From 4a3aef3f7236d2b3267aead61f11c587c6f4bddb Mon Sep 17 00:00:00 2001 From: Joseph Hunkeler Date: Thu, 5 Mar 2015 18:05:27 -0500 Subject: Further improvements --- src/Makefile.in | 2 +- src/analysis/Makefile.am | 2 +- src/analysis/Makefile.in | 6 +- src/analysis/cf_make_900_obs.csh | 193 -------------- src/analysis/cf_make_all_obs.csh | 555 --------------------------------------- src/analysis/gethmjd.h | 0 src/cal/Makefile.in | 2 +- src/cal/jitter/Makefile.am | 2 +- src/cal/jitter/Makefile.in | 6 +- src/fes/Makefile.am | 2 +- src/fes/Makefile.in | 6 +- src/fuv/Makefile.am | 27 +- src/fuv/Makefile.in | 306 ++++----------------- src/libcf/Makefile.am | 3 +- src/libcf/Makefile.in | 7 +- src/slalib/Makefile.am | 2 +- src/slalib/Makefile.in | 6 +- 17 files changed, 76 insertions(+), 1051 deletions(-) delete mode 100755 src/analysis/cf_make_900_obs.csh delete mode 100755 src/analysis/cf_make_all_obs.csh delete mode 100644 src/analysis/gethmjd.h (limited to 'src') diff --git a/src/Makefile.in b/src/Makefile.in index c617f20..df509b3 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -97,7 +97,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = AM_V_P = $(am__v_P_@AM_V@) diff --git a/src/analysis/Makefile.am b/src/analysis/Makefile.am index 42e9122..5c9d665 100644 --- a/src/analysis/Makefile.am +++ b/src/analysis/Makefile.am @@ -51,4 +51,4 @@ ttag_lightcurve_mjd2hmjd_SOURCES = ttag_lightcurve_mjd2hmjd.c gethmjd.c ttag_lightcurve_periodogram_SOURCES = ttag_lightcurve_periodogram.c LDADD = ../libcf/libcf.la ../slalib/libsla.la $(cfitsio_LIBS) -AM_CFLAGS = -I../../include -I./ -DCFORTRAN -Df2cFortran +AM_CFLAGS = -I$(top_srcdir)/include -I./ -DCFORTRAN -Df2cFortran diff --git a/src/analysis/Makefile.in b/src/analysis/Makefile.in index f3d2ddd..02ba382 100644 --- a/src/analysis/Makefile.in +++ b/src/analysis/Makefile.in @@ -110,7 +110,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" @@ -263,7 +263,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles am__mv = mv -f @@ -531,7 +531,7 @@ ttag_lightcurve_combine_SOURCES = ttag_lightcurve_combine.c ttag_lightcurve_mjd2hmjd_SOURCES = ttag_lightcurve_mjd2hmjd.c gethmjd.c ttag_lightcurve_periodogram_SOURCES = ttag_lightcurve_periodogram.c LDADD = ../libcf/libcf.la ../slalib/libsla.la $(cfitsio_LIBS) -AM_CFLAGS = -I../../include -I./ -DCFORTRAN -Df2cFortran +AM_CFLAGS = -I$(top_srcdir)/include -I./ -DCFORTRAN -Df2cFortran all: all-recursive .SUFFIXES: diff --git a/src/analysis/cf_make_900_obs.csh b/src/analysis/cf_make_900_obs.csh deleted file mode 100755 index 9edbc70..0000000 --- a/src/analysis/cf_make_900_obs.csh +++ /dev/null @@ -1,193 +0,0 @@ -#!/usr/local/bin/tcsh -f - -#****************************************************************************** -#* Johns Hopkins University -#* Center For Astrophysical Sciences -#* FUSE -#****************************************************************************** -#* -#* Synopsis: cf_make_900_obs.csh association_file -#* -#* Description: This routine is derived from cf_make_all_obs.csh, but modified -#* to consider only 900+ (airglow) files. Output is a single -#* quick-look image of the airglow spactrum. -#* -#* Extracted spectra are combined, not IDF files. -#* -#* When an expected data set is missing, the script stops, cleans -#* the directory, and returns 1. -#* -#* History: 08/08/08 1.00 wvd Create separate quick-look image -#* for 900+ (airglow) exposures. -#* Always combine extracted spectra. If -#* cf_xcorr fails, combine with no shift. -#* 08/08/08 1.01 wvd Rename airglow quick-look file to -#* M112580100000airgttagf.gif -#* -#*****************************************************************************/ - -# Delete files after processing? (Default is no.) -#set DELETE_IDF # Delete intermediate data files -set DELETE_BPM # Delete bad-pixel map files - -# Set program path -set rm = "/bin/rm -f" - -set cf_xcorr = cf_xcorr -set cf_combine = cf_combine -set cf_pack = cf_pack -set cf_nvo = cf_nvo -set idl_obsplot = idl_obsplot.pl -set modhead = modhead - -# Init var list -set detector = (1a 2b) -set channel = (lif sic) -set resolution = (2 3 4) -set obsmod = (hist ttag) - -# Determine the root name and the program ID -set asnf = $1 -set rn = ${asnf:s/000asnf.fit//} -set pid = `echo $rn | awk '{print substr($1, 1, 4)}'` - -# Determine the object class -set tmp_file = `ls ${rn}*fcal.fit | awk '{if (NR == 1) print}'` -set tmp_buf = `$modhead $tmp_file OBJCLASS` -set objclass = $tmp_buf[2] - -# Clean tmp files that the script will create (safe) -$rm tmp_xcorr.res tmp_combine.lis -$rm tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis -$rm DN_${rn}*.fit - -foreach om ($obsmod) - foreach res ($resolution) - foreach chan ($channel) - foreach det ($detector) - - set ignore_exp_stat = '' - if ($om == hist) set ignore_exp_stat = -a - if ($pid == S100) set ignore_exp_stat = -a - if ($pid == M106) set ignore_exp_stat = -a - - # Find exposures that match the current segment - set seg = $det$chan$res$om - set readfiles = 0 - ls ${rn}9[0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Keep only "9xx" exposures - if ($? == 0) then - set readfiles = 2 - set ignore_exp_stat = -a - endif - - if ($readfiles >= 1) then # There are one or more exposures - - echo " " - echo "*** Processing: $seg ***" - # [1a][lif] -> [1b][lif], [2b][lif] -> [2a][lif] etc... - if ($det == 1a) set det2 = 1b - if ($det == 2b) set det2 = 2a - set seg2 = $det2$chan$res$om - - echo "----- cf_xcorr input -----" - cat tmp_exp.lis - echo "----------------------------" - $cf_xcorr tmp_exp.lis tmp_xcorr.res # Compute shift and sigma_shift - echo "----- cf_xcorr results -----" - cat tmp_xcorr.res - echo "----------------------------" - - awk '{if ($3 >= 0) {print $6, $2} else {print $6}}' tmp_xcorr.res > tmp_good_exp.lis - - # - # --- Path 1: Optimize resolution --- - # - - echo "Optimize resolution..." - set n_good = `cat tmp_good_exp.lis | wc -l` - - # Extract [Day + Night] spectra - set s = DN_${rn}900${seg}fcal.fit - awk '{print "'$rn'"$1"'$seg'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg [dn] - # echo "----- Combining Files ----- " - # cat tmp_combine.lis - # echo "Output: " $s - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_good - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_dn.lis - - set s = DN_${rn}900${seg2}fcal.fit - awk '{print "'$rn'"$1"'$seg2'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg2 [dn] - # echo "----- Combining Files ----- " - # cat tmp_combine.lis - # echo "Output: " $s - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_good - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_dn.lis - - endif - end - - $rm tmp_xcorr.res tmp_combine.lis - $rm tmp_good_exp.lis tmp_exp.lis - - end - - # Pack the 8 [detector][channel] pairs together - if (-e tmp_seg_dn.lis) then - - set fcal_all = ${rn}00900all$res${om}fcal.fit # Final output name - $rm $fcal_all # Clean (safe) - set n_segs = `cat tmp_seg_dn.lis | wc -l` - - if (!($n_segs == 8)) then - - @ mseg = 8 - $n_segs - echo "ERROR: $mseg (day + night) segments are missing" - $rm tmp_seg_dn.lis - goto crash - - else - - $cf_pack tmp_seg_dn.lis $fcal_all - $rm tmp_seg_dn.lis - - # Plot figures, delete unwanted files - $idl_obsplot {$rn} airglow - mv ${rn}00900spec${om}f.gif ${rn}00000airg${om}f.gif - $rm ${rn}00900lif*.gif ${rn}00900sic*.gif - $rm $fcal_all - - endif - endif - end -end - -# Clean [dn] files. -$rm DN_${rn}*.fit - -# Delete IDF files -if $?DELETE_IDF then - echo "NOTE: Deleting intermediate data files." - $rm ${rn}*idf.fit -endif - -# Delete bad-pixel-map (bpm) files -if $?DELETE_BPM then - echo "NOTE: Deleting bad pixel map (bpm) files." - $rm ${rn}*bpm.fit -endif - -exit(0) - -crash: # Procedure when script crashes - -# Clean directory -$rm tmp_xcorr.res tmp_combine.lis -$rm tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis -$rm DN_*.fit - -# Return 1 -exit(1) diff --git a/src/analysis/cf_make_all_obs.csh b/src/analysis/cf_make_all_obs.csh deleted file mode 100755 index 2a97247..0000000 --- a/src/analysis/cf_make_all_obs.csh +++ /dev/null @@ -1,555 +0,0 @@ -#!/usr/local/bin/tcsh -f - -#****************************************************************************** -#* Johns Hopkins University -#* Center For Astrophysical Sciences -#* FUSE -#****************************************************************************** -#* -#* Synopsis: cf_make_all_obs.csh association_file -#* -#* Description: Creates 3 files from Calfuse output (properly run): -#* -#* 1) An "all" file containing 1 extension per detector (= 8). -#* Each extension contains a combined spectrum from the set -#* of exposures, using "Xcorr" or "Background" method. -#* 2) In the case of TTAG data, creates an "ano" file. Same as -#* the "all" file but considering "night only" exposure time. -#* 3) A National Virtual Observatory "nvo" file. One extension -#* containing wavelengths that span the whole FUSE range. -#* -#* The Xcorr method consists of co-adding spectra, the latter -#* being corrected for a possible shift. The Background method -#* consists of combining all the IDF files. -#* -#* The Xcorr test is performed on 4 (detector, channel) pairs, the -#* method of other pairs are given by them: -#* LiF 1a -> Lif 1b -#* LiF 2b -> LiF 2a -#* SiC 1a -> Sic 1b -#* Sic 2b -> Sic 2a -#* In the script, the left segments are referred as to $seg (or -#* $det) and the right segments are referred as to $seg2 (or -#* $det2). -#* -#* When an expected data set is missing, the script stops, cleans -#* the directory, and returns 1. -#* -#* History: 04/15/05 1.0 tc First release -#* 08/22/05 1.1 wvd Argument is name of association file. -#* 10/20/05 1.2 wvd Use idl_obsplot.pl to call cf_obsplot. -#* 10/25/05 1.3 wvd Add option to delete BPM or IDF files. -#* 03/21/06 1.4 wvd If there's only one exposure, always -#* follow the cross-correlation path. -#* Don't check the number of night-only -#* spectra before calling cf_pack. -#* 03/28/06 1.5 wvd If there's no good time in any exposure, -#* follow the cross-correlation path. -#* 04/27/06 1.6 wvd Be smarter when discarding 000 files. -#* Always use cross-corr for HIST data. -#* 05/23/06 1.7 wvd Move -k to proper spot after cf_combine. -#* 06/02/06 1.8 wvd If OBJCLASS = 7 (Sky Background) -#* always combine IDF files. -#* 06/22/06 1.9 wvd Call idf_combine with -z flag. -#* 05/24/07 1.10 bot If only 900+ spectra are available, -#* use them. -#* 04/04/08 1.11 bot Ignore EXP_STAT in cf_combine for HIST -#* data. -#* 07/25/08 1.12 wvd Ignore EXP_STAT in cf_combine and -#* idf_combine for BR-EARTH observations -#* (S100, M106, and 900+ exposures). -#* 08/08/08 1.13 wvd Don't ignore EXP_STAT for 900+ exposures. -#* 08/15/08 1.14 wvd Call cf_make_900_obs.csh -#* to make quick-look airglow plot. -#* -#*****************************************************************************/ - -# Delete files after processing? (Default is no.) -#set DELETE_IDF # Delete intermediate data files -#set DELETE_BPM # Delete bad-pixel map files - -# Set program path -set rm = "/bin/rm -f" - -set cf_xcorr = cf_xcorr -set cf_combine = cf_combine -set cf_pack = cf_pack -set cf_nvo = cf_nvo -set idl_obsplot = idl_obsplot.pl -set modhead = modhead - -#set cf_xcorr = /home/vela/civeit/Work/CalFuse/Xcorr/New/cf_xcorr -#set cf_combine = /home/vela/civeit/Work/CalFuse/Shiftexp/cf_combine -#set cf_pack = /home/vela/civeit/Work/CalFuse/Pack/cf_pack -#set cf_nvo = /home/vela/civeit/Work/CalFuse/Nvo/cf_nvo -#set modhead = /home/vela/civeit/local/bin/modhead - -#set cf_obsplot = /data1/fuse/calfuse/v3.1/idl/cf_obsplot.pro - -# Init var list -set detector = (1a 2b) -set channel = (lif sic) -set resolution = (2 3 4) -set obsmod = (hist ttag) - -# Determine the root name and the program ID -set asnf = $1 -set rn = ${asnf:s/000asnf.fit//} -set pid = `echo $rn | awk '{print substr($1, 1, 4)}'` - -# Determine the object class -set tmp_file = `ls ${rn}*fcal.fit | awk '{if (NR == 1) print}'` -set tmp_buf = `$modhead $tmp_file OBJCLASS` -set objclass = $tmp_buf[2] - -# Clean tmp files that the script will create (safe) -$rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis tmp_night_exp.lis -$rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis tmp_seg_no.lis -$rm DN_${rn}*.fit NO_${rn}*.fit - -foreach om ($obsmod) - foreach res ($resolution) - foreach chan ($channel) - foreach det ($detector) - - set ignore_exp_stat = '' - if ($om == hist) set ignore_exp_stat = -a - if ($pid == S100) set ignore_exp_stat = -a - if ($pid == M106) set ignore_exp_stat = -a - - # Find exposures that match the current segment - set seg = $det$chan$res$om - set readfiles = 0 - ls ${rn}[0-8][0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Reject EXP "9xx" and "000" - - if ($? == 0) then - set readfiles = 1 - else - ls ${rn}9[0-9][0-9]${seg}fcal.fit |& grep -v 000${seg} > tmp_exp.lis # Keep only "9xx" exposures - if ($? == 0) set readfiles = 2 - endif - - if ($readfiles >= 1) then # There are one or more exposures - - echo " " - echo "*** Processing: $seg ***" - # [1a][lif] -> [1b][lif], [2b][lif] -> [2a][lif] etc... - if ($det == 1a) set det2 = 1b - if ($det == 2b) set det2 = 2a - set seg2 = $det2$chan$res$om - - echo "----- cf_xcorr input -----" - cat tmp_exp.lis - echo "----------------------------" - $cf_xcorr tmp_exp.lis tmp_xcorr.res # Compute shift and sigma_shift - echo "----- cf_xcorr results -----" - cat tmp_xcorr.res - echo "----------------------------" - - awk '{if ($5 > 0) print $6, $4, $5}' tmp_xcorr.res > tmp_all_night_exp.lis - awk '{if ($3 >= 0) print $6, $2}' tmp_xcorr.res > tmp_good_exp.lis - awk '{if (($3 >= 0) && ($5 > 0)) print $6, $2, $4, $5}' tmp_xcorr.res > tmp_night_exp.lis - set time_good = `awk 'BEGIN{$t = 0} {if ($3 >= 0) $t = $t + $4} END{print $t}' tmp_xcorr.res` - set time_bad = `awk 'BEGIN{$t = 0} {if ($3 < 0) $t = $t + $4} END{print $t}' tmp_xcorr.res` - echo "Xcorr time: $time_good - Background time: $time_bad" - set n_exp = `cat tmp_xcorr.res | wc -l` - - if (($time_good > 2 * $time_bad && $objclass != 7) || ($time_good == 0 && $time_bad == 0) || $n_exp == 1 || $om == hist) then - - # - # --- Path 1: Optimize resolution --- - # - - echo "Optimize resolution..." - set n_good = `cat tmp_good_exp.lis | wc -l` - - # Extract [Day + Night] spectra - set s = DN_${rn}000${seg}fcal.fit - awk '{print "'$rn'"$1"'$seg'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg [dn] - # echo "----- Combining Files ----- " - # cat tmp_combine.lis - # echo "Output: " $s - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_good - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_dn.lis - - set s = DN_${rn}000${seg2}fcal.fit - awk '{print "'$rn'"$1"'$seg2'fcal.fit",$2}' tmp_good_exp.lis > tmp_combine.lis # Combine $seg2 [dn] - # echo "----- Combining Files ----- " - # cat tmp_combine.lis - # echo "Output: " $s - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_good - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_dn.lis - - set n_night = `cat tmp_night_exp.lis | wc -l` - if ($om == ttag && $n_night > 0) then # Create and combine night only files - - echo "*** Creating night only files ***" - set exp_nums = `awk '{print $1}' tmp_night_exp.lis` - - foreach exp ($exp_nums) - - # Create night-only BPM and FCAL files if they do not already exist. - set bno1 = NO_$rn$exp$det${om}fbpm.fit # Bad-pixel maps - set bno2 = NO_$rn$exp$det2${om}fbpm.fit - set cno1 = NO_$rn$exp${seg}fcal.fit # Extracted spectra - set cno2 = NO_$rn$exp${seg2}fcal.fit - - set etime = `egrep "^$exp" tmp_night_exp.lis | awk '{print $3}'` - set ntime = `egrep "^$exp" tmp_night_exp.lis | awk '{print $4}'` - set ratio = `egrep "^$exp" tmp_night_exp.lis | awk '{printf "%.0f", 0.5+$4/$3*10.}'` - - if (!(-e $cno1)) then - if ($etime == $ntime) then - echo "$cno1 is a symbolic link to $rn$exp${seg}fcal.fit" - ln -s $rn$exp${seg}fcal.fit $cno1 - else - - set idf_file = $rn$exp$det${om}fidf.fit - if (!(-e $bno1)) then - if ($ratio > 9) then - echo "$bno1 is a symbolic link to $rn$exp$det${om}fbpm.fit" - ln -s $rn$exp$det${om}fbpm.fit $bno1 - else - echo "Creating BPM: $bno1 ..." - cf_bad_pixels -n $bno1 $idf_file - endif - endif - - echo "Creating (LiF + SiC) FCAL: $cno1 ..." - cf_extract_spectra -n $bno1 -r NO_$rn$exp $idf_file # Existence of $bno1 is not required - endif - endif - - if (!(-e $cno2)) then - if ($etime == $ntime) then - echo "Using a symbolic link to $cno2" - ln -s $rn$exp${seg2}fcal.fit NO_$rn$exp${seg2}fcal.fit - else - - set idf_file = $rn$exp$det2${om}fidf.fit - if (!(-e $bno2)) then - if ($ratio > 9) then - echo "Using a symbolic link to $bno2" - ln -s $rn$exp$det2${om}fbpm.fit NO_$rn$exp$det2${om}fbpm.fit - else - echo "Creating BPM: $bno2 ..." - cf_bad_pixels -n $bno2 $idf_file - endif - endif - - echo "Creating (LiF + SiC) FCAL: $cno2 ..." - cf_extract_spectra -n $bno2 -r NO_$rn$exp $idf_file # Existence of $bno2 is not required - endif - endif - - end - - # Combine exposures into a single spectrum. - set s = NO_${rn}000${seg}fcal.fit - awk '{print "NO_'$rn'"$1"'$seg'fcal.fit",$2}' tmp_night_exp.lis > tmp_combine.lis # Combine $seg [no] - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_night - $modhead "${s}[0]" DAYNIGHT NIGHT - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_no.lis - - set s = NO_${rn}000${seg2}fcal.fit - awk '{print "NO_'$rn'"$1"'$seg2'fcal.fit",$2}' tmp_night_exp.lis > tmp_combine.lis # Combine $seg2 [no] - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - # $modhead "${s}[1]" NUM_EXP $n_night - $modhead "${s}[0]" DAYNIGHT NIGHT - $modhead "${s}[1]" COMBMETH XCORR - echo $s >> tmp_seg_no.lis - - endif - - else - - # - # --- Path 2: Optimize background --- - # - - echo "Optimize background..." - - # Combine IDF files - set idf1_all = DN_${rn}000$det${om}fidf.fit # Same for [dn] and [no] - set idf2_all = DN_${rn}000$det2${om}fidf.fit - - if (!(-e $idf1_all)) then - echo "Creating IDF: $idf1_all ..." - if ($readfiles == 1) then - ls ${rn}[0-8][0-9][0-9]$det${om}fidf.fit |& grep -v 000${det} > tmp_idf.lis # Reject EXP "9xx" and "000" - else - ls ${rn}9[0-9][0-9]$det${om}fidf.fit |& grep -v 000${det} > tmp_idf.lis # Consider only airglow - endif - if ($? == 0) then # IDF files exist - - set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis` - # echo "Combining IDF files: " $idf_lis - idf_combine -cz $ignore_exp_stat $idf1_all $idf_lis # Create combined IDF file for $seg - $rm tmp_idf.lis - - else - - echo "ERROR: IDF files are missing" - $rm tmp_idf.lis - goto crash - - endif - endif - - if (!(-e $idf2_all)) then - echo "Creating IDF: $idf2_all ..." - if ($readfiles == 1) then - ls ${rn}[0-8][0-9][0-9]$det2${om}fidf.fit |& grep -v 000${det2} > tmp_idf.lis # Reject EXP "9xx" and "000" - else - ls ${rn}9[0-9][0-9]$det2${om}fidf.fit |& grep -v 000${det2} > tmp_idf.lis # Consider only airglow - endif - if ($? == 0) then # IDF files exist - - set idf_lis = `awk '{printf "%s ",$1}' tmp_idf.lis` - # echo "Combining IDF files: " $idf_lis - idf_combine -cz $ignore_exp_stat $idf2_all $idf_lis # Create combined IDF file for $seg2 - $rm tmp_idf.lis - - else - - echo "ERROR: IDF files are missing" - $rm tmp_idf.lis - goto crash - - endif - endif - - # Get the number of (valid) combined IDF files - set tmp_buf = `$modhead $idf1_all NSPEC` - set n_comb1 = $tmp_buf[3] - set tmp_buf = `$modhead $idf1_all SPEC001` - set idf1_1 = $tmp_buf[3] - set tmp_buf = `$modhead $idf2_all NSPEC` - set n_comb2 = $tmp_buf[3] - set tmp_buf = `$modhead $idf2_all SPEC001` - set idf2_1 = $tmp_buf[3] - - # Combine BPM files - set bpm1_all = DN_${rn}000$det${om}fbpm.fit - set bpm2_all = DN_${rn}000$det2${om}fbpm.fit - - if (!(-e $bpm1_all)) then - echo "Combine all BPM (from IDF): $bpm1_all ..." - bpm_combine $bpm1_all $idf1_all # Create combined BPM file [dn] for $seg - endif - - if (!(-e $bpm2_all)) then - echo "Combine all BPM (from IDF): $bpm2_all ..." - bpm_combine $bpm2_all $idf2_all # Idem for $seg2 - endif - - # Extract [Day + Night] spectra - set s = DN_${rn}000${seg}fcal.fit - set xxx = DN_${rn}xxx${seg}fcal.fit - if (!(-e $xxx)) cf_extract_spectra -r DN_${rn}xxx $idf1_all # Avoid overwrite LiF | SiC - echo $xxx > tmp_combine.lis - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - $modhead "${s}[0]" NSPEC $n_comb1 - $modhead "${s}[0]" SPEC001 $idf1_1 - $modhead "${s}[1]" COMBMETH BACKGRND - echo $s >> tmp_seg_dn.lis - - set s = DN_${rn}000${seg2}fcal.fit - set xxx = DN_${rn}xxx${seg2}fcal.fit - if (!(-e $xxx)) cf_extract_spectra -r DN_${rn}xxx $idf2_all # Avoid overwrite LiF | SiC - echo $xxx > tmp_combine.lis - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - $modhead "${s}[0]" NSPEC $n_comb2 - $modhead "${s}[0]" SPEC001 $idf2_1 - $modhead "${s}[1]" COMBMETH BACKGRND - echo $s >> tmp_seg_dn.lis - - set n_night = `cat tmp_all_night_exp.lis | wc -l` - if ($om == ttag && $n_night > 0) then # Create and combine night only files - - echo "*** Creating night only files ***" - set exp_nums = `awk '{print $1}' tmp_all_night_exp.lis` - $rm tmp_bpm1.lis tmp_bpm2.lis - - foreach exp ($exp_nums) - - # Create bpm night only files (if they do not exist yet) - set bno1 = NO_$rn$exp$det${om}fbpm.fit - set bno2 = NO_$rn$exp$det2${om}fbpm.fit - - set idf_file = $rn$exp$det${om}fidf.fit - if (!(-e $bno1)) then - echo "Creating BPM: $bno1 ..." - cf_bad_pixels -n $bno1 $idf_file - endif - if (-e $bno1) echo $bno1 >> tmp_bpm1.lis # If valid, add in $seg list - - set idf_file = $rn$exp$det2${om}fidf.fit - if (!(-e $bno2)) then - echo "Creating BPM: $bno2 ..." - cf_bad_pixels -n $bno2 $idf_file - endif - if (-e $bno2) echo $bno2 >> tmp_bpm2.lis # If valid, add in $seg2 list - - end - - - # Combine BPM for $seg and extract spectra - - set bpm1_all = NO_${rn}000$det${om}fbpm.fit - set n_bpm = `cat tmp_bpm1.lis | wc -l` - echo "Number of valid BPM files: $n_bpm" - - if ($n_bpm > 0) then - - echo $n_bpm > tmp_bpm.lis - cat tmp_bpm1.lis >> tmp_bpm.lis - - if (!(-e $bpm1_all)) then - echo "Combine all BPM (from list): $bpm1_all ..." - bpm_combine $bpm1_all tmp_bpm.lis # Create combined BPM file [no] for $seg - endif - $rm tmp_bpm.lis - - endif - - # Extract [Night only] spectra. The existence of $bpm1_all is not required - set s = NO_${rn}000${seg}fcal.fit - set xxx = NO_${rn}xxx${seg}fcal.fit - if (!(-e $xxx)) cf_extract_spectra -n $bpm1_all -r NO_${rn}xxx $idf1_all # Avoid overwrite LiF | SiC - echo $xxx > tmp_combine.lis - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - $modhead "${s}[0]" NSPEC $n_comb1 - $modhead "${s}[0]" SPEC001 $idf1_1 - $modhead "${s}[1]" COMBMETH BACKGRND - echo $s >> tmp_seg_no.lis - - - # Combine BPM for $seg2 and extract spectra - - set bpm2_all = NO_${rn}000$det2${om}fbpm.fit - set n_bpm = `cat tmp_bpm2.lis | wc -l` - echo "Number of valid BPM files: $n_bpm" - - if ($n_bpm > 0) then - - echo $n_bpm > tmp_bpm.lis - cat tmp_bpm2.lis >> tmp_bpm.lis - - if (!(-e $bpm2_all)) then - echo "Combine all BPM (from list): $bpm2_all ..." - bpm_combine $bpm2_all tmp_bpm.lis # Create combined BPM file [no] for $seg2 - endif - $rm tmp_bpm.lis - - endif - - # Extract [Night only] spectra. The existence of $bpm2_all is not required - set s = NO_${rn}000${seg2}fcal.fit - set xxx = NO_${rn}xxx${seg2}fcal.fit - if (!(-e $xxx)) cf_extract_spectra -n $bpm2_all -r NO_${rn}xxx $idf2_all # Avoid overwrite LiF | SiC - echo $xxx > tmp_combine.lis - $cf_combine -k $ignore_exp_stat tmp_combine.lis $s - $modhead "${s}[0]" NSPEC $n_comb2 - $modhead "${s}[0]" SPEC001 $idf2_1 - $modhead "${s}[1]" COMBMETH BACKGRND - echo $s >> tmp_seg_no.lis - - endif - endif - endif - end - - $rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis - $rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_night_exp.lis - - end - - # Pack the 8 [detector][channel] pairs together ([dn] and [no] for ttag) - if (-e tmp_seg_dn.lis) then - - set fcal_all = ${rn}00000all$res${om}fcal.fit # Final output name - $rm $fcal_all # Clean (safe) - set n_segs = `cat tmp_seg_dn.lis | wc -l` - - if (!($n_segs == 8)) then - - @ mseg = 8 - $n_segs - echo "ERROR: $mseg (day + night) segments are missing" - $rm tmp_seg_dn.lis - goto crash - - else - - $cf_pack tmp_seg_dn.lis $fcal_all - $rm tmp_seg_dn.lis - - # Plot figures - $idl_obsplot {$rn} - - # Create National Virtual Observatory file - set nvo_file = ${rn}00000nvo$res${om}fcal.fit - $rm $nvo_file # Clean (safe) - $cf_nvo $fcal_all $nvo_file # Create file - - if (-e tmp_seg_no.lis) then - - set fcal_all = ${rn}00000ano$res${om}fcal.fit # Final output name - $rm $fcal_all # Clean (safe) - set n_segs = `cat tmp_seg_no.lis | wc -l` - - # if (!($n_segs == 8)) then - # - # @ mseg = 8 - $n_segs - # echo "ERROR: $mseg (night only) segments are missing" - # $rm tmp_seg_no.lis - # # goto crash - # - # else - - $cf_pack tmp_seg_no.lis $fcal_all - $rm tmp_seg_no.lis - - # endif - - endif - endif - endif - end -end - -# Clean [dn] and [no] files. Just keep all, (ano) and nvo -$rm DN_${rn}*.fit NO_${rn}*.fit - -# Delete IDF files -if $?DELETE_IDF then - echo "NOTE: Deleting intermediate data files." - $rm ${rn}*idf.fit -endif - -# Delete bad-pixel-map (bpm) files -if $?DELETE_BPM then - echo "NOTE: Deleting bad pixel map (bpm) files." - $rm ${rn}*bpm.fit -endif - -# Call routine to make quick-look airglow plot. -cf_make_900_obs.csh $1 - -exit(0) - -crash: # Procedure when script crashes - -# Clean directory -$rm tmp_xcorr.res tmp_bpm1.lis tmp_bpm2.lis tmp_combine.lis tmp_night_exp.lis -$rm tmp_all_night_exp.lis tmp_good_exp.lis tmp_exp.lis tmp_seg_dn.lis tmp_seg_no.lis -$rm DN_*.fit NO_*.fit - -# Return 1 -exit(1) diff --git a/src/analysis/gethmjd.h b/src/analysis/gethmjd.h deleted file mode 100644 index e69de29..0000000 diff --git a/src/cal/Makefile.in b/src/cal/Makefile.in index d419942..7bd0ca3 100644 --- a/src/cal/Makefile.in +++ b/src/cal/Makefile.in @@ -97,7 +97,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = AM_V_P = $(am__v_P_@AM_V@) diff --git a/src/cal/jitter/Makefile.am b/src/cal/jitter/Makefile.am index 693ae7a..2eaa6d0 100644 --- a/src/cal/jitter/Makefile.am +++ b/src/cal/jitter/Makefile.am @@ -4,4 +4,4 @@ bin_PROGRAMS = cf_jitter_diag \ cf_jitter_diag_SOURCES = cf_jitter_diag.c cf_jitter_SOURCES = cf_jitter.c LDADD = ../../libcf/libcf.la ../../slalib/libsla.la $(cfitsio_LIBS) -AM_CFLAGS = -I../../../include -I./ -DCFORTRAN -Df2cFortran $(cfitsio_CFLAGS) +AM_CFLAGS = -I$(top_srcdir)/include -I./ -DCFORTRAN -Df2cFortran $(cfitsio_CFLAGS) diff --git a/src/cal/jitter/Makefile.in b/src/cal/jitter/Makefile.in index 31675d5..17bfb6f 100644 --- a/src/cal/jitter/Makefile.in +++ b/src/cal/jitter/Makefile.in @@ -99,7 +99,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" @@ -131,7 +131,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles am__mv = mv -f @@ -351,7 +351,7 @@ SUBDIRS = . cf_jitter_diag_SOURCES = cf_jitter_diag.c cf_jitter_SOURCES = cf_jitter.c LDADD = ../../libcf/libcf.la ../../slalib/libsla.la $(cfitsio_LIBS) -AM_CFLAGS = -I../../../include -I./ -DCFORTRAN -Df2cFortran $(cfitsio_CFLAGS) +AM_CFLAGS = -I$(top_srcdir)/include -I./ -DCFORTRAN -Df2cFortran $(cfitsio_CFLAGS) all: all-recursive .SUFFIXES: diff --git a/src/fes/Makefile.am b/src/fes/Makefile.am index 7aba311..ffeee17 100644 --- a/src/fes/Makefile.am +++ b/src/fes/Makefile.am @@ -5,4 +5,4 @@ cf_calfes_SOURCES = \ cf_fes_cal.c cf_fes_get_cal_image.c cf_limbang.c \ cf_fes_apply_bias.c cf_fes_apply_flat.c cf_fes_apply_mask.c cf_calfes_LDADD = ../slalib/libsla.la ../libcf/libcf.la -cf_calfes_CFLAGS = -I../../include -I./ +cf_calfes_CFLAGS = -I$(top_srcdir)/include -I./ diff --git a/src/fes/Makefile.in b/src/fes/Makefile.in index f63f549..2a1d28f 100644 --- a/src/fes/Makefile.in +++ b/src/fes/Makefile.in @@ -99,7 +99,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" @@ -135,7 +135,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles am__mv = mv -f @@ -358,7 +358,7 @@ cf_calfes_SOURCES = \ cf_fes_apply_bias.c cf_fes_apply_flat.c cf_fes_apply_mask.c cf_calfes_LDADD = ../slalib/libsla.la ../libcf/libcf.la -cf_calfes_CFLAGS = -I../../include -I./ +cf_calfes_CFLAGS = -I$(top_srcdir)/include -I./ all: all-recursive .SUFFIXES: diff --git a/src/fuv/Makefile.am b/src/fuv/Makefile.am index 2772a69..efeaa71 100644 --- a/src/fuv/Makefile.am +++ b/src/fuv/Makefile.am @@ -1,6 +1,6 @@ SUBDIRS = . BUILD_LIBS = ../slalib/libsla.la ../libcf/libcf.la $(cfitsio_LIBS) -BUILD_FLAGS = -I../../include -I./ $(cfitsio_CFLAGS) +BUILD_FLAGS = -I../include -I./ $(cfitsio_CFLAGS) bin_PROGRAMS = cf_assign_wavelength \ cf_bad_pixels \ cf_convert_to_farf \ @@ -24,26 +24,5 @@ cf_remove_motions_SOURCES = cf_remove_motions.c cf_screen_photons_SOURCES = cf_screen_photons.c cf_ttag_init_SOURCES = cf_ttag_init.c -cf_assign_wavelength_LDADD = $(BUILD_LIBS) -cf_bad_pixels_LDADD = $(BUILD_LIBS) -cf_convert_to_farf_LDADD = $(BUILD_LIBS) -cf_countmap_LDADD = $(BUILD_LIBS) -cf_extract_spectra_LDADD = $(BUILD_LIBS) -cf_flux_calibrate_LDADD = $(BUILD_LIBS) -cf_gainmap_LDADD = $(BUILD_LIBS) -cf_hist_init_LDADD = $(BUILD_LIBS) -cf_remove_motions_LDADD = $(BUILD_LIBS) -cf_screen_photons_LDADD = $(BUILD_LIBS) -cf_ttag_init_LDADD = $(BUILD_LIBS) - -cf_assign_wavelength_CFLAGS = $(BUILD_FLAGS) -cf_bad_pixels_CFLAGS = $(BUILD_FLAGS) -cf_convert_to_farf_CFLAGS = $(BUILD_FLAGS) -cf_countmap_CFLAGS = $(BUILD_FLAGS) -cf_extract_spectra_CFLAGS = $(BUILD_FLAGS) -cf_flux_calibrate_CFLAGS = $(BUILD_FLAGS) -cf_gainmap_CFLAGS = $(BUILD_FLAGS) -cf_hist_init_CFLAGS = $(BUILD_FLAGS) -cf_remove_motions_CFLAGS = $(BUILD_FLAGS) -cf_screen_photons_CFLAGS = $(BUILD_FLAGS) -cf_ttag_init_CFLAGS = $(BUILD_FLAGS) +LDADD = $(BUILD_LIBS) +AM_CFLAGS = $(BUILD_FLAGS) diff --git a/src/fuv/Makefile.in b/src/fuv/Makefile.in index d40613a..80d7a39 100644 --- a/src/fuv/Makefile.in +++ b/src/fuv/Makefile.in @@ -104,14 +104,14 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" PROGRAMS = $(bin_PROGRAMS) -am_cf_assign_wavelength_OBJECTS = \ - cf_assign_wavelength-cf_assign_wavelength.$(OBJEXT) +am_cf_assign_wavelength_OBJECTS = cf_assign_wavelength.$(OBJEXT) cf_assign_wavelength_OBJECTS = $(am_cf_assign_wavelength_OBJECTS) +cf_assign_wavelength_LDADD = $(LDADD) am__DEPENDENCIES_1 = am__DEPENDENCIES_2 = ../slalib/libsla.la ../libcf/libcf.la \ $(am__DEPENDENCIES_1) @@ -120,80 +120,46 @@ AM_V_lt = $(am__v_lt_@AM_V@) am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@) am__v_lt_0 = --silent am__v_lt_1 = -cf_assign_wavelength_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_assign_wavelength_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \ - $(LDFLAGS) -o $@ -am_cf_bad_pixels_OBJECTS = cf_bad_pixels-cf_bad_pixels.$(OBJEXT) +am_cf_bad_pixels_OBJECTS = cf_bad_pixels.$(OBJEXT) cf_bad_pixels_OBJECTS = $(am_cf_bad_pixels_OBJECTS) +cf_bad_pixels_LDADD = $(LDADD) cf_bad_pixels_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_bad_pixels_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cf_bad_pixels_CFLAGS) \ - $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ -am_cf_convert_to_farf_OBJECTS = \ - cf_convert_to_farf-cf_convert_to_farf.$(OBJEXT) +am_cf_convert_to_farf_OBJECTS = cf_convert_to_farf.$(OBJEXT) cf_convert_to_farf_OBJECTS = $(am_cf_convert_to_farf_OBJECTS) +cf_convert_to_farf_LDADD = $(LDADD) cf_convert_to_farf_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_convert_to_farf_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_convert_to_farf_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \ - $(LDFLAGS) -o $@ -am_cf_countmap_OBJECTS = cf_countmap-cf_countmap.$(OBJEXT) +am_cf_countmap_OBJECTS = cf_countmap.$(OBJEXT) cf_countmap_OBJECTS = $(am_cf_countmap_OBJECTS) +cf_countmap_LDADD = $(LDADD) cf_countmap_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_countmap_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cf_countmap_CFLAGS) \ - $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ -am_cf_extract_spectra_OBJECTS = \ - cf_extract_spectra-cf_extract_spectra.$(OBJEXT) +am_cf_extract_spectra_OBJECTS = cf_extract_spectra.$(OBJEXT) cf_extract_spectra_OBJECTS = $(am_cf_extract_spectra_OBJECTS) +cf_extract_spectra_LDADD = $(LDADD) cf_extract_spectra_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_extract_spectra_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_extract_spectra_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \ - $(LDFLAGS) -o $@ -am_cf_flux_calibrate_OBJECTS = \ - cf_flux_calibrate-cf_flux_calibrate.$(OBJEXT) +am_cf_flux_calibrate_OBJECTS = cf_flux_calibrate.$(OBJEXT) cf_flux_calibrate_OBJECTS = $(am_cf_flux_calibrate_OBJECTS) +cf_flux_calibrate_LDADD = $(LDADD) cf_flux_calibrate_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_flux_calibrate_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_flux_calibrate_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ - -o $@ -am_cf_gainmap_OBJECTS = cf_gainmap-cf_gainmap.$(OBJEXT) +am_cf_gainmap_OBJECTS = cf_gainmap.$(OBJEXT) cf_gainmap_OBJECTS = $(am_cf_gainmap_OBJECTS) +cf_gainmap_LDADD = $(LDADD) cf_gainmap_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_gainmap_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cf_gainmap_CFLAGS) \ - $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ -am_cf_hist_init_OBJECTS = cf_hist_init-cf_hist_init.$(OBJEXT) +am_cf_hist_init_OBJECTS = cf_hist_init.$(OBJEXT) cf_hist_init_OBJECTS = $(am_cf_hist_init_OBJECTS) +cf_hist_init_LDADD = $(LDADD) cf_hist_init_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_hist_init_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cf_hist_init_CFLAGS) \ - $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ -am_cf_remove_motions_OBJECTS = \ - cf_remove_motions-cf_remove_motions.$(OBJEXT) +am_cf_remove_motions_OBJECTS = cf_remove_motions.$(OBJEXT) cf_remove_motions_OBJECTS = $(am_cf_remove_motions_OBJECTS) +cf_remove_motions_LDADD = $(LDADD) cf_remove_motions_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_remove_motions_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_remove_motions_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ - -o $@ -am_cf_screen_photons_OBJECTS = \ - cf_screen_photons-cf_screen_photons.$(OBJEXT) +am_cf_screen_photons_OBJECTS = cf_screen_photons.$(OBJEXT) cf_screen_photons_OBJECTS = $(am_cf_screen_photons_OBJECTS) +cf_screen_photons_LDADD = $(LDADD) cf_screen_photons_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_screen_photons_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC \ - $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) --mode=link $(CCLD) \ - $(cf_screen_photons_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ - -o $@ -am_cf_ttag_init_OBJECTS = cf_ttag_init-cf_ttag_init.$(OBJEXT) +am_cf_ttag_init_OBJECTS = cf_ttag_init.$(OBJEXT) cf_ttag_init_OBJECTS = $(am_cf_ttag_init_OBJECTS) +cf_ttag_init_LDADD = $(LDADD) cf_ttag_init_DEPENDENCIES = $(am__DEPENDENCIES_2) -cf_ttag_init_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(cf_ttag_init_CFLAGS) \ - $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ AM_V_P = $(am__v_P_@AM_V@) am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) am__v_P_0 = false @@ -206,7 +172,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles am__mv = mv -f @@ -434,7 +400,7 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ SUBDIRS = . BUILD_LIBS = ../slalib/libsla.la ../libcf/libcf.la $(cfitsio_LIBS) -BUILD_FLAGS = -I../../include -I./ $(cfitsio_CFLAGS) +BUILD_FLAGS = -I../include -I./ $(cfitsio_CFLAGS) cf_assign_wavelength_SOURCES = cf_assign_wavelength.c cf_bad_pixels_SOURCES = cf_bad_pixels.c cf_convert_to_farf_SOURCES = cf_convert_to_farf.c @@ -446,28 +412,8 @@ cf_hist_init_SOURCES = cf_hist_init.c cf_remove_motions_SOURCES = cf_remove_motions.c cf_screen_photons_SOURCES = cf_screen_photons.c cf_ttag_init_SOURCES = cf_ttag_init.c -cf_assign_wavelength_LDADD = $(BUILD_LIBS) -cf_bad_pixels_LDADD = $(BUILD_LIBS) -cf_convert_to_farf_LDADD = $(BUILD_LIBS) -cf_countmap_LDADD = $(BUILD_LIBS) -cf_extract_spectra_LDADD = $(BUILD_LIBS) -cf_flux_calibrate_LDADD = $(BUILD_LIBS) -cf_gainmap_LDADD = $(BUILD_LIBS) -cf_hist_init_LDADD = $(BUILD_LIBS) -cf_remove_motions_LDADD = $(BUILD_LIBS) -cf_screen_photons_LDADD = $(BUILD_LIBS) -cf_ttag_init_LDADD = $(BUILD_LIBS) -cf_assign_wavelength_CFLAGS = $(BUILD_FLAGS) -cf_bad_pixels_CFLAGS = $(BUILD_FLAGS) -cf_convert_to_farf_CFLAGS = $(BUILD_FLAGS) -cf_countmap_CFLAGS = $(BUILD_FLAGS) -cf_extract_spectra_CFLAGS = $(BUILD_FLAGS) -cf_flux_calibrate_CFLAGS = $(BUILD_FLAGS) -cf_gainmap_CFLAGS = $(BUILD_FLAGS) -cf_hist_init_CFLAGS = $(BUILD_FLAGS) -cf_remove_motions_CFLAGS = $(BUILD_FLAGS) -cf_screen_photons_CFLAGS = $(BUILD_FLAGS) -cf_ttag_init_CFLAGS = $(BUILD_FLAGS) +LDADD = $(BUILD_LIBS) +AM_CFLAGS = $(BUILD_FLAGS) all: all-recursive .SUFFIXES: @@ -553,47 +499,47 @@ clean-binPROGRAMS: cf_assign_wavelength$(EXEEXT): $(cf_assign_wavelength_OBJECTS) $(cf_assign_wavelength_DEPENDENCIES) $(EXTRA_cf_assign_wavelength_DEPENDENCIES) @rm -f cf_assign_wavelength$(EXEEXT) - $(AM_V_CCLD)$(cf_assign_wavelength_LINK) $(cf_assign_wavelength_OBJECTS) $(cf_assign_wavelength_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_assign_wavelength_OBJECTS) $(cf_assign_wavelength_LDADD) $(LIBS) cf_bad_pixels$(EXEEXT): $(cf_bad_pixels_OBJECTS) $(cf_bad_pixels_DEPENDENCIES) $(EXTRA_cf_bad_pixels_DEPENDENCIES) @rm -f cf_bad_pixels$(EXEEXT) - $(AM_V_CCLD)$(cf_bad_pixels_LINK) $(cf_bad_pixels_OBJECTS) $(cf_bad_pixels_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_bad_pixels_OBJECTS) $(cf_bad_pixels_LDADD) $(LIBS) cf_convert_to_farf$(EXEEXT): $(cf_convert_to_farf_OBJECTS) $(cf_convert_to_farf_DEPENDENCIES) $(EXTRA_cf_convert_to_farf_DEPENDENCIES) @rm -f cf_convert_to_farf$(EXEEXT) - $(AM_V_CCLD)$(cf_convert_to_farf_LINK) $(cf_convert_to_farf_OBJECTS) $(cf_convert_to_farf_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_convert_to_farf_OBJECTS) $(cf_convert_to_farf_LDADD) $(LIBS) cf_countmap$(EXEEXT): $(cf_countmap_OBJECTS) $(cf_countmap_DEPENDENCIES) $(EXTRA_cf_countmap_DEPENDENCIES) @rm -f cf_countmap$(EXEEXT) - $(AM_V_CCLD)$(cf_countmap_LINK) $(cf_countmap_OBJECTS) $(cf_countmap_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_countmap_OBJECTS) $(cf_countmap_LDADD) $(LIBS) cf_extract_spectra$(EXEEXT): $(cf_extract_spectra_OBJECTS) $(cf_extract_spectra_DEPENDENCIES) $(EXTRA_cf_extract_spectra_DEPENDENCIES) @rm -f cf_extract_spectra$(EXEEXT) - $(AM_V_CCLD)$(cf_extract_spectra_LINK) $(cf_extract_spectra_OBJECTS) $(cf_extract_spectra_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_extract_spectra_OBJECTS) $(cf_extract_spectra_LDADD) $(LIBS) cf_flux_calibrate$(EXEEXT): $(cf_flux_calibrate_OBJECTS) $(cf_flux_calibrate_DEPENDENCIES) $(EXTRA_cf_flux_calibrate_DEPENDENCIES) @rm -f cf_flux_calibrate$(EXEEXT) - $(AM_V_CCLD)$(cf_flux_calibrate_LINK) $(cf_flux_calibrate_OBJECTS) $(cf_flux_calibrate_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_flux_calibrate_OBJECTS) $(cf_flux_calibrate_LDADD) $(LIBS) cf_gainmap$(EXEEXT): $(cf_gainmap_OBJECTS) $(cf_gainmap_DEPENDENCIES) $(EXTRA_cf_gainmap_DEPENDENCIES) @rm -f cf_gainmap$(EXEEXT) - $(AM_V_CCLD)$(cf_gainmap_LINK) $(cf_gainmap_OBJECTS) $(cf_gainmap_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_gainmap_OBJECTS) $(cf_gainmap_LDADD) $(LIBS) cf_hist_init$(EXEEXT): $(cf_hist_init_OBJECTS) $(cf_hist_init_DEPENDENCIES) $(EXTRA_cf_hist_init_DEPENDENCIES) @rm -f cf_hist_init$(EXEEXT) - $(AM_V_CCLD)$(cf_hist_init_LINK) $(cf_hist_init_OBJECTS) $(cf_hist_init_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_hist_init_OBJECTS) $(cf_hist_init_LDADD) $(LIBS) cf_remove_motions$(EXEEXT): $(cf_remove_motions_OBJECTS) $(cf_remove_motions_DEPENDENCIES) $(EXTRA_cf_remove_motions_DEPENDENCIES) @rm -f cf_remove_motions$(EXEEXT) - $(AM_V_CCLD)$(cf_remove_motions_LINK) $(cf_remove_motions_OBJECTS) $(cf_remove_motions_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_remove_motions_OBJECTS) $(cf_remove_motions_LDADD) $(LIBS) cf_screen_photons$(EXEEXT): $(cf_screen_photons_OBJECTS) $(cf_screen_photons_DEPENDENCIES) $(EXTRA_cf_screen_photons_DEPENDENCIES) @rm -f cf_screen_photons$(EXEEXT) - $(AM_V_CCLD)$(cf_screen_photons_LINK) $(cf_screen_photons_OBJECTS) $(cf_screen_photons_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_screen_photons_OBJECTS) $(cf_screen_photons_LDADD) $(LIBS) cf_ttag_init$(EXEEXT): $(cf_ttag_init_OBJECTS) $(cf_ttag_init_DEPENDENCIES) $(EXTRA_cf_ttag_init_DEPENDENCIES) @rm -f cf_ttag_init$(EXEEXT) - $(AM_V_CCLD)$(cf_ttag_init_LINK) $(cf_ttag_init_OBJECTS) $(cf_ttag_init_LDADD) $(LIBS) + $(AM_V_CCLD)$(LINK) $(cf_ttag_init_OBJECTS) $(cf_ttag_init_LDADD) $(LIBS) mostlyclean-compile: -rm -f *.$(OBJEXT) @@ -601,17 +547,17 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_assign_wavelength-cf_assign_wavelength.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_bad_pixels-cf_bad_pixels.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_convert_to_farf-cf_convert_to_farf.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_countmap-cf_countmap.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_extract_spectra-cf_extract_spectra.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_flux_calibrate-cf_flux_calibrate.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_gainmap-cf_gainmap.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_hist_init-cf_hist_init.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_remove_motions-cf_remove_motions.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_screen_photons-cf_screen_photons.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_ttag_init-cf_ttag_init.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_assign_wavelength.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_bad_pixels.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_convert_to_farf.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_countmap.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_extract_spectra.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_flux_calibrate.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_gainmap.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_hist_init.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_remove_motions.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_screen_photons.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cf_ttag_init.Po@am__quote@ .c.o: @am__fastdepCC_TRUE@ $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< @@ -634,160 +580,6 @@ distclean-compile: @AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@ @am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(LTCOMPILE) -c -o $@ $< -cf_assign_wavelength-cf_assign_wavelength.o: cf_assign_wavelength.c -@am__fastdepCC_TRUE@ $(AM_V_CC)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cf_assign_wavelength_CFLAGS) $(CFLAGS) -MT cf_assign_wavelength-cf_assign_wavelength.o -MD -MP -MF $(DEPDIR)/cf_assign_wavelength-cf_assign_wavelength.Tpo -c -o cf_assign_wavelength-cf_assign_wavelength.o `test -f 'cf_assign_wavelength.c' || echo '$(srcdir)/'`cf_assign_wavelength.c -@am__fastdepCC_TRUE@ $(AM_V_at)$(am__mv) $(DEPDIR)/cf_assign_wavelength-cf_assign_wavelength.Tpo $(DEPDIR)/cf_assign_wavelength-cf_assign_wavelength.Po -@AMDEP_TRUE@@am__fastdepCC_FALSE@ $(AM_V_CC)source='cf_assign_wavelength.c' object='cf_assign_wavelength-cf_assign_wavelength.o' libtool=no @AMDEPBACKSLASH@ -@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@ -@am__fastdepCC_FALSE@ $(AM_V_CC@am__nodep@)$(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cf_assign_wavelength_CFLAGS) $(CFLAGS) -c -o cf_assign_wavelength-cf_assign_wavelength.o `test -f 'cf_assign_wavelength.c' || echo '$(srcdir)/'`cf_assign_wavelength.c - 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mostlyclean-libtool: -rm -f *.lo diff --git a/src/libcf/Makefile.am b/src/libcf/Makefile.am index 5d45f30..d59fc62 100644 --- a/src/libcf/Makefile.am +++ b/src/libcf/Makefile.am @@ -32,6 +32,7 @@ libcf_la_SOURCES = \ cf_init_support.c cf_modify_hist_pha.c \ cf_fes_proc_check.c cf_fes_proc_update.c libcf_la_LDFLAGS = -lm -lgfortran -libcf_la_CFLAGS = $(cfitsio_CFLAGS) -I../include -I./ -I../../include +libcf_la_CFLAGS = $(cfitsio_CFLAGS) libcf_la_LIBADD = $(cfitsio_LIBS) +AM_CFLAGS = -I$(top_srcdir)/include diff --git a/src/libcf/Makefile.in b/src/libcf/Makefile.in index 2b20728..c04b91d 100644 --- a/src/libcf/Makefile.in +++ b/src/libcf/Makefile.in @@ -98,7 +98,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; @@ -200,7 +200,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include depcomp = $(SHELL) $(top_srcdir)/depcomp am__depfiles_maybe = depfiles am__mv = mv -f @@ -409,8 +409,9 @@ libcf_la_SOURCES = \ cf_fes_proc_check.c cf_fes_proc_update.c libcf_la_LDFLAGS = -lm -lgfortran -libcf_la_CFLAGS = $(cfitsio_CFLAGS) -I../include -I./ -I../../include +libcf_la_CFLAGS = $(cfitsio_CFLAGS) libcf_la_LIBADD = $(cfitsio_LIBS) +AM_CFLAGS = -I$(top_srcdir)/include all: all-am .SUFFIXES: diff --git a/src/slalib/Makefile.am b/src/slalib/Makefile.am index 895eea9..7b5f1e1 100644 --- a/src/slalib/Makefile.am +++ b/src/slalib/Makefile.am @@ -184,4 +184,4 @@ libsla_la_SOURCES = \ xy2xy.f \ zd.f -AM_CFLAGS = -I../include -I./ +AM_CFLAGS = -I$(top_srcdir)/include -I./ diff --git a/src/slalib/Makefile.in b/src/slalib/Makefile.in index 643c07f..c175c19 100644 --- a/src/slalib/Makefile.in +++ b/src/slalib/Makefile.in @@ -98,7 +98,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ $(ACLOCAL_M4) DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) mkinstalldirs = $(install_sh) -d -CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_HEADER = $(top_builddir)/src/include/config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; @@ -175,7 +175,7 @@ AM_V_at = $(am__v_at_@AM_V@) am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) am__v_at_0 = @ am__v_at_1 = -DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)/src/include F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS) LTF77COMPILE = $(LIBTOOL) $(AM_V_lt) --tag=F77 $(AM_LIBTOOLFLAGS) \ $(LIBTOOLFLAGS) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) @@ -529,7 +529,7 @@ libsla_la_SOURCES = \ xy2xy.f \ zd.f -AM_CFLAGS = -I../include -I./ +AM_CFLAGS = -I$(top_srcdir)/include -I./ all: all-am .SUFFIXES: -- cgit