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-rw-r--r--include/tng_io.h29
-rw-r--r--src/lib/tng_io.c277
2 files changed, 249 insertions, 57 deletions
diff --git a/include/tng_io.h b/include/tng_io.h
index 9cc8a8a..e46cd60 100644
--- a/include/tng_io.h
+++ b/include/tng_io.h
@@ -4293,6 +4293,35 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write
const double time,
const double *box_shape);
+/**
+ * @brief High-level function for getting the compression method and
+ * multiplication factor of the next frame of a specific data block.
+ * @param tng_data is the trajectory to use.
+ * @param block_id is the ID number of the block containing the data of
+ * interest.
+ * @param codec_id will be set to the value of the codec_id of the
+ * compression of the data block. See tng_compression for more details.
+ * @param factor will be set to the multiplication factor applied to
+ * the values before compression, in order to get integers from them.
+ * factor is 1/precision.
+ * @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
+ * must be initialised before using it.
+ * @pre \code codec_id != 0 \endcode The pointer to the returned codec id
+ * must not be a NULL pointer.
+ * @pre \code factor != 0 \endcode The pointer to the returned multiplication
+ * factor must not be a NULL pointer.
+ * @details This function reads ahead until a data block of the requested ID
+ * is found.
+ * @return TNG_SUCCESS (0) if successful, TNG_FAILURE (1) if a minor error
+ * has occured (such as invalid mode) or TNG_CRITICAL (2) if a major error
+ * has occured.
+ */
+tng_function_status DECLSPECDLLEXPORT tng_util_compression_next_frame_get
+ (tng_trajectory_t tng_data,
+ const int64_t block_id,
+ char *codec_id,
+ float *factor);
+
/** @} */ /* end of group2 */
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index e60aab5..97fb283 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -722,6 +722,35 @@ static tng_function_status tng_output_file_init(tng_trajectory_t tng_data)
return(TNG_SUCCESS);
}
+static tng_function_status DECLSPECDLLEXPORT tng_frame_set_particle_mapping_free(tng_trajectory_t tng_data)
+{
+ tng_trajectory_frame_set_t frame_set;
+ tng_particle_mapping_t mapping;
+ int64_t i;
+
+ TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
+
+ frame_set = &tng_data->current_trajectory_frame_set;
+
+ if(frame_set->n_mapping_blocks && frame_set->mappings)
+ {
+ for(i = frame_set->n_mapping_blocks; i--;)
+ {
+ mapping = &frame_set->mappings[i];
+ if(mapping->real_particle_numbers)
+ {
+ free(mapping->real_particle_numbers);
+ mapping->real_particle_numbers = 0;
+ }
+ }
+ free(frame_set->mappings);
+ frame_set->mappings = 0;
+ frame_set->n_mapping_blocks = 0;
+ }
+
+ return(TNG_SUCCESS);
+}
+
/** Setup a file block container.
* @param block_p a pointer to memory to initialise as a file block container.
* @details Memory is allocated during initialisation.
@@ -2974,7 +3003,6 @@ static tng_function_status tng_frame_set_block_read
tng_bool same_hash;
tng_trajectory_frame_set_t frame_set =
&tng_data->current_trajectory_frame_set;
- tng_particle_mapping_t mapping;
if(tng_input_file_init(tng_data) != TNG_SUCCESS)
{
@@ -3023,21 +3051,7 @@ static tng_function_status tng_frame_set_block_read
tng_data->current_trajectory_frame_set_input_file_pos = file_pos;
- if(frame_set->n_mapping_blocks && frame_set->mappings)
- {
- for(i = frame_set->n_mapping_blocks; i--;)
- {
- mapping = &frame_set->mappings[i];
- if(mapping->real_particle_numbers)
- {
- free(mapping->real_particle_numbers);
- mapping->real_particle_numbers = 0;
- }
- }
- free(frame_set->mappings);
- frame_set->mappings = 0;
- frame_set->n_mapping_blocks = 0;
- }
+ tng_frame_set_particle_mapping_free(tng_data);
if(tng_data->first_trajectory_frame_set_input_file_pos <= 0)
{
@@ -3847,6 +3861,7 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
{
int nalgo;
int new_len;
+ int *alt_algo = 0;
char *dest, *temp;
int64_t algo_find_n_frames;
unsigned long offset;
@@ -3866,7 +3881,32 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
if(block->id == TNG_TRAJ_POSITIONS)
{
- if(!tng_data->compress_algo_pos)
+ /* If there is only one frame in this frame set and there might be more
+ * do not store the algorithm as the compression algorithm, but find
+ * the best one without storing it */
+ if(n_frames == 1 && tng_data->frame_set_n_frames > 1)
+ {
+ nalgo = tng_compress_nalgo();
+ alt_algo=malloc(nalgo * sizeof *tng_data->compress_algo_pos);
+ if(type == TNG_FLOAT_DATA)
+ {
+ dest = tng_compress_pos_float_find_algo(start_pos, (int)n_particles,
+ (int)n_frames,
+ (float)tng_data->compression_precision,
+ 0, alt_algo,
+ &new_len);
+
+ }
+ else
+ {
+ dest = tng_compress_pos_find_algo(start_pos, (int)n_particles,
+ (int)n_frames,
+ tng_data->compression_precision,
+ 0, alt_algo,
+ &new_len);
+ }
+ }
+ else if(!tng_data->compress_algo_pos)
{
if(n_frames > 10)
{
@@ -3938,7 +3978,32 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
}
else if(block->id == TNG_TRAJ_VELOCITIES)
{
- if(!tng_data->compress_algo_vel)
+ /* If there is only one frame in this frame set and there might be more
+ * do not store the algorithm as the compression algorithm, but find
+ * the best one without storing it */
+ if(n_frames == 1 && tng_data->frame_set_n_frames > 1)
+ {
+ nalgo = tng_compress_nalgo();
+ alt_algo=malloc(nalgo * sizeof *tng_data->compress_algo_pos);
+ if(type == TNG_FLOAT_DATA)
+ {
+ dest = tng_compress_vel_float_find_algo(start_pos, (int)n_particles,
+ (int)n_frames,
+ (float)tng_data->compression_precision,
+ 0, alt_algo,
+ &new_len);
+
+ }
+ else
+ {
+ dest = tng_compress_vel_find_algo(start_pos, (int)n_particles,
+ (int)n_frames,
+ tng_data->compression_precision,
+ 0, alt_algo,
+ &new_len);
+ }
+ }
+ else if(!tng_data->compress_algo_vel)
{
if(n_frames > 10)
{
@@ -4017,6 +4082,11 @@ static tng_function_status tng_compress(tng_trajectory_t tng_data,
offset = (unsigned long)((char *)start_pos - block->block_contents);
+ if(alt_algo)
+ {
+ free(alt_algo);
+ }
+
block->block_contents_size = new_len + offset;
temp = realloc(block->block_contents, block->block_contents_size);
@@ -4859,6 +4929,8 @@ static tng_function_status tng_particle_data_block_write
/* If the frame set is finished before writing the full number of frames
make sure the data block is not longer than the frame set. */
n_frames = tng_min_i64(n_frames, frame_set->n_frames);
+
+ n_frames -= (data->first_frame_with_data - frame_set->first_frame);
}
frame_step = (n_frames % stride_length) ? n_frames / stride_length + 1:
@@ -5775,6 +5847,8 @@ static tng_function_status tng_data_block_write(tng_trajectory_t tng_data,
/* If the frame set is finished before writing the full number of frames
make sure the data block is not longer than the frame set. */
n_frames = tng_min_i64(n_frames, frame_set->n_frames);
+
+ n_frames -= (data->first_frame_with_data - frame_set->first_frame);
}
frame_step = (n_frames % stride_length) ? n_frames / stride_length + 1:
@@ -6285,13 +6359,15 @@ static tng_function_status tng_data_block_contents_read
}
}
offset += sizeof(stride_length);
+ n_frames = first_frame_with_data -
+ tng_data->current_trajectory_frame_set.n_frames;
}
else
{
first_frame_with_data = 0;
stride_length = 1;
+ n_frames = tng_data->current_trajectory_frame_set.n_frames;
}
- n_frames = tng_data->current_trajectory_frame_set.n_frames;
}
else
{
@@ -8699,8 +8775,6 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t
tng_trajectory_t tng_data = *tng_data_p;
tng_trajectory_frame_set_t frame_set;
- tng_particle_mapping_t mapping;
-
if(!*tng_data_p)
{
return(TNG_SUCCESS);
@@ -8788,21 +8862,7 @@ tng_function_status DECLSPECDLLEXPORT tng_trajectory_destroy(tng_trajectory_t *t
tng_data->forcefield_name = 0;
}
- if(frame_set->mappings)
- {
- for(i = frame_set->n_mapping_blocks; i--;)
- {
- mapping = &frame_set->mappings[i];
- if(mapping->real_particle_numbers)
- {
- free(mapping->real_particle_numbers);
- mapping->real_particle_numbers = 0;
- }
- }
- free(frame_set->mappings);
- frame_set->mappings = 0;
- frame_set->n_mapping_blocks = 0;
- }
+ tng_frame_set_particle_mapping_free(tng_data);
if(frame_set->molecule_cnt_list)
{
@@ -11804,10 +11864,8 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
const int64_t first_frame,
const int64_t n_frames)
{
- int64_t i;
tng_gen_block_t block;
tng_trajectory_frame_set_t frame_set;
- tng_particle_mapping_t mapping;
FILE *temp = tng_data->input_file;
int64_t curr_pos;
@@ -11838,21 +11896,7 @@ tng_function_status DECLSPECDLLEXPORT tng_frame_set_new
ftell(tng_data->output_file);
/* Clear mappings if they remain. */
- if(frame_set->n_mapping_blocks && frame_set->mappings)
- {
- for(i = frame_set->n_mapping_blocks; i--;)
- {
- mapping = &frame_set->mappings[i];
- if(mapping->real_particle_numbers)
- {
- free(mapping->real_particle_numbers);
- mapping->real_particle_numbers = 0;
- }
- }
- free(frame_set->mappings);
- frame_set->mappings = 0;
- frame_set->n_mapping_blocks = 0;
- }
+ tng_frame_set_particle_mapping_free(tng_data);
tng_data->n_trajectory_frame_sets++;
@@ -12168,6 +12212,8 @@ tng_function_status DECLSPECDLLEXPORT tng_data_block_add
data->n_frames = n_frames;
data->codec_id = codec_id;
data->compression_multiplier = 1.0;
+ /* FIXME: This can cause problems. */
+ data->first_frame_with_data = frame_set->first_frame;
switch(datatype)
{
@@ -12320,6 +12366,8 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_block_add
data->n_frames = n_frames;
data->codec_id = codec_id;
data->compression_multiplier = 1.0;
+ /* FIXME: This can cause problems. */
+ data->first_frame_with_data = frame_set->first_frame;
if(block_type_flag == TNG_TRAJECTORY_BLOCK && tng_data->var_num_atoms_flag)
{
@@ -15703,8 +15751,6 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read
*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);
if(data->stride_length > 1)
@@ -15713,7 +15759,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_particle_data_next_frame_read
}
else
{
- i = (i - frame_set->first_frame) / data->stride_length;
+ i = (i - frame_set->first_frame);
}
tng_num_particles_get(tng_data, &n_particles);
@@ -15845,7 +15891,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_non_particle_data_next_frame_read
}
else
{
- i = (i - frame_set->first_frame) / data->stride_length;
+ i = (i - frame_set->first_frame);
}
*data_type = data->datatype;
@@ -17189,3 +17235,120 @@ tng_function_status DECLSPECDLLEXPORT tng_util_box_shape_with_time_double_write
TNG_GZIP_COMPRESSION));
}
+tng_function_status DECLSPECDLLEXPORT tng_util_compression_next_frame_get
+ (tng_trajectory_t tng_data,
+ const int64_t block_id,
+ char *codec_id,
+ float *factor)
+{
+ tng_trajectory_frame_set_t frame_set;
+ tng_particle_data_t p_data;
+ tng_non_particle_data_t np_data;
+ tng_function_status stat;
+ int64_t i;
+ long file_pos;
+ int block_type = -1;
+
+ TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
+ TNG_ASSERT(codec_id, "TNG library: The pointer to the returned codec id must not be a NULL pointer.");
+ TNG_ASSERT(factor, "TNG library: The pointer to the returned multiplication factor must not be a NULL pointer.");
+
+ frame_set = &tng_data->current_trajectory_frame_set;
+
+ stat = tng_particle_data_find(tng_data, block_id, &p_data);
+ if(stat == TNG_SUCCESS)
+ {
+ block_type = TNG_PARTICLE_BLOCK_DATA;
+ }
+ else
+ {
+ stat = tng_data_find(tng_data, block_id, &np_data);
+ if(stat == TNG_SUCCESS)
+ {
+ block_type = TNG_NON_PARTICLE_BLOCK_DATA;
+ }
+ else
+ {
+ 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);
+ }
+ stat = tng_particle_data_find(tng_data, block_id, &p_data);
+ if(stat == TNG_SUCCESS)
+ {
+ block_type = TNG_PARTICLE_BLOCK_DATA;
+ }
+ else
+ {
+ stat = tng_data_find(tng_data, block_id, &np_data);
+ if(stat == TNG_SUCCESS)
+ {
+ block_type = TNG_NON_PARTICLE_BLOCK_DATA;
+ }
+ else
+ {
+ return(stat);
+ }
+ }
+ }
+ }
+ if(block_type == TNG_PARTICLE_BLOCK_DATA)
+ {
+ if(p_data->last_retrieved_frame < 0)
+ {
+ i = p_data->first_frame_with_data;
+ }
+ else
+ {
+ i = p_data->last_retrieved_frame + p_data->stride_length;
+ }
+ }
+ else if(block_type == TNG_NON_PARTICLE_BLOCK_DATA)
+ {
+ if(np_data->last_retrieved_frame < 0)
+ {
+ i = np_data->first_frame_with_data;
+ }
+ else
+ {
+ i = np_data->last_retrieved_frame + np_data->stride_length;
+ }
+ }
+ else
+ {
+ return(TNG_FAILURE);
+ }
+ if(i < frame_set->first_frame || i >= frame_set->first_frame + frame_set->n_frames)
+ {
+ 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);
+ }
+ }
+ if(block_type == TNG_PARTICLE_BLOCK_DATA)
+ {
+ *codec_id = p_data->codec_id;
+ *factor = p_data->compression_multiplier;
+ }
+ else if(block_type == TNG_NON_PARTICLE_BLOCK_DATA)
+ {
+ *codec_id = np_data->codec_id;
+ *factor = np_data->compression_multiplier;
+ }
+ return(TNG_SUCCESS);
+}
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