more changes

scripts/compute_psdlags.sh

@@ -3,6 +3,7 @@
 mkdir -p data
 
 ref_band="1367A"
+refpsd_tabfile=data/tables/psd_${ref_band}.tab
 
 for lightcurve in data/lc/*.lc
 do
@@ -11,20 +12,21 @@ do
     if [[ $ref_band == $echo_band ]]; then continue; fi
     err_str="LF"
 
-echo -n "Running psdlag using ref band ${ref_band}"
-echo " and echo band $echo_band{${err_str}}."
+    # Save tables with these filenames
+    echopsd_tabfile=data/tables/psd_${echo_band}.tab
+    timelag_tabfile=data/tables/lag_${ref_band}_${echo_band}.tab
 
-scripts/psdlag_4bin.py
+    echo -n "Running psdlag using ref band ${ref_band}"
+    echo " and echo band $echo_band{${err_str}}."
+
+    # psdlag python script will call clag and print tables
+    # tmp.* files.
+    echo scripts/psdlag_4bin.py ${ref_band}.lc $lightcurve
 
 
-    # Propagate tables into analyses/tables
-    echoPSD_tabfile=analyses/tables/PSD_${echo_band}_\{${err_str}\}.tab
-    refPSD_tabfile=analyses/tables/PSD_${ref_band}_\{${err_str}\}.tab
-    timelag_tabfile=analyses/tables/timelag_${ref_band}_≺_${echo_band}_\{${err_str}\}.tab
-
-    # Output curves to temporary files using perl script, move tables to
-    # permanent location. This just assumes there are no conflicts.
-    scripts/extract_tables.pl $lightcurve > /dev/null
+    # process_tables perl script reads tmp.* files and creates some
+    # other useful tables
+    scripts/process_tables.pl $lightcurve > /dev/null
     mv tmp.echoPSD $echoPSD_tabfile
     mv tmp.refPSD $refPSD_tabfile
     mv tmp.timelag $timelag_tabfile

scripts/plot.sh

@@ -3,16 +3,14 @@
 # This metascript uses the available plotting scripts to produce a list of
 # document-rady plots.
 
-# Only analyses with this error type will be represented in the atlas
-errtype=$(cat err_type)
-ref_band="1367Å"
+ref_band="1367A"
 
 case $1 in
     "PSD"|"psd"|"PSDs"|"PSDS"|"psds")
         gnuplot_file=psd_atlas.gp
         scripts/propagate_tables.sh
         gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
-        for tabfile in analyses/tables/PSD_*${errtype}*.tab;
+        for tabfile in data/tables/PSD_*${errtype}*.tab;
         do
             echo_band=$(basename $tabfile|
                         sed 's|PSD[_ ]\(.\{5\}\)[_ ]{[^_ ]*}.tab|\1|')
@@ -30,7 +28,7 @@ case $1 in
         gnuplot_file=timelag_atlas.gp
         gnuplot_input=$(cat scripts/templates/${gnuplot_file}|perl -pe 's|\n|␤|g')
         scripts/propagate_tables.sh
-        for tabfile in analyses/tables/timelag_*${errtype}*.tab;
+        for tabfile in data/tables/timelag_*${errtype}*.tab;
         do
             ref_band_extracted=$(basename $tabfile|sed 's|timelag_\([^≺]*\)[_ ]≺[_ ][^≺_ ]*[_ ]{[^_ ]*}.tab|\1|')
             echo_band=$(basename $tabfile|sed 's|timelag_[^≺]*[_ ]≺[_ ]\([^≺_ ]*\)[_ ]{[^_ ]*}.tab|\1|')
@@ -45,7 +43,7 @@ case $1 in
     ;;
 
     "tophat"|"th")
-        mkdir -p analyses/tables/
+        mkdir -p data/tables/
         scripts/tophat_fft.pl
         gnuplot scripts/templates/tophat_freqdomain.gp
         gnuplot scripts/templates/tophat_timedomain.gp