diff options
| -rw-r--r-- | src/lib/tng_io.c | 556 |
1 files changed, 285 insertions, 271 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index 0bf9d18..243f41b 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -3734,13 +3734,16 @@ static tng_function_status tng_allocate_particle_data_mem union data_values ***values; int64_t i, j, k; - for(i = data->n_frames; i--;) + if(data->values) { - for(j = n_particles; j--;) + for(i = data->n_frames; i--;) { - free(data->values[i][j]); + for(j = n_particles; j--;) + { + free(data->values[i][j]); + } + free(data->values[i]); } - free(data->values[i]); } data->n_frames = n_frames; n_frames = tng_max(1, n_frames); @@ -4422,126 +4425,77 @@ static tng_function_status tng_particle_data_block_write offset += sizeof(n_particles); - /* FIXME: If not using a union to store data a whole dimension or the - * whole block can be written at once if byte swapping is not needed */ - switch(data->datatype) + if(data->values) { - case TNG_FLOAT_DATA: - /* For speed reasons the compression multiplier is not used if the data - * is not compressed. */ - if(data->codec_id == TNG_UNCOMPRESSED) + /* FIXME: If not using a union to store data a whole dimension or the + * whole block can be written at once if byte swapping is not needed */ + switch(data->datatype) { - for(i = 0; i < data->n_frames / stride_length; i++) + case TNG_FLOAT_DATA: + /* For speed reasons the compression multiplier is not used if the data + * is not compressed. */ + if(data->codec_id == TNG_UNCOMPRESSED) { - first_dim_values = data->values[i]; - for(j = num_first_particle; j < num_first_particle + n_particles; - j++) + for(i = 0; i < data->n_frames / stride_length; i++) { - second_dim_values = first_dim_values[j]; - for(k = 0; k < data->n_values_per_frame; k++) + first_dim_values = data->values[i]; + for(j = num_first_particle; j < num_first_particle + n_particles; + j++) { - memcpy(block->block_contents+offset, - &second_dim_values[k].f, - size); - if(tng_data->output_endianness_swap_func_32) + second_dim_values = first_dim_values[j]; + for(k = 0; k < data->n_values_per_frame; k++) { - if(tng_data->output_endianness_swap_func_32(tng_data, - (int32_t *)block->header_contents+offset) - != TNG_SUCCESS) + memcpy(block->block_contents+offset, + &second_dim_values[k].f, + size); + if(tng_data->output_endianness_swap_func_32) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_32(tng_data, + (int32_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } + offset += size; } - offset += size; } } } - } - else - { - multiplier = data->compression_multiplier; - for(i = 0; i < data->n_frames / stride_length; i++) + else { - first_dim_values = data->values[i]; - for(j = num_first_particle; j < num_first_particle + n_particles; - j++) + multiplier = data->compression_multiplier; + for(i = 0; i < data->n_frames / stride_length; i++) { - second_dim_values = first_dim_values[j]; - for(k = 0; k < data->n_values_per_frame; k++) + first_dim_values = data->values[i]; + for(j = num_first_particle; j < num_first_particle + n_particles; + j++) { - f_temp = second_dim_values[k].f * multiplier; - memcpy(block->block_contents+offset, - &f_temp, size); - if(tng_data->output_endianness_swap_func_32) + second_dim_values = first_dim_values[j]; + for(k = 0; k < data->n_values_per_frame; k++) { - if(tng_data->output_endianness_swap_func_32(tng_data, - (int32_t *)block->header_contents+offset) - != TNG_SUCCESS) + f_temp = second_dim_values[k].f * multiplier; + memcpy(block->block_contents+offset, + &f_temp, size); + if(tng_data->output_endianness_swap_func_32) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_32(tng_data, + (int32_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } + offset += size; } - offset += size; } } } - } - break; + break; - case TNG_INT_DATA: - for(i = 0; i < data->n_frames / stride_length; i++) - { - first_dim_values = data->values[i]; - for(j = num_first_particle; j < num_first_particle + n_particles; - j++) - { - second_dim_values = first_dim_values[j]; - for(k = 0; k < data->n_values_per_frame; k++) - { - memcpy(block->block_contents+offset, - &second_dim_values[k].i, - size); - if(tng_data->output_endianness_swap_func_64) - { - if(tng_data->output_endianness_swap_func_64(tng_data, - (int64_t *)block->header_contents+offset) - != TNG_SUCCESS) - { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); - } - } - offset += size; - } - } - } - break; - case TNG_CHAR_DATA: - for(i = 0; i < data->n_frames / stride_length; i++) - { - first_dim_values = data->values[i]; - for(j = num_first_particle; j < num_first_particle + n_particles; - j++) - { - second_dim_values = first_dim_values[j]; - for(k = 0; k < data->n_values_per_frame; k++) - { - len = strlen(second_dim_values[k].c) + 1; - strncpy(block->block_contents+offset, - second_dim_values[k].c, len); - offset += len; - } - } - } - break; - case TNG_DOUBLE_DATA: - default: - /* For speed reasons the compression multiplier is not used if the data - * is not compressed.*/ - if(data->codec_id == TNG_UNCOMPRESSED) - { + case TNG_INT_DATA: for(i = 0; i < data->n_frames / stride_length; i++) { first_dim_values = data->values[i]; @@ -4552,8 +4506,8 @@ static tng_function_status tng_particle_data_block_write for(k = 0; k < data->n_values_per_frame; k++) { memcpy(block->block_contents+offset, - &second_dim_values[k].d, - size); + &second_dim_values[k].i, + size); if(tng_data->output_endianness_swap_func_64) { if(tng_data->output_endianness_swap_func_64(tng_data, @@ -4568,10 +4522,8 @@ static tng_function_status tng_particle_data_block_write } } } - } - else - { - multiplier = data->compression_multiplier; + break; + case TNG_CHAR_DATA: for(i = 0; i < data->n_frames / stride_length; i++) { first_dim_values = data->values[i]; @@ -4581,26 +4533,84 @@ static tng_function_status tng_particle_data_block_write second_dim_values = first_dim_values[j]; for(k = 0; k < data->n_values_per_frame; k++) { - d_temp = second_dim_values[k].d * multiplier; - memcpy(block->block_contents+offset, - &d_temp, - size); - if(tng_data->output_endianness_swap_func_64) + len = strlen(second_dim_values[k].c) + 1; + strncpy(block->block_contents+offset, + second_dim_values[k].c, len); + offset += len; + } + } + } + break; + case TNG_DOUBLE_DATA: + default: + /* For speed reasons the compression multiplier is not used if the data + * is not compressed.*/ + if(data->codec_id == TNG_UNCOMPRESSED) + { + for(i = 0; i < data->n_frames / stride_length; i++) + { + first_dim_values = data->values[i]; + for(j = num_first_particle; j < num_first_particle + n_particles; + j++) + { + second_dim_values = first_dim_values[j]; + for(k = 0; k < data->n_values_per_frame; k++) { - if(tng_data->output_endianness_swap_func_64(tng_data, - (int64_t *)block->header_contents+offset) - != TNG_SUCCESS) + memcpy(block->block_contents+offset, + &second_dim_values[k].d, + size); + if(tng_data->output_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_64(tng_data, + (int64_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } + offset += size; + } + } + } + } + else + { + multiplier = data->compression_multiplier; + for(i = 0; i < data->n_frames / stride_length; i++) + { + first_dim_values = data->values[i]; + for(j = num_first_particle; j < num_first_particle + n_particles; + j++) + { + second_dim_values = first_dim_values[j]; + for(k = 0; k < data->n_values_per_frame; k++) + { + d_temp = second_dim_values[k].d * multiplier; + memcpy(block->block_contents+offset, + &d_temp, + size); + if(tng_data->output_endianness_swap_func_64) + { + if(tng_data->output_endianness_swap_func_64(tng_data, + (int64_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } + } + offset += size; } - offset += size; } } } } } + else + { + memset(block->block_contents+offset, 0, block->block_contents_size - offset); + } switch(data->codec_id) @@ -4720,20 +4730,23 @@ static tng_function_status tng_allocate_data_mem union data_values **values; int64_t i, j; - for(i = data->n_frames; i--;) + if(data->values) { - if(data->datatype == TNG_CHAR_DATA) + for(i = data->n_frames; i--;) { - for(j = data->n_values_per_frame; j--;) + if(data->datatype == TNG_CHAR_DATA) { - if(data->values[i][j].c) + for(j = data->n_values_per_frame; j--;) { - free(data->values[i][j].c); - data->values[i][j].c = 0; + if(data->values[i][j].c) + { + free(data->values[i][j].c); + data->values[i][j].c = 0; + } } } + free(data->values[i]); } - free(data->values[i]); } data->n_frames = n_frames; data->stride_length = tng_max(1, stride_length); @@ -5297,104 +5310,68 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, offset += sizeof(data->stride_length); } - /* FIXME: If not using a union to store data a whole dimension or the - * whole block can be written at once if byte swapping is not needed */ - switch(data->datatype) + if(data->values) { - case TNG_FLOAT_DATA: - /* For speed reasons the compression multiplier is not used if the data - * is not compressed.*/ - if(data->codec_id == TNG_UNCOMPRESSED) + /* FIXME: If not using a union to store data a whole dimension or the + * whole block can be written at once if byte swapping is not needed */ + switch(data->datatype) { - for(i = 0; i < n_frames / stride_length; i++) + case TNG_FLOAT_DATA: + /* For speed reasons the compression multiplier is not used if the data + * is not compressed.*/ + if(data->codec_id == TNG_UNCOMPRESSED) { - for(j = 0; j < data->n_values_per_frame; j++) + for(i = 0; i < n_frames / stride_length; i++) { - memcpy(block->block_contents+offset, &data->values[i][j].f, - size); - if(tng_data->output_endianness_swap_func_32) + for(j = 0; j < data->n_values_per_frame; j++) { - if(tng_data->output_endianness_swap_func_32(tng_data, - (int32_t *)block->header_contents+offset) - != TNG_SUCCESS) + memcpy(block->block_contents+offset, &data->values[i][j].f, + size); + if(tng_data->output_endianness_swap_func_32) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_32(tng_data, + (int32_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } + offset += size; } - offset += size; } } - } - else - { - multiplier = data->compression_multiplier; - for(i = 0; i < n_frames / stride_length; i++) + else { - for(j = 0; j < data->n_values_per_frame; j++) + multiplier = data->compression_multiplier; + for(i = 0; i < n_frames / stride_length; i++) { - f_temp = data->values[i][j].f * multiplier; - memcpy(block->block_contents+offset, &f_temp, - size); - if(tng_data->output_endianness_swap_func_32) + for(j = 0; j < data->n_values_per_frame; j++) { - if(tng_data->output_endianness_swap_func_32(tng_data, - (int32_t *)block->header_contents+offset) - != TNG_SUCCESS) + f_temp = data->values[i][j].f * multiplier; + memcpy(block->block_contents+offset, &f_temp, + size); + if(tng_data->output_endianness_swap_func_32) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_32(tng_data, + (int32_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } - } - offset += size; - } - } - } - break; - case TNG_INT_DATA: - for(i = 0; i < n_frames / stride_length; i++) - { - for(j = 0; j < data->n_values_per_frame; j++) - { - memcpy(block->block_contents+offset, &data->values[i][j].i, - size); - if(tng_data->output_endianness_swap_func_64) - { - if(tng_data->output_endianness_swap_func_64(tng_data, - (int64_t *)block->header_contents+offset) - != TNG_SUCCESS) - { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + offset += size; } } - offset += size; } - } - break; - case TNG_CHAR_DATA: - for(i = 0; i < n_frames / stride_length; i++) - { - for(j = 0; j < data->n_values_per_frame; j++) - { - len = strlen(data->values[i][j].c) + 1; - strncpy(block->block_contents+offset, data->values[i][j].c, - len); - offset += len; - } - } - break; - case TNG_DOUBLE_DATA: - default: - /* For speed reasons the compression multiplier is not used if the data - * is not compressed.*/ - if(data->codec_id == TNG_UNCOMPRESSED) - { + break; + case TNG_INT_DATA: for(i = 0; i < n_frames / stride_length; i++) { for(j = 0; j < data->n_values_per_frame; j++) { - memcpy(block->block_contents+offset, &data->values[i][j].d, + memcpy(block->block_contents+offset, &data->values[i][j].i, size); if(tng_data->output_endianness_swap_func_64) { @@ -5409,32 +5386,75 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data, offset += size; } } - } - else - { - multiplier = data->compression_multiplier; + break; + case TNG_CHAR_DATA: for(i = 0; i < n_frames / stride_length; i++) { for(j = 0; j < data->n_values_per_frame; j++) { - d_temp = data->values[i][j].d * multiplier; - memcpy(block->block_contents+offset, &d_temp, - size); - if(tng_data->output_endianness_swap_func_64) + len = strlen(data->values[i][j].c) + 1; + strncpy(block->block_contents+offset, data->values[i][j].c, + len); + offset += len; + } + } + break; + case TNG_DOUBLE_DATA: + default: + /* For speed reasons the compression multiplier is not used if the data + * is not compressed.*/ + if(data->codec_id == TNG_UNCOMPRESSED) + { + for(i = 0; i < n_frames / stride_length; i++) + { + for(j = 0; j < data->n_values_per_frame; j++) { - if(tng_data->output_endianness_swap_func_64(tng_data, - (int64_t *)block->header_contents+offset) - != TNG_SUCCESS) + memcpy(block->block_contents+offset, &data->values[i][j].d, + size); + if(tng_data->output_endianness_swap_func_64) { - printf("Cannot swap byte order. %s: %d\n", - __FILE__, __LINE__); + if(tng_data->output_endianness_swap_func_64(tng_data, + (int64_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } } + offset += size; + } + } + } + else + { + multiplier = data->compression_multiplier; + for(i = 0; i < n_frames / stride_length; i++) + { + for(j = 0; j < data->n_values_per_frame; j++) + { + d_temp = data->values[i][j].d * multiplier; + memcpy(block->block_contents+offset, &d_temp, + size); + if(tng_data->output_endianness_swap_func_64) + { + if(tng_data->output_endianness_swap_func_64(tng_data, + (int64_t *)block->header_contents+offset) + != TNG_SUCCESS) + { + printf("Cannot swap byte order. %s: %d\n", + __FILE__, __LINE__); + } + } + offset += size; } - offset += size; } } } } + else + { + memset(block->block_contents+offset, 0, block->block_contents_size - offset); + } switch(data->codec_id) { @@ -7254,6 +7274,8 @@ tng_function_status tng_trajectory_init(tng_trajectory_t *tng_data_p) frame_set->tr_particle_data = 0; frame_set->tr_data = 0; + frame_set->n_written_frames = 0; + frame_set->next_frame_set_file_pos = -1; frame_set->prev_frame_set_file_pos = -1; frame_set->medium_stride_next_frame_set_file_pos = -1; @@ -9931,28 +9953,14 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, data->datatype = datatype; - data->stride_length = 1; + data->stride_length = tng_max(stride_length, 1); data->values = 0; - data->n_values_per_frame = 0; - data->n_frames = 0; + data->n_values_per_frame = n_values_per_frame; + data->n_frames = n_frames; data->codec_id = codec_id; data->compression_multiplier = 1.0; } - /* Allocate memory */ - if(!data->values || data->n_frames != n_frames || - data->n_values_per_frame != n_values_per_frame) - { - if(tng_allocate_data_mem(tng_data, data, n_frames, stride_length, - n_values_per_frame) != - TNG_SUCCESS) - { - printf("Cannot allocate data memory. %s: %d\n", - __FILE__, __LINE__); - return(TNG_CRITICAL); - } - } - switch(datatype) { case TNG_FLOAT_DATA: @@ -9971,6 +9979,16 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, if(new_data) { + /* Allocate memory */ + if(tng_allocate_data_mem(tng_data, data, n_frames, stride_length, + n_values_per_frame) != + TNG_SUCCESS) + { + printf("Cannot allocate data memory. %s: %d\n", + __FILE__, __LINE__); + return(TNG_CRITICAL); + } + orig = new_data; if(n_frames > frame_set->n_written_frames) @@ -10045,17 +10063,17 @@ tng_function_status tng_data_block_add(tng_trajectory_t tng_data, new_data = orig; } - else - { - for(i = 0; i < n_frames / stride_length; i++) - { - first_dim_values = data->values[i]; - for(j = 0; j < n_values_per_frame; j++) - { - first_dim_values[j].d = 0; - } - } - } +// else +// { +// for(i = 0; i < n_frames / stride_length; i++) +// { +// first_dim_values = data->values[i]; +// for(j = 0; j < n_values_per_frame; j++) +// { +// first_dim_values[j].d = 0; +// } +// } +// } return(TNG_SUCCESS); } @@ -10148,10 +10166,10 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, data->datatype = datatype; - data->stride_length = 1; + data->stride_length = tng_max(stride_length, 1); data->values = 0; - data->n_values_per_frame = 0; - data->n_frames = 0; + data->n_values_per_frame = n_values_per_frame; + data->n_frames = n_frames; data->codec_id = codec_id; data->compression_multiplier = 1.0; } @@ -10165,24 +10183,20 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, tot_n_particles = tng_data->n_particles; } - /* Allocate memory */ - if(!data->values || data->n_frames != n_frames || - data->n_values_per_frame != n_values_per_frame) + /* If data values are supplied add that data to the data block. */ + if(new_data) { + /* Allocate memory */ if(tng_allocate_particle_data_mem(tng_data, data, n_frames, stride_length, tot_n_particles, n_values_per_frame) != - TNG_SUCCESS) + TNG_SUCCESS) { printf("Cannot allocate particle data memory. %s: %d\n", - __FILE__, __LINE__); + __FILE__, __LINE__); return(TNG_CRITICAL); } - } - /* If data values are supplied add that data to the data block. */ - if(new_data) - { orig = new_data; if(n_frames > frame_set->n_written_frames) @@ -10282,22 +10296,22 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, new_data = orig; } /* Otherwise fill the data block with zeroes */ - else - { - for(i = 0; i < n_frames / stride_length; i++) - { - first_dim_values = data->values[i]; - for(j = num_first_particle; j < num_first_particle + n_particles; - j++) - { - second_dim_values = first_dim_values[j]; - for(k = 0; k < n_values_per_frame; k++) - { - second_dim_values[k].d = 0; - } - } - } - } +// else +// { +// for(i = 0; i < n_frames / stride_length; i++) +// { +// first_dim_values = data->values[i]; +// for(j = num_first_particle; j < num_first_particle + n_particles; +// j++) +// { +// second_dim_values = first_dim_values[j]; +// for(k = 0; k < n_values_per_frame; k++) +// { +// second_dim_values[k].d = 0; +// } +// } +// } +// } return(TNG_SUCCESS); |