diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 351 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 38 |
2 files changed, 373 insertions, 16 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index fcd6080..cb24104 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -6725,14 +6725,22 @@ tng_function_status tng_num_molecules_get(const tng_trajectory_t tng_data, return(TNG_SUCCESS); } -tng_function_status tng_num_frames_per_frame_set_get(const tng_trajectory_t tng_data, - int64_t *n) +tng_function_status tng_num_frames_per_frame_set_get + (const tng_trajectory_t tng_data, + int64_t *n) { *n = tng_data->frame_set_n_frames; return(TNG_SUCCESS); } +tng_function_status tng_num_frame_sets_get(const tng_trajectory_t tng_data, + int64_t *n) +{ + *n = tng_data->n_trajectory_frame_sets; + + return(TNG_SUCCESS); +} tng_function_status tng_current_frame_set_get (const tng_trajectory_t tng_data, @@ -6743,7 +6751,303 @@ tng_function_status tng_current_frame_set_get return(TNG_SUCCESS); } -tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, + const int64_t nr) +{ + int64_t long_stride_length, medium_stride_length; + int64_t file_pos, curr_nr = 0; + tng_trajectory_frame_set_t frame_set = + &tng_data->current_trajectory_frame_set; + tng_gen_block_t block; + tng_function_status stat; + + if(nr > tng_data->n_trajectory_frame_sets) + { + return(TNG_FAILURE); + } + + long_stride_length = tng_data->long_stride_length; + medium_stride_length = tng_data->medium_stride_length; + + /* FIXME: The frame set number of the current frame set is not stored */ + + if(nr < tng_data->n_trajectory_frame_sets - 1 - nr) + { + /* Start from the beginning */ + file_pos = tng_data->first_trajectory_frame_set_input_file_pos; + } + else + { + /* Start from the end */ + file_pos = tng_data->last_trajectory_frame_set_input_file_pos; + curr_nr = tng_data->n_trajectory_frame_sets - 1; + } + if(file_pos <= 0) + { + return(TNG_FAILURE); + } + + tng_block_init(&block); + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + tng_data->current_trajectory_frame_set_input_file_pos = file_pos; + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + + file_pos = tng_data->current_trajectory_frame_set_input_file_pos; + + /* Take long steps forward until a long step forward would be too long or + * the right frame set is found */ + while(file_pos > 0 && curr_nr + long_stride_length <= nr) + { + file_pos = frame_set->long_stride_next_frame_set_file_pos; + curr_nr += long_stride_length; + if(file_pos > 0) + { + fseek(tng_data->input_file, file_pos, SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Take medium steps forward until a medium step forward would be too long + * or the right frame set is found */ + while(file_pos > 0 && curr_nr + medium_stride_length <= nr) + { + file_pos = frame_set->medium_stride_next_frame_set_file_pos; + curr_nr += medium_stride_length; + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Take one step forward until the right frame set is found */ + while(file_pos > 0 && curr_nr < nr) + { + file_pos = frame_set->next_frame_set_file_pos; + ++curr_nr; + + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Take long steps backward until a long step backward would be too long + * or the right frame set is found */ + while(file_pos > 0 && curr_nr - long_stride_length >= nr) + { + file_pos = frame_set->long_stride_prev_frame_set_file_pos; + curr_nr -= long_stride_length; + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Take medium steps backward until a medium step backward would be too long + * or the right frame set is found */ + while(file_pos > 0 && curr_nr - medium_stride_length >= nr) + { + file_pos = frame_set->medium_stride_prev_frame_set_file_pos; + curr_nr -= medium_stride_length; + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* Take one step backward until the right frame set is found */ + while(file_pos > 0 && curr_nr > nr) + { + file_pos = frame_set->prev_frame_set_file_pos; + --curr_nr; + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + /* If for some reason the current frame set is not yet found, + * take one step forward until the right frame set is found */ + while(file_pos > 0 && curr_nr < nr) + { + file_pos = frame_set->next_frame_set_file_pos; + ++curr_nr; + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + /* Read block headers first to see what block is found. */ + stat = tng_block_header_read(tng_data, block); + if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + + if(tng_block_read_next(tng_data, block, + TNG_SKIP_HASH) != TNG_SUCCESS) + { + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + } + if(curr_nr == nr) + { + tng_block_destroy(&block); + return(TNG_SUCCESS); + } + } + + tng_block_destroy(&block); + return(TNG_FAILURE); +} + +tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, const int64_t frame) { int64_t first_frame, last_frame, n_frames_per_frame_set; @@ -6779,6 +7083,7 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, if(file_pos <= 0) { + tng_block_destroy(&block); return(TNG_FAILURE); } } @@ -6816,16 +7121,19 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, first_frame = max(frame_set->first_frame, 0); last_frame = first_frame + frame_set->n_frames - 1; - file_pos = tng_data->current_trajectory_frame_set_input_file_pos; - + if(frame >= first_frame && frame <= last_frame) { tng_block_destroy(&block); return(TNG_SUCCESS); } + file_pos = tng_data->current_trajectory_frame_set_input_file_pos; + + /* Take long steps forward until a long step forward would be too long or + * the right frame set is found */ while(file_pos > 0 && first_frame + long_stride_length * - n_frames_per_frame_set < frame) + n_frames_per_frame_set <= frame) { file_pos = frame_set->long_stride_next_frame_set_file_pos; if(file_pos > 0) @@ -6854,8 +7162,11 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* Take medium steps forward until a medium step forward would be too long + * or the right frame set is found */ while(file_pos > 0 && first_frame + medium_stride_length * - n_frames_per_frame_set < frame) + n_frames_per_frame_set <= frame) { file_pos = frame_set->medium_stride_next_frame_set_file_pos; if(file_pos > 0) @@ -6886,6 +7197,8 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* Take one step forward until the right frame set is found */ while(file_pos > 0 && first_frame < frame && last_frame < frame) { file_pos = frame_set->next_frame_set_file_pos; @@ -6917,8 +7230,11 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* Take long steps backward until a long step backward would be too long + * or the right frame set is found */ while(file_pos > 0 && first_frame - long_stride_length * - n_frames_per_frame_set > frame) + n_frames_per_frame_set >= frame) { file_pos = frame_set->long_stride_prev_frame_set_file_pos; if(file_pos > 0) @@ -6949,8 +7265,11 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* Take medium steps backward until a medium step backward would be too long + * or the right frame set is found */ while(file_pos > 0 && first_frame - medium_stride_length * - n_frames_per_frame_set > frame) + n_frames_per_frame_set >= frame) { file_pos = frame_set->medium_stride_prev_frame_set_file_pos; if(file_pos > 0) @@ -6981,6 +7300,8 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* Take one step backward until the right frame set is found */ while(file_pos > 0 && first_frame > frame && last_frame > frame) { file_pos = frame_set->prev_frame_set_file_pos; @@ -7012,6 +7333,9 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + + /* If for some reason the current frame set is not yet found, + * take one step forward until the right frame set is found */ while(file_pos > 0 && first_frame < frame && last_frame < frame) { file_pos = frame_set->next_frame_set_file_pos; @@ -7043,6 +7367,7 @@ tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, return(TNG_SUCCESS); } } + tng_block_destroy(&block); return(TNG_FAILURE); } @@ -8086,7 +8411,7 @@ tng_function_status tng_frame_data_write(tng_trajectory_t tng_data, tng_data->input_file = tng_data->output_file; - stat = tng_frame_set_find(tng_data, frame_nr); + stat = tng_frame_set_of_frame_find(tng_data, frame_nr); if(stat != TNG_SUCCESS) { @@ -8424,7 +8749,7 @@ tng_function_status tng_frame_particle_data_write(tng_trajectory_t tng_data, tng_data->input_file = tng_data->output_file; - stat = tng_frame_set_find(tng_data, frame_nr); + stat = tng_frame_set_of_frame_find(tng_data, frame_nr); frame_set = &tng_data->current_trajectory_frame_set; @@ -9068,7 +9393,7 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, block_index = -1; - stat = tng_frame_set_find(tng_data, start_frame_nr); + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { return(stat); @@ -9412,7 +9737,7 @@ tng_function_status tng_particle_data_interval_get(tng_trajectory_t tng_data, block_index = -1; - stat = tng_frame_set_find(tng_data, start_frame_nr); + stat = tng_frame_set_of_frame_find(tng_data, start_frame_nr); if(stat != TNG_SUCCESS) { return(stat); diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 0530112..3de8d67 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -924,6 +924,22 @@ tng_function_status tng_num_frames_per_frame_set_get_ } /** + * @brief Get the number of frame sets. + * @param tng_data is the trajectory from which to get the number of frame sets. + * @param n is pointing to a value set to the number of frame sets. + * @return TNG_SUCCESS (0) if successful. + */ +tng_function_status tng_num_frame_sets_get + (const tng_trajectory_t tng_data, + int64_t *n); +tng_function_status tng_num_frame_sets_get_ + (const tng_trajectory_t tng_data, + int64_t *n) +{ + return(tng_num_frame_sets_get(tng_data, n)); +} + +/** * @brief Get the current trajectory frame set. * @param tng_data is the trajectory from which to get the frame set. * @param frame_set is pointing to the memory position of the found frame set. @@ -939,6 +955,22 @@ tng_function_status tng_current_frame_set_get_ return(tng_current_frame_set_get(tng_data, frame_set)); } +/** + * @brief Find the requested frame set number. + * @param tng_data is the trajectory from which to get the frame set. + * @param nr is the frame set number to search for. + * @details tng_data->current_trajectory_frame_set will contain the + * found trajectory if successful. + * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error + * has occurred or TNG_CRITICAL (2) if a major error has occured. + */ +tng_function_status tng_frame_set_nr_find(tng_trajectory_t tng_data, + const int64_t nr); +tng_function_status tng_frame_set_nr_find_(tng_trajectory_t tng_data, + const int64_t *nr) +{ + return(tng_frame_set_nr_find(tng_data, *nr)); +} /** * @brief Find the frame set containing a specific frame. @@ -949,12 +981,12 @@ tng_function_status tng_current_frame_set_get_ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error * has occurred or TNG_CRITICAL (2) if a major error has occured. */ -tng_function_status tng_frame_set_find(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_of_frame_find(tng_trajectory_t tng_data, const int64_t frame); -tng_function_status tng_frame_set_find_(tng_trajectory_t tng_data, +tng_function_status tng_frame_set_of_frame_find_(tng_trajectory_t tng_data, const int64_t *frame) { - return(tng_frame_set_find(tng_data, *frame)); + return(tng_frame_set_of_frame_find(tng_data, *frame)); } /** |