commit c0e460c8be6d1918f9f94add2200bbb661139b32
parent dc23cbec38fe2f895266b35db84d9e55d8621b91
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Mon, 30 Oct 2023 11:49:16 +0100
Merge branch 'release_0.1'
Diffstat:
| M | .gitignore | | | 14 | +++++++------- |
| A | Makefile | | | 150 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| M | README.md | | | 49 | ++++++++++++++++++++++++++++--------------------- |
| D | cmake/CMakeLists.txt | | | 118 | ------------------------------------------------------------------------------- |
| A | config.mk | | | 77 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| D | doc/sars.5.scd | | | 94 | ------------------------------------------------------------------------------- |
| A | make.sh | | | 71 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | sars.5 | | | 105 | +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
| A | sars.pc.in | | | 10 | ++++++++++ |
| M | src/sars.c | | | 425 | ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++----------- |
| M | src/sars.h | | | 38 | +++++++++++++++++++++++++++++++++++--- |
| M | src/sars_c.h | | | 16 | ++++++++++++++++ |
| M | src/test_sars_load.c | | | 100 | +++++++++++++++++++++++++++++++++++++++++++++++++++++-------------------------- |
13 files changed, 936 insertions(+), 331 deletions(-)
diff --git a/.gitignore b/.gitignore
@@ -1,12 +1,12 @@
.gitignore
-CMakeCache.txt
-CMakeFiles
-Makefile
-tmp
[Bb]uild*
*.sw[po]
-*.[ao]
-*.orig
+*.[aod]
+*.so
*~
+test*
+!test*.[ch]
+.config
+.test
tags
-
+*.pc
diff --git a/Makefile b/Makefile
@@ -0,0 +1,150 @@
+# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+#
+# 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/>.
+
+.POSIX:
+.SUFFIXES: # Clean up default inference rules
+
+include config.mk
+
+LIBNAME_STATIC = libsars.a
+LIBNAME_SHARED = libsars.so
+LIBNAME = $(LIBNAME_$(LIB_TYPE))
+
+################################################################################
+# Library building
+################################################################################
+SRC = src/sars.c src/sars_log.c
+OBJ = $(SRC:.c=.o)
+DEP = $(SRC:.c=.d)
+
+build_library: .config $(DEP)
+ @$(MAKE) -fMakefile $$(for i in $(DEP); do echo -f $${i}; done) \
+ $$(if [ -n "$(LIBNAME)" ]; then \
+ echo "$(LIBNAME)"; \
+ else \
+ echo "$(LIBNAME_SHARED)"; \
+ fi)
+
+$(DEP) $(OBJ): config.mk
+
+$(LIBNAME_SHARED): $(OBJ)
+ $(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -o $@ $(OBJ) $(LDFLAGS_SO) $(RSYS_LIBS)
+
+$(LIBNAME_STATIC): libsars.o
+ $(AR) -rc $@ $?
+ $(RANLIB) $@
+
+libsars.o: $(OBJ)
+ $(LD) -r $(OBJ) -o $@
+ $(OBJCOPY) $(OCPFLAGS) $@
+
+.config: config.mk
+ @if ! $(PKG_CONFIG) --atleast-version $(RSYS_VERSION) rsys; then \
+ echo "rsys $(RSYS_VERSION) not found" >&2; exit 1; fi
+ @echo "config done" > $@
+
+.SUFFIXES: .c .d .o
+.c.d:
+ @$(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -MM -MT "$(@:.d=.o) $@" $< -MF $@
+
+.c.o:
+ $(CC) $(CFLAGS_SO) $(RSYS_CFLAGS) -DSARS_SHARED_BUILD -c $< -o $@
+
+################################################################################
+# Installation
+################################################################################
+pkg:
+ sed -e 's#@PREFIX@#$(PREFIX)#g'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ sars.pc.in > sars.pc
+
+sars-local.pc: sars.pc.in
+ sed -e '1d'\
+ -e 's#^includedir=.*#includedir=./src/#'\
+ -e 's#^libdir=.*#libdir=./#'\
+ -e 's#@VERSION@#$(VERSION)#g'\
+ -e 's#@RSYS_VERSION@#$(RSYS_VERSION)#g'\
+ sars.pc.in > $@
+
+install: build_library pkg
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib" $(LIBNAME)
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/lib/pkgconfig" sars.pc
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/include/star" src/sars.h
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/doc/star-aerosol" COPYING README.md
+ @$(SHELL) make.sh install "$(DESTDIR)$(PREFIX)/share/man/man5" sars.5
+
+uninstall:
+ rm -f "$(DESTDIR)$(PREFIX)/lib/$(LIBNAME)"
+ rm -f "$(DESTDIR)$(PREFIX)/lib/pkgconfig/sars.pc"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/star-aerosol/COPYING"
+ rm -f "$(DESTDIR)$(PREFIX)/share/doc/star-aerosol/README.md"
+ rm -f "$(DESTDIR)$(PREFIX)/include/star/sars.h"
+ rm -f "$(DESTDIR)$(PREFIX)/share/man/man5/sars.5"
+
+################################################################################
+# Miscellaneous targets
+################################################################################
+all: build_library build_tests
+
+clean: clean_test
+ rm -f $(OBJ) $(TEST_OBJ) $(LIBNAME)
+ rm -f .config .test libsars.o sars.pc sars-local.pc
+
+distclean: clean
+ rm -f $(DEP) $(TEST_DEP)
+
+lint:
+ shellcheck -o all make.sh
+ mandoc -Tlint -Wall sars.5 || [ $$? -le 1 ]
+
+################################################################################
+# Tests
+################################################################################
+TEST_SRC =\
+ src/test_sars.c\
+ src/test_sars_load.c
+TEST_OBJ = $(TEST_SRC:.c=.o)
+TEST_DEP = $(TEST_SRC:.c=.d)
+
+PKG_CONFIG_LOCAL = PKG_CONFIG_PATH="./:$${PKG_CONFIG_PATH}" $(PKG_CONFIG)
+SARS_CFLAGS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --cflags sars-local.pc)
+SARS_LIBS = $$($(PKG_CONFIG_LOCAL) $(PCFLAGS) --libs sars-local.pc)
+
+build_tests: build_library $(TEST_DEP) .test
+ @$(MAKE) -fMakefile -f.test $$(for i in $(TEST_DEP); do echo -f"$${i}"; done) test_bin
+
+test: build_tests
+ @$(SHELL) make.sh run_test $(TEST_SRC)
+
+.test: Makefile
+ @$(SHELL) make.sh config_test $(TEST_SRC) > $@
+
+clean_test:
+ $(SHELL) make.sh clean_test $(TEST_SRC)
+ rm -f test_file.sars
+
+$(TEST_DEP): config.mk sars-local.pc
+ @$(CC) $(CFLAGS_EXE) $(SARS_CFLAGS) $(RSYS_CFLAGS) \
+ -MM -MT "$(@:.d=.o) $@" $(@:.d=.c) -MF $@
+
+$(TEST_OBJ): config.mk sars-local.pc
+ $(CC) $(CFLAGS_EXE) $(SARS_CFLAGS) $(RSYS_CFLAGS) -c $(@:.o=.c) -o $@
+
+test_sars: config.mk sars-local.pc $(LIBNAME)
+ $(CC) $(CFLAGS_EXE) -o $@ src/$@.o $(LDFLAGS_EXE) $(SARS_LIBS) $(RSYS_LIBS)
+
+test_sars_load: config.mk sars-local.pc $(LIBNAME)
+ $(CC) $(CFLAGS_EXE) -o $@ src/$@.o $(LDFLAGS_EXE) $(SARS_LIBS) $(RSYS_LIBS) -lm
diff --git a/README.md b/README.md
@@ -1,31 +1,38 @@
-# Star-Aerosol
+# Star Aerosol
-This C library loads the radiative properties of an aerosol saved wrt the
-Star-Aerosol file format.
+This C library loads the radiative properties of an aerosol saved in
+sars format. See `sars.5` for the format specification.
-## How to build
+## Requirements
-This library is compatible with 64-bits POSIX systems. It relies the
-[CMake](http://www.cmake.org) and the
-[RCMake](https://gitlab.com/vaplv/rcmake/) packages to build. It also depends
-on the [RSys](https://gitlab.com/vaplv/rsys/) library. It optionally depends on
-[scdoc](https://sr.ht/~sircmpwn/scdoc/) which, if available, is used to
-generate the man page of the Star-Aerosol file format.
+- C compiler
+- POSIX make
+- pkg-config
+- [RSys](https://gitlab.com/vaplv/rsys)
+- [mandoc](https://mandoc.bsd.lv)
-First ensure that CMake is installed on your system. Then install the RCMake
-package as well as the aforementioned prerequisites. Finally generate the
-project from the `cmake/CMakeLists.txt` file by appending to the
-`CMAKE_PREFIX_PATH` variable the install directories of its dependencies. The
-resulting project can be edited, built, tested and installed as any CMake
-project. Refer to the [CMake documentation](https://cmake.org/documentation)
-for further informations on CMake.
+## Installation
-## Copyright notice
+Edit config.mk as needed, then run:
-Copyright (C) 2022, 2023 [|Méso|Star>](https://www.meso-star.com) (<contact@meso-star.com>).
+ make clean install
+
+## Release notes
+
+### Version 0.1
+
+- Write the man page directly in mdoc's roff macros, instead of using
+ the intermediate scdoc source.
+- Replace CMake by Makefile as build system.
+- Update compiler and linker flags to increase the security and
+ robustness of generated binaries.
+- Provide a pkg-config file to link the library as an external
+ dependency.
## License
-Star-Aerosol is free software released under the GPL v3+ license: GNU GPL
-version 3 or later. You are welcome to redistribute it under certain
+Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+
+Star-Aerosol is free software released under the GPL v3+ license: GNU
+GPL version 3 or later. You are welcome to redistribute it under certain
conditions; refer to the COPYING file for details.
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -1,118 +0,0 @@
-# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
-#
-# 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/>.
-
-cmake_minimum_required(VERSION 3.1)
-project(sars C)
-enable_testing()
-
-set(SARS_SOURCE_DIR ${PROJECT_SOURCE_DIR}/../src)
-option(NO_TEST "Do not build tests" OFF)
-
-################################################################################
-# Check dependencies
-################################################################################
-find_package(RCMake 0.4 REQUIRED)
-find_package(RSys 0.13 REQUIRED)
-
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${RCMAKE_SOURCE_DIR})
-include(rcmake)
-include(rcmake_runtime)
-
-include_directories(${RSys_INCLUDE_DIR})
-
-################################################################################
-# Configure and define targets
-################################################################################
-set(VERSION_MAJOR 0)
-set(VERSION_MINOR 0)
-set(VERSION_PATCH 0)
-set(VERSION ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})
-
-set(SARS_FILES_SRC
- sars.c
- sars_log.c)
-set(SARS_FILES_INC
- sars_c.h
- sars_log.h)
-set(SARS_FILES_INC_API
- sars.h)
-
-set(SARS_FILES_DOC COPYING README.md)
-
-# Prepend each file in the `SARS_FILES_<SRC|INC>' list by `SARS_SOURCE_DIR'
-rcmake_prepend_path(SARS_FILES_SRC ${SARS_SOURCE_DIR})
-rcmake_prepend_path(SARS_FILES_INC ${SARS_SOURCE_DIR})
-rcmake_prepend_path(SARS_FILES_INC_API ${SARS_SOURCE_DIR})
-rcmake_prepend_path(SARS_FILES_DOC ${PROJECT_SOURCE_DIR}/../)
-
-add_library(sars SHARED ${SARS_FILES_SRC} ${SARS_FILES_INC} ${SARS_FILES_INC_API})
-target_link_libraries(sars RSys)
-
-if(CMAKE_COMPILER_IS_GNUCC)
- target_link_libraries(sars m)
-endif()
-
-set_target_properties(sars PROPERTIES
- DEFINE_SYMBOL SARS_SHARED_BUILD
- VERSION ${VERSION}
- SOVERSION ${VERSION_MAJOR})
-
-rcmake_setup_devel(sars StarAerosol ${VERSION} star/sars_version.h)
-
-################################################################################
-# Add tests
-################################################################################
-if(NOT NO_TEST)
- function(new_test _name)
- add_executable(${_name} ${SARS_SOURCE_DIR}/${_name}.c)
- target_link_libraries(${_name} sars RSys ${ARGN})
- add_test(${_name} ${_name})
- endfunction()
-
- new_test(test_sars)
- new_test(test_sars_load)
-endif()
-
-################################################################################
-# Man page
-###############################################################################
-find_program(SCDOC NAMES scdoc)
-if(NOT SCDOC)
- message(WARNING
- "The `scdoc' program is missing. "
- "The Star-Aerosol man page cannot be generated.")
-else()
- set(_src ${PROJECT_SOURCE_DIR}/../doc/sars.5.scd)
- add_custom_command(
- OUTPUT sars.5
- COMMAND ${SCDOC} < ${_src} > sars.5
- DEPENDS ${_src}
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "Buid ROFF man page sars.5"
- VERBATIM)
- add_custom_target(man-roff ALL DEPENDS sars.5)
- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/sars.5 DESTINATION share/man/man5)
-endif()
-
-################################################################################
-# Define output & install directories
-################################################################################
-install(TARGETS sars
- ARCHIVE DESTINATION bin
- LIBRARY DESTINATION lib
- RUNTIME DESTINATION bin)
-install(FILES ${SARS_FILES_INC_API} DESTINATION include/star)
-install(FILES ${SARS_FILES_DOC} DESTINATION share/doc/star-aerosol)
-
diff --git a/config.mk b/config.mk
@@ -0,0 +1,77 @@
+VERSION = 0.1.0
+PREFIX = /usr/local
+
+LIB_TYPE = SHARED
+#LIB_TYPE = STATIC
+
+BUILD_TYPE = RELEASE
+#BUILD_TYPE = DEBUG
+
+################################################################################
+# Tools
+################################################################################
+AR = ar
+CC = cc
+LD = ld
+OBJCOPY = objcopy
+PKG_CONFIG = pkg-config
+RANLIB = ranlib
+
+################################################################################
+# Dependencies
+################################################################################
+PCFLAGS_SHARED =
+PCFLAGS_STATIC = --static
+PCFLAGS = $(PCFLAGS_$(LIB_TYPE))
+
+RSYS_VERSION = 0.14
+RSYS_CFLAGS = $$($(PKG_CONFIG) $(PCFLAGS) --cflags rsys)
+RSYS_LIBS = $$($(PKG_CONFIG) $(PCFLAGS) --libs rsys)
+
+################################################################################
+# Compilation options
+################################################################################
+WFLAGS =\
+ -Wall\
+ -Wcast-align\
+ -Wconversion\
+ -Wextra\
+ -Wmissing-declarations\
+ -Wmissing-prototypes\
+ -Wshadow
+
+CFLAGS_HARDENED =\
+ -D_FORTIFY_SOURCES=2\
+ -fcf-protection=full\
+ -fstack-clash-protection\
+ -fstack-protector-strong
+
+CFLAGS_COMMON =\
+ -std=c89\
+ -pedantic\
+ -fvisibility=hidden\
+ -fstrict-aliasing\
+ $(CFLAGS_HARDENED)\
+ $(WFLAGS)
+
+CFLAGS_DEBUG = -g $(CFLAGS_COMMON)
+CFLAGS_RELEASE = -O2 -DNDEBUG $(CFLAGS_COMMON)
+CFLAGS = $(CFLAGS_$(BUILD_TYPE))
+
+CFLAGS_SO = $(CFLAGS) -fPIC
+CFLAGS_EXE = $(CFLAGS) -fPIE
+
+################################################################################
+# Linker options
+################################################################################
+LDFLAGS_HARDENED = -Wl,-z,relro,-z,now
+LDFLAGS_DEBUG = $(LDFLAGS_HARDENED)
+LDFLAGS_RELEASE = -s $(LDFLAGS_HARDENED)
+LDFLAGS = $(LDFLAGS_$(BUILD_TYPE))
+
+LDFLAGS_SO = $(LDFLAGS) -shared -Wl,--no-undefined
+LDFLAGS_EXE = $(LDFLAGS) -pie
+
+OCPFLAGS_DEBUG = --localize-hidden
+OCPFLAGS_RELEASE = --localize-hidden --strip-unneeded
+OCPFLAGS = $(OCPFLAGS_$(BUILD_TYPE))
diff --git a/doc/sars.5.scd b/doc/sars.5.scd
@@ -1,94 +0,0 @@
-sars(5)
-
-; Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
-;
-; 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/>.
-
-# NAME
-
-sars - Star AeoRoSol file format
-
-# DESCRIPTION
-
-*sars* is a binary file format for storing the radiative properties of an
-aerosol. The volumetric mesh to which the CKs are attached is _not_ described
-there but must be defined in a separated file via, for example, the *smsh*(5)
-file format.
-
-An *sars* file begins by a header that describes the layout of the data. Next
-the spectral bands on which the radiative coefficients were defined are listed.
-Finally, the entire list of the scattering coefficients and absorption
-coefficients are stored.
-
-The header consists of 3 64-bit integers. The first integer is a power of two
-(usually 4096) that defines the _pagesize_ in bytes on which the radiative
-coefficients are aligned. The remaining two integers store the number of bands
-and the number of nodes, that is, the number of radiative coefficients per band
-which is actually the number of nodes in the volumetric mesh to which these
-coefficients are attached.
-
-After the header comes the list of spectral bands sorted in ascending order
-relative to their interval. Each spectral band is defined by 2 double-precision
-floating-point numbers that represent the lower and upper limits of the band in
-nanometers.
-
-Fill bytes follow the list of spectral bands to ensure alignment of the
-radiative coefficients on _pagesize_. By aligning data on _pagesize_, and
-depending on system requirements, memory mapping can be used to automatically
-load/unload the radiative coefficients on demand (see *mmap*(2)). For each band,
-the absorption coefficient and diffusion coefficient are listed per node. This
-list is followed by a _padding_, which is a list of bytes that provides memory
-alignment of the following data to _pagesize_. Bands are sorted according to the
-order in which they were previously declared.
-
-# BINARY FILE FORMAT
-
-Data are encoded with respect to the little endian bytes ordering, i.e. least
-significant bytes are stored first.
-
-```
-<sars> ::= <pagesize> <#bands> <#nodes>
- <bands>
- <padding>
- <rad-coefs>
-
-<pagesize> ::= UINT64
-<#bands> ::= UINT64
-<#nodes> ::= UINT64
-<padding> ::= [ BYTE ... ] #ensure alignment on <pagesize>
-
----
-
-<band-list> ::= <band> [ <band> ... ]
-<band> ::= <band-low> <band-upp>
-
-<band-id> ::= UINT64
-<band-low> ::= DOUBLE # In nm (inclusive)
-<band-upp> ::= DOUBLE # In nm (exclusive)
-
----
-
-<rad-coefs> ::= <per-band-k>
- [ <per-band-k> ... ]
-
-<per-band-k> ::= <ka-ks> [ <ka-ks> ... ] <padding>
-
-<ka-ks> ::= <ka> <ks>
-<ka> ::= FLOAT # in m^-1
-<ks> ::= FLOAT # in m^-1
-```
-
-# SEE ALSO
-
-*mmap*(2), *smsh*(5)
diff --git a/make.sh b/make.sh
@@ -0,0 +1,71 @@
+#!/bin/sh
+
+# Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+#
+# 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/>.
+
+set -e
+
+config_test()
+{
+ for i in "$@"; do
+ test=$(basename "${i}" ".c")
+ test_list="${test_list} ${test}"
+ printf "%s: %s\n" "${test}" "src/${test}.o"
+ done
+ printf "test_bin: %s\n" "${test_list}"
+}
+
+run_test()
+{
+ for i in "$@"; do
+ test=$(basename "${i}" ".c")
+
+ printf "%s " "${test}"
+ if "./${test}" > /dev/null 2>&1; then
+ printf "\033[1;32mOK\033[m\n"
+ else
+ printf "\033[1;31mError\033[m\n"
+ fi
+ done 2> /dev/null
+}
+
+
+clean_test()
+{
+ for i in "$@"; do
+ rm -f "$(basename "${i}" ".c")"
+ done
+}
+
+install()
+{
+ prefix=$1
+ shift 1
+
+ mkdir -p "${prefix}"
+
+ for i in "$@"; do
+ dst="${prefix}/${i##*/}"
+
+ if cmp -s "${i}" "${dst}"; then
+ printf "Up to date %s\n" "${dst}"
+ else
+ printf "Installing %s\n" "${dst}"
+ cp "${i}" "${prefix}"
+ fi
+ done
+}
+
+"$@"
diff --git a/sars.5 b/sars.5
@@ -0,0 +1,105 @@
+.\" Copyright (C) 2022, 2023 |Méso|Star> (contact@meso-star.com)
+.\"
+.\" 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/>.
+.Dd July 28, 2023
+.Dt SARS 5
+.Os
+.Sh NAME
+.Nm sars
+.Nd Star AeRoSol file format
+.Sh DESCRIPTION
+.Nm
+is a binary file format for storing the radiative properties of an
+aerosol.
+The volumetric mesh to which the CKs are attached is
+.Em not
+described there but must be defined in a separated file via, for example, the
+.Xr smsh 5
+file format.
+.Pp
+A
+.Nm
+file begins by a header that describes the layout of the data.
+Next the spectral bands on which the radiative coefficients were defined are
+listed.
+Finally, the entire list of the scattering coefficients and absorption
+coefficients are stored.
+.Pp
+The header consists of 3 64-bit integers.
+The first integer is a power of two
+.Pq usually 4096
+that defines the
+.Va pagesize
+in bytes on which the radiative coefficients are aligned.
+The remaining two integers store the number of bands and the number of nodes,
+that is, the number of radiative coefficients per band which is actually the
+number of nodes in the volumetric mesh to which these coefficients are
+attached.
+.Pp
+After the header comes the list of spectral bands sorted in ascending order
+relative to their interval.
+Each spectral band is defined by 2 double-precision floating-point numbers that
+represent the lower and upper limits of the band in nanometers.
+.Pp
+Fill bytes follow the list of spectral bands to ensure alignment of the
+radiative coefficients on
+.Va pagesize .
+By aligning data on
+.Va pagesize ,
+and depending on system requirements, memory mapping can be used to
+automatically load/unload the radiative coefficients on demand
+.Pq see Xr mmap 2 .
+For each band, the absorption coefficient and diffusion coefficient are listed
+per node.
+This list is followed by a
+.Va padding ,
+which is a list of bytes that provides memory alignment of the following data
+to
+.Va pagesize .
+Bands are sorted according to the order in which they were previously declared.
+.Pp
+Data are encoded with respect to the little endian bytes ordering, i.e. least
+significant bytes are stored first.
+.Pp
+The file format is as follows:
+.Bl -column (per-band-k) (::=) ()
+.It Ao Va sars Ac Ta ::= Ta Ao Va pagesize Ac Ao Va #bands Ac Ao Va #nodes Ac
+.It Ta Ta Aq Va bands
+.It Ta Ta Aq Va padding
+.It Ta Ta Aq Va rad-coefs
+.It \ Ta Ta
+.It Ao Va pagesize Ac Ta ::= Ta Vt uint64_t
+.It Ao Va #bands Ac Ta ::= Ta Vt uint64_t
+.It Ao Va #nodes Ac Ta ::= Ta Vt uint64_t
+.It Ao Va padding Ac Ta ::= Ta Op Va int8_t ...
+# Ensure alignment on
+.Va pagesize
+.It \ Ta Ta
+.It Ao Va bands Ac Ta ::= Ta Ao Va band Ac Va ...
+.It Ao Va band Ac Ta ::= Ta Ao Va band-low Ac Ao Va band-upp Ac
+.It Ao Va band-low Ac Ta ::= Ta Vt double
+# Inclusive bound in nm
+.It Ao Va band-upp Ac Ta ::= Ta Vt double
+# Excusive bound in nm
+.It \ Ta Ta
+.It Ao Va rad-coefs Ac Ta ::= Ta Ao Va per-band-k Ac Va ...
+.It Ao Va ka-ks Ac Ta ::= Ta Ao Va ka Ac Ao Va ks Ac
+.It Ao Va ka Ac Ta ::= Ta Vt float
+# In m^-1
+.It Ao Va ks Ac Ta ::= Ta Vt float
+# In m^-1
+.El
+.Sh SEE ALSO
+.Xr mmap 2 ,
+.Xr smsh 5
diff --git a/sars.pc.in b/sars.pc.in
@@ -0,0 +1,10 @@
+prefix=@PREFIX@
+includedir=${prefix}/include
+libdir=${prefix}/lib
+
+Requires: rsys >= @RSYS_VERSION@
+Name: Star-AeRoSol
+Description: Star Aerosol library
+Version: @VERSION@
+Libs: -L${libdir} -lsars
+CFlags: -I${includedir}
diff --git a/src/sars.c b/src/sars.c
@@ -22,16 +22,29 @@
#include "sars_log.h"
#include <rsys/algorithm.h>
+#include <rsys/cstr.h>
#include <rsys/hash.h>
#include <unistd.h> /* sysconf support */
#include <errno.h>
#include <sys/mman.h> /* mmap */
+#include <sys/stat.h> /* fstat */
/*******************************************************************************
* Helper functions
******************************************************************************/
+static INLINE int
+is_stdin(FILE* stream)
+{
+ struct stat stream_buf;
+ struct stat stdin_buf;
+ ASSERT(stream);
+ CHK(fstat(fileno(stream), &stream_buf) == 0);
+ CHK(fstat(STDIN_FILENO, &stdin_buf) == 0);
+ return stream_buf.st_dev == stdin_buf.st_dev;
+}
+
static INLINE res_T
check_sars_create_args(const struct sars_create_args* args)
{
@@ -39,6 +52,28 @@ check_sars_create_args(const struct sars_create_args* args)
return args ? RES_OK : RES_BAD_ARG;
}
+static INLINE res_T
+check_sars_load_args(const struct sars_load_args* args)
+{
+ if(!args || !args->path) return RES_BAD_ARG;
+ return RES_OK;
+}
+
+static INLINE res_T
+check_sars_load_stream_args
+ (struct sars* sars,
+ const struct sars_load_stream_args* args)
+{
+ if(!args || !args->stream || !args->name) return RES_BAD_ARG;
+ if(args->memory_mapping && is_stdin(args->stream)) {
+ log_err(sars,
+ "%s: unable to use memory mapping on data loaded from stdin\n",
+ args->name);
+ return RES_BAD_ARG;
+ }
+ return RES_OK;
+}
+
static void
reset_sars(struct sars* sars)
{
@@ -52,20 +87,20 @@ static res_T
read_band
(struct sars* sars,
struct band* band,
- FILE* stream,
- const char* stream_name)
+ FILE* stream)
{
size_t iband;
res_T res = RES_OK;
- ASSERT(sars && band && stream_name);
+ ASSERT(sars && band);
+ band->sars = sars;
iband = (size_t)(band - darray_band_cdata_get(&sars->bands));
/* Read band definition */
#define READ(Var, Name) { \
if(fread((Var), sizeof(*(Var)), 1, stream) != 1) { \
log_err(sars, "%s: band %lu: could not read the %s.\n", \
- stream_name, (unsigned long)iband, (Name)); \
+ sars_get_name(sars), (unsigned long)iband, (Name)); \
res = RES_IO_ERR; \
goto error; \
} \
@@ -78,7 +113,7 @@ read_band
if(band->low < 0 || band->low >= band->upp) {
log_err(sars,
"%s: band %lu: invalid band range [%g, %g[.\n",
- stream_name, (unsigned long)iband, band->low, band->upp);
+ sars_get_name(sars), (unsigned long)iband, band->low, band->upp);
res = RES_BAD_ARG;
goto error;
}
@@ -89,23 +124,223 @@ error:
goto exit;
}
+static res_T
+map_data
+ (struct sars* sars,
+ const int fd, /* File descriptor */
+ const size_t filesz, /* Overall filesize */
+ const char* data_name,
+ const off_t offset, /* Offset of the data into file */
+ const size_t map_len,
+ void** out_map) /* Lenght of the data to map */
+{
+ void* map = NULL;
+ res_T res = RES_OK;
+ ASSERT(sars && filesz && data_name && map_len && out_map);
+ ASSERT(IS_ALIGNED((size_t)offset, (size_t)sars->pagesize));
+
+ if((size_t)offset + map_len > filesz) {
+ log_err(sars, "%s: the %s to map exceed the file size\n",
+ sars_get_name(sars), data_name);
+ res = RES_IO_ERR;
+ goto error;
+ }
+
+ map = mmap(NULL, map_len, PROT_READ, MAP_PRIVATE|MAP_POPULATE, fd, offset);
+ if(map == MAP_FAILED) {
+ log_err(sars, "%s: could not map the %s -- %s\n",
+ sars_get_name(sars), data_name, strerror(errno));
+ res = RES_IO_ERR;
+ goto error;
+ }
+
+exit:
+ *out_map = map;
+ return res;
+error:
+ if(map == MAP_FAILED) map = NULL;
+ goto exit;
+}
static res_T
-load_stream(struct sars* sars, FILE* stream, const char* stream_name)
+map_file(struct sars* sars, FILE* stream)
{
+ size_t filesz;
size_t map_len;
size_t iband;
+ size_t nbands;
+ off_t offset;
+ res_T res = RES_OK;
+ ASSERT(sars && stream);
+
+ /* Compute the length in bytes of the k to map for each band/quadrature point */
+ map_len = ALIGN_SIZE(sars->nnodes * sizeof(float)*2, sars->pagesize);
+
+ /* Compute the offset toward the 1st list of radiative coefficients */
+ offset = ftell(stream);
+ offset = (off_t)ALIGN_SIZE((uint64_t)offset, sars->pagesize);
+
+ /* Retrieve the overall filesize */
+ fseek(stream, 0, SEEK_END);
+ filesz = (size_t)ftell(stream);
+
+ nbands = sars_get_bands_count(sars);
+ FOR_EACH(iband, 0, nbands) {
+ struct band* band = NULL;
+
+ band = darray_band_data_get(&sars->bands) + iband;
+ band->map_len = map_len;
+
+ /* Mapping per band radiative coefficients */
+ res = map_data(sars, fileno(stream), filesz, "radiative coefficients",
+ offset, band->map_len, (void**)&band->k_list);
+ if(res != RES_OK) {
+ log_err(sars,
+ "%s: data mapping error for band %lu\n",
+ sars_get_name(sars), (unsigned long)iband);
+ res = RES_IO_ERR;
+ goto error;
+ }
+
+ offset = (off_t)((size_t)offset + map_len);
+ }
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+read_padding(FILE* stream, const size_t padding)
+{
+ char chunk[1024];
+ size_t remaining_nbytes = padding;
+
+ while(remaining_nbytes) {
+ const size_t nbytes = MMIN(sizeof(chunk), remaining_nbytes);
+ if(fread(chunk, 1, nbytes, stream) != nbytes) return RES_IO_ERR;
+ remaining_nbytes -= nbytes;
+ }
+ return RES_OK;
+}
+
+/* Return the size in bytes of the data layout and band descriptors */
+static INLINE size_t
+compute_sizeof_header(struct sars* sars)
+{
+ size_t sizeof_header = 0;
+ ASSERT(sars);
+
+ sizeof_header =
+ sizeof(uint64_t) /* pagesize */
+ + sizeof(uint64_t) /* #bands */
+ + sizeof(uint64_t) /* #nodes */
+ + sizeof(double[2]) * sars_get_bands_count(sars); /* Bands */
+ return sizeof_header;
+}
+
+static res_T
+load_data
+ (struct sars* sars,
+ FILE* stream,
+ const char* data_name,
+ float** out_data)
+{
+ float* data = NULL;
+ res_T res = RES_OK;
+ ASSERT(sars && stream && data_name && out_data);
+
+ data = MEM_ALLOC(sars->allocator, sizeof(float[2]/*ka and ks*/)*sars->nnodes);
+ if(!data) {
+ res = RES_MEM_ERR;
+ log_err(sars, "%s: could not allocate the %s -- %s\n",
+ sars_get_name(sars), data_name, res_to_cstr(res));
+ goto error;
+ }
+
+ if(fread(data, sizeof(float[2]), sars->nnodes, stream) != sars->nnodes) {
+ res = RES_IO_ERR;
+ log_err(sars, "%s: could not read the %s -- %s\n",
+ sars_get_name(sars), data_name, res_to_cstr(res));
+ goto error;
+ }
+
+exit:
+ *out_data = data;
+ return res;
+error:
+ if(data) { MEM_RM(sars->allocator, data); data = NULL; }
+ goto exit;
+}
+
+static res_T
+load_file(struct sars* sars, FILE* stream)
+{
+ size_t sizeof_header;
+ size_t sizeof_k_list;
+ size_t padding_bytes;
+ size_t iband;
+ size_t nbands;
+ res_T res = RES_OK;
+ ASSERT(sars && stream);
+
+ sizeof_header = compute_sizeof_header(sars);
+ sizeof_k_list = sizeof(float[2])*sars->nnodes;
+
+ padding_bytes = ALIGN_SIZE(sizeof_header, sars->pagesize) - sizeof_header;
+ if((res = read_padding(stream, padding_bytes)) != RES_OK) goto error;
+
+ /* Calculate the padding between the lists of radiative coefficients. Note
+ * that this padding is the same between each list */
+ padding_bytes = ALIGN_SIZE(sizeof_k_list, sars->pagesize) - sizeof_k_list;
+
+ nbands = sars_get_bands_count(sars);
+ FOR_EACH(iband, 0, nbands) {
+ struct band* band = NULL;
+
+ band = darray_band_data_get(&sars->bands) + iband;
+ ASSERT(!band->k_list && band->sars == sars);
+
+ /* Loading per band scattering coefficients */
+ res = load_data(sars, stream, "radiative coefficients", &band->k_list);
+ if(res != RES_OK) {
+ log_err(sars,
+ "%s: data loading error for band %lu\n",
+ sars_get_name(sars), (unsigned long)iband);
+ goto error;
+ }
+
+ if((res = read_padding(stream, padding_bytes)) != RES_OK) goto error;
+ }
+
+exit:
+ return res;
+error:
+ goto exit;
+}
+
+static res_T
+load_stream(struct sars* sars, const struct sars_load_stream_args* args)
+{
+ size_t iband;
uint64_t nbands;
- off_t offset = 0;
res_T res = RES_OK;
- ASSERT(sars && stream && stream_name);
+ ASSERT(sars && check_sars_load_stream_args(sars, args) == RES_OK);
reset_sars(sars);
+ res = str_set(&sars->name, args->name);
+ if(res != RES_OK) {
+ log_err(sars, "%s: unable to duplicate path to loaded data or stream name\n",
+ args->name);
+ goto error;
+ }
+
/* Read file header */
#define READ(Var, Name) { \
- if(fread((Var), sizeof(*(Var)), 1, stream) != 1) { \
- log_err(sars, "%s: could not read the %s.\n", stream_name, (Name)); \
+ if(fread((Var), sizeof(*(Var)), 1, args->stream) != 1) { \
+ log_err(sars, "%s: could not read the %s.\n", sars_get_name(sars), (Name));\
res = RES_IO_ERR; \
goto error; \
} \
@@ -120,7 +355,7 @@ load_stream(struct sars* sars, FILE* stream, const char* stream_name)
log_err(sars,
"%s: invalid page size %lu. The page size attribute must be aligned on "
"the page size of the operating system (%lu).\n",
- stream_name,
+ sars_get_name(sars),
(unsigned long)sars->pagesize,
(unsigned long)sars->pagesize_os);
res = RES_BAD_ARG;
@@ -128,13 +363,13 @@ load_stream(struct sars* sars, FILE* stream, const char* stream_name)
}
if(!nbands) {
log_err(sars, "%s: invalid number of bands %lu.\n",
- stream_name, (unsigned long)nbands);
+ sars_get_name(sars), (unsigned long)nbands);
res = RES_BAD_ARG;
goto error;
}
if(!sars->nnodes) {
log_err(sars, "%s: invalid number of nodes %lu.\n",
- stream_name, (unsigned long)sars->nnodes);
+ sars_get_name(sars), (unsigned long)sars->nnodes);
res = RES_BAD_ARG;
goto error;
}
@@ -143,20 +378,20 @@ load_stream(struct sars* sars, FILE* stream, const char* stream_name)
res = darray_band_resize(&sars->bands, nbands);
if(res != RES_OK) {
log_err(sars, "%s: could not allocate the list of bands (#bands=%lu).\n",
- stream_name, (unsigned long)nbands);
+ sars_get_name(sars), (unsigned long)nbands);
goto error;
}
/* Read the band description */
FOR_EACH(iband, 0, nbands) {
struct band* band = darray_band_data_get(&sars->bands) + iband;
- res = read_band(sars, band, stream, stream_name);
+ res = read_band(sars, band, args->stream);
if(res != RES_OK) goto error;
if(iband > 0 && band[0].low < band[-1].upp) {
log_err(sars,
"%s: bands must be sorted in ascending order and must not "
"overlap (band %lu in [%g, %g[ nm; band %lu in [%g, %g[ nm).\n",
- stream_name,
+ sars_get_name(sars),
(unsigned long)(iband-1), band[-1].low, band[-1].upp,
(unsigned long)(iband), band[ 0].low, band[ 0].upp);
res = RES_BAD_ARG;
@@ -164,30 +399,12 @@ load_stream(struct sars* sars, FILE* stream, const char* stream_name)
}
}
- /* Compute the length in bytes of the k to map for each band/quadrature point */
- map_len = ALIGN_SIZE(sars->nnodes * sizeof(float)*2, sars->pagesize);
-
- /* Compute the offset toward the 1st list of radiative coefficients */
- offset = ftell(stream);
- offset = (off_t)ALIGN_SIZE((uint64_t)offset, sars->pagesize);
-
- FOR_EACH(iband, 0, nbands) {
- struct band* band = NULL;
-
- band = darray_band_data_get(&sars->bands) + iband;
- band->map_len = map_len;
-
- /* Map the per band scattering coefficient */
- band->k_list = mmap(NULL, band->map_len, PROT_READ,
- MAP_PRIVATE|MAP_POPULATE, fileno(stream), offset);
- if(band->k_list == MAP_FAILED) {
- log_err(sars,
- "%s: band %lu: could not map the radiative coefficients -- %s\n",
- stream_name, (unsigned long)iband, strerror(errno));
- res = RES_IO_ERR;
- goto error;
- }
- offset = (off_t)((size_t)offset + map_len);
+ if(args->memory_mapping) {
+ res = map_file(sars, args->stream);
+ if(res != RES_OK) goto error;
+ } else {
+ res = load_file(sars, args->stream);
+ if(res != RES_OK) goto error;
}
exit:
@@ -233,6 +450,7 @@ release_sars(ref_T* ref)
ASSERT(ref);
sars = CONTAINER_OF(ref, struct sars, ref);
if(sars->logger == &sars->logger__) logger_release(&sars->logger__);
+ str_release(&sars->name);
darray_band_release(&sars->bands);
MEM_RM(sars->allocator, sars);
}
@@ -273,6 +491,7 @@ sars_create
sars->allocator = allocator;
sars->verbose = args->verbose;
sars->pagesize_os = (size_t)sysconf(_SC_PAGESIZE);
+ str_init(allocator, &sars->name);
darray_band_init(allocator, &sars->bands);
if(args->logger) {
sars->logger = args->logger;
@@ -305,24 +524,27 @@ sars_ref_put(struct sars* sars)
}
res_T
-sars_load(struct sars* sars, const char* path)
+sars_load(struct sars* sars, const struct sars_load_args* args)
{
+ struct sars_load_stream_args stream_args = SARS_LOAD_STREAM_ARGS_NULL;
FILE* file = NULL;
res_T res = RES_OK;
- if(!sars || !path) {
- res = RES_BAD_ARG;
- goto error;
- }
+ if(!sars) { res = RES_BAD_ARG; goto error; }
+ res = check_sars_load_args(args);
+ if(res != RES_OK) goto error;
- file = fopen(path, "r");
+ file = fopen(args->path, "r");
if(!file) {
- log_err(sars, "%s: error opening file `%s'.\n", FUNC_NAME, path);
+ log_err(sars, "%s: error opening file `%s'.\n", FUNC_NAME, args->path);
res = RES_IO_ERR;
goto error;
}
- res = load_stream(sars, file, path);
+ stream_args.stream = file;
+ stream_args.name = args->path;
+ stream_args.memory_mapping = args->memory_mapping;
+ res = load_stream(sars, &stream_args);
if(res != RES_OK) goto error;
exit:
@@ -333,13 +555,59 @@ error:
}
res_T
-sars_load_stream
- (struct sars* sars,
- FILE* stream,
- const char* stream_name)
+sars_load_stream(struct sars* sars, const struct sars_load_stream_args* args)
{
- if(!sars || !stream) return RES_BAD_ARG;
- return load_stream(sars, stream, stream_name ? stream_name : "<stream>");
+ res_T res = RES_OK;
+ if(!sars) return RES_BAD_ARG;
+ res = check_sars_load_stream_args(sars, args);
+ if(res != RES_OK) return res;
+ return load_stream(sars, args);
+}
+
+res_T
+sars_validate(const struct sars* sars)
+{
+ size_t iband;
+ size_t nbands;
+ if(!sars) return RES_BAD_ARG;
+
+ nbands = sars_get_bands_count(sars);
+ FOR_EACH(iband, 0, nbands) {
+ struct sars_band band = SARS_BAND_NULL;
+ size_t inode;
+ size_t nnodes;
+
+ SARS(get_band(sars, iband, &band));
+
+ /* Check band limits */
+ if(band.lower != band.lower /* NaN? */
+ || band.upper != band.upper) { /* NaN? */
+ log_err(sars,
+ "%s: invalid limits for band %lu: [%g, %g[\n",
+ sars_get_name(sars), (unsigned long)iband, band.lower, band.upper);
+ return RES_BAD_ARG;
+ }
+
+ /* Check radiative coefficients */
+ nnodes = sars_get_nodes_count(sars);
+ FOR_EACH(inode, 0, nnodes) {
+ const float ka = sars_band_get_ka(&band, inode);
+ const float ks = sars_band_get_ks(&band, inode);
+ if(ka != ka /* NaN? */ || ka < 0) {
+ log_err(sars,
+ "%s: invalid absorption coefficient for band %lu at node %lu: %g\n",
+ sars_get_name(sars), (unsigned long)iband, (unsigned long)inode, ka);
+ return RES_BAD_ARG;
+ }
+ if(ks != ks /* NaN? */ || ks < 0) {
+ log_err(sars,
+ "%s: invalid scattering coefficient for band %lu at node %lu: %g\n",
+ sars_get_name(sars), (unsigned long)iband, (unsigned long)inode, ka);
+ return RES_BAD_ARG;
+ }
+ }
+ }
+ return RES_OK;
}
size_t
@@ -513,6 +781,13 @@ error:
goto exit;
}
+const char*
+sars_get_name(const struct sars* sars)
+{
+ ASSERT(sars);
+ return str_cget(&sars->name);
+}
+
/*******************************************************************************
* Local functions
******************************************************************************/
@@ -520,7 +795,47 @@ void
band_release(struct band* band)
{
ASSERT(band);
- if(band->k_list && band->k_list != MAP_FAILED) {
+ if(!band->k_list) return;
+
+ if(!band->map_len) {
+ MEM_RM(band->sars->allocator, band->k_list);
+ } else if(band->k_list != MAP_FAILED) {
munmap(band->k_list, band->map_len);
}
}
+
+res_T
+band_copy(struct band* dst, const struct band* src)
+{
+ ASSERT(dst && src);
+
+ dst->sars = src->sars;
+ dst->low = src->low;
+ dst->upp = dst->upp;
+ dst->map_len = src->map_len;
+ dst->k_list = NULL;
+
+ if(src->map_len) {
+ /* The k are mapped: copy the pointer */
+ dst->k_list = src->k_list;
+ } else if(src->k_list != NULL) {
+ /* The k are loaded: duplicate thable contents */
+ const size_t memsz = sizeof(*dst->k_list)*src->sars->nnodes*2/*ka & ks*/;
+ dst->k_list = MEM_ALLOC(src->sars->allocator, memsz);
+ if(!dst->k_list) return RES_MEM_ERR;
+ memcpy(dst->k_list, src->k_list, memsz);
+ }
+ return RES_OK;
+}
+
+res_T
+band_copy_and_release(struct band* dst, struct band* src)
+{
+ ASSERT(dst && src);
+ dst->sars = src->sars;
+ dst->low = src->low;
+ dst->upp = dst->upp;
+ dst->map_len = src->map_len;
+ dst->k_list = src->k_list;
+ return RES_OK;
+}
diff --git a/src/sars.h b/src/sars.h
@@ -50,6 +50,24 @@ struct sars_create_args {
static const struct sars_create_args SARS_CREATE_ARGS_DEFAULT =
SARS_CREATE_ARGS_DEFAULT__;
+struct sars_load_args {
+ const char* path;
+ int memory_mapping; /* Use memory mapping instead of normal loading */
+};
+#define SARS_LOAD_ARGS_NULL__ {NULL, 0}
+static const struct sars_load_args SARS_LOAD_ARGS_NULL = SARS_LOAD_ARGS_NULL__;
+
+struct sars_load_stream_args {
+ FILE* stream;
+ const char* name; /* Stream name */
+ /* Use memory mapping instead of normal loading. Note that memory mapping
+ * cannot be used on some stream like stdin */
+ int memory_mapping;
+};
+#define SARS_LOAD_STREAM_ARGS_NULL__ {NULL, "stream", 0}
+static const struct sars_load_stream_args SARS_LOAD_STREAM_ARGS_NULL =
+ SARS_LOAD_STREAM_ARGS_NULL__;
+
struct sars_band {
double lower; /* Lower band wavelength in nm (inclusive) */
double upper; /* Upper band wavelength in nm (exclusive) */
@@ -84,13 +102,23 @@ sars_ref_put
SARS_API res_T
sars_load
(struct sars* sars,
- const char* path);
+ const struct sars_load_args* args);
SARS_API res_T
sars_load_stream
(struct sars* sars,
- FILE* stream,
- const char* stream_name); /* Can be NULL */
+ const struct sars_load_stream_args* args);
+
+/* Validates radiative coefficients. Data checks have already been carried out
+ * during loading, notably on spectral bands, but this function performs longer
+ * and more thorough tests. It reviews all scattering and absorption
+ * coefficients to check their validity, i.e. whether they are positive or zero.
+ * Note that checking radiative coefficients is not mandatory, in order to speed
+ * up the loading step and avoid loading/unloading them when using memory
+ * mapping. */
+SARS_API res_T
+sars_validate
+ (const struct sars* sars);
SARS_API size_t
sars_get_bands_count
@@ -126,6 +154,10 @@ sars_compute_hash
(const struct sars* sars,
hash256_T hash);
+SARS_API const char*
+sars_get_name
+ (const struct sars* sars);
+
static INLINE float
sars_band_get_ka(const struct sars_band* band, const size_t inode)
{
diff --git a/src/sars_c.h b/src/sars_c.h
@@ -19,8 +19,10 @@
#include <rsys/dynamic_array.h>
#include <rsys/logger.h>
#include <rsys/ref_count.h>
+#include <rsys/str.h>
struct band {
+ struct sars* sars;
double low; /* Lower bound in nm (inclusive) */
double upp; /* Upper bound in nm (exclusive) */
size_t map_len;
@@ -32,6 +34,7 @@ band_init(struct mem_allocator* allocator, struct band* band)
{
ASSERT(band);
(void)allocator;
+ band->sars = NULL;
band->low = DBL_MAX;
band->upp =-DBL_MAX;
band->map_len = 0;
@@ -42,11 +45,23 @@ extern LOCAL_SYM void
band_release
(struct band* band);
+extern LOCAL_SYM res_T
+band_copy
+ (struct band* dst,
+ const struct band* src);
+
+extern LOCAL_SYM res_T
+band_copy_and_release
+ (struct band* dst,
+ struct band* src);
+
/* Generate the dynamic array of bands */
#define DARRAY_NAME band
#define DARRAY_DATA struct band
#define DARRAY_FUNCTOR_INIT band_init
#define DARRAY_FUNCTOR_RELEASE band_release
+#define DARRAY_FUNCTOR_COPY band_copy
+#define DARRAY_FUNCTOR_COPY_AND_RELEASE band_copy_and_release
#include <rsys/dynamic_array.h>
struct mem_allocator;
@@ -58,6 +73,7 @@ struct sars {
struct darray_band bands;
size_t pagesize_os;
+ struct str name;
struct mem_allocator* allocator;
struct logger* logger;
diff --git a/src/test_sars_load.c b/src/test_sars_load.c
@@ -19,6 +19,7 @@
#include <rsys/hash.h>
#include <rsys/mem_allocator.h>
#include <math.h>
+#include <string.h>
/*******************************************************************************
* Helper functions
@@ -114,6 +115,9 @@ test_load(struct sars* sars)
hash256_T hash1;
hash256_T band_hash0;
hash256_T band_hash1;
+ struct sars_load_args args = SARS_LOAD_ARGS_NULL;
+ struct sars_load_stream_args stream_args = SARS_LOAD_STREAM_ARGS_NULL;
+
FILE* fp = NULL;
const char* filename = "test_file.sars";
const uint64_t pagesize = 16384;
@@ -124,13 +128,16 @@ test_load(struct sars* sars)
write_sars(fp, pagesize, nbands, nnodes);
rewind(fp);
- CHK(sars_load_stream(NULL, fp, filename) == RES_BAD_ARG);
- CHK(sars_load_stream(sars, NULL, filename) == RES_BAD_ARG);
- CHK(sars_load_stream(sars, fp, NULL) == RES_OK);
- check_sars_load(sars, nbands, nnodes);
+ stream_args.stream =fp;
+ stream_args.name = filename;
+ CHK(sars_load_stream(NULL, &stream_args) == RES_BAD_ARG);
+ CHK(sars_load_stream(sars, NULL) == RES_BAD_ARG);
+ stream_args.stream = NULL;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_OK);
- rewind(fp);
- CHK(sars_load_stream(sars, fp, filename) == RES_OK);
+ CHK(!strcmp(sars_get_name(sars), filename));
CHK(sars_compute_hash(NULL, hash0) == RES_BAD_ARG);
CHK(sars_compute_hash(sars, NULL) == RES_BAD_ARG);
@@ -145,10 +152,23 @@ test_load(struct sars* sars)
CHK(sars_band_compute_hash(sars, 0, band_hash1) == RES_OK);
CHK(hash256_eq(band_hash0, band_hash1));
- CHK(sars_load(NULL, filename) == RES_BAD_ARG);
+ check_sars_load(sars, nbands, nnodes);
+ rewind(fp);
+
+ stream_args.name = NULL;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
+ stream_args.name = SARS_LOAD_STREAM_ARGS_NULL.name;
+ stream_args.memory_mapping = 1;
+ CHK(sars_load_stream(sars, &stream_args) == RES_OK);
+ CHK(!strcmp(sars_get_name(sars), SARS_LOAD_STREAM_ARGS_NULL.name));
+ check_sars_load(sars, nbands, nnodes);
+
+ args.path = "nop";
+ CHK(sars_load(NULL, &args) == RES_BAD_ARG);
CHK(sars_load(sars, NULL) == RES_BAD_ARG);
- CHK(sars_load(sars, "nop") == RES_IO_ERR);
- CHK(sars_load(sars, filename) == RES_OK);
+ CHK(sars_load(sars, &args) == RES_IO_ERR);
+ args.path = filename;
+ CHK(sars_load(sars, &args) == RES_OK);
check_sars_load(sars, nbands, nnodes);
CHK(sars_compute_hash(sars, hash1) == RES_OK);
@@ -158,7 +178,9 @@ test_load(struct sars* sars)
write_sars(fp, pagesize, nbands+1, nnodes);
rewind(fp);
- CHK(sars_load_stream(sars, fp, filename) == RES_OK);
+ stream_args.stream = fp;
+ stream_args.name = filename;
+ CHK(sars_load_stream(sars, &stream_args) == RES_OK);
CHK(sars_compute_hash(sars, hash1) == RES_OK);
CHK(!hash256_eq(hash0, hash1));
@@ -171,6 +193,7 @@ test_load(struct sars* sars)
static void
test_load_fail(struct sars* sars)
{
+ struct sars_load_stream_args stream_args = SARS_LOAD_STREAM_ARGS_NULL;
FILE* fp = NULL;
double low;
double upp;
@@ -179,28 +202,32 @@ test_load_fail(struct sars* sars)
CHK(fp = tmpfile());
write_sars(fp, 2048, 1, 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* The pagesize is not a power of two */
CHK(fp = tmpfile());
write_sars(fp, 4100, 1, 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* Wrong #bands */
CHK(fp = tmpfile());
write_sars(fp, 4096, 0, 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* Wrong #nodes */
CHK(fp = tmpfile());
write_sars(fp, 4096, 1, 0);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* Wrong band boundaries */
@@ -212,7 +239,8 @@ test_load_fail(struct sars* sars)
CHK(fwrite(&low, sizeof(low), 1, fp) == 1);
CHK(fwrite(&upp, sizeof(upp), 1, fp) == 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* Unsorted bands */
@@ -226,7 +254,8 @@ test_load_fail(struct sars* sars)
CHK(fwrite(&low, sizeof(low), 1, fp) == 1);
CHK(fwrite(&upp, sizeof(upp), 1, fp) == 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
/* Bands overlap */
@@ -240,7 +269,8 @@ test_load_fail(struct sars* sars)
CHK(fwrite(&low, sizeof(low), 1, fp) == 1);
CHK(fwrite(&upp, sizeof(upp), 1, fp) == 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_BAD_ARG);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_BAD_ARG);
CHK(fclose(fp) == 0);
}
@@ -255,9 +285,22 @@ test_load_files(struct sars* sars, int argc, char** argv)
size_t nbands;
size_t iband;
- printf("Load %s\n", argv[1]);
-
- CHK(sars_load(sars, argv[i]) == RES_OK);
+ if(!strcmp(argv[i], "-")) { /* Read from stdin */
+ struct sars_load_stream_args args = SARS_LOAD_STREAM_ARGS_NULL;
+ printf("Load from stdin\n");
+ args.stream = stdin;
+ args.name = "stdin";
+ args.memory_mapping = 1;
+ CHK(sars_load_stream(sars, &args) == RES_BAD_ARG);
+ args.memory_mapping = 0;
+ CHK(sars_load_stream(sars, &args) == RES_OK);
+ } else {
+ struct sars_load_args args = SARS_LOAD_ARGS_NULL;
+ printf("Load %s\n", argv[1]);
+ args.path = argv[i];
+ args.memory_mapping = 1;
+ CHK(sars_load(sars, &args) == RES_OK);
+ }
nbands = sars_get_bands_count(sars);
nnodes = sars_get_nodes_count(sars);
CHK(nbands);
@@ -265,25 +308,14 @@ test_load_files(struct sars* sars, int argc, char** argv)
FOR_EACH(iband, 0, nbands) {
struct sars_band band = SARS_BAND_NULL;
- size_t inode;
CHK(sars_get_band(sars, iband, &band) == RES_OK);
printf("band %lu in [%g, %g[ nm\n",
(unsigned long)band.id,
band.lower, band.upper);
-
- CHK(band.lower == band.lower); /* !NaN */
- CHK(band.upper == band.upper); /* !NaN */
- CHK(band.lower < band.upper);
-
- FOR_EACH(inode, 0, nnodes) {
- const float ka = sars_band_get_ka(&band, inode);
- const float ks = sars_band_get_ks(&band, inode);
- CHK(ka == ka); /* !NaN */
- CHK(ks == ks); /* !NaN */
- }
}
+ CHK(sars_validate(sars) == RES_OK);
CHK(sars_compute_hash(sars, hash) == RES_OK);
}
}
@@ -291,6 +323,7 @@ test_load_files(struct sars* sars, int argc, char** argv)
static void
test_find(struct sars* sars)
{
+ struct sars_load_stream_args stream_args = SARS_LOAD_STREAM_ARGS_NULL;
size_t ibands[2];
double range[2];
FILE* fp;
@@ -298,7 +331,8 @@ test_find(struct sars* sars)
CHK(fp = tmpfile());
write_sars(fp, 4096, 10, 1);
rewind(fp);
- CHK(sars_load_stream(sars, fp, NULL) == RES_OK);
+ stream_args.stream = fp;
+ CHK(sars_load_stream(sars, &stream_args) == RES_OK);
range[0] = 0;
range[1] = 10;
