment(i));
}
ExtSed sed = new ExtSed(fileURL.getPath());
sed.addSegment(segList);
File output = File.createTempFile("writeAsciiTest_3c273", ".dat");
SaveSedDialog ssd = new SaveSedDialog(SedBuilder.getWorkspace().getRootFrame(), sed, false);
ssd.setXunit("Hz");
ssd.setYunit("erg/s/cm2/Angstrom");
ssd.setFilePath("file:///" + output.getPath());
ssd.writeAscii(sed, output, false);
URL url = new URL(ssd.getFilePath());
SetupBean result = new AsciiConf().makeConf(url);
Segment segment = SegmentImporter.getSegments(result).get(0);
assertEquals(segment.getSpectralAxisUnits(), "Hz");
assertEquals(segment.getFluxAxisUnits(), "erg/s/cm2/Angstrom");
// Test SED created in Science window (from calculated fluxes
File output2 = File.createTempFile("writeAsciiTest_3c273-2", ".dat");
ssd.setFilePath("file:///" + output2.getPath());
ssd.writeAscii(sed, output2, true);
URL url2 = new URL(ssd.getFilePath());
URLConnection urlConnection = url2.openConnection();
BufferedReader bufferedReader =
new BufferedReader(new InputStreamReader(urlConnection.getInputStream()));
String line;
String metadata = "";
while ((line = bufferedReader.readLine()).startsWith("#")) {
metadata = metadata + line;
}
SetupBean result2 = new AsciiConf().makeConf(url2);
Segment segment2 = SegmentImporter.getSegments(result2).get(0);
assertEquals(segment2.getSpectralAxisUnits(), "Hz");
assertEquals(segment2.getFluxAxisUnits(), "erg/s/cm2/Angstrom");
assert (metadata.contains("Iris Flux Integration output"));
output.deleteOnExit();
output2.deleteOnExit();
}
@Test
public void testNormalizer() throws Exception {
ExtSed sed1 = new ExtSed("Sed1");
ExtSed sed2 = new ExtSed("Sed2");
ExtSed sed3 = new ExtSed("Sed3");
Segment seg1 = new Segment();
for (int k = 0; k < x1.length; k++) {
y1[k] = y1[k] * 1e23;
yerr1[k] = yerr1[k] * 1e23;
}
seg1.setFluxAxisValues(y1);
seg1.setSpectralAxisValues(x1);
seg1.setFluxAxisUnits("Jy");
seg1.setSpectralAxisUnits("Angstrom");
seg1.setDataValues(yerr1, UTYPE.FLUX_STAT_ERROR);
sed1.addSegment(seg1);
Segment seg2 = new Segment();
seg2.setFluxAxisValues(y2);
seg2.setSpectralAxisValues(x2);
seg2.setFluxAxisUnits("erg/s/cm2/Hz");
seg2.setSpectralAxisUnits("Angstrom");
seg2.setDataValues(yerr2, UTYPE.FLUX_STAT_ERROR);
sed2.addSegment(seg2);
Segment seg3 = new Segment();
seg3.setFluxAxisValues(y3);
// convert the values in x3 to nm so I can test the unit conversions
// too.
for (int k = 0; k < x3.length; k++) {
x3[k] = x3[k] * 0.1;
}
seg3.setSpectralAxisValues(x3);
seg3.setFluxAxisUnits("erg/s/cm2/Hz");
seg3.setSpectralAxisUnits("nm");
seg3.setDataValues(yerr3, UTYPE.FLUX_STAT_ERROR);
sed3.addSegment(seg3);
SedStack stack = new SedStack("Stack");
stack.add(sed1);
stack.add(sed2);
stack.add(sed3);
// setup the redshift configuration
NormalizationConfiguration config = new NormalizationConfiguration();
config.setMultiply(true);
config.setIntegrate(true);
config.setStats("Average");
config.setXUnits("Angstrom");
config.setXmax(Double.POSITIVE_INFINITY);
config.setXmin(Double.NEGATIVE_INFINITY);
config.setIntegrateValueYUnits("erg/s/cm2/Hz");
config.setYValue(1.0);
// normalize the Stack
SedStackerNormalizer normalizer =
new SedStackerNormalizer(client, Default.getInstance().getUnitsManager());
normalizer.normalize(stack, config);
List<double[]> xs = new ArrayList<>();
List<double[]> ys = new ArrayList<>();
xs.add(x1);
xs.add(x2);
xs.add(x3);
ys.add(y1);
ys.add(y2);
ys.add(y3);
// stack.getOrigSeds() should return original seds
for (int j = 0; j < stack.getOrigSeds().size(); j++) {
ExtSed origSed = stack.getOrigSeds().get(j);
double[] x = xs.get(j);
double[] y = ys.get(j);
for (int i = 0; i < stack.getOrigSeds().get(j).getSegment(0).getLength(); i++) {
double xOrigValue = origSed.getSegment(0).getSpectralAxisValues()[i];
double yOrigValue = origSed.getSegment(0).getFluxAxisValues()[i];
assertEquals(xOrigValue, x[i], EPSILON);
assertEquals(yOrigValue, y[i], EPSILON);
}
}
for (int j = 0; j < stack.getSed(0).getSegment(0).getLength(); j++)
assertEquals(
0.49234923 * y1[j],
stack.getSed(0).getSegment(0).getFluxAxisValues()[j],
EPSILON * 0.49234923 * y1[j]);
for (int j = 0; j < stack.getSed(1).getSegment(0).getLength(); j++)
assertEquals(9.846 * y2[j], stack.getSed(1).getSegment(0).getFluxAxisValues()[j], EPSILON);
assertEquals(
1.1529274,
Double.valueOf(stack.getSed(2).getAttachment(NORM_CONSTANT).toString()),
EPSILON);
}
@Test
public void testNormalizerOutsideRange() throws Exception {
ExtSed sed1 = new ExtSed("Sed1");
ExtSed sed2 = new ExtSed("Sed2");
ExtSed sed3 = new ExtSed("Sed3");
Segment seg1 = new Segment();
// for (int k=0; k<x1.length; k++) {
// y1[k] = y1[k]*1e23;
// yerr1[k] = yerr1[k]*1e23;
// }
seg1.setFluxAxisValues(y1);
seg1.setSpectralAxisValues(x1);
seg1.setFluxAxisUnits("erg/s/cm2/Angstrom");
seg1.setSpectralAxisUnits("Angstrom");
seg1.setDataValues(yerr1, UTYPE.FLUX_STAT_ERROR);
sed1.addSegment(seg1);
Segment seg2 = new Segment();
seg2.setFluxAxisValues(y2);
seg2.setSpectralAxisValues(x2);
seg2.setFluxAxisUnits("erg/s/cm2/Angstrom");
seg2.setSpectralAxisUnits("Angstrom");
seg2.setDataValues(yerr2, UTYPE.FLUX_STAT_ERROR);
sed2.addSegment(seg2);
Segment seg3 = new Segment();
seg3.setFluxAxisValues(y3);
// convert the values in x3 to nm so I can test the unit conversions
// too.
for (int k = 0; k < x3.length; k++) {
x3[k] = x3[k] * 0.1;
}
seg3.setSpectralAxisValues(x3);
seg3.setFluxAxisUnits("erg/s/cm2/Angstrom");
seg3.setSpectralAxisUnits("nm");
seg3.setDataValues(yerr3, UTYPE.FLUX_STAT_ERROR);
sed3.addSegment(seg3);
SedStack stack = new SedStack("Stack");
stack.add(sed1);
stack.add(sed2);
stack.add(sed3);
// setup the redshift configuration
NormalizationConfiguration config = new NormalizationConfiguration();
config.setMultiply(true);
config.setIntegrate(true);
config.setStats("Value");
config.setXUnits("Angstrom");
config.setXmax(9.0);
config.setXmin(1.5);
config.setIntegrateValueYUnits("erg/s/cm2");
config.setYValue(1.0);
// normalize the Stack
normalizeWithWindowInterceptor(stack, config);
List<double[]> xs = new ArrayList<>();
List<double[]> ys = new ArrayList<>();
xs.add(x1);
xs.add(x2);
xs.add(x3);
ys.add(y1);
ys.add(y2);
ys.add(y3);
// stack.getOrigSeds() should return original seds
for (int j = 0; j < stack.getOrigSeds().size(); j++) {
ExtSed origSed = stack.getOrigSeds().get(j);
double[] x = xs.get(j);
double[] y = ys.get(j);
for (int i = 0; i < stack.getOrigSeds().get(j).getSegment(0).getLength(); i++) {
double xOrigValue = origSed.getSegment(0).getSpectralAxisValues()[i];
double yOrigValue = origSed.getSegment(0).getFluxAxisValues()[i];
assertEquals(xOrigValue, x[i], EPSILON);
assertEquals(yOrigValue, y[i], EPSILON);
}
}
for (int j = 0; j < stack.getSed(0).getSegment(0).getLength(); j++)
assertEquals(y1[j], stack.getSed(0).getSegment(0).getFluxAxisValues()[j], EPSILON);
for (int j = 0; j < stack.getSed(1).getSegment(0).getLength(); j++)
assertEquals(0.0625 * y2[j], stack.getSed(1).getSegment(0).getFluxAxisValues()[j], EPSILON);
assertEquals(
0.035714285714,
Double.valueOf(stack.getSed(2).getAttachment(NORM_CONSTANT).toString()),
EPSILON);
}