@Test
public void testreadWriteHdu() throws Exception {
byte[] undefinedData = new byte[1000];
for (int index = 0; index < undefinedData.length; index++) {
undefinedData[index] = (byte) index;
}
UndefinedData data = UndefinedHDU.encapsulate(undefinedData);
Header header = new Header();
header.pointToData(data);
UndefinedHDU hdu = new UndefinedHDU(header, data);
hdu.getHeader().deleteKey("EXTEND");
BufferedFile stream = new BufferedFile("target/rewriteHduTest.bin", "rw");
hdu.write(stream);
stream.close();
stream = new BufferedFile("target/rewriteHduTest.bin", "rw");
data = UndefinedHDU.encapsulate(new byte[0]);
hdu = new UndefinedHDU(new Header(data), data);
hdu.read(stream);
hdu.addValue("TESTER", "WRITE", null);
hdu.rewrite();
hdu.reset();
hdu.read(stream);
hdu.getHeader().getStringValue("TESTER");
byte[] rereadUndefinedData = (byte[]) hdu.getData().getData();
Assert.assertArrayEquals(undefinedData, rereadUndefinedData);
}
/** Create the WCS using the definition given in the FITS header. */
public WCS(Header h) throws TransformationException {
wcsKeys = new HashMap<String, Object>();
this.h = h;
headerNaxis = new int[2];
if (checkDSS()) {
headerNaxis[0] = h.getIntValue("NAXIS1");
headerNaxis[1] = h.getIntValue("NAXIS2");
if (headerNaxis[0] == 0) {
headerNaxis[0] = h.getIntValue("XPIXELS");
headerNaxis[1] = h.getIntValue("YPIXELS");
}
doDSSWCS();
stdWCS = false;
} else if (checkNeat()) {
headerNaxis[0] = h.getIntValue("NAXIS1");
headerNaxis[1] = h.getIntValue("NAXIS2");
doNeatWCS();
stdWCS = false;
} else { // More or less standard FITS WCS
getAxes();
if (lonAxis == -1 || latAxis == -1) {
throw new TransformationException("Unable to find coordinate axes");
}
headerNaxis[0] = h.getIntValue("NAXIS" + lonAxis);
headerNaxis[1] = h.getIntValue("NAXIS" + latAxis);
extractCoordinateSystem();
extractProjection();
extractScaler();
}
}
@Test
public void testFitsUndefinedHdu4() throws Exception {
Fits fits1 = makeAsciiTable();
fits1.read();
byte[] undefinedData = new byte[1000];
for (int index = 0; index < undefinedData.length; index++) {
undefinedData[index] = (byte) index;
}
Data data = UndefinedHDU.encapsulate(undefinedData);
Header header = new Header();
header.pointToData(data);
fits1.addHDU(FitsFactory.hduFactory(header, data));
BufferedDataOutputStream os =
new BufferedDataOutputStream(new FileOutputStream("target/UndefindedHDU4.fits"));
fits1.write(os);
os.close();
Fits fits2 = new Fits("target/UndefindedHDU4.fits");
BasicHDU<?>[] hdus = fits2.read();
byte[] rereadUndefinedData =
(byte[]) ((UndefinedData) hdus[hdus.length - 1].getData()).getData();
Assert.assertArrayEquals(undefinedData, rereadUndefinedData);
ByteArrayOutputStream out = new ByteArrayOutputStream();
hdus[hdus.length - 1].info(new PrintStream(out));
String undefinedInfo = new String(out.toByteArray());
Assert.assertTrue(undefinedInfo.indexOf("Apparent size:1000") >= 0);
}
static void initPlotTitle(
PlotState state,
ImagePlot plot,
ActiveFitsReadGroup frGroup,
String dataDesc,
boolean isMultiImage) {
WebPlotRequest req = state.getPrimaryWebPlotRequest();
WebPlotRequest.TitleOptions titleOps = req.getTitleOptions();
String headerKey = req.getHeaderKeyForTitle();
if ((isMultiImage
&& (titleOps == WebPlotRequest.TitleOptions.NONE
|| titleOps == WebPlotRequest.TitleOptions.FILE_NAME))
|| (titleOps == WebPlotRequest.TitleOptions.HEADER_KEY && StringUtils.isEmpty(headerKey))) {
titleOps = WebPlotRequest.TitleOptions.HEADER_KEY;
headerKey = "EXTNAME";
}
String s = req.getPlotDescAppend();
plot.setPlotDesc("");
Header header = frGroup.getFitsRead(state.firstBand()).getHeader();
switch (titleOps) {
case NONE:
plot.setPlotDesc("");
break;
case PLOT_DESC:
String base = req.getTitle() == null ? "" : req.getTitle();
plot.setPlotDesc(base + dataDesc);
break;
case FILE_NAME:
break;
case HEADER_KEY:
HeaderCard card = header.findCard(headerKey);
if (card == null && state.getCubeCnt(state.firstBand()) > 0) {
card = header.findCard("PLANE" + state.getImageIdx(state.firstBand()));
}
String hTitle = card != null ? card.getValue() : "";
plot.setPlotDesc(hTitle);
break;
case PLOT_DESC_PLUS:
plot.setPlotDesc(req.getTitle() + (s != null ? " " + s : ""));
break;
case SERVICE_OBS_DATE:
if (req.getRequestType() == RequestType.SERVICE) {
// String desc= req.getServiceType()== WebPlotRequest.ServiceType.WISE
// ? MID_OBS : OBS_DATE;
String title =
req.getTitle()
+ ": "
+
// desc + ": " +
PlotServUtils.getDateValueFromServiceFits(req.getServiceType(), header);
plot.setPlotDesc(title);
}
break;
}
}
@Test
public void testHduFromHeader() throws Exception {
Header header = new Header();
header.addValue("SIMPLE", true, "");
header.addValue("BITPIX", 8, "");
header.addValue("NAXIS", 2, "");
header.addValue("NAXIS1", 4, "");
header.addValue("NAXIS3", 4, "");
ImageHDU hdu = (ImageHDU) Fits.makeHDU(header);
Assert.assertNotNull(hdu);
}
private double equinox() {
double equin = h.getDoubleValue("EQUINOX", NaN);
if (isNaN(equin)) {
equin = h.getDoubleValue("EPOCH", NaN);
}
if (isNaN(equin)) {
equin = 2000;
}
wcsKeys.put("EQUINOX", 2000);
return equin;
}
@Test
public void testBigDataSegments() throws Exception {
ImageData data = new ImageData(new float[4][4]);
Header manufactureHeader = ImageHDU.manufactureHeader(data);
manufactureHeader.card(Standard.END).comment("");
manufactureHeader.findCard(Standard.NAXIS1).setValue(25000);
manufactureHeader.findCard(Standard.NAXIS2).setValue(25000);
long value = manufactureHeader.getDataSize();
int intValue = (int) manufactureHeader.getDataSize();
assertEquals(2500001280L, value);
Assert.assertTrue(intValue != value);
}
public void copyToHeader(Header h) throws nom.tam.fits.HeaderCardException {
String[] srt = wcsKeys.keySet().toArray(new String[0]);
java.util.Arrays.sort(srt);
for (String key : srt) {
Object o = wcsKeys.get(key);
if (o instanceof Integer) {
h.addValue(key, ((Integer) o).intValue(), "Copied WCS eleemnt");
} else if (o instanceof Double) {
h.addValue(key, ((Double) o).doubleValue(), "Copied WCS element");
} else if (o instanceof String) {
h.addValue(key, (String) o, "Copied WCS element");
}
}
}
public String getHeaderString() {
Header hdr = hdu.getHeader();
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
hdr.dumpHeader(ps);
String hdrString = baos.toString();
try {
baos.close();
} catch (IOException e) {
e.printStackTrace();
}
ps.close();
return hdrString;
}
/** Get the scaling between the projection plane and pixel coordinates */
private void extractScaler() throws TransformationException {
// There are three ways that scaling information may be provided:
// CDELTn, CRPIXn, and CROTAn
// CDm_n, CRPIXn
// PCm_n, CDELTn, CRPIXn
// We look for them in this sequence.
//
double crpix1 = h.getDoubleValue("CRPIX" + lonAxis, NaN);
double crpix2 = h.getDoubleValue("CRPIX" + latAxis, NaN);
wcsKeys.put("CRPIX1", crpix1);
wcsKeys.put("CRPIX2", crpix2);
if (isNaN(crpix1) || isNaN(crpix2)) {
throw new TransformationException("CRPIXn not found in header");
}
// Note that in FITS files, the center of the first pixel is
// assumed to be at coordinates 1,1. Thus the corner of the image
// is at pixels coordinates 1/2, 1/2.
crpix1 -= 0.5;
crpix2 -= 0.5;
if (extractScaler1(crpix1, crpix2)) {
return;
}
if (extractScaler2(crpix1, crpix2)) {
return;
}
// No scaling information found.
throw new TransformationException("No scaling information found in FITS header");
}
private void extractCoordinateSystem() throws TransformationException {
// To get the coordinate system we look at the CTYPEn, EQUINOX, RADESYSm
String lonType = h.getStringValue("CTYPE" + lonAxis).substring(0, 4);
String latType = h.getStringValue("CTYPE" + latAxis).substring(0, 4);
String coordSym = null;
CoordinateSystem coords;
if (lonType.equals("RA--") && latType.equals("DEC-")) {
coordSym = frame() + equinox();
} else {
if (lonType.charAt(0) != latType.charAt(0)) {
throw new TransformationException(
"Inconsistent axes definitions:" + lonType + "," + latType);
}
if (lonType.equals("GLON")) {
coordSym = "G";
} else if (lonType.equals("ELON")) {
coordSym = "E" + equinox();
} else if (lonType.equals("HLON")) {
coordSym = "H" + equinox();
}
}
coords = CoordinateSystem.factory(coordSym);
this.csys = coords;
add(coords.getSphereDistorter());
add(coords.getRotater());
}
/** Is this a DSS projection? */
private boolean checkDSS() throws TransformationException {
String origin = h.getStringValue("ORIGIN");
if (origin == null || h.getStringValue("CTYPE1") != null) {
return false;
}
wcsKeys.put("ORIGIN", origin);
// If we have a local solution use it unless told
// to prefer the DSS solution.
if (h.getStringValue("CTYPE1") != null && !preferDSS) {
return false;
}
if (h.getDoubleValue("XPIXELSZ", -1) == -1) {
return false;
}
return origin.startsWith("CASB") || origin.startsWith("STScI");
}
/** Get the scaling when it is described as a matrix */
private boolean extractScaler2(double crpix1, double crpix2) throws TransformationException {
// Look for the CD matrix...
//
double m11 = h.getDoubleValue("CD" + lonAxis + "_" + lonAxis, NaN);
double m12 = h.getDoubleValue("CD" + lonAxis + "_" + latAxis, NaN);
double m21 = h.getDoubleValue("CD" + latAxis + "_" + lonAxis, NaN);
double m22 = h.getDoubleValue("CD" + latAxis + "_" + latAxis, NaN);
boolean matrix = !isNaN(m11 + m12 + m21 + m22);
if (!matrix) {
return false;
}
wcsKeys.put("CD1_1", m11);
wcsKeys.put("CD1_2", m12);
wcsKeys.put("CD2_1", m21);
wcsKeys.put("CD2_2", m22);
m11 = toRadians(m11);
m12 = toRadians(m12);
m21 = toRadians(m21);
m22 = toRadians(m22);
// we have
// t = a11 (x-x0) + a12 (y-y0); u = a21(x-x0) + a22(y-y0)
// t = a11x + a12y - a11 x0 - a12 y0;
//
Scaler s =
new Scaler(-m11 * crpix1 - m12 * crpix2, -m21 * crpix1 - m22 * crpix2, m11, m12, m21, m22);
s = s.inverse();
// Are longitude and latitude in unusual order?
if (lonAxis > latAxis) {
s.interchangeAxes();
}
this.scale = s;
add(s);
setWCSScale(s);
return true;
}
/** Update the display to show the FITS headers of the spectrum */
public void updateDisplay() {
Header header = null;
if (specData != null) {
header = specData.getHeaders();
}
// Stop with null table if no spectrum or no headers.
if (specData == null || header == null) {
table.setModel(new DefaultTableModel());
return;
}
String[] columnNames = {"Keyword", "Value", "Comment"};
int numKeywords = header.getNumberOfCards();
String[][] values = new String[numKeywords][3];
Iterator it = header.iterator();
int n = 0;
while (it.hasNext()) {
HeaderCard card = (HeaderCard) (it.next());
String key = card.getKey();
String value = card.getValue();
String comment = card.getComment();
// A blank keyword is really a comment line.
if ("".equals(key)) {
value = comment;
comment = "";
}
values[n][0] = key;
values[n][1] = value;
values[n++][2] = comment;
}
table.setModel(new DefaultTableModel(values, columnNames));
// Set default widths, matched to FITS format.
TableColumn column = table.getColumnModel().getColumn(0);
column.setPreferredWidth(100);
column = table.getColumnModel().getColumn(1);
column.setPreferredWidth(300);
column = table.getColumnModel().getColumn(2);
column.setPreferredWidth(450);
}
/**
* Find which axes are being used for coordinates. Normally this will just be 1 and 2, but
* occasionally we may be surprised.
*/
private void getAxes() {
int naxes = h.getIntValue("NAXIS");
// The first axes match are assumed to be correct.
for (int i = 1; i <= naxes; i += 1) {
String axis = h.getStringValue("CTYPE" + i);
if (axis != null && axis.length() >= 4) {
axis = axis.substring(0, 4);
} else {
continue;
}
if (lonAxis == -1) {
if (axis.equals("RA--")
|| axis.equals("GLON")
|| axis.equals("ELON")
|| axis.equals("HLON")) {
lonAxis = i;
}
}
if (latAxis == -1) {
if (axis.equals("DEC-")
|| axis.equals("GLAT")
|| axis.equals("ELAT")
|| axis.equals("HLAT")) {
latAxis = i;
}
}
}
if (lonAxis > -1) {
wcsKeys.put("CTYPE1", h.getStringValue("CTYPE" + lonAxis));
}
if (latAxis > -1) {
wcsKeys.put("CTYPE2", h.getStringValue("CTYPE" + latAxis));
}
}
private String frame() {
String sys = h.getStringValue("RADESYS");
if (sys != null) {
wcsKeys.put("RADESYS", sys);
}
if (sys == null) {
double equin = equinox();
if (equin >= 1984) {
return "J";
} else {
return "B";
}
}
if (sys.length() > 3 && sys.substring(0, 3).equals("FK4")) {
return "B";
} else {
return "J";
}
}
@Test
public void testFitsUndefinedHdu3() throws Exception {
Fits fits1 = makeAsciiTable();
fits1.read();
byte[] undefinedData = new byte[1000];
for (int index = 0; index < undefinedData.length; index++) {
undefinedData[index] = (byte) index;
}
Data data = UndefinedHDU.encapsulate(undefinedData);
Header header = new Header(data);
Cursor<String, HeaderCard> iter = header.iterator();
String[] headers = new String[header.getNumberOfCards() - 1];
int index = 0;
while (iter.hasNext()) {
HeaderCard headerCard = iter.next();
// the EXTEND key will be deleted later on because the header is no
// primary header so don't use it
if (!headerCard.getKey().equals("EXTEND")) {
headers[index++] = headerCard.toString();
}
}
Header newHeader = new Header(headers);
for (index = 0; index < headers.length; index++) {
Assert.assertEquals(header.getCard(index), newHeader.getCard(index));
}
fits1.addHDU(FitsFactory.hduFactory(newHeader, data));
BufferedDataOutputStream os =
new BufferedDataOutputStream(new FileOutputStream("target/UndefindedHDU3.fits"));
fits1.write(os);
os.close();
Fits fits2 = new Fits("target/UndefindedHDU3.fits");
BasicHDU[] hdus = fits2.read();
for (index = 0; index < headers.length; index++) {
Assert.assertEquals(header.getCard(index), hdus[5].getHeader().getCard(index));
}
}
@Test
public void testFitsUndefinedHdu5() throws Exception {
Header head = new Header();
head.setXtension("UNKNOWN");
head.setBitpix(BasicHDU.BITPIX_BYTE);
head.setNaxes(1);
head.addValue("NAXIS1", 1000, null);
head.addValue("PCOUNT", 0, null);
head.addValue("GCOUNT", 2, null);
UndefinedHDU hdu = (UndefinedHDU) FitsFactory.hduFactory(head);
byte[] data = (byte[]) hdu.getData().getData();
Assert.assertEquals(2000, data.length);
Arrays.fill(data, (byte) 1);
BufferedFile buf = new BufferedFile("target/testFitsUndefinedHdu5", "rw");
hdu.write(buf);
buf.close();
Arrays.fill(data, (byte) 2);
buf = new BufferedFile("target/testFitsUndefinedHdu5", "rw");
hdu.read(buf);
data = (byte[]) hdu.getData().getData();
buf.close();
Assert.assertEquals((byte) 1, data[0]);
}
public String getWcsHeaderCardsString() {
Header header = hdu.getHeader();
Header filteredHeader = new Header();
// now adjust WCS values:
ArrayList<HeaderCard> cards = new ArrayList<HeaderCard>();
cards.add(header.findCard("CTYPE1"));
cards.add(header.findCard("CTYPE2"));
cards.add(header.findCard("RADESYS"));
cards.add(header.findCard("RADECSYS"));
cards.add(header.findCard("CRVAL1"));
cards.add(header.findCard("CRVAL2"));
cards.add(header.findCard("CDELT1"));
cards.add(header.findCard("CDELT2"));
cards.add(header.findCard("EQUINOX"));
cards.add(header.findCard("BUNIT"));
cards.add(header.findCard("EPOCH"));
cards.add(header.findCard("CD1_1"));
cards.add(header.findCard("CD1_2"));
cards.add(header.findCard("CD2_1"));
cards.add(header.findCard("CD2_2"));
cards.add(header.findCard("CRPIX1"));
cards.add(header.findCard("CRPIX2"));
cards.add(header.findCard("END"));
cards.forEach(
(card) -> {
if (card != null) {
try {
filteredHeader.addLine(card);
} catch (Exception e) {
e.printStackTrace();
}
}
});
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
filteredHeader.dumpHeader(ps);
String wcsHdrString = baos.toString();
try {
baos.close();
} catch (IOException e) {
e.printStackTrace();
}
ps.close();
return wcsHdrString;
}
/**
* Write FITS WCS keywords given key values. Only relatively simple WCSs are handled here. We
* assume we are dealing with axes 1 and 2.
*
* @param h The header to be updated.
* @param s A Scaler giving the transformation between standard projection coordinates and
* pixel/device coordinates.
* @param projString A three character string giving the projection used. Supported projections
* are: "Tan", "Sin", "Ait", "Car", "Zea".
* @param coordString A string giving the coordinate system used. The first character gives the
* general frame. For most frames the remainder of the string gives the equinox of the
* coordinate system. E.g., J2000, B1950, Galactic, "E2000", "H2020.10375".
*/
public void updateHeader(
Header h, Scaler s, double[] crval, String projString, String coordString) throws Exception {
if (proj.isFixedProjection()) {
h.addValue("CRVAL1", toDegrees(proj.getReferencePoint()[0]), "Fixed reference center");
h.addValue("CRVAL2", toDegrees(proj.getReferencePoint()[1]), "Fixed reference center");
} else {
h.addValue("CRVAL1", crval[0], "Reference longitude");
h.addValue("CRVAL2", crval[1], "Reference latitude");
}
coordString = coordString.toUpperCase();
String[] prefixes = new String[2];
char c = coordString.charAt(0);
if (c == 'J' || c == 'I') {
h.addValue("RADESYS", "FK5", "Coordinate system");
prefixes[0] = "RA--";
prefixes[1] = "DEC-";
} else if (c == 'B') {
h.addValue("RADESYS", "FK4", "Coordinate system");
prefixes[0] = "RA--";
prefixes[1] = "DEC-";
} else {
prefixes[0] = c + "LON";
prefixes[1] = c + "LAT";
}
if (c != 'G' && c != 'I') {
try {
double equinox = Double.parseDouble(coordString.substring(1));
h.addValue("EQUINOX", equinox, "Epoch of the equinox");
} catch (Exception e) {
// Couldn't parse out the equinox
}
}
if (c == 'I') {
h.addValue("EQUINOX", 2000, "ICRS coordinates");
}
String upProj = projString.toUpperCase();
h.addValue("CTYPE1", prefixes[0] + "-" + upProj, "Coordinates -- projection");
h.addValue("CTYPE2", prefixes[1] + "-" + upProj, "Coordinates -- projection");
// Note that the scaler transforms from the standard projection
// coordinates to the pixel coordinates.
// P = P0 + M X where X is the standard coordinates and P is the
// pixel coordinates. So the reference pixels are just the constants
// in the scaler.
// Remember that FITS pixels are offset by 0.5 from 0 offset pixels.
h.addValue("CRPIX1", s.x0 + 0.5, "X reference pixel");
h.addValue("CRPIX2", s.y0 + 0.5, "Y reference pixel");
// Remember that the FITS values are of the form
// X = M(P-P0)
// so we'll need to invert the scaler.
//
// Do we need a matrix?
if (abs(s.a01) < 1.e-14 && abs(s.a10) < 1.e-14) {
// No cross terms, so we'll just use CDELTs
h.addValue("CDELT1", toDegrees(1 / s.a00), "X scale");
h.addValue("CDELT2", toDegrees(1 / s.a11), "Y scale");
} else {
// We have cross terms. It's simplest
// just to use the CD matrix and not worry about
// normalization. First invert the matrix to get
// the transformation in the direction that FITS uses.
Scaler rev = s.inverse();
h.addValue("CD1_1", toDegrees(rev.a00), "Matrix element");
h.addValue("CD1_2", toDegrees(rev.a01), "Matrix element");
h.addValue("CD2_1", toDegrees(rev.a10), "Matrix element");
h.addValue("CD2_2", toDegrees(rev.a11), "Matrix element");
}
}
/** Handle the NEAT special projection */
private void doNeatWCS() throws TransformationException {
// The NEAT transformation from the standard spherical system
// includes:
// Transformation to J2000 spherical coordinates (a null operation)
// A tangent plane projection to the standard plane
// A scaler transformation to corrected pixel coordinates.
// A distorter to distorted pixel coordinates
// A scaler transformation of distorted coordinates to actual pixels
CoordinateSystem csys = CoordinateSystem.factory("J2000");
this.csys = csys;
// The RA0/DEC0 pair are the actual center of the projection.
double cv1 = toRadians(h.getDoubleValue("RA0"));
double cv2 = toRadians(h.getDoubleValue("DEC0"));
wcsKeys.put("CRVAL1", toDegrees(cv1));
wcsKeys.put("CRVAL2", toDegrees(cv2));
Projection proj = new Projection("Tan", new double[] {cv1, cv2});
this.proj = proj;
double cd1 = toRadians(h.getDoubleValue("CDELT1"));
double cd2 = toRadians(h.getDoubleValue("CDELT2"));
wcsKeys.put("CDELT1", toDegrees(cd1));
wcsKeys.put("CDELT2", toDegrees(cd2));
wcsScale = abs(cd1);
double cp1 = h.getDoubleValue("CRPIX1");
double cp2 = h.getDoubleValue("CRPIX2");
wcsKeys.put("CPRIX1", cp1);
wcsKeys.put("CRPIX2", cp2);
wcsKeys.put("CTYPE1", "RA---XTN");
wcsKeys.put("CTYPE2", "DEC--XTN");
Scaler s1 = new Scaler(0., 0., -1 / cd1, 0, 0, -1 / cd2);
// Note that the the A0,A1,A2, B0,B1,B2 rotation
// is relative to the original pixel values, so
// we need to put this in the secondary scaler.
//
double x0 = h.getDoubleValue("X0");
double y0 = h.getDoubleValue("Y0");
Distorter dis =
new skyview.geometry.distorter.Neat(
h.getDoubleValue("RADIAL"), h.getDoubleValue("XRADIAL"), h.getDoubleValue("YRADIAL"));
double a0 = h.getDoubleValue("A0");
double a1 = h.getDoubleValue("A1");
double a2 = h.getDoubleValue("A2");
double b0 = h.getDoubleValue("B0");
double b1 = h.getDoubleValue("B1");
double b2 = h.getDoubleValue("B2");
// The reference pixel is to be computed in the distorted frame.
double[] cpix = new double[] {cp1, cp2};
double[] cout = new double[2];
dis.transform(cpix, cout);
Scaler s2 =
new Scaler(
cout[0] - a0 - a1 * x0 - a2 * y0,
cout[1] - b0 - b2 * x0 - b1 * y0,
-(1 + a1),
-a2,
-b2,
-(1 + b1));
wcsKeys.put("A0", a0);
wcsKeys.put("A1", a1);
wcsKeys.put("A2", a2);
wcsKeys.put("B0", b0);
wcsKeys.put("B1", b1);
wcsKeys.put("B2", b2);
this.distort = dis;
add(csys.getSphereDistorter());
add(csys.getRotater());
add(proj.getRotater());
add(proj.getProjecter());
this.scale = s1;
// Note that s1 is defined from the projection plane to the pixels coordinates,
// so we don't need to invert it.
//
// But the second scaler, s2, used in the NEAT correction
// is defined in the direction from pixels to sphere, so we
// need to take its inverse.
this.scale = this.scale.add(s2.inverse());
add(this.scale);
add(dis);
}
/** Is this a NEAT special projection? */
private boolean checkNeat() {
return h.getStringValue("CTYPE1").equals("RA---XTN");
}
/** Handle a DSS projection */
private void doDSSWCS() throws TransformationException {
double plateRA =
h.getDoubleValue("PLTRAH")
+ h.getDoubleValue("PLTRAM") / 60
+ h.getDoubleValue("PLTRAS") / 3600;
plateRA = toRadians(15 * plateRA);
wcsKeys.put("PLTRAH", h.getDoubleValue("PLTRAH"));
wcsKeys.put("PLTRAM", h.getDoubleValue("PLTRAM"));
wcsKeys.put("PLTRAS", h.getDoubleValue("PLTRAS"));
double plateDec =
h.getDoubleValue("PLTDECD")
+ h.getDoubleValue("PLTDECM") / 60
+ h.getDoubleValue("PLTDECS") / 3600;
plateDec = toRadians(plateDec);
if (h.getStringValue("PLTDECSN").substring(0, 1).equals("-")) {
plateDec = -plateDec;
}
wcsKeys.put("PLTDECD", h.getDoubleValue("PLTDECD"));
wcsKeys.put("PLTDECM", h.getDoubleValue("PLTDECM"));
wcsKeys.put("PLTDECS", h.getDoubleValue("PLTDECS"));
wcsKeys.put("PLTDECSN", h.getStringValue("PLTDECSN"));
double plateScale = h.getDoubleValue("PLTSCALE");
double xPixelSize = h.getDoubleValue("XPIXELSZ");
double yPixelSize = h.getDoubleValue("YPIXELSZ");
wcsKeys.put("PLTSCALE", plateScale);
wcsKeys.put("XPIXELSZ", xPixelSize);
wcsKeys.put("YPIXELSZ", yPixelSize);
double[] xCoeff = new double[20];
double[] yCoeff = new double[20];
for (int i = 1; i <= 20; i += 1) {
xCoeff[i - 1] = h.getDoubleValue("AMDX" + i);
yCoeff[i - 1] = h.getDoubleValue("AMDY" + i);
wcsKeys.put("AMDX" + i, xCoeff[i - 1]);
wcsKeys.put("AMDY" + i, yCoeff[i - 1]);
}
double[] ppo = new double[6];
for (int i = 1; i <= 6; i += 1) {
ppo[i - 1] = h.getDoubleValue("PPO" + i);
wcsKeys.put("PPO" + i, ppo[i - 1]);
}
double plateCenterX = ppo[2];
double plateCenterY = ppo[5];
double cdelt1 = -plateScale / 1000 * xPixelSize / 3600;
double cdelt2 = plateScale / 1000 * yPixelSize / 3600;
wcsScale = abs(cdelt1);
// This gives cdelts in degrees per pixel.
// CNPIX pixels use a have the first pixel going from 1 - 2 so they are
// off by 0.5 from FITS (which in turn is offset by 0.5 from the internal
// scaling, but we handle that elsewhere).
double crpix1 = plateCenterX / xPixelSize - h.getDoubleValue("CNPIX1", 0) - 0.5;
double crpix2 = plateCenterY / yPixelSize - h.getDoubleValue("CNPIX2", 0) - 0.5;
wcsKeys.put("CNPIX1", h.getDoubleValue("CNPIX1", 0));
wcsKeys.put("CNPIX2", h.getDoubleValue("CNPIX2", 0));
Projection proj = new Projection("Tan", new double[] {plateRA, plateDec});
this.proj = proj;
CoordinateSystem coords = CoordinateSystem.factory("J2000");
this.csys = coords;
cdelt1 = toRadians(cdelt1);
cdelt2 = toRadians(cdelt2);
Scaler s = new Scaler(-cdelt1 * crpix1, -cdelt2 * crpix2, cdelt1, 0, 0, cdelt2);
// Got the transformers ready. Add them in properly.
add(coords.getSphereDistorter());
add(coords.getRotater());
add(proj.getRotater());
add(proj.getProjecter());
this.distort =
new skyview.geometry.distorter.DSS(
plateRA, plateDec, xPixelSize, yPixelSize, plateScale, ppo, xCoeff, yCoeff);
add(this.distort);
this.scale = s.inverse();
add(this.scale);
}
private void extractProjection() throws TransformationException {
Projection proj = null;
Scaler ncpScale = null;
String lonType = h.getStringValue("CTYPE" + lonAxis).substring(5, 8);
String latType = h.getStringValue("CTYPE" + latAxis).substring(5, 8);
if (!lonType.equals(latType)) {
throw new TransformationException(
"Inconsistent projection in FITS header: " + lonType + "," + latType);
}
if (lonType.equals("AIT")) {
proj = new Projection("Ait");
} else if (lonType.equals("CAR")) {
proj = new Projection("Car");
// Allow non-central latitudes for the Cartesian projection.
try {
double lon = h.getDoubleValue("CRVAL" + lonAxis);
if (lon != 0) {
proj.setReference(toRadians(lon), 0);
}
} catch (Exception e) {
System.err.println("Unable to read reference longitude in Cartesian projection");
}
} else if (lonType.equals("CSC")) {
proj = new Projection("Csc");
} else if (lonType.equals("SFL") || lonType.equals("GLS")) {
proj = new Projection("Sfl");
} else if (lonType.equals("TOA")) {
proj = new Projection("Toa");
} else {
double crval1 = h.getDoubleValue("CRVAL" + lonAxis, NaN);
double crval2 = h.getDoubleValue("CRVAL" + latAxis, NaN);
if (isNaN(crval1 + crval2)) {
throw new TransformationException("Unable to find reference coordinates in FITS header");
}
wcsKeys.put("CRVAL1", crval1);
wcsKeys.put("CRVAL2", crval2);
if (lonType.equals("TAN")
|| lonType.equals("SIN")
|| lonType.equals("ZEA")
|| lonType.equals("ARC")
|| lonType.equals("STG")) {
String type = lonType.substring(0, 1) + lonType.substring(1, 3).toLowerCase();
proj = new Projection(type, new double[] {toRadians(crval1), toRadians(crval2)});
double lonpole = h.getDoubleValue("LONPOLE", NaN);
if (!isNaN(lonpole)) {
wcsKeys.put("LONPOLE", lonpole);
}
// ---- Following is probably erroneous -----
// The WCS standard indicates that the default LONPOLE for
// a projection is 180 when the CRVAL latitude is less than
// the native latitude of the projection (90 degrees for the projections
// handled here) and 0 otherwise. This means that for a projection
// around the pole the default lonpole is 0. Some data (the SFD surveys)
// seem to require that we do a rotation of 180 degrees to accommodate
// this. However we do not implement this unless the LONPOLE is
// explicitly given since this seems non-intuitive to me and I suspect
// that a user who is not careful enough to specify a LONPOLE in this
// situation probably doesn't understand what is going on anyway.
// ----- We now assume that our standard processing of
// ----- zenithal projections handles lonpole of 180 and that
// ----- this is the default for all zenithal images.
// ----- Previously we assumed that we were using lonPole=0 at
// ----- at the poles, but we weren't....
//
if (!isNaN(lonpole)) {
double lonDefault = 180;
if (lonpole != lonDefault) {
Rotater r = proj.getRotater();
Rotater lon = new Rotater("Z", toRadians(lonpole - lonDefault), 0, 0);
if (r != null) {
proj.setRotater(r.add(lon));
} else {
proj.setRotater(lon);
}
}
}
} else if (lonType.equals("NCP")) {
// Sin projection with projection centered at pole.
double[] xproj = new double[] {toRadians(crval1), PI / 2};
if (crval2 < 0) {
xproj[1] = -xproj[1];
}
double poleOffset = sin(xproj[1] - toRadians(crval2));
// Have we handled South pole here?
proj = new Projection("Sin", xproj);
// NCP scales the Y-axis to accommodate the distortion of the SIN projection away
// from the pole.
ncpScale = new Scaler(0, poleOffset, 1, 0, 0, 1);
ncpScale = ncpScale.add(new Scaler(0., 0., 1, 0, 0, 1 / sin(toRadians(crval2))));
} else {
throw new TransformationException("Unsupported projection type:" + lonType);
}
}
this.proj = proj;
if (ncpScale != null) {
this.scale = ncpScale;
}
add(proj.getRotater());
add(proj.getProjecter());
add(ncpScale); // Ignored if null
}
/** Get the scaling when CDELT is specified */
private boolean extractScaler1(double crpix1, double crpix2) throws TransformationException {
boolean matrix = false;
double cdelt1 = h.getDoubleValue("CDELT" + lonAxis, NaN);
double cdelt2 = h.getDoubleValue("CDELT" + latAxis, NaN);
wcsKeys.put("CDELT1", cdelt1);
wcsKeys.put("CDELT2", cdelt2);
if (isNaN(cdelt1) || isNaN(cdelt2)) {
return false;
}
// We use 1 indexing to match better with the FITS files.
double m11, m12, m21, m22;
// We've got minimal information... We might have more.
double crota = h.getDoubleValue("CROTA" + latAxis, NaN);
if (!isNaN(crota) && crota != 0) {
wcsKeys.put("CROTA2", crota);
crota = toRadians(crota);
m11 = cos(crota);
m12 = sin(crota);
m21 = -sin(crota);
m22 = cos(crota);
matrix = true;
} else {
m11 = h.getDoubleValue("PC" + lonAxis + "_" + lonAxis, NaN);
m12 = h.getDoubleValue("PC" + lonAxis + "_" + latAxis, NaN);
m21 = h.getDoubleValue("PC" + latAxis + "_" + lonAxis, NaN);
m22 = h.getDoubleValue("PC" + latAxis + "_" + latAxis, NaN);
matrix = !isNaN(m11 + m12 + m21 + m22);
if (matrix) {
wcsKeys.put("PC1_1", m11);
wcsKeys.put("PC1_2", m12);
wcsKeys.put("PC2_1", m21);
wcsKeys.put("PC2_2", m22);
}
}
// Note that Scaler is defined with parameters t = x0 + a00 x + a01 y; u = y0 + a10 x + a11 y
// which is different from what we have here...
// t = scalex (x-x0), u = scaley (y-y0)
// t = scalex x - scalex x0; u = scaley y - scaley y0
// or
// t = scalex [a11 (x-x0) + a12 (y-y0)], u = scaley [a21 (x-x0) + a22 (y-y0)] ->
// t = scalex a11 x - scalex a11 x0 + scalex a12 y + scalex a12 y0 ->
// t = - scalex (a11 x0 + a12 y0) + scalex a11 x + scalex a12 y (and similarly for u)
Scaler s;
cdelt1 = toRadians(cdelt1);
cdelt2 = toRadians(cdelt2);
if (!matrix) {
s = new Scaler(-cdelt1 * crpix1, -cdelt2 * crpix2, cdelt1, 0, 0, cdelt2);
} else {
s =
new Scaler(
-cdelt1 * (m11 * crpix1 + m12 * crpix2),
-cdelt2 * (m21 * crpix1 + m22 * crpix2),
cdelt1 * m11,
cdelt1 * m12,
cdelt2 * m21,
cdelt2 * m22);
}
// Note that this scaler transforms from pixel coordinates to standard projection
// plane coordinates. We want the inverse transformation as the scaler.
s = s.inverse();
// Are lon and lat in unusual order?
if (lonAxis > latAxis) {
s.interchangeAxes();
}
this.scale = s;
add(s);
setWCSScale(s);
return true;
}
protected void customisePrimaryHeader(Header hdr) throws HeaderCardException {
hdr.addValue("VOTMETA", true, "Table metadata in VOTable format");
}
public Header getHeader() throws HeaderCardException {
/* Work out the dimensions in columns and bytes of the table. */
int rowLength = 0;
int nUseCol = 0;
int ncol = table.getColumnCount();
for (int icol = 0; icol < ncol; icol++) {
ColumnWriter writer = colWriters[icol];
if (writer != null) {
nUseCol++;
rowLength += writer.getLength();
}
}
/* Prepare a FITS header block. */
Header hdr = new Header();
/* Add HDU layout metadata. */
hdr.addValue("XTENSION", "BINTABLE", "binary table extension");
hdr.addValue("BITPIX", 8, "8-bit bytes");
hdr.addValue("NAXIS", 2, "2-dimensional table");
hdr.addValue("NAXIS1", rowLength, "width of table in bytes");
hdr.addValue("NAXIS2", rowCount, "number of rows in table");
hdr.addValue("PCOUNT", 0, "size of special data area");
hdr.addValue("GCOUNT", 1, "one data group");
hdr.addValue("TFIELDS", nUseCol, "number of columns");
/* Add EXTNAME record containing table name. */
String tname = table.getName();
if (tname != null && tname.trim().length() > 0) {
FitsConstants.addTrimmedValue(hdr, "EXTNAME", tname, "table name");
}
/* Add HDU metadata describing columns. */
int jcol = 0;
for (int icol = 0; icol < ncol; icol++) {
ColumnWriter colwriter = colWriters[icol];
if (colwriter != null) {
jcol++;
String forcol = " for column " + jcol;
ColumnInfo colinfo = colInfos[icol];
/* Name. */
String name = colinfo.getName();
if (name != null && name.trim().length() > 0) {
FitsConstants.addTrimmedValue(hdr, "TTYPE" + jcol, name, "label" + forcol);
}
/* Format. */
String form = colwriter.getFormat();
hdr.addValue("TFORM" + jcol, form, "format" + forcol);
/* Units. */
String unit = colinfo.getUnitString();
if (unit != null && unit.trim().length() > 0) {
FitsConstants.addTrimmedValue(hdr, "TUNIT" + jcol, unit, "units" + forcol);
}
/* Blank. */
Number bad = colwriter.getBadNumber();
if (bad != null) {
hdr.addValue("TNULL" + jcol, bad.longValue(), "blank value" + forcol);
}
/* Shape. */
int[] dims = colwriter.getDims();
if (dims != null && dims.length > 1) {
StringBuffer sbuf = new StringBuffer();
for (int i = 0; i < dims.length; i++) {
sbuf.append(i == 0 ? '(' : ',');
sbuf.append(dims[i]);
}
sbuf.append(')');
hdr.addValue("TDIM" + jcol, sbuf.toString(), "dimensions" + forcol);
}
/* Scaling. */
double zero = colwriter.getZero();
double scale = colwriter.getScale();
if (zero != 0.0) {
hdr.addValue("TZERO" + jcol, zero, "base" + forcol);
}
if (scale != 1.0) {
hdr.addValue("TSCALE" + jcol, scale, "factor" + forcol);
}
/* Comment (non-standard). */
String comm = colinfo.getDescription();
if (comm != null && comm.trim().length() > 0) {
try {
hdr.addValue("TCOMM" + jcol, comm, null);
} catch (HeaderCardException e) {
// never mind.
}
}
/* UCD (non-standard). */
String ucd = colinfo.getUCD();
if (ucd != null && ucd.trim().length() > 0 && ucd.length() < 68) {
try {
hdr.addValue("TUCD" + jcol, ucd, null);
} catch (HeaderCardException e) {
// never mind.
}
}
/* Utype (non-standard). */
String utype = colinfo.getUtype();
if (utype != null && utype.trim().length() > 0 && utype.trim().length() < 68) {
try {
hdr.addValue("TUTYP" + jcol, utype, null);
} catch (HeaderCardException e) {
// never mind.
}
}
}
}
return hdr;
}
