From 45e7470e730c8d99728a4c8b4275b07a2b098ee5 Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 6 Dec 2018 12:48:58 -0500 Subject: [PATCH 01/37] adding searching for IRIS library and headers --- configure | 435 ++++++++++++++++++++++++++++++++++++++++++++++++--- configure.in | 96 +++++++++++- def.mk.in | 6 + 3 files changed, 516 insertions(+), 21 deletions(-) diff --git a/configure b/configure index 3101643a..a05f93b1 100755 --- a/configure +++ b/configure @@ -621,6 +621,12 @@ ac_includes_default="\ ac_subst_vars='LTLIBOBJS LIBOBJS LD_PRINTOUT +GOT_IRIS_LIB +IRIS_LIB +IRIS_CFLAG +IRIS_LIBRARY_FLAG +IRIS_INCLUDE_FLAG +GOT_RSL_LIB RSL_LIB RSL_CFLAG RSL_LIBRARY_FLAG @@ -701,6 +707,7 @@ with_confuse with_gsl with_rsl with_rave +with_iris ' ac_precious_vars='build_alias host_alias @@ -1323,6 +1330,7 @@ Optional Packages: --with-gsl=DIR|INC,LIB The GSL (GNU Scientific Library) installation directory --with-rsl=DIR The RSL root installation directory --with-rave=ROOT The RAVE root installation directory + --with-iris=DIR The IRIS root installation directory Some influential environment variables: CC C compiler command @@ -2845,25 +2853,6 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -LIBS=-lm - - -CONFUSE_INCLUDE_DIR= -CONFUSE_LIB_DIR= -GOT_CONFUSE_INC=no -GOT_CONFUSE_LIB=no -CONFUSE_SUPPRESSED=no - -# Check whether --with-confuse was given. -if test "${with_confuse+set}" = set; then : - withval=$with_confuse; -else - withval=yes -fi - -case $withval in - yes) - ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' @@ -3002,6 +2991,26 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu +LIBS=-lm + + +CONFUSE_INCLUDE_DIR= +CONFUSE_LIB_DIR= +GOT_CONFUSE_INC=no +GOT_CONFUSE_LIB=no +CONFUSE_SUPPRESSED=no + +# Check whether --with-confuse was given. +if test "${with_confuse+set}" = set; then : + withval=$with_confuse; +else + withval=yes +fi + +case $withval in + yes) + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 $as_echo_n "checking for grep that handles long lines and -e... " >&6; } if ${ac_cv_path_GREP+:} false; then : @@ -4193,6 +4202,7 @@ RSL_LIBRARY_FLAG=${RSL_LIB_DIR} RSL_INCLUDE_FLAG=${RSL_INCLUDE_DIR} { $as_echo "$as_me:${as_lineno-$LINENO}: checking for RSL installation" >&5 $as_echo_n "checking for RSL installation... " >&6; } + if [ "$GOT_RSL_INC" = "yes" ]; then if [ "$GOT_RSL_LIB" = "yes" ]; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 @@ -4208,6 +4218,7 @@ else $as_echo "no" >&6; } fi + RAVE_ROOT_DIR= RAVE_INCLUDE_FLAG= RAVE_LIB_FLAG= @@ -4268,6 +4279,385 @@ as_fn_error $? "The RAVE installation does not contain def.mk. Is this an old in See \`config.log' for more details" "$LINENO" 5; }; fi + +IRIS_INCLUDE_DIR= +IRIS_LIB_DIR= +IRIS_CFLAG= +IRIS_LIB= +GOT_IRIS_INC=no +GOT_IRIS_LIB=no +IRIS_SUPPRESSED=no + +# Check whether --with-iris was given. +if test "${with_iris+set}" = set; then : + withval=$with_iris; +else + withval=yes +fi + +case $withval in + yes) + for ac_header in iris2odim.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" +if test "x$ac_cv_header_iris2odim_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_IRIS2ODIM_H 1 +_ACEOF + GOT_IRIS_INC=yes +fi + +done + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 +$as_echo_n "checking for populateObject in -liris2odim... " >&6; } +if ${ac_cv_lib_iris2odim_populateObject+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-liris2odim $LIBS" +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char populateObject (); +int +main () +{ +return populateObject (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_lib_iris2odim_populateObject=yes +else + ac_cv_lib_iris2odim_populateObject=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iris2odim_populateObject" >&5 +$as_echo "$ac_cv_lib_iris2odim_populateObject" >&6; } +if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : + GOT_IRIS_LIB=yes +fi + + ;; + no) + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS library" >&5 +$as_echo_n "checking for IRIS library... " >&6; } + { $as_echo "$as_me:${as_lineno-$LINENO}: result: suppressed" >&5 +$as_echo "suppressed" >&6; } + IRIS_SUPPRESSED=yes + ;; + *) + if [ "$withval" != "" ]; then + if [ "`echo $withval | grep ','`" = "" ]; then + iris_inc=$withval/include + iris_lib=$withval/lib + else + iris_inc="`echo $withval |cut -f1 -d,`" + iris_lib="`echo $withval |cut -f2 -d,`" + fi + + if [ "$iris_inc" != "" ]; then + saved_CPPFLAGS="$CPPFLAGS" + CPPFLAGS="$CPPFLAGS -I$iris_inc" + echo FUCK!!!! + ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 +$as_echo_n "checking how to run the C preprocessor... " >&6; } +# On Suns, sometimes $CPP names a directory. +if test -n "$CPP" && test -d "$CPP"; then + CPP= +fi +if test -z "$CPP"; then + if ${ac_cv_prog_CPP+:} false; then : + $as_echo_n "(cached) " >&6 +else + # Double quotes because CPP needs to be expanded + for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" + do + ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + +else + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.i conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + # Broken: success on invalid input. +continue +else + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.i conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : + break +fi + + done + ac_cv_prog_CPP=$CPP + +fi + CPP=$ac_cv_prog_CPP +else + ac_cv_prog_CPP=$CPP +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 +$as_echo "$CPP" >&6; } +ac_preproc_ok=false +for ac_c_preproc_warn_flag in '' yes +do + # Use a header file that comes with gcc, so configuring glibc + # with a fresh cross-compiler works. + # Prefer to if __STDC__ is defined, since + # exists even on freestanding compilers. + # On the NeXT, cc -E runs the code through the compiler's parser, + # not just through cpp. "Syntax error" is here to catch this case. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#ifdef __STDC__ +# include +#else +# include +#endif + Syntax error +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + +else + # Broken: fails on valid input. +continue +fi +rm -f conftest.err conftest.i conftest.$ac_ext + + # OK, works on sane cases. Now check whether nonexistent headers + # can be detected and how. + cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ +#include +_ACEOF +if ac_fn_c_try_cpp "$LINENO"; then : + # Broken: success on invalid input. +continue +else + # Passes both tests. +ac_preproc_ok=: +break +fi +rm -f conftest.err conftest.i conftest.$ac_ext + +done +# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. +rm -f conftest.i conftest.err conftest.$ac_ext +if $ac_preproc_ok; then : + +else + { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details" "$LINENO" 5; } +fi + +ac_ext=c +ac_cpp='$CPP $CPPFLAGS' +ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' +ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' +ac_compiler_gnu=$ac_cv_c_compiler_gnu + + for ac_header in iris2odim.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" +if test "x$ac_cv_header_iris2odim_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_IRIS2ODIM_H 1 +_ACEOF + GOT_IRIS_INC=yes +fi + +done + + echo $GOT_IRIS_INC + if [ "$GOT_IRIS_INC" = "yes" ]; then + IRIS_INCLUDE_DIR="-I$iris_inc" + else + CPPFLAGS="$saved_CPPFLAGS" + fi + else + for ac_header in iris2odim.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" +if test "x$ac_cv_header_iris2odim_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_IRIS2ODIM_H 1 +_ACEOF + GOT_IRIS_INC=yes +fi + +done + + fi + + if [ "$iris_lib" != "" ]; then + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -L$iris_lib" + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 +$as_echo_n "checking for populateObject in -liris2odim... " >&6; } +if ${ac_cv_lib_iris2odim_populateObject+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-liris2odim $LIBS" +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char populateObject (); +int +main () +{ +return populateObject (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_lib_iris2odim_populateObject=yes +else + ac_cv_lib_iris2odim_populateObject=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iris2odim_populateObject" >&5 +$as_echo "$ac_cv_lib_iris2odim_populateObject" >&6; } +if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : + GOT_IRIS_LIB=yes +fi + + if [ "$GOT_IRIS_LIB" = "yes" ]; then + IRIS_LIB_DIR="-L$iris_lib" + else + LDFLAGS="$saved_LDFLAGS" + fi + else + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 +$as_echo_n "checking for populateObject in -liris2odim... " >&6; } +if ${ac_cv_lib_iris2odim_populateObject+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-liris2odim $LIBS" +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char populateObject (); +int +main () +{ +return populateObject (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_lib_iris2odim_populateObject=yes +else + ac_cv_lib_iris2odim_populateObject=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iris2odim_populateObject" >&5 +$as_echo "$ac_cv_lib_iris2odim_populateObject" >&6; } +if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : + GOT_IRIS_LIB=yes +fi + + fi + else + as_fn_error $? "\"Odd argument passed for iris\"" "$LINENO" 5 + fi + ;; +esac + +IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} +IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS installation" >&5 +$as_echo_n "checking for IRIS installation... " >&6; } +if [ "$GOT_IRIS_INC" = "yes" ]; then + if [ "$GOT_IRIS_LIB" = "yes" ]; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + IRIS_CFLAG=-DIRIS + IRIS_LIB=-iris2odim + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + fi +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc compiler" >&5 $as_echo_n "checking for RAVE cc compiler... " >&6; } RAVECC=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^CC=/p" | sed -n -e"s/^CC=[ \t]*\(.*\)/\1/p"` @@ -4438,6 +4828,13 @@ fi + + + + + + + diff --git a/configure.in b/configure.in index 0681c136..bc973e4e 100644 --- a/configure.in +++ b/configure.in @@ -14,6 +14,7 @@ if test "${localstatedir}" = "\${prefix}/var"; then fi AC_PROG_CC +AC_PROG_CPP LIBS=-lm @@ -50,14 +51,14 @@ case $withval in if [[ "$confuse_inc" != "" ]]; then saved_CPPFLAGS="$CPPFLAGS" CPPFLAGS="$CPPFLAGS -I$confuse_inc" - AC_CHECK_HEADERS(confuse.h,GOT_CONFUSE_INC=yes) + AC_CHECK_HEADERS([confuse.h],GOT_CONFUSE_INC=yes) if [[ "$GOT_CONFUSE_INC" = "yes" ]]; then CONFUSE_INCLUDE_DIR="-I$confuse_inc" else CPPFLAGS="$saved_CPPFLAGS" fi else - AC_CHECK_HEADERS(confuse.h,GOT_CONFUSE_INC=yes) + AC_CHECK_HEADERS([confuse.h],GOT_CONFUSE_INC=yes) fi if [[ "$confuse_lib" != "" ]]; then @@ -230,6 +231,7 @@ esac RSL_LIBRARY_FLAG=${RSL_LIB_DIR} RSL_INCLUDE_FLAG=${RSL_INCLUDE_DIR} AC_MSG_CHECKING(for RSL installation) + if [[ "$GOT_RSL_INC" = "yes" ]]; then if [[ "$GOT_RSL_LIB" = "yes" ]]; then AC_MSG_RESULT(yes) @@ -242,6 +244,7 @@ else AC_MSG_RESULT(no) fi + dnl First verify that we have a proper rave installation. We can not live without it dnl RAVE_ROOT_DIR= @@ -289,6 +292,88 @@ else AC_MSG_FAILURE(The RAVE installation does not contain def.mk. Is this an old installation); fi + +dnl Check that we have Vaisala IRIS library installed as part of RAVE +dnl +IRIS_INCLUDE_DIR= +IRIS_LIB_DIR= +IRIS_CFLAG= +IRIS_LIB= +GOT_IRIS_INC=no +GOT_IRIS_LIB=no +IRIS_SUPPRESSED=no +AC_ARG_WITH(iris,[ --with-iris=DIR The IRIS root installation directory], + ,withval=yes) +case $withval in + yes) + AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + ;; + no) + AC_MSG_CHECKING(for IRIS library) + AC_MSG_RESULT(suppressed) + IRIS_SUPPRESSED=yes + ;; + *) + if [[ "$withval" != "" ]]; then + if [[ "`echo $withval | grep ','`" = "" ]]; then + iris_inc=$withval/include + iris_lib=$withval/lib + else + iris_inc="`echo $withval |cut -f1 -d,`" + iris_lib="`echo $withval |cut -f2 -d,`" + fi + + if [[ "$iris_inc" != "" ]]; then + saved_CPPFLAGS="$CPPFLAGS" + CPPFLAGS="$CPPFLAGS -I$iris_inc" + AC_PROG_CPP + AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) + echo $GOT_IRIS_INC + if [[ "$GOT_IRIS_INC" = "yes" ]]; then + IRIS_INCLUDE_DIR="-I$iris_inc" + else + CPPFLAGS="$saved_CPPFLAGS" + fi + else + AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) + fi + + if [[ "$iris_lib" != "" ]]; then + saved_LDFLAGS="$LDFLAGS" + LDFLAGS="$LDFLAGS -L$iris_lib" + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + if [[ "$GOT_IRIS_LIB" = "yes" ]]; then + IRIS_LIB_DIR="-L$iris_lib" + else + LDFLAGS="$saved_LDFLAGS" + fi + else + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + fi + else + AC_MSG_ERROR("Odd argument passed for iris") + fi + ;; +esac + +IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} +IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} +AC_MSG_CHECKING(for IRIS installation) +if [[ "$GOT_IRIS_INC" = "yes" ]]; then + if [[ "$GOT_IRIS_LIB" = "yes" ]]; then + AC_MSG_RESULT(yes) + IRIS_CFLAG=-DIRIS + IRIS_LIB=-iris2odim + else + AC_MSG_RESULT(no) + fi +else + AC_MSG_RESULT(no) +fi + + + dnl Now we should extract some variables from raves def.mk file to give user a possibility to change dnl then when necessary AC_MSG_CHECKING(for RAVE cc compiler) @@ -431,6 +516,13 @@ AC_SUBST(RSL_LIBRARY_FLAG) AC_SUBST(RSL_CFLAG) AC_SUBST(RSL_LIB) AC_SUBST(GOT_RSL_LIB) +AC_SUBST(IRIS_INCLUDE_FLAG) +AC_SUBST(IRIS_LIBRARY_FLAG) +AC_SUBST(IRIS_CFLAG) +AC_SUBST(IRIS_LIB) +AC_SUBST(GOT_IRIS_LIB) + + AC_SUBST(LD_PRINTOUT) AC_CONFIG_FILES(def.mk) diff --git a/def.mk.in b/def.mk.in index e7ecc174..9915f767 100644 --- a/def.mk.in +++ b/def.mk.in @@ -48,6 +48,12 @@ RSL_INCLUDE_FLAG=@RSL_INCLUDE_FLAG@ RSL_CFLAG=@RSL_CFLAG@ RSL_LIB=@RSL_LIB@ +# IRIS +IRIS_LIBRARY_FLAG=@IRIS_LIBRARY_FLAG@ +IRIS_INCLUDE_FLAG=@IRIS_INCLUDE_FLAG@ +IRIS_CFLAG=@IRIS_CFLAG@ +IRIS_LIB=@IRIS_LIB@ + # Special flag to be used for printouts of the necessary LD_LIBRARY_PATH # LD_PRINTOUT= @LD_PRINTOUT@ From 9ba6120395ef20def1ac90893dfafd418b6f3f67 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 13:12:59 -0500 Subject: [PATCH 02/37] testing on linux --- configure | 169 +++++++-------------------------------------------- configure.in | 19 +++--- 2 files changed, 32 insertions(+), 156 deletions(-) diff --git a/configure b/configure index a05f93b1..2a9097df 100755 --- a/configure +++ b/configure @@ -681,6 +681,7 @@ infodir docdir oldincludedir includedir +runstatedir localstatedir sharedstatedir sysconfdir @@ -756,6 +757,7 @@ datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' +runstatedir='${localstatedir}/run' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' @@ -1008,6 +1010,15 @@ do | -silent | --silent | --silen | --sile | --sil) silent=yes ;; + -runstatedir | --runstatedir | --runstatedi | --runstated \ + | --runstate | --runstat | --runsta | --runst | --runs \ + | --run | --ru | --r) + ac_prev=runstatedir ;; + -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ + | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ + | --run=* | --ru=* | --r=*) + runstatedir=$ac_optarg ;; + -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ @@ -1145,7 +1156,7 @@ fi for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ - libdir localedir mandir + libdir localedir mandir runstatedir do eval ac_val=\$$ac_var # Remove trailing slashes. @@ -1298,6 +1309,7 @@ Fine tuning of the installation directories: --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] @@ -2852,7 +2864,6 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu - ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' @@ -4280,6 +4291,7 @@ See \`config.log' for more details" "$LINENO" 5; }; fi + IRIS_INCLUDE_DIR= IRIS_LIB_DIR= IRIS_CFLAG= @@ -4351,11 +4363,11 @@ fi ;; no) - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS library" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS library" >&5 $as_echo_n "checking for IRIS library... " >&6; } - { $as_echo "$as_me:${as_lineno-$LINENO}: result: suppressed" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: result: suppressed" >&5 $as_echo "suppressed" >&6; } - IRIS_SUPPRESSED=yes + IRIS_SUPPRESSED=yes ;; *) if [ "$withval" != "" ]; then @@ -4370,144 +4382,6 @@ $as_echo "suppressed" >&6; } if [ "$iris_inc" != "" ]; then saved_CPPFLAGS="$CPPFLAGS" CPPFLAGS="$CPPFLAGS -I$iris_inc" - echo FUCK!!!! - ac_ext=c -ac_cpp='$CPP $CPPFLAGS' -ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 -$as_echo_n "checking how to run the C preprocessor... " >&6; } -# On Suns, sometimes $CPP names a directory. -if test -n "$CPP" && test -d "$CPP"; then - CPP= -fi -if test -z "$CPP"; then - if ${ac_cv_prog_CPP+:} false; then : - $as_echo_n "(cached) " >&6 -else - # Double quotes because CPP needs to be expanded - for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" - do - ac_preproc_ok=false -for ac_c_preproc_warn_flag in '' yes -do - # Use a header file that comes with gcc, so configuring glibc - # with a fresh cross-compiler works. - # Prefer to if __STDC__ is defined, since - # exists even on freestanding compilers. - # On the NeXT, cc -E runs the code through the compiler's parser, - # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#ifdef __STDC__ -# include -#else -# include -#endif - Syntax error -_ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - -else - # Broken: fails on valid input. -continue -fi -rm -f conftest.err conftest.i conftest.$ac_ext - - # OK, works on sane cases. Now check whether nonexistent headers - # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#include -_ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - # Broken: success on invalid input. -continue -else - # Passes both tests. -ac_preproc_ok=: -break -fi -rm -f conftest.err conftest.i conftest.$ac_ext - -done -# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : - break -fi - - done - ac_cv_prog_CPP=$CPP - -fi - CPP=$ac_cv_prog_CPP -else - ac_cv_prog_CPP=$CPP -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 -$as_echo "$CPP" >&6; } -ac_preproc_ok=false -for ac_c_preproc_warn_flag in '' yes -do - # Use a header file that comes with gcc, so configuring glibc - # with a fresh cross-compiler works. - # Prefer to if __STDC__ is defined, since - # exists even on freestanding compilers. - # On the NeXT, cc -E runs the code through the compiler's parser, - # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#ifdef __STDC__ -# include -#else -# include -#endif - Syntax error -_ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - -else - # Broken: fails on valid input. -continue -fi -rm -f conftest.err conftest.i conftest.$ac_ext - - # OK, works on sane cases. Now check whether nonexistent headers - # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#include -_ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - # Broken: success on invalid input. -continue -else - # Passes both tests. -ac_preproc_ok=: -break -fi -rm -f conftest.err conftest.i conftest.$ac_ext - -done -# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : - -else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "C preprocessor \"$CPP\" fails sanity check -See \`config.log' for more details" "$LINENO" 5; } -fi - -ac_ext=c -ac_cpp='$CPP $CPPFLAGS' -ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' -ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' -ac_compiler_gnu=$ac_cv_c_compiler_gnu - for ac_header in iris2odim.h do : ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" @@ -4520,7 +4394,6 @@ fi done - echo $GOT_IRIS_INC if [ "$GOT_IRIS_INC" = "yes" ]; then IRIS_INCLUDE_DIR="-I$iris_inc" else @@ -4627,12 +4500,12 @@ fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iris2odim_populateObject" >&5 $as_echo "$ac_cv_lib_iris2odim_populateObject" >&6; } if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : - GOT_IRIS_LIB=yes + GOT_RSL_LIB=yes fi fi else - as_fn_error $? "\"Odd argument passed for iris\"" "$LINENO" 5 + as_fn_error $? "\"Odd argument passed for IRIS\"" "$LINENO" 5 fi ;; esac @@ -4641,12 +4514,13 @@ IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS installation" >&5 $as_echo_n "checking for IRIS installation... " >&6; } + if [ "$GOT_IRIS_INC" = "yes" ]; then if [ "$GOT_IRIS_LIB" = "yes" ]; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } IRIS_CFLAG=-DIRIS - IRIS_LIB=-iris2odim + IRIS_LIB=-liris2odim else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } @@ -4656,6 +4530,7 @@ else $as_echo "no" >&6; } fi +echo "PROBLEMS!!!" { $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc compiler" >&5 diff --git a/configure.in b/configure.in index bc973e4e..c672b286 100644 --- a/configure.in +++ b/configure.in @@ -293,6 +293,7 @@ else fi + dnl Check that we have Vaisala IRIS library installed as part of RAVE dnl IRIS_INCLUDE_DIR= @@ -303,16 +304,16 @@ GOT_IRIS_INC=no GOT_IRIS_LIB=no IRIS_SUPPRESSED=no AC_ARG_WITH(iris,[ --with-iris=DIR The IRIS root installation directory], - ,withval=yes) + ,withval=yes) case $withval in yes) AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) ;; no) - AC_MSG_CHECKING(for IRIS library) - AC_MSG_RESULT(suppressed) - IRIS_SUPPRESSED=yes + AC_MSG_CHECKING(for IRIS library) + AC_MSG_RESULT(suppressed) + IRIS_SUPPRESSED=yes ;; *) if [[ "$withval" != "" ]]; then @@ -327,9 +328,7 @@ case $withval in if [[ "$iris_inc" != "" ]]; then saved_CPPFLAGS="$CPPFLAGS" CPPFLAGS="$CPPFLAGS -I$iris_inc" - AC_PROG_CPP AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - echo $GOT_IRIS_INC if [[ "$GOT_IRIS_INC" = "yes" ]]; then IRIS_INCLUDE_DIR="-I$iris_inc" else @@ -349,10 +348,10 @@ case $withval in LDFLAGS="$saved_LDFLAGS" fi else - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_RSL_LIB=yes) fi else - AC_MSG_ERROR("Odd argument passed for iris") + AC_MSG_ERROR("Odd argument passed for IRIS") fi ;; esac @@ -360,11 +359,12 @@ esac IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} AC_MSG_CHECKING(for IRIS installation) + if [[ "$GOT_IRIS_INC" = "yes" ]]; then if [[ "$GOT_IRIS_LIB" = "yes" ]]; then AC_MSG_RESULT(yes) IRIS_CFLAG=-DIRIS - IRIS_LIB=-iris2odim + IRIS_LIB=-liris2odim else AC_MSG_RESULT(no) fi @@ -372,6 +372,7 @@ else AC_MSG_RESULT(no) fi +echo "PROBLEMS!!!" dnl Now we should extract some variables from raves def.mk file to give user a possibility to change From b5b1cb18483c9e47c580c7343b01d305bbc4086e Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 6 Dec 2018 16:58:01 -0500 Subject: [PATCH 03/37] updated configure.in to detect iris and rainbow rave modules --- configure | 475 +++++++++++++++++++++++++++++---------------------- configure.in | 185 ++++++++++---------- def.mk.in | 6 +- 3 files changed, 371 insertions(+), 295 deletions(-) diff --git a/configure b/configure index 2a9097df..0eae52fd 100755 --- a/configure +++ b/configure @@ -621,11 +621,12 @@ ac_includes_default="\ ac_subst_vars='LTLIBOBJS LIBOBJS LD_PRINTOUT +GOT_RAINBOW_LIB +RAINBOW_LIB +RAINBOW_CFLAG GOT_IRIS_LIB IRIS_LIB IRIS_CFLAG -IRIS_LIBRARY_FLAG -IRIS_INCLUDE_FLAG GOT_RSL_LIB RSL_LIB RSL_CFLAG @@ -681,7 +682,6 @@ infodir docdir oldincludedir includedir -runstatedir localstatedir sharedstatedir sysconfdir @@ -709,6 +709,7 @@ with_gsl with_rsl with_rave with_iris +with_rainbow ' ac_precious_vars='build_alias host_alias @@ -757,7 +758,6 @@ datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' -runstatedir='${localstatedir}/run' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' @@ -1010,15 +1010,6 @@ do | -silent | --silent | --silen | --sile | --sil) silent=yes ;; - -runstatedir | --runstatedir | --runstatedi | --runstated \ - | --runstate | --runstat | --runsta | --runst | --runs \ - | --run | --ru | --r) - ac_prev=runstatedir ;; - -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ - | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ - | --run=* | --ru=* | --r=*) - runstatedir=$ac_optarg ;; - -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ @@ -1156,7 +1147,7 @@ fi for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ - libdir localedir mandir runstatedir + libdir localedir mandir do eval ac_val=\$$ac_var # Remove trailing slashes. @@ -1309,7 +1300,6 @@ Fine tuning of the installation directories: --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] - --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] @@ -1342,7 +1332,8 @@ Optional Packages: --with-gsl=DIR|INC,LIB The GSL (GNU Scientific Library) installation directory --with-rsl=DIR The RSL root installation directory --with-rave=ROOT The RAVE root installation directory - --with-iris=DIR The IRIS root installation directory + --with-iris Add Vaisala IRIS support using iris2odim rave module + --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module Some influential environment variables: CC C compiler command @@ -3004,7 +2995,6 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu LIBS=-lm - CONFUSE_INCLUDE_DIR= CONFUSE_LIB_DIR= GOT_CONFUSE_INC=no @@ -4291,9 +4281,129 @@ See \`config.log' for more details" "$LINENO" 5; }; fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc compiler" >&5 +$as_echo_n "checking for RAVE cc compiler... " >&6; } +RAVECC=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^CC=/p" | sed -n -e"s/^CC=[ \t]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECC" >&5 +$as_echo "$RAVECC" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc options" >&5 +$as_echo_n "checking for RAVE cc options... " >&6; } +RAVECCOPTS=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^OPTS=/p" | sed -n -e"s/^OPTS=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECCOPTS" >&5 +$as_echo "$RAVECCOPTS" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for cpp options" >&5 +$as_echo_n "checking for cpp options... " >&6; } +CPPOPTS=`echo "$RAVECCOPTS" | sed -e "s/-Wstrict-prototypes//"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPPOPTS" >&5 +$as_echo "$CPPOPTS" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE ld flags" >&5 +$as_echo_n "checking for RAVE ld flags... " >&6; } +RAVELDFLAGS=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^LDFLAGS=/p" | sed -n -e"s/^LDFLAGS=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVELDFLAGS" >&5 +$as_echo "$RAVELDFLAGS" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE shared flag" >&5 +$as_echo_n "checking for RAVE shared flag... " >&6; } +RAVECCSHARED=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^CCSHARED=/p" | sed -n -e"s/^CCSHARED=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECCSHARED" >&5 +$as_echo "$RAVECCSHARED" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python include flag" >&5 +$as_echo_n "checking for Python include flag... " >&6; } +PYTHON_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^INCLUDE_PYTHON=/p" | sed -n -e"s/^INCLUDE_PYTHON=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INCLUDE_PYTHON" >&5 +$as_echo "$INCLUDE_PYTHON" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for numpy include flag" >&5 +$as_echo_n "checking for numpy include flag... " >&6; } +NUMPY_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^NUMPY_INCLUDE_DIR=/p" | sed -n -e"s/^NUMPY_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 +$as_echo "$PROJ_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for proj include flag used by RAVE" >&5 +$as_echo_n "checking for proj include flag used by RAVE... " >&6; } +PROJ_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^PROJ_INCLUDE_DIR=/p" | sed -n -e"s/^PROJ_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 +$as_echo "$PROJ_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for proj library flag used by RAVE" >&5 +$as_echo_n "checking for proj library flag used by RAVE... " >&6; } +PROJ_LIBRARY_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^PROJ_LIB_DIR=/p" | sed -n -e"s/^PROJ_LIB_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 +$as_echo "$PROJ_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for expat include flag used by RAVE" >&5 +$as_echo_n "checking for expat include flag used by RAVE... " >&6; } +EXPAT_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_INCLUDE_DIR=/p" | sed -n -e"s/^EXPAT_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_INCLUDE_FLAG" >&5 +$as_echo "$EXPAT_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for expat library flag used by RAVE" >&5 +$as_echo_n "checking for expat library flag used by RAVE... " >&6; } +EXPAT_LIBRARY_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_LIB_DIR=/p" | sed -n -e"s/^EXPAT_LIB_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_INCLUDE_FLAG" >&5 +$as_echo "$EXPAT_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if expat is supressed" >&5 +$as_echo_n "checking if expat is supressed... " >&6; } +EXPAT_SUPPRESSED=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_SUPPRESSED=/p" | sed -n -e"s/^EXPAT_SUPPRESSED=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_SUPPRESSED" >&5 +$as_echo "$EXPAT_SUPPRESSED" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf include flag used by RAVE" >&5 +$as_echo_n "checking for hlhdf include flag used by RAVE... " >&6; } +HLHDF_INCLUDE_FLAG=-I`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_INCLUDE_DIR=/p" | sed -n -e"s/^HLHDF_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_INCLUDE_FLAG" >&5 +$as_echo "$HLHDF_INCLUDE_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf library flag used by RAVE" >&5 +$as_echo_n "checking for hlhdf library flag used by RAVE... " >&6; } +HLHDF_LIBRARY_FLAG=-L`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_LIB_DIR=/p" | sed -n -e"s/^HLHDF_LIB_DIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_LIBRARY_FLAG" >&5 +$as_echo "$HLHDF_LIBRARY_FLAG" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf config file" >&5 +$as_echo_n "checking for hlhdf config file... " >&6; } +HLHDF_MK_FILE=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_HLDEF_MK_FILE=/p" | sed -n -e"s/^HLHDF_HLDEF_MK_FILE=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_MK_FILE" >&5 +$as_echo "$HLHDF_MK_FILE" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf ld shared" >&5 +$as_echo_n "checking for hlhdf ld shared... " >&6; } +HLHDFLDSHARED=`cat $HLHDF_MK_FILE | sed -n "/^LDSHARED=/p" | sed -n -e"s/^LDSHARED=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDFLDSHARED" >&5 +$as_echo "$HLHDFLDSHARED" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for g++ ld shared options" >&5 +$as_echo_n "checking for g++ ld shared options... " >&6; } +LDCPPSHARED=`echo "$HLHDFLDSHARED" | awk '{$1=""}1'` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $LDCPPSHARED" >&5 +$as_echo "$LDCPPSHARED" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hdf5 software used by hlhdf" >&5 +$as_echo_n "checking for hdf5 software used by hlhdf... " >&6; } +HLHDF_HDF5_LIB=`cat $HLHDF_MK_FILE | sed -n "/^HDF5_LIBDIR=/p" | sed -n -e"s/^HDF5_LIBDIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_HDF5_LIB" >&5 +$as_echo "$HLHDF_HDF5_LIB" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for zlib software used by hlhdf" >&5 +$as_echo_n "checking for zlib software used by hlhdf... " >&6; } +HLHDF_ZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^ZLIB_LIBDIR=/p" | sed -n -e"s/^ZLIB_LIBDIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_ZLIB_LIB" >&5 +$as_echo "$HLHDF_ZLIB_LIB" >&6; } + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for szlib software used by hlhdf" >&5 +$as_echo_n "checking for szlib software used by hlhdf... " >&6; } +HLHDF_SZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^SZLIB_LIBDIR=/p" | sed -n -e"s/^SZLIB_LIBDIR=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_SZLIB_LIB" >&5 +$as_echo "$HLHDF_SZLIB_LIB" >&6; } + +LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" +CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" -IRIS_INCLUDE_DIR= -IRIS_LIB_DIR= IRIS_CFLAG= IRIS_LIB= GOT_IRIS_INC=no @@ -4363,44 +4473,17 @@ fi ;; no) - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS library" >&5 -$as_echo_n "checking for IRIS library... " >&6; } + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for iris2odim rave module" >&5 +$as_echo_n "checking for iris2odim rave module... " >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: result: suppressed" >&5 $as_echo "suppressed" >&6; } IRIS_SUPPRESSED=yes ;; *) if [ "$withval" != "" ]; then - if [ "`echo $withval | grep ','`" = "" ]; then - iris_inc=$withval/include - iris_lib=$withval/lib - else - iris_inc="`echo $withval |cut -f1 -d,`" - iris_lib="`echo $withval |cut -f2 -d,`" - fi - - if [ "$iris_inc" != "" ]; then - saved_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$iris_inc" - for ac_header in iris2odim.h -do : - ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" -if test "x$ac_cv_header_iris2odim_h" = xyes; then : - cat >>confdefs.h <<_ACEOF -#define HAVE_IRIS2ODIM_H 1 -_ACEOF - GOT_IRIS_INC=yes -fi - -done - - if [ "$GOT_IRIS_INC" = "yes" ]; then - IRIS_INCLUDE_DIR="-I$iris_inc" - else - CPPFLAGS="$saved_CPPFLAGS" - fi - else - for ac_header in iris2odim.h + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"iris2odim should be installed as a library module of RAVE - ignoring specified path '$withval'\"" >&5 +$as_echo "$as_me: WARNING: \"iris2odim should be installed as a library module of RAVE - ignoring specified path '$withval'\"" >&2;} + for ac_header in iris2odim.h do : ac_fn_c_check_header_mongrel "$LINENO" "iris2odim.h" "ac_cv_header_iris2odim_h" "$ac_includes_default" if test "x$ac_cv_header_iris2odim_h" = xyes; then : @@ -4412,12 +4495,7 @@ fi done - fi - - if [ "$iris_lib" != "" ]; then - saved_LDFLAGS="$LDFLAGS" - LDFLAGS="$LDFLAGS -L$iris_lib" - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 $as_echo_n "checking for populateObject in -liris2odim... " >&6; } if ${ac_cv_lib_iris2odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 @@ -4457,19 +4535,66 @@ if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : GOT_IRIS_LIB=yes fi - if [ "$GOT_IRIS_LIB" = "yes" ]; then - IRIS_LIB_DIR="-L$iris_lib" - else - LDFLAGS="$saved_LDFLAGS" - fi - else - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -liris2odim" >&5 -$as_echo_n "checking for populateObject in -liris2odim... " >&6; } -if ${ac_cv_lib_iris2odim_populateObject+:} false; then : + else + as_fn_error $? "\"Odd argument passed for iris\"" "$LINENO" 5 + fi + ;; +esac + +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Vaisala IRIS support" >&5 +$as_echo_n "checking for Vaisala IRIS support... " >&6; } + +if [ "$GOT_IRIS_INC" = "yes" ]; then + if [ "$GOT_IRIS_LIB" = "yes" ]; then + { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +$as_echo "yes" >&6; } + IRIS_CFLAG=-DIRIS + IRIS_LIB=-liris2odim + else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } + fi +else + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 +$as_echo "no" >&6; } +fi + + + +RAINBOW_CFLAG= +RAINBOW_LIB= +GOT_RAINBOW_INC=no +GOT_RAINBOW_LIB=no +RAINBOW_SUPPRESSED=no + +# Check whether --with-rainbow was given. +if test "${with_rainbow+set}" = set; then : + withval=$with_rainbow; +else + withval=yes +fi + +case $withval in + yes) + for ac_header in rb52odim.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "rb52odim.h" "ac_cv_header_rb52odim_h" "$ac_includes_default" +if test "x$ac_cv_header_rb52odim_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_RB52ODIM_H 1 +_ACEOF + GOT_RAINBOW_INC=yes +fi + +done + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -lrb52odim" >&5 +$as_echo_n "checking for populateObject in -lrb52odim... " >&6; } +if ${ac_cv_lib_rb52odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-liris2odim $LIBS" +LIBS="-lrb52odim $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ @@ -4489,38 +4614,99 @@ return populateObject (); } _ACEOF if ac_fn_c_try_link "$LINENO"; then : - ac_cv_lib_iris2odim_populateObject=yes + ac_cv_lib_rb52odim_populateObject=yes else - ac_cv_lib_iris2odim_populateObject=no + ac_cv_lib_rb52odim_populateObject=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_iris2odim_populateObject" >&5 -$as_echo "$ac_cv_lib_iris2odim_populateObject" >&6; } -if test "x$ac_cv_lib_iris2odim_populateObject" = xyes; then : - GOT_RSL_LIB=yes +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_rb52odim_populateObject" >&5 +$as_echo "$ac_cv_lib_rb52odim_populateObject" >&6; } +if test "x$ac_cv_lib_rb52odim_populateObject" = xyes; then : + GOT_RAINBOW_LIB=yes +fi + + ;; + no) + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for rb52odim rave module" >&5 +$as_echo_n "checking for rb52odim rave module... " >&6; } + { $as_echo "$as_me:${as_lineno-$LINENO}: result: suppressed" >&5 +$as_echo "suppressed" >&6; } + IRIS_SUPPRESSED=yes + ;; + *) + if [ "$withval" != "" ]; then + { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"rb52odim should be installed as a library module of RAVE - ignoring specified path '$withval'\"" >&5 +$as_echo "$as_me: WARNING: \"rb52odim should be installed as a library module of RAVE - ignoring specified path '$withval'\"" >&2;} + for ac_header in rb52odim.h +do : + ac_fn_c_check_header_mongrel "$LINENO" "rb52odim.h" "ac_cv_header_rb52odim_h" "$ac_includes_default" +if test "x$ac_cv_header_rb52odim_h" = xyes; then : + cat >>confdefs.h <<_ACEOF +#define HAVE_RB52ODIM_H 1 +_ACEOF + GOT_RAINBOW_INC=yes +fi + +done + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for populateObject in -lrb52odim" >&5 +$as_echo_n "checking for populateObject in -lrb52odim... " >&6; } +if ${ac_cv_lib_rb52odim_populateObject+:} false; then : + $as_echo_n "(cached) " >&6 +else + ac_check_lib_save_LIBS=$LIBS +LIBS="-lrb52odim $LIBS" +cat confdefs.h - <<_ACEOF >conftest.$ac_ext +/* end confdefs.h. */ + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char populateObject (); +int +main () +{ +return populateObject (); + ; + return 0; +} +_ACEOF +if ac_fn_c_try_link "$LINENO"; then : + ac_cv_lib_rb52odim_populateObject=yes +else + ac_cv_lib_rb52odim_populateObject=no +fi +rm -f core conftest.err conftest.$ac_objext \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_rb52odim_populateObject" >&5 +$as_echo "$ac_cv_lib_rb52odim_populateObject" >&6; } +if test "x$ac_cv_lib_rb52odim_populateObject" = xyes; then : + GOT_RAINBOW_LIB=yes fi - fi else - as_fn_error $? "\"Odd argument passed for IRIS\"" "$LINENO" 5 + as_fn_error $? "\"Odd argument passed for rainbow\"" "$LINENO" 5 fi ;; esac -IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} -IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for IRIS installation" >&5 -$as_echo_n "checking for IRIS installation... " >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for SELEX Rainbow support" >&5 +$as_echo_n "checking for SELEX Rainbow support... " >&6; } -if [ "$GOT_IRIS_INC" = "yes" ]; then - if [ "$GOT_IRIS_LIB" = "yes" ]; then +if [ "$GOT_RAINBOW_INC" = "yes" ]; then + if [ "$GOT_RAINBOW_LIB" = "yes" ]; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } - IRIS_CFLAG=-DIRIS - IRIS_LIB=-liris2odim + RAINBOW_CFLAG=-DRAINBOW + RAINBOW_LIB=-lrb52odim else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } @@ -4530,129 +4716,6 @@ else $as_echo "no" >&6; } fi -echo "PROBLEMS!!!" - - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc compiler" >&5 -$as_echo_n "checking for RAVE cc compiler... " >&6; } -RAVECC=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^CC=/p" | sed -n -e"s/^CC=[ \t]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECC" >&5 -$as_echo "$RAVECC" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE cc options" >&5 -$as_echo_n "checking for RAVE cc options... " >&6; } -RAVECCOPTS=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^OPTS=/p" | sed -n -e"s/^OPTS=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECCOPTS" >&5 -$as_echo "$RAVECCOPTS" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for cpp options" >&5 -$as_echo_n "checking for cpp options... " >&6; } -CPPOPTS=`echo "$RAVECCOPTS" | sed -e "s/-Wstrict-prototypes//"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPPOPTS" >&5 -$as_echo "$CPPOPTS" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE ld flags" >&5 -$as_echo_n "checking for RAVE ld flags... " >&6; } -RAVELDFLAGS=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^LDFLAGS=/p" | sed -n -e"s/^LDFLAGS=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVELDFLAGS" >&5 -$as_echo "$RAVELDFLAGS" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE shared flag" >&5 -$as_echo_n "checking for RAVE shared flag... " >&6; } -RAVECCSHARED=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^CCSHARED=/p" | sed -n -e"s/^CCSHARED=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVECCSHARED" >&5 -$as_echo "$RAVECCSHARED" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python include flag" >&5 -$as_echo_n "checking for Python include flag... " >&6; } -PYTHON_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^INCLUDE_PYTHON=/p" | sed -n -e"s/^INCLUDE_PYTHON=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INCLUDE_PYTHON" >&5 -$as_echo "$INCLUDE_PYTHON" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for numpy include flag" >&5 -$as_echo_n "checking for numpy include flag... " >&6; } -NUMPY_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^NUMPY_INCLUDE_DIR=/p" | sed -n -e"s/^NUMPY_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 -$as_echo "$PROJ_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for proj include flag used by RAVE" >&5 -$as_echo_n "checking for proj include flag used by RAVE... " >&6; } -PROJ_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^PROJ_INCLUDE_DIR=/p" | sed -n -e"s/^PROJ_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 -$as_echo "$PROJ_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for proj library flag used by RAVE" >&5 -$as_echo_n "checking for proj library flag used by RAVE... " >&6; } -PROJ_LIBRARY_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^PROJ_LIB_DIR=/p" | sed -n -e"s/^PROJ_LIB_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $PROJ_INCLUDE_FLAG" >&5 -$as_echo "$PROJ_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for expat include flag used by RAVE" >&5 -$as_echo_n "checking for expat include flag used by RAVE... " >&6; } -EXPAT_INCLUDE_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_INCLUDE_DIR=/p" | sed -n -e"s/^EXPAT_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_INCLUDE_FLAG" >&5 -$as_echo "$EXPAT_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for expat library flag used by RAVE" >&5 -$as_echo_n "checking for expat library flag used by RAVE... " >&6; } -EXPAT_LIBRARY_FLAG=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_LIB_DIR=/p" | sed -n -e"s/^EXPAT_LIB_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_INCLUDE_FLAG" >&5 -$as_echo "$EXPAT_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking if expat is supressed" >&5 -$as_echo_n "checking if expat is supressed... " >&6; } -EXPAT_SUPPRESSED=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^EXPAT_SUPPRESSED=/p" | sed -n -e"s/^EXPAT_SUPPRESSED=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $EXPAT_SUPPRESSED" >&5 -$as_echo "$EXPAT_SUPPRESSED" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf include flag used by RAVE" >&5 -$as_echo_n "checking for hlhdf include flag used by RAVE... " >&6; } -HLHDF_INCLUDE_FLAG=-I`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_INCLUDE_DIR=/p" | sed -n -e"s/^HLHDF_INCLUDE_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_INCLUDE_FLAG" >&5 -$as_echo "$HLHDF_INCLUDE_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf library flag used by RAVE" >&5 -$as_echo_n "checking for hlhdf library flag used by RAVE... " >&6; } -HLHDF_LIBRARY_FLAG=-L`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_LIB_DIR=/p" | sed -n -e"s/^HLHDF_LIB_DIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_LIBRARY_FLAG" >&5 -$as_echo "$HLHDF_LIBRARY_FLAG" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf config file" >&5 -$as_echo_n "checking for hlhdf config file... " >&6; } -HLHDF_MK_FILE=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^HLHDF_HLDEF_MK_FILE=/p" | sed -n -e"s/^HLHDF_HLDEF_MK_FILE=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_MK_FILE" >&5 -$as_echo "$HLHDF_MK_FILE" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hlhdf ld shared" >&5 -$as_echo_n "checking for hlhdf ld shared... " >&6; } -HLHDFLDSHARED=`cat $HLHDF_MK_FILE | sed -n "/^LDSHARED=/p" | sed -n -e"s/^LDSHARED=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDFLDSHARED" >&5 -$as_echo "$HLHDFLDSHARED" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for g++ ld shared options" >&5 -$as_echo_n "checking for g++ ld shared options... " >&6; } -LDCPPSHARED=`echo "$HLHDFLDSHARED" | awk '{$1=""}1'` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $LDCPPSHARED" >&5 -$as_echo "$LDCPPSHARED" >&6; } - - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for hdf5 software used by hlhdf" >&5 -$as_echo_n "checking for hdf5 software used by hlhdf... " >&6; } -HLHDF_HDF5_LIB=`cat $HLHDF_MK_FILE | sed -n "/^HDF5_LIBDIR=/p" | sed -n -e"s/^HDF5_LIBDIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_HDF5_LIB" >&5 -$as_echo "$HLHDF_HDF5_LIB" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for zlib software used by hlhdf" >&5 -$as_echo_n "checking for zlib software used by hlhdf... " >&6; } -HLHDF_ZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^ZLIB_LIBDIR=/p" | sed -n -e"s/^ZLIB_LIBDIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_ZLIB_LIB" >&5 -$as_echo "$HLHDF_ZLIB_LIB" >&6; } - -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for szlib software used by hlhdf" >&5 -$as_echo_n "checking for szlib software used by hlhdf... " >&6; } -HLHDF_SZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^SZLIB_LIBDIR=/p" | sed -n -e"s/^SZLIB_LIBDIR=[ ]*\(.*\)/\1/p"` -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_SZLIB_LIB" >&5 -$as_echo "$HLHDF_SZLIB_LIB" >&6; } LD_PRINTOUT=$prefix/lib if [ "$RAVE_LIB_FLAG" != "" ]; then diff --git a/configure.in b/configure.in index c672b286..bddb0da6 100644 --- a/configure.in +++ b/configure.in @@ -18,7 +18,6 @@ AC_PROG_CPP LIBS=-lm - dnl Check that we have libconfuse installed dnl CONFUSE_INCLUDE_DIR= @@ -293,88 +292,6 @@ else fi - -dnl Check that we have Vaisala IRIS library installed as part of RAVE -dnl -IRIS_INCLUDE_DIR= -IRIS_LIB_DIR= -IRIS_CFLAG= -IRIS_LIB= -GOT_IRIS_INC=no -GOT_IRIS_LIB=no -IRIS_SUPPRESSED=no -AC_ARG_WITH(iris,[ --with-iris=DIR The IRIS root installation directory], - ,withval=yes) -case $withval in - yes) - AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) - ;; - no) - AC_MSG_CHECKING(for IRIS library) - AC_MSG_RESULT(suppressed) - IRIS_SUPPRESSED=yes - ;; - *) - if [[ "$withval" != "" ]]; then - if [[ "`echo $withval | grep ','`" = "" ]]; then - iris_inc=$withval/include - iris_lib=$withval/lib - else - iris_inc="`echo $withval |cut -f1 -d,`" - iris_lib="`echo $withval |cut -f2 -d,`" - fi - - if [[ "$iris_inc" != "" ]]; then - saved_CPPFLAGS="$CPPFLAGS" - CPPFLAGS="$CPPFLAGS -I$iris_inc" - AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - if [[ "$GOT_IRIS_INC" = "yes" ]]; then - IRIS_INCLUDE_DIR="-I$iris_inc" - else - CPPFLAGS="$saved_CPPFLAGS" - fi - else - AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - fi - - if [[ "$iris_lib" != "" ]]; then - saved_LDFLAGS="$LDFLAGS" - LDFLAGS="$LDFLAGS -L$iris_lib" - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) - if [[ "$GOT_IRIS_LIB" = "yes" ]]; then - IRIS_LIB_DIR="-L$iris_lib" - else - LDFLAGS="$saved_LDFLAGS" - fi - else - AC_CHECK_LIB(iris2odim,populateObject,GOT_RSL_LIB=yes) - fi - else - AC_MSG_ERROR("Odd argument passed for IRIS") - fi - ;; -esac - -IRIS_LIBRARY_FLAG=${IRIS_LIB_DIR} -IRIS_INCLUDE_FLAG=${IRIS_INCLUDE_DIR} -AC_MSG_CHECKING(for IRIS installation) - -if [[ "$GOT_IRIS_INC" = "yes" ]]; then - if [[ "$GOT_IRIS_LIB" = "yes" ]]; then - AC_MSG_RESULT(yes) - IRIS_CFLAG=-DIRIS - IRIS_LIB=-liris2odim - else - AC_MSG_RESULT(no) - fi -else - AC_MSG_RESULT(no) -fi - -echo "PROBLEMS!!!" - - dnl Now we should extract some variables from raves def.mk file to give user a possibility to change dnl then when necessary AC_MSG_CHECKING(for RAVE cc compiler) @@ -447,7 +364,6 @@ AC_MSG_CHECKING(for g++ ld shared options) LDCPPSHARED=`echo "$HLHDFLDSHARED" | awk '{$1=""}1'` AC_MSG_RESULT($LDCPPSHARED) - AC_MSG_CHECKING(for hdf5 software used by hlhdf) HLHDF_HDF5_LIB=`cat $HLHDF_MK_FILE | sed -n "/^HDF5_LIBDIR=/p" | sed -n -e"s/^HDF5_LIBDIR=[[ ]]*\(.*\)/\1/p"` AC_MSG_RESULT($HLHDF_HDF5_LIB) @@ -460,6 +376,101 @@ AC_MSG_CHECKING(for szlib software used by hlhdf) HLHDF_SZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^SZLIB_LIBDIR=/p" | sed -n -e"s/^SZLIB_LIBDIR=[[ ]]*\(.*\)/\1/p"` AC_MSG_RESULT($HLHDF_SZLIB_LIB) +dnl Update LDFLAGS and CPPFLAGS with those obtained from RAVE +LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" +CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" + +dnl Check that we have Vaisala IRIS library installed as part of RAVE +dnl +IRIS_CFLAG= +IRIS_LIB= +GOT_IRIS_INC=no +GOT_IRIS_LIB=no +IRIS_SUPPRESSED=no +AC_ARG_WITH(iris,[ --with-iris Add Vaisala IRIS support using iris2odim rave module], + ,withval=yes) +case $withval in + yes) + AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + ;; + no) + AC_MSG_CHECKING(for iris2odim rave module) + AC_MSG_RESULT(suppressed) + IRIS_SUPPRESSED=yes + ;; + *) + if [[ "$withval" != "" ]]; then + AC_MSG_WARN("iris2odim should be installed as a library module of RAVE - ignoring specified path '$withval'") + AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + else + AC_MSG_ERROR("Odd argument passed for iris") + fi + ;; +esac + +AC_MSG_CHECKING(for Vaisala IRIS support) + +if [[ "$GOT_IRIS_INC" = "yes" ]]; then + if [[ "$GOT_IRIS_LIB" = "yes" ]]; then + AC_MSG_RESULT(yes) + IRIS_CFLAG=-DIRIS + IRIS_LIB=-liris2odim + else + AC_MSG_RESULT(no) + fi +else + AC_MSG_RESULT(no) +fi + + + +dnl Check that we have SELEX Rainbow library installed as part of RAVE +dnl +RAINBOW_CFLAG= +RAINBOW_LIB= +GOT_RAINBOW_INC=no +GOT_RAINBOW_LIB=no +RAINBOW_SUPPRESSED=no +AC_ARG_WITH(rainbow,[ --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module], + ,withval=yes) +case $withval in + yes) + AC_CHECK_HEADERS(rb52odim.h,GOT_RAINBOW_INC=yes) + AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes) + ;; + no) + AC_MSG_CHECKING(for rb52odim rave module) + AC_MSG_RESULT(suppressed) + IRIS_SUPPRESSED=yes + ;; + *) + if [[ "$withval" != "" ]]; then + AC_MSG_WARN("rb52odim should be installed as a library module of RAVE - ignoring specified path '$withval'") + AC_CHECK_HEADERS(rb52odim.h,GOT_RAINBOW_INC=yes) + AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes) + else + AC_MSG_ERROR("Odd argument passed for rainbow") + fi + ;; +esac + +AC_MSG_CHECKING(for SELEX Rainbow support) + +if [[ "$GOT_RAINBOW_INC" = "yes" ]]; then + if [[ "$GOT_RAINBOW_LIB" = "yes" ]]; then + AC_MSG_RESULT(yes) + RAINBOW_CFLAG=-DRAINBOW + RAINBOW_LIB=-lrb52odim + else + AC_MSG_RESULT(no) + fi +else + AC_MSG_RESULT(no) +fi + + dnl Generate the ld library printout dnl LD_PRINTOUT=$prefix/lib @@ -517,12 +528,12 @@ AC_SUBST(RSL_LIBRARY_FLAG) AC_SUBST(RSL_CFLAG) AC_SUBST(RSL_LIB) AC_SUBST(GOT_RSL_LIB) -AC_SUBST(IRIS_INCLUDE_FLAG) -AC_SUBST(IRIS_LIBRARY_FLAG) AC_SUBST(IRIS_CFLAG) AC_SUBST(IRIS_LIB) AC_SUBST(GOT_IRIS_LIB) - +AC_SUBST(RAINBOW_CFLAG) +AC_SUBST(RAINBOW_LIB) +AC_SUBST(GOT_RAINBOW_LIB) AC_SUBST(LD_PRINTOUT) diff --git a/def.mk.in b/def.mk.in index 9915f767..3a57cd1f 100644 --- a/def.mk.in +++ b/def.mk.in @@ -49,11 +49,13 @@ RSL_CFLAG=@RSL_CFLAG@ RSL_LIB=@RSL_LIB@ # IRIS -IRIS_LIBRARY_FLAG=@IRIS_LIBRARY_FLAG@ -IRIS_INCLUDE_FLAG=@IRIS_INCLUDE_FLAG@ IRIS_CFLAG=@IRIS_CFLAG@ IRIS_LIB=@IRIS_LIB@ +# RAINBOW +RAINBOW_CFLAG=@RAINBOW_CFLAG@ +RAINBOW_LIB=@RAINBOW_LIB@ + # Special flag to be used for printouts of the necessary LD_LIBRARY_PATH # LD_PRINTOUT= @LD_PRINTOUT@ From bab7364081c1f36912aad7082c7e6457a999a512 Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 6 Dec 2018 17:41:34 -0500 Subject: [PATCH 04/37] fix typo --- configure | 1 - configure.in | 1 - 2 files changed, 2 deletions(-) diff --git a/configure b/configure index 0eae52fd..61b76db9 100755 --- a/configure +++ b/configure @@ -4783,7 +4783,6 @@ fi ac_config_files="$ac_config_files def.mk" -# lib/config.h) cat >confcache <<\_ACEOF # This file is a shell script that caches the results of configure # tests run on this system so they can be shared between configure diff --git a/configure.in b/configure.in index bddb0da6..1d7bf6e0 100644 --- a/configure.in +++ b/configure.in @@ -538,6 +538,5 @@ AC_SUBST(GOT_RAINBOW_LIB) AC_SUBST(LD_PRINTOUT) AC_CONFIG_FILES(def.mk) -# lib/config.h) AC_OUTPUT From 40d5f155ef7016e7399b5aaa363187bd5bc502e1 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 17:43:29 -0500 Subject: [PATCH 05/37] run autoconf on linux --- configure | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/configure b/configure index 0eae52fd..f970a087 100755 --- a/configure +++ b/configure @@ -682,6 +682,7 @@ infodir docdir oldincludedir includedir +runstatedir localstatedir sharedstatedir sysconfdir @@ -758,6 +759,7 @@ datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' +runstatedir='${localstatedir}/run' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' @@ -1010,6 +1012,15 @@ do | -silent | --silent | --silen | --sile | --sil) silent=yes ;; + -runstatedir | --runstatedir | --runstatedi | --runstated \ + | --runstate | --runstat | --runsta | --runst | --runs \ + | --run | --ru | --r) + ac_prev=runstatedir ;; + -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ + | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ + | --run=* | --ru=* | --r=*) + runstatedir=$ac_optarg ;; + -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ @@ -1147,7 +1158,7 @@ fi for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ - libdir localedir mandir + libdir localedir mandir runstatedir do eval ac_val=\$$ac_var # Remove trailing slashes. @@ -1300,6 +1311,7 @@ Fine tuning of the installation directories: --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] From fa8cf568c03670b75acfd31c66b380bf115ee028 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 17:50:45 -0500 Subject: [PATCH 06/37] debugging --- configure | 5 ++++- configure.in | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/configure b/configure index 1d286a2c..ecd49bf8 100755 --- a/configure +++ b/configure @@ -1345,7 +1345,7 @@ Optional Packages: --with-rsl=DIR The RSL root installation directory --with-rave=ROOT The RAVE root installation directory --with-iris Add Vaisala IRIS support using iris2odim rave module - --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module + --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module Some influential environment variables: CC C compiler command @@ -4416,6 +4416,9 @@ $as_echo "$HLHDF_SZLIB_LIB" >&6; } LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" +echo SHITSHOW +echo $LDFLAGS + IRIS_CFLAG= IRIS_LIB= GOT_IRIS_INC=no diff --git a/configure.in b/configure.in index 1d7bf6e0..0cc4a3a2 100644 --- a/configure.in +++ b/configure.in @@ -380,6 +380,9 @@ dnl Update LDFLAGS and CPPFLAGS with those obtained from RAVE LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" +echo PRINTING LDFLAGS: +echo $LDFLAGS + dnl Check that we have Vaisala IRIS library installed as part of RAVE dnl IRIS_CFLAG= @@ -433,7 +436,7 @@ RAINBOW_LIB= GOT_RAINBOW_INC=no GOT_RAINBOW_LIB=no RAINBOW_SUPPRESSED=no -AC_ARG_WITH(rainbow,[ --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module], +AC_ARG_WITH(rainbow,[ --with-rainbow Add SELEX Rainbow 5 support using rb52odim rave module], ,withval=yes) case $withval in yes) From cc6b494d83048c47144aaa949a3fd900dbcda92b Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 17:51:48 -0500 Subject: [PATCH 07/37] debugging --- configure | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure b/configure index ecd49bf8..1140a8f1 100755 --- a/configure +++ b/configure @@ -4416,7 +4416,7 @@ $as_echo "$HLHDF_SZLIB_LIB" >&6; } LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" -echo SHITSHOW +echo PRINTING LDFLAGS: echo $LDFLAGS IRIS_CFLAG= From 287c4421a8fe0660e8f2d27defe81c84bc8c2b4d Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 18:11:13 -0500 Subject: [PATCH 08/37] debugging --- configure | 4 +++- configure.in | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/configure b/configure index 1140a8f1..144bba0c 100755 --- a/configure +++ b/configure @@ -3005,7 +3005,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -LIBS=-lm +LIBS=-lm -liris2odim CONFUSE_INCLUDE_DIR= CONFUSE_LIB_DIR= @@ -4418,6 +4418,8 @@ CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" echo PRINTING LDFLAGS: echo $LDFLAGS +echo $CPPFLAGS +echo $LIBS IRIS_CFLAG= IRIS_LIB= diff --git a/configure.in b/configure.in index 0cc4a3a2..6f6f881a 100644 --- a/configure.in +++ b/configure.in @@ -382,6 +382,8 @@ CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" echo PRINTING LDFLAGS: echo $LDFLAGS +echo $CPPFLAGS +echo $LIBS dnl Check that we have Vaisala IRIS library installed as part of RAVE dnl From 335e67f86f69f07b04540492fb4affd17b70975f Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 18:25:35 -0500 Subject: [PATCH 09/37] adding other-libraries argument to AC_CHECK_LIB --- configure | 18 ++++++++++-------- configure.in | 14 +++++++------- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/configure b/configure index 144bba0c..951e2f29 100755 --- a/configure +++ b/configure @@ -3005,7 +3005,7 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -LIBS=-lm -liris2odim +LIBS=-lm CONFUSE_INCLUDE_DIR= CONFUSE_LIB_DIR= @@ -4413,14 +4413,16 @@ HLHDF_SZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^SZLIB_LIBDIR=/p" | sed -n -e"s/^ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $HLHDF_SZLIB_LIB" >&5 $as_echo "$HLHDF_SZLIB_LIB" >&6; } +{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for RAVE module libraries" >&5 +$as_echo_n "checking for RAVE module libraries... " >&6; } +RAVE_MODULE_LIBRARIES=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^RAVE_MODULE_LIBRARIES=/p" | sed -n -e"s/^RAVE_MODULE_LIBRARIES=[ ]*\(.*\)/\1/p"` +{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $RAVE_MODULE_LIBRARIES" >&5 +$as_echo "$RAVE_MODULE_LIBRARIES" >&6; } + + LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" -echo PRINTING LDFLAGS: -echo $LDFLAGS -echo $CPPFLAGS -echo $LIBS - IRIS_CFLAG= IRIS_LIB= GOT_IRIS_INC=no @@ -4454,7 +4456,7 @@ if ${ac_cv_lib_iris2odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-liris2odim $LIBS" +LIBS="-liris2odim $RAVE_MODULE_LIBRARIES $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ @@ -4518,7 +4520,7 @@ if ${ac_cv_lib_iris2odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-liris2odim $LIBS" +LIBS="-liris2odim $RAVE_MODULE_LIBARIES $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ diff --git a/configure.in b/configure.in index 6f6f881a..60e8b309 100644 --- a/configure.in +++ b/configure.in @@ -376,15 +376,15 @@ AC_MSG_CHECKING(for szlib software used by hlhdf) HLHDF_SZLIB_LIB=`cat $HLHDF_MK_FILE | sed -n "/^SZLIB_LIBDIR=/p" | sed -n -e"s/^SZLIB_LIBDIR=[[ ]]*\(.*\)/\1/p"` AC_MSG_RESULT($HLHDF_SZLIB_LIB) +AC_MSG_CHECKING(for RAVE module libraries) +RAVE_MODULE_LIBRARIES=`cat $RAVE_ROOT_DIR/mkf/def.mk | sed -n "/^RAVE_MODULE_LIBRARIES=/p" | sed -n -e"s/^RAVE_MODULE_LIBRARIES=[[ ]]*\(.*\)/\1/p"` +AC_MSG_RESULT($RAVE_MODULE_LIBRARIES) + + dnl Update LDFLAGS and CPPFLAGS with those obtained from RAVE LDFLAGS="$LDFLAGS $RAVE_LIB_FLAG $HLHDF_LIBRARY_FLAG $PROJ_LIBRARY_FLAG" CPPFLAGS="$CPPFLAGS $RAVE_INCLUDE_FLAG $HLHDF_INCLUDE_FLAG $PROJ_INCLUDE_FLAG" -echo PRINTING LDFLAGS: -echo $LDFLAGS -echo $CPPFLAGS -echo $LIBS - dnl Check that we have Vaisala IRIS library installed as part of RAVE dnl IRIS_CFLAG= @@ -397,7 +397,7 @@ AC_ARG_WITH(iris,[ --with-iris Add Vaisala IRIS support using iris2odim rave case $withval in yes) AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes,,[$RAVE_MODULE_LIBRARIES]) ;; no) AC_MSG_CHECKING(for iris2odim rave module) @@ -408,7 +408,7 @@ case $withval in if [[ "$withval" != "" ]]; then AC_MSG_WARN("iris2odim should be installed as a library module of RAVE - ignoring specified path '$withval'") AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes,,[$RAVE_MODULE_LIBARIES]) else AC_MSG_ERROR("Odd argument passed for iris") fi From 6d1668c5fe16479270105299eb32d7015be199c0 Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 6 Dec 2018 19:20:30 -0500 Subject: [PATCH 10/37] dirty fix for rb52odim --- configure | 15 ++------------- configure.in | 5 ++++- 2 files changed, 6 insertions(+), 14 deletions(-) diff --git a/configure b/configure index 951e2f29..d21e78f1 100755 --- a/configure +++ b/configure @@ -682,7 +682,6 @@ infodir docdir oldincludedir includedir -runstatedir localstatedir sharedstatedir sysconfdir @@ -759,7 +758,6 @@ datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' -runstatedir='${localstatedir}/run' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' @@ -1012,15 +1010,6 @@ do | -silent | --silent | --silen | --sile | --sil) silent=yes ;; - -runstatedir | --runstatedir | --runstatedi | --runstated \ - | --runstate | --runstat | --runsta | --runst | --runs \ - | --run | --ru | --r) - ac_prev=runstatedir ;; - -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ - | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ - | --run=* | --ru=* | --r=*) - runstatedir=$ac_optarg ;; - -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ @@ -1158,7 +1147,7 @@ fi for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ - libdir localedir mandir runstatedir + libdir localedir mandir do eval ac_val=\$$ac_var # Remove trailing slashes. @@ -1311,7 +1300,6 @@ Fine tuning of the installation directories: --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] - --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] @@ -4579,6 +4567,7 @@ $as_echo "no" >&6; } fi +CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" RAINBOW_CFLAG= RAINBOW_LIB= diff --git a/configure.in b/configure.in index 60e8b309..5c33347b 100644 --- a/configure.in +++ b/configure.in @@ -430,9 +430,12 @@ else fi - dnl Check that we have SELEX Rainbow library installed as part of RAVE dnl +dnl rb52odim depends on libxml, including it here hard-coded +dnl TODO: add explicit checking for presence of xml2 +CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" + RAINBOW_CFLAG= RAINBOW_LIB= GOT_RAINBOW_INC=no From 9785695fdd2047a55e1a1eed7a73a97a007f1f1b Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 19:35:15 -0500 Subject: [PATCH 11/37] debugging linux --- configure | 20 ++++++++++++++++---- configure.in | 6 +++--- 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/configure b/configure index d21e78f1..8fbf8582 100755 --- a/configure +++ b/configure @@ -682,6 +682,7 @@ infodir docdir oldincludedir includedir +runstatedir localstatedir sharedstatedir sysconfdir @@ -758,6 +759,7 @@ datadir='${datarootdir}' sysconfdir='${prefix}/etc' sharedstatedir='${prefix}/com' localstatedir='${prefix}/var' +runstatedir='${localstatedir}/run' includedir='${prefix}/include' oldincludedir='/usr/include' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' @@ -1010,6 +1012,15 @@ do | -silent | --silent | --silen | --sile | --sil) silent=yes ;; + -runstatedir | --runstatedir | --runstatedi | --runstated \ + | --runstate | --runstat | --runsta | --runst | --runs \ + | --run | --ru | --r) + ac_prev=runstatedir ;; + -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \ + | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \ + | --run=* | --ru=* | --r=*) + runstatedir=$ac_optarg ;; + -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb) ac_prev=sbindir ;; -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \ @@ -1147,7 +1158,7 @@ fi for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \ datadir sysconfdir sharedstatedir localstatedir includedir \ oldincludedir docdir infodir htmldir dvidir pdfdir psdir \ - libdir localedir mandir + libdir localedir mandir runstatedir do eval ac_val=\$$ac_var # Remove trailing slashes. @@ -1300,6 +1311,7 @@ Fine tuning of the installation directories: --sysconfdir=DIR read-only single-machine data [PREFIX/etc] --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com] --localstatedir=DIR modifiable single-machine data [PREFIX/var] + --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run] --libdir=DIR object code libraries [EPREFIX/lib] --includedir=DIR C header files [PREFIX/include] --oldincludedir=DIR C header files for non-gcc [/usr/include] @@ -4508,7 +4520,7 @@ if ${ac_cv_lib_iris2odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-liris2odim $RAVE_MODULE_LIBARIES $LIBS" +LIBS="-liris2odim $RAVE_MODULE_LIBRARIES $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ @@ -4602,7 +4614,7 @@ if ${ac_cv_lib_rb52odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-lrb52odim $LIBS" +LIBS="-lrb52odim $RAVE_MODULE_LIBRARIES -lxml2 $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ @@ -4666,7 +4678,7 @@ if ${ac_cv_lib_rb52odim_populateObject+:} false; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS -LIBS="-lrb52odim $LIBS" +LIBS="-lrb52odim $RAVE_MODULE_LIBRARIES -lxml2 $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ diff --git a/configure.in b/configure.in index 5c33347b..7e8a1cdd 100644 --- a/configure.in +++ b/configure.in @@ -408,7 +408,7 @@ case $withval in if [[ "$withval" != "" ]]; then AC_MSG_WARN("iris2odim should be installed as a library module of RAVE - ignoring specified path '$withval'") AC_CHECK_HEADERS(iris2odim.h,GOT_IRIS_INC=yes) - AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes,,[$RAVE_MODULE_LIBARIES]) + AC_CHECK_LIB(iris2odim,populateObject,GOT_IRIS_LIB=yes,,[$RAVE_MODULE_LIBRARIES]) else AC_MSG_ERROR("Odd argument passed for iris") fi @@ -446,7 +446,7 @@ AC_ARG_WITH(rainbow,[ --with-rainbow Add SELEX Rainbow 5 support using rb52od case $withval in yes) AC_CHECK_HEADERS(rb52odim.h,GOT_RAINBOW_INC=yes) - AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes) + AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes,,[$RAVE_MODULE_LIBRARIES -lxml2]) ;; no) AC_MSG_CHECKING(for rb52odim rave module) @@ -457,7 +457,7 @@ case $withval in if [[ "$withval" != "" ]]; then AC_MSG_WARN("rb52odim should be installed as a library module of RAVE - ignoring specified path '$withval'") AC_CHECK_HEADERS(rb52odim.h,GOT_RAINBOW_INC=yes) - AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes) + AC_CHECK_LIB(rb52odim,populateObject,GOT_RAINBOW_LIB=yes,,[$RAVE_MODULE_LIBRARIES -lxml2]) else AC_MSG_ERROR("Odd argument passed for rainbow") fi From 79d3d06e1e2addf9dda35e857e56c8ccfb9e74b2 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Thu, 6 Dec 2018 19:45:01 -0500 Subject: [PATCH 12/37] debugging --- configure | 2 +- configure.in | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/configure b/configure index 8fbf8582..e0f19049 100755 --- a/configure +++ b/configure @@ -4579,7 +4579,7 @@ $as_echo "no" >&6; } fi -CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" +CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" RAINBOW_CFLAG= RAINBOW_LIB= diff --git a/configure.in b/configure.in index 7e8a1cdd..d814b133 100644 --- a/configure.in +++ b/configure.in @@ -434,7 +434,8 @@ dnl Check that we have SELEX Rainbow library installed as part of RAVE dnl dnl rb52odim depends on libxml, including it here hard-coded dnl TODO: add explicit checking for presence of xml2 -CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" +dnl BUG: this solution works on Mac OSX but not on linux +CPPFLAGS="$CPPFLAGS -I/usr/include/libxml2" RAINBOW_CFLAG= RAINBOW_LIB= From ad6c87f87607382fdb44903c10c03adf577d3777 Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 12 Dec 2018 18:36:51 -0500 Subject: [PATCH 13/37] vol2bird now reads polar volumes in IRIS RAW format --- lib/Makefile | 4 +-- lib/libvol2bird.c | 73 +++++++++++++++++++++++++++++++++++++++++++++-- 2 files changed, 72 insertions(+), 5 deletions(-) diff --git a/lib/Makefile b/lib/Makefile index 026236e5..dc2f835c 100644 --- a/lib/Makefile +++ b/lib/Makefile @@ -18,7 +18,7 @@ # use gcc if not set already CC ?= gcc #CFLAGS += ${RSL_CFLAG} -fPIC -x c -DFPRINTFON -CFLAGS += ${RSL_CFLAG} -fPIC -g -x c +CFLAGS += ${RSL_CFLAG} ${IRIS_CFLAG} -fPIC -g -x c LDFLAGS += -shared -Wall # define where the vol2bird stuff is @@ -48,7 +48,7 @@ libvol2bird.so : $(LIBVOL2BIRD_DEPS) $(SRC_VOL2BIRD_DIR)/libdealias.c \ $(SRC_VOL2BIRD_DIR)/librsl.c \ $(LDFLAGS) \ - -Wall -o libvol2bird.so $(RAVE_MODULE_LIBRARIES) -lconfuse -lgsl -lgslcblas $(RSL_LIB) -lm + -Wall -o libvol2bird.so $(RAVE_MODULE_LIBRARIES) -lconfuse -lgsl -lgslcblas $(RSL_LIB) ${IRIS_LIB} -lm .PHONY : install install : libvol2bird.so diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 9915cd4d..9e84caae 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -36,6 +36,10 @@ #include "librsl.h" #endif +#ifdef IRIS +#include "iris2odim.h" +#endif + // non-public function prototypes (local to this file/translation unit) @@ -131,7 +135,9 @@ static void updateFlagFieldsInPointsArray(const float* yObs, const float* yFitte static int updateMap(PolarScan_t* scan, CELLPROP *cellProp, const int nCells, vol2bird_t* alldata); - +#ifdef IRIS +PolarVolume_t* vol2birdGetIRISVolume(char* filename, float rangeMax, int small); +#endif // non-public function declarations (local to this file/translation unit) @@ -4191,6 +4197,14 @@ PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small){ PolarVolume_t* volume = NULL; + #ifdef IRIS + // test whether the file is in IRIS format + if (isIRIS(filename)==0){ + volume = vol2birdGetIRISVolume(filename, rangeMax, small); + goto done; + } + #endif + RaveIO_t* raveio = RaveIO_open(filename); // check that a valid RaveIO_t pointer was returned @@ -4211,15 +4225,68 @@ PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small){ // not a rave complient file, attempt to read the file with the RSL library instead #ifdef RSL else{ - volume = vol2birdGetRSLVolume(filename, rangeMax, small); + volume = vol2birdGetRSLVolume(filename, rangeMax, small); } #endif RAVE_OBJECT_RELEASE(raveio); - return volume; + done: + return volume; } +#ifdef IRIS +PolarVolume_t* vol2birdGetIRISVolume(char* filename, float rangeMax, int small) { + + // initialize a polar volume to return + PolarVolume_t* volume = NULL; + + // initialize the rave object type of filename + int rot = Rave_ObjectType_UNDEFINED; + + int ret = 0; + + // read the iris file + file_element_s* file_element_p = readIRIS(filename); + + if(file_element_p == NULL){ + fprintf(stderr, "Error: could not read IRIS file.\n"); + return volume; + } + + rot = objectTypeFromIRIS(file_element_p); + + if (rot == Rave_ObjectType_PVOL) { + volume = RAVE_OBJECT_NEW(&PolarVolume_TYPE); + + if (volume == NULL) { + RAVE_CRITICAL0("Error: failed to create polarvolume instance"); + goto done; + } + } + else{ + fprintf(stderr, "Error: IRIS file does not contain a polar volume.\n"); + goto done; + } + + // read iris data into rave polar volume object + ret = populateObject((RaveCoreObject*) volume, file_element_p); + + if( ret != 0) { + fprintf(stderr, "Error: could not populate IRIS data into a polar volume object\n"); + RAVE_OBJECT_RELEASE(volume); + volume = (PolarVolume_t*) NULL; + } + + // clean up + if(file_element_p != NULL) { + free_IRIS(&file_element_p); + } + + done: + return volume; +} +#endif RaveIO_t* vol2birdIO_open(const char* filename) From 7a4c5c726a94863d861b6c76832b02298142d579 Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 13 Dec 2018 12:32:32 -0500 Subject: [PATCH 14/37] added github links to repo --- README.md | 7 +++++++ docs/index.html | 4 ++++ 2 files changed, 11 insertions(+) diff --git a/README.md b/README.md index 1b5419c3..4fa061a8 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,13 @@ Dokter AM, Desmet P, Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson C, Haas Ecography, 2018, DOI [10.1111/ecog.04028](https://doi.org/10.1111/ecog.04028) ### repository contents + +Browse source code at: +[https://github.com/adokter/vol2bird](https://github.com/adokter/vol2bird) + +Report a bug at: +[https://github.com/adokter/vol2bird/issues](https://github.com/adokter/vol2bird/issues) + * `data` contains two polar volume radar files for testing * `doc` documentation on ODIM hdf5 data format * `docs` html pages of this documentation diff --git a/docs/index.html b/docs/index.html index 5e39d872..bb8b03bb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -52,6 +52,10 @@ Dokter AM, Desmet P, Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson C, Haase G, Leijnse H, Farnsworth A, Bouten W, Shamoun-Baranes J.
Ecography, 2018, DOI 10.1111/ecog.04028

repository contents

+

Browse source code at:
+https://github.com/adokter/vol2bird

+

Report a bug at:
+https://github.com/adokter/vol2bird/issues

  • data contains two polar volume radar files for testing
  • doc documentation on ODIM hdf5 data format
    • From 44c692bd43227de766c453ed71f833a86a33ba1a Mon Sep 17 00:00:00 2001 From: adokter Date: Thu, 3 Jan 2019 12:18:15 +0100 Subject: [PATCH 15/37] match default nlayer in options.conf match hard-coded default --- etc/options.conf | 2 +- src/vol2bird.c | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/etc/options.conf b/etc/options.conf index b635b641..225ab4ee 100644 --- a/etc/options.conf +++ b/etc/options.conf @@ -1,6 +1,6 @@ # the number of layers in an altitude profile -NLAYER = 20 +NLAYER = 25 # the width/thickness of a layer [m] HLAYER = 200.0 diff --git a/src/vol2bird.c b/src/vol2bird.c index 3c9c84bd..ec34df6b 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -42,6 +42,7 @@ int main(int argc, char** argv) { // cfg_t* cfg; vol2bird_t alldata; + // make sure executable and library version match if (strcmp(VERSION,libvol2bird_version()) != 0){ fprintf(stderr,"Error: incorrect vol2bird installation: executable version (%s) has to match shared library version (%s).\n",VERSION,libvol2bird_version()); return -1; From c2a02d80923d965cbc6e6fdc44d4963255ac6526 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 7 Jan 2019 15:26:42 +0100 Subject: [PATCH 16/37] fix brackets Makefile --- lib/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/Makefile b/lib/Makefile index dc2f835c..a9824631 100644 --- a/lib/Makefile +++ b/lib/Makefile @@ -48,7 +48,7 @@ libvol2bird.so : $(LIBVOL2BIRD_DEPS) $(SRC_VOL2BIRD_DIR)/libdealias.c \ $(SRC_VOL2BIRD_DIR)/librsl.c \ $(LDFLAGS) \ - -Wall -o libvol2bird.so $(RAVE_MODULE_LIBRARIES) -lconfuse -lgsl -lgslcblas $(RSL_LIB) ${IRIS_LIB} -lm + -Wall -o libvol2bird.so $(RAVE_MODULE_LIBRARIES) -lconfuse -lgsl -lgslcblas $(RSL_LIB) $(IRIS_LIB) -lm .PHONY : install install : libvol2bird.so From 0ce8f36b645b418e442a8c7a89290982e85a9994 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 7 Jan 2019 15:28:43 +0100 Subject: [PATCH 17/37] fix brackets Makefile --- lib/Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/Makefile b/lib/Makefile index a9824631..d16aee85 100644 --- a/lib/Makefile +++ b/lib/Makefile @@ -17,8 +17,8 @@ # use gcc if not set already CC ?= gcc -#CFLAGS += ${RSL_CFLAG} -fPIC -x c -DFPRINTFON -CFLAGS += ${RSL_CFLAG} ${IRIS_CFLAG} -fPIC -g -x c +#CFLAGS += $(RSL_CFLAG) -fPIC -x c -DFPRINTFON +CFLAGS += $(RSL_CFLAG) $(IRIS_CFLAG) -fPIC -g -x c LDFLAGS += -shared -Wall # define where the vol2bird stuff is From 68733ba7cb74f5896ac1bbfb5c03de481dec9af2 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 7 Jan 2019 15:38:10 +0100 Subject: [PATCH 18/37] fix iris library in vol2bird binary source makefile --- src/Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/Makefile b/src/Makefile index 77622201..4ae5415d 100644 --- a/src/Makefile +++ b/src/Makefile @@ -51,7 +51,7 @@ vol2bird : ../lib/libvol2bird.so $(VOL2BIRD_DEPS) $(RAVE_MODULE_LDFLAGS) \ $(PROJ_LIBRARY_FLAG) \ $(RSL_LIBRARY_FLAG) \ - -lvol2bird $(RAVE_MODULE_LIBRARIES) -lm $(RSL_LIB) -o vol2bird $(LDFLAGS) + -lvol2bird $(RAVE_MODULE_LIBRARIES) -lm $(RSL_LIB) $(IRIS_LIB) -o vol2bird $(LDFLAGS) rsl2odim : ../lib/libvol2bird.so $(RSL2ODIM_DEPS) # @@ -65,7 +65,8 @@ rsl2odim : ../lib/libvol2bird.so $(RSL2ODIM_DEPS) $(RAVE_MODULE_LDFLAGS) \ $(PROJ_LIBRARY_FLAG) \ $(RSL_LIBRARY_FLAG) \ - -lvol2bird $(RAVE_MODULE_LIBRARIES) -lm $(RSL_LIB) -o rsl2odim $(LDFLAGS) + $(IRIS_LIBRARY_FLAG) \ + -lvol2bird $(RAVE_MODULE_LIBRARIES) -lm $(RSL_LIB) $(IRIS_LIB) -o rsl2odim $(LDFLAGS) # # (You may still have to change your LD_LIBRARY_PATH) From c1aaa5b40702e8410c03ac72d7b72e024f5f0897 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 12 Mar 2019 17:46:40 -0400 Subject: [PATCH 19/37] prototype getopt options --- lib/constants.h | 2 + src/vol2bird.c | 193 ++++++++++++++++++++++++++++++++++++++---------- 2 files changed, 158 insertions(+), 37 deletions(-) diff --git a/lib/constants.h b/lib/constants.h index 279703dd..460b5b75 100644 --- a/lib/constants.h +++ b/lib/constants.h @@ -82,6 +82,8 @@ // other hard-coded options // //-------------------------------------------------------// +// maximum number of input files +#define INPUTFILESMAX 50 // Raw value used for gates or layers void of data (never ra-diated) #define UNDETECT -999 // Raw value used for gates or layers when below the measurement detection threshold diff --git a/src/vol2bird.c b/src/vol2bird.c index ec34df6b..04903e42 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -30,6 +30,7 @@ #include #include +#include #include "rave_io.h" #include "polarvolume.h" #include "libvol2bird.h" @@ -38,19 +39,12 @@ #include "hlhdf_debug.h" #include "rave_debug.h" -int main(int argc, char** argv) { -// cfg_t* cfg; - vol2bird_t alldata; - - // make sure executable and library version match - if (strcmp(VERSION,libvol2bird_version()) != 0){ - fprintf(stderr,"Error: incorrect vol2bird installation: executable version (%s) has to match shared library version (%s).\n",VERSION,libvol2bird_version()); - return -1; - } +void usage(char* programName, int verbose){ + fprintf(stderr,"usage: %s [ []]\n",programName); + fprintf(stderr,"usage: %s -i [-i [-i ] ...] [-o [-p ]]\n",programName); + fprintf(stderr,"usage: %s --help\n", programName); - // print default message when no input arguments - if (argc == 1) { - fprintf(stderr,"usage: %s [ []]\n",argv[0]); + if(verbose){ fprintf(stderr," Version %s (%s)\n", VERSION, VERSIONDATE); fprintf(stderr," expects OPERA ODIM hdf5 input format, see \n"); fprintf(stderr," or input formats compatible with RSL, see \n\n"); @@ -75,49 +69,174 @@ int main(int argc, char** argv) { fprintf(stderr," n_dbz_all - number of points total reflectivity estimate (DBZH)\n\n"); fprintf(stderr," Report bugs to: a.m.dokter@uva.nl or on http://github.com/adokter/vol2bird/issues \n"); fprintf(stderr," vol2bird home page: \n"); + } +} + +int main(int argc, char** argv) { +// cfg_t* cfg; + vol2bird_t alldata; + + // make sure executable and library version match + if (strcmp(VERSION,libvol2bird_version()) != 0){ + fprintf(stderr,"Error: incorrect vol2bird installation: executable version (%s) has to match shared library version (%s).\n",VERSION,libvol2bird_version()); return -1; } - // check to see if we have the right number of input arguments - if (argc > 4) { - fprintf(stderr, "Up to three arguments are allowed\n"); + + // print default message when no input arguments + if (argc == 1) { + usage(argv[0], 0); return -1; } - // ------------------------------------------------------------- // - // initialization of variables // - // ------------------------------------------------------------- // - + // number of input files specified on command line + int nInputFiles = 0; // the polar volume file that the user provided as input - char* fileVolIn = argv[1]; + char* fileVolIn[INPUTFILESMAX]; // the (optional) vertical profile file that the user specified as output - const char* fileVpOut; + const char* fileVpOut = NULL; // the (optional) vertical profile file that the user specified as output - const char* fileVolOut; - - if (argc == 3){ - fileVpOut = argv[2]; - fileVolOut = NULL; + const char* fileVolOut = NULL; + + // determine whether we deal with legacy command line format (0) or getopt command line format (1) + int commandLineFormat = 0; + for (int i=0; i 4) { + fprintf(stderr, "Error: Invalid command line arguments\n"); + usage(argv[0], 0); + return -1; + } + + // ------------------------------------------------------------- // + // initialization of variables // + // ------------------------------------------------------------- // + + // the polar volume file that the user provided as input + fileVolIn[0] = argv[1]; + nInputFiles = 1; + + if (argc == 3){ + fileVpOut = argv[2]; + fileVolOut = NULL; + } + else if (argc == 4){ + fileVpOut = argv[2]; + fileVolOut = argv[3]; + } + else{ + fileVpOut = NULL; + fileVolOut = NULL; + } } - else{ - fileVpOut = NULL; - fileVolOut = NULL; + else{ // interpret command line input using getopt library + + int c; + + while (1) { + static struct option long_options[] = + { + /* These options don’t set a flag. + We distinguish them by their indices. */ + {"help", no_argument, 0, 'h'}, + {"version", no_argument, 0, 'v'}, + {"input", required_argument, 0, 'i'}, + {"output", required_argument, 0, 'o'}, + {"pvol", required_argument, 0, 'p'}, + {0, 0, 0, 0} + }; + + /* getopt_long stores the option index here. */ + int option_index = 0; + + c = getopt_long (argc, argv, "hvi:o:p:", + long_options, &option_index); + + /* Detect the end of the options. */ + if (c == -1) break; + + switch (c){ + case 0: + /* If this option set a flag, do nothing else now. */ + if (long_options[option_index].flag != 0) + break; + printf ("option %s", long_options[option_index].name); + if (optarg) + printf (" with arg %s", optarg); + printf ("\n"); + break; + + case 'h': + usage(argv[0],1); + return -1; + break; + + case 'v': + fprintf(stderr,"%s version %s (%s)\n", argv[0], VERSION, VERSIONDATE); + return -1; + break; + + case 'i': + printf ("option -i with value `%s'\n", optarg); + fileVolIn[nInputFiles] = optarg; + nInputFiles++; + break; + + case 'o': + printf ("option -o with value `%s'\n", optarg); + fileVpOut = optarg; + break; + + case 'p': + printf ("option -p with value `%s'\n", optarg); + fileVolOut = optarg; + break; + + case '?': + /* getopt_long already printed an error message. */ + break; + + default: + abort (); + } + } + + /* Print any remaining command line arguments (not options). */ + if (optind < argc) { + printf ("unknown function argument(s): "); + while (optind < argc) + printf ("%s ", argv[optind++]); + putchar ('\n'); + } + printf("%i input files found\n",nInputFiles); + printf("vp output file: %s\n",fileVpOut); + printf("pvol output file: %s\n",fileVolOut); + } + // Initialize hlhdf library HL_init(); - //HL_setDebugLevel(HLHDF_SPEWDEBUG); - // Make rave library print debugging error messages + // Make rave and hlhdf library print debugging error messages + //HL_setDebugLevel(HLHDF_SPEWDEBUG); //Rave_initializeDebugger(); //Rave_setDebugLevel(RAVE_WARNING); //Rave_setDebugLevel(RAVE_INFO); // store the input filename - strcpy(alldata.misc.filename_pvol,fileVolIn); + strcpy(alldata.misc.filename_pvol,fileVolIn[0]); if (fileVpOut != NULL){ strcpy(alldata.misc.filename_vp,fileVpOut); } @@ -134,7 +253,7 @@ int main(int argc, char** argv) { // we do not read in the full volume for speed/memory PolarVolume_t* volume = NULL; - volume = vol2birdGetVolume(fileVolIn, alldata.misc.rCellMax,1); + volume = vol2birdGetVolume(fileVolIn[0], alldata.misc.rCellMax,1); if (volume == NULL) { fprintf(stderr,"Error: failed to read radar volume\n"); @@ -199,7 +318,7 @@ int main(int argc, char** argv) { fprintf(stdout, "# vol2bird Vertical Profile of Birds (VPB)\n"); fprintf(stdout, "# source: %s\n",source); - fprintf(stdout, "# polar volume input: %s\n",fileVolIn); + fprintf(stdout, "# polar volume input: %s\n",fileVolIn[0]); if (alldata.misc.vcp > 0) fprintf(stdout, "# volume coverage pattern (VCP): %i\n", alldata.misc.vcp); printf("# date time HGHT u v w ff dd sd_vvp gap dbz eta dens DBZH n n_dbz n_all n_dbz_all\n"); From d1ab49db9fc3c45601b7aa5402a450d6d2b68daa Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 13 Mar 2019 18:31:55 -0400 Subject: [PATCH 20/37] testing for file existence. radarDataFormat struct added --- lib/libvol2bird.c | 10 +++++++++- lib/libvol2bird.h | 10 ++++++++++ src/vol2bird.c | 38 ++++++++++++++++++++++++-------------- 3 files changed, 43 insertions(+), 15 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index fb8caf65..a4a393d9 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -24,6 +24,7 @@ #include #include #include +#include #include #include "rave_io.h" @@ -2642,7 +2643,14 @@ static int includeGate(const int iProfileType, const int iQuantityType, const un } // includeGate - +/** + * Function name: isRegularFile + * Intent: determines whether the given path is to a regular file + * Note: also returns true on existing directories + */ +int isRegularFile(const char *path) { + return (access(path, F_OK) != -1); +} /* end function is_regular_file */ static int readUserConfigOptions(cfg_t** cfg, const char * optsConfFilename) { diff --git a/lib/libvol2bird.h b/lib/libvol2bird.h index 858ff315..26f20f9f 100644 --- a/lib/libvol2bird.h +++ b/lib/libvol2bird.h @@ -381,10 +381,20 @@ struct vol2bird { }; typedef struct vol2bird vol2bird_t; +typedef enum radarDataFormat { + radarDataFormat_UNKNOWN = 0, + radarDataFormat_ODIM = 1, /** Opera Data Information Model (ODIM) */ + radarDataFormat_RSL = 2, /** TRMM radar solftware library (including NEXRAD) */ + radarDataFormat_IRIS = 3 /** Vaisala IRIS */ +} radarDataFormat; + + // ***************************************************************************** // Public function prototypes // ***************************************************************************** +int isRegularFile(const char *path); + void vol2birdCalcProfiles(vol2bird_t* alldata); float* vol2birdGetProfile(int iProfileType, vol2bird_t* alldata); diff --git a/src/vol2bird.c b/src/vol2bird.c index 04903e42..0eee1d79 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -31,6 +31,7 @@ #include #include #include +#include #include "rave_io.h" #include "polarvolume.h" #include "libvol2bird.h" @@ -91,7 +92,7 @@ int main(int argc, char** argv) { // number of input files specified on command line int nInputFiles = 0; // the polar volume file that the user provided as input - char* fileVolIn[INPUTFILESMAX]; + char* fileIn[INPUTFILESMAX]; // the (optional) vertical profile file that the user specified as output const char* fileVpOut = NULL; // the (optional) vertical profile file that the user specified as output @@ -124,7 +125,7 @@ int main(int argc, char** argv) { // ------------------------------------------------------------- // // the polar volume file that the user provided as input - fileVolIn[0] = argv[1]; + fileIn[0] = argv[1]; nInputFiles = 1; if (argc == 3){ @@ -140,6 +141,7 @@ int main(int argc, char** argv) { fileVolOut = NULL; } } + else{ // interpret command line input using getopt library int c; @@ -188,18 +190,15 @@ int main(int argc, char** argv) { break; case 'i': - printf ("option -i with value `%s'\n", optarg); - fileVolIn[nInputFiles] = optarg; + fileIn[nInputFiles] = optarg; nInputFiles++; break; case 'o': - printf ("option -o with value `%s'\n", optarg); fileVpOut = optarg; break; case 'p': - printf ("option -p with value `%s'\n", optarg); fileVolOut = optarg; break; @@ -219,12 +218,23 @@ int main(int argc, char** argv) { printf ("%s ", argv[optind++]); putchar ('\n'); } - printf("%i input files found\n",nInputFiles); - printf("vp output file: %s\n",fileVpOut); - printf("pvol output file: %s\n",fileVolOut); + + printf("%i input files found in command line\n",nInputFiles); + for (int i=0; i 0) fprintf(stdout, "# volume coverage pattern (VCP): %i\n", alldata.misc.vcp); printf("# date time HGHT u v w ff dd sd_vvp gap dbz eta dens DBZH n n_dbz n_all n_dbz_all\n"); From 9d085adb1e1cdfdd172c1d57cc032e0684863659 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 18 Mar 2019 15:08:56 -0400 Subject: [PATCH 21/37] added determineRadarFormat() function --- lib/librsl.h | 1 + lib/libvol2bird.c | 29 +++++++++++++++++++++++++++++ lib/libvol2bird.h | 2 ++ src/vol2bird.c | 17 ++++++++--------- 4 files changed, 40 insertions(+), 9 deletions(-) diff --git a/lib/librsl.h b/lib/librsl.h index 30bc65a9..303a3f72 100644 --- a/lib/librsl.h +++ b/lib/librsl.h @@ -1,5 +1,6 @@ #ifdef RSL +#include "rsl.h" PolarVolume_t* vol2birdGetRSLVolume(char* filename, float rangeMax, int small); diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index a4a393d9..d101ac16 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -40,6 +40,7 @@ #include "libdealias.h" #ifdef RSL +#include "rsl.h" #include "librsl.h" #endif @@ -3335,6 +3336,34 @@ static void sortCellsByArea(CELLPROP *cellProp, const int nCells) { +radarDataFormat determineRadarFormat(char* filename){ + +#ifdef IRIS + if (isIRIS(filename)==0){ + return radarDataFormat_ODIM; + } +#endif + +#ifdef RSL + if(RSL_filetype(filename) != UNKNOWN){ + return radarDataFormat_RSL; + } +#endif + + // try to load the file using Rave + // unfortunately this loads the entire file into memory, + // but no other file type check function available in Rave. + RaveIO_t* raveio = RaveIO_open(filename); + + // check that a valid RaveIO_t pointer was returned + if (raveio != (RaveIO_t*) NULL){ + RAVE_OBJECT_RELEASE(raveio); + return radarDataFormat_ODIM; + } + + return radarDataFormat_UNKNOWN; +} + static int removeDroppedCells(CELLPROP *cellProp, const int nCells) { int iCell; diff --git a/lib/libvol2bird.h b/lib/libvol2bird.h index 26f20f9f..6cc3b0da 100644 --- a/lib/libvol2bird.h +++ b/lib/libvol2bird.h @@ -393,6 +393,8 @@ typedef enum radarDataFormat { // Public function prototypes // ***************************************************************************** +radarDataFormat determineRadarFormat(char* filename); + int isRegularFile(const char *path); void vol2birdCalcProfiles(vol2bird_t* alldata); diff --git a/src/vol2bird.c b/src/vol2bird.c index 0eee1d79..90d8205b 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -217,15 +217,7 @@ int main(int argc, char** argv) { while (optind < argc) printf ("%s ", argv[optind++]); putchar ('\n'); - } - - printf("%i input files found in command line\n",nInputFiles); - for (int i=0; i Date: Mon, 18 Mar 2019 15:44:07 -0400 Subject: [PATCH 22/37] prepare vol2birdGetVolume() to take an array of files as input --- lib/libvol2bird.c | 12 ++++++------ lib/libvol2bird.h | 2 +- src/rsl2odim.c | 2 +- src/vol2bird.c | 11 ++++++++--- 4 files changed, 16 insertions(+), 11 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index d101ac16..253359ab 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -1920,7 +1920,7 @@ static int getListOfSelectedGates(PolarScan_t* scan, vol2birdScanUse_t scanUse, int vol2birdLoadClutterMap(PolarVolume_t* volume, char* file, float rangeMax){ PolarVolume_t* clutVol = NULL; - clutVol = vol2birdGetVolume(file, rangeMax,1); + clutVol = vol2birdGetVolume(&file, 1, rangeMax,1); if(clutVol == NULL){ fprintf(stderr, "Error: function loadClutterMap: failed to load file '%s'\n",file); @@ -4236,19 +4236,19 @@ void printProfile(vol2bird_t* alldata) { // reads a polar volume from file and returns it as a RAVE polar volume object // remember to release the polar volume object when done with it -PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small){ +PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float rangeMax, int small){ PolarVolume_t* volume = NULL; #ifdef IRIS // test whether the file is in IRIS format - if (isIRIS(filename)==0){ - volume = vol2birdGetIRISVolume(filename, rangeMax, small); + if (isIRIS(filenames[0])==0){ + volume = vol2birdGetIRISVolume(filenames[0], rangeMax, small); goto done; } #endif - RaveIO_t* raveio = RaveIO_open(filename); + RaveIO_t* raveio = RaveIO_open(filenames[0]); // check that a valid RaveIO_t pointer was returned if (raveio != (RaveIO_t*) NULL){ @@ -4268,7 +4268,7 @@ PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small){ // not a rave complient file, attempt to read the file with the RSL library instead #ifdef RSL else{ - volume = vol2birdGetRSLVolume(filename, rangeMax, small); + volume = vol2birdGetRSLVolume(filenames[0], rangeMax, small); } #endif diff --git a/lib/libvol2bird.h b/lib/libvol2bird.h index 6cc3b0da..1ceaf01a 100644 --- a/lib/libvol2bird.h +++ b/lib/libvol2bird.h @@ -401,7 +401,7 @@ void vol2birdCalcProfiles(vol2bird_t* alldata); float* vol2birdGetProfile(int iProfileType, vol2bird_t* alldata); -PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small); +PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float rangeMax, int small); PolarVolume_t* PolarVolume_resample(PolarVolume_t* volume, double rscale_proj, long nbins_proj, long nrays_proj); diff --git a/src/rsl2odim.c b/src/rsl2odim.c index 5d442e09..f5745103 100644 --- a/src/rsl2odim.c +++ b/src/rsl2odim.c @@ -34,7 +34,7 @@ int main(int argc, char** argv) { // read in data up to a distance of alldata.misc.rCellMax // we do not read in the full volume for speed/memory PolarVolume_t* volume = NULL; - volume = vol2birdGetVolume(fileVolIn, 1000000, 0); + volume = vol2birdGetVolume(&fileVolIn, 1, 1000000, 0); if (volume == NULL) { fprintf(stderr,"Error: failed to read radar volume\n"); diff --git a/src/vol2bird.c b/src/vol2bird.c index 90d8205b..c464cbc8 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -190,8 +190,13 @@ int main(int argc, char** argv) { break; case 'i': - fileIn[nInputFiles] = optarg; - nInputFiles++; + if (nInputFiles < INPUTFILESMAX){ + fileIn[nInputFiles] = optarg; + nInputFiles++; + } + else{ + fprintf(stderr, "Warning: too many input files, ignoring file %s ...\n", optarg); + } break; case 'o': @@ -262,7 +267,7 @@ int main(int argc, char** argv) { // we do not read in the full volume for speed/memory PolarVolume_t* volume = NULL; - volume = vol2birdGetVolume(fileIn[0], alldata.misc.rCellMax,1); + volume = vol2birdGetVolume(fileIn, nInputFiles, alldata.misc.rCellMax,1); if (volume == NULL) { fprintf(stderr,"Error: failed to read radar volume\n"); From 5d89a119c33c98c8c5ddaf4b18b416bf228494a7 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 18 Mar 2019 20:01:21 -0400 Subject: [PATCH 23/37] new code to read and merge multiple IRIS scans into a polar volume (issue #116) --- lib/libvol2bird.c | 142 ++++++++++++++++++++++++++++++++++------------ 1 file changed, 106 insertions(+), 36 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 253359ab..9b747f01 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -144,7 +144,7 @@ static void updateFlagFieldsInPointsArray(const float* yObs, const float* yFitte static int updateMap(PolarScan_t* scan, CELLPROP *cellProp, const int nCells, vol2bird_t* alldata); #ifdef IRIS -PolarVolume_t* vol2birdGetIRISVolume(char* filename, float rangeMax, int small); +PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles, float rangeMax, int small); #endif // non-public function declarations (local to this file/translation unit) @@ -4243,7 +4243,7 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range #ifdef IRIS // test whether the file is in IRIS format if (isIRIS(filenames[0])==0){ - volume = vol2birdGetIRISVolume(filenames[0], rangeMax, small); + volume = vol2birdGetIRISVolume(filenames, nInputFiles, rangeMax, small); goto done; } #endif @@ -4279,55 +4279,125 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range } #ifdef IRIS -PolarVolume_t* vol2birdGetIRISVolume(char* filename, float rangeMax, int small) { - +PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles, float rangeMax, int small) { // initialize a polar volume to return PolarVolume_t* volume = NULL; - + PolarVolume_t* output = NULL; + PolarScan_t* scan = NULL; + + int outputInitialised = FALSE; + // initialize the rave object type of filename int rot = Rave_ObjectType_UNDEFINED; int ret = 0; + + file_element_s* file_element_p; - // read the iris file - file_element_s* file_element_p = readIRIS(filename); - - if(file_element_p == NULL){ - fprintf(stderr, "Error: could not read IRIS file.\n"); - return volume; - } - - rot = objectTypeFromIRIS(file_element_p); - - if (rot == Rave_ObjectType_PVOL) { - volume = RAVE_OBJECT_NEW(&PolarVolume_TYPE); + for (int i=0; i Date: Mon, 18 Mar 2019 20:11:47 -0400 Subject: [PATCH 24/37] also add source attribute of first scan to volume --- lib/libvol2bird.c | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 9b747f01..ca8a5eec 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -144,7 +144,7 @@ static void updateFlagFieldsInPointsArray(const float* yObs, const float* yFitte static int updateMap(PolarScan_t* scan, CELLPROP *cellProp, const int nCells, vol2bird_t* alldata); #ifdef IRIS -PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles, float rangeMax, int small); +PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles); #endif // non-public function declarations (local to this file/translation unit) @@ -4243,7 +4243,7 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range #ifdef IRIS // test whether the file is in IRIS format if (isIRIS(filenames[0])==0){ - volume = vol2birdGetIRISVolume(filenames, nInputFiles, rangeMax, small); + volume = vol2birdGetIRISVolume(filenames, nInputFiles); goto done; } #endif @@ -4279,10 +4279,11 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range } #ifdef IRIS -PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles, float rangeMax, int small) { +PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles) { // initialize a polar volume to return - PolarVolume_t* volume = NULL; PolarVolume_t* output = NULL; + // initialize helper volume and scan to store intermediate file reads + PolarVolume_t* volume = NULL; PolarScan_t* scan = NULL; int outputInitialised = FALSE; @@ -4374,6 +4375,7 @@ PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles, float r PolarVolume_setLatitude(output, PolarScan_getLatitude(scan)); PolarVolume_setLongitude(output, PolarScan_getLongitude(scan)); PolarVolume_setHeight(output, PolarScan_getHeight(scan)); + PolarVolume_setSource(output, PolarScan_getSource(scan)); outputInitialised = TRUE; } From c1d3fb5fb95409b9af5a6bf09a541abe18991958 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 19 Mar 2019 12:28:30 -0400 Subject: [PATCH 25/37] add functionality to read and merge multiple ODIM scans. --- lib/libvol2bird.c | 149 ++++++++++++++++++++++++++++++++++++++-------- src/vol2bird.c | 7 ++- 2 files changed, 128 insertions(+), 28 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index ca8a5eec..018f1b3d 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -147,6 +147,8 @@ static int updateMap(PolarScan_t* scan, CELLPROP *cellProp, const int nCells, vo PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles); #endif +PolarVolume_t* vol2birdGetODIMVolume(char* filenames[], int nInputFiles); + // non-public function declarations (local to this file/translation unit) static int analyzeCells(PolarScan_t *scan, vol2birdScanUse_t scanUse, const int nCells, int dualpol, vol2bird_t *alldata) { @@ -4248,31 +4250,19 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range } #endif - RaveIO_t* raveio = RaveIO_open(filenames[0]); - - // check that a valid RaveIO_t pointer was returned - if (raveio != (RaveIO_t*) NULL){ - // check that the Rave object is a polar volume - if (RaveIO_getObjectType(raveio) == Rave_ObjectType_PVOL) { - - // the if statement above tests whether we are dealing with a - // PVOL object, so we can safely cast the generic object to - // the PolarVolume_t type: - - volume = (PolarVolume_t*) RaveIO_getObject(raveio); - } - else{ - fprintf(stderr,"Error: ODIM HDF5 file is not a polar volume\n"); - } - } // not a rave complient file, attempt to read the file with the RSL library instead #ifdef RSL - else{ - volume = vol2birdGetRSLVolume(filenames[0], rangeMax, small); + if(RSL_filetype(filenames[0]) != UNKNOWN){ + if (nInputFiles > 1){ + fprintf(stderr,"Multiple input files detected in RSL format. \ + Only single polar volume file import supported, using file %s only.\n", filenames[0]); + } + volume = vol2birdGetRSLVolume(filenames[0], rangeMax, small); + goto done; } #endif - RAVE_OBJECT_RELEASE(raveio); + volume = vol2birdGetODIMVolume(filenames, nInputFiles); done: return volume; @@ -4293,7 +4283,7 @@ PolarVolume_t* vol2birdGetIRISVolume(char* filenames[], int nInputFiles) { int ret = 0; - file_element_s* file_element_p; + file_element_s* file_element_p = NULL; for (int i=0; i\n"); - fprintf(stderr," or input formats compatible with RSL, see \n\n"); + fprintf(stderr," or input formats compatible with RSL, see \n"); + fprintf(stderr," or Vaisala Sigmet IRIS format, see \n\n"); fprintf(stderr," Output fields to stdout:\n"); fprintf(stderr," date - date [UTC]\n"); fprintf(stderr," time - time [UTC]\n"); @@ -68,7 +69,7 @@ void usage(char* programName, int verbose){ fprintf(stderr," n_dbz - number of points bird density estimate (dbz,eta,dens)\n"); fprintf(stderr," n_all - number of points VVP st.dev. estimate (sd_vvp)\n"); fprintf(stderr," n_dbz_all - number of points total reflectivity estimate (DBZH)\n\n"); - fprintf(stderr," Report bugs to: a.m.dokter@uva.nl or on http://github.com/adokter/vol2bird/issues \n"); + fprintf(stderr," Report bugs at: http://github.com/adokter/vol2bird/issues \n"); fprintf(stderr," vol2bird home page: \n"); } } From 72e8ff622a7917f42b430d76efe50e9a8bf7dee8 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 19 Mar 2019 12:34:43 -0400 Subject: [PATCH 26/37] updates to help message --- src/vol2bird.c | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/src/vol2bird.c b/src/vol2bird.c index 33624fd8..c574e5eb 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -41,15 +41,16 @@ #include "rave_debug.h" void usage(char* programName, int verbose){ - fprintf(stderr,"usage: %s [ []]\n",programName); - fprintf(stderr,"usage: %s -i [-i [-i ] ...] [-o [-p ]]\n",programName); - fprintf(stderr,"usage: %s --help\n", programName); + fprintf(stderr,"vol2bird version %s (%s)\n", VERSION, VERSIONDATE); + fprintf(stderr," usage: %s [ []]\n",programName); + fprintf(stderr," usage: %s -i [-i [-i ] ...] [-o [-p ]]\n",programName); + fprintf(stderr," usage: %s --help\n", programName); if(verbose){ - fprintf(stderr,"\n Version %s (%s)\n", VERSION, VERSIONDATE); - fprintf(stderr," expects OPERA ODIM hdf5 input format, see \n"); - fprintf(stderr," or input formats compatible with RSL, see \n"); - fprintf(stderr," or Vaisala Sigmet IRIS format, see \n\n"); + fprintf(stderr,"\n Supported radar data formats:\n"); + fprintf(stderr," * OPERA ODIM hdf5 input format, see \n"); + fprintf(stderr," * input formats compatible with RSL, see \n"); + fprintf(stderr," * Vaisala Sigmet IRIS format, see \n\n"); fprintf(stderr," Output fields to stdout:\n"); fprintf(stderr," date - date [UTC]\n"); fprintf(stderr," time - time [UTC]\n"); From fb3b7b2aac2be982b4acb211e2ed266d07af18af Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 19 Mar 2019 13:05:42 -0400 Subject: [PATCH 27/37] minor cosmetic changes --- lib/libvol2bird.c | 7 +++---- lib/libvol2bird.h | 2 +- src/vol2bird.c | 7 ------- 3 files changed, 4 insertions(+), 12 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 018f1b3d..5d3b69cf 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -88,7 +88,7 @@ static int hasAzimuthGap(const float *points_local, const int nPoints, vol2bird_ static int includeGate(const int iProfileType, const int iQuantityType, const unsigned int gateCode, vol2bird_t* alldata); -const char* libvol2bird_version(); +const char* libvol2bird_version(void); static int verticalProfile_AddCustomField(VerticalProfile_t* self, RaveField_t* field, const char* quantity); @@ -2418,7 +2418,7 @@ static int hasAzimuthGap(const float* points_local, const int nPoints, vol2bird_ } // hasAzimuthGap -const char* libvol2bird_version(){ +const char* libvol2bird_version(void){ return VERSION; }; @@ -4254,8 +4254,7 @@ PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float range #ifdef RSL if(RSL_filetype(filenames[0]) != UNKNOWN){ if (nInputFiles > 1){ - fprintf(stderr,"Multiple input files detected in RSL format. \ - Only single polar volume file import supported, using file %s only.\n", filenames[0]); + fprintf(stderr,"Multiple input files detected in RSL format. Only single polar volume file import supported, using file %s only.\n", filenames[0]); } volume = vol2birdGetRSLVolume(filenames[0], rangeMax, small); goto done; diff --git a/lib/libvol2bird.h b/lib/libvol2bird.h index 1ceaf01a..2055e26a 100644 --- a/lib/libvol2bird.h +++ b/lib/libvol2bird.h @@ -433,4 +433,4 @@ float nanify(float value); int saveToODIM(RaveCoreObject* object, const char* filename); -const char* libvol2bird_version(); +const char* libvol2bird_version(void); diff --git a/src/vol2bird.c b/src/vol2bird.c index c574e5eb..fd2fd050 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -233,13 +233,6 @@ int main(int argc, char** argv) { fprintf(stderr, "Error: input file '%s' does not exist.\n", fileIn[i]); return -1; } - else{ - radarDataFormat format = determineRadarFormat(fileIn[i]); - if (format == radarDataFormat_RSL) fprintf(stderr, "File %s file type: RSL\n",fileIn[i]); - if (format == radarDataFormat_ODIM) fprintf(stderr, "File %s file type: ODIM\n",fileIn[i]); - if (format == radarDataFormat_IRIS) fprintf(stderr, "File %s file type: IRIS\n",fileIn[i]); - if (format == radarDataFormat_UNKNOWN) fprintf(stderr, "File %s file type: UNKNOWN\n",fileIn[i]); - } } // Initialize hlhdf library From 8cb01153c532bc170792b32ed1ab6d865753b892 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 19 Mar 2019 13:14:40 -0400 Subject: [PATCH 28/37] added NEWS.md --- NEWS.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 00000000..5ff349ef --- /dev/null +++ b/NEWS.md @@ -0,0 +1,12 @@ +# vol2bird 0.4.0 + +All issues included in this release can be found [here](https://github.com/adokter/vol2bird/milestone/2?closed=1). + +* added Vaisala Sigmet IRIS support, a widely used weather radar data format (e.g. in Canada) (#112) + +* added functionality to read files containing single scans (sweeps) and merge them into polar volumes (#116) + +# vol2bird 0.3.20 and older + +All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/3?closed=1). + From dc5ccdc958c8f168758e0237464ffa01cfb90292 Mon Sep 17 00:00:00 2001 From: adokter Date: Tue, 19 Mar 2019 14:54:22 -0400 Subject: [PATCH 29/37] generated site with doxygen --- docs/globals.html | 54 ++++++++++++++++++++++++++++++++++++++++++ docs/globals_func.html | 54 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 docs/globals.html create mode 100644 docs/globals_func.html diff --git a/docs/globals.html b/docs/globals.html new file mode 100644 index 00000000..fcfc6617 --- /dev/null +++ b/docs/globals.html @@ -0,0 +1,54 @@ + + + + + + + +vol2bird: File Members + + + + + + +
    +
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    +
    vol2bird +
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    +
    +
    Here is a list of all documented file members with links to the documentation:
    +
    + +
    +Generated by   +doxygen + 1.8.14 +
    + + diff --git a/docs/globals_func.html b/docs/globals_func.html new file mode 100644 index 00000000..0529cb12 --- /dev/null +++ b/docs/globals_func.html @@ -0,0 +1,54 @@ + + + + + + + +vol2bird: File Members + + + + + + +
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    + + From d610ca5952d4f9798dd023dc748a525bcf2a4ba0 Mon Sep 17 00:00:00 2001 From: adokter Date: Wed, 20 Mar 2019 21:42:12 -0400 Subject: [PATCH 30/37] rsl2odim can now read iris format (renaming of rsl2odim needed in future) --- docs/constants_8h_source.html | 2 +- docs/librsl_8h_source.html | 2 +- docs/libvol2bird_8c.html | 46 +++++++-- docs/libvol2bird_8h_source.html | 3 +- docs/menudata.js | 5 +- docs/vol2bird_8c.html | 5 + src/rsl2odim.c | 168 +++++++++++++++++++++++++++++--- 7 files changed, 206 insertions(+), 25 deletions(-) diff --git a/docs/constants_8h_source.html b/docs/constants_8h_source.html index a1e702e9..c4e5da48 100644 --- a/docs/constants_8h_source.html +++ b/docs/constants_8h_source.html @@ -46,7 +46,7 @@
    constants.h
    -
    1 //-------------------------------------------------------------//
    2 // hard-coded constants assigned to vol2birdConstants struct //
    3 //-------------------------------------------------------------//
    4 
    5 #include <float.h>
    6 
    7 // when analyzing cells, AREACELL determines the minimum size of a
    8 // cell to be considered in the rest of the analysis [km^2]
    9 #define AREACELL 0.5
    10 // minimum standard deviation of the fit
    11 #define CHISQMIN 1e-5
    12 // cells with clutter fractions above this value are likely not birds
    13 #define CLUTPERCCELL 0.5
    14 // threshold value (on the external static clutter map!) above which gates are excluded as clutter
    15 #define CLUTTERVALUEMIN 0.1
    16 // each weather cell identified by findWeatherCells() is grown by a distance
    17 // equal to 'fringeDist' using a region-growing approach
    18 #define FRINGEDIST 5000.0
    19 // when determining whether there are enough vrad observations in
    20 // each direction, use NBINSGAP sectors
    21 #define NBINSGAP 8
    22 // there should be at least NOBSGAPMIN vrad observations in each sector
    23 #define NOBSGAPMIN 5
    24 // when calculating the altitude-layer averaged dbz, there should
    25 // be at least NDBZMIN valid data points
    26 #define NDBZMIN 25
    27 // the minimum number of direct neighbors with dbz value above
    28 // dbzThresMin as used in findWeatherCells()
    29 #define NEIGHBORS 5
    30 // vrad's texture is calculated based on the local neighborhood. The
    31 // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    32 // static int nAzimNeighborhood;
    33 #define NTEXBINAZIM 3
    34 // vrad's texture is calculated based on the local neighborhood. The
    35 // neighborhood size in the range direction is equal to NTEXBINRANG
    36 // static int nRangNeighborhood;
    37 #define NTEXBINRANG 3
    38 // the minimum number of neighbors for the texture value to be
    39 // considered valid, as used in calcTexture()
    40 #define NTEXMIN 4
    41 // the refractive index of water
    42 #define REFRACTIVE_INDEX_OF_WATER 0.964
    43 // range gates up to a distance of RANGE_MAX+RCELLMAX_OFFSET are read into memory
    44 // the extra offset allows for the raincell search to extend somewhat further
    45 // than the maximum range used in the profile generation (RANGE_MAX).
    46 #define RCELLMAX_OFFSET 5000.0f
    47 // smallest range bin size to accept in metres
    48 #define RSCALEMIN 10
    49 // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    50 // from the fitted value, since these are likely outliers
    51 #define VDIFMAX 10.0
    52 // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    53 #define VRADMIN 1.0
    54 
    55 
    56 //-------------------------------------------------------//
    57 // hard-coded options for use RSL library //
    58 //-------------------------------------------------------//
    59 
    60 #ifdef RSL
    61 // By how much the elevation angle of sweeps of different quantities
    62 // is allowed to differ for them to be included into the same scan object.
    63 // Applies to data read with the RSL library only
    64 #define ELEVTOL 0.3
    65 // Offsets and gains for encoding reflectivity, velocity
    66 // and correlation coefficient
    67 // Once encoded values should be positive for storage in RAVE objects
    68 // Used with data read by the RSL library only
    69 #define RSL_OFFSET_DBZ 0
    70 #define RSL_GAIN_DBZ 1
    71 #define RSL_OFFSET_VRAD 0
    72 #define RSL_GAIN_VRAD 1
    73 #define RSL_OFFSET_RHOHV 0
    74 #define RSL_GAIN_RHOHV 1
    75 // Encoded values reserved for nodata and undetects.
    76 // Should be positive integers larger than zero
    77 #define RSL_NODATA -1000
    78 #define RSL_UNDETECT -999
    79 #endif
    80 
    81 //-------------------------------------------------------//
    82 // other hard-coded options //
    83 //-------------------------------------------------------//
    84 
    85 // Raw value used for gates or layers void of data (never ra-diated)
    86 #define UNDETECT -999
    87 // Raw value used for gates or layers when below the measurement detection threshold
    88 // or when information could not be retrieved (radiated but nothing detected or calculated)
    89 #define NODATA -1000
    90 // name under which the calculated texture quantity will be stored
    91 #define TEXNAME "VTEX"
    92 // name under which the calculated raincell masking quantity will be stored
    93 #define CELLNAME "CELL"
    94 // name of the parameter containing the static cluttermap
    95 #define CLUTNAME "OCCULT"
    96 // Name of the program, to be stored as task attribute in ODIM
    97 #define PROGRAM "vol2bird"
    98 // Version of the program, to be stored as task_version attribute in ODIM
    99 #define VERSION "0.3.20"
    100 // Date of latest version of the program
    101 #define VERSIONDATE "24-Oct-2018"
    102 
    103 //-------------------------------------------------------//
    104 // user options defaults (to be set in options.conf) //
    105 //-------------------------------------------------------//
    106 
    107 // the number of layers in an altitude profile
    108 #define NLAYER 25
    109 // the width/thickness of a layer [m]
    110 #define HLAYER 200.0f
    111 // the minimum range [m] used for constructing the bird density profile
    112 #define RANGEMIN 5000.0f
    113 // the maximum range [m] used for constructing the bird density profile
    114 #define RANGEMAX 25000.0f
    115 // the minimum azimuth [degrees] used for constructing the bird density profile
    116 #define AZIMMIN 0.0f
    117 // the maximum range [degrees] used for constructing the bird density profile
    118 #define AZIMMAX 360.0f
    119 // the minimum scan elevation [degrees] used for constructing the bird density profile
    120 #define ELEVMIN 0.0f
    121 // the maximum scan elevation used for constructing the bird density profile
    122 #define ELEVMAX 90.0f
    123 // the wavelength [cm] of the radar
    124 #define RADAR_WAVELENGTH_CM 5.3f
    125 // whether a static clutter map is used
    126 #define USE_CLUTTERMAP 0
    127 // clutter map path and filename
    128 #define CLUTTERMAP ""
    129 // print options to stderr
    130 #define PRINT_OPTIONS 0
    131 // name of (optional) environmental variable containing path to user configuration file
    132 #define OPTIONS_CONF "OPTIONS_CONF"
    133 // default user configuration file name to search for in working directory
    134 #define OPTIONS_FILE "options.conf"
    135 // FIXME: add description
    136 #define VERBOSE_OUTPUT_REQUIRED 0
    137 // print dbz to stderr
    138 #define PRINT_DBZ 0
    139 // print aliased and dealiased vrad pairs to stderr
    140 #define PRINT_DEALIAS 0
    141 // print vrad to stderr
    142 #define PRINT_VRAD 0
    143 // print rhohv to stderr
    144 #define PRINT_RHOHV 0
    145 // print cell to stderr
    146 #define PRINT_CELL 0
    147 // print cell properties to stderr
    148 #define PRINT_CELL_PROP 0
    149 // print texture to stderr
    150 #define PRINT_TEXTURE 0
    151 // print clutter to stderr
    152 #define PRINT_CLUT 0
    153 // print profile data to stderr
    154 #define PRINT_PROFILE 0
    155 // whether or not to print the 'points' array
    156 #define PRINT_POINTS_ARRAY 0
    157 // Whether or not to fit a model to the observed vrad
    158 #define FIT_VRAD 1
    159 // Whether to export bird profile as JSON
    160 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    161 // Scans with Nyquist velocity lower than this value are excluded
    162 #define MIN_NYQUIST_VELOCITY 5.0f
    163 // When all scans have nyquist velocity higher than this value, dealiasing is suppressed
    164 #define MAX_NYQUIST_DEALIAS 25.0f
    165 // when analyzing cells, only cells for which the stddev of vrad
    166 // (aka the texture) is less than cellStdDevMax are considered in the
    167 // rest of the analysis
    168 #define STDEV_CELL 5.0f
    169 // VVP Radial velocity standard deviation threshold
    170 #define STDEV_BIRD 2.0f
    171 // Bird radar cross section [cm^2]
    172 #define SIGMA_BIRD 11.0f
    173 // Maximum mean reflectivity [cm^2/km^3] for cells containing birds
    174 #define ETACELL 11500.0f
    175 // Maximum reflectivity [cm^2/km^3] for single gates containing birds
    176 #define ETAMAX 36000.0f
    177 // minimum dbz of a gate to be considered for inclusion in a weather cell
    178 #define DBZMIN 0.0
    179 // reflectivity quantity to use, one of "DBZH", "DBZV", "TH", "TV"
    180 #define DBZTYPE "DBZH"
    181 // for a range gate to contribute it should have a valid radial velocity
    182 #define REQUIRE_VRAD 0
    183 // whether we should dealias the radial velocities
    184 #define DEALIAS_VRAD 1
    185 // whether we should dealias all data once (default), or dealias for each profile individually
    186 #define DEALIAS_RECYCLE 1
    187 // Test dealiasing field velocities up to VMAX m/s
    188 #define DEALIAS_VMAX 50.0
    189 // Test field velocities increase in steps VMAX/VAF
    190 #define DEALIAS_VAF 15.0
    191 // Test field directions increase by 360/NF degrees
    192 #define DEALIAS_NF 12.0
    193 // whether you want to export the vertical bird profile as JSON
    194 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    195 // whether to use dual-pol moments for filtering meteorological echoes
    196 #define DUALPOL 1
    197 // whether to use single-pol moments for filtering meteorological echoes
    198 #define SINGLEPOL 1
    199 // correlation coefficients higher than this threshold will be classified as precipitation
    200 #define RHOHVMIN 0.95f
    201 // whether to resample the input polar volume
    202 #define RESAMPLE 0
    203 // resampled range gate length in m
    204 #define RESAMPLE_RSCALE 500.0f
    205 // resampled number of range bins
    206 #define RESAMPLE_NBINS 100
    207 // resampled number of azimuth bins
    208 #define RESAMPLE_NRAYS 360
    +
    1 //-------------------------------------------------------------//
    2 // hard-coded constants assigned to vol2birdConstants struct //
    3 //-------------------------------------------------------------//
    4 
    5 #include <float.h>
    6 
    7 // when analyzing cells, AREACELL determines the minimum size of a
    8 // cell to be considered in the rest of the analysis [km^2]
    9 #define AREACELL 0.5
    10 // minimum standard deviation of the fit
    11 #define CHISQMIN 1e-5
    12 // cells with clutter fractions above this value are likely not birds
    13 #define CLUTPERCCELL 0.5
    14 // threshold value (on the external static clutter map!) above which gates are excluded as clutter
    15 #define CLUTTERVALUEMIN 0.1
    16 // each weather cell identified by findWeatherCells() is grown by a distance
    17 // equal to 'fringeDist' using a region-growing approach
    18 #define FRINGEDIST 5000.0
    19 // when determining whether there are enough vrad observations in
    20 // each direction, use NBINSGAP sectors
    21 #define NBINSGAP 8
    22 // there should be at least NOBSGAPMIN vrad observations in each sector
    23 #define NOBSGAPMIN 5
    24 // when calculating the altitude-layer averaged dbz, there should
    25 // be at least NDBZMIN valid data points
    26 #define NDBZMIN 25
    27 // the minimum number of direct neighbors with dbz value above
    28 // dbzThresMin as used in findWeatherCells()
    29 #define NEIGHBORS 5
    30 // vrad's texture is calculated based on the local neighborhood. The
    31 // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    32 // static int nAzimNeighborhood;
    33 #define NTEXBINAZIM 3
    34 // vrad's texture is calculated based on the local neighborhood. The
    35 // neighborhood size in the range direction is equal to NTEXBINRANG
    36 // static int nRangNeighborhood;
    37 #define NTEXBINRANG 3
    38 // the minimum number of neighbors for the texture value to be
    39 // considered valid, as used in calcTexture()
    40 #define NTEXMIN 4
    41 // the refractive index of water
    42 #define REFRACTIVE_INDEX_OF_WATER 0.964
    43 // range gates up to a distance of RANGE_MAX+RCELLMAX_OFFSET are read into memory
    44 // the extra offset allows for the raincell search to extend somewhat further
    45 // than the maximum range used in the profile generation (RANGE_MAX).
    46 #define RCELLMAX_OFFSET 5000.0f
    47 // smallest range bin size to accept in metres
    48 #define RSCALEMIN 10
    49 // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    50 // from the fitted value, since these are likely outliers
    51 #define VDIFMAX 10.0
    52 // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    53 #define VRADMIN 1.0
    54 
    55 
    56 //-------------------------------------------------------//
    57 // hard-coded options for use RSL library //
    58 //-------------------------------------------------------//
    59 
    60 #ifdef RSL
    61 // By how much the elevation angle of sweeps of different quantities
    62 // is allowed to differ for them to be included into the same scan object.
    63 // Applies to data read with the RSL library only
    64 #define ELEVTOL 0.3
    65 // Offsets and gains for encoding reflectivity, velocity
    66 // and correlation coefficient
    67 // Once encoded values should be positive for storage in RAVE objects
    68 // Used with data read by the RSL library only
    69 #define RSL_OFFSET_DBZ 0
    70 #define RSL_GAIN_DBZ 1
    71 #define RSL_OFFSET_VRAD 0
    72 #define RSL_GAIN_VRAD 1
    73 #define RSL_OFFSET_RHOHV 0
    74 #define RSL_GAIN_RHOHV 1
    75 // Encoded values reserved for nodata and undetects.
    76 // Should be positive integers larger than zero
    77 #define RSL_NODATA -1000
    78 #define RSL_UNDETECT -999
    79 #endif
    80 
    81 //-------------------------------------------------------//
    82 // other hard-coded options //
    83 //-------------------------------------------------------//
    84 
    85 // maximum number of input files
    86 #define INPUTFILESMAX 50
    87 // Raw value used for gates or layers void of data (never ra-diated)
    88 #define UNDETECT -999
    89 // Raw value used for gates or layers when below the measurement detection threshold
    90 // or when information could not be retrieved (radiated but nothing detected or calculated)
    91 #define NODATA -1000
    92 // name under which the calculated texture quantity will be stored
    93 #define TEXNAME "VTEX"
    94 // name under which the calculated raincell masking quantity will be stored
    95 #define CELLNAME "CELL"
    96 // name of the parameter containing the static cluttermap
    97 #define CLUTNAME "OCCULT"
    98 // Name of the program, to be stored as task attribute in ODIM
    99 #define PROGRAM "vol2bird"
    100 // Version of the program, to be stored as task_version attribute in ODIM
    101 #define VERSION "0.3.20"
    102 // Date of latest version of the program
    103 #define VERSIONDATE "24-Oct-2018"
    104 
    105 //-------------------------------------------------------//
    106 // user options defaults (to be set in options.conf) //
    107 //-------------------------------------------------------//
    108 
    109 // the number of layers in an altitude profile
    110 #define NLAYER 25
    111 // the width/thickness of a layer [m]
    112 #define HLAYER 200.0f
    113 // the minimum range [m] used for constructing the bird density profile
    114 #define RANGEMIN 5000.0f
    115 // the maximum range [m] used for constructing the bird density profile
    116 #define RANGEMAX 25000.0f
    117 // the minimum azimuth [degrees] used for constructing the bird density profile
    118 #define AZIMMIN 0.0f
    119 // the maximum range [degrees] used for constructing the bird density profile
    120 #define AZIMMAX 360.0f
    121 // the minimum scan elevation [degrees] used for constructing the bird density profile
    122 #define ELEVMIN 0.0f
    123 // the maximum scan elevation used for constructing the bird density profile
    124 #define ELEVMAX 90.0f
    125 // the wavelength [cm] of the radar
    126 #define RADAR_WAVELENGTH_CM 5.3f
    127 // whether a static clutter map is used
    128 #define USE_CLUTTERMAP 0
    129 // clutter map path and filename
    130 #define CLUTTERMAP ""
    131 // print options to stderr
    132 #define PRINT_OPTIONS 0
    133 // name of (optional) environmental variable containing path to user configuration file
    134 #define OPTIONS_CONF "OPTIONS_CONF"
    135 // default user configuration file name to search for in working directory
    136 #define OPTIONS_FILE "options.conf"
    137 // FIXME: add description
    138 #define VERBOSE_OUTPUT_REQUIRED 0
    139 // print dbz to stderr
    140 #define PRINT_DBZ 0
    141 // print aliased and dealiased vrad pairs to stderr
    142 #define PRINT_DEALIAS 0
    143 // print vrad to stderr
    144 #define PRINT_VRAD 0
    145 // print rhohv to stderr
    146 #define PRINT_RHOHV 0
    147 // print cell to stderr
    148 #define PRINT_CELL 0
    149 // print cell properties to stderr
    150 #define PRINT_CELL_PROP 0
    151 // print texture to stderr
    152 #define PRINT_TEXTURE 0
    153 // print clutter to stderr
    154 #define PRINT_CLUT 0
    155 // print profile data to stderr
    156 #define PRINT_PROFILE 0
    157 // whether or not to print the 'points' array
    158 #define PRINT_POINTS_ARRAY 0
    159 // Whether or not to fit a model to the observed vrad
    160 #define FIT_VRAD 1
    161 // Whether to export bird profile as JSON
    162 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    163 // Scans with Nyquist velocity lower than this value are excluded
    164 #define MIN_NYQUIST_VELOCITY 5.0f
    165 // When all scans have nyquist velocity higher than this value, dealiasing is suppressed
    166 #define MAX_NYQUIST_DEALIAS 25.0f
    167 // when analyzing cells, only cells for which the stddev of vrad
    168 // (aka the texture) is less than cellStdDevMax are considered in the
    169 // rest of the analysis
    170 #define STDEV_CELL 5.0f
    171 // VVP Radial velocity standard deviation threshold
    172 #define STDEV_BIRD 2.0f
    173 // Bird radar cross section [cm^2]
    174 #define SIGMA_BIRD 11.0f
    175 // Maximum mean reflectivity [cm^2/km^3] for cells containing birds
    176 #define ETACELL 11500.0f
    177 // Maximum reflectivity [cm^2/km^3] for single gates containing birds
    178 #define ETAMAX 36000.0f
    179 // minimum dbz of a gate to be considered for inclusion in a weather cell
    180 #define DBZMIN 0.0
    181 // reflectivity quantity to use, one of "DBZH", "DBZV", "TH", "TV"
    182 #define DBZTYPE "DBZH"
    183 // for a range gate to contribute it should have a valid radial velocity
    184 #define REQUIRE_VRAD 0
    185 // whether we should dealias the radial velocities
    186 #define DEALIAS_VRAD 1
    187 // whether we should dealias all data once (default), or dealias for each profile individually
    188 #define DEALIAS_RECYCLE 1
    189 // Test dealiasing field velocities up to VMAX m/s
    190 #define DEALIAS_VMAX 50.0
    191 // Test field velocities increase in steps VMAX/VAF
    192 #define DEALIAS_VAF 15.0
    193 // Test field directions increase by 360/NF degrees
    194 #define DEALIAS_NF 12.0
    195 // whether you want to export the vertical bird profile as JSON
    196 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    197 // whether to use dual-pol moments for filtering meteorological echoes
    198 #define DUALPOL 1
    199 // whether to use single-pol moments for filtering meteorological echoes
    200 #define SINGLEPOL 1
    201 // correlation coefficients higher than this threshold will be classified as precipitation
    202 #define RHOHVMIN 0.95f
    203 // whether to resample the input polar volume
    204 #define RESAMPLE 0
    205 // resampled range gate length in m
    206 #define RESAMPLE_RSCALE 500.0f
    207 // resampled number of range bins
    208 #define RESAMPLE_NBINS 100
    209 // resampled number of azimuth bins
    210 #define RESAMPLE_NRAYS 360
    Generated by   diff --git a/docs/librsl_8h_source.html b/docs/librsl_8h_source.html index ef0038b1..051d45a4 100644 --- a/docs/librsl_8h_source.html +++ b/docs/librsl_8h_source.html @@ -46,7 +46,7 @@
    librsl.h
    -
    1 #ifdef RSL
    2 
    3 
    4 PolarVolume_t* vol2birdGetRSLVolume(char* filename, float rangeMax, int small);
    5 
    6 #endif
    +
    1 #ifdef RSL
    2 
    3 #include "rsl.h"
    4 
    5 PolarVolume_t* vol2birdGetRSLVolume(char* filename, float rangeMax, int small);
    6 
    7 #endif
    Generated by   diff --git a/docs/libvol2bird_8c.html b/docs/libvol2bird_8c.html index ef4f0a62..0778ed12 100644 --- a/docs/libvol2bird_8c.html +++ b/docs/libvol2bird_8c.html @@ -57,6 +57,7 @@ #include <confuse.h>
    #include <stdlib.h>
    #include <math.h>
    +#include <unistd.h>
    #include <vertical_profile.h>
    #include "rave_io.h"
    #include "rave_debug.h"
    @@ -66,6 +67,7 @@ #include "libsvdfit.h"
    #include "constants.h"
    #include "libdealias.h"
    +#include "rsl.h"
    #include "librsl.h"
    - - + + @@ -109,6 +111,9 @@ + + @@ -124,6 +129,9 @@ + + + @@ -133,6 +141,9 @@ + + @@ -157,9 +168,9 @@ - - + + @@ -177,7 +188,28 @@

    vol2bird main functions

    Author
    Adriaan Dokter & Netherlands eScience Centre
    Date
    2015-05-05
    -
    +

    Function Documentation

    + +

    ◆ isRegularFile()

    + +
    +
    +

    @@ -73,9 +75,9 @@

    CELLPROP * getCellProperties (PolarScan_t *scan, vol2birdScanUse_t scanUse, const int nCells, vol2bird_t *alldata)
     
    -const char * libvol2bird_version ()
     
    +const char * libvol2bird_version (void)
     
    PolarScanParam_t * PolarScan_newParam (PolarScan_t *scan, const char *quantity, RaveDataType type)
     
    PolarScanParam_t * PolarScanParam_resample (PolarScanParam_t *param, double rscale, double rscale_proj, long nbins_proj, long nrays_proj)
     
    +PolarVolume_t * vol2birdGetODIMVolume (char *filenames[], int nInputFiles)
     
    int vol2birdLoadClutterMap (PolarVolume_t *volume, char *file, float rangeMax)
     
    PolarVolume_t * PolarVolume_resample (PolarVolume_t *volume, double rscale_proj, long nbins_proj, long nrays_proj)
     
    int isRegularFile (const char *path)
     Function name: isRegularFile Intent: determines whether the given path is to a regular file Note: also returns true on existing directories. More...
     
    int mapDataToRave (PolarVolume_t *volume, vol2bird_t *alldata)
     
    int saveToODIM (RaveCoreObject *object, const char *filename)
     
    +radarDataFormat determineRadarFormat (char *filename)
     
    void vol2birdCalcProfiles (vol2bird_t *alldata)
     
    void vol2birdPrintPointsArraySimple (vol2bird_t *alldata)
     
    -PolarVolume_t * vol2birdGetVolume (char *filename, float rangeMax, int small)
     
    +PolarVolume_t * vol2birdGetVolume (char *filenames[], int nInputFiles, float rangeMax, int small)
     
    RaveIO_t * vol2birdIO_open (const char *filename)
     
     + + + + + + + +
    int isRegularFile (const char * path)
    +
    + +

    Function name: isRegularFile Intent: determines whether the given path is to a regular file Note: also returns true on existing directories.

    + +
    + +
    Generated by   diff --git a/docs/libvol2bird_8h_source.html b/docs/libvol2bird_8h_source.html index 2adfab4b..52d22987 100644 --- a/docs/libvol2bird_8h_source.html +++ b/docs/libvol2bird_8h_source.html @@ -46,7 +46,8 @@
    libvol2bird.h
    -
    1 /*
    2  * Copyright 2015 Adriaan Dokter & Netherlands eScience Centre
    3  * If you want to use this software, please contact me at a.m.dokter@uva.nl
    4  *
    5  * This program calculates Vertical Profiles of Birds (VPBs) as described in
    6  *
    7  * Bird migration flight altitudes studied by a network of operational weather radars
    8  * Dokter A.M., Liechti F., Stark H., Delobbe L., Tabary P., Holleman I.
    9  * J. R. Soc. Interface, 8, 30–43, 2011
    10  * DOI: 10.1098/rsif.2010.0116
    11  *
    12  */
    13 
    14 #include <confuse.h>
    15 #include <polarvolume.h>
    16 #include <vertical_profile.h>
    17 
    18 // ****************************************************************************
    19 // Definition of standard parameters.
    20 // ****************************************************************************
    21 
    22 #define DEG2RAD (0.017453293) // Degrees to radians.
    23 #define RAD2DEG (57.29578) // Radians to degrees.
    24 
    25 // ****************************************************************************
    26 // Definition of general macros:
    27 // ****************************************************************************
    28 
    29 #define XABS(x) (((x) < 0) ? (-(x)) : (x))
    30 #define ROUND(x) (((x) > 0) ? (int)((x) + 0.5) : (int)((x)-0.5))
    31 #define SQUARE(x) ((x) * (x))
    32 
    33 // ****************************************************************************
    34 // Defined (default) parameters.
    35 // ****************************************************************************
    36 
    37 #ifndef PI
    38 #define PI (3.14159265358979323846)
    39 #endif
    40 
    41 #ifndef TRUE
    42 #define TRUE 1
    43 #endif
    44 
    45 #ifndef FALSE
    46 #define FALSE 0
    47 #endif
    48 
    49 // ****************************************************************************
    50 // Structure for containing SCAN metadata:
    51 // ****************************************************************************
    52 
    53 struct cellprop {
    54  int iRangOfMax;
    55  int iAzimOfMax;
    56  float dbzAvg;
    57  float texAvg;
    58  float cv;
    59  int nGates;
    60  int nGatesClutter;
    61  double area;
    62  float dbzMax;
    63  int index;
    64  int drop;
    65 };
    66 
    67 struct scanmeta {
    68  float heig; // Height of radar antenna in km.
    69  float elev; // Elevation of scan in deg.
    70  int nRang; // Number of range bins in scan.
    71  int nAzim; // Number of azimuth rays in scan.
    72  float rangeScale; // Size of range bins in scan in km.
    73  float azimScale; // Size of azimuth steps in scan in deg.
    74  float valueOffset; // Offset value of quantity contained by scan.
    75  float valueScale; // Scale of value of quantity contained by scan.
    76  float missing; // Missing value of quantity contained by scan.
    77  double nyquist; // Nyquist velocity of the scan
    78 };
    79 
    80 typedef struct cellprop CELLPROP;
    81 typedef struct scanmeta SCANMETA;
    82 
    83 // *****************************************************************************
    84 // Structures for internal use
    85 // *****************************************************************************
    86 
    87 // ------------------------------------------------------------- //
    88 // vol2bird options from options.conf //
    89 // ------------------------------------------------------------- //
    90 
    91 struct vol2birdOptions {
    92  int nLayers; /* the number of layers in an altitude profile */
    93  float layerThickness; /* the width/thickness of a layer [m] */
    94  float rangeMin; /* the minimum range [m] used for constructing the bird density profile */
    95  float rangeMax; /* the maximum range [m] used for constructing the bird density profile */
    96  float azimMin; /* the minimum azimuth [degrees] used for constructing the bird density profile */
    97  float azimMax; /* the maximum azimuth [degrees] used for constructing the bird density profile */
    98  float elevMin; /* the minimum scan elevation [degrees] used for constructing the bird density profile */
    99  float elevMax; /* the maximum scan elevation [degrees] used for constructing the bird density profile */
    100  float radarWavelength; /* the default wavelength [cm] of the radar if it is not included in the metadata */
    101  int useClutterMap; /* whether a static clutter map is used */
    102  char clutterMap[1000]; /* path and filename of static cluttermap / beam occultation map to use */
    103  float clutterValueMin; /* positions in static clutter map with value above this value are excluded as clutter */
    104  int printOptions; /* print options to stderr */
    105  int printDbz; /* print dbz to stderr */
    106  int printDealias; /* print aliased and dealiased vrad pairs to stderr */
    107  int printVrad; /* print vrad to stderr */
    108  int printRhohv; /* print rhohv to stderr */
    109  int printCell; /* print cell to stderr */
    110  int printCellProp; /* print cell properties to stderr */
    111  int printTex; /* print texture to stderr */
    112  int printClut; /* print clutter to stderr */
    113  int printProfileVar; /* print profile data to stderr */
    114  int printPointsArray; /* whether or not to print the 'points' array */
    115  int fitVrad; /* Whether or not to fit a model to the observed vrad */
    116  int exportBirdProfileAsJSONVar; /* whether you want to export the vertical bird profile as JSON */
    117  float minNyquist; /* Minimum Nyquist velocity [m/s] to include a scan; */
    118  float maxNyquistDealias; /* When all scans (except those excluded by minNyquist) have nyquist velocity */
    119  /* higher than this value, dealiasing is suppressed; */
    120  float birdRadarCrossSection; /* Bird radar cross section [cm^2] */
    121  float etaMax; /* Maximum reflectivity factor of reflectivity gates containing birds */
    122  float cellEtaMin; /* Maximum mean reflectivity [cm^2/km^3] of cells of birds */
    123  float cellStdDevMax; /* When analyzing cells, only cells for which the stddev of vrad */
    124  /* (aka the texture) is less than cellStdDevMax are considered in the */
    125  /* rest of the analysis*/
    126  float stdDevMinBird; /* Minimum VVP radial velocity standard deviation for layer containing birds*/
    127  char dbzType[10]; /* Preferred dBZ quantity to use */
    128  int requireVrad; /* require range gates to have a valid radial velocity measurement */
    129  int dealiasVrad; /* dealias radial velocities using torus mapping method by Haase et al. */
    130  int dealiasRecycle; /* whether we should dealias once, or separately for each profile type */
    131  int dualPol; /* whether to use dual-polarization moments for filtering meteorological echoes */
    132  int singlePol; /* whether to use single-polarization moments for filtering meteorological echoes */
    133  float dbzThresMin; /* reflectivities above this threshold will be checked as potential precipitation */
    134  float rhohvThresMin; /* correlation coefficients above this threshold will be removed as precipitation */
    135  int resample; /* whether to resample the input polar volume */
    136  float resampleRscale; /* resampled range gate length in m */
    137  int resampleNbins; /* resampled number of range bins */
    138  int resampleNrays; /* resampled number of azimuth bins */
    139 };
    140 typedef struct vol2birdOptions vol2birdOptions_t;
    141 
    142 // ------------------------------------------------------------- //
    143 // vol2bird options from constants.h //
    144 // ------------------------------------------------------------- //
    145 
    146 struct vol2birdConstants {
    147  // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    148  // from the fitted value, since these are likely outliers
    149  float absVDifMax;
    150  // when analyzing cells, areaCellMin determines the minimum size of a
    151  // cell in km^2 to be considered in the rest of the analysis
    152  float areaCellMin;
    153  // cells with clutter fractions above this value are likely not birds
    154  float cellClutterFractionMax;
    155  // minimum standard deviation of the VVP fit
    156  float chisqMin;
    157  // threshold dbz value for excluding gates as clutter (static clutter only)
    158  float clutterValueMin;
    159  // maximum dbz used in calculation of profile dbzAvg
    160  float dbzMax;
    161  // minimum dbz for inclusion in a cell
    162  float dbzThresMin;
    163  // each weather cell identified by findWeatherCells() is grown by a distance
    164  // equal to 'fringeDist' using a region-growing approach
    165  float fringeDist;
    166  // the refractive index of water
    167  float refracIndex;
    168  // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    169  float vradMin;
    170  // when determining whether there are enough vrad observations in
    171  // each direction, use NBINSGAP sectors
    172  int nBinsGap;
    173  // when calculating the altitude-layer averaged dbz, there should
    174  // be at least NDBZMIN valid data points
    175  int nPointsIncludedMin;
    176  // the minimum number of direct neighbors with dbz value above
    177  // dbzThresMin as used in findWeatherCells()
    178  int nNeighborsMin;
    179  // there should be at least NOBSGAPMIN vrad observations in each
    180  // sector
    181  int nObsGapMin;
    182  // vrad's texture is calculated based on the local neighborhood. The
    183  // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    184  // static int nAzimNeighborhood;
    185  int nAzimNeighborhood;
    186  // vrad's texture is calculated based on the local neighborhood. The
    187  // neighborhood size in the range direction is equal to NTEXBINRANG
    188  // static int nRangNeighborhood;
    189  int nRangNeighborhood;
    190  // the minimum number of neighbors for the texture value to be
    191  // considered valid, as used in calcTexture()
    192  int nCountMin;
    193 };
    194 
    195 typedef struct vol2birdConstants vol2birdConstants_t;
    196 
    197 // ------------------------------------------------------------- //
    198 // information about the 'points' array //
    199 // ------------------------------------------------------------- //
    200 
    201 // The data needed for calculating bird densities are collected
    202 // in one big array, 'points'. Although this array is one
    203 // variable, it is partitioned into 'nLayers' parts. The parts
    204 // are not equal in size, therefore we need to keep track of
    205 // where the data pertaining to a certain altitude bin can be
    206 // written. The valid range of indexes into 'points' are stored
    207 // in arrays 'indexFrom' and 'indexTo'.
    208 
    209 struct vol2birdPoints {
    210  // the 'points' array has this many pseudo-columns
    211  int nColsPoints;
    212  // the 'points' array has this many rows
    213  int nRowsPoints;
    214  // the psuedo-column in 'points' that holds the azimuth angle
    215  int azimAngleCol;
    216  // the psuedo-column in 'points' that holds the elevation angle
    217  int elevAngleCol;
    218  // the psuedo-column in 'points' that holds the dbz value
    219  int dbzValueCol;
    220  // the psuedo-column in 'points' that holds the vrad value
    221  int vradValueCol;
    222  // the psuedo-column in 'points' that holds the cell value
    223  int cellValueCol;
    224  // the psuedo-column in 'points' that holds the gate classification code
    225  int gateCodeCol;
    226  // the psuedo-column in 'points' that holds the nyquist velocity
    227  int nyquistCol;
    228  // the psuedo-column in 'points' that holds the dealiased vrad value
    229  int vraddValueCol;
    230  // the psuedo-column in 'points' that holds the static clutter map value
    231  int clutValueCol;
    232  // the 'points' array itself
    233  float* points; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    234  // for a given altitude layer in the profile, only part of the 'points'
    235  // array is relevant. The 'indexFrom' and 'indexTo' arrays keep track
    236  // which rows in 'points' pertains to a given layer
    237  int* indexFrom; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    238  int* indexTo; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    239  // nPointsWritten stores the number of points that was copied from one
    240  // of the scan elevations to the 'points' array; it should therefore
    241  // never exceed indexTo[i]-indexFrom[i]
    242  int* nPointsWritten; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    243 };
    244 typedef struct vol2birdPoints vol2birdPoints_t;
    245 
    246 // ------------------------------------------------------------- //
    247 // information about the flagfields of 'gateCode' //
    248 // ------------------------------------------------------------- //
    249 
    250 struct vol2birdFlags {
    251  // the bit in 'gateCode' that says whether this gate is true in the static
    252  // clutter map (which we don't have yet TODO)
    253  int flagPositionStaticClutter;
    254  // the bit in 'gateCode' that says whether this gate is part of the
    255  // calculated cluttermap (without fringe)
    256  int flagPositionDynamicClutter;
    257  // the bit in 'gateCode' that says whether this gate is part of the
    258  // fringe of the calculated cluttermap
    259  int flagPositionDynamicClutterFringe;
    260  // the bit in 'gateCode' that says whether this gate has reflectivity data
    261  // but no corresponding radial velocity data
    262  int flagPositionVradMissing;
    263  // the bit in 'gateCode' the psuedo-columnsays whether this gate's dbz value is too
    264  // high to be due to birds, it must be caused by something else
    265  int flagPositionDbzTooHighForBirds;
    266  // the bit in 'gateCode' the psuedo-columnsays whether this gate's radial velocity is
    267  // close to zero. These gates are all discarded to exclude ground
    268  // clutter, which often has a radial velocity near zero.
    269  int flagPositionVradTooLow;
    270  // the bit in 'gateCode' that says whether this gate passed the VDIFMAX test
    271  int flagPositionVDifMax;
    272  // the bit in 'gateCode' that says whether the gate's azimuth angle was too low
    273  int flagPositionAzimTooLow;
    274  // the bit in 'gateCode' that says whether the gate's azimuth angle was too high
    275  int flagPositionAzimTooHigh;
    276 };
    277 typedef struct vol2birdFlags vol2birdFlags_t;
    278 
    279 // ------------------------------------------------------------- //
    280 // information about the 'profile' array //
    281 // ------------------------------------------------------------- //
    282 
    283 struct vol2birdProfiles {
    284  // the number of different types of profile we're making
    285  int nProfileTypes;
    286  // how many rows there are in a profile
    287  int nRowsProfile;
    288  // columns in profile contain
    289  // [altmin,altmax,u,v,w,hSpeed,hDir,chi,hasGap,dbzAvg,nPointsCopied,reflectivity,birdDensity]
    290  int nColsProfile;
    291  // the profile array itself
    292  float* profile; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    293  // these next 3 profile arrays are an ugly way to make sure
    294  // vol2birdGetProfile() can deliver its data
    295  float* profile1;
    296  float* profile2;
    297  float* profile3;
    298  // the type of profile that was last calculated
    299  int iProfileTypeLast;
    300 };
    301 typedef struct vol2birdProfiles vol2birdProfiles_t;
    302 
    303 // ------------------------------------------------------------- //
    304 // some other variables //
    305 // ------------------------------------------------------------- //
    306 
    307 struct vol2birdMisc {
    308  // rCellMax is defined as rangeMax + 5000.0f in order to avoid
    309  // edge effects when calculating the fringe
    310  float rCellMax;
    311  // the number of dimensions to describe the location of an echo
    312  // (azimuth and elevAngle) as used in the 'pointsSelection' array
    313  // that is passed to svdfit
    314  int nDims;
    315  // how many parameters are fitted by the svdfit procedure
    316  int nParsFitted;
    317  // the factor that is used when converting from Z to eta, calculated from radar wavelength
    318  float dbzFactor;
    319  //Maximum mean reflectivity factor of cells of birds (conversion of cellEtaMin)
    320  float cellDbzMin;
    321  //Maximum reflectivity factor of reflectivity factor gates containing birds (conversion of cellEtaMax)
    322  float dbzMax;
    323  // whether the vol2bird module has been initialized
    324  int initializationSuccessful;
    325  // whether vol2bird calculated a valid bird profile
    326  int vol2birdSuccessful;
    327  // number of scans used to calculate the profile
    328  int nScansUsed;
    329  // lowest Nyquist velocity of scans present
    330  double nyquistMin;
    331  // lowest Nyquist velocity of scans used
    332  double nyquistMinUsed;
    333  // highest Nyquist velocity of scans used
    334  double nyquistMax;
    335  // whether configuration was loaded successfully
    336  int loadConfigSuccessful;
    337  // during calculation of iProfileType == 3, use this array to store the
    338  // result of (chi < stdDevMinBird), such that it can be used later during
    339  // calculation of iProfileType == 1
    340  int* scatterersAreNotBirds; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    341  // this string contains all the user options and constants, for storage in ODIM task_args attribute
    342  char task_args[3000];
    343  // the polar volume input file name
    344  char filename_pvol[1000];
    345  // the vertical profile output file name
    346  char filename_vp[1000];
    347  // the volume coverage pattern of the polar volume input file (NEXRAD specific)
    348  int vcp;
    349 };
    350 typedef struct vol2birdMisc vol2birdMisc_t;
    351 
    352 // structure for storing scan properties
    353 struct vol2birdScanUse {
    354  // whether to use this scan in calculation of the profiles
    355  int useScan;
    356  // the reflectivity quantity used for this scan
    357  char dbzName[10];
    358  // the radial velocity quantity used for this scan
    359  char vradName[10];
    360  // the correlation coefficient quantity used for this scan
    361  char rhohvName[10];
    362  // the texture field quantity used for this scan
    363  char texName[10];
    364  // the raincell masking quantity used for this scan
    365  char cellName[10];
    366  // the static clutter map quantity used for this scan
    367  char clutName[10];
    368 };
    369 typedef struct vol2birdScanUse vol2birdScanUse_t;
    370 
    371 // root structure, containing all data
    372 struct vol2bird {
    373  vol2birdOptions_t options;
    374  vol2birdConstants_t constants;
    375  vol2birdPoints_t points;
    376  vol2birdFlags_t flags;
    377  vol2birdProfiles_t profiles;
    378  vol2birdMisc_t misc;
    379  VerticalProfile_t* vp;
    380  cfg_t* cfg;
    381 };
    382 typedef struct vol2bird vol2bird_t;
    383 
    384 // *****************************************************************************
    385 // Public function prototypes
    386 // *****************************************************************************
    387 
    388 void vol2birdCalcProfiles(vol2bird_t* alldata);
    389 
    390 float* vol2birdGetProfile(int iProfileType, vol2bird_t* alldata);
    391 
    392 PolarVolume_t* vol2birdGetVolume(char* filename, float rangeMax, int small);
    393 
    394 PolarVolume_t* PolarVolume_resample(PolarVolume_t* volume, double rscale_proj, long nbins_proj, long nrays_proj);
    395 
    396 PolarScanParam_t* PolarScanParam_project_on_scan(PolarScanParam_t* param, PolarScan_t* scan, double rscale);
    397 
    398 int vol2birdGetNColsProfile(vol2bird_t* alldata);
    399 
    400 int vol2birdGetNRowsProfile(vol2bird_t* alldata);
    401 
    402 int vol2birdLoadClutterMap(PolarVolume_t* volume, char* file, float rangeMax);
    403 
    404 void vol2birdPrintIndexArrays(vol2bird_t* alldata);
    405 
    406 void vol2birdPrintOptions(vol2bird_t* alldata);
    407 
    408 void vol2birdPrintPointsArray(vol2bird_t* alldata);
    409 
    410 void vol2birdPrintPointsArraySimple(vol2bird_t* alldata);
    411 
    412 int vol2birdLoadConfig(vol2bird_t* alldata);
    413 
    414 int vol2birdSetUp(PolarVolume_t* volume, vol2bird_t* alldata);
    415 
    416 void vol2birdTearDown(vol2bird_t* alldata);
    417 
    418 int mapDataToRave(PolarVolume_t* volume, vol2bird_t* alldata);
    419 
    420 float nanify(float value);
    421 
    422 int saveToODIM(RaveCoreObject* object, const char* filename);
    423 
    424 const char* libvol2bird_version();
    vol2birdProfiles
    Definition: libvol2bird.h:283
    +
    1 /*
    2  * Copyright 2015 Adriaan Dokter & Netherlands eScience Centre
    3  * If you want to use this software, please contact me at a.m.dokter@uva.nl
    4  *
    5  * This program calculates Vertical Profiles of Birds (VPBs) as described in
    6  *
    7  * Bird migration flight altitudes studied by a network of operational weather radars
    8  * Dokter A.M., Liechti F., Stark H., Delobbe L., Tabary P., Holleman I.
    9  * J. R. Soc. Interface, 8, 30–43, 2011
    10  * DOI: 10.1098/rsif.2010.0116
    11  *
    12  */
    13 
    14 #include <confuse.h>
    15 #include <polarvolume.h>
    16 #include <vertical_profile.h>
    17 
    18 // ****************************************************************************
    19 // Definition of standard parameters.
    20 // ****************************************************************************
    21 
    22 #define DEG2RAD (0.017453293) // Degrees to radians.
    23 #define RAD2DEG (57.29578) // Radians to degrees.
    24 
    25 // ****************************************************************************
    26 // Definition of general macros:
    27 // ****************************************************************************
    28 
    29 #define XABS(x) (((x) < 0) ? (-(x)) : (x))
    30 #define ROUND(x) (((x) > 0) ? (int)((x) + 0.5) : (int)((x)-0.5))
    31 #define SQUARE(x) ((x) * (x))
    32 
    33 // ****************************************************************************
    34 // Defined (default) parameters.
    35 // ****************************************************************************
    36 
    37 #ifndef PI
    38 #define PI (3.14159265358979323846)
    39 #endif
    40 
    41 #ifndef TRUE
    42 #define TRUE 1
    43 #endif
    44 
    45 #ifndef FALSE
    46 #define FALSE 0
    47 #endif
    48 
    49 // ****************************************************************************
    50 // Structure for containing SCAN metadata:
    51 // ****************************************************************************
    52 
    53 struct cellprop {
    54  int iRangOfMax;
    55  int iAzimOfMax;
    56  float dbzAvg;
    57  float texAvg;
    58  float cv;
    59  int nGates;
    60  int nGatesClutter;
    61  double area;
    62  float dbzMax;
    63  int index;
    64  int drop;
    65 };
    66 
    67 struct scanmeta {
    68  float heig; // Height of radar antenna in km.
    69  float elev; // Elevation of scan in deg.
    70  int nRang; // Number of range bins in scan.
    71  int nAzim; // Number of azimuth rays in scan.
    72  float rangeScale; // Size of range bins in scan in km.
    73  float azimScale; // Size of azimuth steps in scan in deg.
    74  float valueOffset; // Offset value of quantity contained by scan.
    75  float valueScale; // Scale of value of quantity contained by scan.
    76  float missing; // Missing value of quantity contained by scan.
    77  double nyquist; // Nyquist velocity of the scan
    78 };
    79 
    80 typedef struct cellprop CELLPROP;
    81 typedef struct scanmeta SCANMETA;
    82 
    83 // *****************************************************************************
    84 // Structures for internal use
    85 // *****************************************************************************
    86 
    87 // ------------------------------------------------------------- //
    88 // vol2bird options from options.conf //
    89 // ------------------------------------------------------------- //
    90 
    91 struct vol2birdOptions {
    92  int nLayers; /* the number of layers in an altitude profile */
    93  float layerThickness; /* the width/thickness of a layer [m] */
    94  float rangeMin; /* the minimum range [m] used for constructing the bird density profile */
    95  float rangeMax; /* the maximum range [m] used for constructing the bird density profile */
    96  float azimMin; /* the minimum azimuth [degrees] used for constructing the bird density profile */
    97  float azimMax; /* the maximum azimuth [degrees] used for constructing the bird density profile */
    98  float elevMin; /* the minimum scan elevation [degrees] used for constructing the bird density profile */
    99  float elevMax; /* the maximum scan elevation [degrees] used for constructing the bird density profile */
    100  float radarWavelength; /* the default wavelength [cm] of the radar if it is not included in the metadata */
    101  int useClutterMap; /* whether a static clutter map is used */
    102  char clutterMap[1000]; /* path and filename of static cluttermap / beam occultation map to use */
    103  float clutterValueMin; /* positions in static clutter map with value above this value are excluded as clutter */
    104  int printOptions; /* print options to stderr */
    105  int printDbz; /* print dbz to stderr */
    106  int printDealias; /* print aliased and dealiased vrad pairs to stderr */
    107  int printVrad; /* print vrad to stderr */
    108  int printRhohv; /* print rhohv to stderr */
    109  int printCell; /* print cell to stderr */
    110  int printCellProp; /* print cell properties to stderr */
    111  int printTex; /* print texture to stderr */
    112  int printClut; /* print clutter to stderr */
    113  int printProfileVar; /* print profile data to stderr */
    114  int printPointsArray; /* whether or not to print the 'points' array */
    115  int fitVrad; /* Whether or not to fit a model to the observed vrad */
    116  int exportBirdProfileAsJSONVar; /* whether you want to export the vertical bird profile as JSON */
    117  float minNyquist; /* Minimum Nyquist velocity [m/s] to include a scan; */
    118  float maxNyquistDealias; /* When all scans (except those excluded by minNyquist) have nyquist velocity */
    119  /* higher than this value, dealiasing is suppressed; */
    120  float birdRadarCrossSection; /* Bird radar cross section [cm^2] */
    121  float etaMax; /* Maximum reflectivity factor of reflectivity gates containing birds */
    122  float cellEtaMin; /* Maximum mean reflectivity [cm^2/km^3] of cells of birds */
    123  float cellStdDevMax; /* When analyzing cells, only cells for which the stddev of vrad */
    124  /* (aka the texture) is less than cellStdDevMax are considered in the */
    125  /* rest of the analysis*/
    126  float stdDevMinBird; /* Minimum VVP radial velocity standard deviation for layer containing birds*/
    127  char dbzType[10]; /* Preferred dBZ quantity to use */
    128  int requireVrad; /* require range gates to have a valid radial velocity measurement */
    129  int dealiasVrad; /* dealias radial velocities using torus mapping method by Haase et al. */
    130  int dealiasRecycle; /* whether we should dealias once, or separately for each profile type */
    131  int dualPol; /* whether to use dual-polarization moments for filtering meteorological echoes */
    132  int singlePol; /* whether to use single-polarization moments for filtering meteorological echoes */
    133  float dbzThresMin; /* reflectivities above this threshold will be checked as potential precipitation */
    134  float rhohvThresMin; /* correlation coefficients above this threshold will be removed as precipitation */
    135  int resample; /* whether to resample the input polar volume */
    136  float resampleRscale; /* resampled range gate length in m */
    137  int resampleNbins; /* resampled number of range bins */
    138  int resampleNrays; /* resampled number of azimuth bins */
    139 };
    140 typedef struct vol2birdOptions vol2birdOptions_t;
    141 
    142 // ------------------------------------------------------------- //
    143 // vol2bird options from constants.h //
    144 // ------------------------------------------------------------- //
    145 
    146 struct vol2birdConstants {
    147  // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    148  // from the fitted value, since these are likely outliers
    149  float absVDifMax;
    150  // when analyzing cells, areaCellMin determines the minimum size of a
    151  // cell in km^2 to be considered in the rest of the analysis
    152  float areaCellMin;
    153  // cells with clutter fractions above this value are likely not birds
    154  float cellClutterFractionMax;
    155  // minimum standard deviation of the VVP fit
    156  float chisqMin;
    157  // threshold dbz value for excluding gates as clutter (static clutter only)
    158  float clutterValueMin;
    159  // maximum dbz used in calculation of profile dbzAvg
    160  float dbzMax;
    161  // minimum dbz for inclusion in a cell
    162  float dbzThresMin;
    163  // each weather cell identified by findWeatherCells() is grown by a distance
    164  // equal to 'fringeDist' using a region-growing approach
    165  float fringeDist;
    166  // the refractive index of water
    167  float refracIndex;
    168  // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    169  float vradMin;
    170  // when determining whether there are enough vrad observations in
    171  // each direction, use NBINSGAP sectors
    172  int nBinsGap;
    173  // when calculating the altitude-layer averaged dbz, there should
    174  // be at least NDBZMIN valid data points
    175  int nPointsIncludedMin;
    176  // the minimum number of direct neighbors with dbz value above
    177  // dbzThresMin as used in findWeatherCells()
    178  int nNeighborsMin;
    179  // there should be at least NOBSGAPMIN vrad observations in each
    180  // sector
    181  int nObsGapMin;
    182  // vrad's texture is calculated based on the local neighborhood. The
    183  // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    184  // static int nAzimNeighborhood;
    185  int nAzimNeighborhood;
    186  // vrad's texture is calculated based on the local neighborhood. The
    187  // neighborhood size in the range direction is equal to NTEXBINRANG
    188  // static int nRangNeighborhood;
    189  int nRangNeighborhood;
    190  // the minimum number of neighbors for the texture value to be
    191  // considered valid, as used in calcTexture()
    192  int nCountMin;
    193 };
    194 
    195 typedef struct vol2birdConstants vol2birdConstants_t;
    196 
    197 // ------------------------------------------------------------- //
    198 // information about the 'points' array //
    199 // ------------------------------------------------------------- //
    200 
    201 // The data needed for calculating bird densities are collected
    202 // in one big array, 'points'. Although this array is one
    203 // variable, it is partitioned into 'nLayers' parts. The parts
    204 // are not equal in size, therefore we need to keep track of
    205 // where the data pertaining to a certain altitude bin can be
    206 // written. The valid range of indexes into 'points' are stored
    207 // in arrays 'indexFrom' and 'indexTo'.
    208 
    209 struct vol2birdPoints {
    210  // the 'points' array has this many pseudo-columns
    211  int nColsPoints;
    212  // the 'points' array has this many rows
    213  int nRowsPoints;
    214  // the psuedo-column in 'points' that holds the azimuth angle
    215  int azimAngleCol;
    216  // the psuedo-column in 'points' that holds the elevation angle
    217  int elevAngleCol;
    218  // the psuedo-column in 'points' that holds the dbz value
    219  int dbzValueCol;
    220  // the psuedo-column in 'points' that holds the vrad value
    221  int vradValueCol;
    222  // the psuedo-column in 'points' that holds the cell value
    223  int cellValueCol;
    224  // the psuedo-column in 'points' that holds the gate classification code
    225  int gateCodeCol;
    226  // the psuedo-column in 'points' that holds the nyquist velocity
    227  int nyquistCol;
    228  // the psuedo-column in 'points' that holds the dealiased vrad value
    229  int vraddValueCol;
    230  // the psuedo-column in 'points' that holds the static clutter map value
    231  int clutValueCol;
    232  // the 'points' array itself
    233  float* points; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    234  // for a given altitude layer in the profile, only part of the 'points'
    235  // array is relevant. The 'indexFrom' and 'indexTo' arrays keep track
    236  // which rows in 'points' pertains to a given layer
    237  int* indexFrom; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    238  int* indexTo; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    239  // nPointsWritten stores the number of points that was copied from one
    240  // of the scan elevations to the 'points' array; it should therefore
    241  // never exceed indexTo[i]-indexFrom[i]
    242  int* nPointsWritten; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    243 };
    244 typedef struct vol2birdPoints vol2birdPoints_t;
    245 
    246 // ------------------------------------------------------------- //
    247 // information about the flagfields of 'gateCode' //
    248 // ------------------------------------------------------------- //
    249 
    250 struct vol2birdFlags {
    251  // the bit in 'gateCode' that says whether this gate is true in the static
    252  // clutter map (which we don't have yet TODO)
    253  int flagPositionStaticClutter;
    254  // the bit in 'gateCode' that says whether this gate is part of the
    255  // calculated cluttermap (without fringe)
    256  int flagPositionDynamicClutter;
    257  // the bit in 'gateCode' that says whether this gate is part of the
    258  // fringe of the calculated cluttermap
    259  int flagPositionDynamicClutterFringe;
    260  // the bit in 'gateCode' that says whether this gate has reflectivity data
    261  // but no corresponding radial velocity data
    262  int flagPositionVradMissing;
    263  // the bit in 'gateCode' the psuedo-columnsays whether this gate's dbz value is too
    264  // high to be due to birds, it must be caused by something else
    265  int flagPositionDbzTooHighForBirds;
    266  // the bit in 'gateCode' the psuedo-columnsays whether this gate's radial velocity is
    267  // close to zero. These gates are all discarded to exclude ground
    268  // clutter, which often has a radial velocity near zero.
    269  int flagPositionVradTooLow;
    270  // the bit in 'gateCode' that says whether this gate passed the VDIFMAX test
    271  int flagPositionVDifMax;
    272  // the bit in 'gateCode' that says whether the gate's azimuth angle was too low
    273  int flagPositionAzimTooLow;
    274  // the bit in 'gateCode' that says whether the gate's azimuth angle was too high
    275  int flagPositionAzimTooHigh;
    276 };
    277 typedef struct vol2birdFlags vol2birdFlags_t;
    278 
    279 // ------------------------------------------------------------- //
    280 // information about the 'profile' array //
    281 // ------------------------------------------------------------- //
    282 
    283 struct vol2birdProfiles {
    284  // the number of different types of profile we're making
    285  int nProfileTypes;
    286  // how many rows there are in a profile
    287  int nRowsProfile;
    288  // columns in profile contain
    289  // [altmin,altmax,u,v,w,hSpeed,hDir,chi,hasGap,dbzAvg,nPointsCopied,reflectivity,birdDensity]
    290  int nColsProfile;
    291  // the profile array itself
    292  float* profile; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    293  // these next 3 profile arrays are an ugly way to make sure
    294  // vol2birdGetProfile() can deliver its data
    295  float* profile1;
    296  float* profile2;
    297  float* profile3;
    298  // the type of profile that was last calculated
    299  int iProfileTypeLast;
    300 };
    301 typedef struct vol2birdProfiles vol2birdProfiles_t;
    302 
    303 // ------------------------------------------------------------- //
    304 // some other variables //
    305 // ------------------------------------------------------------- //
    306 
    307 struct vol2birdMisc {
    308  // rCellMax is defined as rangeMax + 5000.0f in order to avoid
    309  // edge effects when calculating the fringe
    310  float rCellMax;
    311  // the number of dimensions to describe the location of an echo
    312  // (azimuth and elevAngle) as used in the 'pointsSelection' array
    313  // that is passed to svdfit
    314  int nDims;
    315  // how many parameters are fitted by the svdfit procedure
    316  int nParsFitted;
    317  // the factor that is used when converting from Z to eta, calculated from radar wavelength
    318  float dbzFactor;
    319  //Maximum mean reflectivity factor of cells of birds (conversion of cellEtaMin)
    320  float cellDbzMin;
    321  //Maximum reflectivity factor of reflectivity factor gates containing birds (conversion of cellEtaMax)
    322  float dbzMax;
    323  // whether the vol2bird module has been initialized
    324  int initializationSuccessful;
    325  // whether vol2bird calculated a valid bird profile
    326  int vol2birdSuccessful;
    327  // number of scans used to calculate the profile
    328  int nScansUsed;
    329  // lowest Nyquist velocity of scans present
    330  double nyquistMin;
    331  // lowest Nyquist velocity of scans used
    332  double nyquistMinUsed;
    333  // highest Nyquist velocity of scans used
    334  double nyquistMax;
    335  // whether configuration was loaded successfully
    336  int loadConfigSuccessful;
    337  // during calculation of iProfileType == 3, use this array to store the
    338  // result of (chi < stdDevMinBird), such that it can be used later during
    339  // calculation of iProfileType == 1
    340  int* scatterersAreNotBirds; // Is allocated in vol2birdSetUp() and freed in vol2birdTearDown()
    341  // this string contains all the user options and constants, for storage in ODIM task_args attribute
    342  char task_args[3000];
    343  // the polar volume input file name
    344  char filename_pvol[1000];
    345  // the vertical profile output file name
    346  char filename_vp[1000];
    347  // the volume coverage pattern of the polar volume input file (NEXRAD specific)
    348  int vcp;
    349 };
    350 typedef struct vol2birdMisc vol2birdMisc_t;
    351 
    352 // structure for storing scan properties
    353 struct vol2birdScanUse {
    354  // whether to use this scan in calculation of the profiles
    355  int useScan;
    356  // the reflectivity quantity used for this scan
    357  char dbzName[10];
    358  // the radial velocity quantity used for this scan
    359  char vradName[10];
    360  // the correlation coefficient quantity used for this scan
    361  char rhohvName[10];
    362  // the texture field quantity used for this scan
    363  char texName[10];
    364  // the raincell masking quantity used for this scan
    365  char cellName[10];
    366  // the static clutter map quantity used for this scan
    367  char clutName[10];
    368 };
    369 typedef struct vol2birdScanUse vol2birdScanUse_t;
    370 
    371 // root structure, containing all data
    372 struct vol2bird {
    373  vol2birdOptions_t options;
    374  vol2birdConstants_t constants;
    375  vol2birdPoints_t points;
    376  vol2birdFlags_t flags;
    377  vol2birdProfiles_t profiles;
    378  vol2birdMisc_t misc;
    379  VerticalProfile_t* vp;
    380  cfg_t* cfg;
    381 };
    382 typedef struct vol2bird vol2bird_t;
    383 
    384 typedef enum radarDataFormat {
    385  radarDataFormat_UNKNOWN = 0,
    386  radarDataFormat_ODIM = 1,
    387  radarDataFormat_RSL = 2,
    388  radarDataFormat_IRIS = 3
    389 } radarDataFormat;
    390 
    391 
    392 // *****************************************************************************
    393 // Public function prototypes
    394 // *****************************************************************************
    395 
    396 radarDataFormat determineRadarFormat(char* filename);
    397 
    398 int isRegularFile(const char *path);
    399 
    400 void vol2birdCalcProfiles(vol2bird_t* alldata);
    401 
    402 float* vol2birdGetProfile(int iProfileType, vol2bird_t* alldata);
    403 
    404 PolarVolume_t* vol2birdGetVolume(char* filenames[], int nInputFiles, float rangeMax, int small);
    405 
    406 PolarVolume_t* PolarVolume_resample(PolarVolume_t* volume, double rscale_proj, long nbins_proj, long nrays_proj);
    407 
    408 PolarScanParam_t* PolarScanParam_project_on_scan(PolarScanParam_t* param, PolarScan_t* scan, double rscale);
    409 
    410 int vol2birdGetNColsProfile(vol2bird_t* alldata);
    411 
    412 int vol2birdGetNRowsProfile(vol2bird_t* alldata);
    413 
    414 int vol2birdLoadClutterMap(PolarVolume_t* volume, char* file, float rangeMax);
    415 
    416 void vol2birdPrintIndexArrays(vol2bird_t* alldata);
    417 
    418 void vol2birdPrintOptions(vol2bird_t* alldata);
    419 
    420 void vol2birdPrintPointsArray(vol2bird_t* alldata);
    421 
    422 void vol2birdPrintPointsArraySimple(vol2bird_t* alldata);
    423 
    424 int vol2birdLoadConfig(vol2bird_t* alldata);
    425 
    426 int vol2birdSetUp(PolarVolume_t* volume, vol2bird_t* alldata);
    427 
    428 void vol2birdTearDown(vol2bird_t* alldata);
    429 
    430 int mapDataToRave(PolarVolume_t* volume, vol2bird_t* alldata);
    431 
    432 float nanify(float value);
    433 
    434 int saveToODIM(RaveCoreObject* object, const char* filename);
    435 
    436 const char* libvol2bird_version(void);
    vol2birdProfiles
    Definition: libvol2bird.h:283
    +
    isRegularFile
    int isRegularFile(const char *path)
    Function name: isRegularFile Intent: determines whether the given path is to a regular file Note: als...
    Definition: libvol2bird.c:2654
    vol2bird
    Definition: libvol2bird.h:372
    vol2birdConstants
    Definition: libvol2bird.h:146
    vol2birdMisc
    Definition: libvol2bird.h:307
    diff --git a/docs/menudata.js b/docs/menudata.js index 2cbab142..9e07629b 100644 --- a/docs/menudata.js +++ b/docs/menudata.js @@ -27,4 +27,7 @@ var menudata={children:[ {text:"Classes",url:"annotated.html",children:[ {text:"Class List",url:"annotated.html"}]}, {text:"Files",url:"files.html",children:[ -{text:"File List",url:"files.html"}]}]} +{text:"File List",url:"files.html"}, +{text:"File Members",url:"globals.html",children:[ +{text:"All",url:"globals.html"}, +{text:"Functions",url:"globals_func.html"}]}]}]} diff --git a/docs/vol2bird_8c.html b/docs/vol2bird_8c.html index b9b40ce9..2a791c63 100644 --- a/docs/vol2bird_8c.html +++ b/docs/vol2bird_8c.html @@ -53,6 +53,8 @@ More...

    #include <stdio.h>
    #include <time.h>
    +#include <getopt.h>
    +#include <string.h>
    #include "rave_io.h"
    #include "polarvolume.h"
    #include "libvol2bird.h"
    @@ -63,6 +65,9 @@
    + + diff --git a/src/rsl2odim.c b/src/rsl2odim.c index f5745103..a05d9e5a 100644 --- a/src/rsl2odim.c +++ b/src/rsl2odim.c @@ -6,35 +6,175 @@ #include #include +#include #include "rave_io.h" #include "polarvolume.h" #include "libvol2bird.h" +#include "constants.h" + +void usage(char* programName, int verbose){ + fprintf(stderr,"usage: %s \n",programName); + fprintf(stderr,"usage: %s -i [-i [-i ] ...] -o \n",programName); + fprintf(stderr,"usage: %s --help\n", programName); + + if (verbose){ + fprintf(stderr,"\n Expects input formats compatible with RSL, see \n"); + fprintf(stderr," or Vaisala Sigmet IRIS format, see \n"); + fprintf(stderr," Outputs OPERA ODIM hdf5 input format, see \n"); + } +} int main(int argc, char** argv) { // cfg_t* cfg; // print default message when no input arguments if (argc == 1) { - fprintf(stderr,"usage: %s \n",argv[0]); - fprintf(stderr," expects input formats compatible with RSL, see \n"); - fprintf(stderr," outputs OPERA ODIM hdf5 input format, see \n"); - return -1; - } - // check to see if we have the right number of input arguments - if (argc != 3) { - fprintf(stderr, "Error: two arguments required: RSL volume in, and ODIM volume out\n"); + usage(argv[0], 0); return -1; } + // number of input files specified on command line + int nInputFiles = 0; // the polar volume file that the user provided as input - char* fileVolIn = argv[1]; - // the volume file that the user specified as output - const char* fileVolOut = argv[2]; + char* fileIn[INPUTFILESMAX]; + // the (optional) vertical profile file that the user specified as output + const char* fileVolOut = NULL; + + // determine whether we deal with legacy command line format (0) or getopt command line format (1) + int commandLineFormat = 0; + for (int i=0; i Date: Fri, 12 Apr 2019 12:42:22 +0200 Subject: [PATCH 31/37] fix issue #123 --- lib/libvol2bird.c | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 5d3b69cf..2fc7f463 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -3784,6 +3784,13 @@ void vol2birdCalcProfiles(vol2bird_t* alldata) { else { birdDensity = UNDETECT; } + + // birdDensity and reflectivity should also be UNDETECT when undbzAvg is + if (undbzAvg == UNDETECT){ + reflectivity = UNDETECT + birdDensity = UNDETECT + } + //Prepare the arguments of svdfit iPointIncluded = 0; From 7a7bcf28ca8029f26b715536cd6fdce0b25aa938 Mon Sep 17 00:00:00 2001 From: adokter Date: Fri, 12 Apr 2019 12:44:32 +0200 Subject: [PATCH 32/37] fix issue #123 continued --- lib/libvol2bird.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/libvol2bird.c b/lib/libvol2bird.c index 2fc7f463..1bcc0426 100644 --- a/lib/libvol2bird.c +++ b/lib/libvol2bird.c @@ -3787,8 +3787,8 @@ void vol2birdCalcProfiles(vol2bird_t* alldata) { // birdDensity and reflectivity should also be UNDETECT when undbzAvg is if (undbzAvg == UNDETECT){ - reflectivity = UNDETECT - birdDensity = UNDETECT + reflectivity = UNDETECT; + birdDensity = UNDETECT; } From 96112d029dbd8787af1b0b7c24e4df0e3008ae28 Mon Sep 17 00:00:00 2001 From: adokter Date: Fri, 12 Apr 2019 15:26:17 +0200 Subject: [PATCH 33/37] remove % symbol --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 4fa061a8..516982c7 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ ## Vertical profiling of biological scatterers -**%vol2bird** is an algorithm that calculates vertical profiles of birds and other biological scatterers from weather radar data. **%vol2bird** is written in C. +**vol2bird** is an algorithm that calculates vertical profiles of birds and other biological scatterers from weather radar data. **vol2bird** is written in C. See this publications for a description of the methodology: @@ -24,13 +24,13 @@ Report a bug at: * `data` contains two polar volume radar files for testing * `doc` documentation on ODIM hdf5 data format * `docs` html pages of this documentation -* `docker` scripts for generating and running a Docker container for %vol2bird +* `docker` scripts for generating and running a Docker container for vol2bird * `doxygen` doxygen configuration for generating this documentation -* `etc` contains the user configuration file `options.conf`. Put your own modified copy in your working directory to run %vol2bird with non-default settings. +* `etc` contains the user configuration file `options.conf`. Put your own modified copy in your working directory to run vol2bird with non-default settings. * `lib` contains the main library * `pgfplugin` product generation framework (PGF) plugin for the BALTRAD system * `pyvol2bird` is a python wrapper for the library -* `src` contains main executables for %vol2bird (main program) and rsl2odim (converts NEXRAD to ODIM data format) +* `src` contains main executables for vol2bird (main program) and rsl2odim (converts NEXRAD to ODIM data format) * `tests` unit tests for pgfplugin Copyright 2010-2018 Adriaan M. Dokter (University of Amsterdam, Cornell lab of ornithology) & Netherlands eScience Centre From 0dbcc0756bb340ee08ccc8c341a973bd518df6e6 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 22 Apr 2019 22:35:40 -0400 Subject: [PATCH 34/37] fix issue #117 --- etc/options.conf | 2 +- src/rsl2odim.c | 2 +- src/vol2bird.c | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/etc/options.conf b/etc/options.conf index 225ab4ee..efe65a8a 100644 --- a/etc/options.conf +++ b/etc/options.conf @@ -9,7 +9,7 @@ HLAYER = 200.0 RANGEMIN = 5000.0 # the maximum range [m] used for constructing the bird density profile -RANGEMAX = 25000.0 +RANGEMAX = 35000.0 # the minimum azimuth [degrees] used for constructing the bird density profile AZIMMIN = 0.0 diff --git a/src/rsl2odim.c b/src/rsl2odim.c index a05d9e5a..00a2753b 100644 --- a/src/rsl2odim.c +++ b/src/rsl2odim.c @@ -116,7 +116,7 @@ int main(int argc, char** argv) { break; case 'v': - fprintf(stderr,"%s version %s (%s)\n", argv[0], VERSION, VERSIONDATE); + fprintf(stdout,"%s version %s (%s)\n", argv[0], VERSION, VERSIONDATE); return -1; break; diff --git a/src/vol2bird.c b/src/vol2bird.c index fd2fd050..0c9e0243 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -187,7 +187,7 @@ int main(int argc, char** argv) { break; case 'v': - fprintf(stderr,"%s version %s (%s)\n", argv[0], VERSION, VERSIONDATE); + fprintf(stdout,"%s version %s (%s)\n", argv[0], VERSION, VERSIONDATE); return -1; break; From 8ecd3f30d53d8559598049b2d63e79d7718cadb6 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 22 Apr 2019 23:44:14 -0400 Subject: [PATCH 35/37] bump version, add release notes, usage message typo correction --- NEWS.md | 16 +++++++++++++++- lib/constants.h | 4 ++-- src/vol2bird.c | 2 +- 3 files changed, 18 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index 5ff349ef..a0d7b348 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,10 +2,24 @@ All issues included in this release can be found [here](https://github.com/adokter/vol2bird/milestone/2?closed=1). -* added Vaisala Sigmet IRIS support, a widely used weather radar data format (e.g. in Canada) (#112) +* vol2bird now reads Vaisala Sigmet IRIS (Iris RAW) format, the native radar data format of Vaisala radar processors (e.g. used in Canada, Portugal, Finland) (#112) * added functionality to read files containing single scans (sweeps) and merge them into polar volumes (#116) +* rsl2odim now also converts Vaisala IRIS format and ODIM hdf5 format and can merge files containing scans / sweeps into a polar volume. + +* new input argument format that generalizes to multiple input files + +* change default maximum range to 35 km (#117) + +* fixed a bug that in rare cases produced a negative reflectivity eta (#123) + +* new determineRadarFormat() function to check whether a file is in ODIM, IRIS or RSL format + +* added a documentation webpage gnerated by doxygen (available at http://adokter.github.io/vol2bird) + +* added this NEWS.md file to document releases + # vol2bird 0.3.20 and older All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/3?closed=1). diff --git a/lib/constants.h b/lib/constants.h index 460b5b75..e1d786fb 100644 --- a/lib/constants.h +++ b/lib/constants.h @@ -98,9 +98,9 @@ // Name of the program, to be stored as task attribute in ODIM #define PROGRAM "vol2bird" // Version of the program, to be stored as task_version attribute in ODIM -#define VERSION "0.3.20" +#define VERSION "0.4.0" // Date of latest version of the program -#define VERSIONDATE "24-Oct-2018" +#define VERSIONDATE "23-Apr-2019" //-------------------------------------------------------// // user options defaults (to be set in options.conf) // diff --git a/src/vol2bird.c b/src/vol2bird.c index 0c9e0243..0c271125 100644 --- a/src/vol2bird.c +++ b/src/vol2bird.c @@ -43,7 +43,7 @@ void usage(char* programName, int verbose){ fprintf(stderr,"vol2bird version %s (%s)\n", VERSION, VERSIONDATE); fprintf(stderr," usage: %s [ []]\n",programName); - fprintf(stderr," usage: %s -i [-i [-i ] ...] [-o [-p ]]\n",programName); + fprintf(stderr," usage: %s -i [-i [-i ] ...] [-o ] [-p ]\n",programName); fprintf(stderr," usage: %s --help\n", programName); if(verbose){ From d1a71777ce3c6f4b3447eaa583c8141a52c15ee0 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 22 Apr 2019 23:46:14 -0400 Subject: [PATCH 36/37] ran doxygen --- docs/constants_8h_source.html | 2 +- docs/index.html | 14 ++++---------- docs/rsl2odim_8c.html | 5 +++++ 3 files changed, 10 insertions(+), 11 deletions(-) diff --git a/docs/constants_8h_source.html b/docs/constants_8h_source.html index c4e5da48..a1535ae7 100644 --- a/docs/constants_8h_source.html +++ b/docs/constants_8h_source.html @@ -46,7 +46,7 @@
    constants.h
    -
    1 //-------------------------------------------------------------//
    2 // hard-coded constants assigned to vol2birdConstants struct //
    3 //-------------------------------------------------------------//
    4 
    5 #include <float.h>
    6 
    7 // when analyzing cells, AREACELL determines the minimum size of a
    8 // cell to be considered in the rest of the analysis [km^2]
    9 #define AREACELL 0.5
    10 // minimum standard deviation of the fit
    11 #define CHISQMIN 1e-5
    12 // cells with clutter fractions above this value are likely not birds
    13 #define CLUTPERCCELL 0.5
    14 // threshold value (on the external static clutter map!) above which gates are excluded as clutter
    15 #define CLUTTERVALUEMIN 0.1
    16 // each weather cell identified by findWeatherCells() is grown by a distance
    17 // equal to 'fringeDist' using a region-growing approach
    18 #define FRINGEDIST 5000.0
    19 // when determining whether there are enough vrad observations in
    20 // each direction, use NBINSGAP sectors
    21 #define NBINSGAP 8
    22 // there should be at least NOBSGAPMIN vrad observations in each sector
    23 #define NOBSGAPMIN 5
    24 // when calculating the altitude-layer averaged dbz, there should
    25 // be at least NDBZMIN valid data points
    26 #define NDBZMIN 25
    27 // the minimum number of direct neighbors with dbz value above
    28 // dbzThresMin as used in findWeatherCells()
    29 #define NEIGHBORS 5
    30 // vrad's texture is calculated based on the local neighborhood. The
    31 // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    32 // static int nAzimNeighborhood;
    33 #define NTEXBINAZIM 3
    34 // vrad's texture is calculated based on the local neighborhood. The
    35 // neighborhood size in the range direction is equal to NTEXBINRANG
    36 // static int nRangNeighborhood;
    37 #define NTEXBINRANG 3
    38 // the minimum number of neighbors for the texture value to be
    39 // considered valid, as used in calcTexture()
    40 #define NTEXMIN 4
    41 // the refractive index of water
    42 #define REFRACTIVE_INDEX_OF_WATER 0.964
    43 // range gates up to a distance of RANGE_MAX+RCELLMAX_OFFSET are read into memory
    44 // the extra offset allows for the raincell search to extend somewhat further
    45 // than the maximum range used in the profile generation (RANGE_MAX).
    46 #define RCELLMAX_OFFSET 5000.0f
    47 // smallest range bin size to accept in metres
    48 #define RSCALEMIN 10
    49 // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    50 // from the fitted value, since these are likely outliers
    51 #define VDIFMAX 10.0
    52 // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    53 #define VRADMIN 1.0
    54 
    55 
    56 //-------------------------------------------------------//
    57 // hard-coded options for use RSL library //
    58 //-------------------------------------------------------//
    59 
    60 #ifdef RSL
    61 // By how much the elevation angle of sweeps of different quantities
    62 // is allowed to differ for them to be included into the same scan object.
    63 // Applies to data read with the RSL library only
    64 #define ELEVTOL 0.3
    65 // Offsets and gains for encoding reflectivity, velocity
    66 // and correlation coefficient
    67 // Once encoded values should be positive for storage in RAVE objects
    68 // Used with data read by the RSL library only
    69 #define RSL_OFFSET_DBZ 0
    70 #define RSL_GAIN_DBZ 1
    71 #define RSL_OFFSET_VRAD 0
    72 #define RSL_GAIN_VRAD 1
    73 #define RSL_OFFSET_RHOHV 0
    74 #define RSL_GAIN_RHOHV 1
    75 // Encoded values reserved for nodata and undetects.
    76 // Should be positive integers larger than zero
    77 #define RSL_NODATA -1000
    78 #define RSL_UNDETECT -999
    79 #endif
    80 
    81 //-------------------------------------------------------//
    82 // other hard-coded options //
    83 //-------------------------------------------------------//
    84 
    85 // maximum number of input files
    86 #define INPUTFILESMAX 50
    87 // Raw value used for gates or layers void of data (never ra-diated)
    88 #define UNDETECT -999
    89 // Raw value used for gates or layers when below the measurement detection threshold
    90 // or when information could not be retrieved (radiated but nothing detected or calculated)
    91 #define NODATA -1000
    92 // name under which the calculated texture quantity will be stored
    93 #define TEXNAME "VTEX"
    94 // name under which the calculated raincell masking quantity will be stored
    95 #define CELLNAME "CELL"
    96 // name of the parameter containing the static cluttermap
    97 #define CLUTNAME "OCCULT"
    98 // Name of the program, to be stored as task attribute in ODIM
    99 #define PROGRAM "vol2bird"
    100 // Version of the program, to be stored as task_version attribute in ODIM
    101 #define VERSION "0.3.20"
    102 // Date of latest version of the program
    103 #define VERSIONDATE "24-Oct-2018"
    104 
    105 //-------------------------------------------------------//
    106 // user options defaults (to be set in options.conf) //
    107 //-------------------------------------------------------//
    108 
    109 // the number of layers in an altitude profile
    110 #define NLAYER 25
    111 // the width/thickness of a layer [m]
    112 #define HLAYER 200.0f
    113 // the minimum range [m] used for constructing the bird density profile
    114 #define RANGEMIN 5000.0f
    115 // the maximum range [m] used for constructing the bird density profile
    116 #define RANGEMAX 25000.0f
    117 // the minimum azimuth [degrees] used for constructing the bird density profile
    118 #define AZIMMIN 0.0f
    119 // the maximum range [degrees] used for constructing the bird density profile
    120 #define AZIMMAX 360.0f
    121 // the minimum scan elevation [degrees] used for constructing the bird density profile
    122 #define ELEVMIN 0.0f
    123 // the maximum scan elevation used for constructing the bird density profile
    124 #define ELEVMAX 90.0f
    125 // the wavelength [cm] of the radar
    126 #define RADAR_WAVELENGTH_CM 5.3f
    127 // whether a static clutter map is used
    128 #define USE_CLUTTERMAP 0
    129 // clutter map path and filename
    130 #define CLUTTERMAP ""
    131 // print options to stderr
    132 #define PRINT_OPTIONS 0
    133 // name of (optional) environmental variable containing path to user configuration file
    134 #define OPTIONS_CONF "OPTIONS_CONF"
    135 // default user configuration file name to search for in working directory
    136 #define OPTIONS_FILE "options.conf"
    137 // FIXME: add description
    138 #define VERBOSE_OUTPUT_REQUIRED 0
    139 // print dbz to stderr
    140 #define PRINT_DBZ 0
    141 // print aliased and dealiased vrad pairs to stderr
    142 #define PRINT_DEALIAS 0
    143 // print vrad to stderr
    144 #define PRINT_VRAD 0
    145 // print rhohv to stderr
    146 #define PRINT_RHOHV 0
    147 // print cell to stderr
    148 #define PRINT_CELL 0
    149 // print cell properties to stderr
    150 #define PRINT_CELL_PROP 0
    151 // print texture to stderr
    152 #define PRINT_TEXTURE 0
    153 // print clutter to stderr
    154 #define PRINT_CLUT 0
    155 // print profile data to stderr
    156 #define PRINT_PROFILE 0
    157 // whether or not to print the 'points' array
    158 #define PRINT_POINTS_ARRAY 0
    159 // Whether or not to fit a model to the observed vrad
    160 #define FIT_VRAD 1
    161 // Whether to export bird profile as JSON
    162 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    163 // Scans with Nyquist velocity lower than this value are excluded
    164 #define MIN_NYQUIST_VELOCITY 5.0f
    165 // When all scans have nyquist velocity higher than this value, dealiasing is suppressed
    166 #define MAX_NYQUIST_DEALIAS 25.0f
    167 // when analyzing cells, only cells for which the stddev of vrad
    168 // (aka the texture) is less than cellStdDevMax are considered in the
    169 // rest of the analysis
    170 #define STDEV_CELL 5.0f
    171 // VVP Radial velocity standard deviation threshold
    172 #define STDEV_BIRD 2.0f
    173 // Bird radar cross section [cm^2]
    174 #define SIGMA_BIRD 11.0f
    175 // Maximum mean reflectivity [cm^2/km^3] for cells containing birds
    176 #define ETACELL 11500.0f
    177 // Maximum reflectivity [cm^2/km^3] for single gates containing birds
    178 #define ETAMAX 36000.0f
    179 // minimum dbz of a gate to be considered for inclusion in a weather cell
    180 #define DBZMIN 0.0
    181 // reflectivity quantity to use, one of "DBZH", "DBZV", "TH", "TV"
    182 #define DBZTYPE "DBZH"
    183 // for a range gate to contribute it should have a valid radial velocity
    184 #define REQUIRE_VRAD 0
    185 // whether we should dealias the radial velocities
    186 #define DEALIAS_VRAD 1
    187 // whether we should dealias all data once (default), or dealias for each profile individually
    188 #define DEALIAS_RECYCLE 1
    189 // Test dealiasing field velocities up to VMAX m/s
    190 #define DEALIAS_VMAX 50.0
    191 // Test field velocities increase in steps VMAX/VAF
    192 #define DEALIAS_VAF 15.0
    193 // Test field directions increase by 360/NF degrees
    194 #define DEALIAS_NF 12.0
    195 // whether you want to export the vertical bird profile as JSON
    196 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    197 // whether to use dual-pol moments for filtering meteorological echoes
    198 #define DUALPOL 1
    199 // whether to use single-pol moments for filtering meteorological echoes
    200 #define SINGLEPOL 1
    201 // correlation coefficients higher than this threshold will be classified as precipitation
    202 #define RHOHVMIN 0.95f
    203 // whether to resample the input polar volume
    204 #define RESAMPLE 0
    205 // resampled range gate length in m
    206 #define RESAMPLE_RSCALE 500.0f
    207 // resampled number of range bins
    208 #define RESAMPLE_NBINS 100
    209 // resampled number of azimuth bins
    210 #define RESAMPLE_NRAYS 360
    +
    1 //-------------------------------------------------------------//
    2 // hard-coded constants assigned to vol2birdConstants struct //
    3 //-------------------------------------------------------------//
    4 
    5 #include <float.h>
    6 
    7 // when analyzing cells, AREACELL determines the minimum size of a
    8 // cell to be considered in the rest of the analysis [km^2]
    9 #define AREACELL 0.5
    10 // minimum standard deviation of the fit
    11 #define CHISQMIN 1e-5
    12 // cells with clutter fractions above this value are likely not birds
    13 #define CLUTPERCCELL 0.5
    14 // threshold value (on the external static clutter map!) above which gates are excluded as clutter
    15 #define CLUTTERVALUEMIN 0.1
    16 // each weather cell identified by findWeatherCells() is grown by a distance
    17 // equal to 'fringeDist' using a region-growing approach
    18 #define FRINGEDIST 5000.0
    19 // when determining whether there are enough vrad observations in
    20 // each direction, use NBINSGAP sectors
    21 #define NBINSGAP 8
    22 // there should be at least NOBSGAPMIN vrad observations in each sector
    23 #define NOBSGAPMIN 5
    24 // when calculating the altitude-layer averaged dbz, there should
    25 // be at least NDBZMIN valid data points
    26 #define NDBZMIN 25
    27 // the minimum number of direct neighbors with dbz value above
    28 // dbzThresMin as used in findWeatherCells()
    29 #define NEIGHBORS 5
    30 // vrad's texture is calculated based on the local neighborhood. The
    31 // neighborhood size in the azimuth direction is equal to NTEXBINAZIM
    32 // static int nAzimNeighborhood;
    33 #define NTEXBINAZIM 3
    34 // vrad's texture is calculated based on the local neighborhood. The
    35 // neighborhood size in the range direction is equal to NTEXBINRANG
    36 // static int nRangNeighborhood;
    37 #define NTEXBINRANG 3
    38 // the minimum number of neighbors for the texture value to be
    39 // considered valid, as used in calcTexture()
    40 #define NTEXMIN 4
    41 // the refractive index of water
    42 #define REFRACTIVE_INDEX_OF_WATER 0.964
    43 // range gates up to a distance of RANGE_MAX+RCELLMAX_OFFSET are read into memory
    44 // the extra offset allows for the raincell search to extend somewhat further
    45 // than the maximum range used in the profile generation (RANGE_MAX).
    46 #define RCELLMAX_OFFSET 5000.0f
    47 // smallest range bin size to accept in metres
    48 #define RSCALEMIN 10
    49 // after fitting the vrad data, throw out any vrad observations that are more that VDIFMAX away
    50 // from the fitted value, since these are likely outliers
    51 #define VDIFMAX 10.0
    52 // When analyzing cells, radial velocities lower than VRADMIN are treated as clutter
    53 #define VRADMIN 1.0
    54 
    55 
    56 //-------------------------------------------------------//
    57 // hard-coded options for use RSL library //
    58 //-------------------------------------------------------//
    59 
    60 #ifdef RSL
    61 // By how much the elevation angle of sweeps of different quantities
    62 // is allowed to differ for them to be included into the same scan object.
    63 // Applies to data read with the RSL library only
    64 #define ELEVTOL 0.3
    65 // Offsets and gains for encoding reflectivity, velocity
    66 // and correlation coefficient
    67 // Once encoded values should be positive for storage in RAVE objects
    68 // Used with data read by the RSL library only
    69 #define RSL_OFFSET_DBZ 0
    70 #define RSL_GAIN_DBZ 1
    71 #define RSL_OFFSET_VRAD 0
    72 #define RSL_GAIN_VRAD 1
    73 #define RSL_OFFSET_RHOHV 0
    74 #define RSL_GAIN_RHOHV 1
    75 // Encoded values reserved for nodata and undetects.
    76 // Should be positive integers larger than zero
    77 #define RSL_NODATA -1000
    78 #define RSL_UNDETECT -999
    79 #endif
    80 
    81 //-------------------------------------------------------//
    82 // other hard-coded options //
    83 //-------------------------------------------------------//
    84 
    85 // maximum number of input files
    86 #define INPUTFILESMAX 50
    87 // Raw value used for gates or layers void of data (never ra-diated)
    88 #define UNDETECT -999
    89 // Raw value used for gates or layers when below the measurement detection threshold
    90 // or when information could not be retrieved (radiated but nothing detected or calculated)
    91 #define NODATA -1000
    92 // name under which the calculated texture quantity will be stored
    93 #define TEXNAME "VTEX"
    94 // name under which the calculated raincell masking quantity will be stored
    95 #define CELLNAME "CELL"
    96 // name of the parameter containing the static cluttermap
    97 #define CLUTNAME "OCCULT"
    98 // Name of the program, to be stored as task attribute in ODIM
    99 #define PROGRAM "vol2bird"
    100 // Version of the program, to be stored as task_version attribute in ODIM
    101 #define VERSION "0.4.0"
    102 // Date of latest version of the program
    103 #define VERSIONDATE "23-Apr-2019"
    104 
    105 //-------------------------------------------------------//
    106 // user options defaults (to be set in options.conf) //
    107 //-------------------------------------------------------//
    108 
    109 // the number of layers in an altitude profile
    110 #define NLAYER 25
    111 // the width/thickness of a layer [m]
    112 #define HLAYER 200.0f
    113 // the minimum range [m] used for constructing the bird density profile
    114 #define RANGEMIN 5000.0f
    115 // the maximum range [m] used for constructing the bird density profile
    116 #define RANGEMAX 25000.0f
    117 // the minimum azimuth [degrees] used for constructing the bird density profile
    118 #define AZIMMIN 0.0f
    119 // the maximum range [degrees] used for constructing the bird density profile
    120 #define AZIMMAX 360.0f
    121 // the minimum scan elevation [degrees] used for constructing the bird density profile
    122 #define ELEVMIN 0.0f
    123 // the maximum scan elevation used for constructing the bird density profile
    124 #define ELEVMAX 90.0f
    125 // the wavelength [cm] of the radar
    126 #define RADAR_WAVELENGTH_CM 5.3f
    127 // whether a static clutter map is used
    128 #define USE_CLUTTERMAP 0
    129 // clutter map path and filename
    130 #define CLUTTERMAP ""
    131 // print options to stderr
    132 #define PRINT_OPTIONS 0
    133 // name of (optional) environmental variable containing path to user configuration file
    134 #define OPTIONS_CONF "OPTIONS_CONF"
    135 // default user configuration file name to search for in working directory
    136 #define OPTIONS_FILE "options.conf"
    137 // FIXME: add description
    138 #define VERBOSE_OUTPUT_REQUIRED 0
    139 // print dbz to stderr
    140 #define PRINT_DBZ 0
    141 // print aliased and dealiased vrad pairs to stderr
    142 #define PRINT_DEALIAS 0
    143 // print vrad to stderr
    144 #define PRINT_VRAD 0
    145 // print rhohv to stderr
    146 #define PRINT_RHOHV 0
    147 // print cell to stderr
    148 #define PRINT_CELL 0
    149 // print cell properties to stderr
    150 #define PRINT_CELL_PROP 0
    151 // print texture to stderr
    152 #define PRINT_TEXTURE 0
    153 // print clutter to stderr
    154 #define PRINT_CLUT 0
    155 // print profile data to stderr
    156 #define PRINT_PROFILE 0
    157 // whether or not to print the 'points' array
    158 #define PRINT_POINTS_ARRAY 0
    159 // Whether or not to fit a model to the observed vrad
    160 #define FIT_VRAD 1
    161 // Whether to export bird profile as JSON
    162 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    163 // Scans with Nyquist velocity lower than this value are excluded
    164 #define MIN_NYQUIST_VELOCITY 5.0f
    165 // When all scans have nyquist velocity higher than this value, dealiasing is suppressed
    166 #define MAX_NYQUIST_DEALIAS 25.0f
    167 // when analyzing cells, only cells for which the stddev of vrad
    168 // (aka the texture) is less than cellStdDevMax are considered in the
    169 // rest of the analysis
    170 #define STDEV_CELL 5.0f
    171 // VVP Radial velocity standard deviation threshold
    172 #define STDEV_BIRD 2.0f
    173 // Bird radar cross section [cm^2]
    174 #define SIGMA_BIRD 11.0f
    175 // Maximum mean reflectivity [cm^2/km^3] for cells containing birds
    176 #define ETACELL 11500.0f
    177 // Maximum reflectivity [cm^2/km^3] for single gates containing birds
    178 #define ETAMAX 36000.0f
    179 // minimum dbz of a gate to be considered for inclusion in a weather cell
    180 #define DBZMIN 0.0
    181 // reflectivity quantity to use, one of "DBZH", "DBZV", "TH", "TV"
    182 #define DBZTYPE "DBZH"
    183 // for a range gate to contribute it should have a valid radial velocity
    184 #define REQUIRE_VRAD 0
    185 // whether we should dealias the radial velocities
    186 #define DEALIAS_VRAD 1
    187 // whether we should dealias all data once (default), or dealias for each profile individually
    188 #define DEALIAS_RECYCLE 1
    189 // Test dealiasing field velocities up to VMAX m/s
    190 #define DEALIAS_VMAX 50.0
    191 // Test field velocities increase in steps VMAX/VAF
    192 #define DEALIAS_VAF 15.0
    193 // Test field directions increase by 360/NF degrees
    194 #define DEALIAS_NF 12.0
    195 // whether you want to export the vertical bird profile as JSON
    196 #define EXPORT_BIRD_PROFILE_AS_JSON 0
    197 // whether to use dual-pol moments for filtering meteorological echoes
    198 #define DUALPOL 1
    199 // whether to use single-pol moments for filtering meteorological echoes
    200 #define SINGLEPOL 1
    201 // correlation coefficients higher than this threshold will be classified as precipitation
    202 #define RHOHVMIN 0.95f
    203 // whether to resample the input polar volume
    204 #define RESAMPLE 0
    205 // resampled range gate length in m
    206 #define RESAMPLE_RSCALE 500.0f
    207 // resampled number of range bins
    208 #define RESAMPLE_NBINS 100
    209 // resampled number of azimuth bins
    210 #define RESAMPLE_NRAYS 360
    Generated by   diff --git a/docs/index.html b/docs/index.html index 9de34bd9..f26edfde 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@
    Vertical profiling of biological scatterers
    -

    vol2bird is an algorithm that calculates vertical profiles of birds and other biological scatterers from weather radar data. vol2bird is written in C.

    +

    vol2bird is an algorithm that calculates vertical profiles of birds and other biological scatterers from weather radar data. vol2bird is written in C.

    See this publications for a description of the methodology:

    Bird migration flight altitudes studied by a network of operational weather radars
    Dokter AM, Liechti F, Stark H, Delobbe L, Tabary P, Holleman I
    @@ -52,26 +52,20 @@ Dokter AM, Desmet P, Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson C, Haase G, Leijnse H, Farnsworth A, Bouten W, Shamoun-Baranes J.
    Ecography, 2018, DOI 10.1111/ecog.04028

    repository contents

    -<<<<<<< HEAD

    Browse source code at:
    https://github.com/adokter/vol2bird

    -

    Report a bug at:
    -https://github.com/adokter/vol2bird/issues

    -======= -

    Browse source code at: https://github.com/adokter/vol2bird

    Report a bug at: https://github.com/adokter/vol2bird/issues

    ->>>>>>> master
    • data contains two polar volume radar files for testing
    • doc documentation on ODIM hdf5 data format
    • docs html pages of this documentation
      • -
    • docker scripts for generating and running a Docker container for vol2bird
      • +
    • docker scripts for generating and running a Docker container for vol2bird
    • doxygen doxygen configuration for generating this documentation
      • -
    • etc contains the user configuration file options.conf. Put your own modified copy in your working directory to run vol2bird with non-default settings.
      • +
    • etc contains the user configuration file options.conf. Put your own modified copy in your working directory to run vol2bird with non-default settings.
    • lib contains the main library
    • pgfplugin product generation framework (PGF) plugin for the BALTRAD system
    • pyvol2bird is a python wrapper for the library
      • -
    • src contains main executables for vol2bird (main program) and rsl2odim (converts NEXRAD to ODIM data format)
      • +
    • src contains main executables for vol2bird (main program) and rsl2odim (converts NEXRAD to ODIM data format)
    • tests unit tests for pgfplugin

    Copyright 2010-2018 Adriaan M. Dokter (University of Amsterdam, Cornell lab of ornithology) & Netherlands eScience Centre

    diff --git a/docs/rsl2odim_8c.html b/docs/rsl2odim_8c.html index dc5d4107..2c9631c8 100644 --- a/docs/rsl2odim_8c.html +++ b/docs/rsl2odim_8c.html @@ -53,12 +53,17 @@ More...

    #include <stdio.h>
    #include <float.h>
    +#include <getopt.h>
    #include "rave_io.h"
    #include "polarvolume.h"
    #include "libvol2bird.h"
    +#include "constants.h"

    Functions

    +void usage (char *programName, int verbose)
     
    int main (int argc, char **argv)
     
    + + From f58cafe23a98081db94d049f3820c919f4911799 Mon Sep 17 00:00:00 2001 From: adokter Date: Mon, 22 Apr 2019 23:49:09 -0400 Subject: [PATCH 37/37] update release notes --- NEWS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/NEWS.md b/NEWS.md index a0d7b348..0680d433 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,13 +4,13 @@ All issues included in this release can be found [here](https://github.com/adokt * vol2bird now reads Vaisala Sigmet IRIS (Iris RAW) format, the native radar data format of Vaisala radar processors (e.g. used in Canada, Portugal, Finland) (#112) -* added functionality to read files containing single scans (sweeps) and merge them into polar volumes (#116) +* added functionality to vol2bird to read files containing single scans (sweeps) and merge them into polar volumes (#116) -* rsl2odim now also converts Vaisala IRIS format and ODIM hdf5 format and can merge files containing scans / sweeps into a polar volume. +* rsl2odim now converts Vaisala IRIS format and ODIM hdf5 format and can merge files containing scans / sweeps into a polar volume. -* new input argument format that generalizes to multiple input files +* new input argument format that allows specifying multiple input files -* change default maximum range to 35 km (#117) +* change default maximum range from 25 km to 35 km (#117) * fixed a bug that in rare cases produced a negative reflectivity eta (#123)

    Functions

    +void usage (char *programName, int verbose)
     
    int main (int argc, char **argv)