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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Copyright by The HDF Group. * * All rights reserved. * * * * This file is part of HDF5. The full HDF5 copyright notice, including * * terms governing use, modification, and redistribution, is contained in * * the LICENSE file, which can be found at the root of the source code * * distribution tree, or in https://www.hdfgroup.org/licenses. * * If you do not have access to either file, you may request a copy from * * help@hdfgroup.org. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ #ifndef H5DOpublic_H #define H5DOpublic_H #ifdef __cplusplus extern "C" { #endif /** \page H5DO_UG HDF5 High Level Optimizations * * Navigate back: \ref index "Main" / \ref UG *
* * \section sec_hldo_intro Introduction * * The HDF5 Dataset Optimization (H5DO) interface provides high-performance functions for specialized * dataset I/O operations that bypass standard HDF5 processing layers when appropriate. * * @see H5DO Reference Manual * * Since version 1.10.3 these functions are deprecated in favor of #H5Dwrite_chunk and #H5Dread_chunk. * * \section sec_hldo_direct_chunk Direct Chunk Write Function * When a user application has a chunked dataset and is trying to write a single chunk of data with * #H5Dwrite, the data goes through several steps inside the HDF5 library. The library first examines the * hyperslab selection. Then it converts the data from the datatype in memory to the datatype in the file if * they are different. Finally, the library processes the data in the filter pipeline. Starting with * the 1.8.11 release, a new high-level C function called #H5DOwrite_chunk becomes available. It writes a data * chunk directly to the file bypassing the library’s hyperslab selection, data conversion, and filter * pipeline processes. In other words, if an application can pre-process the data, then the application can * use #H5DOwrite_chunk to write the data much faster. * * #H5DOwrite_chunk was developed in response to a client request. The client builds X-ray pixel * detectors for use at synchrotron light sources. These detectors can produce data at the rate of tens of * gigabytes per second. Before transferring the data over their network, the detectors compress the data * by a factor of 10 or more. The modular architecture of the detectors can scale up its data stream in * parallel and maps well to current parallel computing and storage systems. * See the \ref_rfc20121114 for the original proposal. * * \subsection subsec_hldo_direct_chunk_using Using the Direct Chunk Write Function * Basically, the #H5DOwrite_chunk function takes a pre-processed data chunk (buf) and its size * (data_size) and writes to the chunk location (offset) in the dataset ( dset_id). * * The function prototype is shown below: * \code * herr_t H5DOwrite_chunk( * hid_t dset_id, // the dataset * hid_t dxpl_id, // data transfer property list * uint32_t filter_mask, // indicates which filters are used * hsize_t* offset, // position of the chunk * size_t data_size, // size of the actual data * const void* buf // buffer with data to be written * ) * \endcode * * Below is a simple example showing how to use the function: * Example 1. Using H5DOwrite_chunk * \code * hsize_t offset[2] = {4, 4}; * uint32_t filter_mask = 0; * size_t nbytes = 40; * if(H5DOwrite_chunk(dset_id, dxpl, filter_mask, offset, nbytes, data_buf) < 0) * goto error; * \endcode * * In the example above, the dataset is 8x8 elements of int. Each chunk is 4x4. The offset of the first * element of the chunk to be written is 4 and 4. In the diagram below, the shaded chunk is the data to be * written. The function is writing a pre-compressed data chunk of 40 bytes (assumed) to the dataset. The * zero value of the filter mask means that all filters have been applied to the pre-processed data. * * * * * *
* \image html DOChunks_fig1.png "Figure 1. Illustration of the chunk to be written" *
* * The complete code example at the end of this topic shows how to set the value of the filter mask to * indicate a filter being skipped. The corresponding bit in the filter mask is turned on when a filter is * skipped. For example, if the second filter is skipped, the second bit of the filter mask should be turned * on. For more information, see the #H5DOwrite_chunk entry in the \ref RM. * * \subsection subsec_hldo_direct_chunk_design The Design * The following diagram shows how the function #H5DOwrite_chunk bypasses hyperslab selection, data * conversion, and filter pipeline inside the HDF5 library. * * * * * *
* \image html DOChunks_fig2.png "Figure 2. Diagram for H5DOwrite_chunk" *
* * \subsection subsec_hldo_direct_chunk_perf Performance * The table below describes the results of performance benchmark tests run by HDF developers. It shows * that using the new function #H5DOwrite_chunk to write pre-compressed data is much faster than using * the #H5Dwrite function to compress and write the same data with the filter pipeline. Measurements * involving #H5Dwrite include compression time in the filter pipeline. Since the data is already * compressed before #H5DOwrite_chunk is called, use of #H5DOwrite_chunk to write compressed data * avoids the performance bottleneck in the HDF5 filter pipeline. * * The test was run on a Linux 2.6.18 / 64-bit Intel x86_64 machine. The dataset contained 100 chunks. * Only one chunk was written to the file per write call. The number of writes was 100. The time * measurement was for the entire dataset with the Unix system function gettimeofday. Writing the * entire dataset with one write call took almost the same amount of time as writing chunk by chunk. In * order to force the system to flush the data to the file, the O_SYNC flag was used to open the file. * * Table 1. Performance result for H5DOwrite_chunk in the high-level library * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Dataset size (MB)95.37762.942288.82
Size after compression (MB)64.14512.941538.81
Dataset dimensionality100x1000x250100x2000x1000100x2000x3000
Chunk dimensionality1000x2502000x10002000x3000
Datatype4-byte integer4-byte integer4-byte * integer
IO speed is in MB/s and Time is in second * (s).speed1time2speedtimespeedtime
H5Dwrite writes without compression * filter77.271.2397.027.8691.7724.94
H5DOwrite_chunk writes uncompressed * data791.2195.717.9789.1725.67
H5Dwrite writes with compression * filter2.6835.592.67285.752.67857.24
H5DOwrite_chunk writes compressed * data77.190.8378.566.5396.2815.98
Unix writes compressed data to Unix * file76.490.84955.498.5915.61
* * \subsection subsec_hldo_direct_chunk_caution A Word of Caution * Since #H5DOwrite_chunk writes data chunks directly in a file, developers must be careful when using it. * The function bypasses hyperslab selection, the conversion of data from one datatype to another, and * the filter pipeline to write the chunk. Developers should have experience with these processes before * they use this function. * * \subsection subsec_hldo_direct_chunk_example A Complete Code Example * The following is an example of using #H5DOwrite_chunk to write an entire dataset by chunk. * \code * #include * #include * #define DEFLATE_SIZE_ADJUST(s) (ceil(((double)(s))*1.001)+12) * * size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); * const Bytef *z_src = (const Bytef*)(direct_buf); * Bytef *z_dst; // destination buffer * uLongf z_dst_nbytes = (uLongf)DEFLATE_SIZE_ADJUST(buf_size); * uLong z_src_nbytes = (uLong)buf_size; * int aggression = 9; // Compression aggression setting * uint32_t filter_mask = 0; * size_t buf_size = CHUNK_NX*CHUNK_NY*sizeof(int); * * // Create the data space * if((dataspace = H5Screate_simple(RANK, dims, maxdims)) < 0) * goto error; * // Create a new file * if((file = H5Fcreate(FILE_NAME5, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0) * goto error; * // Modify dataset creation properties, i.e. enable chunking and compression * if((cparms = H5Pcreate(H5P_DATASET_CREATE)) < 0) * goto error; * if((status = H5Pset_chunk( cparms, RANK, chunk_dims)) < 0) * goto error; * if((status = H5Pset_deflate( cparms, aggression)) < 0) * goto error; * // Create a new dataset within the file using cparms creation properties * if((dset_id = H5Dcreate2(file, DATASETNAME, H5T_NATIVE_INT, dataspace, H5P_DEFAULT,cparms, * H5P_DEFAULT)) < 0) goto error; * // Initialize data for one chunk * for(i = n = 0; i < CHUNK_NX; i++) * for(j = 0; j < CHUNK_NY; j++) * direct_buf[i][j] = n++; * // Allocate output (compressed) buffer * outbuf = malloc(z_dst_nbytes); * z_dst = (Bytef *)outbuf; * // Perform compression from the source to the destination buffer * ret = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression); * // Check for various zlib errors * if(Z_BUF_ERROR == ret) { * fprintf(stderr, "overflow"); * goto error; * } else if(Z_MEM_ERROR == ret) { * fprintf(stderr, "deflate memory error"); * goto error; * } else if(Z_OK != ret) { * fprintf(stderr, "other deflate error"); * goto error; * } * // Write the compressed chunk data repeatedly to cover all the chunks in the dataset, using the direct * write function. for(i=0; i * Navigate back: \ref index "Main" / \ref UG */ /**\defgroup H5DO HDF5 Optimizations APIs (H5DO) * * Bypassing default HDF5 behavior in order to optimize for specific * use cases (H5DO) * * HDF5 functions described is this section are implemented in the HDF5 High-level * library as optimized functions. These functions generally require careful setup * and testing as they enable an application to bypass portions of the HDF5 * library's I/O pipeline for performance purposes. * * These functions are distributed in the standard HDF5 distribution and are * available any time the HDF5 High-level library is available. * * - \ref H5DOappend * \n Appends data to a dataset along a specified dimension. * - \ref H5DOread_chunk * \n Reads a raw data chunk directly from a dataset in a file into a buffer (DEPRECATED) * - \ref H5DOwrite_chunk * \n Writes a raw data chunk from a buffer directly to a dataset in a file (DEPRECATED) * */ /*------------------------------------------------------------------------- * * "Optimized dataset" routines. * *------------------------------------------------------------------------- */ /** * -------------------------------------------------------------------------- * \ingroup H5DO * * \brief Appends data to a dataset along a specified dimension. * * \param[in] dset_id Dataset identifier * \param[in] dxpl_id Dataset transfer property list identifier * \param[in] axis Dataset Dimension (0-based) for the append * \param[in] extension Number of elements to append for the * axis-th dimension * \param[in] memtype The memory datatype identifier * \param[in] buf Buffer with data for the append * * \return \herr_t * * \details The H5DOappend() routine extends a dataset by \p extension * number of elements along a dimension specified by a * dimension \p axis and writes \p buf of elements to the * dataset. Dimension \p axis is 0-based. Elements’ type * is described by \p memtype. * * This routine combines calling H5Dset_extent(), * H5Sselect_hyperslab(), and H5Dwrite() into a single routine * that simplifies application development for the common case * of appending elements to an existing dataset. * * For a multi-dimensional dataset, appending to one dimension * will write a contiguous hyperslab over the other dimensions. * For example, if a 3-D dataset has dimension sizes (3, 5, 8), * extending the 0th dimension (currently of size 3) by 3 will * append 3*5*8 = 120 elements (which must be pointed to by the * \p buffer parameter) to the dataset, making its final * dimension sizes (6, 5, 8). * * If a dataset has more than one unlimited dimension, any of * those dimensions may be appended to, although only along * one dimension per call to H5DOappend(). * * \since 1.10.0 * */ H5HL_DLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension, hid_t memtype, const void *buf); /* Symbols defined for compatibility with previous versions of the HDF5 API. * * Use of these symbols is deprecated. */ #ifndef H5_NO_DEPRECATED_SYMBOLS /* Compatibility wrappers for functionality moved to H5D */ /** * -------------------------------------------------------------------------- * \ingroup H5DO * * \brief Writes a raw data chunk from a buffer directly to a dataset in a file. * * \param[in] dset_id Identifier for the dataset to write to * \param[in] dxpl_id Transfer property list identifier for * this I/O operation * \param[in] filters Mask for identifying the filters in use * \param[in] offset Logical position of the chunk's first element * in the dataspace * \param[in] data_size Size of the actual data to be written in bytes * \param[in] buf Buffer containing data to be written to the chunk * * \return \herr_t * * \deprecated This function was deprecated in favor of the function * H5Dwrite_chunk() of HDF5-1.10.3. * The functionality of H5DOwrite_chunk() was moved * to H5Dwrite_chunk(). * \deprecated For compatibility, this API call has been left as a stub which * simply calls H5Dwrite_chunk(). New code should use H5Dwrite_chunk(). * * \details The H5DOwrite_chunk() writes a raw data chunk as specified by its * logical \p offset in a chunked dataset \p dset_id from the application * memory buffer \p buf to the dataset in the file. Typically, the data * in \p buf is preprocessed in memory by a custom transformation, such as * compression. The chunk will bypass the library's internal data * transfer pipeline, including filters, and will be written directly to the file. * * \p dxpl_id is a data transfer property list identifier. * * \p filters is a mask providing a record of which filters are used * with the chunk. The default value of the mask is zero (\c 0), * indicating that all enabled filters are applied. A filter is skipped * if the bit corresponding to the filter's position in the pipeline * (0 ≤ position < 32) is turned on. This mask is saved * with the chunk in the file. * * \p offset is an array specifying the logical position of the first * element of the chunk in the dataset's dataspace. The length of the * offset array must equal the number of dimensions, or rank, of the * dataspace. The values in \p offset must not exceed the dimension limits * and must specify a point that falls on a dataset chunk boundary. * * \p data_size is the size in bytes of the chunk, representing the number of * bytes to be read from the buffer \p buf. If the data chunk has been * precompressed, \p data_size should be the size of the compressed data. * * \p buf is the memory buffer containing data to be written to the chunk in the file. * * \attention Exercise caution when using H5DOread_chunk() and H5DOwrite_chunk(), * as they read and write data chunks directly in a file. * H5DOwrite_chunk() bypasses hyperslab selection, the conversion of data * from one datatype to another, and the filter pipeline to write the chunk. * Developers should have experience with these processes before * using this function. Please see \ref H5DO_UG * for more information. * * \note H5DOread_chunk() and H5DOwrite_chunk() are not * supported under parallel and do not support variable length types. * * \par Example * The following code illustrates the use of H5DOwrite_chunk to write * an entire dataset, chunk by chunk: * \snippet H5DO_examples.c H5DOwrite * * \version 1.10.3 Function deprecated in favor of H5Dwrite_chunk. * * \since 1.8.11 */ H5HL_DLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, size_t data_size, const void *buf); /** * -------------------------------------------------------------------------- * \ingroup H5DO * * \brief Reads a raw data chunk directly from a dataset in a file into a buffer. * * \param[in] dset_id Identifier for the dataset to be read * \param[in] dxpl_id Transfer property list identifier for * this I/O operation * \param[in] offset Logical position of the chunk's first element in the dataspace * \param[in,out] filters Mask for identifying the filters used * with the chunk * \param[in] buf Buffer containing the chunk read from * the dataset * * \return \herr_t * * \deprecated This function was deprecated in favor of the function * H5Dread_chunk() as of HDF5-1.10.3. * In HDF5 1.10.3, the functionality of H5DOread_chunk() * was moved to H5Dread_chunk(). * \deprecated For compatibility, this API call has been left as a stub which * simply calls H5Dread_chunk(). New code should use H5Dread_chunk(). * * \details The H5DOread_chunk() reads a raw data chunk as specified * by its logical \p offset in a chunked dataset \p dset_id * from the dataset in the file into the application memory * buffer \p buf. The data in \p buf is read directly from the file * bypassing the library's internal data transfer pipeline, * including filters. * * \p dxpl_id is a data transfer property list identifier. * * The mask \p filters indicates which filters are used with the * chunk when written. A zero value indicates that all enabled filters * are applied on the chunk. A filter is skipped if the bit corresponding * to the filter's position in the pipeline * (0 ≤ position < 32) is turned on. * * \p offset is an array specifying the logical position of the first * element of the chunk in the dataset's dataspace. The length of the * offset array must equal the number of dimensions, or rank, of the * dataspace. The values in \p offset must not exceed the dimension * limits and must specify a point that falls on a dataset chunk boundary. * * \p buf is the memory buffer containing the chunk read from the dataset * in the file. * * \par Example * The following code illustrates the use of H5DOread_chunk() * to read a chunk from a dataset: * \snippet H5DO_examples.c H5DOread * * \version 1.10.3 Function deprecated in favor of H5Dread_chunk. * * \since 1.10.2, 1.8.19 */ H5HL_DLL herr_t H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters /*out*/, void *buf /*out*/); #endif /* H5_NO_DEPRECATED_SYMBOLS */ #ifdef __cplusplus } #endif #endif