commit c67215c15a7603efc011203a477c8dff0d9b5f46
parent 9f23dda14b1405092614e70a9778e723a14ed28d
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Fri, 11 Mar 2022 09:31:52 +0100
Add isotope selection per molecule to the lines view
Diffstat:
| M | src/shtr.h | | | 58 | +++++++++++++++++++++++++++++++++++++--------------------- |
| M | src/shtr_lines_view.c | | | 79 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-------------- |
| M | src/test_shtr_lines.c | | | 51 | ++++++++++++++++++++++++++++++++++++++++++--------- |
3 files changed, 144 insertions(+), 44 deletions(-)
diff --git a/src/shtr.h b/src/shtr.h
@@ -40,27 +40,7 @@
#endif
#define SHTR_MAX_MOLECULES_COUNT 100
-
-struct shtr_create_args {
- struct logger* logger; /* May be NULL <=> default logger */
- struct mem_allocator* allocator; /* NULL <=> use default allocator */
- int verbose; /* Verbosity level */
-};
-#define SHTR_CREATE_ARGS_DEFAULT__ {NULL, NULL, 0}
-static const struct shtr_create_args SHTR_CREATE_ARGS_DEFAULT =
- SHTR_CREATE_ARGS_DEFAULT__;
-
-struct shtr_lines_view_create_args {
- double wavenumber_range[2]; /* Spectral range */
-
- /* List of molecule identifiers to consider sorted in ascending order */
- int32_t molecules[SHTR_MAX_MOLECULES_COUNT];
- size_t nmolecules;
-};
-#define SHTR_LINES_VIEW_CREATE_ARGS_NULL__ {{0,0},{0}, 0}
-static const struct shtr_lines_view_create_args
-SHTR_LINES_VIEW_CREATE_ARGS_NULL =
- SHTR_LINES_VIEW_CREATE_ARGS_NULL__;
+#define SHTR_MAX_ISOTOPES_COUNT 10
struct shtr_isotope {
double abundance; /* in ]0, 1] */
@@ -119,6 +99,42 @@ struct shtr_isotope_metadata;
struct shtr_lines_list;
struct shtr_lines_view;
+/*******************************************************************************
+ * Input arguments for API functions
+ ******************************************************************************/
+struct shtr_create_args {
+ struct logger* logger; /* May be NULL <=> default logger */
+ struct mem_allocator* allocator; /* NULL <=> use default allocator */
+ int verbose; /* Verbosity level */
+};
+#define SHTR_CREATE_ARGS_DEFAULT__ {0}
+static const struct shtr_create_args SHTR_CREATE_ARGS_DEFAULT =
+ SHTR_CREATE_ARGS_DEFAULT__;
+
+struct shtr_isotope_selection {
+ /* List of isotopes identifier to consider for this molecule. The listed
+ * idenfiers are _local_ to the molecule */
+ int32_t isotope_ids_local[SHTR_MAX_ISOTOPES_COUNT];
+ size_t nisotopes; /* 0 <=> select all the isotopes */
+
+ int32_t id; /* Molecule to which the isotopes belongs */
+};
+#define SHTR_ISOTOPE_SELECTION_NULL__ {0}
+static const struct shtr_isotope_selection
+SHTR_ISOTOPE_SELECTION_NULL = SHTR_ISOTOPE_SELECTION_NULL__;
+
+struct shtr_lines_view_create_args {
+ double wavenumber_range[2]; /* Spectral range */
+
+ /* List of molecule be selected */
+ struct shtr_isotope_selection molecules[SHTR_MAX_MOLECULES_COUNT];
+ size_t nmolecules;
+};
+#define SHTR_LINES_VIEW_CREATE_ARGS_NULL__ {0}
+static const struct shtr_lines_view_create_args
+SHTR_LINES_VIEW_CREATE_ARGS_NULL =
+ SHTR_LINES_VIEW_CREATE_ARGS_NULL__;
+
BEGIN_DECLS
/*******************************************************************************
diff --git a/src/shtr_lines_view.c b/src/shtr_lines_view.c
@@ -120,25 +120,58 @@ error:
}
static int
+cmp_isotope_selection(const void* a, const void* b)
+{
+ const struct shtr_isotope_selection* molecule0 = a;
+ const struct shtr_isotope_selection* molecule1 = b;
+ ASSERT(a && b);
+ return molecule0->id - molecule1->id;
+}
+
+static int
+cmp_isotope_selection_molecule_id(const void* key, const void* val)
+{
+ const int32_t* molecule_id = key;
+ const struct shtr_isotope_selection* molecule = val;
+ ASSERT(key && val);
+ return *molecule_id - molecule->id;
+}
+
+static int
cmp_int32(const void* a, const void* b)
{
ASSERT(a && b);
return *((int32_t*)a) - *((int32_t*)b);
}
-/* Return 1 if `molecule' is in `molecules' and 0 otherwise */
+/* Return 1 if the line belongs to an isotope to be selected and 0 otherwise */
static INLINE int
-include_molecule
- (const int32_t molecules[],
- const size_t nmolecules,
- const int32_t molecule)
+is_the_line_to_select
+ (const struct shtr_line* line,
+ const struct shtr_isotope_selection* molecules,
+ const size_t nmolecules)
{
- int32_t* i = NULL;
+ const struct shtr_isotope_selection* molecule = NULL;
+ int32_t* isotope = NULL;
ASSERT(molecules);
- i = search_lower_bound
- (&molecule, molecules, nmolecules, sizeof(int32_t), cmp_int32);
- return i != NULL && *i == molecule;
+ molecule = search_lower_bound(&line->molecule_id, molecules, nmolecules,
+ sizeof(*molecules), cmp_isotope_selection_molecule_id);
+
+ if(molecule == NULL || molecule->id != line->molecule_id)
+ return 0; /* The lines does not belongs to a molecule to be selected */
+
+ if(molecule->nisotopes == 0) /* <=> All the isotopes are accepted */
+ return 1;
+
+ isotope = search_lower_bound(&line->isotope_id_local,
+ molecule->isotope_ids_local, molecule->nisotopes,
+ sizeof(*molecule->isotope_ids_local), cmp_int32);
+
+ if(isotope == NULL || *isotope != line->isotope_id_local)
+ return 0; /* The lines does not belongs to an isotope to be selected */
+
+ return 1;
}
static res_T
@@ -147,7 +180,7 @@ select_lines
const struct shtr_lines_view_create_args* args)
{
const struct shtr_line* lines;
- int32_t molecules[SHTR_MAX_MOLECULES_COUNT];
+ struct shtr_isotope_selection molecules[SHTR_MAX_MOLECULES_COUNT];
size_t line_id_range[2];
size_t i;
res_T res = RES_OK;
@@ -156,12 +189,30 @@ select_lines
/* Nothing to do */
if(args->nmolecules == 0) goto exit;
- /* Sort in ascending order the indices of the molecules to include */
+ /* Sort in ascending order the ids of the molecules to include */
memcpy(molecules, args->molecules, args->nmolecules*sizeof(molecules[0]));
- qsort(molecules, args->nmolecules, sizeof(molecules[0]), cmp_int32);
+ qsort
+ (molecules,
+ args->nmolecules,
+ sizeof(molecules[0]),
+ cmp_isotope_selection);
+
+ /* Sort in ascending order the ids of the par molecule isotopes to include */
+ FOR_EACH(i, 0, args->nmolecules) {
+ qsort
+ (molecules[i].isotope_ids_local,
+ molecules[i].nisotopes,
+ sizeof(molecules[i].isotope_ids_local[0]),
+ cmp_int32);
+ }
+
#ifndef NDEBUG
FOR_EACH(i, 1, args->nmolecules) {
- ASSERT(molecules[i] >= molecules[i-1]);
+ size_t j;
+ ASSERT(molecules[i].id >= molecules[i-1].id);
+ FOR_EACH(j, 1, molecules[i].nisotopes) {
+ ASSERT(molecules[i].isotope_ids_local[j] >= molecules[i].isotope_ids_local[j-1]);
+ }
}
#endif
@@ -170,7 +221,7 @@ select_lines
lines = darray_line_cdata_get(&view->list->lines);
FOR_EACH(i, line_id_range[0], line_id_range[1]+1) {
- if(include_molecule(molecules, args->nmolecules, lines[i].molecule_id)) {
+ if(is_the_line_to_select(&lines[i], molecules, args->nmolecules)) {
res = darray_size_t_push_back(&view->line_ids, &i);
if(res != RES_OK) {
log_err(view->list->shtr,
diff --git a/src/test_shtr_lines.c b/src/test_shtr_lines.c
@@ -232,9 +232,22 @@ check_view
/* Discard lines that does not belongs to a listed molecule */
FOR_EACH(imolecule, 0, args->nmolecules) {
- if(lines[i].molecule_id == args->molecules[imolecule]) break;
+ if(lines[i].molecule_id == args->molecules[imolecule].id) break;
+ }
+ if(imolecule >= args->nmolecules)
+ continue; /* Skip the molecule */
+
+ /* nisotope == 0 <=> All isotopes must be selected */
+ if(args->molecules[imolecule].nisotopes) {
+ size_t iisotope;
+ FOR_EACH(iisotope, 0, args->molecules[imolecule].nisotopes) {
+ if(lines[i].isotope_id_local
+ == args->molecules[imolecule].isotope_ids_local[iisotope])
+ break;
+ }
+ if(iisotope >= args->molecules[imolecule].nisotopes)
+ continue; /* Skip the isotope */
}
- if(imolecule >= args->nmolecules) continue;
CHK(shtr_lines_view_get_line(view, nlines_selected, &line) == RES_OK);
CHK(line_eq(line, lines+i));
@@ -331,9 +344,9 @@ test_view(struct shtr* shtr)
args.wavenumber_range[0] = 0;
args.wavenumber_range[1] = INF;
- args.molecules[0] = 1;
- args.molecules[1] = 2;
- args.molecules[2] = 3;
+ args.molecules[0].id = 1;
+ args.molecules[1].id = 2;
+ args.molecules[2].id = 3;
args.nmolecules = 3;
CHK(shtr_lines_view_create(NULL, &args, &view) == RES_BAD_ARG);
CHK(shtr_lines_view_create(list, NULL, &view) == RES_BAD_ARG);
@@ -408,14 +421,14 @@ test_view(struct shtr* shtr)
check_view(list, view, &args);
CHK(shtr_lines_view_ref_put(view) == RES_OK);
- args.molecules[0] = 2;
+ args.molecules[0].id = 2;
args.nmolecules = 1;
CHK(shtr_lines_view_create(list, &args, &view) == RES_OK);
CHK(shtr_lines_view_get_size(view, &n) == RES_OK);
CHK(n == 0);
CHK(shtr_lines_view_ref_put(view) == RES_OK);
- args.molecules[1] = 1;
+ args.molecules[1].id = 1;
args.nmolecules = 2;
CHK(shtr_lines_view_create(list, &args, &view) == RES_OK);
CHK(shtr_lines_view_get_size(view, &n) == RES_OK);
@@ -423,7 +436,7 @@ test_view(struct shtr* shtr)
check_view(list, view, &args);
CHK(shtr_lines_view_ref_put(view) == RES_OK);
- args.molecules[1] = 3;
+ args.molecules[1].id = 3;
args.nmolecules = 2;
CHK(shtr_lines_view_create(list, &args, &view) == RES_OK);
CHK(shtr_lines_view_get_size(view, &n) == RES_OK);
@@ -433,12 +446,32 @@ test_view(struct shtr* shtr)
args.wavenumber_range[0] = 0;
args.wavenumber_range[1] = INF;
- args.molecules[0] = 2;
+ args.molecules[0].id = 2;
args.nmolecules = 1;
CHK(shtr_lines_view_create(list, &args, &view) == RES_OK);
check_view(list, view, &args);
CHK(shtr_lines_view_ref_put(view) == RES_OK);
+ args.wavenumber_range[0] = 0;
+ args.wavenumber_range[1] = INF;
+ args.molecules[0].id = 3; /* 24 */
+ args.molecules[0].isotope_ids_local[0] = 4;
+ args.molecules[0].isotope_ids_local[1] = 1;
+ args.molecules[0].isotope_ids_local[2] = 2;
+ args.molecules[0].isotope_ids_local[3] = 0;
+ args.molecules[0].nisotopes = 4;
+ args.molecules[1].id = 1; /* 11 */
+ args.molecules[1].isotope_ids_local[0] = 4;
+ args.molecules[1].isotope_ids_local[1] = 3;
+ args.molecules[1].nisotopes = 2;
+ args.nmolecules = 2;
+ CHK(shtr_lines_view_create(list, &args, &view) == RES_OK);
+ CHK(shtr_lines_view_get_size(view, &n) == RES_OK);
+ CHK(n == 35);
+ check_view(list, view, &args);
+ CHK(shtr_lines_view_ref_put(view) == RES_OK);
+
+
CHK(shtr_lines_list_ref_put(list) == RES_OK);
CHK(fclose(fp) == 0);
}
