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Java library for reading and writing FITS files. FITS, the Flexible Image Transport System, is the format commonly used in the archiving and transport of astronomical data.
/*
* #%L
* nom.tam FITS library
* %%
* Copyright (C) 2004 - 2024 nom-tam-fits
* %%
* This is free and unencumbered software released into the public domain.
*
* Anyone is free to copy, modify, publish, use, compile, sell, or
* distribute this software, either in source code form or as a compiled
* binary, for any purpose, commercial or non-commercial, and by any
* means.
*
* In jurisdictions that recognize copyright laws, the author or authors
* of this software dedicate any and all copyright interest in the
* software to the public domain. We make this dedication for the benefit
* of the public at large and to the detriment of our heirs and
* successors. We intend this dedication to be an overt act of
* relinquishment in perpetuity of all present and future rights to this
* software under copyright law.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
* OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
* #L%
*/
package nom.tam.fits;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.util.Locale;
import java.util.StringTokenizer;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.regex.Pattern;
import nom.tam.util.ComplexValue;
import nom.tam.util.FlexFormat;
import static nom.tam.fits.header.NonStandard.HIERARCH;
import static nom.tam.fits.header.Standard.CONTINUE;
/**
*
* Converts a single 80-character wide FITS header record into a header card. See {@link HeaderCard#create(String)} for
* a description of the rules that guide parsing.
*
*
* When parsing header records that violate FITS standards, the violations can be logged or will throw appropriate
* excpetions (depending on the severity of the standard violation and whether
* {@link FitsFactory#setAllowHeaderRepairs(boolean)} is enabled or not. The logging of violations is disabled by
* default, but may be controlled via {@link Header#setParserWarningsEnabled(boolean)}.
*
*
* @author Attila Kovacs
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
* @see Header#setParserWarningsEnabled(boolean)
*/
class HeaderCardParser {
private static final Logger LOG = Logger.getLogger(HeaderCardParser.class.getName());
static {
// Do not log warnings by default.
LOG.setLevel(Level.SEVERE);
}
/** regexp for IEEE floats */
private static final Pattern DECIMAL_REGEX = Pattern.compile("[+-]?\\d+(\\.\\d*)?([dDeE][+-]?\\d+)?");
/** regexp for complex numbers */
private static final Pattern COMPLEX_REGEX = Pattern
.compile("\\(\\s*" + DECIMAL_REGEX + "\\s*,\\s*" + DECIMAL_REGEX + "\\s*\\)");
/** regexp for decimal integers. */
private static final Pattern INT_REGEX = Pattern.compile("[+-]?\\d+");
/** The header line (usually 80-character width), which to parse. */
private String line;
/**
* the value of the card. (trimmed and standardized with . in HIERARCH)
*/
private String key = null;
/**
* the value of the card. (trimmed)
*/
private String value = null;
/**
* the comment specified with the value.
*/
private String comment = null;
/**
* was the value quoted?
*/
private Class type = null;
/**
* The position in the string that right after the last character processed by this parser
*/
private int parsePos = 0;
/**
* Instantiates a new parser for a FITS header line.
*
* @param line a line in the FITS header, normally exactly 80-characters wide (but need not
* be).
*
* @see #getKey()
* @see #getValue()
* @see #getComment()
* @see #isString()
*
* @throws UnclosedQuoteException if there is a missing end-quote and header repairs aren't allowed.
* @throws IllegalArgumentException if the record contained neither a key or a value.
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
*/
HeaderCardParser(String line) throws UnclosedQuoteException, IllegalArgumentException {
this.line = line;
// TODO HeaderCard never calls this with a null argument, so the check below is dead code here...
// if (line == null) {
// throw new IllegalArgumentException("Cannot parse null string");
// }
parseKey();
parseValue();
parseComment();
}
/**
* Returns the keyword component of the parsed header line. If the processing of HIERARCH keywords is enabled, it
* may be a `HIERARCH` style long key with the components separated by dots (e.g.
* `HIERARCH.ORG.SYSTEM.SUBSYS.ELEMENT`). Otherwise, it will be a standard 0--8 character standard uppercase FITS
* keyword (including simply `HIERARCH` if {@link FitsFactory#setUseHierarch(boolean)} was set false).
*
* @return the FITS header keyword for the line.
*
* @see FitsFactory#setUseHierarch(boolean)
*/
String getKey() {
return key;
}
/**
* Returns the value component of the parsed header line.
*
* @return the value part of the line or null if the line contained no value.
*
* @see FitsFactory#setUseHierarch(boolean)
*/
String getValue() {
return value;
}
/**
* Returns the comment component of the parsed header line, with all leading and trailing spaces preserved.
*
* @return the comment part of the line or null if the line contained no comment.
*
* @see #getTrimmedComment()
*/
String getUntrimmedComment() {
return comment;
}
/**
* Returns the comment component of the parsed header line, with both leading and trailing spaces removed
*
* @return the comment part of the line or null if the line contained no comment.
*
* @see #getUntrimmedComment()
*/
String getTrimmedComment() {
return comment == null ? null : comment.trim();
}
/**
* Returns whether the line contained a quoted string value. By default, strings with missing end quotes are no
* considered string values, but rather as comments. To allow processing lines with missing quotes as string values,
* you must set {@link FitsFactory#setAllowHeaderRepairs(boolean)} to true prior to parsing a header
* line with the missing end quote.
*
* @return true if the value was quoted.
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
*/
boolean isString() {
if (type == null) {
return false;
}
return String.class.isAssignableFrom(type);
}
/**
*
* Returns the inferred Java class for the value stored in the header record, such as a {@link String} class, a
* {@link Boolean} class, an integer type ({@link Integer}, {@link Long}, or {@link BigInteger}) class, a decimal
* type ({@link Float}, {@link Double}, or {@link BigDecimal}) class, a {@link ComplexValue} class, or
* null. For number types, it returns the 'smallest' type that can be used to represent the string
* value.
*
*
* Its an inferred type as the true underlying type that was used to create the value is lost. For example, the
* value 42 may have been written from any integer type, including byte or
* short, but this routine will guess it to be an int ({@link Integer} type. As such, it
* may not be equal to {@link HeaderCard#valueType()} from which the record was created, and hence should not be
* used for round-trip testing of type equality.
*
*
* @return the inferred type of the stored serialized (string) value, or null if the value does not
* seem to match any of the supported value types.
*
* @see HeaderCard#valueType()
*/
Class getInferredType() {
return type;
}
/**
* Parses a fits keyword from a card and standardizes it (trim, uppercase, and hierarch with dots).
*/
private void parseKey() {
/*
* AK: The parsing of headers should never be stricter that the writing, such that any header written by this
* library can be parsed back without errors. (And, if anything, the parsing should be more permissive to allow
* reading FITS produced by other libraries, which may be less stringent in their rules). The original
* implementation strongly enforced the ESO HIERARCH convention when reading, but not at all for writing. Here
* is a tolerant hierarch parser that will read back any hierarch key that was written by this library. The
* input FITS can use any space or even '.' to separate the hierarchies, and the hierarchical elements may
* contain any ASCII characters other than those used for separating. It is more in line with what we do with
* standard keys too.
*/
// Find the '=' in the line, if any...
int iEq = line.indexOf('=');
// The stem is in the first 8 characters or what precedes an '=' character
// before that.
int endStem = (iEq >= 0 && iEq <= HeaderCard.MAX_KEYWORD_LENGTH) ? iEq : HeaderCard.MAX_KEYWORD_LENGTH;
endStem = Math.min(line.length(), endStem);
String rawStem = line.substring(0, endStem).trim();
// Check for space at the start of the keyword...
if (endStem > 0 && !rawStem.isEmpty()) {
if (Character.isSpaceChar(line.charAt(0))) {
LOG.warning("[" + sanitize(rawStem) + "] Non-standard starting with a space (trimming).");
}
}
String stem = rawStem.toUpperCase();
if (!stem.equals(rawStem)) {
LOG.warning("[" + sanitize(rawStem) + "] Non-standard lower-case letter(s) in base keyword.");
}
key = stem;
parsePos = endStem;
// If not using HIERARCH, then be very resilient, and return whatever key the first 8 chars make...
// If the line does not have an '=', can only be a simple key
// If it's not a HIERARCH keyword, then return the simple key.
if (!FitsFactory.getUseHierarch() || (iEq < 0) || !stem.equals(HIERARCH.key())) {
return;
}
// Compose the hierarchical key...
StringTokenizer tokens = new StringTokenizer(line.substring(stem.length(), iEq), " \t\r\n.");
StringBuilder builder = new StringBuilder(stem);
while (tokens.hasMoreTokens()) {
String token = tokens.nextToken();
parsePos = line.indexOf(token, parsePos) + token.length();
// Add a . to separate hierarchies
builder.append('.');
builder.append(token);
}
key = builder.toString();
if (HIERARCH.key().equals(key)) {
// The key is only HIERARCH, without a hierarchical keyword after it...
LOG.warning("HIERARCH base keyword without HIERARCH-style long key after it.");
return;
}
if (!FitsFactory.getHierarchFormater().isCaseSensitive()) {
key = key.toUpperCase(Locale.US);
}
try {
HeaderCard.validateKey(key);
} catch (IllegalArgumentException e) {
LOG.warning(e.getMessage());
}
}
/**
* Advances the parse position to skip any spaces at the current parse position, and returns whether there is
* anything left in the line after the spaces...
*
* @return true if there is more non-space characters in the string, otherwise false
*/
private boolean skipSpaces() {
for (; parsePos < line.length(); parsePos++) {
if (!Character.isSpaceChar(line.charAt(parsePos))) {
// Line has non-space characters left to parse...
return true;
}
}
// nothing left to parse.
return false;
}
/**
* Parses the comment components starting from the current parse position. After this call the parse position is set
* to the end of the string. The leading '/' (if found) is not included in the comment.
*/
private void parseComment() {
if (!skipSpaces()) {
// nothing left to parse.
return;
}
// if no value, then everything is comment from here on...
if (value != null) {
if (line.charAt(parsePos) == '/') {
// Skip the '/' itself, the comment is whatever is after it.
parsePos++;
} else {
// Junk after a string value -- interpret it as the start of the comment...
LOG.warning("[" + sanitize(getKey()) + "] Junk after value (included in the comment).");
}
}
comment = line.substring(parsePos);
parsePos = line.length();
try {
HeaderCard.validateChars(comment);
} catch (IllegalArgumentException e) {
LOG.warning("[" + sanitize(getKey()) + "]: " + e.getMessage());
}
}
/**
* Parses the value component from the current parse position. The parse position is advanced to the first character
* after the value specification in the line. If the header line does not contain a value component, then the value
* field of this object is set to null.
*
* @throws UnclosedQuoteException if there is a missing end-quote and header repairs aren't allowed.
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
*/
private void parseValue() throws UnclosedQuoteException {
if (key.isEmpty() || !skipSpaces()) {
// nothing left to parse.
return;
}
if (CONTINUE.key().equals(key)) {
parseValueBody();
} else if (line.charAt(parsePos) == '=') {
if (parsePos < HeaderCard.MAX_KEYWORD_LENGTH) {
LOG.warning("[" + sanitize(key) + "] assigmment before byte " + (HeaderCard.MAX_KEYWORD_LENGTH + 1)
+ " for key '" + sanitize(key) + "'.");
}
if (parsePos + 1 >= line.length()) {
LOG.warning("[" + sanitize(key) + "] Record ends with '='.");
} else if (line.charAt(parsePos + 1) != ' ') {
LOG.warning("[" + sanitize(key) + "] Missing required standard space after '='.");
}
if (parsePos > HeaderCard.MAX_KEYWORD_LENGTH) {
// equal sign = after the 9th char -- only supported with hierarch keys...
if (!key.startsWith(HIERARCH.key() + ".")) {
LOG.warning("[" + sanitize(key) + "] Possibly misplaced '=' (after byte 9).");
// It's not a HIERARCH key
return;
}
}
parsePos++;
parseValueBody();
}
try {
HeaderCard.validateChars(value);
} catch (IllegalArgumentException e) {
LOG.warning("[" + sanitize(getKey()) + "] " + e.getMessage());
}
}
/**
* Parses the value body from the current parse position. The parse position is advanced to the first character
* after the value specification in the line. If the header line does not contain a value component, then the value
* field of this object is set to null.
*
* @throws UnclosedQuoteException if there is a missing end-quote and header repairs aren't allowed.
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
*/
private void parseValueBody() throws UnclosedQuoteException {
if (!skipSpaces()) {
// nothing left to parse.
return;
}
if (isNextQuote()) {
// Parse as a string value, or else throw an exception.
parseStringValue();
} else {
int end = line.indexOf('/', parsePos);
if (end < 0) {
end = line.length();
}
value = line.substring(parsePos, end).trim();
parsePos = end;
type = getInferredValueType(key, value);
}
}
/**
* Checks if the next character, at the current parse position, is a single quote.
*
* @return true if the next character on the line exists and is a single quote, otherwise
* false.
*/
private boolean isNextQuote() {
if (parsePos >= line.length()) {
// nothing left to parse.
return false;
}
return line.charAt(parsePos) == '\'';
}
/**
* Returns the string fom a parsed string value component, with trailing spaces removed. It preserves leading
* spaces.
*
* @param buf the parsed string value.
*
* @return the string value with trailing spaces removed.
*/
private static String getNoTrailingSpaceString(StringBuilder buf) {
int to = buf.length();
// Remove trailing spaces only!
while (--to >= 0) {
if (!Character.isSpaceChar(buf.charAt(to))) {
break;
}
}
return to < 0 ? "" : buf.substring(0, to + 1);
}
/**
* Parses a quoted string value starting at the current parse position. If successful, the parse position is updated
* to after the string. Otherwise, the parse position is advanced only to skip leading spaces starting from the
* input position.
*
* @throws UnclosedQuoteException if there is a missing end-quote and header repairs aren't allowed.
*
* @see FitsFactory#setAllowHeaderRepairs(boolean)
*/
private void parseStringValue() throws UnclosedQuoteException {
type = String.class;
StringBuilder buf = new StringBuilder(HeaderCard.MAX_VALUE_LENGTH);
// Build the string value, up to the end quote and paying attention to double
// quotes inside the string, which are translated to single quotes within
// the string value itself.
for (++parsePos; parsePos < line.length(); parsePos++) {
if (isNextQuote()) {
parsePos++;
if (!isNextQuote()) {
// Closing single quote;
value = getNoTrailingSpaceString(buf);
return;
}
}
buf.append(line.charAt(parsePos));
}
// String with missing end quote
if (!FitsFactory.isAllowHeaderRepairs()) {
throw new UnclosedQuoteException(line);
}
LOG.warning("[" + sanitize(key) + "] Ignored missing end quote (value parsed to end of record).");
value = getNoTrailingSpaceString(buf);
}
/**
* Returns the inferred Java class for the specified value. See {@link #getInferredType()} for a more detailed
* description.
*
* @param value the serialized (string) representation of a FITS header value.
*
* @return the inferred type of the specified serialized (string) value, or null if the value
* does not seem to match any of the supported value types. null values default to
* Boolean.class.
*/
private static Class getInferredValueType(String key, String value) {
// TODO We never call this with null locally, so the following check is dead code here...
// if (value == null) {
// return Boolean.class;
// }
if (value.isEmpty()) {
LOG.warning("[" + sanitize(key) + "] Null non-string value (defaulted to Boolean.class).");
return Boolean.class;
}
String trimmedValue = value.trim().toUpperCase();
if ("T".equals(trimmedValue) || "F".equals(trimmedValue)) {
return Boolean.class;
}
if (INT_REGEX.matcher(trimmedValue).matches()) {
return getIntegerType(trimmedValue);
}
if (DECIMAL_REGEX.matcher(trimmedValue).matches()) {
return getDecimalType(trimmedValue);
}
if (COMPLEX_REGEX.matcher(trimmedValue).matches()) {
return ComplexValue.class;
}
LOG.warning("[" + sanitize(key) + "] Unrecognised non-string value type '" + sanitize(trimmedValue) + "'.");
return null;
}
/**
* Returns the guessed decimal type of a string representation of a decimal value.
*
* @param value the string representation of a decimal value.
*
* @return the The Java class ({@link Float}, {@link Double}, or {@link BigDecimal}) that can be used to
* represent the value with the precision provided.
*
* @see #getInferredValueType()
* @see #getIntegerType(String)
*/
private static Class getDecimalType(String value) {
value = value.toUpperCase(Locale.US);
boolean hasD = (value.indexOf('D') >= 0);
if (hasD) {
// Convert the Double Scientific Notation specified by FITS to pure IEEE.
value = value.replace('D', 'E');
}
BigDecimal big = new BigDecimal(value);
// Check for zero, and deal with it separately...
if (big.stripTrailingZeros().equals(BigDecimal.ZERO)) {
int decimals = big.scale();
if (decimals <= FlexFormat.FLOAT_DECIMALS) {
return hasD ? Double.class : Float.class;
}
if (decimals <= FlexFormat.DOUBLE_DECIMALS) {
return Double.class;
}
return BigDecimal.class;
}
// Now non-zero values...
int decimals = big.precision() - 1;
float f = big.floatValue();
if (decimals <= FlexFormat.FLOAT_DECIMALS && (f != 0.0F) && Float.isFinite(f)) {
return hasD ? Double.class : Float.class;
}
double d = big.doubleValue();
if (decimals <= FlexFormat.DOUBLE_DECIMALS && (d != 0.0) && Double.isFinite(d)) {
return Double.class;
}
return BigDecimal.class;
}
/**
* Returns the guessed integer type of a string representation of a integer value.
*
* @param value the string representation of an integer value.
*
* @return the The Java class ({@link Integer}, {@link Long}, or {@link BigInteger}) that can be used to
* represent the value with the number of digits provided.
*
* @see #getInferredValueType()
* @see #getDecimalType(String)
*/
private static Class getIntegerType(String value) {
int bits = new BigInteger(value).bitLength();
if (bits < Integer.SIZE) {
return Integer.class;
}
if (bits < Long.SIZE) {
return Long.class;
}
return BigInteger.class;
}
private static String sanitize(String text) {
return HeaderCard.sanitize(text);
}
static Logger getLogger() {
return LOG;
}
}
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