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Conform to CFITSIO hierarch specification #159

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merged 2 commits into from Sep 28, 2021
Merged

Conform to CFITSIO hierarch specification #159

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94677c0
HeaderCard: Fix when long string are used with long hierarch keywords.
attipaci Sep 28, 2021
fa82cec
Conform to CFITSIO hieratch specification with space before =.
attipaci Sep 28, 2021
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13 changes: 9 additions & 4 deletions src/main/java/nom/tam/fits/HeaderCard.java
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Expand Up @@ -199,7 +199,7 @@ public class HeaderCard implements CursorValue<String> {
* <li>If {@link FitsFactory#setUseHierarch(boolean)} is enabled, structured longer keywords can be composed
* after a <code>HIERARCH</code> base key, followed by space (and/or dot ].]) separated parts, up to an
* equal sign [=]. The library will represent the same components (including <code>HIERARCH</code>) but
* separated by single dots [.]. For example, the header line starting with [<code>HIERARCH SMA OBS TARGET=</code>],
* separated by single dots [.]. For example, the header line starting with [<code>HIERARCH SMA OBS TARGET =</code>],
* will be referred as [<code>HIERARCH.SMA.OBS.TARGET</code>] withing this library. The keyword parts
* can be composed of any ASCII characters except dot [.], white spaces, or equal [=].</li>
* <li>By default, all parts of the key are converted to upper-case. Case sensitive HIERARCH keywords can be
Expand Down Expand Up @@ -1375,7 +1375,11 @@ private int maxStringValueLength() {

private boolean stringValueToString(int alignSmallString, int alignPosition, FitsLineAppender buf, boolean commentHandled) {
String stringValue = this.value.replace("'", "''");
if (FitsFactory.isLongStringsEnabled() && stringValue.length() > maxStringValueLength()) {

// We can only write a single-line string, including the quotes, in the space left on the line...
int spaceLeft = FITS_HEADER_CARD_SIZE - buf.length() % FITS_HEADER_CARD_SIZE - 2;

if (FitsFactory.isLongStringsEnabled() && stringValue.length() > spaceLeft) {
writeLongStringValue(buf, stringValue);
commentHandled = true;
} else {
Expand Down Expand Up @@ -1459,7 +1463,8 @@ void setKey(String newKey) {

/**
* A helper utility class to parse header cards for there value (especially
* strings) and comments.
* strings) and comments. See {@link HeaderCard#create(String)} for a description
* of the rules that guide parsing.
*
* @author Attila Kovacs
* @author Richard van Nieuwenhoven
Expand Down Expand Up @@ -1826,7 +1831,7 @@ private void parseStringValue() throws IllegalArgumentException {
} else {
value = null;
parsePos = from;
throw new IllegalArgumentException("Missing or unexpected single quotes in value");
throw new IllegalArgumentException("Missing end quote in [" + line + "]");
}
}
}
Expand Down
4 changes: 3 additions & 1 deletion src/main/java/nom/tam/fits/header/hierarch/BlanksDotHierarchKeyFormatter.java
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Expand Up @@ -62,7 +62,9 @@ public void append(String key, FitsLineAppender buffer) {

buffer.append(HIERARCH_TEXT);
buffer.append(blanks);
buffer.append(key, HIERARCH_KEY_OFFSET, key.length());
buffer.append(key, HIERARCH_KEY_OFFSET, key.length());
// cfitsio specifies a required space before the '=', so let's play nice with it.
buffer.append(' ');
}

@Override
Expand Down
2 changes: 2 additions & 0 deletions src/main/java/nom/tam/fits/header/hierarch/StandardIHierarchKeyFormatter.java
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Expand Up @@ -44,6 +44,8 @@ public void append(String key, FitsLineAppender buffer) {
key = key.toUpperCase(Locale.US);
}
buffer.appendReplacing(key, '.', ' ');
// cfitsio specifies a required space before the '=', so let's play nice with it.
buffer.append(' ');
}

@Override
Expand Down
33 changes: 17 additions & 16 deletions src/test/java/nom/tam/fits/test/HeaderCardTest.java
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Expand Up @@ -446,11 +446,11 @@ public void testHierarchFormatting() throws Exception {
FitsFactory.setUseHierarch(true);
HeaderCard hc;
hc = new HeaderCard("HIERARCH.TEST1.INT", "xx", "Comment");
assertEquals("HIERARCH TEST1 INT= 'xx' / Comment ", hc.toString());
assertEquals("HIERARCH TEST1 INT = 'xx' / Comment ", hc.toString());
hc = new HeaderCard("HIERARCH.TEST1.TEST2.INT", "xx", "Comment");
assertEquals("HIERARCH TEST1 TEST2 INT= 'xx' / Comment ", hc.toString());
assertEquals("HIERARCH TEST1 TEST2 INT = 'xx' / Comment ", hc.toString());
hc = new HeaderCard("HIERARCH.TEST1.TEST3.B", "xx", "Comment");
assertEquals("HIERARCH TEST1 TEST3 B= 'xx' / Comment ", hc.toString());
assertEquals("HIERARCH TEST1 TEST3 B = 'xx' / Comment ", hc.toString());
}

@Test
Expand All @@ -469,6 +469,7 @@ public void testSimpleHierarch() throws Exception {
assertEquals("HIERARCH", hc.getKey());
assertEquals("0.123", hc.getValue());
assertEquals("Comment", hc.getComment());
assertEquals("HIERARCH= 0.123 / Comment", hc.toString().trim());
}

@Test
Expand Down Expand Up @@ -497,7 +498,7 @@ public void testHierarch() throws Exception {

hc = new HeaderCard(key, 123, "Comment");

assertEquals("HIERARCH TEST1 TEST2 INT= 123 / Comment", hc.toString().trim());
assertEquals("HIERARCH TEST1 TEST2 INT = 123 / Comment", hc.toString().trim());

assertEquals("h5", key, hc.getKey());
assertEquals("h6", "123", hc.getValue());
Expand All @@ -516,8 +517,8 @@ public void testHierarch() throws Exception {

hc = new HeaderCard(key, "a verly long value that must be splitted over multiple lines to fit the card", "the comment is also not the smallest");

assertEquals("HIERARCH TEST1 TEST2 INT= 'a verly long value that must be splitted over multi&'" + //
"CONTINUE 'ple lines to fit the card' / the comment is also not the smallest ", hc.toString());
assertEquals("HIERARCH TEST1 TEST2 INT = 'a verly long value that must be splitted over mult&'" + //
"CONTINUE 'iple lines to fit the card' / the comment is also not the smallest ", hc.toString());

}

Expand Down Expand Up @@ -586,8 +587,8 @@ public void testLongStringWithSkippedBlank() throws Exception {

HeaderCard hc = new HeaderCard(key, "a verly long value that must be splitted over multiple lines to fit the card", "the comment is also not the smallest");

assertEquals("HIERARCH TEST1 TEST2 INT='a verly long value that must be splitted over multip&'" + //
"CONTINUE 'le lines to fit the card' / the comment is also not the smallest ", hc.toString());
assertEquals("HIERARCH TEST1 TEST2 INT ='a verly long value that must be splitted over multi&'" + //
"CONTINUE 'ple lines to fit the card' / the comment is also not the smallest ", hc.toString());

}

Expand Down Expand Up @@ -860,17 +861,17 @@ public void testHierarchAlternatives() throws Exception {
FitsFactory.setUseHierarch(true);
HeaderCard headerCard = new HeaderCard("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", "xy", null);
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1 TEST2 TEST3 TEST4 TEST5 TEST6= 'xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1 TEST2 TEST3 TEST4 TEST5 TEST6 = 'xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

FitsFactory.setHierarchFormater(new BlanksDotHierarchKeyFormatter(1));
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6= 'xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6 = 'xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

FitsFactory.setHierarchFormater(new BlanksDotHierarchKeyFormatter(2));
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6= 'xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6 = 'xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

}
Expand Down Expand Up @@ -901,17 +902,17 @@ public void testHierarchAlternativesWithSkippedBlank() throws Exception {
FitsFactory.setUseHierarch(true);
HeaderCard headerCard = new HeaderCard("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", "xy", null);
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1 TEST2 TEST3 TEST4 TEST5 TEST6='xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1 TEST2 TEST3 TEST4 TEST5 TEST6 ='xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

FitsFactory.setHierarchFormater(new BlanksDotHierarchKeyFormatter(1));
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6='xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6 ='xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

FitsFactory.setHierarchFormater(new BlanksDotHierarchKeyFormatter(2));
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", headerCard.getKey());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6='xy' ", headerCard.toString());
assertEquals("HIERARCH TEST1.TEST2.TEST3.TEST4.TEST5.TEST6 ='xy' ", headerCard.toString());
assertEquals("HIERARCH.TEST1.TEST2.TEST3.TEST4.TEST5.TEST6", new HeaderCard(headerCardToStream(headerCard)).getKey());

}
Expand Down Expand Up @@ -1024,12 +1025,12 @@ public void testHeaderCardFormatHierarch() throws Exception {
assertEquals("UTC", card.getValue());
assertEquals("All dates are in UTC time", card.getComment());
assertEquals("HIERARCH.TIMESYS.BBBB.CCCC", card.getKey());
assertEquals("HIERARCH TIMESYS BBBB CCCC='UTC' / All dates are in UTC time ", card.toString());
assertEquals("HIERARCH TIMESYS BBBB CCCC ='UTC' / All dates are in UTC time ", card.toString());

card = HeaderCard.create("HIERARCH TIMESYS.BBBB.CCCC ='UTC ' / All dates are in UTC time");
assertEquals("UTC", card.getValue());
assertEquals("All dates are in UTC time", card.getComment());
assertEquals("HIERARCH.TIMESYS.BBBB.CCCC", card.getKey());
assertEquals("HIERARCH TIMESYS BBBB CCCC='UTC' / All dates are in UTC time ", card.toString());
assertEquals("HIERARCH TIMESYS BBBB CCCC ='UTC' / All dates are in UTC time ", card.toString());
}
}
36 changes: 19 additions & 17 deletions src/test/java/nom/tam/fits/test/HeaderTest.java
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Expand Up @@ -171,7 +171,7 @@ public void cursorTest() throws Exception {
hdr.addValue("FLT1", 1.34, "A float value");
hdr.addValue("FLT2", -1.234567890e-134, "A very long float");
hdr.insertComment("Comment after flt2");

c.setKey("INTVAL1");
hc = (HeaderCard) c.next();
assertEquals("INTVAL1", "INTVAL1", hc.getKey());
Expand Down Expand Up @@ -204,8 +204,8 @@ public void cursorTest() throws Exception {
SafeClose.close(f);
}
}


/** Confirm initial location versus EXTEND keyword (V. Forchi). */
@Test
public void extendTest() throws Exception {
Expand Down Expand Up @@ -366,7 +366,7 @@ public void longStringNullComment() throws Exception {
assertNull(card.getComment());
assertFalse(new HeaderCard("STRKEY",
"This is a very long string keyword value that is continued over at least three keywords in the FITS header even if it has no comment.", null).toString()
.contains("/"));
.contains("/"));
FitsFactory.setLongStringsEnabled(false);
}

Expand Down Expand Up @@ -411,7 +411,7 @@ private void checkOneCombination(String cardValue, String cardComment) throws Ex
Arrays.fill(bytes, (byte) ' ');
System.arraycopy(AsciiFuncs.getBytes(cardString), 0, bytes, 0, cardString.length());
HeaderCard rereadCard = new HeaderCard(new BufferedDataInputStream(new ByteArrayInputStream(bytes)));

assertEquals(cardValue, rereadCard.getValue());
assertEquals(headerCard.getValue(), rereadCard.getValue());
assertEquals(cardComment, headerCard.getComment());
Expand Down Expand Up @@ -487,7 +487,7 @@ public void testBadHeader() throws Exception {
SafeClose.close(f);
}
}


@Test
public void testHeaderCommentsDrift() throws Exception {
Expand Down Expand Up @@ -530,7 +530,7 @@ public void testHeaderCommentsDrift() throws Exception {
@Test
public void testHierachKeyWordParsing() {
FitsFactory.setUseHierarch(true);

String keyword = HeaderCard.create("HIERARCH test this = 'bla bla' ").getKey();
assertEquals("HIERARCH.TEST.THIS", keyword);

Expand Down Expand Up @@ -657,11 +657,11 @@ public void testUpdateHeaderComments() throws Exception {
SafeClose.close(f);
}
}

@Test
public void orderTest() throws Exception {
Header h = new Header();

// Start with an 'existing' header
h.addValue("BLAH1", 0, "");
h.addValue("BLAH2", 0, "");
Expand All @@ -670,8 +670,8 @@ public void orderTest() throws Exception {
h.addValue("MARKER", 0, "");
h.addValue("BLAH4", 0, "");
h.addValue("KEY2", 0, "");


// Now insert some keys before MARKER
h.findCard("MARKER");
h.addValue("KEY1", 1, "");
Expand All @@ -680,21 +680,21 @@ public void orderTest() throws Exception {
h.addValue("KEY4", 1, "");
h.addValue("KEY5", 1, "");


// Now do an in-place update and a deletion, which should not affect
// the position. The position should remain before MARKER.
h.updateLine("BLAH2", new HeaderCard("BLAH2A", 1, ""));
h.deleteKey("BLAH1");
h.addValue("KEY6", 1, "");

// Use updateLine for a non-existent key. This should result in
// adding a new card at the current position
h.updateLine("KEY7", new HeaderCard("KEY7", 1, ""));

// Check to that the keys appear in the expected order...
Cursor<String, HeaderCard> c = h.iterator();
c.setKey("KEY1");

for(int i=1; i<=7; i++) {
HeaderCard card = c.next();
assertEquals("KEY" + i, card.getKey());
Expand Down Expand Up @@ -747,7 +747,7 @@ public void addValueTests() throws Exception {
assertEquals(hdr.getDoubleValue(CTYPE2.name()), 5.0, 0.000001);
assertEquals(hdr.getDoubleValue(CTYPE2), 5.0, 0.000001);
assertEquals(hdr.getDoubleValue("ZZZ", -1.0), -1.0, 0.000001);

hdr.addValue(CTYPE2.name(), BigDecimal.valueOf(5.0), "nothing special");
assertEquals(hdr.getDoubleValue(CTYPE2.name()), 5.0, 0.000001);
assertEquals(hdr.getDoubleValue(CTYPE2, -1d), 5.0, 0.000001);
Expand Down Expand Up @@ -879,7 +879,7 @@ private Header invalidHeaderTests() throws HeaderCardException {
iterator.add(new HeaderCard(NAXIS.name(), 1, ""));
Assert.assertEquals(0, header.getSize());
header.addValue("END", "", "");

Assert.assertEquals(2880, header.getSize());
return header;
}
Expand Down Expand Up @@ -980,7 +980,9 @@ public void testHierarchLongStringIssue44() throws Exception {
*/
try {
f = new Fits(filename);

Header headerRewriter = f.getHDU(0).getHeader();

assertEquals("aaaaaaaabbbbbbbbbcccccccccccdddddddddddeeeeeeeeeee", headerRewriter.findCard("HIERARCH.TEST.THIS.LONG.HEADER").getValue());
for (int index = 1; index < 60; index++) {
StringBuilder buildder = new StringBuilder();
Expand Down