commit 0137c8983b0702bc42a1274518917f870f0c6d0a
parent 8b72b53d71c91a7ca6bc66b53bbeea4c92027ff8
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Mon, 14 Feb 2022 12:03:20 +0100
Refactor the isotope metadata
Rename the shitran_isotope member variable imolecule to
molecule_id_local. Move the parse_param_<type> internal functions to a
separate file and minor rename of internal functions.
Diffstat:
6 files changed, 166 insertions(+), 95 deletions(-)
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -46,7 +46,8 @@ set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
set(SHITRAN_FILES_SRC
shitran.c
shitran_log.c
- shitran_isotope_metadata.c)
+ shitran_isotope_metadata.c
+ shitran_param.c)
set(SHITRAN_FILES_INC
shitran_c.h
shitran_log.h)
diff --git a/src/shitran.h b/src/shitran.h
@@ -52,17 +52,17 @@ struct shitran_isotope {
double abundance; /* in ]0, 1] */
double Q296K; /* Partition function at Tref = 296K */
double molar_mass; /* In g */
- size_t imolecule; /* Index of the molecule to which the isotope belongs */
+
+ /* Local idx of the molecule to which the isotope belongs */
+ size_t molecule_id_local;
+
int gj; /* State independent degeneracy factor */
- int id; /* Identifier of the isotope */
+ int id; /* Identifier of the isotope <=> Global index */
};
#define SHITRAN_ISOTOPE_NULL__ {0,0,0,0,0,-1}
static const struct shitran_isotope SHITRAN_ISOTOPE_NULL =
SHITRAN_ISOTOPE_NULL__;
-#define SHITRAN_ISOTOPE_IS_NULL(Isotope) \
- ((Isotope)->id == SHITRAN_ISOTOPE_NULL.id)
-
struct shitran_molecule {
const char* name;
size_t nisotopes; /* Number of isotopes */
diff --git a/src/shitran_isotope_metadata.c b/src/shitran_isotope_metadata.c
@@ -21,6 +21,7 @@
#include "shitran.h"
#include "shitran_c.h"
#include "shitran_log.h"
+#include "shitran_param.h"
#include <rsys/cstr.h>
#include <rsys/dynamic_array.h>
@@ -32,22 +33,6 @@
#include <ctype.h>
#include <string.h>
-#define C_FORMAT_double "%g"
-#define C_FORMAT_int "%d"
-
-struct param_desc {
- const char* path; /* Path where the param lies */
- const char* name; /* Name of the param */
- size_t iline; /* Line number of the param */
-
- /* Domain of the param */
- double low, upp;
- int is_low_incl; /* Define if the lower bound is inclusive */
- int is_upp_incl; /* Define if the upper bound is inclusive */
-};
-#define PARAM_DESC_NULL__ {NULL, NULL, 0, 0, 0, 0, 0}
-static const struct param_desc PARAM_DESC_NULL = PARAM_DESC_NULL__;
-
/* Generate the dynamic array of isotopes */
#define DARRAY_NAME isotope
#define DARRAY_DATA struct shitran_isotope
@@ -131,61 +116,8 @@ struct shitran_isotope_metadata {
/*******************************************************************************
* Helper functions
******************************************************************************/
-#define DEFINE_PARSE_PARAM_FUNCTION(Type) \
- static res_T \
- parse_param_##Type \
- (struct shitran* shitran, \
- const char* str, \
- const char* path, \
- size_t line_num, \
- const struct param_desc* desc, \
- Type* out_param) \
- { \
- Type param = 0; \
- res_T res = RES_OK; \
- ASSERT(shitran && path && desc && out_param); \
- ASSERT(desc->low < desc->upp \
- || (desc->low == desc->upp && desc->is_low_incl && desc->is_upp_incl));\
- \
- if(!str) { \
- log_err(shitran, "%s:%lu: %s is missing.\n", \
- path, (unsigned long)line_num, desc->name); \
- res = RES_BAD_ARG; \
- goto error; \
- } \
- \
- res = cstr_to_##Type(str, ¶m); \
- if(res != RES_OK) { \
- log_err(shitran, "%s:%lu: invalid %s `%s'.\n", \
- desc->path, (unsigned long)desc->iline, desc->name, str); \
- res = RES_BAD_ARG; \
- goto error; \
- } \
- \
- if(param < desc->low || (param == desc->low && !desc->is_low_incl) \
- || param > desc->upp || (param == desc->upp && !desc->is_upp_incl)) { \
- log_err(shitran, \
- "%s:%lu: invalid %s `%s'. It must be in " \
- "%c"CONCAT(C_FORMAT_, Type)", "CONCAT(C_FORMAT_, Type)"%c.\n", \
- path, (unsigned long)line_num, desc->name, str, \
- desc->is_low_incl ? '[' : ']', (Type)desc->low, \
- (Type)desc->upp, desc->is_upp_incl ? ']' : '['); \
- res = RES_BAD_ARG; \
- goto error; \
- } \
- \
- exit: \
- *out_param = param; \
- return res; \
- error: \
- goto exit; \
- }
-DEFINE_PARSE_PARAM_FUNCTION(double)
-DEFINE_PARSE_PARAM_FUNCTION(int)
-#undef DEFINE_PARSE_PARAM_FUNCTION
-
static res_T
-create_isotoplogues
+create_isotope_metadata
(struct shitran* shitran,
struct shitran_isotope_metadata** out_isotopes)
{
@@ -195,7 +127,8 @@ create_isotoplogues
metadata = MEM_CALLOC(shitran->allocator, 1, sizeof(*metadata));
if(!metadata) {
- log_err(shitran, "Could not allocate the metadata data structure.\n");
+ log_err(shitran,
+ "Could not allocate the isotope metadata data structure.\n");
res = RES_MEM_ERR;
goto error;
}
@@ -355,18 +288,16 @@ parse_isotope
struct shitran* shitran = NULL;
char* tk = NULL;
char* tk_ctx = NULL;
- const char* path = NULL;
- size_t line_num = 0;
size_t local_id = SIZE_MAX;
res_T res = RES_OK;
ASSERT(metadata && txtrdr);
shitran = metadata->shitran;
- path = txtrdr_get_name(txtrdr);
- line_num = txtrdr_get_line_num(txtrdr);
+ param_desc.path = txtrdr_get_name(txtrdr);
+ param_desc.line = txtrdr_get_line_num(txtrdr);
/* Fetch the index of the molecule to which the isotope belongs */
- isotope.imolecule = darray_molecule_size_get(&metadata->molecules);
+ isotope.molecule_id_local = darray_molecule_size_get(&metadata->molecules);
tk = strtok_r(txtrdr_get_line(txtrdr), " \t", &tk_ctx);
param_desc.name = "isotope id";
@@ -374,7 +305,7 @@ parse_isotope
param_desc.upp = INT_MAX;
param_desc.is_low_incl = 1;
param_desc.is_upp_incl = 1;
- res = parse_param_int(shitran, tk, path, line_num, ¶m_desc, &isotope.id);
+ res = parse_param_int(shitran, tk, ¶m_desc, &isotope.id);
if(res != RES_OK) goto error;
tk = strtok_r(NULL, " \t", &tk_ctx);
@@ -383,8 +314,7 @@ parse_isotope
param_desc.upp = 1;
param_desc.is_low_incl = 0;
param_desc.is_upp_incl = 1;
- res = parse_param_double
- (shitran, tk, path, line_num, ¶m_desc, &isotope.abundance);
+ res = parse_param_double(shitran, tk, ¶m_desc, &isotope.abundance);
if(res != RES_OK) goto error;
tk = strtok_r(NULL, " \t", &tk_ctx);
@@ -393,8 +323,7 @@ parse_isotope
param_desc.upp = INF;
param_desc.is_low_incl = 0;
param_desc.is_upp_incl = 1;
- res = parse_param_double
- (shitran, tk, path, line_num, ¶m_desc, &isotope.Q296K);
+ res = parse_param_double(shitran, tk, ¶m_desc, &isotope.Q296K);
if(res != RES_OK) goto error;
tk = strtok_r(NULL, " \t", &tk_ctx);
@@ -403,8 +332,7 @@ parse_isotope
param_desc.upp = INT_MAX;
param_desc.is_low_incl = 1;
param_desc.is_upp_incl = 1;
- res = parse_param_int
- (shitran, tk, path, line_num, ¶m_desc, &isotope.gj);
+ res = parse_param_int(shitran, tk, ¶m_desc, &isotope.gj);
if(res != RES_OK) goto error;
tk = strtok_r(NULL, " \t", &tk_ctx),
@@ -413,8 +341,7 @@ parse_isotope
param_desc.upp = INF;
param_desc.is_low_incl = 0;
param_desc.is_upp_incl = 1;
- res = parse_param_double
- (shitran, tk, path, line_num, ¶m_desc, &isotope.molar_mass);
+ res = parse_param_double(shitran, tk, ¶m_desc, &isotope.molar_mass);
if(res != RES_OK) goto error;
local_id = darray_isotope_size_get(&metadata->isotopes);
@@ -423,7 +350,7 @@ parse_isotope
res = darray_isotope_push_back(&metadata->isotopes, &isotope);
if(res != RES_OK) {
log_err(shitran, "%s:%lu: error storing the isotope %d -- %s.\n",
- path, (unsigned long)line_num, isotope.id, res_to_cstr(res));
+ param_desc.path, param_desc.line, isotope.id, res_to_cstr(res));
res = RES_OK;
goto error;
}
@@ -490,7 +417,7 @@ load_stream
molecule_init(shitran->allocator, &molecule);
- res = create_isotoplogues(shitran, &metadata);
+ res = create_isotope_metadata(shitran, &metadata);
if(res != RES_OK) goto error;
res = txtrdr_stream(metadata->shitran->allocator, stream, name,
diff --git a/src/shitran_param.c b/src/shitran_param.c
@@ -0,0 +1,82 @@
+/* Copyright (C) 2022 CNRS - LMD
+ * Copyright (C) 2022 |Meso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022 Université Paul Sabatier - IRIT
+ * Copyright (C) 2022 Université Paul Sabatier - 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/>. */
+
+#include "shitran_c.h"
+#include "shitran_log.h"
+#include "shitran_param.h"
+
+#include <rsys/cstr.h>
+
+#define C_FORMAT_double "%g"
+#define C_FORMAT_float "%g"
+#define C_FORMAT_int "%d"
+
+/*******************************************************************************
+ * Local functions
+ ******************************************************************************/
+#define DEFINE_PARSE_PARAM_FUNCTION(Type) \
+ res_T \
+ parse_param_##Type \
+ (struct shitran* shitran, \
+ const char* str, \
+ const struct param_desc* desc, \
+ Type* out_param) \
+ { \
+ Type param = 0; \
+ res_T res = RES_OK; \
+ ASSERT(shitran && desc && out_param); \
+ ASSERT(desc->low < desc->upp \
+ || (desc->low == desc->upp && desc->is_low_incl && desc->is_upp_incl));\
+ \
+ if(!str) { \
+ log_err(shitran, "%s:%lu: %s is missing.\n", \
+ desc->path, (unsigned long)desc->line, desc->name); \
+ res = RES_BAD_ARG; \
+ goto error; \
+ } \
+ \
+ res = cstr_to_##Type(str, ¶m); \
+ if(res != RES_OK) { \
+ log_err(shitran, "%s:%lu: invalid %s `%s'.\n", \
+ desc->path, (unsigned long)desc->line, desc->name, str); \
+ res = RES_BAD_ARG; \
+ goto error; \
+ } \
+ \
+ if(param < desc->low || (param == desc->low && !desc->is_low_incl) \
+ || param > desc->upp || (param == desc->upp && !desc->is_upp_incl)) { \
+ log_err(shitran, \
+ "%s:%lu: invalid %s `%s'. It must be in " \
+ "%c"CONCAT(C_FORMAT_, Type)", "CONCAT(C_FORMAT_, Type)"%c.\n", \
+ desc->path, (unsigned long)desc->line, desc->name, str, \
+ desc->is_low_incl ? '[' : ']', (Type)desc->low, \
+ (Type)desc->upp, desc->is_upp_incl ? ']' : '['); \
+ res = RES_BAD_ARG; \
+ goto error; \
+ } \
+ \
+ exit: \
+ *out_param = param; \
+ return res; \
+ error: \
+ goto exit; \
+ }
+DEFINE_PARSE_PARAM_FUNCTION(int)
+DEFINE_PARSE_PARAM_FUNCTION(double)
+DEFINE_PARSE_PARAM_FUNCTION(float)
+#undef DEFINE_PARSE_PARAM_FUNCTION
diff --git a/src/shitran_param.h b/src/shitran_param.h
@@ -0,0 +1,61 @@
+/* Copyright (C) 2022 CNRS - LMD
+ * Copyright (C) 2022 |Meso|Star> (contact@meso-star.com)
+ * Copyright (C) 2022 Université Paul Sabatier - IRIT
+ * Copyright (C) 2022 Université Paul Sabatier - 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/>. */
+
+#ifndef SHITRAN_PARAM_H
+#define SHITRAN_PARAM_H
+
+#include <rsys/rsys.h>
+
+struct param_desc {
+ const char* path; /* Path where the param lies */
+ const char* name; /* Name of the param */
+ size_t line; /* Line number of the param */
+
+ /* Domain of the param */
+ double low, upp;
+ int is_low_incl; /* Define if the lower bound is inclusive */
+ int is_upp_incl; /* Define if the upper bound is inclusive */
+};
+#define PARAM_DESC_NULL__ {NULL, NULL, 0, 0, 0, 0, 0}
+static const struct param_desc PARAM_DESC_NULL = PARAM_DESC_NULL__;
+
+/* Forware declaration */
+struct shitran;
+
+extern LOCAL_SYM res_T
+parse_param_int
+ (struct shitran* shitran,
+ const char* str,
+ const struct param_desc* desc,
+ int* param);
+
+extern LOCAL_SYM res_T
+parse_param_double
+ (struct shitran* shitran,
+ const char* str,
+ const struct param_desc* desc,
+ double* param);
+
+extern LOCAL_SYM res_T
+parse_param_float
+ (struct shitran* shitran,
+ const char* str,
+ const struct param_desc* desc,
+ float* param);
+
+#endif /* SHITRAN_PARAM_H */
diff --git a/src/test_shitran_isotope_metadata.c b/src/test_shitran_isotope_metadata.c
@@ -88,7 +88,7 @@ isotope_eq(const struct shitran_isotope* i0, const struct shitran_isotope* i1)
return i0->abundance == i1->abundance
&& i0->Q296K == i1->Q296K
&& i0->molar_mass == i1->molar_mass
- && i0->imolecule == i1->imolecule
+ && i0->molecule_id_local == i1->molecule_id_local
&& i0->gj == i1->gj
&& i0->id == i1->id;
}
@@ -130,7 +130,7 @@ check_isotope
CHK(isotope->id >= 0);
CHK(shitran_isotope_metadata_get_molecule
- (mdata, isotope->imolecule, &molecule2) == RES_OK);
+ (mdata, isotope->molecule_id_local, &molecule2) == RES_OK);
CHK(molecule_eq(molecule, &molecule2));
}
