Skip to content

Commit

Permalink
Code review rework and adjust CDELT values when present.
Browse files Browse the repository at this point in the history
  • Loading branch information
@at88mph
at88mph committed Aug 14, 2024
1 parent 1dcc0e3 commit 78bd159
Show file tree
Hide file tree
Showing 3 changed files with 48 additions and 18 deletions.
30 changes: 15 additions & 15 deletions cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/WCSCutoutUtil.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -150,16 +150,15 @@ public static PixelRange[] getBounds(final Header header, final Cutout cutout)
static void adjustHeaders(final Header header, final int dimensionLength, final int[] corners, final int[] steps) {
// CRPIX values are not set automatically. Adjust them here, if present.
for (int i = 0; i < dimensionLength; i++) {

final HeaderCard crPixCard = header.findCard(Standard.CRPIXn.n(i + 1));
if (crPixCard != null) {
// Need to run backwards (reverse order) to match the dimensions.
final double nextValue = corners[corners.length - i - 1];
final int stepValue = steps[corners.length - i - 1];
final double crPixValue = (Double.parseDouble(crPixCard.getValue()) - nextValue) / stepValue;
final int stepValue = steps[steps.length - i - 1];
final double crPixValue = Double.parseDouble(crPixCard.getValue()) - nextValue;

if (stepValue > 1) {
final double newValue = crPixValue + (1.0 - (1.0 / stepValue));
final double newValue = (crPixValue / stepValue) + (1.0 - (1.0 / stepValue));
crPixCard.setValue(newValue);
LOGGER.debug("Adjusted " + crPixCard.getKey() + " to " + newValue);
} else {
Expand All @@ -168,19 +167,20 @@ static void adjustHeaders(final Header header, final int dimensionLength, final
}
}

// Handle PC values. These typically override CD values, but as this is operating on Archive data, we'll simply
// modify the values as-is, meaning the CD values will be left even if a PC matrix is included.
//
// TODO: Does CDELTn need to come into play somewhere?
// jenkinsd 2024.08.13
// CDELTn cards are typically present for PC matrices, but due to the nature of Archive data,
// they could be present even if a CD matrix is present. Since PC matrices are the default in
// the absence of a CD matrix, it's not unusual for it to be absent.
// See https://www.aanda.org/articles/aa/pdf/2002/45/aah3859.pdf
//
for (int j = 0; j < dimensionLength; j++) {
final HeaderCard pcMatrixCard = header.findCard(String.format("PC%d_%d", i + 1, j + 1));
if (pcMatrixCard != null) {
final double pcMatrixValue = Double.parseDouble(pcMatrixCard.getValue());
pcMatrixCard.setValue(pcMatrixValue * (double) steps[i]);
}
final HeaderCard cDeltCard = header.findCard(Standard.CDELTn.n(i + 1));
if (cDeltCard != null) {
final double cDeltValue = Double.parseDouble(cDeltCard.getValue());
final int stepValue = steps[steps.length - i - 1];
cDeltCard.setValue(cDeltValue * (double) stepValue);
}

// Handle the entire CD matrix.
for (int j = 0; j < dimensionLength; j++) {
final HeaderCard cdMatrixCard = header.findCard(String.format("CD%d_%d", i + 1, j + 1));
if (cdMatrixCard != null) {
final double cdMatrixValue = Double.parseDouble(cdMatrixCard.getValue());
Expand Down
5 changes: 2 additions & 3 deletions cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,6 @@
import nom.tam.fits.HeaderCard;
import nom.tam.fits.header.IFitsHeader;
import nom.tam.fits.header.Standard;
import nom.tam.fits.header.WCS;
import nom.tam.fits.header.extra.NOAOExt;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
Expand All @@ -93,10 +92,10 @@ public class FitsTest {

private static final IFitsHeader[] HEADER_CARD_KEYS_TO_CHECK = new IFitsHeader[]{
Standard.BITPIX, Standard.NAXIS, Standard.EXTNAME, Standard.XTENSION, Standard.SIMPLE, Standard.EXTVER,
Standard.BSCALE, Standard.BUNIT, NOAOExt.CD1_1
Standard.BSCALE, Standard.BUNIT, NOAOExt.CD1_1, Standard.CDELTn.n(1), Standard.CRPIXn.n(1)
};

public static void assertFitsEqual(final Fits expected, final Fits result) throws Exception {
public static void assertFitsEqual(final Fits expected, final Fits result) {
final BasicHDU<?>[] expectedHDUList = expected.read();
final BasicHDU<?>[] resultHDUList = result.read();

Expand Down
31 changes: 31 additions & 0 deletions cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/NDimensionalSlicerTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
import org.junit.Ignore;
import org.junit.Test;
import org.opencadc.fits.FitsTest;
import org.opencadc.fits.NoOverlapException;
Expand All @@ -101,6 +102,36 @@ public class NDimensionalSlicerTest {
Log4jInit.setLevel("org.opencadc.fits", Level.DEBUG);
}

@Test
@Ignore("Requires larger ALMA file. Useful for running locally.")
public void testIncorrectWCS() throws Exception {
ExtensionSliceFormat fmt = new ExtensionSliceFormat();
List<ExtensionSlice> slices = new ArrayList<>();
slices.add(fmt.parse("[*:4,*:5,*:4]"));
final Cutout cutout = new Cutout();
cutout.pixelCutouts = slices;

final NDimensionalSlicer slicer = new NDimensionalSlicer();
final File file = FileUtil.getFileFromResource("test-alma-cube.fits", NDimensionalSlicerTest.class);

final String configuredTestWriteDir = System.getenv("TEST_WRITE_DIR");
final String testWriteDir = configuredTestWriteDir == null ? "/tmp" : configuredTestWriteDir;
final File expectedFile = FileUtil.getFileFromResource("test-alma-cube-cutout.fits",
NDimensionalSlicerTest.class);
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-alma-cube-cutout", ".fits");
LOGGER.debug("Writing out to " + outputPath);

try (final OutputStream outputStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(file, cutout, outputStream);
}

final Fits expectedFits = new Fits(expectedFile);
final Fits resultFits = new Fits(outputPath.toFile());

FitsTest.assertFitsEqual(expectedFits, resultFits);
Files.deleteIfExists(outputPath);
}

@Test
public void testMEFFileSlice() throws Exception {
ExtensionSliceFormat fmt = new ExtensionSliceFormat();
Expand Down

0 comments on commit 78bd159

Please sign in to comment.