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diff --git a/doc/html/Datasets.html b/doc/html/Datasets.html new file mode 100644 index 0000000..e0f9680 --- /dev/null +++ b/doc/html/Datasets.html @@ -0,0 +1,839 @@ +<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"> +<html> + <head> + <title>The Dataset Interface (H5D)</title> + </head> + + <body> + <h1>The Dataset Interface (H5D)</h1> + + <h2>1. Introduction</h2> + + <p>The purpose of the dataset interface is to provide a mechanism + to describe properties of datasets and to transfer data between + memory and disk. A dataset is composed of a collection of raw + data points and four classes of meta data to describe the data + points. The interface is hopefully designed in such a way as to + allow new features to be added without disrupting current + applications that use the dataset interface. + + <p>The four classes of meta data are: + + <dl> + <dt>Constant Meta Data + <dd>Meta data that is created when the dataset is created and + exists unchanged for the life of the dataset. For instance, + the data type of stored array elements is defined when the + dataset is created and cannot be subsequently changed. + + <dt>Persistent Meta Data + <dd>Meta data that is an integral and permanent part of a + dataset but can change over time. For instance, the size in + any dimension can increase over time if such an increase is + allowed when the dataset was created. + + <dt>Memory Meta Data + <dd>Meta data that exists to describe how raw data is organized + in the application's memory space. For instance, the data + type of elements in an application array might not be the same + as the data type of those elements as stored in the HDF5 file. + + <dt>Transport Meta Data + <dd>Meta data that is used only during the transfer of raw data + from one location to another. For instance, the number of + processes participating in a collective I/O request or hints + to the library to control caching of raw data. + </dl> + + <p>Each of these classes of meta data is handled differently by + the library although the same API might be used to create them. + For instance, the data type exists as constant meta data and as + memory meta data; the same API (the <code>H5T</code> API) is + used to manipulate both pieces of meta data but they're handled + by the dataset API (the <code>H5D</code> API) in different + manners. + + + + <h2>2. Storage Layout Properties</h2> + + <p>The dataset API partitions these terms on three orthogonal axes + (layout, compression, and external storage) and uses a + <em>dataset creation property list</em> to hold the various + settings and pass them through the dataset interface. This is + similar to the way HDF5 files are created with a file creation + property list. A dataset creation property list is always + derived from the default dataset creation property list (use + <code>H5Pcreate()</code> to get a copy of the default property + list) by modifying properties with various + <code>H5Pset_<em>property</em>()</code> functions. + + <dl> + <dt><code>herr_t H5Pset_layout (hid_t <em>plist_id</em>, + H5D_layout_t <em>layout</em>)</code> + <dd>The storage layout is a piece of constant meta data that + describes what method the library uses to organize the raw + data on disk. The default layout is contiguous storage. + + <br><br> + <dl> + <dt><code>H5D_COMPACT</code> + <dd>The raw data is presumably small and can be stored + directly in the object header. Such data is + non-extendible, non-compressible, non-sparse, and cannot + be stored externally. Most of these restrictions are + arbitrary but are enforced because of the small size of + the raw data. Storing data in this format eliminates the + disk seek/read request normally necessary to read raw + data. <b>This layout is not implemented yet.</b> + + <br><br> + <dt><code>H5D_CONTIGUOUS</code> + <dd>The raw data is large, non-extendible, non-compressible, + non-sparse, and can be stored externally. This is the + default value for the layout property. The term + <em>large</em> means that it may not be possible to hold + the entire dataset in memory. The non-compressibility is + a side effect of the data being large, contiguous, and + fixed-size at the physical level, which could cause + partial I/O requests to be extremely expensive if + compression were allowed. + + <br><br> + <dt><code>H5D_CHUNKED</code> + <dd>The raw data is large and can be extended in any + dimension at any time (provided the data space also allows + the extension). It may be sparse at the chunk level (each + chunk is non-sparse, but there might only be a few chunks) + and each chunk can be compressed and/or stored externally. + A dataset is partitioned into chunks so each chunk is the + same logical size. The chunks are indexed by a B-tree and + are allocated on demand (although it might be useful to be + able to preallocate storage for parts of a chunked array + to reduce contention for the B-tree in a parallel + environment). The chunk size must be defined with + <code>H5Pset_chunk()</code>. + + <br><br> + <dt><em>others...</em> + <dd>Other layout types may be defined later without breaking + existing code. However, to be able to correctly read or + modify data stored with one of these new layouts, the + application will need to be linked with a new version of + the library. This happens automatically on systems with + dynamic linking. + </dl> + </dl> + + <p>Once the general layout is defined, the user can define + properties of that layout. Currently, the only layout that has + user-settable properties is the <code>H5D_CHUNKED</code> layout, + which needs to know the dimensionality and chunk size. + + <dl> + <dt><code>herr_t H5Pset_chunk (hid_t <em>plist_id</em>, int + <em>ndims</em>, hsize_t <em>dim</em>[])</code> + <dd>This function defines the logical size of a chunk for + chunked layout. If the layout property is set to + <code>H5D_CHUNKED</code> and the chunk size is set to + <em>dim</em>. The number of elements in the <em>dim</em> array + is the dimensionality, <em>ndims</em>. One need not call + <code>H5Dset_layout()</code> when using this function since + the chunked layout is implied. + </dl> + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example: Chunked Storage</h4></caption> + <tr> + <td> + <p>This example shows how a two-dimensional dataset + is partitioned into chunks. The library can manage file + memory by moving the chunks around, and each chunk could be + compressed. The chunks are allocated in the file on demand + when data is written to the chunk. + <center> + <img alt="Chunked Storage" src="chunk1.gif"> + </center> + + <p><code><pre> +size_t hsize[2] = {1000, 1000}; +plist = H5Pcreate (H5P_DATASET_CREATE); +H5Pset_chunk (plist, 2, size); + </pre></code> + </td> + </tr> + </table> + </center> + + + <p>Although it is most efficient if I/O requests are aligned on chunk + boundaries, this is not a constraint. The application can perform I/O + on any set of data points as long as the set can be described by the + data space. The set on which I/O is performed is called the + <em>selection</em>. + + <h2>3. Compression Properties</h2> + + <p>Some types of storage layout allow data compression which is + defined by the functions described here. <b>Compression is not + implemented yet.</b> + + <dl> + <dt><code>herr_t H5Pset_compression (hid_t <em>plist_id</em>, + H5Z_method_t <em>method</em>)</code> + <dt><code>H5Z_method_t H5Pget_compression (hid_t + <em>plist_id</em>)</code> + <dd>These functions set and query the compression method that + is used to compress the raw data of a dataset. The + <em>plist_id</em> is a dataset creation property list. The + possible values for the compression method are: + + <br><br> + <dl> + <dt><code>H5Z_NONE</code> + <dd>This is the default and specifies that no compression is + to be performed. + + <br><br> + <dt><code>H5Z_DEFLATE</code> + <dd>This specifies that a variation of the Lempel-Ziv 1977 + (LZ77) encoding is used, the same encoding used by the + free GNU <code>gzip</code> program. + </dl> + + <br><br> + <dt><code>herr_t H5Pset_deflate (hid_t <em>plist_id</em>, + int <em>level</em>)</code> + <dt><code>int H5Pget_deflate (hid_t <em>plist_id</em>)</code> + <dd>These functions set or query the deflate level of + dataset creation property list <em>plist_id</em>. The + <code>H5Pset_deflate()</code> sets the compression method to + <code>H5Z_DEFLATE</code> and sets the compression level to + some integer between one and nine (inclusive). One results in + the fastest compression while nine results in the best + compression ratio. The default value is six if + <code>H5Pset_deflate()</code> isn't called. The + <code>H5Pget_deflate()</code> returns the compression level + for the deflate method, or negative if the method is not the + deflate method. + </dl> + + <h2>4. External Storage Properties</h2> + + <p>Some storage formats may allow storage of data across a set of + non-HDF5 files. Currently, only the <code>H5D_CONTIGUOUS</code> storage + format allows external storage. A set segments (offsets and sizes) in + one or more files is defined as an external file list, or <em>EFL</em>, + and the contiguous logical addresses of the data storage are mapped onto + these segments. + + <dl> + <dt><code>herr_t H5Pset_external (hid_t <em>plist</em>, const + char *<em>name</em>, off_t <em>offset</em>, hsize_t + <em>size</em>)</code> + <dd>This function adds a new segment to the end of the external + file list of the specified dataset creation property list. The + segment begins a byte <em>offset</em> of file <em>name</em> and + continues for <em>size</em> bytes. The space represented by this + segment is adjacent to the space already represented by the external + file list. The last segment in a file list may have the size + <code>H5F_UNLIMITED</em>. + + <br><br> + <dt><code>int H5Pget_external_count (hid_t <em>plist</em>)</code> + <dd>Calling this function returns the number of segments in an + external file list. If the dataset creation property list has no + external data then zero is returned. + + <br><br> + <dt><code>herr_t H5Pget_external (hid_t <em>plist</em>, int + <em>idx</em>, size_t <em>name_size</em>, char *<em>name</em>, off_t + *<em>offset</em>, hsize_t *<em>size</em>)</code> + <dd>This is the counterpart for the <code>H5Pset_external()</code> + function. Given a dataset creation property list and a zero-based + index into that list, the file name, byte offset, and segment size are + returned through non-null arguments. At most <em>name_size</em> + characters are copied into the <em>name</em> argument which is not + null terminated if the file name is longer than the supplied name + buffer (this is similar to <code>strncpy()</code>). + </dl> + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example: Multiple Segments</h4></caption> + <tr> + <td> + <p>This example shows how a contiguous, one-dimensional dataset + is partitioned into three parts and each of those parts is + stored in a segment of an external file. The top rectangle + represents the logical address space of the dataset + while the bottom rectangle represents an external file. + <center> + <img alt="Multiple Segments" src="extern1.gif"> + </center> + + <p><code><pre> +plist = H5Pcreate (H5P_DATASET_CREATE); +H5Pset_external (plist, "velocity.data", 3000, 1000); +H5Pset_external (plist, "velocity.data", 0, 2500); +H5Pset_external (plist, "velocity.data", 4500, 1500); + </pre></code> + + <p>One should note that the segments are defined in order of the + logical addresses they represent, not their order within the + external file. It would also have been possible to put the + segments in separate files. Care should be taken when setting + up segments in a single file since the library doesn't + automatically check for segments that overlap. + </td> + </tr> + </table> + </center> + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example: Multi-Dimensional</h4></caption> + <tr> + <td> + <p>This example shows how a contiguous, two-dimensional dataset + is partitioned into three parts and each of those parts is + stored in a separate external file. The top rectangle + represents the logical address space of the dataset + while the bottom rectangles represent external files. + <center> + <img alt="Multiple Dimensions" src="extern2.gif"> + </center> + + <p><code><pre> +plist = H5Pcreate (H5P_DATASET_CREATE); +H5Pset_external (plist, "scan1.data", 0, 24); +H5Pset_external (plist, "scan2.data", 0, 24); +H5Pset_external (plist, "scan3.data", 0, 16); + </pre></code> + + <p>The library maps the multi-dimensional array onto a linear + address space like normal, and then maps that address space + into the segments defined in the external file list. + </td> + </tr> + </table> + </center> + + <p>The segments of an external file can exist beyond the end of the + file. The library reads that part of a segment as zeros. When writing + to a segment that exists beyond the end of a file, the file is + automatically extended. Using this feature, one can create a segment + (or set of segments) which is larger than the current size of the + dataset, which allows to dataset to be extended at a future time + (provided the data space also allows the extension). + + <p>All referenced external data files must exist before performing raw + data I/O on the dataset. This is normally not a problem since those + files are being managed directly by the application, or indirectly + through some other library. + + + <h2>5. Data Type</h2> + + <p>Raw data has a constant data type which describes the data type + of the raw data stored in the file, and a memory data type that + describes the data type stored in application memory. Both data + types are manipulated with the <a + href="Datatypes.html"><code>H5T</code></a> API. + + <p>The constant file data type is associated with the dataset when + the dataset is created in a manner described below. Once + assigned, the constant datatype can never be changed. + + <p>The memory data type is specified when data is transferred + to/from application memory. In the name of data sharability, + the memory data type must be specified, but can be the same + type identifier as the constant data type. + + <p>During dataset I/O operations, the library translates the raw + data from the constant data type to the memory data type or vice + versa. Structured data types include member offsets to allow + reordering of struct members and/or selection of a subset of + members and array data types include index permutation + information to allow things like transpose operations (<b>the + prototype does not support array reordering</b>) Permutations + are relative to some extrinsic descritpion of the dataset. + + + + <h2>6. Data Space</h2> + + <p>The dataspace of a dataset defines the number of dimensions + and the size of each dimension and is manipulated with the + <code>H5S</code> API. The <em>simple</em> dataspace consists of + maximum dimension sizes and actual dimension sizes, which are + usually the same. However, maximum dimension sizes can be the + constant <code>H5D_UNLIMITED</code> in which case the actual + dimension size can be incremented with calls to + <code>H5Dextend()</code>. The maximium dimension sizes are + constant meta data while the actual dimension sizes are + persistent meta data. Initial actual dimension sizes are + supplied at the same time as the maximum dimension sizes when + the dataset is created. + + <p>The dataspace can also be used to define partial I/O + operations. Since I/O operations have two end-points, the raw + data transfer functions take two data space arguments: one which + describes the application memory data space or subset thereof + and another which describes the file data space or subset + thereof. + + + <h2>7. Setting Constant or Persistent Properties</h2> + + <p>Each dataset has a set of constant and persistent properties + which describe the layout method, pre-compression + transformation, compression method, data type, external storage, + and data space. The constant properties are set as described + above in a dataset creation property list whose identifier is + passed to <code>H5Dcreate()</code>. + + <dl> + <dt><code>hid_t H5Dcreate (hid_t <em>file_id</em>, const char + *<em>name</em>, hid_t <em>type_id</em>, hid_t + <em>space_id</em>, hid_t <em>create_plist_id</em>)</code> + <dd>A dataset is created by calling <code>H5Dcreate</code> with + a file identifier, a dataset name, a data type, a data space, + and constant properties. The data type and data space are the + type and space of the dataset as it will exist in the file, + which may be different than in application memory. The + <em>create_plist_id</em> is a <code>H5P_DATASET_CREATE</code> + property list created with <code>H5Pcreate()</code> and + initialized with the various functions described above. + <code>H5Dcreate()</code> returns a dataset handle for success + or negative for failure. The handle should eventually be + closed by calling <code>H5Dclose()</code> to release resources + it uses. + + <br><br> + <dt><code>hid_t H5Dopen (hid_t <em>file_id</em>, const char + *<em>name</em>)</code> + <dd>An existing dataset can be opened for access by calling this + function. A dataset handle is returned for success or a + negative value is returned for failure. The handle should + eventually be closed by calling <code>H5Dclose()</code> to + release resources it uses. + + <br><br> + <dt><code>herr_t H5Dclose (hid_t <em>dataset_id</em>)</code> + <dd>This function closes a dataset handle and releases all + resources it might have been using. The handle should not be + used in subsequent calls to the library. + + <br><br> + <dt><code>herr_t H5Dextend (hid_t <em>dataset_id</em>, + hsize_t <em>dim</em>[])</code> + <dd>This function extends a dataset by increasing the size in + one or more dimensions. Not all datasets can be extended. + </dl> + + + + <h2>8. Querying Constant or Persistent Properties</h2> + + <p>Constant or persistent properties can be queried with a set of + three functions. Each function returns an identifier for a copy + of the requested properties. The identifier can be passed to + various functions which modify the underlying object to derive a + new object; the original dataset is completely unchanged. The + return values from these functions should be properly destroyed + when no longer needed. + + <dl> + <dt><code>hid_t H5Dget_type (hid_t <em>dataset_id</em>)</code> + <dd>Returns an identifier for a copy of the dataset permanent + data type or negative for failure. + + <dt><code>hid_t H5Dget_space (hid_t <em>dataset_id</em>)</code> + <dd>Returns an identifier for a copy of the dataset permanent + data space, which also contains information about the current + size of the dataset if the data set is extendable with + <code>H5Dextend()</code>. + + <dt><code>hid_t H5Dget_create_plist (hid_t + <em>dataset_id</em>)</code> + <dd>Returns an identifier for a copy of the dataset creation + property list. The new property list is created by examining + various permanent properties of the dataset. This is mostly a + catch-all for everything but type and space. + </dl> + + + + <h2>9. Setting Memory and Transfer Properties</h2> + + <p>A dataset also has memory properties which describe memory + within the application, and transfer properties that control + various aspects of the I/O operations. The memory can have a + data type different than the permanent file data type (different + number types, different struct member offsets, different array + element orderings) and can also be a different size (memory is a + subset of the permanent dataset elements, or vice versa). The + transfer properties might provide caching hints or collective + I/O information. Therefore, each I/O operation must specify + memory and transfer properties. + + <p>The memory properties are specified with <em>type_id</em> and + <em>space_id</em> arguments while the transfer properties are + specified with the <em>transfer_id</em> property list for the + <code>H5Dread()</code> and <code>H5Dwrite()</code> functions + (these functions are described below). + + <dl> + <dt><code>herr_t H5Pset_buffer (hid_t <em>xfer_plist</em>, + size_t <em>max_buf_size</em>, void *<em>tconv_buf</em>, void + *<em>bkg_buf</em>)</code> + <dt><code>size_t H5Pget_buffer (hid_t <em>xfer_plist</em>, void + **<em>tconv_buf</em>, void **<em>bkg_buf</em>)</code> + <dd>Sets or retrieves the maximum size in bytes of the temporary + buffer used for data type conversion in the I/O pipeline. An + application-defined buffer can also be supplied as the + <em>tconv_buf</em> argument, otherwise a buffer will be + allocated and freed on demand by the library. A second + temporary buffer <em>bkg_buf</em> can also be supplied and + should be the same size as the <em>tconv_buf</em>. The + default values are 1MB for the maximum buffer size, and null + pointers for each buffer indicating that they should be + allocated on demand and freed when no longer needed. The + <code>H5Pget_buffer()</code> function returns the maximum + buffer size or zero on error. + </dl> + + <p>If the maximum size of the temporary I/O pipeline buffers is + too small to hold the entire I/O request, then the I/O request + will be fragmented and the transfer operation will be strip + mined. However, certain restrictions apply to the strip + mining. For instance, when performing I/O on a hyperslab of a + simple data space the strip mining is in terms of the slowest + varying dimension. So if a 100x200x300 hyperslab is requested, + the temporary buffer must be large enough to hold a 1x200x300 + sub-hyperslab. + + <p>To prevent strip mining from happening, the application should + use <code>H5Pset_buffer()</code> to set the size of the + temporary buffer so it's large enough to hold the entire + request. + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example</h4></caption> + <tr> + <td> + <p>This example shows how to define a function that sets + a dataset transfer property list so that strip mining + does not occur. It takes an (optional) dataset transfer + property list, a dataset, a data space that describes + what data points are being transfered, and a data type + for the data points in memory. It returns a (new) + dataset transfer property list with the temporary + buffer size set to an appropriate value. The return + value should be passed as the fifth argument to + <code>H5Dread()</code> or <code>H5Dwrite()</code>. + <p><code><pre> + 1 hid_t + 2 disable_strip_mining (hid_t xfer_plist, hid_t dataset, + 3 hid_t space, hid_t mem_type) + 4 { + 5 hid_t file_type; /* File data type */ + 6 size_t type_size; /* Sizeof larger type */ + 7 size_t size; /* Temp buffer size */ + 8 hid_t xfer_plist; /* Return value */ + 9 +10 file_type = H5Dget_type (dataset); +11 type_size = MAX(H5Tget_size(file_type), H5Tget_size(mem_type)); +12 H5Tclose (file_type); +13 size = H5Sget_npoints(space) * type_size; +14 if (xfer_plist<0) xfer_plist = H5Pcreate (H5P_DATASET_XFER); +15 H5Pset_buffer(xfer_plist, size, NULL, NULL); +16 return xfer_plist; +17 } + </pre></code> + </td> + </tr> + </table> + </center> + + + + <h2>10. Querying Memory or Transfer Properties</h2> + + <p>Unlike constant and persistent properties, a dataset cannot be + queried for it's memory or transfer properties. Memory + properties cannot be queried because the application already + stores those properties separate from the buffer that holds the + raw data, and the buffer may hold multiple segments from various + datasets and thus have more than one set of memory properties. + The transfer properties cannot be queried from the dataset + because they're associated with the transfer itself and not with + the dataset (but one can call + <code>H5Pget_<em>property</em>()</code> to query transfer + properties from a tempalate). + + + <h2>11. Raw Data I/O</h2> + + <p>All raw data I/O is accomplished through these functions which + take a dataset handle, a memory data type, a memory data space, + a file data space, transfer properties, and an application + memory buffer. They translate data between the memory data type + and space and the file data type and space. The data spaces can + be used to describe partial I/O operations. + + <dl> + <dt><code>herr_t H5Dread (hid_t <em>dataset_id</em>, hid_t + <em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t + <em>file_space_id</em>, hid_t <em>xfer_plist_id</em>, + void *<em>buf</em>/*out*/)</code> + <dd>Reads raw data from the specified dataset into <em>buf</em> + converting from file data type and space to memory data type + and space. + + <br><br> + <dt><code>herr_t H5Dwrite (hid_t <em>dataset_id</em>, hid_t + <em>mem_type_id</em>, hid_t <em>mem_space_id</em>, hid_t + <em>file_space_id</em>, hid_t <em>xfer_plist_id</em>, + const void *<em>buf</em>)</code> + <dd>Writes raw data from an application buffer <em>buf</em> to + the specified dataset converting from memory data type and + space to file data type and space. + </dl> + + + <p>In the name of sharability, the memory datatype must be + supplied. However, it can be the same identifier as was used to + create the dataset or as was returned by + <code>H5Dget_type()</code>; the library will not implicitly + derive memory data types from constant data types. + + <p>For complete reads of the dataset one may supply + <code>H5S_ALL</code> as the argument for the file data space. + If <code>H5S_ALL</code> is also supplied as the memory data + space then no data space conversion is performed. This is a + somewhat dangerous situation since the file data space might be + different than what the application expects. + + + + <h2>12. Examples</h2> + + <p>The examples in this section illustrate some common dataset + practices. + + + <p>This example shows how to create a dataset which is stored in + memory as a two-dimensional array of native <code>double</code> + values but is stored in the file in Cray <code>float</code> + format using LZ77 compression. The dataset is written to the + HDF5 file and then read back as a two-dimensional array of + <code>float</code> values. + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example 1</h4></caption> + <tr> + <td> + <p><code><pre> + 1 hid_t file, data_space, dataset, properties; + 2 double dd[500][600]; + 3 float ff[500][600]; + 4 hsize_t dims[2], chunk_size[2]; + 5 + 6 /* Describe the size of the array */ + 7 dims[0] = 500; + 8 dims[1] = 600; + 9 data_space = H5Screate_simple (2, dims); +10 +11 +12 /* +13 * Create a new file using with read/write access, +14 * default file creation properties, and default file +15 * access properties. +16 */ +17 file = H5Fcreate ("test.h5", H5F_ACC_RDWR, H5P_DEFAULT, +18 H5P_DEFAULT); +19 +20 /* +21 * Set the dataset creation plist to specify that +22 * the raw data is to be partitioned into 100x100 element +23 * chunks and that each chunk is to be compressed with +24 * LZ77. +25 */ +26 chunk_size[0] = chunk_size[1] = 100; +27 properties = H5Pcreate (H5P_DATASET_CREATE); +28 H5Pset_chunk (properties, 2, chunk_size); +29 H5Pset_compression (properties, H5D_COMPRESS_LZ77); +30 +31 /* +32 * Create a new dataset within the file. The data type +33 * and data space describe the data on disk, which may +34 * be different than the format used in the application's +35 * memory. +36 */ +37 dataset = H5Dcreate (file, "dataset", H5T_CRAY_FLOAT, +38 data_space, properties); +39 +40 /* +41 * Write the array to the file. The data type and data +42 * space describe the format of the data in the `dd' +43 * buffer. The raw data is translated to the format +44 * required on disk defined above. We use default raw +45 * data transfer properties. +46 */ +47 H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, +48 H5P_DEFAULT, dd); +49 +50 /* +51 * Read the array as floats. This is similar to writing +52 * data except the data flows in the opposite direction. +53 */ +54 H5Dread (dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, +55 H5P_DEFAULT, ff); +56 +64 H5Dclose (dataset); +65 H5Sclose (data_space); +66 H5Pclose (properties); +67 H5Fclose (file); + </pre></code> + </td> + </tr> + </table> + </center> + + <p>This example uses the file created in Example 1 and reads a + hyperslab of the 500x600 file dataset. The hyperslab size is + 100x200 and it is located beginning at element + <200,200>. We read the hyperslab into an 200x400 array in + memory beginning at element <0,0> in memory. Visually, + the transfer looks something like this: + + <center> + <img alt="Raw Data Transfer" src="dataset_p1.gif"> + </center> + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example 2</h4></caption> + <tr> + <td> + <p><code><pre> + 1 hid_t file, mem_space, file_space, dataset; + 2 double dd[200][400]; + 3 hssize_t offset[2]; + 4 hsize size[2]; + 5 + 6 /* + 7 * Open an existing file and its dataset. + 8 */ + 9 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT); +10 dataset = H5Dopen (file, "dataset"); +11 +12 /* +13 * Describe the file data space. +14 */ +15 offset[0] = 200; /*offset of hyperslab in file*/ +16 offset[1] = 200; +17 size[0] = 100; /*size of hyperslab*/ +18 size[1] = 200; +19 file_space = H5Dget_space (dataset); +20 H5Sset_hyperslab (file_space, 2, offset, size); +21 +22 /* +23 * Describe the memory data space. +24 */ +25 size[0] = 200; /*size of memory array*/ +26 size[1] = 400; +27 mem_space = H5Screate_simple (2, size); +28 +29 offset[0] = 0; /*offset of hyperslab in memory*/ +30 offset[1] = 0; +31 size[0] = 100; /*size of hyperslab*/ +32 size[1] = 200; +33 H5Sset_hyperslab (mem_space, 2, offset, size); +34 +35 /* +36 * Read the dataset. +37 */ +38 H5Dread (dataset, H5T_NATIVE_DOUBLE, mem_space, +39 file_space, H5P_DEFAULT, dd); +40 +41 /* +42 * Close/release resources. +43 */ +44 H5Dclose (dataset); +45 H5Sclose (mem_space); +46 H5Sclose (file_space); +47 H5Fclose (file); + </pre></code> + </td> + </tr> + </table> + </center> + + <p>If the file contains a compound data structure one of whose + members is a floating point value (call it "delta") but the + application is interested in reading an array of floating point + values which are just the "delta" values, then the application + should cast the floating point array as a struct with a single + "delta" member. + + <p> + <center> + <table border align=center width="100%"> + <caption align=bottom><h4>Example 3</h4></caption> + <tr> + <td> + <p><code><pre> + 1 hid_t file, dataset, type; + 2 double delta[200]; + 3 + 4 /* + 5 * Open an existing file and its dataset. + 6 */ + 7 file = H5Fopen ("test.h5", H5F_ACC_RDONLY, H5P_DEFAULT); + 8 dataset = H5Dopen (file, "dataset"); + 9 +10 /* +11 * Describe the memory data type, a struct with a single +12 * "delta" member. +13 */ +14 type = H5Tcreate (H5T_COMPOUND, sizeof(double)); +15 H5Tinsert (type, "delta", 0, H5T_NATIVE_DOUBLE); +16 +17 /* +18 * Read the dataset. +19 */ +20 H5Dread (dataset, type, H5S_ALL, H5S_ALL, +21 H5P_DEFAULT, dd); +22 +23 /* +24 * Close/release resources. +25 */ +26 H5Dclose (dataset); +27 H5Tclose (type); +28 H5Fclose (file); + </pre></code> + </td> + </tr> + </table> + </center> + + <hr> + <address><a href="mailto:matzke@llnl.gov">Robb Matzke</a></address> +<!-- Created: Tue Dec 2 09:17:09 EST 1997 --> +<!-- hhmts start --> +Last modified: Wed May 13 18:57:47 EDT 1998 +<!-- hhmts end --> + </body> +</html> |