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diff --git a/doc/html/Compression.html b/doc/html/Compression.html deleted file mode 100644 index c3a2a45..0000000 --- a/doc/html/Compression.html +++ /dev/null @@ -1,409 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"> -<html> - <head> - <title>Compression</title> - </head> - - <body> - <h1>Compression</h1> - - <h2>1. Introduction</h2> - - <p>HDF5 supports compression of raw data by compression methods - built into the library or defined by an application. A - compression method is associated with a dataset when the dataset - is created and is applied independently to each storage chunk of - the dataset. - - The dataset must use the <code>H5D_CHUNKED</code> storage - layout. The library doesn't support compression for contiguous - datasets because of the difficulty of implementing random access - for partial I/O, and compact dataset compression is not - supported because it wouldn't produce significant results. - - <h2>2. Supported Compression Methods</h2> - - <p>The library identifies compression methods with small - integers, with values less than 16 reserved for use by NCSA and - values between 16 and 255 (inclusive) available for general - use. This range may be extended in the future if it proves to - be too small. - - <p> - <center> - <table align=center width="80%"> - <tr> - <th width="30%">Method Name</th> - <th width="70%">Description</th> - </tr> - - <tr valign=top> - <td><code>H5Z_NONE</code></td> - <td>The default is to not use compression. Specifying - <code>H5Z_NONE</code> as the compression method results - in better perfomance than writing a function that just - copies data because the library's I/O pipeline - recognizes this method and is able to short circuit - parts of the pipeline.</td> - </tr> - - <tr valign=top> - <td><code>H5Z_DEFLATE</code></td> - <td>The <em>deflate</em> method is the algorithm used by - the GNU <code>gzip</code>program. It's a combination of - a Huffman encoding followed by a 1977 Lempel-Ziv (LZ77) - dictionary encoding. The aggressiveness of the - compression can be controlled by passing an integer value - to the compressor with <code>H5Pset_deflate()</code> - (see below). In order for this compression method to be - used, the HDF5 library must be configured and compiled - in the presence of the GNU zlib version 1.1.2 or - later.</td> - </tr> - - <tr valign=top> - <td><code>H5Z_RES_<em>N</em></code></td> - <td>These compression methods (where <em>N</em> is in the - range two through 15, inclusive) are reserved by NCSA - for future use.</td> - </tr> - - <tr valign=top> - <td>Values of <em>N</em> between 16 and 255, inclusive</td> - <td>These values can be used to represent application-defined - compression methods. We recommend that methods under - testing should be in the high range and when a method is - about to be published it should be given a number near - the low end of the range (or even below 16). Publishing - the compression method and its numeric ID will make a - file sharable.</td> - </tr> - </table> - </center> - - <p>Setting the compression for a dataset to a method which was - not compiled into the library and/or not registered by the - application is allowed, but writing to such a dataset will - silently <em>not</em> compress the data. Reading a compressed - dataset for a method which is not available will result in - errors (specifically, <code>H5Dread()</code> will return a - negative value). The errors will be displayed in the - compression statistics if the library was compiled with - debugging turned on for the "z" package. See the - section on diagnostics below for more details. - - <h2>3. Application-Defined Methods</h2> - - <p>Compression methods 16 through 255 can be defined by an - application. As mentioned above, methods that have not been - released should use high numbers in that range while methods - that have been published will be assigned an official number in - the low region of the range (possibly less than 16). Users - should be aware that using unpublished compression methods - results in unsharable files. - - <p>A compression method has two halves: one have handles - compression and the other half handles uncompression. The - halves are implemented as functions - <code><em>method</em>_c</code> and - <code><em>method</em>_u</code> respectively. One should not use - the names <code>compress</code> or <code>uncompress</code> since - they are likely to conflict with other compression libraries - (like the GNU zlib). - - <p>Both the <code><em>method</em>_c</code> and - <code><em>method</em>_u</code> functions take the same arguments - and return the same values. They are defined with the type: - - <dl> - <dt><code>typedef size_t (*H5Z_func_t)(unsigned int - <em>flags</em>, size_t <em>cd_size</em>, const void - *<em>client_data</em>, size_t <em>src_nbytes</em>, const - void *<em>src</em>, size_t <em>dst_nbytes</em>, void - *<em>dst</em>/*out*/)</code> - <dd>The <em>flags</em> are an 8-bit vector which is stored in - the file and which is defined when the compression method is - defined. The <em>client_data</em> is a pointer to - <em>cd_size</em> bytes of configuration data which is also - stored in the file. The function compresses or uncompresses - <em>src_nbytes</em> from the source buffer <em>src</em> into - at most <em>dst_nbytes</em> of the result buffer <em>dst</em>. - The function returns the number of bytes written to the result - buffer or zero if an error occurs. But if a result buffer - overrun occurs the function should return a value at least as - large as <em>dst_size</em> (the uncompressor will see an - overrun only for corrupt data). - </dl> - - <p>The application associates the pair of functions with a name - and a method number by calling <code>H5Zregister()</code>. This - function can also be used to remove a compression method from - the library by supplying null pointers for the functions. - - <dl> - <dt><code>herr_t H5Zregister (H5Z_method_t <em>method</em>, - const char *<em>name</em>, H5Z_func_t <em>method_c</em>, - H5Z_func_t <em>method_u</em>)</code> - <dd>The pair of functions to be used for compression - (<em>method_c</em>) and uncompression (<em>method_u</em>) are - associated with a short <em>name</em> used for debugging and a - <em>method</em> number in the range 16 through 255. This - function can be called as often as desired for a particular - compression method with each call replacing the information - stored by the previous call. Sometimes it's convenient to - supply only one half of the compression, for instance in an - application that opens files for read-only. Compression - statistics for the method are accumulated across calls to this - function. - </dl> - - <p> - <center> - <table border align=center width="100%"> - <caption align=bottom><h4>Example: Registering an - Application-Defined Compression Method</h4></caption> - <tr> - <td> - <p>Here's a simple-minded "compression" method - that just copies the input value to the output. It's - similar to the <code>H5Z_NONE</code> method but - slower. Compression and uncompression are performed - by the same function. - - <p><code><pre> -size_t -bogus (unsigned int flags, - size_t cd_size, const void *client_data, - size_t src_nbytes, const void *src, - size_t dst_nbytes, void *dst/*out*/) -{ - memcpy (dst, src, src_nbytes); - return src_nbytes; -} - </pre></code> - - <p>The function could be registered as method 250 as - follows: - - <p><code><pre> -#define H5Z_BOGUS 250 -H5Zregister (H5Z_BOGUS, "bogus", bogus, bogus); - </pre></code> - - <p>The function can be unregistered by saying: - - <p><code><pre> -H5Zregister (H5Z_BUGUS, "bogus", NULL, NULL); - </pre></code> - - <p>Notice that we kept the name "bogus" even - though we unregistered the functions that perform the - compression and uncompression. This makes compression - statistics more understandable when they're printed. - </td> - </tr> - </table> - </center> - - <h2>4. Enabling Compression for a Dataset</h2> - - <p>If a dataset is to be compressed then the compression - information must be specified when the dataset is created since - once a dataset is created compression parameters cannot be - adjusted. The compression is specified through the dataset - creation property list (see <code>H5Pcreate()</code>). - - <dl> - <dt><code>herr_t H5Pset_deflate (hid_t <em>plist</em>, int - <em>level</em>)</code> - <dd>The compression method for dataset creation property list - <em>plist</em> is set to <code>H5Z_DEFLATE</code> and the - aggression level is set to <em>level</em>. The <em>level</em> - must be a value between one and nine, inclusive, where one - indicates no (but fast) compression and nine is aggressive - compression. - - <br><br> - <dt><code>int H5Pget_deflate (hid_t <em>plist</em>)</code> - <dd>If dataset creation property list <em>plist</em> is set to - use <code>H5Z_DEFLATE</code> compression then this function - will return the aggression level, an integer between one and - nine inclusive. If <em>plist</em> isn't a valid dataset - creation property list or it isn't set to use the deflate - method then a negative value is returned. - - <br><br> - <dt><code>herr_t H5Pset_compression (hid_t <em>plist</em>, - H5Z_method_t <em>method</em>, unsigned int <em>flags</em>, - size_t <em>cd_size</em>, const void *<em>client_data</em>)</code> - <dd>This is a catch-all function for defining compresion methods - and is intended to be called from a wrapper such as - <code>H5Pset_deflate()</code>. The dataset creation property - list <em>plist</em> is adjusted to use the specified - compression method. The <em>flags</em> is an 8-bit vector - which is stored in the file as part of the compression message - and passed to the compress and uncompress functions. The - <em>client_data</em> is a byte array of length - <em>cd_size</em> which is copied to the file and passed to the - compress and uncompress methods. - - <br><br> - <dt><code>H5Z_method_t H5Pget_compression (hid_t <em>plist</em>, - unsigned int *<em>flags</em>, size_t *<em>cd_size</em>, void - *<em>client_data</em>)</code> - <dd>This is a catch-all function for querying the compression - method associated with dataset creation property list - <em>plist</em> and is intended to be called from a wrapper - function such as <code>H5Pget_deflate()</code>. The - compression method (or a negative value on error) is returned - by value, and compression flags and client data is returned by - argument. The application should allocate the - <em>client_data</em> and pass its size as the - <em>cd_size</em>. On return, <em>cd_size</em> will contain - the actual size of the client data. If <em>client_data</em> - is not large enough to hold the entire client data then - <em>cd_size</em> bytes are copied into <em>client_data</em> - and <em>cd_size</em> is set to the total size of the client - data, a value larger than the original. - </dl> - - <p>It is possible to set the compression to a method which hasn't - been defined with <code>H5Zregister()</code> and which isn't - supported as a predefined method (for instance, setting the - method to <code>H5Z_DEFLATE</code> when the GNU zlib isn't - available). If that happens then data will be written to the - file in its uncompressed form and the compression statistics - will show failures for the compression. - - <p> - <center> - <table border align=center width="100%"> - <caption align=bottom><h4>Example: Statistics for an - Unsupported Compression Method</h4></caption> - <tr> - <td> - <p>If an application attempts to use an unsupported - method then the compression statistics will show large - numbers of compression errors and no data - uncompressed. - - <p><code><pre> -H5Z: compression statistics accumulated over life of library: - Method Total Overrun Errors User System Elapsed Bandwidth - ------ ----- ------- ------ ---- ------ ------- --------- - deflate-c 160000 0 160000 0.00 0.01 0.01 1.884e+07 - deflate-u 0 0 0 0.00 0.00 0.00 NaN - </pre></code> - - <p>This example is from a program that tried to use - <code>H5Z_DEFLATE</code> on a system that didn't have - the GNU zlib to write to a dataset and then read the - result. The read and write both succeeded but the - data was not compressed. - </td> - </tr> - </table> - </center> - - <h2>5. Compression Diagnostics</h2> - - <p>If the library is compiled with debugging turned on for the H5Z - layer (usually as a result of <code>configure --enable-debug=z</code>) - then statistics about data compression are printed when the - application exits normally or the library is closed. The - statistics are written to the standard error stream and include - two lines for each compression method that was used: the first - line shows compression statistics while the second shows - uncompression statistics. The following fields are displayed: - - <p> - <center> - <table align=center width="80%"> - <tr> - <th width="30%">Field Name</th> - <th width="70%">Description</th> - </tr> - - <tr valign=top> - <td>Method</td> - <td>This is the name of the method as defined with - <code>H5Zregister()</code> with the letters - "-c" or "-u" appended to indicate - compression or uncompression.</td> - </tr> - - <tr valign=top> - <td>Total</td> - <td>The total number of bytes compressed or decompressed - including buffer overruns and errors. Bytes of - non-compressed data are counted.</td> - </tr> - - <tr valign=top> - <td>Overrun</td> - <td>During compression, if the algorithm causes the result - to be at least as large as the input then a buffer - overrun error occurs. This field shows the total number - of bytes from the Total column which can be attributed to - overruns. Overruns for decompression can only happen if - the data has been corrupted in some way and will result - in failure of <code>H5Dread()</code>.</td> - </tr> - - <tr valign=top> - <td>Errors</td> - <td>If an error occurs during compression the data is - stored in it's uncompressed form; and an error during - uncompression causes <code>H5Dread()</code> to return - failure. This field shows the number of bytes of the - Total column which can be attributed to errors.</td> - </tr> - - <tr valign=top> - <td>User, System, Elapsed</td> - <td>These are the amount of user time, system time, and - elapsed time in seconds spent by the library to perform - compression. Elapsed time is sensitive to system - load. These times may be zero on operating systems that - don't support the required operations.</td> - </tr> - - <tr valign=top> - <td>Bandwidth</td> - <td>This is the compression bandwidth which is the total - number of bytes divided by elapsed time. Since elapsed - time is subject to system load the bandwidth numbers - cannot always be trusted. Furthermore, the bandwidth - includes overrun and error bytes which may significanly - taint the value.</td> - </tr> - </table> - </center> - - <p> - <center> - <table border align=center width="100%"> - <caption align=bottom><h4>Example: Compression - Statistics</h4></caption> - <tr> - <td> - <p><code><pre> -H5Z: compression statistics accumulated over life of library: - Method Total Overrun Errors User System Elapsed Bandwidth - ------ ----- ------- ------ ---- ------ ------- --------- - deflate-c 160000 200 0 0.62 0.74 1.33 1.204e+05 - deflate-u 120000 0 0 0.11 0.00 0.12 9.885e+05 - </pre></code> - </td> - </tr> - </table> - </center> - - <hr> - <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address> -<!-- Created: Fri Apr 17 13:39:35 EDT 1998 --> -<!-- hhmts start --> -Last modified: Fri Apr 17 16:15:21 EDT 1998 -<!-- hhmts end --> - </body> -</html> |