commit b0567f25e66c2a10117e40b4efa7667f3b1f6658
parent 818b197f8e47232d2fd283b6ceafc90dc2c8c14f
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Fri, 4 Feb 2022 18:07:38 +0100
Begin loading isotopologues metadata
Diffstat:
4 files changed, 454 insertions(+), 4 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -44,7 +44,8 @@ set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
set(SHITRAN_FILES_SRC
shitran.c
- shitran_log.c)
+ shitran_log.c
+ shitran_isotopologues.c)
set(SHITRAN_FILES_INC
shitran_c.h
shitran_log.h)
diff --git a/src/shitran.c b/src/shitran.c
@@ -32,6 +32,7 @@ static void
release_shitran(ref_T* ref)
{
struct shitran* shitran = CONTAINER_OF(ref, struct shitran, ref);
+ ASSERT(ref);
if(shitran->logger == &shitran->logger__) logger_release(&shitran->logger__);
MEM_RM(shitran->allocator, shitran);
}
diff --git a/src/shitran.h b/src/shitran.h
@@ -49,12 +49,12 @@ static const struct shitran_create_args SHITRAN_CREATE_ARGS_DEFAULT =
/* Forware declarations */
struct shitran;
-struct shitran_isotopologue_metadata;
+struct shitran_isotopologues;
BEGIN_DECLS
/*******************************************************************************
- * SHITRAN API
+ * Device API
******************************************************************************/
SHITRAN_API res_T
shitran_create
@@ -69,7 +69,30 @@ SHITRAN_API res_T
shitran_ref_put
(struct shitran* shitran);
+/*******************************************************************************
+ * Isotopologues API
+ ******************************************************************************/
+SHITRAN_API res_T
+shitran_isotopologues_load
+ (struct shitran* shitran,
+ const char* path,
+ struct shitran_isotopologues** isotopologues);
+
+SHITRAN_API res_T
+shitran_isotopologues_load_from_stream
+ (struct shitran* shitran,
+ FILE* stream,
+ const char* stream_name, /* NULL <=> use default stream name */
+ struct shitran_isotopologues** isotopologues);
+
+SHITRAN_API res_T
+shitran_isotopologues_ref_get
+ (struct shitran_isotopologues* isotopologues);
+
+SHITRAN_API res_T
+shitran_isotopologues_ref_put
+ (struct shitran_isotopologues* isotopologues);
+
END_DECLS
#endif /* SHITRAN_H */
-
diff --git a/src/shitran_isotopologues.c b/src/shitran_isotopologues.c
@@ -0,0 +1,425 @@
+/* Copyright (C) 2022 CNRS - LMD
+ * Copyright (C) 2022 |Meso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022 Université Paul Sabatier - IRIT/Laplace
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. */
+
+#define _POSIX_C_SOURCE 200112L /* strtok_r support */
+
+#include "shitran.h"
+#include "shitran_c.h"
+#include "shitran_log.h"
+
+#include <rsys/cstr.h>
+#include <rsys/dynamic_array.h>
+#include <rsys/hash_table.h>
+#include <rsys/ref_count.h>
+#include <rsys/str.h>
+#include <rsys/text_reader.h>
+
+#include <ctype.h>
+#include <string.h>
+
+struct isotope {
+ double abundance;
+ double Q; /* At 296 K */
+ double gj;
+ double molar_mass; /* In g */
+ size_t molecule; /* Index of the molecule to which the isotope belongs */
+ int id; /* Unique identifier of the isotope */
+};
+
+/* Generate the dynamic array of isotopes */
+#define DARRAY_NAME isotope
+#define DARRAY_DATA struct isotope
+#include <rsys/dynamic_array.h>
+
+struct molecule {
+ struct str name;
+ size_t isotopes_range[2]; /* Range of the 1st and last regisered isotopes */
+ int id; /* Unique identifier of the molecule */
+};
+#define MOLECULE_IS_VALID(Molecule) ((Molecule)->id >= 0)
+
+static INLINE void
+molecule_clear(struct molecule* molecule)
+{
+ ASSERT(molecule);
+ molecule->isotopes_range[0] = SIZE_MAX;
+ molecule->isotopes_range[1] = 0;
+ molecule->id = -1;
+}
+
+static INLINE void
+molecule_init(struct mem_allocator* allocator, struct molecule* molecule)
+{
+ str_init(allocator, &molecule->name);
+ molecule_clear(molecule);
+}
+
+static INLINE void
+molecule_release(struct molecule* molecule)
+{
+ str_release(&molecule->name);
+}
+
+static INLINE res_T
+molecule_copy(struct molecule* dst, const struct molecule* src)
+{
+ dst->isotopes_range[0] = src->isotopes_range[0];
+ dst->isotopes_range[1] = src->isotopes_range[1];
+ dst->id = src->id;
+ return str_copy(&dst->name, &src->name);
+}
+
+static INLINE res_T
+molecule_copy_and_release(struct molecule* dst, struct molecule* src)
+{
+ dst->isotopes_range[0] = src->isotopes_range[0];
+ dst->isotopes_range[1] = src->isotopes_range[1];
+ dst->id = src->id;
+ return str_copy_and_release(&dst->name, &src->name);
+}
+
+/* Generate the dynamic array of molecules */
+#define DARRAY_NAME molecule
+#define DARRAY_DATA struct molecule
+#define DARRAY_FUNCTOR_INIT molecule_init
+#define DARRAY_FUNCTOR_RELEASE molecule_release
+#define DARRAY_FUNCTOR_COPY molecule_copy
+#define DARRAY_FUNCTOR_COPY_AND_RELEASE molecule_copy_and_release
+#include <rsys/dynamic_array.h>
+
+/* Generate the hash table that map a unique identifier to its index */
+#define HTABLE_NAME id2entry
+#define HTABLE_KEY int /* Unique identifier */
+#define HTABLE_DATA size_t /* Index of the corresponding registered data */
+#include <rsys/hash_table.h>
+
+struct shitran_isotopologues {
+
+ /* List of molecules and isotopes */
+ struct darray_molecule molecules;
+ struct darray_isotope isotopes;
+
+ /* Map the identifier of a molecule/isotope to its correspond index into
+ * their corresponding dynamic arays into which they are registered */
+ struct htable_id2entry molid2idx;
+ struct htable_id2entry isoid2idx;
+
+ struct shitran* shitran;
+ ref_T ref;
+};
+
+/*******************************************************************************
+ * Helper functions
+ ******************************************************************************/
+static res_T
+create_isotoplogues
+ (struct shitran* shitran,
+ struct shitran_isotopologues** out_isotopologues)
+{
+ struct shitran_isotopologues* isotopologues = NULL;
+ res_T res = RES_OK;
+ ASSERT(shitran && out_isotopologues);
+
+ isotopologues = MEM_CALLOC(shitran->allocator, 1, sizeof(*isotopologues));
+ if(!isotopologues) {
+ log_err(shitran, "Could not allocate the isotopologues data structure.\n");
+ res = RES_MEM_ERR;
+ goto error;
+ }
+ ref_init(&isotopologues->ref);
+ SHITRAN(ref_get(shitran));
+ isotopologues->shitran = shitran;
+ darray_molecule_init(shitran->allocator, &isotopologues->molecules);
+ darray_isotope_init(shitran->allocator, &isotopologues->isotopes);
+ htable_id2entry_init(shitran->allocator, &isotopologues->molid2idx);
+ htable_id2entry_init(shitran->allocator, &isotopologues->isoid2idx);
+
+exit:
+ *out_isotopologues = isotopologues;
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+flush_molecule
+ (struct shitran_isotopologues* isotopologues,
+ struct molecule* molecule, /* Currently parsed molecule */
+ struct txtrdr* txtrdr)
+{
+ size_t entry = 0;
+ res_T res = RES_OK;
+ ASSERT(isotopologues && molecule && MOLECULE_IS_VALID(molecule));
+
+ /* Fetch _exclusive_ upper bound */
+ molecule->isotopes_range[1] = darray_isotope_size_get(&isotopologues->isotopes);
+ if(molecule->isotopes_range[0] >= molecule->isotopes_range[1]) {
+ log_warn(isotopologues->shitran,
+ "%s: the %s molecule does not have any isotopes.\n",
+ txtrdr_get_name(txtrdr), str_cget(&molecule->name));
+ }
+
+ /* Fetch the index of the registered molecule */
+ entry = darray_molecule_size_get(&isotopologues->molecules);
+
+ /* Storing the molecule */
+ res = darray_molecule_push_back(&isotopologues->molecules, molecule);
+ if(res != RES_OK) {
+ log_err(isotopologues->shitran,
+ "%s: error storing the %s molecule -- %s.\n",
+ txtrdr_get_name(txtrdr), str_cget(&molecule->name), res_to_cstr(res));
+ goto error;
+ }
+
+ /* Registering the molecule */
+ ASSERT(!htable_id2entry_find(&isotopologues->molid2idx, &molecule->id));
+ res = htable_id2entry_set(&isotopologues->molid2idx, &molecule->id, &entry);
+ if(res != RES_OK) {
+ log_err(isotopologues->shitran,
+ "%s: error registering the %s molecule -- %s.\n",
+ txtrdr_get_name(txtrdr), str_cget(&molecule->name), res_to_cstr(res));
+ goto error;
+ }
+
+ molecule_clear(molecule);
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+parse_molecule
+ (struct shitran_isotopologues* isotopologues,
+ struct molecule* molecule,
+ struct txtrdr* txtrdr)
+{
+ char* name = NULL;
+ char* id = NULL;
+ char* tk = NULL;
+ char* tk_ctx = NULL;
+ size_t len;
+ res_T res = RES_OK;
+ ASSERT(molecule && txtrdr);
+
+ name = strtok_r(txtrdr_get_line(txtrdr), " \t", &tk_ctx);
+ id = strtok_r(NULL, " \t", &tk_ctx);
+
+ if(!name) {
+ log_err(isotopologues->shitran, "%s:%lu: molecule name is missing.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr));
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+ len = strlen(id);
+ if(!id || !len || id[0] != '(' || id[len-1] != ')') {
+ log_err(isotopologues->shitran, "%s:%lu: invalid molecule identifier.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr));
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+ id[len-1] = '\0'; /* Rm trailing parenthesis */
+ res = cstr_to_int(id+1/*Rm leading parenthesis*/, &molecule->id);
+ if(res != RES_OK || !MOLECULE_IS_VALID(molecule)) {
+ id[len-1] = ')'; /* Re-add the trailing parenthesis */
+ log_err(isotopologues->shitran, "%s:%lu: invalid molecule identifier `%s'.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr), id);
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+ tk = strtok_r(NULL, " \t", &tk_ctx);
+ if(tk) {
+ log_warn(isotopologues->shitran, "%s:%lu: unexpected text `%s'.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr), tk);
+ }
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+parse_line
+ (struct shitran_isotopologues* isotopologues,
+ struct molecule* molecule, /* Currently parsed molecule */
+ struct txtrdr* txtrdr)
+{
+ const char* line = NULL;
+ size_t i;
+ res_T res = RES_OK;
+ ASSERT(isotopologues && molecule && txtrdr);
+
+ line = txtrdr_get_cline(txtrdr);
+ ASSERT(line);
+ i = strcspn(line, " \t");
+ ASSERT(i < strlen(line));
+
+ if(isalpha(line[i])) {
+ if(MOLECULE_IS_VALID(molecule)) {
+ res = flush_molecule(isotopologues, molecule, txtrdr);
+ if(res != RES_OK) goto error;
+ }
+ res = parse_molecule(isotopologues, molecule, txtrdr);
+ if(res != RES_OK) goto error;
+ } else {
+ /* TODO parse the isotope */
+ }
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+load_stream
+ (struct shitran* shitran,
+ FILE* stream,
+ const char* name,
+ struct shitran_isotopologues** out_isotopologues)
+{
+ struct molecule molecule; /* Current molecule */
+ struct shitran_isotopologues* isotopologues = NULL;
+ struct txtrdr* txtrdr = NULL;
+ res_T res = RES_OK;
+ ASSERT(shitran && stream && name && out_isotopologues);
+
+ molecule_init(shitran->allocator, &molecule);
+
+ res = create_isotoplogues(shitran, &isotopologues);
+ if(res != RES_OK) goto error;
+
+ res = txtrdr_stream(isotopologues->shitran->allocator, stream, name,
+ 0/*comment char*/, &txtrdr);
+ if(res != RES_OK) {
+ log_err(shitran, "%s: error creating the text reader -- %s.\n",
+ name, res_to_cstr(res));
+ goto error;
+ }
+
+ #define READ_LINE { \
+ res = txtrdr_read_line(txtrdr); \
+ if(res != RES_OK) { \
+ log_err(shitran, "%s: error reading the line `%lu' -- %s.\n", \
+ name, (unsigned long)txtrdr_get_line_num(txtrdr), res_to_cstr(res)); \
+ goto error; \
+ } \
+ } (void)0
+
+ /* Skip the 1st line that is a comment line*/
+ READ_LINE;
+ if(!txtrdr_get_cline(txtrdr)) goto exit;
+
+ for(;;) {
+ READ_LINE;
+
+ if(!txtrdr_get_cline(txtrdr)) break; /* No more parsed line */
+ res = parse_line(isotopologues, &molecule, txtrdr);
+ if(res != RES_OK) goto error;
+ }
+ #undef READ_LINE
+
+exit:
+ *out_isotopologues = isotopologues;
+ molecule_release(&molecule);
+ return res;
+error:
+ goto exit;
+}
+
+static void
+release_isotopologues(ref_T* ref)
+{
+ struct shitran* shitran = NULL;
+ struct shitran_isotopologues* isotopologues = CONTAINER_OF
+ (ref, struct shitran_isotopologues, ref);
+ ASSERT(ref);
+ shitran = isotopologues->shitran;
+ darray_molecule_release(&isotopologues->molecules);
+ darray_isotope_release(&isotopologues->isotopes);
+ htable_id2entry_release(&isotopologues->molid2idx);
+ htable_id2entry_release(&isotopologues->isoid2idx);
+ MEM_RM(shitran->allocator, isotopologues);
+ SHITRAN(ref_put(shitran));
+}
+
+/*******************************************************************************
+ * Exported functions
+ ******************************************************************************/
+res_T
+shitran_isotopologues_load
+ (struct shitran* shitran,
+ const char* path,
+ struct shitran_isotopologues** isotopologues)
+{
+ FILE* file = NULL;
+ res_T res = RES_OK;
+
+ if(!shitran || !path) {
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+ file = fopen(path, "r");
+ if(!file) {
+ log_err(shitran, "%s: error opening file `%s'.\n", FUNC_NAME, path);
+ res = RES_IO_ERR;
+ goto error;
+ }
+
+ res = load_stream(shitran, file, path, isotopologues);
+ if(res != RES_OK) goto error;
+
+exit:
+ if(file) fclose(file);
+ return res;
+error:
+ goto exit;
+}
+
+res_T
+shitran_isotopologues_load_from_stream
+ (struct shitran* shitran,
+ FILE* stream,
+ const char* stream_name,
+ struct shitran_isotopologues** isotopologues)
+{
+ if(!shitran || !stream) return RES_BAD_ARG;
+ return load_stream
+ (shitran, stream, stream_name ? stream_name : "<stream>", isotopologues);
+}
+
+res_T
+shitran_isotopologues_ref_get(struct shitran_isotopologues* isotopologues)
+{
+ if(!isotopologues) return RES_BAD_ARG;
+ ref_get(&isotopologues->ref);
+ return RES_OK;
+}
+
+res_T
+shitran_isotopologues_ref_put(struct shitran_isotopologues* isotopologues)
+{
+ if(!isotopologues) return RES_BAD_ARG;
+ ref_put(&isotopologues->ref, release_isotopologues);
+ return RES_OK;
+}
