def create_replace_links(self):
replace_ln_file_path = os.path.join(self.pwd, 'replace_links.sh')
try:
replace_ln_file = file_open(replace_ln_file_path, 'w')
except (OSError, IOError):
raise Exception('could not open file ' + replace_ln_file_path)
replace_ln_file.write("""#!/bin/bash
set -e
for link; do
test -h "$link" || continue
dir=$(dirname "$link")
reltarget=$(readlink "$link")
case $reltarget in
/*) abstarget=$reltarget;;
*) abstarget=$dir/$reltarget;;
esac
rm -fv "$link"
cp -afv "$abstarget" "$link" || {
# on failure, restore the symlink
rm -rfv "$link"
ln -sfv "$reltarget" "$link"
}
done
""")
replace_ln_file.close()
chmod_exec(replace_ln_file_path)
def link_tables(self):
script_path = 'link_tables.sh'
try:
link_tables = file_open(script_path, 'w')
except (OSError, IOError):
raise GamitSessionException('Could not create script file link_tables.sh')
# link the apr file as the lfile.
contents = \
"""#!/bin/bash
# set up links
cd %s;
sh_links.tables -frame J2000 -year %s -eop %s -topt none &> sh_links.out;
# kill the earthquake rename file
rm eq_rename
# create an empty rename file
echo "" > eq_rename
cd ..;
""" % (self.pwd_tables, self.date.yyyy(), self.GamitOpts['eop_type'])
link_tables.write(contents)
link_tables.close()
chmod_exec(script_path)
os.system('./'+script_path)
def linktables(self, year, eop_type):
script_path = os.path.join(self.pwd_comb, 'link_tables.sh')
try:
link_tables = file_open(script_path, 'w')
except:
raise GlobkException('could not open file link_tables.sh')
# link the apr file as the lfile.
with link_tables:
contents = \
"""#!/bin/bash
# set up links
sh_links.tables -frame J2000 -year %s -eop %s -topt none &> sh_links.out;
# link the bulletin A
ln -s ~/gg/tables/pmu.usno .
""" % (year, eop_type)
link_tables.write(contents)
chmod_exec(script_path)
def create_combination_script(self, date, org):
# extract the gps week and convert to string
gpsWeek_str = date.wwww()
# set the path and name for the run script
run_file_path = os.path.join(self.pwd_comb, 'globk.sh')
try:
run_file = file_open(run_file_path, 'w')
except:
raise GlobkException('could not open file '+run_file_path)
with run_file:
contents = \
"""#!/bin/bash
export INSTITUTE=%s
# data product file names
OUT_FILE=%s%s%s;
# mk solutions directory for prt files etc
[ ! -d tables ] && mkdir tables
cd tables
../link_tables.sh
# create global directory listing for globk
for file in $(find .. -name "*.glx" -print);do echo $file;done | grep "\/n0\/" > globk.gdl
for file in $(find .. -name "*.glx" -print);do echo $file;done | grep -v "\/n0\/" >> globk.gdl
# create the globk cmd file
echo " app_ptid all" > globk.cmd
echo " prt_opt GDLF MIDP CMDS" >> globk.cmd
echo " out_glb ../file.GLX" >> globk.cmd
echo " in_pmu pmu.usno" >> globk.cmd
echo " descript Daily combination of global and regional solutions" >> globk.cmd
""" % (org, org, gpsWeek_str, str(date.gpsWeekDay))
if self.net_type == 'global':
contents += \
"""
echo "# activated for global network merge" >> globk.cmd
echo " apr_wob 10 10 10 10 " >> globk.cmd
echo " apr_ut1 10 10 " >> globk.cmd
echo " apr_svs all 0.05 0.05 0.05 0.005 0.005 0.005 0.01 0.01 0.00 0.01 FR" >> globk.cmd
"""
contents += \
"""
echo " max_chii 1. 0.6" >> globk.cmd
echo " apr_site all 1 1 1 0 0 0" >> globk.cmd
echo " apr_atm all 1 1 1" >> globk.cmd
# create the sinex header file
echo "+FILE/REFERENCE " > head.snx
echo " DESCRIPTION Instituto Geografico Nacional " >> head.snx
echo " OUTPUT Solucion GPS combinada " >> head.snx
echo " CONTACT [email protected] " >> head.snx
echo " SOFTWARE glbtosnx Version " >> head.snx
echo " HARDWARE . " >> head.snx
echo " INPUT Archivos binarios Globk " >> head.snx
echo "-FILE/REFERENCE " >> head.snx
# run globk
globk 0 ../file.prt ../globk.log globk.gdl globk.cmd 2>&1 > ../globk.out
# convert the GLX file into sinex
glbtosnx . ./head.snx ../file.GLX ../${OUT_FILE}.snx 2>&1 > ../glbtosnx.out
# restore original directory
cd ..;
# figure out where the parameters start in the prt file
LINE=`grep -n "PARAMETER ESTIMATES" file.prt | cut -d ":" -f1`
# reduce line by one to make a little cleaner
let LINE--;
# print prt header
sed -n 1,${LINE}p file.prt > ${OUT_FILE}.out
# append the log file
cat globk.log >> ${OUT_FILE}.out
# create the fsnx file which contains only the solution estimate
lineNumber=`grep --binary-file=text -m 1 -n "\-SOLUTION/ESTIMATE" ${OUT_FILE}.snx | cut -d : -f 1`
# extract the solution estimate
head -$lineNumber ${OUT_FILE}.snx > ${OUT_FILE}.fsnx;
# move the H file to a meaningful name
mv file.GLX ${OUT_FILE}.GLX
# clear out log files
rm -rf tables
rm -f file*
rm -f globk*
rm -f glb*
rm -f *.sh
# compress sinex file
# gzip --force *.snx
gzip --force *.fsnx
gzip --force *.out
gzip --force *.glx
gzip --force *.GLX
"""
run_file.write(contents)
# all done
# add executable permissions
chmod_exec(run_file_path)
def create_finish_script(self):
year = self.date.yyyy()
doy = self.date.ddd()
# extract the gps week and convert to string
gpsWeek_str = str(self.date.gpsWeek)
# normalize gps week string
if self.date.gpsWeek < 1000: gpsWeek_str = '0' + gpsWeek_str
# extract the gps week and day of week
gps_week = self.date.gpsWeek
gps_week_day = self.date.gpsWeekDay
finish_file_path = os.path.join(self.pwd, 'finish.sh')
try:
finish_file = file_open(finish_file_path,'w')
except (OSError, IOError):
raise Exception('could not open file '+finish_file_path)
contents = """#!/bin/bash
export INSTITUTE=%s
echo "finish.sh (`date +"%%Y-%%m-%%d %%T"`): Finish script started" >> monitor.log
# set the name of the outfile
FILE=%s%s%s
DOY=%s
YEAR=%s
# move to the solution path
if [ ! -d ./glbf ]; then
# something went wrong! no glbf dir
mkdir glbf
fi
cd glbf
# make sure an h file exists, if not exit
if [ ! -f ../$DOY/h*.${YEAR}${DOY} ]; then
echo "FATAL in finish.sh (`date +"%%Y-%%m-%%d %%T"`): h-files not found in $DOY folder. Exit" >> ../monitor.log
exit;
fi
# get the WL and NL ambiguity resolution and the nrms double diff statistics
echo "finish.sh (`date +"%%Y-%%m-%%d %%T"`): NRMS and WL-NL ambiguity summary follows:" >> ../monitor.log
grep 'nrms' ../$DOY/sh_gamit_${DOY}.summary >> ../monitor.log
grep 'WL fixed' ../$DOY/sh_gamit_${DOY}.summary >> ../monitor.log
# link the svnav.dat file
ln -s ../tables/svnav.dat .
# create the binary h-file
htoglb . tmp.svs -a ../$DOY/h*.${YEAR}${DOY} >> ../${FILE}.out
# grep any missing stations to report them to monitor.log
grep 'No data for site ' ../${FILE}.out | sort | uniq >> ../monitor.log
# convert the binary h-file to sinex file
glbtosnx . "" h*.glx ${FILE}.snx >> ../${FILE}.out
# clean up
rm HTOGLB.* tmp.svs l* svnav.dat
# move back to home
cd ..;
""" % (self.gamitopts['org'], self.gamitopts['org'], gpsWeek_str, str(gps_week_day), doy, year[2:4])
# dump contents to the script file
finish_file.write(contents)
# this section is to calculate the orbits
if self.gamitopts['expt_type'] == 'relax':
# create an sp3 file from the g-file
contents = """
# move to the solutions directory
cd ./solutions/*
# make temporary directory
mkdir tmp
# copy the gfile to temp dir
cp gfile* tmp/
# move to the temp dir
cd tmp;
# do the damn thing
mksp3.sh %s %s %s
# copy the sp3 file to solution dir if exists
[ -e *.sp3 ] && mv *.sp3 ..;
# move out of temporary directory
cd ..;
# clean up
rm -rf tmp gfile*;
# back to home directory
cd ../..
""" % (year,doy,self.options['org'])
finish_file.write(contents)
return
contents = """
# move to the solutions directory
cd $DOY
# rename o file to znd file
if [ -f o*a.[0-9][0-9][0-9]* ]; then
mv -f o*a.[0-9][0-9][0-9]* ../glbf/%s%s%s.znd;
fi
# remove a priori o file
if [ -f o*p.[0-9][0-9][0-9]* ]; then
rm -f o*p.[0-9][0-9][0-9]*;
fi
# restore home dir
cd ..
""" % (self.gamitopts['org'], gpsWeek_str, str(gps_week_day))
finish_file.write(contents)
contents = """
# move to the solutions directory
cd $DOY
# clean up
# remove the grid files, rinex files, etc
rm -rf gfile* *.grid ????????.??o
# compress remaining files
for file in $(ls);do gzip --force $file; done
# return to home directory
cd ..
cd rinex
rm -rf *
cd ..
echo "finish.sh (`date +"%Y-%m-%d %T"`): Done processing h-files and generating SINEX." >> monitor.log
"""
finish_file.write(contents)
# make sure to close the file
finish_file.close()
# add executable permissions
chmod_exec(finish_file_path)
def create_run_script(self):
year = self.date.yyyy()
doy = self.date.ddd()
# extract the gps week and convert to string
gpsWeek_str = str(self.date.gpsWeek)
# normalize gps week string
if self.date.gpsWeek < 1000: gpsWeek_str = '0'+gpsWeek_str
# set the path and name for the run script
run_file_path = os.path.join(self.pwd,'run.sh')
try:
run_file = file_open(run_file_path, 'w')
except (OSError, IOError):
raise Exception('could not open file '+run_file_path)
contents = """#!/bin/bash
# just in case, create a temporary dir for fortran
if [ ! -d ./tmp ]; then
mkdir ./tmp
fi
export TMPDIR=`pwd`/tmp
export INSTITUTE=%s
# set max depth for recursion
MAX_LEVEL=3;
# parse input
level=$1; [ $# -eq 0 ] && level=1;
# check that level less than max depth
if [[ $level -gt $MAX_LEVEL ]];then
# if so then exit
echo "run.sh (`date +"%%Y-%%m-%%d %%T"`): MAX ITERATION DEPTH REACHED ... MUST EXIT" >> monitor.log
exit 0;
fi
echo "run.sh (`date +"%%Y-%%m-%%d %%T"`): Iteration depth: $level" >> monitor.log
# set the params
EXPT=%s;
YEAR=%s;
DOY=%s;
MIN_SPAN=%s;
EOP=%s;
NOFPT=%s;
# set the name of the outfile
OUT_FILE=%s%s%s.out
# execution flag for sh_gamit
EXE=1;
COUNTER=0;
while [ $EXE -eq 1 ]; do
if [ $COUNTER -gt 9 ]; then
echo "run.sh (`date +"%%Y-%%m-%%d %%T"`): Maximum number of retries (10) reached. Abnormal exit in run.sh. Check processing log." >> monitor.log
exit 1
fi
# set exe to 0 so that we exit exe loop if no problems found
EXE=0;
# save a copy of the lfile. before running sh_gamit
iter_ext=`printf "l%%02d_i%%02d" $level $COUNTER`
cp ./tables/lfile. ./tables/lfile.${iter_ext}
# do the damn thing
if [ "$NOFTP" = "no" ]; then
sh_gamit -update_l N -topt none -c -copt null -dopt c x -expt $EXPT -d $YEAR $DOY -minspan $MIN_SPAN -remakex Y -eop $EOP &> $OUT_FILE;
else
sh_gamit -update_l N -topt none -c -copt null -noftp -dopt c x -expt $EXPT -d $YEAR $DOY -minspan $MIN_SPAN -remakex Y -eop $EOP &> $OUT_FILE;
fi
""" \
% (self.gamitopts['org'], self.gamitopts['expt'], year, doy, '12', self.gamitopts['eop_type'],
self.gamitopts['noftp'], self.gamitopts['org'], gpsWeek_str, str(self.date.gpsWeekDay))
# if we're in debug mode do not pipe output to file
# if not session.options['debug']: contents += """ &> $OUT_FILE; """;
contents += """
grep -q "Geodetic height unreasonable" $OUT_FILE;
if [ $? -eq 0 ]; then
sstn=`grep "MODEL/open: Site" $OUT_FILE | tail -1 | cut -d ":" -f 5 | cut -d " " -f 3 |tr '[:upper:]' '[:lower:]'`;
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: unreasonable geodetic height" >> monitor.log
rm rinex/${sstn}* ;
rm $DOY/${sstn}* ;
grep "MODEL/open: Site" $OUT_FILE | tail -1
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep "FATAL.*MAKEX/lib/rstnfo: No match for" $OUT_FILE
if [ $? -eq 0 ];then
sstn=`grep "FATAL.*MAKEX/lib/rstnfo: No match for" $OUT_FILE | tail -1 | cut -d ":" -f5 | awk '{print $4}' | tr '[:upper:]' '[:lower:]'`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: no station info" >> monitor.log
rm rinex/${sstn}* ;
rm $DOY/${sstn}* ;
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "Error extracting velocities for" $OUT_FILE;
if [ $? -eq 0 ]; then
sstn=`grep "Error extracting velocities for" $OUT_FILE | head -1 | cut -d ":" -f 5 | cut -d " " -f 6 |tr '[:upper:]' '[:lower:]'`;
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: Error extracting velocities for" >> monitor.log
rm rinex/${sstn}* ;
rm $DOY/${sstn}* ;
grep "Error extracting velocities for" $OUT_FILE | tail -1
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "Bad WAVELENGTH FACT" $OUT_FILE;
if [ $? -eq 0 ]; then
sstn=`grep "Bad WAVELENGTH FACT" $OUT_FILE | tail -1 | cut -d ":" -f 5 | cut -d " " -f 6 | cut -c 3-6`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: Bad WAVELENGTH FACT in rinex header" >> monitor.log
rm rinex/${sstn}*;
rm $DOY/${sstn}* ;
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "Error decoding swver" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "Error decoding swver" $OUT_FILE;
sstn=`grep "Error decoding swver" $OUT_FILE | tail -1 | awk '{print $8}' | tr '[:upper:]' '[:lower:]'`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: Error decoding swver" >> monitor.log
rm rinex/${sstn}*;
rm $DOY/${sstn}* ;
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "FATAL.*MAKEX/lib/hisub: Antenna code.*not in hi.dat" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "FATAL.*MAKEX/lib/hisub: Antenna code.*not in hi.dat" $OUT_FILE;
sstn=`grep "FATAL.*MAKEX/lib/hisub: Antenna code.*not in hi.dat" $OUT_FILE | tail -1 | awk '{print $9}' | cut -c2-5 | tr '[:upper:]' '[:lower:]'`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn}: Antenna code not in hi.dat" >> monitor.log
rm rinex/${sstn}*;
rm $DOY/${sstn}* ;
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "FATAL.*FIXDRV/dcheck: Only one or no existing X-files" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "FATAL.*FIXDRV/dcheck: Only one or no existing X-files" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): FIXDRV/dcheck: Only one or no existing X-files" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "FATAL.*MAKEXP/makexp: No RINEX or X-files found" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "FATAL.*MAKEXP/makexp: No RINEX or X-files found" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): MAKEXP/makexp: No RINEX or X-files found" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "FATAL.*MAKEX/get_rxfiles: Cannot find selected RINEX file" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "FATAL.*MAKEX/get_rxfiles: Cannot find selected RINEX file" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): MAKEX/get_rxfiles: Cannot find selected RINEX file" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "FATAL.*MAKEX/openf: Error opening file:.*" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "FATAL.*MAKEX/openf: Error opening file:.*" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): MAKEX/openf: Error opening file" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "SOLVE/get_widelane: Error reading first record" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "SOLVE/get_widelane: Error reading first record" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): SOLVE/get_widelane: Error reading first record of temp file" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
grep -q "Failure in sh_preproc. STATUS 1 -- sh_gamit terminated" $OUT_FILE;
if [ $? -eq 0 ]; then
grep "Failure in sh_preproc. STATUS 1 -- sh_gamit terminated" $OUT_FILE;
echo "run.sh (`date +"%Y-%m-%d %T"`): Failure in sh_preproc. STATUS 1 -- sh_gamit terminated" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
# problems related to ill conditioned bias matrix
grep -q "FATAL.*SOLVE/lcloos: Inversion error in" $OUT_FILE;
if [ $? -eq 0 ]; then
# remove the FATAL from the message to avoid confusing finish.sh that there was an error during execution
err="SOLVE/lcloos: Inversion error in LCNORM(2)"
# determine which autocln.sum exists and has information in it
if [ -s $DOY/autcln.post.sum ]; then
autocln=autcln.post.sum
# error occurred after the prefit, read the autcln file and remove the station with low obs
echo "run.sh (`date +"%Y-%m-%d %T"`): $err (after prefit) Will remove the station with the lowest obs count in $autocln" >> monitor.log
sstn=`sed -n -e '/Number of data by site/,/^$/ p' $DOY/$autocln | tail -n +3 | sed '$d' | awk '{print $3, $4}' | awk -v min=999999 '{if($2<min){min=$2; stn=$1}}END{print stn}' | tr '[:upper:]' '[:lower:]'`
nobs=`sed -n -e '/Number of data by site/,/^$/ p' $DOY/$autocln | tail -n +3 | sed '$d' | awk '{print $3, $4}' | awk -v min=999999 '{if($2<min){min=$2; stn=$1}}END{print min}'`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${sstn} -> observation count: $nobs" >> monitor.log
rm rinex/${sstn}*;
rm $DOY/${sstn}* ;
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
else
# the error occurred during the prefit, autocln may or may not have gotten the problem. Use the observation count in the $OUTFILE
echo "run.sh (`date +"%Y-%m-%d %T"`): $err. (during prefit) Will analyze the MAKEX output and remove the file with more rejected observations" >> monitor.log
max_rejected=`grep "observations rejected" $OUT_FILE | awk -F ':' '{print $5}' | awk '{print $6}' | awk -v max=0 '{if($1>max){max=$1}}END{print max}'`
sstn=(`sed -n -e '/'$max_rejected' observations rejected/,/End processing/ p' $OUT_FILE | grep 'End' | awk -F ':' '{print $6}' | awk '{print $1'} | uniq | tr '[:upper:]' '[:lower:]'`)
if [ -z "$sstn" ]; then
echo "run.sh (`date +"%Y-%m-%d %T"`): could not determine the station with low observation count. Check $OUT_FILE" >> monitor.log
else
for stn in ${sstn[*]}
do
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting station ${stn} -> rejected observation count: $max_rejected" >> monitor.log
rm rinex/${stn}*;
rm $DOY/${stn}* ;
done
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
fi
# different search methods, deprecated
#sstn=(`sed -n -e '/ .... valid observations/,/stop in MODEL/ p' $OUT_FILE | grep 'Site' | awk -F ':' '{print $5}' | awk '{print $2'} | uniq | tr '[:upper:]' '[:lower:]'`)
fi
# this case after SOLVE/lcloos because it also triggers GAMIT sh_chksolve
grep -q "FATAL GAMIT sh_chksolve: Solve failed to complete normally" $OUT_FILE;
if [ $? -eq 0 ] && [ $EXE -eq 0 ]; then
echo "run.sh (`date +"%Y-%m-%d %T"`): GAMIT sh_chksolve: Solve failed to complete normally" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
# grep over constrained sites
grep -q "over constrained" ./$DOY/sh_gamit_${DOY}.summary;
if [ $? -eq 0 ]; then
# get the number of lines
lines=`cat ./$DOY/sh_gamit_${DOY}.summary | sed -n 's/WARNING: \([0-9]*\) SITES.*$/\\1/p'`
grep -A $lines "over constrained" ./$DOY/sh_gamit_${DOY}.summary >> monitor.log
# DDG: new behavior -> remove the station with the largest over constrained coordinate
# grep the sites and get the unique list separeted by | (to do regex grep)
# stns=`grep "GCR APTOL" monitor.log | awk '{print $4"_GPS"}' | uniq | tr '<line break>' '|'`
# copy the sittbl. (just in case)
# cp tables/sittbl. tables/sittbl.${iter_ext}
# remove those from the sittbl list: this will relax station to 100 m
# grep -v -E "${stns:0:-1}" tables/sittbl.${iter_ext} > tables/sittbl.
stns=`grep "GCR APTOL" ./$DOY/sh_gamit_${DOY}.summary | awk '{print sqrt($(NF) * $(NF)), $4}' | sort -r | head -n1 | awk '{print $2}' | tr '[:upper:]' '[:lower:]'`
echo "run.sh (`date +"%Y-%m-%d %T"`): deleting over constrained station ${stns}" >> monitor.log
rm rinex/${stns}*;
rm $DOY/${stns}* ;
# echo "run.sh (`date +"%Y-%m-%d %T"`): relaxing over constrained stations ${stns:0:-1}" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): replacing lfile. from this run with lfile.${iter_ext}" >> monitor.log
rm ./tables/lfile.
cp ./tables/lfile.${iter_ext} ./tables/lfile.
echo "run.sh (`date +"%Y-%m-%d %T"`): will try sh_gamit again ..." >> monitor.log
EXE=1;
fi
if [ $EXE -eq 1 ]; then
# if it will retry, save the previous output using extension .l00_i00, .l00_i01, ... etc
# where lxx is the level of iteration and iyy is the interation in this level
mv $OUT_FILE $OUT_FILE.${iter_ext}
COUNTER=$((COUNTER+1));
fi
# grep updated coordinates
grep Updated ./tables/lfile.;
if [ $? -eq 0 ]; then
grep Updated ./tables/lfile. >> monitor.log
fi
done
# clean up
rm -rf ionex met teqc*
# blab about failures
grep "FATAL" *.out >> monitor.log
"""
run_file.write(contents)
contents = \
"""
# remove extraneous solution files
# rm ./$DOY/l*[ab].*;
# make sure to rename the gfilea to the correct gfile[0-9].doy
[ -e ./igs/gfilea.* ] && mv -f ./igs/gfilea* ./*/gfile[0-9]*
# see if any of the coordinates were updated, exit if not
# DDG: Actually, sometimes the final updated coordinate only differs by < .3 m when solve is invoked more than
# once from within sh_gamit. Therefore, also check that the updated coordinate is > .3 m from the original APR
# this happens because the first Updated coordinate (lxxxxa.ddd) triggers an iteration in solve (lxxxxb.ddd)
# with a solution that is again close to the original APR. Without this check, PG iterates 3 times unnecessarily
grep Updated ./tables/lfile.;
if [ $? -ne 0 ]; then
echo "run.sh (`date +"%Y-%m-%d %T"`): Normal exit from run.sh" >> monitor.log
# uncompress everything. Will be compressed later on
gunzip ./*/*;
exit
else
updated=(`grep Updated ./tables/lfile. | awk '{print $1}'`)
RERUN=0
for stn in ${updated[*]}
do
coords=`grep $stn ./tables/lfile. | awk '{print $2,$3,$4}'`
# use the copy of the lfile to grep the APR coordinates
aprs=`grep $stn ./tables/lfile.${iter_ext} | awk '{print $2,$3,$4}'`
# get the distance between Updated and APR
dist=`echo $coords $aprs | awk '{print sqrt(($1 - $4)^2 + ($2 - $5)^2 + ($3 - $6)^2)}'`
if (( $(echo "$dist > 0.3" | bc -l) )); then
RERUN=1;
fi
done
# if RERUN = 0, Updated coordinate was < 0.3 m
if [ $RERUN -eq 0 ]; then
echo "run.sh (`date +"%Y-%m-%d %T"`): Updated coordinate detected but final solution within 0.3 m of APR" >> monitor.log
echo "run.sh (`date +"%Y-%m-%d %T"`): Normal exit from run.sh" >> monitor.log
# uncompress everything. Will be compressed later on
gunzip ./*/*;
exit
fi
fi
# iteration detected!
echo "run.sh (`date +"%Y-%m-%d %T"`): Updated coordinate detected in lfile. Iterating..." >> monitor.log
# save this level's out file for debugging
mv $OUT_FILE $OUT_FILE.${iter_ext}
# apr file for updated coordinates
aprfile=${EXPT}.temp
# recreate the apr file with updated coordinates minus the comments
sed -e 's/Updated from l.....\.[0-9][0-9][0-9]//g' ./tables/lfile. > ./tables/${aprfile};
# the copy of the lfile was saved BEFORE running GAMIT. Replace with the updated version
cp ./tables/${aprfile} ./tables/lfile.
# copy over an updated gfile if it exists
# cp ./*/gfile* ./tables/
# update level
level=$((level+1));
# remove the 'old' solution
[ $level -le $MAX_LEVEL ] && rm -rf ./$DOY;
# decompress the remaining solution files
gunzip ./*/*;
# do another iteration
./run.sh $level;
"""
run_file.write(contents)
run_file.close()
chmod_exec(run_file_path)
def create_combination_script(self, org, gpsweek, gpsweekday, sites):
# set the path and name for the run script
run_file_path = os.path.join(self.pwd_comb, 'globk.sh')
try:
run_file = file_open(run_file_path, 'w')
except:
raise GlobkException('could not open file '+run_file_path)
sites = split_string(sites, 80)
site_list_string = []
for s in sites:
site_list_string.append('echo " use_site %s" >> globk.cmd' % s)
site_string = '\n'.join(site_list_string)
contents = \
"""#!/bin/bash
export INSTITUTE=%s
export GPSWEEK=%s
export GPSWEEKDAY=%i
# data product file names
OUT_FILE=${INSTITUTE}${GPSWEEK}${GPSWEEKDAY};
# create global directory listing for globk
for file in $(find . -name "*.GLX" -print | sort);do echo "$file";done | grep "\/n0\/" > globk.gdl
for file in $(find . -name "*.GLX" -print | sort);do echo "$file";done | grep -v "\/n0\/" >> globk.gdl
# create the globk cmd file
echo " eq_file eq_rename.txt" > globk.cmd
echo " use_site clear" >> globk.cmd
%s
echo " prt_opt GDLF MIDP CMDS PLST " >> globk.cmd
echo " out_glb $OUT_FILE.GLX" >> globk.cmd
echo " in_pmu /opt/gamit_globk/tables/pmu.usno" >> globk.cmd
echo " descript Weekly combined solution at $INSTITUTE" >> globk.cmd
echo " max_chii 3. 0.6" >> globk.cmd
echo " apr_site all 1 1 1 0 0 0" >> globk.cmd
# DO NOT ACTIVATE ATM COMBINATION BECAUSE IT WILL NOT WORK!
echo "#apr_atm all 1 1 1" >> globk.cmd
# create the sinex header file
echo "+FILE/REFERENCE " > head.snx
echo " DESCRIPTION Instituto Geografico Nacional " >> head.snx
echo " OUTPUT Solucion GPS combinada " >> head.snx
echo " CONTACT [email protected] " >> head.snx
echo " SOFTWARE glbtosnx Version " >> head.snx
echo " HARDWARE . " >> head.snx
echo " INPUT Archivos binarios Globk " >> head.snx
echo "-FILE/REFERENCE " >> head.snx
# run globk
globk 0 file.prt globk.log globk.gdl globk.cmd 2>&1 > globk.out
# convert the GLX file into sinex
glbtosnx . head.snx $OUT_FILE.GLX ${OUT_FILE}.snx 2>&1 > glbtosnx.out
# figure out where the parameters start in the prt file
LINE=`grep -n "PARAMETER ESTIMATES" file.prt | cut -d ":" -f1`
# reduce line by one to make a little cleaner
let LINE--;
# print prt header
sed -n 1,${LINE}p file.prt > ${OUT_FILE}.out
# append the log file
cat globk.log >> ${OUT_FILE}.out
# create the fsnx file which contains only the solution estimate
lineNumber=`grep --binary-file=text -m 1 -n "\-SOLUTION/ESTIMATE" ${OUT_FILE}.snx | cut -d : -f 1`
# extract the solution estimate
head -$lineNumber ${OUT_FILE}.snx > ${OUT_FILE}.fsnx;
""" % (org, gpsweek, gpsweekday, site_string)
run_file.write(contents)
# all done
run_file.close()
# add executable permissions
chmod_exec(run_file_path)