package nom.tam.fits.utilities;
   
   /*-
    * #%L
    * nom.tam FITS library
    * %%
    * Copyright (C) 1996 - 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.
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   * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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   */
  
  import java.io.DataInputStream;
  import java.io.EOFException;
  import java.io.IOException;
  import java.io.InputStream;
  import java.io.PipedInputStream;
  import java.io.PipedOutputStream;
  import java.nio.ByteBuffer;
  import java.nio.ByteOrder;
  import java.nio.IntBuffer;
  import java.nio.charset.StandardCharsets;
  import java.util.Arrays;
  
  import nom.tam.fits.BasicHDU;
  import nom.tam.fits.Data;
  import nom.tam.fits.FitsDate;
  import nom.tam.fits.FitsElement;
  import nom.tam.fits.FitsException;
  import nom.tam.fits.Header;
  import nom.tam.fits.HeaderCard;
  import nom.tam.util.FitsIO;
  import nom.tam.util.FitsOutputStream;
  import nom.tam.util.RandomAccess;
  
  import static nom.tam.fits.header.Checksum.CHECKSUM;
  import static nom.tam.fits.header.Checksum.DATASUM;
  
  /**
   * <p>
   * Helper class for dealing with FITS checksums. It implements the Seaman-Pence 32-bit 1's complement checksum
   * calculation. The implementation accumulates in two 64-bit integer values the low and high-order 16-bits of adjacent
   * 4-byte groups. A carry-over of bits are calculated only at the end of the loop. Given the use of 64-bit accumulators,
   * overflow would occur approximately at 280 billion short values.
   * </p>
   * <p>
   * This updated version of the class is a little more flexible than the prior incarnation. Specifically it allows
   * incremental updates to data sums, and provides methods for dealing with partial checksums (e.g. from modified
   * segments of the data), which may be used e.g. to calculate delta sums from changed blocks of data. The new
   * implementation provides methods for decoding encoded checksums, and for calculating checksums directly from files
   * without the need to read potentially huge data into RAM first, and for easily accessing the values stored in FITS
   * headers.
   * </p>
   * <p>
   * See <a href="http://arxiv.org/abs/1201.1345" target="@top">FITS Checksum Proposal</a>
   * </p>
   * <p>
   * Note this class probably should be in the <code>nom.tam.util</code> package, but somehow it ended up here and now we
   * are stuck with it.
   * </p>
   *
   * @author R J Mather, Tony Johnson, Attila Kovacs
   *
   * @see    nom.tam.fits.header.Checksum#CHECKSUM
   */
  public final class FitsCheckSum {
  
      private static final int CHECKSUM_BLOCK_SIZE = 4;
      private static final int CHECKSUM_BLOCK_MASK = CHECKSUM_BLOCK_SIZE - 1;
      private static final int CHECKSUM_STRING_SIZE = 16;
      private static final int SHIFT_2_BYTES = 16;
      private static final int MASK_2_BYTES = 0xffff;
      private static final int MASK_4_BYTES = 0xffffffff;
      private static final int MASK_BYTE = 0xff;
      private static final int ASCII_ZERO = '0';
      private static final int BUFFER_SIZE = 0x8000; // 32 kB
  
      private static final int[] SELECT_BYTE = {24, 16, 8, 0};
     private static final String EXCLUDE = ":;<=>?@[\\]^_`";
     private static final String CHECKSUM_DEFAULT = "0000000000000000";
 
     /** The expected checksum for a HDU that already contains a valid CHECKSUM keyword */
     public static final long HDU_CHECKSUM = 0xffffffffL;
 
     private FitsCheckSum() {
     }
 
     /**
      * Internal class for accumulating FITS checksums.
      */
     private static class Checksum {
         private long h, l;
 
         Checksum(long prior) {
             h = (prior >>> SHIFT_2_BYTES) & MASK_2_BYTES;
             l = prior & MASK_2_BYTES;
         }
 
         void add(int i) {
             h += i >>> SHIFT_2_BYTES;
             l += i & MASK_2_BYTES;
         }
 
         long getChecksum() {
             long hi = h & MASK_4_BYTES; // as unsigned 32-bit integer
             long lo = l & MASK_4_BYTES;
 
             for (;;) {
                 long hicarry = hi >>> SHIFT_2_BYTES;
                 long locarry = lo >>> SHIFT_2_BYTES;
                 if ((hicarry | locarry) == 0) {
                     break;
                 }
                 hi = (hi & MASK_2_BYTES) + locarry;
                 lo = (lo & MASK_2_BYTES) + hicarry;
             }
             return (hi << SHIFT_2_BYTES) | lo;
         }
 
     }
 
     private static class PipeWriter extends Thread {
         private Exception exception;
         private PipedOutputStream out;
         private FitsElement data;
 
         PipeWriter(FitsElement data, PipedInputStream in) throws IOException {
             this.data = data;
             out = new PipedOutputStream(in);
         }
 
         @Override
         public void run() {
             exception = null;
             try (FitsOutputStream fos = new FitsOutputStream(out)) {
                 if (data instanceof Header) {
                     ((Header) data).writeUnchecked(fos);
                 } else {
                     data.write(fos);
                 }
             } catch (Exception e) {
                 exception = e;
             }
         }
 
         public Exception getException() {
             return exception;
         }
     }
 
     /**
      * Computes the checksum for a byte array.
      *
      * @param  data the byte sequence for which to calculate a chekcsum
      *
      * @return      the 32bit checksum in the range from 0 to 2^32-1
      *
      * @see         #checksum(byte[], int, int)
      */
     public static long checksum(byte[] data) {
         return checksum(ByteBuffer.wrap(data));
     }
 
     /**
      * Computes the checksum for a segment of a byte array.
      *
      * @param  data the byte sequence for which to calculate a chekcsum
      * @param  from Stating index of bytes to include in checksum calculation
      * @param  to   Ending index (exclusive) of bytes to include in checksum
      *
      * @return      the 32-bit checksum in the range from 0 to 2^32-1
      *
      * @see         #checksum(RandomAccess, long, long)
      *
      * @since       1.17
      */
     public static long checksum(byte[] data, int from, int to) {
         return checksum(ByteBuffer.wrap(data, from, to));
     }
 
     /**
      * Computes the checksum from a buffer. This method can be used to calculate partial checksums for any data that can
      * be wrapped into a buffer one way or another. As such it is suitable for calculating partial sums from segments of
      * data that can be used to update datasums incrementally (e.g. by incrementing the datasum with the difference of
      * the checksum of the new data segment vs the old data segment), or for updating the checksum for new data that has
      * been added to the existing data (e.g. new rows in a binary table) as long as the modified data segment is a
      * multiple of 4 bytes.
      *
      * @param  data the buffer for which to calculate a (partial) checksum
      *
      * @return      the computed 32-bit unsigned checksum as a Java <code>long</code>
      *
      * @since       1.17
      *
      * @see         #checksum(Data)
      * @see         #checksum(Header)
      * @see         #sumOf(long...)
      * @see         #differenceOf(long, long)
      */
     public static long checksum(ByteBuffer data) {
         Checksum sum = new Checksum(0);
         if (!(data.remaining() % CHECKSUM_BLOCK_SIZE == 0)) {
             throw new IllegalArgumentException("fits blocks must always be divisible by 4");
         }
         data.position(0);
         data.order(ByteOrder.BIG_ENDIAN);
         IntBuffer iData = data.asIntBuffer();
         while (iData.hasRemaining()) {
             sum.add(iData.get());
         }
         return sum.getChecksum();
     }
 
     private static long checksum(InputStream in) throws IOException {
         Checksum sum = new Checksum(0);
         DataInputStream din = new DataInputStream(in);
 
         for (;;) {
             try {
                 sum.add(din.readInt());
             } catch (EOFException e) {
                 break;
             }
         }
 
         return sum.getChecksum();
     }
 
     private static long compute(final FitsElement data) throws FitsException {
         try (PipedInputStream in = new PipedInputStream()) {
             PipeWriter writer = new PipeWriter(data, in);
             writer.start();
 
             long sum = checksum(in);
 
             writer.join();
             if (writer.getException() != null) {
                 throw writer.getException();
             }
 
             return sum;
         } catch (Exception e) {
             if (e instanceof FitsException) {
                 throw (FitsException) e;
             }
             throw new FitsException("Exception while checksumming FITS element: " + e.getMessage(), e);
         }
     }
 
     /**
      * Computes the checksum for a FITS data object, e.g. to be used with {@link #setDatasum(Header, long)}. This call
      * will always calculate the checksum for the data in memory, and as such load deferred mode data into RAM as
      * necessary to perform the calculation. If you rather not load a huge amount of data into RAM, you might consider
      * using {@link #checksum(RandomAccess, long, long)} instead.
      * 
      * @deprecated               Use {@link BasicHDU#verifyIntegrity()} instead.
      *
      * @param      data          The FITS data object for which to calculate a checksum
      *
      * @return                   The checksum of the data
      *
      * @throws     FitsException If there was an error serializing the data object
      *
      * @see                      Data#calcChecksum()
      * @see                      BasicHDU#verifyDataIntegrity()
      * @see                      #checksum(RandomAccess, long, long)
      * @see                      #setDatasum(Header, long)
      * @see                      #setChecksum(BasicHDU)
      *
      * @since                    1.17
      */
     @Deprecated
     public static long checksum(Data data) throws FitsException {
         return compute(data);
     }
 
     /**
      * Computes the checksum for a FITS header. It returns the checksum for the header as is, without attempting to
      * validate the header, or modifying it in any way.
      * 
      * @deprecated               Use {@link BasicHDU#verifyIntegrity()} instead.
      *
      * @param      header        The FITS header object for which to calculate a checksum
      *
      * @return                   The checksum of the data
      *
      * @throws     FitsException If there was an error serializing the FITS header
      *
      * @see                      #checksum(Data)
      *
      * @since                    1.17
      */
     @Deprecated
     public static long checksum(Header header) throws FitsException {
         return compute(header);
     }
 
     /**
      * Calculates the FITS checksum for a HDU, e.g to compare agains the value stored under the CHECKSUM header keyword.
      * The
      *
      * @param      hdu           The Fits HDU for which to calculate a checksum, including both the header and data
      *                               segments.
      *
      * @return                   The calculated checksum for the given HDU.
      *
      * @throws     FitsException if there was an error accessing the contents of the HDU.
      *
      * @see                      BasicHDU#verifyIntegrity()
      * @see                      #checksum(Data)
      * @see                      #sumOf(long...)
      *
      * @deprecated               Use {@link BasicHDU#verifyIntegrity()} instead to verify checksums.
      *
      * @since                    1.17
      */
     @Deprecated
     public static long checksum(BasicHDU<?> hdu) throws FitsException {
         return sumOf(checksum(hdu.getHeader()), checksum(hdu.getData()));
     }
 
     /**
      * Computes the checksum directly from a region of a random access file, by buffering moderately sized chunks from
      * the file as necessary. The file may be very large, up to the full range of 64-bit addresses.
      *
      * @param  f           the random access file, from which to compute a checksum
      * @param  from        the starting position in the file, where to start computing the checksum from.
      * @param  size        the number of bytes in the file to include in the checksum calculation.
      *
      * @return             the checksum for the given segment of the file
      *
      * @throws IOException if there was a problem accessing the file during the computation.
      *
      * @since              1.17
      *
      * @see                #checksum(ByteBuffer)
      * @see                #checksum(Data)
      */
     public static long checksum(RandomAccess f, long from, long size) throws IOException {
         if (f == null) {
             return 0L;
         }
 
         int len = (int) Math.min(BUFFER_SIZE, size);
         byte[] buf = new byte[len];
         long oldpos = f.position();
         f.position(from);
         long sum = 0;
 
         while (size > 0) {
             len = (int) Math.min(BUFFER_SIZE, size);
             len = f.read(buf, 0, len);
             sum = sumOf(sum, checksum(buf, 0, len));
             from += len;
             size -= len;
         }
 
         f.position(oldpos);
         return sum;
     }
 
     /**
      * @deprecated       Use {@link #encode(long, boolean)} instead.
      *
      * @param      c     The calculated 32-bit (unsigned) checksum
      * @param      compl Whether to complement the raw checksum (as defined by the convention).
      *
      * @return           The encoded checksum, suitably encoded for use with the CHECKSUM header
      */
     @Deprecated
     public static String checksumEnc(final long c, final boolean compl) {
         return encode(c, compl);
     }
 
     /**
      * Encodes the complemented checksum. It is the same as <code>encode(checksum, true)</code>.
      *
      * @param  checksum The calculated 32-bit (unsigned) checksum
      *
      * @return          The encoded checksum, suitably encoded for use with the CHECKSUM header
      *
      * @see             #decode(String)
      *
      * @since           1.17
      */
     public static String encode(long checksum) {
         return encode(checksum, true);
     }
 
     /**
      * Encodes the given checksum as is or by its complement.
      *
      * @param  checksum The calculated 32-bit (unsigned) checksum
      * @param  compl    If <code>true</code> the complement of the specified value will be encoded. Otherwise, the value
      *                      as is will be encoded. (FITS normally uses the complemenyed value).
      *
      * @return          The encoded checksum, suitably encoded for use with the CHECKSUM header
      *
      * @see             #decode(String, boolean)
      *
      * @since           1.17
      */
     public static String encode(long checksum, boolean compl) {
         if (compl) {
             checksum = ~checksum & FitsIO.INTEGER_MASK;
         }
 
         final byte[] asc = new byte[CHECKSUM_STRING_SIZE];
         final byte[] ch = new byte[CHECKSUM_BLOCK_SIZE];
         final int sum = (int) checksum;
 
         for (int i = 0; i < CHECKSUM_BLOCK_SIZE; i++) {
             // each byte becomes four
             final int byt = MASK_BYTE & (sum >>> SELECT_BYTE[i]);
 
             Arrays.fill(ch, (byte) ((byt >>> 2) + ASCII_ZERO)); // quotient
             ch[0] += (byte) (byt & CHECKSUM_BLOCK_MASK); // remainder
 
             for (int j = 0; j < CHECKSUM_BLOCK_SIZE; j += 2) {
                 while (EXCLUDE.indexOf(ch[j]) >= 0 || EXCLUDE.indexOf(ch[j + 1]) >= 0) {
                     ch[j]++;
                     ch[j + 1]--;
                 }
             }
 
             for (int j = 0; j < CHECKSUM_BLOCK_SIZE; j++) {
                 int k = CHECKSUM_BLOCK_SIZE * j + i + 1;
                 k = (k < CHECKSUM_STRING_SIZE) ? k : 0; // rotate right
                 asc[k] = ch[j];
             }
         }
 
         return new String(asc, StandardCharsets.US_ASCII);
     }
 
     /**
      * Decodes an encoded (and complemented) checksum. The same as <code>decode(encoded, true)</code>, and the the
      * inverse of {@link #encode(long)}.
      *
      * @param  encoded                  The encoded checksum (16 character string)
      *
      * @return                          The unsigned 32-bit integer complemeted checksum.
      *
      * @throws IllegalArgumentException if the checksum string is invalid (wrong length or contains illegal ASCII
      *                                      characters)
      *
      * @see                             #encode(long)
      *
      * @since                           1.17
      */
     public static long decode(String encoded) throws IllegalArgumentException {
         return decode(encoded, true);
     }
 
     /**
      * Decodes an encoded checksum, complementing it as required. It is the inverse of {@link #encode(long, boolean)}.
      *
      * @param  encoded                  the encoded checksum (16 character string)
      * @param  compl                    whether to complement the checksum after decoding. Normally FITS uses
      *                                      complemented 32-bit checksums, so typically this optional argument should be
      *                                      <code>true</code>.
      *
      * @return                          The unsigned 32-bit integer checksum.
      *
      * @throws IllegalArgumentException if the checksum string is invalid (wrong length or contains illegal ASCII
      *                                      characters)
      *
      * @see                             #encode(long, boolean)
      *
      * @since                           1.17
      */
     public static long decode(String encoded, boolean compl) throws IllegalArgumentException {
         byte[] bytes = encoded.getBytes(StandardCharsets.US_ASCII);
         if (bytes.length != CHECKSUM_STRING_SIZE) {
             throw new IllegalArgumentException("Bad checksum with " + bytes.length + " chars (expected 16)");
         }
         // Rotate the bytes one to the left
         byte tmp = bytes[0];
         System.arraycopy(bytes, 1, bytes, 0, CHECKSUM_STRING_SIZE - 1);
         bytes[CHECKSUM_STRING_SIZE - 1] = tmp;
 
         for (int i = 0; i < CHECKSUM_STRING_SIZE; i++) {
             if (bytes[i] < ASCII_ZERO) {
                 throw new IllegalArgumentException("Bad checksum with illegal char " + Integer.toHexString(bytes[i])
                         + " at pos " + i + " (ASCII below 0x30)");
             }
             bytes[i] -= ASCII_ZERO;
         }
 
         ByteBuffer bb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN);
 
         long sum = (bb.getInt() + bb.getInt() + bb.getInt() + bb.getInt());
         return (compl ? ~sum : sum) & FitsIO.INTEGER_MASK;
     }
 
     /**
      * Calculates the total checksum from partial sums. For example combining checksums from a header and data segment
      * of a HDU, or for composing a data checksum from image tiles.
      *
      * @param  parts The partial sums that are to be added together.
      *
      * @return       The aggregated checksum as a 32-bit unsigned value.
      *
      * @see          #differenceOf(long, long)
      *
      * @since        1.17
      */
     public static long sumOf(long... parts) {
         Checksum sum = new Checksum(0);
 
         for (long part : parts) {
             sum.h += part >>> SHIFT_2_BYTES;
             sum.l += part & MASK_2_BYTES;
         }
         return sum.getChecksum();
     }
 
     /**
      * Subtracts a partial checksum from an aggregated total. One may use it, for example to update the datasum of a
      * large data, when modifying only a small segment of it. Thus, one would first subtract the checksum of the old
      * segment from tha prior datasum, and then add the checksum of the new data segment -- without hacing to
      * recalculate the checksum for the entire data again.
      *
      * @deprecated       Not foolproof, because of the carry over handling in checksums, some additionas are not
      *                       reversible. E.g. 0xffffffff + 0xffffffff = 0xffffffff, but 0xffffffff - 0xffffffff = 0;
      *
      * @param      total The total checksum.
      * @param      part  The partial checksum to be subtracted from the total.
      *
      * @return           The checksum after subtracting the partial sum, as a 32-bit unsigned value.
      *
      * @see              #sumOf(long...)
      *
      * @since            1.17
      */
     @Deprecated
     public static long differenceOf(long total, long part) {
         Checksum sum = new Checksum(total);
         sum.h -= part >>> SHIFT_2_BYTES;
         sum.l -= part & MASK_2_BYTES;
         return sum.getChecksum();
     }
 
     /**
      * Sets the <code>DATASUM</code> and <code>CHECKSUM</code> keywords in a FITS header, based on the provided checksum
      * of the data (calculated elsewhere) and the checksum calculated afresh for the header.
      *
      * @param  header        the header in which to store the <code>DATASUM</code> and <code>CHECKSUM</code> values
      * @param  datasum       the checksum for the data segment that follows the header in the HDU.
      *
      * @throws FitsException if there was an error serializing the header. Note, the method never throws any other type
      *                           of exception (including runtime exceptions), which are instead wrapped into a
      *                           <code>FitsException</code> when they occur.
      *
      * @see                  #setChecksum(BasicHDU)
      * @see                  #getStoredDatasum(Header)
      *
      * @since                1.17
      */
     public static void setDatasum(Header header, long datasum) throws FitsException {
         // Add the freshly calculated datasum to the header, before calculating the checksum
         header.seekTail();
         header.updateLine(DATASUM,
                 new HeaderCard(DATASUM.key(), Long.toString(datasum), "data checksum at " + FitsDate.getFitsDateString()));
 
         HeaderCard hc = header.getCard(CHECKSUM);
 
         if (hc != null) {
             hc.setValue(CHECKSUM_DEFAULT);
             hc.setComment("HDU checksum at " + FitsDate.getFitsDateString());
         } else {
             header.seekTail();
             header.addValue(CHECKSUM, CHECKSUM_DEFAULT);
         }
 
         long hsum = checksum(header);
         header.getCard(CHECKSUM).setValue(encode(sumOf(hsum, datasum)));
     }
 
     /**
      * Computes and sets the DATASUM and CHECKSUM keywords for a given HDU. This method calculates the sums from
      * scratch, and can be computationally expensive. There are less expensive incremental update methods that can be
      * used if the HDU already had sums recorded earlier, which need to be updated e.g. because there were modifications
      * to the header, or (parts of) the data.
      *
      * @param  hdu           the HDU to be updated.
      *
      * @throws FitsException if there was an error serializing the HDU. Note, the method never throws any other type of
      *                           exception (including runtime exceptions), which are instead wrapped into a
      *                           <code>FitsException</code> when they occur.
      *
      * @see                  #setDatasum(Header, long)
      * @see                  #sumOf(long...)
      * @see                  #differenceOf(long, long)
      */
     public static void setChecksum(BasicHDU<?> hdu) throws FitsException {
         try {
             setDatasum(hdu.getHeader(), checksum(hdu.getData()));
         } catch (FitsException e) {
             throw e;
         } catch (Exception e) {
             throw new FitsException("Exception while computing data checksum: " + e.getMessage(), e);
         }
     }
 
     /**
      * Returns the DATASUM value stored in a FITS header.
      *
      * @param  header        the FITS header
      *
      * @return               The stored datasum value (unsigned 32-bit integer) as a Java <code>long</code>.
      *
      * @throws FitsException if the header does not contain a <code>DATASUM</code> entry.
      *
      * @since                1.17
      *
      * @see                  #setDatasum(Header, long)
      * @see                  BasicHDU#getStoredDatasum()
      */
     public static long getStoredDatasum(Header header) throws FitsException {
         HeaderCard hc = header.getCard(DATASUM);
 
         if (hc == null) {
             throw new FitsException("Header does not have a DATASUM value.");
         }
 
         return hc.getValue(Long.class, 0L) & FitsIO.INTEGER_MASK;
     }
 
     /**
      * Returns the decoded CHECKSUM value stored in a FITS header.
      *
      * @deprecated               Not very useful, since it has no meaning other than ensuring that the checksum of the
      *                               HDU yields <code>(int) -1</code> (that is <code>0xffffffff</code>) after including
      *                               this value for the CHECKSUM keyword in the header. It will be removed in the
      *                               future.
      *
      * @param      header        the FITS header
      *
      * @return                   The decoded <code>CHECKSUM</code> value (unsigned 32-bit integer) recorded in the
      *                               header as a Java <code>long</code>.
      *
      * @throws     FitsException if the header does not contain a <code>CHECKSUM</code> entry, or it is invalid.
      *
      * @since                    1.17
      *
      * @see                      #getStoredDatasum(Header)
      * @see                      #setChecksum(BasicHDU)
      */
     @Deprecated
     public static long getStoredChecksum(Header header) throws FitsException {
         String encoded = header.getStringValue(CHECKSUM);
 
         if (encoded == null) {
             throw new FitsException("Header does not have a CHECKUM value.");
         }
 
         return decode(encoded);
     }
 }