Modified FitsOperations to use Cutout class. Added test for HDU Iter…

cadc-data-ops-fits/build.gradle

@@ -12,7 +12,7 @@ repositories {
 
 sourceCompatibility = 1.8
 group = 'org.opencadc'
-version = '0.2.2'
+version = '0.2.3'
 
 description = 'OpenCADC FITS cutout library'
 def git_url = 'https://github.com/opencadc/dal'
@@ -24,7 +24,7 @@ dependencies {
     compile 'org.opencadc:cadc-soda-server:[1.2.1,2.0)'
     compile 'org.opencadc:cadc-wcs:[2.0,3.0)'
     compile 'org.opencadc:jsky:[1.0.0,2.0.0)'
-    compile 'org.opencadc:nom-tam-fits:[1.16.1,1.17.0)'
+    compile 'org.opencadc:nom-tam-fits:[1.16.2,1.16.3)'
 
     // Use JUnit test framework
     testCompile 'junit:junit:[4.13,5.0)'

cadc-data-ops-fits/src/main/java/org/opencadc/fits/FitsOperations.java

@@ -84,8 +84,8 @@
 import nom.tam.fits.HeaderCard;
 import nom.tam.util.Cursor;
 import nom.tam.util.RandomAccessDataObject;
+import org.apache.log4j.Logger;
 import org.opencadc.fits.slice.NDimensionalSlicer;
-import org.opencadc.soda.ExtensionSlice;
 import org.opencadc.soda.server.Cutout;
 
 /**
@@ -94,6 +94,8 @@
  * @author pdowler
  */
 public class FitsOperations {
+    private static final Logger log = Logger.getLogger(FitsOperations.class);
+
     private final RandomAccessDataObject src;
 
     public FitsOperations(RandomAccessDataObject src) {
@@ -156,20 +158,22 @@ public void headersToStream(final OutputStream outputStream) throws IOException
     /**
      * Implement prototype SODA pixel cutout action.
      *
-     * @param slices subsets of data to extract
+     * @param cutout cutout spec
      * @param outputStream  The Stream to write out to.
-     * @throws ReadException    Any errors to report back to the caller.
+     * @throws NoOverlapException   A valid cutout was provided, but there is no match (overlap).
+     * @throws ReadException        Any errors reading reported by the storage system.
      */
-    public void cutoutToStream(final List<ExtensionSlice> slices, final OutputStream outputStream) throws ReadException {
+    public void cutoutToStream(final Cutout cutout, final OutputStream outputStream)
+            throws NoOverlapException, ReadException {
+        log.debug("cutoutToStream() start.");
         try {
             final NDimensionalSlicer slicer = new NDimensionalSlicer();
-            final Cutout cutout = new Cutout();
-            cutout.pixelCutouts = slices;
             slicer.slice(src, cutout, outputStream);
         } catch (FitsException | NoSuchKeywordException ex) {
             throw new ReadException("invalid fits data: " + src + " reason: " + ex.getMessage(), ex);
         } catch (IOException ex) {
             throw new ReadException("failed to read " + src + " reason: " + ex.getMessage(), ex);
         }
+        log.debug("cutoutToStream() OK.");
     }
 }

cadc-data-ops-fits/src/main/java/org/opencadc/fits/NoOverlapException.java

@@ -0,0 +1,112 @@
+/*
+************************************************************************
+*******************  CANADIAN ASTRONOMY DATA CENTRE  *******************
+**************  CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES  **************
+*
+*  (c) 2021.                            (c) 2021.
+*  Government of Canada                 Gouvernement du Canada
+*  National Research Council            Conseil national de recherches
+*  Ottawa, Canada, K1A 0R6              Ottawa, Canada, K1A 0R6
+*  All rights reserved                  Tous droits réservés
+*
+*  NRC disclaims any warranties,        Le CNRC dénie toute garantie
+*  expressed, implied, or               énoncée, implicite ou légale,
+*  statutory, of any kind with          de quelque nature que ce
+*  respect to the software,             soit, concernant le logiciel,
+*  including without limitation         y compris sans restriction
+*  any warranty of merchantability      toute garantie de valeur
+*  or fitness for a particular          marchande ou de pertinence
+*  purpose. NRC shall not be            pour un usage particulier.
+*  liable in any event for any          Le CNRC ne pourra en aucun cas
+*  damages, whether direct or           être tenu responsable de tout
+*  indirect, special or general,        dommage, direct ou indirect,
+*  consequential or incidental,         particulier ou général,
+*  arising from the use of the          accessoire ou fortuit, résultant
+*  software.  Neither the name          de l'utilisation du logiciel. Ni
+*  of the National Research             le nom du Conseil National de
+*  Council of Canada nor the            Recherches du Canada ni les noms
+*  names of its contributors may        de ses  participants ne peuvent
+*  be used to endorse or promote        être utilisés pour approuver ou
+*  products derived from this           promouvoir les produits dérivés
+*  software without specific prior      de ce logiciel sans autorisation
+*  written permission.                  préalable et particulière
+*                                       par écrit.
+*
+*  This file is part of the             Ce fichier fait partie du projet
+*  OpenCADC project.                    OpenCADC.
+*
+*  OpenCADC is free software:           OpenCADC est un logiciel libre ;
+*  you can redistribute it and/or       vous pouvez le redistribuer ou le
+*  modify it under the terms of         modifier suivant les termes de
+*  the GNU Affero General Public        la “GNU Affero General Public
+*  License as published by the          License” telle que publiée
+*  Free Software Foundation,            par la Free Software Foundation
+*  either version 3 of the              : soit la version 3 de cette
+*  License, or (at your option)         licence, soit (à votre gré)
+*  any later version.                   toute version ultérieure.
+*
+*  OpenCADC is distributed in the       OpenCADC est distribué
+*  hope that it will be useful,         dans l’espoir qu’il vous
+*  but WITHOUT ANY WARRANTY;            sera utile, mais SANS AUCUNE
+*  without even the implied             GARANTIE : sans même la garantie
+*  warranty of MERCHANTABILITY          implicite de COMMERCIALISABILITÉ
+*  or FITNESS FOR A PARTICULAR          ni d’ADÉQUATION À UN OBJECTIF
+*  PURPOSE.  See the GNU Affero         PARTICULIER. Consultez la Licence
+*  General Public License for           Générale Publique GNU Affero
+*  more details.                        pour plus de détails.
+*
+*  You should have received             Vous devriez avoir reçu une
+*  a copy of the GNU Affero             copie de la Licence Générale
+*  General Public License along         Publique GNU Affero avec
+*  with OpenCADC.  If not, see          OpenCADC ; si ce n’est
+*  <http://www.gnu.org/licenses/>.      pas le cas, consultez :
+*                                       <http://www.gnu.org/licenses/>.
+*
+*
+************************************************************************
+*/
+
+package org.opencadc.fits;
+
+/**
+ * Exception thrown to indicate a client error in the supplied cutout.
+ */
+public class NoOverlapException extends Exception {
+    /**
+     * Constructs an <code>IllegalArgumentException</code> with the
+     * specified detail message.
+     */
+    public NoOverlapException() {
+        this("No overlap found.");
+    }
+
+    /**
+     * Constructs an <code>IllegalArgumentException</code> with the
+     * specified detail message.
+     *
+     * @param s the detail message.
+     */
+    public NoOverlapException(String s) {
+        super(s);
+    }
+
+    /**
+     * Constructs a new exception with the specified detail message and
+     * cause.
+     *
+     * <p>Note that the detail message associated with <code>cause</code> is
+     * <i>not</i> automatically incorporated in this exception's detail
+     * message.
+     *
+     * @param message the detail message (which is saved for later retrieval
+     *                by the {@link Throwable#getMessage()} method).
+     * @param cause   the cause (which is saved for later retrieval by the
+     *                {@link Throwable#getCause()} method).  (A {@code null} value
+     *                is permitted, and indicates that the cause is nonexistent or
+     *                unknown.)
+     * @since 1.5
+     */
+    public NoOverlapException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/NDimensionalSlicer.java

@@ -104,6 +104,7 @@
 import nom.tam.util.RandomAccessFileExt;
 import org.apache.log4j.Logger;
 import org.opencadc.fits.HDUIterator;
+import org.opencadc.fits.NoOverlapException;
 import org.opencadc.soda.ExtensionSlice;
 import org.opencadc.soda.PixelRange;
 import org.opencadc.soda.server.Cutout;
@@ -134,10 +135,11 @@ public NDimensionalSlicer() {
      * @param outputStream Where to write bytes to.  This method will not close this stream.
      * @throws FitsException Any FITS related errors from the NOM TAM Fits library.
      * @throws IOException   Reading Writing errors.
+     * @throws NoOverlapException   Client error to inform that the supplied cutout is valid but yields no results.
      * @throws NoSuchKeywordException   Reading the FITS file failed.
      */
     public void slice(final File fitsFile, final Cutout cutout, final OutputStream outputStream)
-            throws FitsException, IOException, NoSuchKeywordException {
+            throws FitsException, IOException, NoSuchKeywordException, NoOverlapException {
         slice(new RandomAccessFileExt(fitsFile, "r"), cutout, outputStream);
     }
 
@@ -158,18 +160,19 @@ public void slice(final File fitsFile, final Cutout cutout, final OutputStream o
      * @param outputStream           Where to write bytes to.  This method will not close this stream.
      * @throws FitsException Any FITS related errors from the NOM TAM Fits library.
      * @throws IOException   Reading Writing errors.
+     * @throws NoOverlapException   Client error to inform that the supplied cutout is valid but yields no results.
      * @throws NoSuchKeywordException   Reading the FITS file failed.
      */
     public void slice(final RandomAccessDataObject randomAccessDataObject, final Cutout cutout,
                       final OutputStream outputStream)
-            throws FitsException, IOException, NoSuchKeywordException {
+            throws FitsException, IOException, NoOverlapException, NoSuchKeywordException {
         final ArrayDataOutput output = new BufferedDataOutputStream(outputStream);
         slice(randomAccessDataObject, cutout, output);
     }
 
     private void slice(final RandomAccessDataObject randomAccessDataObject, final Cutout cutout,
                        final ArrayDataOutput output)
-            throws FitsException, IOException, NoSuchKeywordException {
+            throws FitsException, IOException, NoOverlapException, NoSuchKeywordException {
         if (isEmpty(cutout)) {
             throw new IllegalStateException("No cutout specified.");
         }
@@ -182,7 +185,7 @@ private void slice(final RandomAccessDataObject randomAccessDataObject, final Cu
         final Map<Integer, List<ExtensionSlice>> overlapHDUs = getOverlap(fitsInput, cutout);
 
         if (overlapHDUs.isEmpty()) {
-            throw new FitsException("No overlap found.");
+            throw new NoOverlapException();
         } else {
             LOGGER.debug("Found " + overlapHDUs.size() + " overlapping slices.");
         }
@@ -282,7 +285,7 @@ private void setupPrimaryHeader(final Header headerCopy, final int nextEndSize)
 
     private void writeSlices(final BasicHDU<?> hdu, List<ExtensionSlice> extensionSliceList, final Fits fitsOutput,
                              final boolean mefOutput, final boolean firstHDUAlreadyWritten, final int nextEndSize)
-            throws FitsException {
+            throws FitsException, NoOverlapException {
         final ImageHDU imageHDU = (hdu instanceof CompressedImageHDU)
                                   ? ((CompressedImageHDU) hdu).asImageHDU() : (ImageHDU) hdu;
         final Header header = imageHDU.getHeader();
@@ -292,7 +295,7 @@ private void writeSlices(final BasicHDU<?> hdu, List<ExtensionSlice> extensionSl
             if (extensionSliceValue.getPixelRanges().isEmpty()) {
                 fitsOutput.addHDU(hdu);
             } else if (dimensions == null) {
-                throw new FitsException("Sub-image not within image");
+                throw new NoOverlapException();
             } else {
                 final int dimensionLength = dimensions.length;
                 final int[] corners = new int[dimensionLength];
@@ -305,7 +308,7 @@ private void writeSlices(final BasicHDU<?> hdu, List<ExtensionSlice> extensionSl
 
                 // The data contained in this HDU cannot be used to slice from.
                 if (corners.length == 0) {
-                    throw new FitsException("Sub-image not within image");
+                    throw new NoOverlapException();
                 }
 
                 LOGGER.debug("Tiling out " + Arrays.toString(lengths) + " at corner "
@@ -563,7 +566,7 @@ private int mapOverlap(final BasicHDU<?> hdu, final int hduIndex, final List<Ext
      * @throws FitsException if the header could not be read
      */
     private Map<Integer, List<ExtensionSlice>> getOverlap(final Fits fits, final Cutout cutout)
-            throws FitsException, NoSuchKeywordException {
+            throws FitsException, NoOverlapException, NoSuchKeywordException {
         if ((cutout.pixelCutouts != null) && !cutout.pixelCutouts.isEmpty()) {
             return getOverlap(fits, cutout.pixelCutouts);
         } else {
@@ -585,7 +588,7 @@ private Map<Integer, List<ExtensionSlice>> getOverlap(final Fits fits, final Cut
     }
 
     private Map<Integer, List<ExtensionSlice>> getOverlap(final Fits fits, final List<ExtensionSlice> extensionSlices)
-            throws FitsException {
+            throws FitsException, NoOverlapException {
         // A Set is used to eliminate duplicates from the inner loop below.
         final Map<Integer, List<ExtensionSlice>> overlapHDUIndexesSlices = new LinkedHashMap<>();
 
@@ -617,7 +620,7 @@ private Map<Integer, List<ExtensionSlice>> getOverlap(final Fits fits, final Lis
                 }).collect(Collectors.toList());
 
         if (!containsAll.isEmpty()) {
-            throw new IllegalArgumentException("One or more requested slices could not be found:\n" + containsAll);
+            throw new NoOverlapException("One or more requested slices could not be found:\n" + containsAll);
         }
 
         return overlapHDUIndexesSlices;

cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/PolarizationCutout.java

@@ -85,6 +85,7 @@
  */
 public class PolarizationCutout extends FITSCutout<PolarizationState[]> {
     private static final Logger LOGGER = Logger.getLogger(PolarizationCutout.class);
+    private static final double DEFAULT_VALUE = 1.0D;
 
     public PolarizationCutout(final Header header) throws HeaderCardException {
         super(header);
@@ -106,16 +107,23 @@ public long[] getBounds(final PolarizationState[] states) {
         final int naxis = this.fitsHeaderWCSKeywords.getIntValue(Standard.NAXIS.key());
         final double crpix = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CRPIXn.n(polarizationAxis).key());
         final double crval = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CRVALn.n(polarizationAxis).key());
-        final double cdelt = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CDELTn.n(polarizationAxis).key());
+        final double cdelt = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CDELTn.n(polarizationAxis).key(),
+                                                                       DEFAULT_VALUE);
+
+        // Nothing to check.
+        if (crpix == 0.0D || crval == 0.0D) {
+            return null;
+        }
 
         double pix1 = Double.MAX_VALUE;
         double pix2 = Double.MIN_VALUE;
-        for (final PolarizationState headerState : getHeaderStates(polarizationAxis)) {
+        for (final PolarizationState headerState : getHeaderStates(polarizationAxis, crpix, crval, cdelt)) {
             LOGGER.debug("Checking next header state " + headerState.name());
             for (final PolarizationState cutoutState : states) {
                 if (cutoutState.equals(headerState)) {
                     final int value = headerState.getValue();
                     final double pix = crpix + (value - crval) / cdelt;
+                    LOGGER.debug("Found pixel value " + crpix + " + (" + value  + "-" + crval + ") / " + cdelt + " = " + pix);
                     pix1 = Math.min(pix1, pix);
                     pix2 = Math.max(pix2, pix);
 
@@ -150,16 +158,14 @@ public long[] getBounds(final PolarizationState[] states) {
      * @param polarizationAxis  The polarization axis to get values from.
      * @return     Array of PolarizationState objects.  Never null.
      */
-    PolarizationState[] getHeaderStates(final int polarizationAxis) {
-        final int naxis = this.fitsHeaderWCSKeywords.getIntValue(Standard.NAXIS.key());
-        final double crpix = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CRPIXn.n(polarizationAxis).key());
-        final double crval = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CRVALn.n(polarizationAxis).key());
-        final double cdelt = this.fitsHeaderWCSKeywords.getDoubleValue(Standard.CDELTn.n(polarizationAxis).key());
+    PolarizationState[] getHeaderStates(final int polarizationAxis, final double crpix, final double crval,
+                                        final double cdelt) {
+        final int naxisValue = this.fitsHeaderWCSKeywords.getIntValue(Standard.NAXISn.n(polarizationAxis).key());
 
         final List<PolarizationState> polarizationStates = new ArrayList<>();
 
-        IntStream.range(1, naxis + 1)
-                 .map(i -> (int) (crpix + (i - crval) / cdelt))
+        IntStream.range(1, naxisValue + 1)
+                 .map(i -> (int) (crval + cdelt * (i - crpix)))
                  .filter(i -> PolarizationState.fromValue(i) != null)
                  .forEach(i -> polarizationStates.add(PolarizationState.fromValue(i)));
 

cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsOperationsTest.java

@@ -93,6 +93,7 @@
 import org.junit.Assert;
 import org.junit.Test;
 import org.opencadc.soda.ExtensionSlice;
+import org.opencadc.soda.server.Cutout;
 
 /**
  *
@@ -227,7 +228,9 @@ public void testSlice() throws Exception {
             cut.add(new ExtensionSlice(3));
             cut.add(new ExtensionSlice(106));
             cut.add(new ExtensionSlice(126));
-            fop.cutoutToStream(cut, fileOutputStream);
+            final Cutout cutout = new Cutout();
+            cutout.pixelCutouts = cut;
+            fop.cutoutToStream(cutout, fileOutputStream);
         }
 
         final Fits resultsFits = new Fits(new RandomAccessFileExt(outputFile, "r"));
@@ -249,4 +252,29 @@ public void testSlice() throws Exception {
             log.info("...");
         }
     }
+
+    @Test
+    public void testNoOverlap() throws Exception {
+        final RandomAccessDataObject randomAccessDataObject =
+                new RandomAccessFileExt(FileUtil.getFileFromResource("test-hst-mef.fits",
+                                                                     FitsOperationsTest.class), "r");
+        final FitsOperations fop = new FitsOperations(randomAccessDataObject);
+        final File outputFile = Files.createTempFile(
+                new File(System.getProperty("user.home")).toPath(),
+                "test-hst-mef-cutout-", ".fits").toFile();
+        outputFile.deleteOnExit();
+
+        // Extension 3 contains non-image Data, but should still be included.
+        try (final FileOutputStream fileOutputStream = new FileOutputStream(outputFile)) {
+            List<ExtensionSlice> cut = new ArrayList<>();
+            // No such extension
+            cut.add(new ExtensionSlice(188));
+            final Cutout cutout = new Cutout();
+            cutout.pixelCutouts = cut;
+            fop.cutoutToStream(cutout, fileOutputStream);
+            Assert.fail("Should throw NoOverlapException");
+        } catch (NoOverlapException noOverlapException) {
+            // Good!
+        }
+    }
 }