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Diffstat (limited to 'include/compression/tng_compress.h')
| -rw-r--r-- | include/compression/tng_compress.h | 165 |
1 files changed, 165 insertions, 0 deletions
diff --git a/include/compression/tng_compress.h b/include/compression/tng_compress.h new file mode 100644 index 0000000..eefcfaa --- /dev/null +++ b/include/compression/tng_compress.h @@ -0,0 +1,165 @@ +/* This code is part of the tng compression routines. + * + * Written by Daniel Spangberg + * Copyright (c) 2010, 2013, The GROMACS development team. + * + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + */ + +#ifndef TNG_COMPRESS_H +#define TNG_COMPRESS_H + +#ifndef USE_WINDOWS +#if defined(WIN32) || defined(_WIN32) || defined(WIN64) || defined(_WIN64) +#define USE_WINDOWS +#endif /* win32... */ +#endif /* not defined USE_WINDOWS */ + +#ifdef USE_WINDOWS +#define DECLSPECDLLEXPORT __declspec(dllexport) +#else +#define DECLSPECDLLEXPORT +#endif + +#ifdef __cplusplus + extern "C" { +#endif + +/* tng_compress_pos expects positions to have the order: + first xyz, then sorted in atom order + then all the frames repeated, i.e.: + nframes * [ + natoms* [ + x, y, z + ] + ] + desired_precision what to round the numbers to, i.e. integers will be created as: + round(pos[]/desired_precision). + + algo should first be determined by calling + tng_compress_pos_find_algo + + The compressed data is returned in a malloced pointer (so free can + be called to free the memory), the number of chars in the compressed + data is put into *nitems. +*/ + +char DECLSPECDLLEXPORT *tng_compress_pos(double *pos, int natoms, int nframes, + double desired_precision, + int speed, int *algo, + int *nitems); + + +/* The tng_compress_pos_find_algo works the same as tng_compress_pos, but + it performs benchmarking to find the algorithms with the best + compression ratio. + The search is controlled by giving speed: + speed=1: Fast algorithms only. This excludes all BWLZH algorithms and + the XTC3 algorithm. + speed=2: Same as 1 and also includes the XTC3 algorithm using base compression + only. + speed=3: Same as 2 and also includes the XTC3 algorithm which will use BWLZH + compression when it seems likely to give better + compression. Also includes the interframe BWLZH algorithm for + coordinates and velocities. + speed=4: Enable the inter frame BWLZH algorithm for the coordinates. + The one-to-one BWLZH algorithm is enabled for velocities. + speed=5: Enable the LZ77 part of the BWLZH algorithm. + speed=6: Enable the intra frame BWLZH algorithm for the coordinates. Always try + the BWLZH compression in the XTC3 algorithm. + + Set speed=0 to allow tng_compression to set the default speed (which is currently 2). + For very good compression it makes sense to choose speed=4 or speed=5 + + The number of items required in the algorithm array can be found + by calling tng_compress_nalgo +*/ + +char DECLSPECDLLEXPORT *tng_compress_pos_find_algo(double *pos, int natoms, int nframes, + double desired_precision, + int speed, + int *algo, + int *nitems); + +/* This returns the number of integers required for the storage of the algorithm + with the best compression ratio. */ +int DECLSPECDLLEXPORT tng_compress_nalgo(void); + +/* The following two routines does the same as the compression of the + positions, but compresses velocities instead. The algorithm + selection for velocities is different, so the position and + velocities routines should not be mixed. */ + +char DECLSPECDLLEXPORT *tng_compress_vel(double *vel, int natoms, int nframes, + double desired_precision, + int speed, int *algo, + int *nitems); + +char DECLSPECDLLEXPORT *tng_compress_vel_find_algo(double *vel, int natoms, int nframes, + double desired_precision, + int speed, + int *algo, + int *nitems); + +/* From a compressed block, obtain information about + whether it is a position or velocity block: + *vel=1 means velocity block, *vel=0 means position block. + It also gives info about the number of atoms, + frames, and the precision used to compress the block, and the algorithms used to + compress the block. The return value=0 if the block looks like a tng compressed block, + and 1 otherwise. If the return value is 1 no information is returned. */ +int DECLSPECDLLEXPORT tng_compress_inquire(char *data,int *vel, int *natoms, + int *nframes, double *precision, + int *algo); + +/* Uncompresses any tng compress block, positions or velocities. It determines whether it is positions or velocities from the data buffer. The return value is 0 if ok, and 1 if not. +*/ +int DECLSPECDLLEXPORT tng_compress_uncompress(char *data,double *posvel); + + + /* Compression algorithms (matching the original trajng + assignments) The compression backends require that some of the + algorithms must have the same value. */ + +#define TNG_COMPRESS_ALGO_STOPBIT 1 +#define TNG_COMPRESS_ALGO_TRIPLET 2 +#define TNG_COMPRESS_ALGO_BWLZH1 8 +#define TNG_COMPRESS_ALGO_BWLZH2 9 + +#define TNG_COMPRESS_ALGO_POS_STOPBIT_INTER TNG_COMPRESS_ALGO_STOPBIT +#define TNG_COMPRESS_ALGO_POS_TRIPLET_INTER TNG_COMPRESS_ALGO_TRIPLET +#define TNG_COMPRESS_ALGO_POS_TRIPLET_INTRA 3 +#define TNG_COMPRESS_ALGO_POS_XTC2 5 +#define TNG_COMPRESS_ALGO_POS_TRIPLET_ONETOONE 7 +#define TNG_COMPRESS_ALGO_POS_BWLZH_INTER TNG_COMPRESS_ALGO_BWLZH1 +#define TNG_COMPRESS_ALGO_POS_BWLZH_INTRA TNG_COMPRESS_ALGO_BWLZH2 +#define TNG_COMPRESS_ALGO_POS_XTC3 10 +#define TNG_COMPRESS_ALGO_VEL_STOPBIT_ONETOONE TNG_COMPRESS_ALGO_STOPBIT +#define TNG_COMPRESS_ALGO_VEL_TRIPLET_INTER TNG_COMPRESS_ALGO_TRIPLET +#define TNG_COMPRESS_ALGO_VEL_TRIPLET_ONETOONE 3 +#define TNG_COMPRESS_ALGO_VEL_STOPBIT_INTER 6 +#define TNG_COMPRESS_ALGO_VEL_BWLZH_INTER TNG_COMPRESS_ALGO_BWLZH1 +#define TNG_COMPRESS_ALGO_VEL_BWLZH_ONETOONE TNG_COMPRESS_ALGO_BWLZH2 +#define TNG_COMPRESS_ALGO_MAX 11 + + + +/* Obtain strings describing the actual algorithms. These point to static memory, so should + not be freed. */ +char DECLSPECDLLEXPORT *tng_compress_initial_pos_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_pos_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_initial_vel_algo(int *algo); +char DECLSPECDLLEXPORT *tng_compress_vel_algo(int *algo); + + + +#ifdef __cplusplus + } +#endif + + +#endif |