diff options
| -rw-r--r-- | src/lib/tng_io.c | 56 | ||||
| -rw-r--r-- | src/lib/tng_io.h | 240 | ||||
| -rw-r--r-- | src/tests/tng_io_testing.c | 1 |
3 files changed, 172 insertions, 125 deletions
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c index b542ddd..559da77 100644 --- a/src/lib/tng_io.c +++ b/src/lib/tng_io.c @@ -6374,34 +6374,26 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, return(TNG_SUCCESS); } -/* UNTESTED */ -tng_function_status tng_add_data_block(tng_trajectory_t tng_data, - const int64_t id, - const char *block_name, - const char datatype, - const int64_t n_frames, - const int64_t n_values_per_frame, - const int64_t stride_length, - int64_t codec_id, - void *new_data) + + +tng_function_status tng_data_block_add(tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const char datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + int64_t codec_id, + void *new_data) { int i, j, block_index, size, len; struct tng_trajectory_frame_set *frame_set; struct tng_data *data; void *orig; - tng_block_type block_type_flag; frame_set = &tng_data->current_trajectory_frame_set; - if(tng_data->current_trajectory_frame_set_output_file_pos > 0) - { - block_type_flag = TNG_TRAJECTORY_BLOCK; - } - else - { - block_type_flag = TNG_NON_TRAJECTORY_BLOCK; - } - block_index = -1; /* See if there is already a data block of this ID */ if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -6418,6 +6410,7 @@ tng_function_status tng_add_data_block(tng_trajectory_t tng_data, } else { + n_frames = 1; for(i = tng_data->n_data_blocks; i-- ;) { data = &tng_data->non_tr_data[i]; @@ -6435,7 +6428,8 @@ tng_function_status tng_add_data_block(tng_trajectory_t tng_data, if(tng_create_data_block(tng_data, block_type_flag) != TNG_SUCCESS) { - printf("Cannot create data block. %s: %d\n", __FILE__, __LINE__); + printf("Cannot create data block. %s: %d\n", + __FILE__, __LINE__); return(TNG_CRITICAL); } if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -6470,8 +6464,7 @@ tng_function_status tng_add_data_block(tng_trajectory_t tng_data, 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, - n_values_per_frame) != + if(tng_allocate_data_mem(tng_data, data, n_frames, n_values_per_frame)!= TNG_SUCCESS) { printf("Cannot allocate data memory. %s: %d\n", @@ -6548,12 +6541,12 @@ tng_function_status tng_add_data_block(tng_trajectory_t tng_data, return(TNG_SUCCESS); } - tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, - const int64_t n_frames, + const tng_block_type block_type_flag, + int64_t n_frames, const int64_t n_values_per_frame, const int64_t stride_length, const int64_t first_particle_number, @@ -6566,19 +6559,9 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, struct tng_trajectory_frame_set *frame_set; struct tng_particle_data *data; void *orig; - tng_block_type block_type_flag; - + frame_set = &tng_data->current_trajectory_frame_set; - if(tng_data->current_trajectory_frame_set_output_file_pos > 0) - { - block_type_flag = TNG_TRAJECTORY_BLOCK; - } - else - { - block_type_flag = TNG_NON_TRAJECTORY_BLOCK; - } - block_index = -1; /* See if there is already a data block of this ID */ if(block_type_flag == TNG_TRAJECTORY_BLOCK) @@ -6595,6 +6578,7 @@ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, } else { + n_frames = 1; for(i = tng_data->n_particle_data_blocks; i-- ;) { data = &tng_data->non_tr_particle_data[i]; diff --git a/src/lib/tng_io.h b/src/lib/tng_io.h index 350739e..3c21c82 100644 --- a/src/lib/tng_io.h +++ b/src/lib/tng_io.h @@ -778,11 +778,65 @@ tng_function_status tng_frame_set_new(tng_trajectory_t tng_data, const int64_t first_frame, const int64_t n_frames); +/** + * @brief Add a non-particle dependent data block. + * @param tng_data is the trajectory data container in which to add the data + * block + * @param id is the block ID of the block to add. + * @param block_name is a descriptive name of the block to add + * @param datatype is the datatype of the data in the block (e.g. int/float) + * @param block_type_flag indicates if this is a non-trajectory block (added + * directly to tng_data) or if it is a trajectory block (added to the + * frame set) + * @param n_frames is the number of frames of the data block (automatically + * set to 1 if adding a non-trajectory data block) + * @param n_values_per_frame is how many values a stored each frame (e.g. 9 + * for a box shape block) + * @param stride_length is how many frames are between each entry in the + * data block + * @param codec_id is the ID of the codec to compress the data. + * @param new_data is an array of data values to add. + */ +tng_function_status tng_data_block_add(tng_trajectory_t tng_data, + const int64_t id, + const char *block_name, + const char datatype, + const tng_block_type block_type_flag, + int64_t n_frames, + const int64_t n_values_per_frame, + const int64_t stride_length, + int64_t codec_id, + void *new_data); + + +/** + * @brief Add a particle dependent data block. + * @param tng_data is the trajectory data container in which to add the data + * block + * @param id is the block ID of the block to add. + * @param block_name is a descriptive name of the block to add + * @param datatype is the datatype of the data in the block (e.g. int/float) + * @param block_type_flag indicates if this is a non-trajectory block (added + * directly to tng_data) or if it is a trajectory block (added to the + * frame set) + * @param n_frames is the number of frames of the data block (automatically + * set to 1 if adding a non-trajectory data block) + * @param n_values_per_frame is how many values a stored each frame (e.g. 9 + * for a box shape block) + * @param stride_length is how many frames are between each entry in the + * data block + * @param first_particle_number is the number of the first particle stored + * in this data block + * @param n_particles is the number of particles stored in this data block + * @param codec_id is the ID of the codec to compress the data. + * @param new_data is an array of data values to add. + */ tng_function_status tng_particle_data_block_add(tng_trajectory_t tng_data, const int64_t id, const char *block_name, const char datatype, - const int64_t n_frames, + const tng_block_type block_type_flag, + int64_t n_frames, const int64_t n_values_per_frame, const int64_t stride_length, const int64_t first_particle_number, @@ -826,13 +880,15 @@ tng_function_status tng_traj_block_write(tng_trajectory_t tng_data, tng_function_status tng_frame_set_read_nr(tng_trajectory_t tng_data, int64_t frame_set_nr); -/* Read a number of consecutive trajectory frames from the input_file of - tng_data. - tng_data is a trajectory data container. tng_data->input_file_path specifies - which file to read from. If the file (input_file) is not open it will be - opened. - start_frame_nr is the index number of the first frame to read. - end_frame_nr is the index number of the last frame to read. +/** + * @brief Read a number of consecutive trajectory frames from the input_file of + * tng_data. + * @param tng_data is a trajectory data container. + * tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param start_frame_nr is the index number of the first frame to read. + * @param end_frame_nr is the index number of the last frame to read. * @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. */ @@ -840,13 +896,14 @@ tng_function_status tng_frame_read_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); -/* Write a number of consecutive trajectory frames to the output_file of - tng_data. - tng_data is a trajectory data container. tng_data->output_file_path specifies - which file to write to. If the file (output_file) is not open it will be - opened. - start_frame_nr is the index number of the first frame to write. - end_frame_nr is the index number of the last frame to write. +/** + * @brief Write a number of consecutive trajectory frames to the output_file of + * tng_data. + * @param tng_data is a trajectory data container. tng_data->output_file_path specifies + * which file to write to. If the file (output_file) is not open it will be + * opened. + * @param start_frame_nr is the index number of the first frame to write. + * @param end_frame_nr is the index number of the last frame to write. * @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. */ @@ -854,11 +911,12 @@ tng_function_status tng_frame_write_interval(tng_trajectory_t tng_data, int64_t start_frame_nr, int64_t end_frame_nr); -/* Free data is an array of values (2D). - **values is the array to free and will be set to 0 afterwards. - n_frames is the number of frames in the data array. - n_values_per_frame is the number of values per frame in the data array. - type is the data type of the data in the array. +/** + * @brief Free data is an array of values (2D). + * @param values is the 2D array to free and will be set to 0 afterwards. + * @param n_frames is the number of frames in the data array. + * @param n_values_per_frame is the number of values per frame in the data array. + * @param type is the data type of the data in the array (e.g. int/float/char). * @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. */ @@ -867,12 +925,13 @@ tng_function_status tng_data_values_free(union data_values **values, int64_t n_values_per_frame, tng_data_type type); -/* Free data is an array of values (3D). - ***values is the array to free and will be set to 0 afterwards. - n_frames is the number of frames in the data array. - n_particles is the number of particles in the data array. - n_values_per_frame is the number of values per frame in the data array. - type is the data type of the data in the array. +/** + * @brief Free data is an array of values (3D). + * @param values is the array to free and will be set to 0 afterwards. + * @param n_frames is the number of frames in the data array. + * @param n_particles is the number of particles in the data array. + * @param n_values_per_frame is the number of values per frame in the data array. + * @param type is the data type of the data in the array (e.g. int/float/char). * @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. */ @@ -882,20 +941,21 @@ tng_function_status tng_particle_data_values_free(union data_values ***values, int64_t n_values_per_frame, tng_data_type type); -/* Retrieve non-particle data from the last read frame set. - tng_data is a trajectory data container. tng_data->input_file_path specifies - which file to read from. If the file (input_file) is not open it will be - opened. - block_id is the id number of the data block to read. - ***values is a pointer to a 2-dimensional array (memory unallocated), which - will point to the data of the requested data block. The array will be sized - (n_frames * n_values_per_frame). - Since ***values is allocated in this function it is the callers - responsibility to free the memory. - *n_frames is set to the number of frames in the data. This is needed to - properly reach and/or free the data. - *n_values_per_frame is set to the number of values per frame in the data. - This is needed to properly reach and/or free the data. +/** + * @brief Retrieve non-particle data, from the last read frame set. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param values is a pointer to a 2-dimensional array (memory unallocated), which + * will be filled with data. The array will be sized + * (n_frames * n_values_per_frame). + * Since ***values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_frames is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. * @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. */ @@ -906,21 +966,21 @@ tng_function_status tng_data_get(tng_trajectory_t tng_data, int64_t *n_values_per_frame, tng_data_type *type); -/* Read and retrieve non-particle data, in a specific interval, from the - trajectory. - tng_data is a trajectory data container. tng_data->input_file_path specifies - which file to read from. If the file (input_file) is not open it will be - opened. - block_id is the id number of the data block to read. - start_frame_nr is the index number of the first frame to read. - end_frame_nr is the index number of the last frame to read. - ***values is a pointer to a 2-dimensional array (memory unallocated), which - will be filled with data. The array will be sized - (n_frames * n_values_per_frame). - Since ***values is allocated in this function it is the callers - responsibility to free the memory. - *n_values_per_frame is set to the number of values per frame in the data. - This is needed to properly reach and/or free the data. +/** + * @brief Read and retrieve non-particle data, in a specific interval. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param start_frame_nr is the index number of the first frame to read. + * @param end_frame_nr is the index number of the last frame to read. + * @param values is a pointer to a 2-dimensional array (memory unallocated), which + * will be filled with data. The array will be sized + * (n_frames * n_values_per_frame). + * Since ***values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. * @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. */ @@ -932,22 +992,23 @@ tng_function_status tng_data_interval_get(tng_trajectory_t tng_data, int64_t *n_values_per_frame, tng_data_type *type); -/* Retrieve particle data, from the last read frame set. - tng_data is a trajectory data container. tng_data->input_file_path specifies - which file to read from. If the file (input_file) is not open it will be - opened. - block_id is the id number of the particle data block to read. - ****values is a pointer to a 3-dimensional array (memory unallocated), which - will point to the data of the requested data block. The array will be sized - (n_frames * n_particles * n_values_per_frame). - Since ****values is allocated in this function it is the callers - responsibility to free the memory. - *n_frames is set to the number of frames in the data. This is needed to - properly reach and/or free the data. - *n_particles is set to the number of particles in the returned data. This is - needed to properly reach and/or free the data. - *n_values_per_frame is set to the number of values per frame in the data. - This is needed to properly reach and/or free the data. +/** + * @brief Retrieve particle data, from the last read frame set. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param values is a pointer to a 3-dimensional array (memory unallocated), which + * will be filled with data. The array will be sized + * (n_frames * n_particles * n_values_per_frame). + * Since ****values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_frames is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_particles is set to the number of particles in the returned data. This is + * needed to properly reach and/or free the data afterwards. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. * @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. */ @@ -959,24 +1020,25 @@ tng_function_status tng_particle_data_get(tng_trajectory_t tng_data, int64_t *n_values_per_frame, tng_data_type *type); -/* Read and retrieve particle data, in a specific interval, from the trajectory. - tng_data is a trajectory data container. tng_data->input_file_path specifies - which file to read from. If the file (input_file) is not open it will be - opened. - block_id is the id number of the particle data block to read. - start_frame_nr is the index number of the first frame to read. - end_frame_nr is the index number of the last frame to read. - first_particle_number is the number of the first particle, for which to - retrive data. - last_particle_number is the number of the last particle, for which to - retrieve data. - ****values is a pointer to a 3-dimensional array (memory unallocated), which - will be filled with data. The array will be sized - (n_frames * n_particles * n_values_per_frame). - Since ****values is allocated in this function it is the callers - responsibility to free the memory. - *n_values_per_frame is set to the number of values per frame in the data. - This is needed to properly reach and/or free the data. +/** + * @brief Read and retrieve particle data, in a specific interval. + * @param tng_data is a trajectory data container. tng_data->input_file_path specifies + * which file to read from. If the file (input_file) is not open it will be + * opened. + * @param block_id is the id number of the particle data block to read. + * @param start_frame_nr is the index number of the first frame to read. + * @param end_frame_nr is the index number of the last frame to read. + * @param first_particle_number is the number of the first particle, for which to + * retrieve data. + * @param last_particle_number is the number of the last particle, for which to + * retrieve data. + * @param values is a pointer to a 3-dimensional array (memory unallocated), which + * will be filled with data. The array will be sized + * (n_frames * n_particles * n_values_per_frame). + * Since ****values is allocated in this function it is the callers + * responsibility to free the memory. + * @param n_values_per_frame is set to the number of values per frame in the data. + * This is needed to properly reach and/or free the data afterwards. * @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. */ diff --git a/src/tests/tng_io_testing.c b/src/tests/tng_io_testing.c index fa23830..a216d97 100644 --- a/src/tests/tng_io_testing.c +++ b/src/tests/tng_io_testing.c @@ -217,6 +217,7 @@ static tng_function_status tng_test_write_and_read_traj(tng_trajectory_t traj) if(tng_particle_data_block_add(traj, TNG_TRAJ_POSITIONS, "POSITIONS", TNG_FLOAT_DATA, + TNG_TRAJECTORY_BLOCK, traj->frame_set_n_frames, 3, 1, 0, traj->n_particles, TNG_UNCOMPRESSED, |