@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);
}
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");
}
}
}
@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]);
}
protected void customisePrimaryHeader(Header hdr) throws HeaderCardException {
hdr.addValue("VOTMETA", true, "Table metadata in VOTable format");
}
/**
* 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");
}
}
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;
}