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diff --git a/doxygen/examples/Filters.html b/doxygen/examples/Filters.html new file mode 100644 index 0000000..7054a3b --- /dev/null +++ b/doxygen/examples/Filters.html @@ -0,0 +1,450 @@ +<html> + <head> + <title>Filters</title> + <h1>Filters in HDF5</h1> + + <b>Note: Transient pipelines described in this document have not + been implemented.</b> + + <h2>Introduction</h2> + + <p>HDF5 allows chunked data to pass through user-defined filters + on the way to or from disk. The filters operate on chunks of an + <code>H5D_CHUNKED</code> dataset can be arranged in a pipeline + so output of one filter becomes the input of the next filter. + + </p><p>Each filter has a two-byte identification number (type + <code>H5Z_filter_t</code>) allocated by The HDF Group and can also be + passed application-defined integer resources to control its + behavior. Each filter also has an optional ASCII comment + string. + + </p> + <table> + <tbody><tr> + <th>Values for <code>H5Z_filter_t</code></th> + <th>Description</th> + </tr> + + <tr valign="top"> + <td><code>0-255</code></td> + <td>These values are reserved for filters predefined and + registered by the HDF5 library and of use to the general + public. They are described in a separate section + below.</td> + </tr> + + <tr valign="top"> + <td><code>256-511</code></td> + <td>Filter numbers in this range are used for testing only + and can be used temporarily by any organization. No + attempt is made to resolve numbering conflicts since all + definitions are by nature temporary.</td> + </tr> + + <tr valign="top"> + <td><code>512-65535</code></td> + <td>Reserved for future assignment. Please contact the + <a href="mailto:help@hdfgroup.org">HDF5 development team</a> + to reserve a value or range of values for + use by your filters.</td> + </tr></tbody></table> + + <h2>Defining and Querying the Filter Pipeline</h2> + + <p>Two types of filters can be applied to raw data I/O: permanent + filters and transient filters. The permanent filter pipeline is + defined when the dataset is created while the transient pipeline + is defined for each I/O operation. During an + <code>H5Dwrite()</code> the transient filters are applied first + in the order defined and then the permanent filters are applied + in the order defined. For an <code>H5Dread()</code> the + opposite order is used: permanent filters in reverse order, then + transient filters in reverse order. An <code>H5Dread()</code> + must result in the same amount of data for a chunk as the + original <code>H5Dwrite()</code>. + + </p><p>The permanent filter pipeline is defined by calling + <code>H5Pset_filter()</code> for a dataset creation property + list while the transient filter pipeline is defined by calling + that function for a dataset transfer property list. + + </p><dl> + <dt><code>herr_t H5Pset_filter (hid_t <em>plist</em>, + H5Z_filter_t <em>filter</em>, unsigned int <em>flags</em>, + size_t <em>cd_nelmts</em>, const unsigned int + <em>cd_values</em>[])</code> + </dt><dd>This function adds the specified <em>filter</em> and + corresponding properties to the end of the transient or + permanent output filter pipeline (depending on whether + <em>plist</em> is a dataset creation or dataset transfer + property list). The <em>flags</em> argument specifies certain + general properties of the filter and is documented below. The + <em>cd_values</em> is an array of <em>cd_nelmts</em> integers + which are auxiliary data for the filter. The integer values + will be stored in the dataset object header as part of the + filter information. + </dd><dt><code>int H5Pget_nfilters (hid_t <em>plist</em>)</code> + </dt><dd>This function returns the number of filters defined in the + permanent or transient filter pipeline depending on whether + <em>plist</em> is a dataset creation or dataset transfer + property list. In each pipeline the filters are numbered from + 0 through <em>N</em>-1 where <em>N</em> is the value returned + by this function. During output to the file the filters of a + pipeline are applied in increasing order (the inverse is true + for input). Zero is returned if there are no filters in the + pipeline and a negative value is returned for errors. + </dd><dt><code>H5Z_filter_t H5Pget_filter (hid_t <em>plist</em>, + int <em>filter_number</em>, unsigned int *<em>flags</em>, + size_t *<em>cd_nelmts</em>, unsigned int + *<em>cd_values</em>, size_t namelen, char name[])</code> + </dt><dd>This is the query counterpart of + <code>H5Pset_filter()</code> and returns information about a + particular filter number in a permanent or transient pipeline + depending on whether <em>plist</em> is a dataset creation or + dataset transfer property list. On input, <em>cd_nelmts</em> + indicates the number of entries in the <em>cd_values</em> + array allocated by the caller while on exit it contains the + number of values defined by the filter. The + <em>filter_number</em> should be a value between zero and + <em>N</em>-1 as described for <code>H5Pget_nfilters()</code> + and the function will return failure (a negative value) if the + filter number is out of range. If <em>name</em> is a pointer + to an array of at least <em>namelen</em> bytes then the filter + name will be copied into that array. The name will be null + terminated if the <em>namelen</em> is large enough. The + filter name returned will be the name appearing in the file or + else the name registered for the filter or else an empty string. + </dd></dl> + + <p>The flags argument to the functions above is a bit vector of + the following fields: + + </p> + <table> + <tbody><tr> + <th>Values for <em>flags</em></th> + <th>Description</th> + </tr> + + <tr valign="top"> + <td><code>H5Z_FLAG_OPTIONAL</code></td> + <td>If this bit is set then the filter is optional. If + the filter fails (see below) during an + <code>H5Dwrite()</code> operation then the filter is + just excluded from the pipeline for the chunk for which + it failed; the filter will not participate in the + pipeline during an <code>H5Dread()</code> of the chunk. + This is commonly used for compression filters: if the + compression result would be larger than the input then + the compression filter returns failure and the + uncompressed data is stored in the file. If this bit is + clear and a filter fails then the + <code>H5Dwrite()</code> or <code>H5Dread()</code> also + fails.</td> + </tr> + </tbody></table> + + <h2>Defining Filters</h2> + + <p>Each filter is bidirectional, handling both input and output to + the file, and a flag is passed to the filter to indicate the + direction. In either case the filter reads a chunk of data from + a buffer, usually performs some sort of transformation on the + data, places the result in the same or new buffer, and returns + the buffer pointer and size to the caller. If something goes + wrong the filter should return zero to indicate a failure. + + </p><p>During output, a filter that fails or isn't defined and is + marked as optional is silently excluded from the pipeline and + will not be used when reading that chunk of data. A required + filter that fails or isn't defined causes the entire output + operation to fail. During input, any filter that has not been + excluded from the pipeline during output and fails or is not + defined will cause the entire input operation to fail. + + </p><p>Filters are defined in two phases. The first phase is to + define a function to act as the filter and link the function + into the application. The second phase is to register the + function, associating the function with an + <code>H5Z_filter_t</code> identification number and a comment. + + </p><dl> + <dt><code>typedef size_t (*H5Z_func_t)(unsigned int + <em>flags</em>, size_t <em>cd_nelmts</em>, const unsigned int + <em>cd_values</em>[], size_t <em>nbytes</em>, size_t + *<em>buf_size</em>, void **<em>buf</em>)</code> + </dt><dd>The <em>flags</em>, <em>cd_nelmts</em>, and + <em>cd_values</em> are the same as for the + <code>H5Pset_filter()</code> function with the additional flag + <code>H5Z_FLAG_REVERSE</code> which is set when the filter is + called as part of the input pipeline. The input buffer is + pointed to by <em>*buf</em> and has a total size of + <em>*buf_size</em> bytes but only <em>nbytes</em> are valid + data. The filter should perform the transformation in place if + possible and return the number of valid bytes or zero for + failure. If the transformation cannot be done in place then + the filter should allocate a new buffer with + <code>malloc()</code> and assign it to <em>*buf</em>, + assigning the allocated size of that buffer to + <em>*buf_size</em>. The old buffer should be freed + by calling <code>free()</code>. + + <br><br> + </dd><dt><code>herr_t H5Zregister (H5Z_filter_t <em>filter_id</em>, + const char *<em>comment</em>, H5Z_func_t + <em>filter</em>)</code> + </dt><dd>The <em>filter</em> function is associated with a filter + number and a short ASCII comment which will be stored in the + hdf5 file if the filter is used as part of a permanent + pipeline during dataset creation. + </dd></dl> + + <h2>Predefined Filters</h2> + + <p>If <code>zlib</code> version 1.1.2 or later was found + during configuration then the library will define a filter whose + <code>H5Z_filter_t</code> number is + <code>H5Z_FILTER_DEFLATE</code>. Since this compression method + has the potential for generating compressed data which is larger + than the original, the <code>H5Z_FLAG_OPTIONAL</code> flag + should be turned on so such cases can be handled gracefully by + storing the original data instead of the compressed data. The + <em>cd_nvalues</em> should be one with <em>cd_value[0]</em> + being a compression aggression level between zero and nine, + inclusive (zero is the fastest compression while nine results in + the best compression ratio). + + </p><p>A convenience function for adding the + <code>H5Z_FILTER_DEFLATE</code> filter to a pipeline is: + + </p><dl> + <dt><code>herr_t H5Pset_deflate (hid_t <em>plist</em>, unsigned + <em>aggression</em>)</code> + </dt><dd>The deflate compression method is added to the end of the + permanent or transient filter pipeline depending on whether + <em>plist</em> is a dataset creation or dataset transfer + property list. The <em>aggression</em> is a number between + zero and nine (inclusive) to indicate the tradeoff between + speed and compression ratio (zero is fastest, nine is best + ratio). + </dd></dl> + + <p>Even if the <code>zlib</code> isn't detected during + configuration the application can define + <code>H5Z_FILTER_DEFLATE</code> as a permanent filter. If the + filter is marked as optional (as with + <code>H5Pset_deflate()</code>) then it will always fail and be + automatically removed from the pipeline. Applications that read + data will fail only if the data is actually compressed; they + won't fail if <code>H5Z_FILTER_DEFLATE</code> was part of the + permanent output pipeline but was automatically excluded because + it didn't exist when the data was written. + + </p><p><code>zlib</code> can be acquired from + <code><a href="http://www.cdrom.com/pub/infozip/zlib/"> + http://www.cdrom.com/pub/infozip/zlib/</a></code>. + + </p><h2>Example</h2> + + <p>This example shows how to define and register a simple filter + that adds a checksum capability to the data stream. + + </p><p>The function that acts as the filter always returns zero + (failure) if the <code>md5()</code> function was not detected at + configuration time (left as an exercise for the reader). + Otherwise the function is broken down to an input and output + half. The output half calculates a checksum, increases the size + of the output buffer if necessary, and appends the checksum to + the end of the buffer. The input half calculates the checksum + on the first part of the buffer and compares it to the checksum + already stored at the end of the buffer. If the two differ then + zero (failure) is returned, otherwise the buffer size is reduced + to exclude the checksum. + + </p> + <table> + <tbody><tr> + <td> + <p><code></code></p><pre><code> + size_t + md5_filter(unsigned int flags, size_t cd_nelmts, + const unsigned int cd_values[], size_t nbytes, + size_t *buf_size, void **buf) + { + #ifdef HAVE_MD5 + unsigned char cksum[16]; + + if (flags & H5Z_REVERSE) { + /* Input */ + assert(nbytes>=16); + md5(nbytes-16, *buf, cksum); + + /* Compare */ + if (memcmp(cksum, (char*)(*buf)+nbytes-16, 16)) { + return 0; /*fail*/ + } + + /* Strip off checksum */ + return nbytes-16; + + } else { + /* Output */ + md5(nbytes, *buf, cksum); + + /* Increase buffer size if necessary */ + if (nbytes+16>*buf_size) { + *buf_size = nbytes + 16; + *buf = realloc(*buf, *buf_size); + } + + /* Append checksum */ + memcpy((char*)(*buf)+nbytes, cksum, 16); + return nbytes+16; + } + #else + return 0; /*fail*/ + #endif + } + </code></pre> + </td> + </tr> + </tbody></table> + + <p>Once the filter function is defined it must be registered so + the HDF5 library knows about it. Since we're testing this + filter we choose one of the <code>H5Z_filter_t</code> numbers + from the reserved range. We'll randomly choose 305. + + </p><p> + </p> + <table> + <tbody><tr> + <td> + <p><code></code></p><pre><code> + #define FILTER_MD5 305 + herr_t status = H5Zregister(FILTER_MD5, "md5 checksum", md5_filter); + </code></pre> + </td> + </tr> + </tbody></table> + + <p>Now we can use the filter in a pipeline. We could have added + the filter to the pipeline before defining or registering the + filter as long as the filter was defined and registered by time + we tried to use it (if the filter is marked as optional then we + could have used it without defining it and the library would + have automatically removed it from the pipeline for each chunk + written before the filter was defined and registered). + + </p><p> + </p> + <table> + <tbody><tr> + <td> + <p><code></code></p><pre><code> + hid_t dcpl = H5Pcreate(H5P_DATASET_CREATE); + hsize_t chunk_size[3] = {10,10,10}; + H5Pset_chunk(dcpl, 3, chunk_size); + H5Pset_filter(dcpl, FILTER_MD5, 0, 0, NULL); + hid_t dset = H5Dcreate(file, "dset", H5T_NATIVE_DOUBLE, space, dcpl); + </code></pre> + </td> + </tr> + </tbody></table> + + <h2>6. Filter 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 filter statistics 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 filter that was used: one for input and one + for output. The following fields are displayed: + + </p><p> + </p> + <table> + <tbody><tr> + <th>Field Name</th> + <th>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 characters + "< or ">" prepended to indicate + input or output.</td> + </tr> + + <tr valign="top"> + <td>Total</td> + <td>The total number of bytes processed by the filter + including errors. This is the maximum of the + <em>nbytes</em> argument or the return value. + </td></tr> + + <tr valign="top"> + <td>Errors</td> + <td>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 in the filter function. + 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 filter bandwidth which is the total + number of bytes processed divided by elapsed time. + Since elapsed time is subject to system load the + bandwidth numbers cannot always be trusted. + Furthermore, the bandwidth includes bytes attributed to + errors which may significanly taint the value if the + function is able to detect errors without much + expense.</td> + </tr> + </tbody></table> + + <p> + </p> + <table> + <caption align="bottom"> + <b>Example: Filter Statistics</b> + </caption> + <tbody><tr> + <td> + <p><code></code></p><pre><code>H5Z: filter statistics accumulated ov= + er life of library: + Method Total Errors User System Elapsed Bandwidth + ------ ----- ------ ---- ------ ------- --------- + >deflate 160000 40000 0.62 0.74 1.33 117.5 kBs + <deflate 120000 0 0.11 0.00 0.12 1.000 MBs + </code></pre> + </td> + </tr> + </tbody></table> + + <hr> + + + <p><a name="fn1">Footnote 1:</a> Dataset chunks can be compressed + through the use of filters. Developers should be aware that + reading and rewriting compressed chunked data can result in holes + in an HDF5 file. In time, enough such holes can increase the + file size enough to impair application or library performance + when working with that file. See + <a href="https://support.hdfgroup.org/HDF5/doc1.6/Performance.html#Freespace"> + Freespace Management</a> + in the chapter + <a href="https://support.hdfgroup.org/HDF5/doc1.6/Performance.html"> + Performance Analysis and Issues</a>.</p> +</html> |