diff --git a/cadc-data-ops-fits/build.gradle b/cadc-data-ops-fits/build.gradle
index c61750d5..d467ef85 100644
--- a/cadc-data-ops-fits/build.gradle
+++ b/cadc-data-ops-fits/build.gradle
@@ -12,21 +12,21 @@ repositories {
sourceCompatibility = 1.8
group = 'org.opencadc'
-version = '0.2.9'
+version = '0.3.0'
description = 'OpenCADC FITS cutout library'
def git_url = 'https://github.com/opencadc/dal'
dependencies {
- compile 'org.opencadc:cadc-dali:[1.2.10,2.0.0)'
- compile 'org.opencadc:cadc-util:[1.6,2.0)'
- 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:[1.16.8,1.17.0)'
+ implementation 'org.opencadc:cadc-dali:[1.2.10,2.0.0)'
+ implementation 'org.opencadc:cadc-util:[1.6,2.0)'
+ implementation 'org.opencadc:cadc-soda-server:[1.2.1,2.0)'
+ implementation 'org.opencadc:cadc-wcs:[2.1.4,3.0)'
+ implementation 'org.opencadc:jsky:[1.0.0,2.0.0)'
+ implementation 'gov.nasa.gsfc.heasarc:nom-tam-fits:1.18.0'
// Use JUnit test framework
- testCompile 'junit:junit:[4.13,5.0)'
+ testImplementation 'junit:junit:[4.13,5.0)'
}
apply from: '../opencadc.gradle'
diff --git a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/FitsOperations.java b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/FitsOperations.java
index ff46cdcf..15485c5a 100644
--- a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/FitsOperations.java
+++ b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/FitsOperations.java
@@ -83,7 +83,7 @@
import nom.tam.fits.Header;
import nom.tam.fits.HeaderCard;
import nom.tam.util.Cursor;
-import nom.tam.util.RandomAccessDataObject;
+import nom.tam.util.RandomAccessFileIO;
import org.apache.log4j.Logger;
import org.opencadc.fits.slice.NDimensionalSlicer;
import org.opencadc.soda.server.Cutout;
@@ -96,9 +96,9 @@
public class FitsOperations {
private static final Logger log = Logger.getLogger(FitsOperations.class);
- private final RandomAccessDataObject src;
+ private final RandomAccessFileIO src;
- public FitsOperations(RandomAccessDataObject src) {
+ public FitsOperations(RandomAccessFileIO src) {
this.src = src;
}
diff --git a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/RandomAccessStorageObject.java b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/RandomAccessStorageObject.java
new file mode 100644
index 00000000..84b291fc
--- /dev/null
+++ b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/RandomAccessStorageObject.java
@@ -0,0 +1,93 @@
+/*
+ ************************************************************************
+ ******************* CANADIAN ASTRONOMY DATA CENTRE *******************
+ ************** CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES **************
+ *
+ * (c) 2023. (c) 2023.
+ * 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
+ * . pas le cas, consultez :
+ * .
+ *
+ *
+ ************************************************************************
+ */
+
+package org.opencadc.fits;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+
+import nom.tam.util.RandomAccessFileIO;
+
+
+public class RandomAccessStorageObject extends RandomAccessFile implements RandomAccessFileIO {
+ public RandomAccessStorageObject(File file, String mode) throws FileNotFoundException {
+ super(file, mode);
+ }
+
+ @Override
+ public long position() throws IOException {
+ return super.getFilePointer();
+ }
+
+ @Override
+ public void position(long n) throws IOException {
+ super.seek(n);
+ }
+}
diff --git a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/FITSHeaderWCSKeywords.java b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/FITSHeaderWCSKeywords.java
index 5e2aae89..c84c9871 100644
--- a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/FITSHeaderWCSKeywords.java
+++ b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/FITSHeaderWCSKeywords.java
@@ -78,6 +78,7 @@
import java.util.Iterator;
import java.util.Map;
+import nom.tam.fits.FitsFactory;
import nom.tam.fits.Header;
import nom.tam.fits.HeaderCard;
import nom.tam.fits.HeaderCardException;
@@ -407,39 +408,54 @@ private Header cloneHeader(final Header source) throws HeaderCardException {
return destination;
}
+ /**
+ * Copy a header card with some potential modifications. COMMENT and HISTORY cards are truncated to the
+ * maximum length.
+ * @param destination The Header to write to.
+ * @param headerCardKey The current key.
+ * @param valueType The class type of the value.
+ * @param comment The comment value for COMMENT or HISTORY values.
+ * @param value The string value.
+ * @throws HeaderCardException
+ */
private void cloneHeaderCard(final Header destination, final String headerCardKey, final Class valueType,
final String comment, final String value) throws HeaderCardException {
// Check for blank lines or just plain comments that are not standard FITS comments.
if (!StringUtil.hasText(headerCardKey)) {
destination.addValue(headerCardKey, (String) null, comment);
} else if (Standard.COMMENT.key().equals(headerCardKey)) {
- destination.insertComment(comment);
+ if (StringUtil.hasText(comment) && comment.length() > HeaderCard.MAX_COMMENT_CARD_COMMENT_LENGTH) {
+ destination.insertComment(comment.substring(0, HeaderCard.MAX_COMMENT_CARD_COMMENT_LENGTH));
+ } else {
+ destination.insertComment(comment);
+ }
} else if (Standard.HISTORY.key().equals(headerCardKey)) {
- destination.insertHistory(comment);
+ if (StringUtil.hasText(comment) && comment.length() > HeaderCard.MAX_COMMENT_CARD_COMMENT_LENGTH) {
+ destination.insertHistory(comment.substring(0, HeaderCard.MAX_COMMENT_CARD_COMMENT_LENGTH));
+ } else {
+ destination.insertHistory(comment);
+ }
} else if (headerCardKey.startsWith(CADCExt.CDELT.key())) {
// CDELT values cannot be zero.
final double cdeltValue = Double.parseDouble(value);
- destination.addValue(headerCardKey, cdeltValue == 0.0D ? 1.0D : cdeltValue,
- comment);
+ destination.addValue(headerCardKey, cdeltValue == 0.0D ? 1.0D : cdeltValue, comment);
} else {
if (valueType == String.class || valueType == null) {
destination.addValue(headerCardKey, value, comment);
} else if (valueType == Boolean.class) {
destination.addValue(headerCardKey, Boolean.parseBoolean(value) || value.equals("T"), comment);
} else if (valueType == Integer.class) {
- destination.addValue(headerCardKey, Integer.parseInt(value),
- comment);
+ destination.addValue(headerCardKey, Integer.parseInt(value), comment);
} else if (valueType == BigInteger.class) {
destination.addValue(headerCardKey, new BigInteger(value), comment);
} else if (valueType == Long.class) {
- destination.addValue(headerCardKey, Long.parseLong(value),
- comment);
+ destination.addValue(headerCardKey, Long.parseLong(value), comment);
} else if (valueType == Double.class) {
- destination.addValue(headerCardKey, Double.parseDouble(value),
- comment);
+ destination.addValue(headerCardKey, Double.parseDouble(value), comment);
} else if (valueType == BigDecimal.class) {
- destination.addValue(headerCardKey, new BigDecimal(value),
- comment);
+ destination.addValue(headerCardKey, new BigDecimal(value), comment);
+ } else if (valueType == Float.class) {
+ destination.addValue(headerCardKey, Float.parseFloat(value), comment);
}
}
}
diff --git a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/NDimensionalSlicer.java b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/NDimensionalSlicer.java
index efcd7233..7d1257c4 100644
--- a/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/NDimensionalSlicer.java
+++ b/cadc-data-ops-fits/src/main/java/org/opencadc/fits/slice/NDimensionalSlicer.java
@@ -96,21 +96,24 @@
import nom.tam.fits.HeaderCardException;
import nom.tam.fits.ImageData;
import nom.tam.fits.ImageHDU;
-import nom.tam.fits.StreamingImageData;
import nom.tam.fits.header.DataDescription;
+import nom.tam.fits.header.IFitsHeader;
import nom.tam.fits.header.Standard;
+import nom.tam.image.StreamingTileImageData;
+import nom.tam.image.compression.CompressedImageTiler;
import nom.tam.image.compression.hdu.CompressedImageHDU;
import nom.tam.util.ArrayDataOutput;
-import nom.tam.util.BufferedDataOutputStream;
-import nom.tam.util.RandomAccessDataObject;
-import nom.tam.util.RandomAccessFileExt;
+import nom.tam.util.FitsOutputStream;
+import nom.tam.util.RandomAccessFileIO;
import org.apache.log4j.Logger;
import org.opencadc.fits.HDUIterator;
import org.opencadc.fits.NoOverlapException;
+import org.opencadc.fits.RandomAccessStorageObject;
import org.opencadc.soda.ExtensionSlice;
import org.opencadc.soda.PixelRange;
import org.opencadc.soda.server.Cutout;
+
/**
* Slice out a portion of an image. This class will support the SODA Shapes and will delegate each cutout to its
* appropriate handler (e.g. CircleCutout, EnergyCutout, etc.).
@@ -142,7 +145,7 @@ public NDimensionalSlicer() {
*/
public void slice(final File fitsFile, final Cutout cutout, final OutputStream outputStream)
throws FitsException, IOException, NoSuchKeywordException, NoOverlapException {
- slice(new RandomAccessFileExt(fitsFile, "r"), cutout, outputStream);
+ slice(new RandomAccessStorageObject(fitsFile, "r"), cutout, outputStream);
}
/**
@@ -165,14 +168,14 @@ public void slice(final File fitsFile, final Cutout cutout, final OutputStream o
* @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,
+ public void slice(final RandomAccessFileIO randomAccessDataObject, final Cutout cutout,
final OutputStream outputStream)
throws FitsException, IOException, NoOverlapException, NoSuchKeywordException {
- final ArrayDataOutput output = new BufferedDataOutputStream(outputStream);
+ final ArrayDataOutput output = new FitsOutputStream(outputStream);
slice(randomAccessDataObject, cutout, output);
}
- private void slice(final RandomAccessDataObject randomAccessDataObject, final Cutout cutout,
+ private void slice(final RandomAccessFileIO randomAccessDataObject, final Cutout cutout,
final ArrayDataOutput output)
throws FitsException, IOException, NoOverlapException, NoSuchKeywordException {
if (isEmpty(cutout)) {
@@ -181,7 +184,6 @@ private void slice(final RandomAccessDataObject randomAccessDataObject, final Cu
// Single Fits object for the slice. It maintains state about itself such as the current read offset.
final Fits fitsInput = new Fits(randomAccessDataObject);
- fitsInput.setStreamWrite(true);
// Reduce the requested extensions to only those that overlap.
final Map> overlapHDUs = getOverlap(fitsInput, cutout);
@@ -216,7 +218,6 @@ private void slice(final RandomAccessDataObject randomAccessDataObject, final Cu
// Will write out to an ArrayDataOutput stream at the end.
final Fits fitsOutput = new Fits();
- fitsOutput.setStreamWrite(true);
LOGGER.debug("\nMEF Output: " + mefOutput + "\nMEF Input: " + mefInput);
@@ -265,43 +266,80 @@ private void slice(final RandomAccessDataObject randomAccessDataObject, final Cu
fitsOutput.write(output);
}
- private void setupPrimaryHeader(final Header headerCopy, final int nextEndSize) throws HeaderCardException {
- final HeaderCard nextEndCard = headerCopy.findCard(DataDescription.NEXTEND);
+ private void setupPrimaryHeader(final Header header, final int nextEndSize) throws HeaderCardException {
+ final HeaderCard nextEndCard = header.findCard(DataDescription.NEXTEND);
// Adjust the NEXTEND appropriately.
if (nextEndCard == null) {
- headerCopy.addValue(DataDescription.NEXTEND, nextEndSize);
+ header.addValue(DataDescription.NEXTEND, nextEndSize);
} else {
nextEndCard.setValue(nextEndSize);
}
- final HeaderCard extendFlagCard = headerCopy.findCard(Standard.EXTEND);
+ final HeaderCard extendFlagCard = header.findCard(Standard.EXTEND);
// Adjust the EXTEND appropriately.
if (extendFlagCard == null) {
- headerCopy.addValue(Standard.EXTEND, true);
+ header.addValue(Standard.EXTEND, true);
} else {
extendFlagCard.setValue(true);
}
}
+ private void setupImageHeader(final Header header, final boolean mefOutput, final boolean firstHDUAlreadyWritten,
+ final int nextEndSize, final int[] dimensions)
+ throws FitsException {
+ header.deleteKey(Standard.SIMPLE);
+ header.deleteKey(Standard.XTENSION);
+ header.deleteKey(Standard.EXTEND);
+ header.deleteKey(Standard.TFIELDS);
+
+ if (mefOutput) {
+ if (firstHDUAlreadyWritten) {
+ header.addValue(Standard.XTENSION, Standard.XTENSION_IMAGE);
+ } else {
+ header.addValue(Standard.SIMPLE, Boolean.TRUE);
+ setupPrimaryHeader(header, nextEndSize);
+ }
+ } else {
+ // MEF input to simple output.
+ header.addValue(Standard.SIMPLE, Boolean.TRUE);
+ }
+
+ // Values set as per FITS standard for IMAGE and SIMPLE extensions.
+ header.addValue(Standard.PCOUNT, 0);
+ header.addValue(Standard.GCOUNT, 1);
+ }
+
private void writeSlices(final BasicHDU hdu, List extensionSliceList, final Fits fitsOutput,
final boolean mefOutput, final boolean firstHDUAlreadyWritten, final int nextEndSize)
throws FitsException, NoOverlapException {
final int[] dimensions;
+ final Header header;
if (hdu instanceof CompressedImageHDU) {
+ final CompressedImageHDU compressedImageHDU = (CompressedImageHDU) hdu;
// Follow the ZNAXISn values, if present.
- dimensions = ((CompressedImageHDU) hdu).getOriginalAxes();
+ dimensions = compressedImageHDU.getImageAxes();
+ header = compressedImageHDU.getImageHeader();
+
+ final Header originalHeader = compressedImageHDU.getHeader();
+
+ // EXTNAME and EXTVER aren't copied for some reason.
+ if (originalHeader.containsKey(Standard.EXTNAME)
+ && !originalHeader.getStringValue(Standard.EXTNAME).equals("COMPRESSED_IMAGE")) {
+ header.addValue(Standard.EXTNAME, originalHeader.getStringValue(Standard.EXTNAME));
+ }
+
+ if (originalHeader.containsKey(Standard.EXTVER)) {
+ header.addValue(Standard.EXTVER, originalHeader.getIntValue(Standard.EXTNAME));
+ }
} else {
dimensions = hdu.getAxes();
+ header = hdu.getHeader();
}
LOGGER.debug("Writing slices with dimensions of " + Arrays.toString(dimensions));
- final ImageHDU imageHDU = (hdu instanceof CompressedImageHDU)
- ? ((CompressedImageHDU) hdu).asImageHDU(true) : (ImageHDU) hdu;
- final Header header = imageHDU.getHeader();
-
for (final ExtensionSlice extensionSliceValue : extensionSliceList) {
if (extensionSliceValue.getPixelRanges().isEmpty()) {
fitsOutput.addHDU(hdu);
@@ -313,6 +351,7 @@ private void writeSlices(final BasicHDU hdu, List extensionSl
final int[] lengths = new int[dimensionLength];
final int[] steps = new int[dimensionLength];
+ // We copy the header to preserve as much as we can, then we'll remove whatever is inappropriate.
final Header headerCopy = copyHeader(header);
fillCornersAndLengths(dimensions, headerCopy, extensionSliceValue, corners, lengths, steps);
@@ -347,35 +386,20 @@ private void writeSlices(final BasicHDU hdu, List extensionSl
}
}
- if (mefOutput) {
- if (firstHDUAlreadyWritten) {
- headerCopy.setXtension(Standard.XTENSION_IMAGE);
- final HeaderCard pcountHeaderCard = headerCopy.findCard(Standard.PCOUNT);
- final HeaderCard gcountHeaderCard = headerCopy.findCard(Standard.GCOUNT);
+ setupImageHeader(headerCopy, mefOutput, firstHDUAlreadyWritten, nextEndSize, dimensions);
- if (pcountHeaderCard == null) {
- headerCopy.addValue(Standard.PCOUNT, 0);
- }
-
- if (gcountHeaderCard == null) {
- headerCopy.addValue(Standard.GCOUNT, 1);
- }
- } else {
- headerCopy.setSimple(true);
- setupPrimaryHeader(headerCopy, nextEndSize);
- }
+ final StreamingTileImageData streamingTileImageData;
+ if (hdu instanceof CompressedImageHDU) {
+ final CompressedImageHDU compressedImageHDU = (CompressedImageHDU) hdu;
+ final CompressedImageTiler compressedImageTiler = new CompressedImageTiler(compressedImageHDU);
+ streamingTileImageData = new StreamingTileImageData(headerCopy, compressedImageTiler, corners,
+ lengths, steps);
} else {
- // MEF input to simple output.
- headerCopy.setSimple(true);
+ // Assume ImageHDU
+ streamingTileImageData = new StreamingTileImageData(headerCopy, ((ImageHDU) hdu).getTiler(),
+ corners, lengths, steps);
}
-
- final StreamingImageData newImageData =
- (StreamingImageData) FitsFactory.dataFactory(headerCopy, true);
- // The tiler is where the source data comes from.
- newImageData.setTiler(imageHDU.getTiler());
- newImageData.setTile(corners, lengths, steps);
-
- fitsOutput.addHDU(FitsFactory.hduFactory(headerCopy, newImageData));
+ fitsOutput.addHDU(new ImageHDU(headerCopy, streamingTileImageData));
}
}
}
@@ -399,7 +423,8 @@ private boolean isEmpty(final Cutout cutout) {
*/
private void fillCornersAndLengths(final int[] dimensions, final Header header,
final ExtensionSlice extensionSliceValue, final int[] corners,
- final int[] lengths, final int[] steps) {
+ final int[] lengths, final int[] steps)
+ throws FitsException {
LOGGER.debug("Full dimensions are " + Arrays.toString(dimensions));
final int dimensionLength = dimensions.length;
@@ -439,7 +464,8 @@ private void fillCornersAndLengths(final int[] dimensions, final Header header,
// Adjust the NAXISn header appropriately. If the step value does not divide perfectly into the length,
// then there will be an extra write, so add 1 where necessary.
- header.setNaxis(i + 1, (nextLength / step) + ((nextLength % step) == 0 ? 0 : 1));
+ header.addValue(Standard.NAXISn.n(i + 1),
+ (nextLength / step) + ((nextLength % step) == 0 ? 0 : 1));
// Need to set the values backwards (reverse order) to match the dimensions.
corners[corners.length - i - 1] = lowerBound;
@@ -476,21 +502,24 @@ private Header copyHeader(final Header source) throws HeaderCardException {
destination.insertHistory(headerCard.getComment());
} else {
if (valueType == String.class || valueType == null) {
- destination.addValue(headerCard.getKey(), headerCard.getValue(), headerCard.getComment());
+ destination.addValue(headerCardKey, headerCard.getValue(), headerCard.getComment());
} else if (valueType == Boolean.class) {
- destination.addValue(headerCard.getKey(), Boolean.parseBoolean(headerCard.getValue()),
+ destination.addValue(headerCardKey, Boolean.parseBoolean(headerCard.getValue()),
headerCard.getComment());
} else if (valueType == Integer.class || valueType == BigInteger.class) {
- destination.addValue(headerCard.getKey(), new BigInteger(headerCard.getValue()),
+ destination.addValue(headerCardKey, new BigInteger(headerCard.getValue()),
headerCard.getComment());
} else if (valueType == Long.class) {
- destination.addValue(headerCard.getKey(), Long.parseLong(headerCard.getValue()),
+ destination.addValue(headerCardKey, Long.parseLong(headerCard.getValue()),
headerCard.getComment());
} else if (valueType == Double.class) {
- destination.addValue(headerCard.getKey(), Double.parseDouble(headerCard.getValue()),
+ destination.addValue(headerCardKey, Double.parseDouble(headerCard.getValue()),
headerCard.getComment());
} else if (valueType == BigDecimal.class) {
- destination.addValue(headerCard.getKey(), new BigDecimal(headerCard.getValue()),
+ destination.addValue(headerCardKey, new BigDecimal(headerCard.getValue()),
+ headerCard.getComment());
+ } else if (valueType == Float.class) {
+ destination.addValue(headerCardKey, Float.parseFloat(headerCard.getValue()),
headerCard.getComment());
}
}
@@ -499,6 +528,43 @@ private Header copyHeader(final Header source) throws HeaderCardException {
return destination;
}
+ private void addHeaderCard(final Header destination, final IFitsHeader headerCard, final Class valueType,
+ final String value)
+ throws FitsException {
+ final String headerCardKey = headerCard.key();
+
+ // Check for blank lines or just plain comments that are not standard FITS comments.
+ if (!StringUtil.hasText(headerCardKey)) {
+ destination.addValue(headerCardKey, (String) null, headerCard.comment());
+ } else if (Standard.COMMENT.key().equals(headerCardKey)) {
+ destination.insertComment(headerCard.comment());
+ } else if (Standard.HISTORY.key().equals(headerCardKey)) {
+ destination.insertHistory(headerCard.comment());
+ } else {
+ if (valueType == String.class || valueType == null) {
+ destination.addValue(headerCardKey, value, headerCard.comment());
+ } else if (valueType == Boolean.class) {
+ destination.addValue(headerCardKey, Boolean.parseBoolean(value),
+ headerCard.comment());
+ } else if (valueType == Integer.class || valueType == BigInteger.class) {
+ destination.addValue(headerCardKey, new BigInteger(value),
+ headerCard.comment());
+ } else if (valueType == Long.class) {
+ destination.addValue(headerCardKey, Long.parseLong(value),
+ headerCard.comment());
+ } else if (valueType == Double.class) {
+ destination.addValue(headerCardKey, Double.parseDouble(value),
+ headerCard.comment());
+ } else if (valueType == BigDecimal.class) {
+ destination.addValue(headerCardKey, new BigDecimal(value),
+ headerCard.comment());
+ } else if (valueType == Float.class) {
+ destination.addValue(headerCardKey, Float.parseFloat(value),
+ headerCard.comment());
+ }
+ }
+ }
+
private boolean matchHDU(final BasicHDU hdu, final String extensionName, final Integer extensionVersion) {
final String extName = hdu.getTrimmedString(Standard.EXTNAME);
@@ -563,7 +629,7 @@ private int mapOverlap(final BasicHDU hdu, final int hduIndex, final Listtr is null, it was a long way away from the WCS and does not
// impose a limit/cutout - so we can safely skip it
if (tr != null) {
LOGGER.debug("Transformed coordinates: " + Arrays.toString(tr.coordinates));
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsOperationsTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsOperationsTest.java
index ce617036..abee0a8f 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsOperationsTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsOperationsTest.java
@@ -86,8 +86,7 @@
import nom.tam.fits.Header;
import nom.tam.fits.HeaderCard;
import nom.tam.util.Cursor;
-import nom.tam.util.RandomAccessDataObject;
-import nom.tam.util.RandomAccessFileExt;
+import nom.tam.util.RandomAccessFileIO;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
@@ -113,8 +112,8 @@ public FitsOperationsTest() {
public void testGetPrimaryHeader() {
try {
// setup
- final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("sample-mef.fits",
+ final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("sample-mef.fits",
FitsOperationsTest.class), "r");
FitsOperations fop = new FitsOperations(randomAccessDataObject);
@@ -140,8 +139,8 @@ public void testGetPrimaryHeader() {
public void testGetHeaders() {
try {
// setup
- final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("sample-mef.fits",
+ final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("sample-mef.fits",
FitsOperationsTest.class), "r");
FitsOperations fop = new FitsOperations(randomAccessDataObject);
@@ -167,54 +166,63 @@ public void testGetHeaders() {
}
@Test
- public void testHeaders() {
-
- try {
- try (final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("sample-mef.fits",
- FitsOperationsTest.class), "r");
- final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
- // setup
- final FitsOperations fop = new FitsOperations(randomAccessDataObject);
- fop.headersToStream(byteArrayOutputStream);
+ public void testHeaders() throws Exception {
+ try (final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("sample-mef.fits",
+ FitsOperationsTest.class), "r");
+ final ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
+ // setup
+ final FitsOperations fop = new FitsOperations(randomAccessDataObject);
+ fop.headersToStream(byteArrayOutputStream);
- final byte[] output = byteArrayOutputStream.toByteArray();
+ final byte[] output = byteArrayOutputStream.toByteArray();
- final File sampleHeaderFile = FileUtil.getFileFromResource("sample-mef.txt",
- FitsOperationsTest.class);
- final List expectedHeaderLines = new ArrayList<>();
- try (final FileInputStream fileInputStream = new FileInputStream(sampleHeaderFile);
- final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(fileInputStream))) {
- String line;
- while ((line = bufferedReader.readLine()) != null) {
- expectedHeaderLines.add(line);
- }
+ final File sampleHeaderFile = FileUtil.getFileFromResource("sample-mef.txt",
+ FitsOperationsTest.class);
+ final List expectedHeaderLines = new ArrayList<>();
+ try (final FileInputStream fileInputStream = new FileInputStream(sampleHeaderFile);
+ final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(fileInputStream))) {
+ String line;
+ while ((line = bufferedReader.readLine()) != null) {
+ expectedHeaderLines.add(line);
}
+ }
- final List resultHeaderLines = new ArrayList<>();
- try (final BufferedReader bufferedReader = new BufferedReader(
- new InputStreamReader(new ByteArrayInputStream(output)))) {
- String line;
- while ((line = bufferedReader.readLine()) != null) {
- resultHeaderLines.add(line);
- }
+ final List resultHeaderLines = new ArrayList<>();
+ try (final BufferedReader bufferedReader = new BufferedReader(
+ new InputStreamReader(new ByteArrayInputStream(output)))) {
+ String line;
+ while ((line = bufferedReader.readLine()) != null) {
+ resultHeaderLines.add(line);
}
-
- Assert.assertEquals("Wrong headers provided.", expectedHeaderLines, resultHeaderLines);
}
+ for (int i = 0; i < expectedHeaderLines.size(); i++) {
+ final String nextExpectedHeaderLine = expectedHeaderLines.get(i);
+ final String nextResultHeaderLine = resultHeaderLines.get(i);
+ final HeaderCard expectedHeaderCard = HeaderCard.create(nextExpectedHeaderLine);
+ final HeaderCard resultHeaderCard = HeaderCard.create(nextResultHeaderLine);
+
+ Assert.assertEquals("Wrong header key at '" + nextExpectedHeaderLine + "' == '"
+ + nextResultHeaderLine + "': " + i, expectedHeaderCard.getKey(),
+ resultHeaderCard.getKey());
+
+ Assert.assertEquals("Wrong header value at '" + nextExpectedHeaderLine + "' == '"
+ + nextResultHeaderLine + "': " + i, expectedHeaderCard.getValue(),
+ resultHeaderCard.getValue());
+ }
} catch (Exception unexpected) {
log.error("unexpected exception", unexpected);
- Assert.fail("unexpected exception: " + unexpected);
+ throw unexpected;
}
}
@Test
public void testSlice() throws Exception {
// setup
- final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("test-hst-mef.fits",
+ final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("test-hst-mef.fits",
FitsOperationsTest.class), "r");
final FitsOperations fop = new FitsOperations(randomAccessDataObject);
final File outputFile = Files.createTempFile(
@@ -233,7 +241,7 @@ public void testSlice() throws Exception {
fop.cutoutToStream(cutout, fileOutputStream);
}
- final Fits resultsFits = new Fits(new RandomAccessFileExt(outputFile, "r"));
+ final Fits resultsFits = new Fits(new RandomAccessStorageObject(outputFile, "r"));
resultsFits.read();
Assert.assertEquals("Wrong HDU count. Extensions 3, 106, and 126 should be available.", 4,
@@ -255,8 +263,8 @@ public void testSlice() throws Exception {
@Test
public void testNoOverlap() throws Exception {
- final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("test-hst-mef.fits",
+ final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("test-hst-mef.fits",
FitsOperationsTest.class), "r");
final FitsOperations fop = new FitsOperations(randomAccessDataObject);
final File outputFile = Files.createTempFile(
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsTest.java
index 604c8d4d..d0728e13 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/FitsTest.java
@@ -128,9 +128,18 @@ public static void assertHeadersEqual(final Header expectedHeader, final Header
if (expectedCard == null) {
Assert.assertNull("Card " + headerCardKey.key() + " should be null.", resultCard);
} else {
+ final Class valueType = expectedCard.valueType();
Assert.assertNotNull("Header " + headerCardKey.key() + " should not be null.", resultCard);
- Assert.assertEquals("Header " + headerCardKey.key() + " has the wrong value.",
- expectedCard.getValue(), resultCard.getValue());
+
+ // Floats have varying decimal place specifications, so compare them separately.
+ if (valueType == Float.class) {
+ Assert.assertEquals("Header " + headerCardKey.key() + " has the wrong value.",
+ Float.parseFloat(expectedCard.getValue()),
+ Float.parseFloat(resultCard.getValue()), 0.0F);
+ } else {
+ Assert.assertEquals("Header " + headerCardKey.key() + " has the wrong value.",
+ expectedCard.getValue(), resultCard.getValue());
+ }
}
});
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/BaseCutoutTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/BaseCutoutTest.java
index 75159894..16c16201 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/BaseCutoutTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/BaseCutoutTest.java
@@ -73,12 +73,10 @@
import org.apache.log4j.Logger;
import org.junit.Assert;
-import java.io.File;
import java.util.Arrays;
public abstract class BaseCutoutTest {
private static final Logger LOGGER = Logger.getLogger(BaseCutoutTest.class);
- final static File DEFAULT_DATA_DIR = new File(System.getProperty("user.home") + "/.config/test-data");
// Concrete tests can set this if desired.
long padding = 2;
@@ -95,9 +93,10 @@ public abstract class BaseCutoutTest {
*/
void assertFuzzyPixelArrayEquals(final String message, final long[] expected, final long[] result) {
if (result == null && expected != null) {
- Assert.fail("Result array is null but expected " + Arrays.toString(expected));
+ Assert.fail("Result array is null but expected " + Arrays.toString(expected)
+ + "\nMessage from test: " + message);
} else if (result != null && expected == null) {
- Assert.fail("Expected null but got " + Arrays.toString(result));
+ Assert.fail("Expected null but got " + Arrays.toString(result) + "\nMessage from test: " + message);
} else if (result != null) {
LOGGER.debug("\n*****\nChecking array \n" + Arrays.toString(result) + "\nagainst\n"
+ Arrays.toString(expected) + "\n allowing a difference of " + padding + ".\n****");
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/CircleCutoutTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/CircleCutoutTest.java
index 7a7ae633..71bd1e8c 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/CircleCutoutTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/CircleCutoutTest.java
@@ -73,17 +73,19 @@
import ca.nrc.cadc.util.FileUtil;
import ca.nrc.cadc.util.Log4jInit;
import nom.tam.fits.Header;
+import nom.tam.fits.HeaderCard;
import nom.tam.util.ArrayDataInput;
-import nom.tam.util.BufferedDataInputStream;
+import nom.tam.util.FitsInputStream;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
-import org.junit.Ignore;
import org.junit.Test;
+import java.io.BufferedReader;
import java.io.File;
-import java.io.FileInputStream;
import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
@@ -107,8 +109,8 @@ public void testALMA() throws Exception {
final String headerFileName = "test-alma-cube-header.txt";
final File testFile = FileUtil.getFileFromResource(headerFileName, CircleCutoutTest.class);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final ArrayDataInput arrayDataInput = new FitsInputStream(inputStream)) {
final Header testHeader = Header.readHeader(arrayDataInput);
final Circle circle = new Circle(new Point(246.52D, -24.33D), 0.01D);
@@ -139,9 +141,15 @@ public void testBLAST() throws Exception {
LOGGER.debug("Reading header file " + headerFileName);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
- final Header testHeader = Header.readHeader(arrayDataInput);
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream))) {
+
+ final Header testHeader = new Header();
+ final char[] buff = new char[80];
+ while (bufferedReader.read(buff) >= 0) {
+ testHeader.addLine(HeaderCard.create(new String(buff)));
+ }
+
final Circle circle = new Circle(new Point(309.8D, 42.7D), 0.3D);
final CircleCutout circleCutout = new CircleCutout(testHeader);
@@ -154,28 +162,6 @@ public void testBLAST() throws Exception {
LOGGER.debug("CircleCutoutTest.testComputeBLAST OK: " + (System.currentTimeMillis() - startMillis) + " ms");
}
- @Test
- @Ignore("Bad header information? Pixels are off by ~5.")
- public void testIRIS() throws Exception {
- final long startMillis = System.currentTimeMillis();
-
- final String headerFileName = "test-iris-header.txt";
- final File testFile = FileUtil.getFileFromResource(headerFileName, CircleCutoutTest.class);
-
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
-
- final Header testHeader = Header.readHeader(arrayDataInput);
- final Circle circle = new Circle(new Point(250.0D, 75.2D), 0.3D);
- final CircleCutout circleCutout = new CircleCutout(testHeader);
-
- final long[] expected = new long[]{431, 463, 79, 110};
- final long[] result = circleCutout.getBounds(circle);
- assertFuzzyPixelArrayEquals("Wrong IRIS circle bounds.", expected, result);
- }
- LOGGER.debug("CircleCutoutTest.testComputeIRIS OK: " + (System.currentTimeMillis() - startMillis) + " ms");
- }
-
@Test
public void testOMM() throws Exception {
final long startMillis = System.currentTimeMillis();
@@ -183,8 +169,8 @@ public void testOMM() throws Exception {
final String headerFileName = "test-omm-header.txt";
final File testFile = FileUtil.getFileFromResource(headerFileName, CircleCutoutTest.class);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final ArrayDataInput arrayDataInput = new FitsInputStream(inputStream)) {
final Header testHeader = Header.readHeader(arrayDataInput);
final Circle circle = new Circle(new Point(20.89D, -59.47D), 0.1D);
@@ -226,8 +212,8 @@ public void testHSTMEF() throws Exception {
final File testFile = FileUtil.getFileFromResource("test-hst-mef/" + headerFileName,
CircleCutoutTest.class);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final ArrayDataInput arrayDataInput = new FitsInputStream(inputStream)) {
final Header testHeader = Header.readHeader(arrayDataInput);
LOGGER.debug("Looking at HDU " + hduIndex);
@@ -270,8 +256,8 @@ public void testNoOverlap() throws Exception {
LOGGER.debug("Reading header file " + headerFileName);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final ArrayDataInput arrayDataInput = new FitsInputStream(inputStream)) {
final Header testHeader = Header.readHeader(arrayDataInput);
final CircleCutout circleCutout = new CircleCutout(testHeader);
assertFuzzyPixelArrayEquals("Should be empty.", null, circleCutout.getBounds(circle));
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/FITSHeaderWCSKeywordsTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/FITSHeaderWCSKeywordsTest.java
index 99dba2a3..4e5d4b91 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/FITSHeaderWCSKeywordsTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/FITSHeaderWCSKeywordsTest.java
@@ -72,12 +72,12 @@
import ca.nrc.cadc.util.Log4jInit;
import nom.tam.fits.Fits;
import nom.tam.fits.Header;
-import nom.tam.util.RandomAccessDataObject;
-import nom.tam.util.RandomAccessFileExt;
+import nom.tam.util.RandomAccessFileIO;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
import org.junit.Test;
+import org.opencadc.fits.RandomAccessStorageObject;
import java.math.BigDecimal;
import java.util.Iterator;
@@ -117,9 +117,9 @@ public void testEmptyHeaderConstructor() throws Exception {
@Test
public void testGet() throws Exception {
final long startMillis = System.currentTimeMillis();
- try (final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("sample-mef.fits",
- FITSHeaderWCSKeywordsTest.class), "r");
+ try (final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("sample-mef.fits",
+ FITSHeaderWCSKeywordsTest.class), "r");
final Fits fits = new Fits(randomAccessDataObject)) {
// Just to cache it up front, and ensure that it can be read.
@@ -137,6 +137,9 @@ public void testGet() throws Exception {
if (valueType == Integer.class) {
Assert.assertEquals("Wrong integer value.", Integer.parseInt(headerCardValue),
testSubject.getIntValue(headerCardKey));
+ } else if (valueType == Float.class) {
+ Assert.assertEquals("Wrong float value.", Float.parseFloat(headerCardValue),
+ testSubject.getFloatValue(headerCardKey), 0.0F);
} else if (valueType == Double.class || valueType == BigDecimal.class) {
Assert.assertEquals("Wrong double value.", Double.parseDouble(headerCardValue),
testSubject.getDoubleValue(headerCardKey), 0.0D);
@@ -157,8 +160,8 @@ public void testGet() throws Exception {
@Test
public void testIterator() throws Exception {
final long startMillis = System.currentTimeMillis();
- try (final RandomAccessDataObject randomAccessDataObject =
- new RandomAccessFileExt(FileUtil.getFileFromResource("sample-mef.fits",
+ try (final RandomAccessFileIO randomAccessDataObject =
+ new RandomAccessStorageObject(FileUtil.getFileFromResource("sample-mef.fits",
FITSHeaderWCSKeywordsTest.class), "r");
final Fits fits = new Fits(randomAccessDataObject)) {
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/NDimensionalSlicerTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/NDimensionalSlicerTest.java
index 937a1f86..e7bb8a35 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/NDimensionalSlicerTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/NDimensionalSlicerTest.java
@@ -72,7 +72,6 @@
import ca.nrc.cadc.util.Log4jInit;
import java.io.DataOutputStream;
import java.io.File;
-import java.io.FileOutputStream;
import java.io.OutputStream;
import java.nio.file.Files;
import java.nio.file.Path;
@@ -81,14 +80,15 @@
import nom.tam.fits.BasicHDU;
import nom.tam.fits.Fits;
-import nom.tam.util.RandomAccessDataObject;
-import nom.tam.util.RandomAccessFileExt;
+import nom.tam.util.FitsOutputStream;
+import nom.tam.util.RandomAccessFileIO;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
import org.junit.Test;
import org.opencadc.fits.FitsTest;
import org.opencadc.fits.NoOverlapException;
+import org.opencadc.fits.RandomAccessStorageObject;
import org.opencadc.soda.ExtensionSlice;
import org.opencadc.soda.ExtensionSliceFormat;
import org.opencadc.soda.server.Cutout;
@@ -123,7 +123,7 @@ public void testMEFFileSlice() throws Exception {
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-hst-mef-cutout", ".fits");
LOGGER.debug("Writing out to " + outputPath);
- try (final OutputStream outputStream = new FileOutputStream(outputPath.toFile())) {
+ try (final OutputStream outputStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(file, cutout, outputStream);
}
@@ -187,8 +187,8 @@ public void testMEFRandomAccessSlice() throws Exception {
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-hst-mef-cutout", ".fits");
LOGGER.debug("Writing out to " + outputPath);
- try (final RandomAccessDataObject randomAccessDataObject = new RandomAccessFileExt(file, "r");
- final OutputStream outputStream = new FileOutputStream(outputPath.toFile());
+ try (final RandomAccessFileIO randomAccessDataObject = new RandomAccessStorageObject(file, "r");
+ final OutputStream outputStream = Files.newOutputStream(outputPath.toFile().toPath());
final OutputStream hstFileCutoutStream = new DataOutputStream(outputStream)) {
slicer.slice(randomAccessDataObject, cutout, hstFileCutoutStream);
hstFileCutoutStream.flush();
@@ -222,8 +222,8 @@ public void testSimpleToMEF() throws Exception {
final String testWriteDir = configuredTestWriteDir == null ? "/tmp" : configuredTestWriteDir;
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-simple-iris-cutout", ".fits");
- try (final RandomAccessDataObject randomAccessDataObject = new RandomAccessFileExt(file, "r");
- final OutputStream outputStream = new FileOutputStream(outputPath.toFile())) {
+ try (final RandomAccessFileIO randomAccessDataObject = new RandomAccessStorageObject(file, "r");
+ final OutputStream outputStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(randomAccessDataObject, cutout, outputStream);
outputStream.flush();
}
@@ -252,8 +252,8 @@ public void testMEFToSimple() throws Exception {
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-simple-hst-cutout", ".fits");
LOGGER.debug("Writing out to " + outputPath);
- try (final RandomAccessDataObject randomAccessDataObject = new RandomAccessFileExt(file, "r");
- final OutputStream hstFileCutoutStream = new FileOutputStream(outputPath.toFile())) {
+ try (final RandomAccessFileIO randomAccessDataObject = new RandomAccessStorageObject(file, "r");
+ final OutputStream hstFileCutoutStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(randomAccessDataObject, cutout, hstFileCutoutStream);
hstFileCutoutStream.flush();
}
@@ -280,8 +280,8 @@ public void testNoSuchExtension() throws Exception {
final Path outputPath = Files.createTempFile(new File(testWriteDir).toPath(), "test-simple-hst-cutout", ".fits");
LOGGER.debug("Writing out to " + outputPath);
- try (final RandomAccessDataObject randomAccessDataObject = new RandomAccessFileExt(file, "r");
- final OutputStream hstFileCutoutStream = new FileOutputStream(outputPath.toFile())) {
+ try (final RandomAccessFileIO randomAccessDataObject = new RandomAccessStorageObject(file, "r");
+ final OutputStream hstFileCutoutStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(randomAccessDataObject, cutout, hstFileCutoutStream);
hstFileCutoutStream.flush();
} catch (NoOverlapException noOverlapException) {
@@ -307,9 +307,8 @@ public void testDataInPrimaryHeader() throws Exception {
final NDimensionalSlicer slicer = new NDimensionalSlicer();
final File file = Files.createTempFile("test-data-primary-", ".fits").toFile();
- try (final DataOutputStream dataOutputStream = new DataOutputStream(new FileOutputStream(file));
+ try (final FitsOutputStream fitsOutputStream = new FitsOutputStream(Files.newOutputStream(file.toPath()));
final Fits fits = new Fits()) {
- fits.setStreamWrite(true);
for (int i = 0; i < 101; i += 1) {
for (int j = 0; j < 101; j += 1) {
data0[i][j] = i * j;
@@ -329,9 +328,10 @@ public void testDataInPrimaryHeader() throws Exception {
data2[i][j] = i * j;
}
}
- fits.addHDU(Fits.makeHDU(data2));
- fits.write(dataOutputStream);
+ fits.addHDU(Fits.makeHDU(data2));
+ fits.write(fitsOutputStream);
+ fitsOutputStream.flush();
}
final String configuredTestWriteDir = System.getenv("TEST_WRITE_DIR");
@@ -344,8 +344,8 @@ public void testDataInPrimaryHeader() throws Exception {
LOGGER.debug("Writing out to " + outputPath);
- try (final RandomAccessDataObject randomAccessDataObject = new RandomAccessFileExt(file, "r");
- final OutputStream outputStream = new FileOutputStream(outputPath.toFile())) {
+ try (final RandomAccessFileIO randomAccessDataObject = new RandomAccessStorageObject(file, "r");
+ final OutputStream outputStream = Files.newOutputStream(outputPath.toFile().toPath())) {
slicer.slice(randomAccessDataObject, cutout, outputStream);
outputStream.flush();
} catch (IllegalArgumentException illegalArgumentException) {
@@ -354,7 +354,6 @@ public void testDataInPrimaryHeader() throws Exception {
}
try (final Fits checkFits = new Fits(outputPath.toFile())) {
- checkFits.setStreamWrite(true);
checkFits.read();
int index = 0;
diff --git a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/WCSCutoutUtilTest.java b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/WCSCutoutUtilTest.java
index b1c9b296..7176b15c 100644
--- a/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/WCSCutoutUtilTest.java
+++ b/cadc-data-ops-fits/src/test/java/org/opencadc/fits/slice/WCSCutoutUtilTest.java
@@ -74,8 +74,7 @@
import ca.nrc.cadc.util.FileUtil;
import ca.nrc.cadc.util.Log4jInit;
import nom.tam.fits.Header;
-import nom.tam.util.ArrayDataInput;
-import nom.tam.util.BufferedDataInputStream;
+import nom.tam.fits.HeaderCard;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import org.junit.Assert;
@@ -83,15 +82,18 @@
import org.opencadc.soda.PixelRange;
import org.opencadc.soda.server.Cutout;
+import java.io.BufferedReader;
import java.io.File;
-import java.io.FileInputStream;
import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
public class WCSCutoutUtilTest extends BaseCutoutTest {
private static final Logger LOGGER = Logger.getLogger(WCSCutoutUtilTest.class);
static {
+ Log4jInit.setLevel("ca.nrc.cadc.wcs", Level.DEBUG);
Log4jInit.setLevel("org.opencadc.fits.slice", Level.DEBUG);
}
@@ -105,9 +107,14 @@ public void testMultipleWCS() throws Exception {
cutout.pos = new Circle(new Point(128.638D, 17.33D), 0.01D);
cutout.band = new Interval<>(1.3606E-3D, 1.3616E-3D);
- try (final InputStream inputStream = new FileInputStream(testFile);
- final ArrayDataInput arrayDataInput = new BufferedDataInputStream(inputStream)) {
- final Header testHeader = Header.readHeader(arrayDataInput);
+ try (final InputStream inputStream = Files.newInputStream(testFile.toPath());
+ final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(inputStream))) {
+ final Header testHeader = new Header();
+ final char[] buff = new char[80];
+ while (bufferedReader.read(buff) >= 0) {
+ testHeader.addLine(HeaderCard.create(new String(buff)));
+ }
+
final PixelRange[] resultRanges = WCSCutoutUtil.getBounds(testHeader, cutout);
// Combined Circle cutout (axes 1 & 2), as well as Band cutout on axis 3.