diff options
| -rw-r--r-- | src/lib/tng_io.c | 162 |
1 files changed, 149 insertions, 13 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 1205d96..527f456 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -27,6 +27,7 @@ #include "tng_io.h" #include "md5.h" +#include "compression/tng_compress.h" struct tng_bond { @@ -337,6 +338,11 @@ struct tng_trajectory { int n_data_blocks; /** A list of frame and particle indepdendent data blocks */ struct tng_non_particle_data *non_tr_data; + + /** TNG compression algorithm for compressing positions */ + int *compress_algo_pos; + /** TNG compression algorithm for compressing velocities */ + int *compress_algo_vel; }; @@ -3606,10 +3612,135 @@ static tng_function_status tng_particle_data_block_create return(TNG_SUCCESS); } +static tng_function_status tng_compress(tng_trajectory_t tng_data, + tng_gen_block_t block, + int64_t n_frames, + int64_t n_particles, + void *start_pos, int len) +{ + int nalgo; + int new_len; + char *dest, *temp; + + if(block->id != TNG_TRAJ_POSITIONS && + block->id != TNG_TRAJ_VELOCITIES) + { + printf("Can only compress positions and velocities with the" + "TNG method.\n"); + return(TNG_FAILURE); + } + + if(block->id == TNG_TRAJ_POSITIONS) + { + if(!tng_data->compress_algo_pos) + { + nalgo = tng_compress_nalgo(); + tng_data->compress_algo_pos=malloc(nalgo * + sizeof *tng_data->compress_algo_pos); + dest = tng_compress_pos_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data->compress_algo_pos, + &new_len); + } + else + { + dest = tng_compress_pos(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data->compress_algo_pos, &new_len); + } + } + else + { + if(!tng_data->compress_algo_vel) + { + nalgo = tng_compress_nalgo(); + tng_data->compress_algo_vel=malloc(nalgo * + sizeof *tng_data->compress_algo_vel); + dest = tng_compress_vel_find_algo(start_pos, n_particles, + n_frames, + 0.01, 0, + tng_data->compress_algo_vel, + &new_len); + } + else + { + dest = tng_compress_vel(start_pos, n_particles, + n_frames, 0.01, 0, + tng_data->compress_algo_vel, &new_len); + } + } + + memcpy(start_pos, dest, new_len); + + free(dest); + + block->block_contents_size = new_len + (block->block_contents_size - len); + + temp = realloc(block->block_contents, block->block_contents_size); + if(!temp) + { + free(block->block_contents); + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + block->block_contents_size, __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + block->block_contents = temp; + + return(TNG_SUCCESS); +} + +static tng_function_status tng_uncompress(tng_trajectory_t tng_data, + tng_gen_block_t block, + void *start_pos, + unsigned long uncompressed_len) +{ + char *temp; + double *dest = 0; + int offset; + + if(block->id != TNG_TRAJ_POSITIONS && + block->id != TNG_TRAJ_VELOCITIES) + { + printf("Can only uncompress positions and velocities with the" + "TNG method.\n"); + return(TNG_FAILURE); + } + + if(tng_compress_uncompress(start_pos, dest) == 1) + { + printf("Cannot uncompress TNG compressed block.\n"); + return(TNG_FAILURE); + } + + offset = start_pos - (void *)block->block_contents; + + + block->block_contents_size = uncompressed_len + offset; + + temp = realloc(block->block_contents, uncompressed_len + offset); + if(!temp) + { + free(block->block_contents); + free(dest); + printf("Cannot allocate memory (%"PRId64" bytes). %s: %d\n", + block->block_contents_size, __FILE__, __LINE__); + return(TNG_CRITICAL); + } + + memcpy(temp + offset, dest, uncompressed_len); + + block->block_contents = temp; + + free(dest); + return(TNG_SUCCESS); +} + #ifdef USE_ZLIB static tng_function_status tng_gzip_compress(tng_trajectory_t tng_data, tng_gen_block_t block, - void *start_pos, int len) + void *start_pos, const int len) { Bytef *dest; char *temp; @@ -4924,12 +5055,6 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, data_size = (n_frames / stride_length) * size * n_values; switch(codec_id) { - case TNG_XTC_COMPRESSION: - printf("XTC compression not implemented yet.\n"); - break; - case TNG_TNG_COMPRESSION: - printf("TNG compression not implemented yet.\n"); - break; #ifdef USE_ZLIB case TNG_GZIP_COMPRESSION: // printf("Before compression: %"PRId64"\n", block->block_contents_size); @@ -5458,12 +5583,6 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, switch(data->codec_id) { - case TNG_XTC_COMPRESSION: - printf("XTC compression not implemented yet.\n"); - break; - case TNG_TNG_COMPRESSION: - printf("TNG compression not implemented yet.\n"); - break; #ifdef USE_ZLIB case TNG_GZIP_COMPRESSION: // printf("Before compression: %"PRId64"\n", block->block_contents_size); @@ -7263,6 +7382,9 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) tng_data->non_tr_particle_data = 0; tng_data->non_tr_data = 0; + tng_data->compress_algo_pos = 0; + tng_data->compress_algo_vel = 0; + frame_set->first_frame = -1; frame_set->n_mapping_blocks = 0; frame_set->mappings = 0; @@ -7527,6 +7649,17 @@ tng_function_status tng_trajectory_destroy(tng_trajectory_t *tng_data_p) tng_data->n_particle_data_blocks = 0; tng_data->n_data_blocks = 0; + if(tng_data->compress_algo_pos) + { + free(tng_data->compress_algo_pos); + tng_data->compress_algo_pos = 0; + } + if(tng_data->compress_algo_vel) + { + free(tng_data->compress_algo_vel); + tng_data->compress_algo_vel = 0; + } + if(frame_set->tr_particle_data) { for(i = frame_set->n_particle_data_blocks; i--; ) @@ -7672,6 +7805,9 @@ tng_function_status tng_trajectory_init_from_src(tng_trajectory_t src, dest->non_tr_particle_data = 0; dest->non_tr_data = 0; + dest->compress_algo_pos = 0; + dest->compress_algo_vel = 0; + frame_set->first_frame = -1; frame_set->n_mapping_blocks = 0; frame_set->mappings = 0; |