mirror of
https://github.com/TREX-CoE/trexio.git
synced 2025-01-03 01:56:13 +01:00
[WIP] working generator for sparse functions
+ remove trailing whitespaces
This commit is contained in:
parent
c1e1176400
commit
d3ba8f3652
@ -2394,21 +2394,21 @@ def has_$group_dset$(trexio_file) -> bool:
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*** C templates for front end
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**** Function declarations
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#+begin_src c :tangle hrw_sparse_front.h :exports none
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#+begin_src c :tangle hrw_dset_sparse_front.h :exports none
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trexio_exit_code trexio_has_$group_sparse_dset$(trexio_t* const file);
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trexio_exit_code trexio_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int64_t size, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int64_t size, const int32_t* index_sparse, const double* value_sparse);
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trexio_exit_code trexio_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_data, const int64_t size, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_data, const int64_t size, const int32_t* index_sparse, const double* value_sparse);
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//trexio_exit_code trexio_read_$group_sparse_dset$_value(trexio_t* const file, const uint64_t offset, const uint_64_t size, int32_t* const value_sparse);
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//trexio_exit_code trexio_write_$group_sparse_dset$_value(trexio_t* const file, const uint64_t offset, const uint_64_t size, double* const value_sparse);
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#+end_src
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**** Source code for default functions
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#+begin_src c :tangle read_sparse_front.c
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#+begin_src c :tangle read_dset_sparse_front.c
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trexio_exit_code
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trexio_read_$group_sparse_dset$(trexio_t* const file,
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const int64_t offset_file,
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const int64_t offset_dset,
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const int64_t offset_data,
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const int64_t size,
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int32_t* const index_sparse,
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double* const value_sparse
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@ -2416,28 +2416,35 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
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if (offset_dset < 0L) return TREXIO_INVALID_ARG_3;
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if (size <= 0L) return TREXIO_INVALID_ARG_4;
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if (index_sparse == NULL) return TREXIO_INVALID_ARG_5;
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if (value_sparse == NULL) return TREXIO_INVALID_ARG_6;
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if (size <= 0L) return TREXIO_INVALID_ARG_3;
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if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
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if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
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const uint32_t rank = $group_sparse_dset_rank$; // To be set by generator : number of indices
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const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
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int64_t size_max; // Max number of integrals (already in the file)
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trexio_exit_code rc;
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// temporary
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size_max = size;
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/* TODO
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rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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*/
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_$group_sparse_dset$(file, offset_file, offset_dset, size, size_max, rank, index_sparse, value_sparse);
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return trexio_text_read_$group_sparse_dset$(file, offset_file, offset_data, size, size_max, index_sparse, value_sparse);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_$group_sparse_dset$(file, offset_file, offset_dset, size, size_max, rank, index_sparse, value_sparse);
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#ifdef HAVE_HDF5
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return trexio_hdf5_read_$group_sparse_dset$(file, offset_file, offset_data, size, size_max, index_sparse, value_sparse);
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break;
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_read_$group_sparse_dset$(...);
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@ -2449,11 +2456,11 @@ trexio_read_$group_sparse_dset$(trexio_t* const file,
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}
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#+end_src
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#+begin_src c :tangle write_sparse_front.c
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#+begin_src c :tangle write_dset_sparse_front.c
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trexio_exit_code
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trexio_write_$group_sparse_dset$(trexio_t* const file,
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const int64_t offset_file,
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const int64_t offset_dset,
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const int64_t offset_data,
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const int64_t size,
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const int32_t* index_sparse,
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const double* value_sparse
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@ -2461,28 +2468,35 @@ trexio_write_$group_sparse_dset$(trexio_t* const file,
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (offset_file < 0L) return TREXIO_INVALID_ARG_2;
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if (offset_dset < 0L) return TREXIO_INVALID_ARG_3;
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if (size <= 0L) return TREXIO_INVALID_ARG_4;
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if (index_sparse == NULL) return TREXIO_INVALID_ARG_5;
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if (value_sparse == NULL) return TREXIO_INVALID_ARG_6;
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if (size <= 0L) return TREXIO_INVALID_ARG_3;
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if (index_sparse == NULL) return TREXIO_INVALID_ARG_4;
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if (value_sparse == NULL) return TREXIO_INVALID_ARG_5;
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const uint32_t rank = $group_sparse_dset_rank$; // To be set by generator : number of indices
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const uint32_t rank = $group_dset_rank$; // To be set by generator : number of indices
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int64_t size_max; // Max number of integrals (already in the file)
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trexio_exit_code rc;
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// temporary
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size_max = size;
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/* TODO
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rc = trexio_read_$group_sparse_dset$_num(file, &size_max);
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if (rc != TREXIO_SUCCESS) return rc;
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*/
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_write_$group_sparse_dset$(file, offset_file, offset_dset, size, size_max, rank, index_sparse, value_sparse);
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return trexio_text_write_$group_sparse_dset$(file, offset_file, offset_data, size, size_max, index_sparse, value_sparse);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_write_$group_sparse_dset$(file, offset_file, offset_dset, size, size_max, rank, index_sparse, value_sparse);
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#ifdef HAVE_HDF5
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return trexio_hdf5_write_$group_sparse_dset$(file, offset_file, offset_data, size, size_max, index_sparse, value_sparse);
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break;
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_write_$group_sparse_dset$(...);
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@ -2495,6 +2509,39 @@ trexio_write_$group_sparse_dset$(trexio_t* const file,
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#+end_src
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#+begin_src c :tangle has_dset_sparse_front.c
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trexio_exit_code
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trexio_has_$group_sparse_dset$ (trexio_t* const file)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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assert(file->back_end < TREXIO_INVALID_BACK_END);
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_has_$group_sparse_dset$(file);
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break;
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case TREXIO_HDF5:
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#ifdef HAVE_HDF5
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return trexio_hdf5_has_$group_sparse_dset$(file);
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break;
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#else
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return TREXIO_BACK_END_MISSING;
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#endif
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/*
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case TREXIO_JSON:
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return trexio_json_has_$group_sparse_dset$(file);
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break;
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,*/
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}
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return TREXIO_FAILURE;
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}
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#+end_src
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** Templates for front end has/read/write a dataset of strings
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*** Introduction
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This section concerns API calls related to datasets of strings.
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@ -19,23 +19,26 @@ cat populated/pop_flush_group_text.h >> trexio_text.h
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cat populated/pop_has_dset_data_text.c >> trexio_text.c
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cat populated/pop_has_dset_str_text.c >> trexio_text.c
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cat populated/pop_has_dset_sparse_text.c >> trexio_text.c
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cat populated/pop_has_attr_num_text.c >> trexio_text.c
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cat populated/pop_has_attr_str_text.c >> trexio_text.c
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cat populated/pop_read_dset_data_text.c >> trexio_text.c
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cat populated/pop_read_dset_str_text.c >> trexio_text.c
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cat populated/pop_read_dset_sparse_text.c >> trexio_text.c
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cat populated/pop_read_attr_str_text.c >> trexio_text.c
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cat populated/pop_read_attr_num_text.c >> trexio_text.c
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cat populated/pop_write_dset_data_text.c >> trexio_text.c
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cat populated/pop_write_dset_str_text.c >> trexio_text.c
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cat populated/pop_write_dset_sparse_text.c >> trexio_text.c
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cat populated/pop_write_attr_str_text.c >> trexio_text.c
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cat populated/pop_write_attr_num_text.c >> trexio_text.c
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cat populated/pop_hrw_dset_data_text.h >> trexio_text.h
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cat populated/pop_hrw_dset_str_text.h >> trexio_text.h
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cat populated/pop_hrw_dset_sparse_text.h >> trexio_text.h
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cat populated/pop_hrw_attr_num_text.h >> trexio_text.h
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cat populated/pop_hrw_attr_str_text.h >> trexio_text.h
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cat rdm_text.c >> trexio_text.c
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cat rdm_text.h >> trexio_text.h
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cat suffix_text.h >> trexio_text.h
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@ -1003,13 +1003,13 @@ trexio_text_has_$group_str$ (trexio_t* const file)
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#+end_src
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** Template for has/read/write the dataset of sparse data
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#+begin_src c :tangle hrw_sparse_text.h :exports none
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#+begin_src c :tangle hrw_dset_sparse_text.h :exports none
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trexio_exit_code trexio_text_has_$group_sparse_dset$(trexio_t* const file);
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trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int_64_t size, const int64_t size_max, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int_64_t size, const int64_t size_max, const int32_t* index_sparse, const double* value_sparse);
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trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int64_t size, const int64_t size_max, int32_t* const index_sparse, double* const value_sparse);
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trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file, const int64_t offset_file, const int64_t offset_dset, const int64_t size, const int64_t size_max, const int32_t* index_sparse, const double* value_sparse);
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#+end_src
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#+begin_src c :tangle write_sparse_text.c
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#+begin_src c :tangle write_dset_sparse_text.c
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trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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const int64_t offset_file,
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const int64_t offset_dset,
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@ -1022,7 +1022,7 @@ trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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/* Build the name of the file with sparse data*/
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const char* $group_sparse_dset$_file_name = "/$group_sparse_dset$.txt";
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const char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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strncpy (file_abs_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
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strncat (file_abs_path, $group_sparse_dset$_file_name,
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@ -1039,10 +1039,11 @@ trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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// in general: 10*n_indices + n_indices + 24 + 1
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const uint64_t line_length = $group_sparse_dset_line_length$L;
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fseek(f, (long) offset_file * line_length, SEEK_SET);
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//fseek(f, (long) offset_file * line_length, SEEK_SET);
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for (uint64_t i=0L+offset_data ; i<size+offset_data ; ++i) {
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int rc = fprintf(f, "$group_sparse_dset_format_printf$\n",
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int rc;
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for (uint64_t i=0L+offset_dset ; i<size+offset_dset ; ++i) {
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rc = fprintf(f, "$group_sparse_dset_format_printf$\n",
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$group_sparse_dset_indices_printf$,
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value_sparse[i]);
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assert(rc > 0);
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@ -1056,13 +1057,15 @@ trexio_exit_code trexio_text_write_$group_sparse_dset$(trexio_t* const file,
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value[i]);
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*/
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fclose(f);
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rc = fclose(f);
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assert(rc == 0);
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle read_sparse_text.c
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#+begin_src c :tangle read_dset_sparse_text.c
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trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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const int64_t offset_file,
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const int64_t offset_dset,
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@ -1075,14 +1078,14 @@ trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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/* Build the name of the file with sparse data*/
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const char* $group_sparse_dset$_file_name = "/$group_sparse_dset$.txt";
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const char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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strncpy (file_abs_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
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strncat (file_abs_path, $group_sparse_dset$_file_name,
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TREXIO_MAX_FILENAME_LENGTH-strlen($group_sparse_dset$_file_name));
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FILE* f = fopen(file_abs_path, "a");
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FILE* f = fopen(file_abs_path, "r");
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//TODO ERROR HANDLING
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assert(f != NULL);
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@ -1094,10 +1097,11 @@ trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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fseek(f, (long) offset_file * line_length, SEEK_SET);
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for (uint64_t i=0L+offset_data ; i<size+offset_data ; ++i) {
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int rc = fprintf(f, "$group_sparse_dset_format_scanf$\n",
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int rc;
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for (uint64_t i=0L+offset_dset ; i<size+offset_dset ; ++i) {
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rc = fscanf(f, "$group_sparse_dset_format_scanf$",
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$group_sparse_dset_indices_scanf$,
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value_sparse[i]);
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&value_sparse[i]);
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// TODO: find a way to indicate the number of elements being read (useful?)
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if (rc == EOF){
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@ -1106,47 +1110,32 @@ trexio_exit_code trexio_text_read_$group_sparse_dset$(trexio_t* const file,
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assert(rc > 0);
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}
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}
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/*
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int rc = fscanf(f, "%d %d %d %d %lf",
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&index[4*i],
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&index[4*i+1],
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&index[4*i+2],N OPEN
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&index[4*i+3],
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&value[i]);
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,*/
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fclose(f);
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rc = fclose(f);
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assert(rc==0);
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return TREXIO_SUCCESS;
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}
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#+end_src
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#+begin_src c :tangle has_sparse_text.c
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#+begin_src c :tangle has_dset_sparse_text.c
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trexio_exit_code trexio_text_has_$group_sparse_dset$(trexio_t* const file)
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{
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if (file == NULL) return TREXIO_FILE_ERROR;
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/* Build the name of the file with sparse data*/
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const char* $group_sparse_dset$_file_name = "/$group_sparse_dset$.txt";
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const char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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char file_abs_path[TREXIO_MAX_FILENAME_LENGTH];
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strncpy (file_abs_path, file->file_name, TREXIO_MAX_FILENAME_LENGTH);
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strncat (file_abs_path, $group_sparse_dset$_file_name,
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TREXIO_MAX_FILENAME_LENGTH-strlen($group_sparse_dset$_file_name));
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/*struct stat buffer;
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int rc = stat(file_abs_path, &buffer)
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if (rc == 0) {
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if (access(file_abs_path, F_OK) == 0){
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return TREXIO_SUCCESS;
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} else {
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return TREXIO_HAS_NOT;
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}*/
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int fd = open(file_abs_path, O_CREAT | O_EXCL | O_RDONLY);
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if (fd < 0) {
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if(errno == EEXIST) return TREXIO_SUCCESS;
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} else {
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return TREXIO_HAS_NOT;
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}
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}
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#+end_src
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@ -1156,4 +1145,3 @@ trexio_exit_code trexio_text_has_$group_sparse_dset$(trexio_t* const file)
|
||||
#+begin_src c :tangle suffix_text.h
|
||||
#endif
|
||||
#+end_src
|
||||
|
||||
|
||||
@ -6,18 +6,13 @@ config_file = 'trex.json'
|
||||
trex_config = read_json(config_file)
|
||||
# --------------------------------------------------------------------------- #
|
||||
|
||||
# -------------------------------- [WIP] ------------------------------------ #
|
||||
# for now remove rdm from config because it functions are hardcoded
|
||||
del trex_config['rdm']
|
||||
# --------------------------------------------------------------------------- #
|
||||
|
||||
# -------------------- GET ATTRIBUTES FROM THE CONFIGURATION ---------------- #
|
||||
group_dict = get_group_dict(trex_config)
|
||||
detailed_nums = get_detailed_num_dict(trex_config)
|
||||
detailed_strs = get_detailed_str_dict(trex_config)
|
||||
# helper dictionaries that contain names of groups, nums or dsets as keys
|
||||
dsets = get_dset_dict(trex_config)
|
||||
detailed_dsets_nostr, detailed_dsets_str = split_dset_dict_detailed(dsets)
|
||||
detailed_dsets_nostr, detailed_dsets_str, detailed_dsets_sparse = split_dset_dict_detailed(dsets)
|
||||
detailed_dsets = detailed_dsets_nostr.copy()
|
||||
detailed_dsets.update(detailed_dsets_str)
|
||||
# consistency check for dimensioning variables
|
||||
@ -56,6 +51,10 @@ for fname in files_todo['dset_data']:
|
||||
for fname in files_todo['dset_str']:
|
||||
recursive_populate_file(fname, template_paths, detailed_dsets_str)
|
||||
|
||||
# populate has/read/write_dset (sparse) functions with recursive scheme
|
||||
for fname in files_todo['dset_sparse']:
|
||||
recursive_populate_file(fname, template_paths, detailed_dsets_sparse)
|
||||
|
||||
# populate group-related functions with mixed (iterative+recursive) scheme [text backend]
|
||||
for fname in files_todo['group']:
|
||||
special_populate_text_group(fname, template_paths, group_dict, detailed_dsets, detailed_nums, detailed_strs)
|
||||
|
||||
@ -39,7 +39,7 @@ def get_files_todo(source_files: dict) -> dict:
|
||||
files_todo = {}
|
||||
#files_todo['all'] = list(filter(lambda x: 'read' in x or 'write' in x or 'has' in x or 'hrw' in x or 'flush' in x or 'free' in x, all_files))
|
||||
files_todo['all'] = [f for f in all_files if 'read' in f or 'write' in f or 'has' in f or 'flush' in f or 'free' in f or 'hrw' in f]
|
||||
for key in ['dset_data', 'dset_str', 'attr_num', 'attr_str', 'group']:
|
||||
for key in ['dset_data', 'dset_str', 'dset_sparse', 'attr_num', 'attr_str', 'group']:
|
||||
files_todo[key] = list(filter(lambda x: key in x, files_todo['all']))
|
||||
|
||||
files_todo['group'].append('struct_text_group_dset.h')
|
||||
@ -107,6 +107,8 @@ def recursive_populate_file(fname: str, paths: dict, detailed_source: dict) -> N
|
||||
'group_num_f_dtype_default', 'group_num_f_dtype_double', 'group_num_f_dtype_single',
|
||||
'group_num_dtype_default', 'group_num_dtype_double', 'group_num_dtype_single',
|
||||
'group_num_h5_dtype', 'group_num_py_dtype',
|
||||
'group_sparse_dset', 'group_sparse_dset_format_scanf', 'group_sparse_dset_format_printf',
|
||||
'group_sparse_dset_line_length', 'group_sparse_dset_indices_printf', 'group_sparse_dset_indices_scanf',
|
||||
'group_dset', 'group_num', 'group_str', 'group']
|
||||
|
||||
for item in detailed_source.keys():
|
||||
@ -571,9 +573,11 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
|
||||
"""
|
||||
dset_numeric_dict = {}
|
||||
dset_string_dict = {}
|
||||
dset_sparse_dict = {}
|
||||
for k,v in datasets.items():
|
||||
# create a temp dictionary
|
||||
tmp_dict = {}
|
||||
is_sparse = False
|
||||
# specify details required to replace templated variables later
|
||||
if v[0] == 'float':
|
||||
datatype = 'double'
|
||||
@ -614,8 +618,25 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
|
||||
group_dset_std_dtype_out = 's'
|
||||
group_dset_std_dtype_in = 's'
|
||||
group_dset_py_dtype = 'str'
|
||||
elif 'sparse' in v[0]:
|
||||
is_sparse = True
|
||||
datatype = 'double'
|
||||
group_dset_h5_dtype = 'native_double'
|
||||
group_dset_f_dtype_default= 'real(8)'
|
||||
group_dset_f_dtype_double = 'real(8)'
|
||||
group_dset_f_dtype_single = 'real(4)'
|
||||
group_dset_dtype_default= 'double'
|
||||
group_dset_dtype_double = 'double'
|
||||
group_dset_dtype_single = 'float'
|
||||
default_prec = '64'
|
||||
group_dset_std_dtype_out = '24.16e'
|
||||
group_dset_std_dtype_in = 'lf'
|
||||
group_dset_py_dtype = 'float'
|
||||
|
||||
# add the dset name for templates
|
||||
if is_sparse:
|
||||
tmp_dict['group_sparse_dset'] = k
|
||||
else:
|
||||
tmp_dict['group_dset'] = k
|
||||
# add flag to detect index types
|
||||
if 'index' == v[0]:
|
||||
@ -656,16 +677,25 @@ def split_dset_dict_detailed (datasets: dict) -> tuple:
|
||||
dim_f_list = "(*)"
|
||||
tmp_dict['group_dset_f_dims'] = dim_f_list
|
||||
|
||||
if is_sparse:
|
||||
tmp_dict['group_sparse_dset_format_scanf'] = "%d %d %d %d %lf"
|
||||
tmp_dict['group_sparse_dset_format_printf'] = "%10d %10d %10d %10d %24.16e"
|
||||
tmp_dict['group_sparse_dset_line_length'] = "69"
|
||||
tmp_dict['group_sparse_dset_indices_printf'] = "index_sparse[4*i], index_sparse[4*i+1], index_sparse[4*i+2], index_sparse[4*i+3]"
|
||||
tmp_dict['group_sparse_dset_indices_scanf'] = "&index_sparse[4*i], &index_sparse[4*i+1], &index_sparse[4*i+2], &index_sparse[4*i+3]"
|
||||
|
||||
# add group name as a key-value pair to the dset dict
|
||||
tmp_dict['group'] = v[2]
|
||||
|
||||
# split datasets in numeric- and string- based
|
||||
if (datatype == 'char*'):
|
||||
dset_string_dict[k] = tmp_dict
|
||||
elif (is_sparse):
|
||||
dset_sparse_dict[k] = tmp_dict
|
||||
else:
|
||||
dset_numeric_dict[k] = tmp_dict
|
||||
|
||||
return (dset_numeric_dict, dset_string_dict)
|
||||
return (dset_numeric_dict, dset_string_dict, dset_sparse_dict)
|
||||
|
||||
|
||||
def check_dim_consistency(num: dict, dset: dict) -> None:
|
||||
|
||||
Loading…
Reference in New Issue
Block a user