diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/lib/tng_io.c | 320 |
1 files changed, 237 insertions, 83 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 492b463..b91db67 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -3906,6 +3906,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, 0, tng_data-> compress_algo_pos, &new_len); + if(algo_find_n_frames < n_frames) { dest = tng_compress_pos(start_pos, (int)n_particles, @@ -4015,9 +4016,9 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data, } offset = (unsigned long)((char *)start_pos - block->block_contents); - + block->block_contents_size = new_len + offset; - + temp = realloc(block->block_contents, block->block_contents_size); if(!temp) { @@ -4054,6 +4055,8 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, unsigned long offset; int result; (void)tng_data; + + TNG_ASSERT(uncompressed_len, "TNG library: The full length of the uncompressed data must be > 0."); if(block->id != TNG_TRAJ_POSITIONS && block->id != TNG_TRAJ_VELOCITIES) @@ -4067,7 +4070,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data, printf("TNG library: Data type not supported.\n"); return(TNG_FAILURE); } - + if(type == TNG_FLOAT_DATA) { f_dest = malloc(uncompressed_len); @@ -4308,7 +4311,7 @@ static tng_function_status tng_allocate_particle_data_mem data->stride_length = tng_max_i64(1, stride_length); data->n_values_per_frame = n_values_per_frame; frame_alloc = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length; - + if(data->datatype == TNG_CHAR_DATA) { data->strings = malloc(sizeof(char ***) * frame_alloc); @@ -4557,7 +4560,7 @@ static tng_function_status tng_particle_data_read default: size = sizeof(double); } - + /* If the block does not exist, create it */ if(tng_particle_data_find(tng_data, block->id, &data) != TNG_SUCCESS) { @@ -4571,7 +4574,7 @@ static tng_function_status tng_particle_data_read } if(tng_particle_data_block_create(tng_data, block_type_flag) != - TNG_SUCCESS) + TNG_SUCCESS) { printf("TNG library: Cannot create particle data block. %s: %d\n", __FILE__, __LINE__); @@ -4606,6 +4609,7 @@ static tng_function_status tng_particle_data_read data->n_frames = 0; data->codec_id = codec_id; data->compression_multiplier = multiplier; + data->last_retrieved_frame = -1; } if(/*block_type_flag == TNG_TRAJECTORY_BLOCK &&*/ @@ -4621,8 +4625,6 @@ static tng_function_status tng_particle_data_read n_frames_div = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length; - data->last_retrieved_frame = -1; - if(codec_id != TNG_UNCOMPRESSED) { data_size = (unsigned long)(n_frames_div * size * n_particles * n_values); @@ -5216,8 +5218,6 @@ static tng_function_status tng_particle_data_block_write data->codec_id = TNG_UNCOMPRESSED; break; case TNG_TNG_COMPRESSION: -/* printf("TNG library: TEST: frame_step: %"PRId64", n_particles: %"PRId64", block_contents_size: %"PRId64", start_pos: %"PRId64"\n", - frame_step, n_particles, block->block_contents_size, data_start_pos);*/ stat = tng_compress(tng_data, block, frame_step, n_particles, data->datatype, block->block_contents + data_start_pos); @@ -5543,12 +5543,11 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data, data->n_frames = 0; data->codec_id = codec_id; data->compression_multiplier = multiplier; + data->last_retrieved_frame = -1; } n_frames_div = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length; - data->last_retrieved_frame = -1; - if(codec_id != TNG_UNCOMPRESSED) { switch(codec_id) @@ -9772,7 +9771,7 @@ tng_function_status DECLSPECDLLEXPORT tng_implicit_num_particles_set TNG_ASSERT(n >= 0, "TNG library: The number of molecules must be >= 0"); diff = n - tng_data->n_particles; - + if(diff == 0) { return(TNG_SUCCESS); @@ -11043,6 +11042,138 @@ tng_function_status DECLSPECDLLEXPORT tng_block_read_next(tng_trajectory_t tng_d } } +tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_current_only_data_from_block_id + (tng_trajectory_t tng_data, + const char hash_mode, + const int64_t block_id) +{ + long file_pos; + tng_gen_block_t block; + tng_function_status stat; + int found_flag = 1; + + TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); + + if(tng_input_file_init(tng_data) != TNG_SUCCESS) + { + return(TNG_CRITICAL); + } + + file_pos = (long)tng_data->current_trajectory_frame_set_input_file_pos; + + if(file_pos < 0) + { + /* No current frame set. This means that the first frame set must be + * read */ + found_flag = 0; + file_pos = (long)tng_data->first_trajectory_frame_set_input_file_pos; + } + + if(file_pos > 0) + { + fseek(tng_data->input_file, + file_pos, + SEEK_SET); + } + else + { + return(TNG_FAILURE); + } + + tng_block_init(&block); + + if(!tng_data->input_file_len) + { + fseek(tng_data->input_file, 0, SEEK_END); + tng_data->input_file_len = ftell(tng_data->input_file); + 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) + { + printf("TNG library: Cannot read block header at pos %ld. %s: %d\n", + file_pos, __FILE__, __LINE__); + tng_block_destroy(&block); + return(TNG_CRITICAL); + } + /* If the current frame set had already been read skip its block contents */ + if(found_flag) + { + fseek(tng_data->input_file, block->block_contents_size, SEEK_CUR); + } + /* Otherwiese read the frame set block */ + else + { + stat = tng_block_read_next(tng_data, block, + hash_mode); + if(stat != TNG_SUCCESS) + { + printf("TNG library: Cannot read frame set block. %s: %d\n", __FILE__, __LINE__); + tng_block_destroy(&block); + return(stat); + } + } + file_pos = ftell(tng_data->input_file); + + found_flag = 0; + + /* Read only blocks of the requested ID + * until next frame set block */ + stat = tng_block_header_read(tng_data, block); + while(file_pos < tng_data->input_file_len && + stat != TNG_CRITICAL && + block->id != TNG_TRAJECTORY_FRAME_SET) + { + if(block->id == block_id) + { + stat = tng_block_read_next(tng_data, block, + hash_mode); + if(stat != TNG_CRITICAL) + { + file_pos = ftell(tng_data->input_file); + found_flag = 1; + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + else + { + file_pos += block->block_contents_size + block->header_contents_size; + fseek(tng_data->input_file, block->block_contents_size, SEEK_CUR); + if(file_pos < tng_data->input_file_len) + { + stat = tng_block_header_read(tng_data, block); + } + } + } + if(stat == TNG_CRITICAL) + { + printf("TNG library: Cannot read block header at pos %ld. %s: %d\n", + file_pos, __FILE__, __LINE__); + tng_block_destroy(&block); + return(stat); + } + + if(block->id == TNG_TRAJECTORY_FRAME_SET) + { + fseek(tng_data->input_file, file_pos, SEEK_SET); + } + + tng_block_destroy(&block); + + if(found_flag) + { + return(TNG_SUCCESS); + } + else + { + return(TNG_FAILURE); + } +} tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next (tng_trajectory_t tng_data, @@ -11197,55 +11328,12 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_read_next_only_data_from_blo if(tng_block_read_next(tng_data, block, hash_mode) == TNG_SUCCESS) { - tng_data->n_trajectory_frame_sets++; - file_pos = ftell(tng_data->input_file); - /* Read only blocks of the requested ID - * until next frame set block */ - stat = tng_block_header_read(tng_data, block); - while(file_pos < tng_data->input_file_len && - stat != TNG_CRITICAL && - block->id != TNG_TRAJECTORY_FRAME_SET) - { - if(block->id == block_id) - { - stat = tng_block_read_next(tng_data, block, - hash_mode); - if(stat != TNG_CRITICAL) - { - file_pos = ftell(tng_data->input_file); - if(file_pos < tng_data->input_file_len) - { - stat = tng_block_header_read(tng_data, block); - } - } - } - else - { - file_pos += block->block_contents_size + block->header_contents_size; - fseek(tng_data->input_file, block->block_contents_size, SEEK_CUR); - if(file_pos < tng_data->input_file_len) - { - stat = tng_block_header_read(tng_data, block); - } - } - } - if(stat == TNG_CRITICAL) - { - printf("TNG library: Cannot read block header at pos %ld. %s: %d\n", - file_pos, __FILE__, __LINE__); - tng_block_destroy(&block); - return(stat); - } - - if(block->id == TNG_TRAJECTORY_FRAME_SET) - { - fseek(tng_data->input_file, file_pos, SEEK_SET); - } + stat = tng_frame_set_read_current_only_data_from_block_id(tng_data, hash_mode, block_id); } tng_block_destroy(&block); - return(TNG_SUCCESS); + return(stat); } tng_function_status tng_frame_set_write(tng_trajectory_t tng_data, @@ -11695,6 +11783,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add data->values = 0; /* FIXME: Memory leak from strings. */ data->strings = 0; + data->last_retrieved_frame = -1; } data->datatype = datatype; @@ -11847,6 +11936,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add data->values = 0; /* FIXME: Memory leak from strings. */ data->strings = 0; + data->last_retrieved_frame = -1; } data->stride_length = tng_max_i64(stride_length, 1); @@ -15033,11 +15123,13 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read int64_t *retrieved_frame_number, double *retrieved_time) { + tng_trajectory_frame_set_t frame_set; tng_particle_data_t data; tng_function_status stat; int size; int64_t i, data_size, n_particles; void *temp; + long file_pos; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(values, "TNG library: The pointer to the values array must not be a NULL pointer"); @@ -15045,10 +15137,18 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read TNG_ASSERT(retrieved_frame_number, "TNG library: The pointer to the frame number of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_time, "TNG library: The pointer to the time of the returned data must not be a NULL pointer"); + frame_set = &tng_data->current_trajectory_frame_set; + stat = tng_particle_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { - stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + stat = tng_frame_set_read_current_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + file_pos = ftell(tng_data->input_file); + while(stat != TNG_SUCCESS && file_pos < tng_data->input_file_len) + { + stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + file_pos = ftell(tng_data->input_file); + } if(stat != TNG_SUCCESS) { return(stat); @@ -15056,7 +15156,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read stat = tng_particle_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { - return(TNG_FAILURE); + return(stat); } } if(data->last_retrieved_frame < 0) @@ -15066,23 +15166,47 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read else { i = data->last_retrieved_frame + data->stride_length; - if(i >= data->n_frames) + if(i < frame_set->first_frame || i >= frame_set->first_frame + frame_set->n_frames) { - stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + stat = tng_frame_set_of_frame_find(tng_data, i); + if(stat != TNG_SUCCESS) + { + return(stat); + } + stat = tng_frame_set_read_current_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); if(stat != TNG_SUCCESS) { + printf("Cannot read data blocks of frame set. %s: %d\n", + __FILE__, __LINE__); return(stat); } - i = data->first_frame_with_data; } } data->last_retrieved_frame = i; *retrieved_frame_number = i; - *retrieved_time = tng_data->current_trajectory_frame_set.first_frame_time + - (i - tng_data->current_trajectory_frame_set.first_frame) * - tng_data->time_per_frame; + if(frame_set->first_frame_time >= 0 && tng_data->time_per_frame >= 0) + { + *retrieved_time = frame_set->first_frame_time + + (i - frame_set->first_frame) * + tng_data->time_per_frame; + } + else + { + *retrieved_time = 0; + } + +// printf("TEMP: First frame time: %e, i: %"PRId64", First frame: %"PRId64", Time per frame: %e\n", +// frame_set->first_frame_time, i, frame_set->first_frame, tng_data->time_per_frame); +// printf("TNG library: TEMP: first_frame_with_data: %"PRId64"\n", data->first_frame_with_data); - i = (i - data->first_frame_with_data) / data->stride_length; + if(data->stride_length > 1) + { + i = (i - data->first_frame_with_data) / data->stride_length; + } + else + { + i = (i - frame_set->first_frame) / data->stride_length; + } tng_num_particles_get(tng_data, &n_particles); @@ -15104,6 +15228,9 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read } data_size = size * n_particles * data->n_values_per_frame; + +// printf("TNG library: TEMP: i = %"PRId64", data_size = %"PRId64", size = %d, n_particles = %"PRId64", n_values_per_frame = %"PRId64"\n", +// i, data_size, size, n_particles, data->n_values_per_frame); temp = realloc(*values, data_size); if(!temp) @@ -15117,7 +15244,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read *values = temp; - memcpy(*values, (char *)data->values + i * data_size, data_size); + memcpy(*values, (char *)(data->values + i * data_size), data_size); return(TNG_SUCCESS); } @@ -15130,11 +15257,13 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read int64_t *retrieved_frame_number, double *retrieved_time) { + tng_trajectory_frame_set_t frame_set; tng_non_particle_data_t data; tng_function_status stat; int size; int64_t i, data_size; void *temp; + long file_pos; TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(values, "TNG library: The pointer to the values array must not be a NULL pointer"); @@ -15142,18 +15271,21 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read TNG_ASSERT(retrieved_frame_number, "TNG library: The pointer to the frame number of the returned data must not be a NULL pointer"); TNG_ASSERT(retrieved_time, "TNG library: The pointer to the time of the returned data must not be a NULL pointer"); + frame_set = &tng_data->current_trajectory_frame_set; + stat = tng_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { - stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); - if(stat != TNG_SUCCESS) + stat = tng_frame_set_read_current_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + file_pos = ftell(tng_data->input_file); + while(stat != TNG_SUCCESS && file_pos < tng_data->input_file_len) { - return(stat); + stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + file_pos = ftell(tng_data->input_file); } - stat = tng_data_find(tng_data, block_id, &data); if(stat != TNG_SUCCESS) { - return(TNG_FAILURE); + return(stat); } } if(data->last_retrieved_frame < 0) @@ -15163,23 +15295,45 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read else { i = data->last_retrieved_frame + data->stride_length; - if(i >= data->n_frames) + if(i < frame_set->first_frame || i >= frame_set->first_frame + frame_set->n_frames) { - stat = tng_frame_set_read_next_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); + stat = tng_frame_set_of_frame_find(tng_data, i); + if(stat != TNG_SUCCESS) + { + printf("Cannot find frame set of frame %"PRId64". %s: %d\n", + frame_set->first_frame + i, __FILE__, __LINE__); + return(stat); + } + stat = tng_frame_set_read_current_only_data_from_block_id(tng_data, TNG_USE_HASH, block_id); if(stat != TNG_SUCCESS) { + printf("Cannot read data blocks of frame set. %s: %d\n", + __FILE__, __LINE__); return(stat); } - i = data->first_frame_with_data; } } data->last_retrieved_frame = i; *retrieved_frame_number = i; - *retrieved_time = tng_data->current_trajectory_frame_set.first_frame_time + - (i - tng_data->current_trajectory_frame_set.first_frame) * - tng_data->time_per_frame; - - i = (i - data->first_frame_with_data) / data->stride_length; + if(frame_set->first_frame_time >= 0 && tng_data->time_per_frame >= 0) + { + *retrieved_time = frame_set->first_frame_time + + (i - frame_set->first_frame) * + tng_data->time_per_frame; + } + else + { + *retrieved_time = 0; + } + + if(data->stride_length > 1) + { + i = (i - data->first_frame_with_data) / data->stride_length; + } + else + { + i = (i - frame_set->first_frame) / data->stride_length; + } *data_type = data->datatype; @@ -15212,7 +15366,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read *values = temp; - memcpy(*values, (char *)data->values + i * data_size, data_size); + memcpy(*values, (char *)(data->values + i * data_size), data_size); return(TNG_SUCCESS); } @@ -16154,7 +16308,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_pos_write TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup."); TNG_ASSERT(frame_nr >= 0, "TNG library: frame_nr must be >= 0."); TNG_ASSERT(positions, "TNG library: positions must not be a NULL pointer"); - + return(tng_util_generic_write(tng_data, frame_nr, positions, 3, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_PARTICLE_BLOCK_DATA, |