#David Shean (David_Shean@Brown.edu)
#1/20/04
#thmirmos
#This tcsh script will process a series of raw RDR.QUB THEMIS Day IR files from level 0 to level 4, producing a "single-stretch" mosaic.  You must enter appropriate latitude and longitude ranges for the final mosaic.  You can also input different sizes for the boxfilters if desired.  After entering custom lat/lon parameters, place the file in the directory with all of your RDR.QUB files.  To make this file executable, type "chmod +x thmirmos" at a tcsh prompt.  Then run "thmirmos".  The output will be two mosaics.  One processes the images using the steps of the hilev4 proc while the other uses a different series of filters.  

#Define boundaries of mosaic
#Olympus
#set lat1 = 13.0
#set lat2 = 24.5
#set lon1 = -142.5
#set lon2 = -132.2
#Arsia
#set lat1 = -13.0 
#set lat2 = -1.0
#set lon1 = -132.0
#set lon2 = -115.0
#Pavonis
#set lat1 = -3.0
#set lat2 = 8.5
#set lon1 = -118.5
#set lon2 = -109.5
#Ascraeus
set lat1 = 6.2
set lat2 = 16.2
set lon1 = -110.2
set lon2 = -100.2
set clon = 0
set box1 = 51 
set box2 = 251
set numimg = 0

#Run thm2isis to convert .RDR to .cub files
foreach i (*RDR.QUB)
$ISISEXE/thm2isis.pl $i $i.l1 -- -- $ISISM01DATA/thm_kernels_both.def.3 -- 180 -- --
#Isolate band 9
dsk2dsk from=$i.l1 to=$i.l1.b9 sfrom='"::9"'
rm $i.l1
#Run thmirmc to map project image - SIMP:0,ocentric will tie images to MOLA
$ISISEXE/thmirmc.pl $i.l1.b9 -- -- -- "SIMP:$clon,ocentric" -- -- -- -- 0.1 #-- -- -- $lat1 $lat2 $lon1 $lon2
rm $i.l1.b9
end

#Apply box1 HPF and box2 HPF to each image
foreach i (*.irmc.cub)
boxfilter from=$i to=$i.box_1 filter=HPF samp=$box1 line=$box1 band=1
boxfilter from=$i to=$i.box_2 filter=HPF samp=$box2 line=$box2 band=1
set numimg = `expr $numimg + 1`
#rm $i.irmc.cub
end

#Clear the history label of each file
foreach i (*.box*)
labels from=$i list=none inithist=yes
end

#Mosaic the box1 HPF images
set j = 0
#Ensure that history file is large enough
set numimg = `expr $numimg + 2`
foreach i (*.box_1)
if ($j == 0) then
#Initializes the mosaic with the input lat/lon range
mosaic from=$i to=mos1.cub init=yes nimgs=$numimg lat="($lat1, $lat2)" lon="($lon1, $lon2)" 
set j = 1
else
#Adds each subsequent image on top of the mosaic
mosaic from=$i to=mos1.cub init=no nimgs=$numimg top=y
set j = `expr $j + 1`
#Clears mosaic history file for every 5 images added - prevents history file size error
if (`expr $j % 5` == 0) then
labels from=mos1.cub list=none inithist=yes
endif
endif
end

rm *.box_1

#Mosaic the box2 HPF images
set j = 0
foreach i (*.box_2)
if ($j == 0) then
mosaic from=$i to=mos2.cub init=yes nimgs=$numimg lat="($lat1, $lat2)" lon="($lon1, $lon2)"
set j = 1
else
mosaic from=$i to=mos2.cub init=no nimgs=$numimg top=y
set j = `expr $j + 1`
if (`expr $j % 5` == 0) then
labels from=mos2.cub list=none inithist=yes
endif
endif
end

rm *.box_2

#box2 LPF on mos1
boxfilter from=mos1.cub to=mos1_lpf_box_2.cub filter=LPFV samp=$box2 line=$box2 band=1
#box1 LPF on mos2
boxfilter from=mos2.cub to=mos2_lpf_box_1.cub filter=LPFV samp=$box1 line=$box1 band=1

#Add box1 LPF of mos2 to mos1 - hilev4 procedures
add from=mos2_lpf_box_1.cub from2=mos1.cub opt=c2c to=mosaic_lev4.cub
#Add box2 LPF of mos1 to mos1 - original procedure
add from=mos1_lpf_box_2.cub from2=mos1.cub opt=c2c to=mosaic_HPF.cub

#Convert to tif with gis headers
dform.pl -t -gis=yes mosaic_lev4.cub
dform.pl -t -gis=yes mosaic_HPF.cub

#Remove intermediate files
rm mos1*
rm mos2*
rm isis_param.out