diff options
| -rw-r--r-- | include/tng_io.h | 35 | ||||
| -rw-r--r-- | src/lib/tng_io.c | 109 |
2 files changed, 115 insertions, 29 deletions
diff --git a/include/tng_io.h b/include/tng_io.h index f6eb637..fb4efd6 100644 --- a/include/tng_io.h +++ b/include/tng_io.h @@ -1072,7 +1072,7 @@ tng_function_status DECLSPECDLLEXPORT tng_input_file_len_get /** * @brief Get the number of frames in the trajectory - * @param tng_data the trajectory of which to get the number of frames. + * @param tng_data is the trajectory of which to get the number of frames. * @param n is pointing to a value set to the number of frames. * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) * must be initialised before using it. @@ -1085,6 +1085,34 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get int64_t *n); /** + * @brief Get the precision of lossy compression + * @param tng_data is the trajectory of which to get the compression precision. + * @param precision will be pointing to the retrieved compression precision. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @details A compression precision of 0.001 (the default) means that the + * compressed values are accurate to the third decimal. + * @return TNG_SUCCESS (0) if successful. + */ +tng_function_status DECLSPECDLLEXPORT tng_compression_precision_get + (const tng_trajectory_t tng_data, + double *precision); + +/** + * @brief Get the precision of lossy compression + * @param tng_data is the trajectory of which to set the compression precision. + * @param precision is the new compression precision. + * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) + * must be initialised before using it. + * @details A compression precision of 0.001 (the default) means that the + * compressed values are accurate to the third decimal. + * @return TNG_SUCCESS (0) if successful. + */ +tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set + (tng_trajectory_t tng_data, + const double precision); + +/** * @brief Set the number of particles, in the case no molecular system is used. * @param tng_data is the trajectory of which to get the number of particles. * @param n is the number of particles to use. @@ -2645,8 +2673,9 @@ tng_function_status DECLSPECDLLEXPORT tng_time_get_str * @param filename is a string containing the name of the trajectory to open. * @param mode specifies the file mode of the trajectory. Can be set to 'r', * 'w' or 'a' for reading, writing or appending respectively. - * @param tng_data_p is a pointer to the opened trajectory. This must be - * closed by the user. + * @param tng_data_p is a pointer to the opened trajectory. This will be + * allocated by the TNG library. The trajectory must be + * closed by the user, whereby memory is freed. * @pre \code tng_data != 0 \endcode The trajectory container (tng_data) * must be initialised before using it. * @pre \code filename != 0 \endcode The pointer to the filename must not be a diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index c5aed0d..fe69ebd 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -366,6 +366,8 @@ struct tng_trajectory { int *compress_algo_pos; /** TNG compression algorithm for compressing velocities */ int *compress_algo_vel; + /** The precision used for lossy compression */ + double compression_precision; }; #ifndef USE_WINDOWS @@ -3878,16 +3880,17 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, { dest = tng_compress_pos_float_find_algo(start_pos, (int)n_particles, (int)algo_find_n_frames, - (float)0.001, 0, - tng_data-> + (float)tng_data->compression_precision, + 0, tng_data-> compress_algo_pos, &new_len); if(algo_find_n_frames < n_frames) { dest = tng_compress_pos_float(start_pos, (int)n_particles, - (int)n_frames, (float)0.001, 0, - tng_data->compress_algo_pos, + (int)n_frames, + (float)tng_data->compression_precision, + 0, tng_data->compress_algo_pos, &new_len); } } @@ -3895,14 +3898,15 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, { dest = tng_compress_pos_find_algo(start_pos, (int)n_particles, (int)algo_find_n_frames, - 0.001, 0, - tng_data-> + tng_data->compression_precision, + 0, tng_data-> compress_algo_pos, &new_len); if(algo_find_n_frames < n_frames) { dest = tng_compress_pos(start_pos, (int)n_particles, - (int)n_frames, 0.001, 0, + (int)n_frames, + tng_data->compression_precision, 0, tng_data->compress_algo_pos, &new_len); } @@ -3913,14 +3917,17 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, if(type == TNG_FLOAT_DATA) { dest = tng_compress_pos_float(start_pos, (int)n_particles, - (int)n_frames, (float)0.001, 0, + (int)n_frames, + (float)tng_data->compression_precision, 0, tng_data->compress_algo_pos, &new_len); } else { dest = tng_compress_pos(start_pos, (int)n_particles, - (int)n_frames, 0.001, 0, - tng_data->compress_algo_pos, &new_len); + (int)n_frames, + tng_data->compression_precision, 0, + tng_data->compress_algo_pos, + &new_len); } } } @@ -3945,15 +3952,16 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, { dest = tng_compress_vel_float_find_algo(start_pos, (int)n_particles, (int)algo_find_n_frames, - (float)0.001, 0, - tng_data-> + (float)tng_data->compression_precision, + 0, tng_data-> compress_algo_vel, &new_len); if(algo_find_n_frames < n_frames) { dest = tng_compress_vel_float(start_pos, (int)n_particles, - (int)n_frames, (float)0.001, 0, - tng_data->compress_algo_vel, + (int)n_frames, + (float)tng_data->compression_precision, + 0, tng_data->compress_algo_vel, &new_len); } } @@ -3961,15 +3969,16 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, { dest = tng_compress_vel_find_algo(start_pos, (int)n_particles, (int)algo_find_n_frames, - 0.001, 0, - tng_data-> + tng_data->compression_precision, + 0, tng_data-> compress_algo_vel, &new_len); if(algo_find_n_frames < n_frames) { dest = tng_compress_vel(start_pos, (int)n_particles, - (int)n_frames, 0.001, 0, - tng_data->compress_algo_vel, + (int)n_frames, + tng_data->compression_precision, + 0, tng_data->compress_algo_vel, &new_len); } } @@ -3979,16 +3988,17 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, if(type == TNG_FLOAT_DATA) { dest = tng_compress_vel_float(start_pos, (int)n_particles, - (int)n_frames, (float)0.001, 0, - tng_data-> + (int)n_frames, + (float)tng_data->compression_precision, + 0, tng_data-> compress_algo_vel, &new_len); } else { dest = tng_compress_vel(start_pos, (int)n_particles, - (int)n_frames, 0.001, 0, - tng_data-> + (int)n_frames, tng_data->compression_precision, + 0, tng_data-> compress_algo_vel, &new_len); } @@ -8254,6 +8264,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init(tng_trajectory_t *tng_ tng_data->compress_algo_pos = 0; tng_data->compress_algo_vel = 0; + tng_data->compression_precision = 0.001; tng_data->distance_unit_exponential = -9; frame_set->first_frame = -1; @@ -8799,6 +8810,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_init_from_src(tng_trajector dest->compress_algo_pos = 0; dest->compress_algo_vel = 0; dest->distance_unit_exponential = -9; + dest->compression_precision = 0.001; frame_set->n_mapping_blocks = 0; frame_set->mappings = 0; @@ -9691,6 +9703,28 @@ tng_function_status DECLSPECDLLEXPORT tng_num_frames_get return(TNG_SUCCESS); } +tng_function_status DECLSPECDLLEXPORT tng_compression_precision_get + (const tng_trajectory_t tng_data, + double *precision) +{ + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + + *precision = tng_data->compression_precision; + + return(TNG_SUCCESS); +} + +tng_function_status DECLSPECDLLEXPORT tng_compression_precision_set + (tng_trajectory_t tng_data, + const double precision) +{ + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + + tng_data->compression_precision = precision; + + return(TNG_SUCCESS); +} + tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set (tng_trajectory_t tng_data, const int64_t n) @@ -11739,10 +11773,15 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_data_write /* If the wanted frame would be in the frame set after the last * frame set create a new frame set. */ if(stat == TNG_FAILURE && - (last_frame < frame_nr && + last_frame < frame_nr) +/* (last_frame < frame_nr && tng_data->current_trajectory_frame_set.first_frame + - tng_data->frame_set_n_frames >= frame_nr)) + tng_data->frame_set_n_frames >= frame_nr))*/ { + if(last_frame + tng_data->frame_set_n_frames < frame_nr) + { + last_frame = frame_nr - 1; + } tng_frame_set_new(tng_data, last_frame+1, tng_data->frame_set_n_frames); @@ -12166,6 +12205,10 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_particle_data_write (last_frame < frame_nr && last_frame + tng_data->frame_set_n_frames >= frame_nr)) { + if(last_frame + tng_data->frame_set_n_frames < frame_nr) + { + last_frame = frame_nr - 1; + } tng_frame_set_new(tng_data, last_frame+1, tng_data->frame_set_n_frames); @@ -15242,6 +15285,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write tng_particle_data_t p_data; tng_non_particle_data_t np_data; int64_t n_particles, n_frames, stride_length = 100, frame_pos; + int64_t last_frame; char block_type_flag; tng_function_status stat; @@ -15287,7 +15331,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write { n_frames = frame_set->n_frames; } - if(frame_nr >= frame_set->first_frame + n_frames) + last_frame = frame_set->first_frame + + frame_set->n_frames - 1; + if(frame_nr > last_frame) { stat = tng_frame_set_write(tng_data, TNG_USE_HASH); if(stat != TNG_SUCCESS) @@ -15296,6 +15342,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write __LINE__); return(stat); } + if(last_frame + tng_data->frame_set_n_frames < frame_nr) + { + last_frame = frame_nr - 1; + } stat = tng_frame_set_new(tng_data, frame_set->first_frame + frame_set->n_frames, n_frames); if(stat != TNG_SUCCESS) @@ -15432,6 +15482,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write tng_particle_data_t p_data; tng_non_particle_data_t np_data; int64_t n_particles, n_frames, stride_length = 100, frame_pos; + int64_t last_frame; char block_type_flag; tng_function_status stat; @@ -15477,7 +15528,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write { n_frames = frame_set->n_frames; } - if(frame_nr >= frame_set->first_frame + n_frames) + last_frame = frame_set->first_frame + + frame_set->n_frames - 1; + if(frame_nr > last_frame) { stat = tng_frame_set_write(tng_data, TNG_USE_HASH); if(stat != TNG_SUCCESS) @@ -15486,6 +15539,10 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_double_write __LINE__); return(stat); } + if(last_frame + tng_data->frame_set_n_frames < frame_nr) + { + last_frame = frame_nr - 1; + } stat = tng_frame_set_new(tng_data, frame_set->first_frame + frame_set->n_frames, n_frames); if(stat != TNG_SUCCESS) |