! jnl file that uses Argo data to make different vertical section temperature plots.  The sections are either
! in a N-s direction or an E-W direction.  This does not make arbitrary section plots.
! requires input arguments for the location of section, the time range, the depth range and the distance range

! to run the program in ferret, you will need to type the following line with or without the various values 
! filled in:

! go fer_temp_section section_direction ylo yhi time_start time_end depth_min depth_max xlo xhi con_lev

! If you choose not to give values for the various variables, default ones will be substituted for you.
! If you only want to choose some values, you can, but you cannot skip any values.  This means you can 
! fill in the first 2 and no others, or if you want to specify the time ranges, you must do the first 4.
! You can't choose to do the section_direction and the depth_min and depth_max without filling in the 
! ylo, yhi, time_start and time_end


! section direction can be "N" for N-S or "E" for E-W

! xlo corresponds to the lowest latitude limit  
! xhi corresponds to the highest latitude limit  
! ylo corresponds to the lowest longitude limit 
! yhi corresponds to the highest longitude limit

! depth values are entered in the range of 0 - 2000dbar with the default being 0 - 1000dbar

! time values are entered corresponding to monthly values starting with Jan, 2004.
! The default is the entire time range.
! con_lev sets the contour and fill levels of the plot.  This is done in the following format:  (lo,hi,delta).  
! More than one can be chosen:  (lo,mid,delta1),(mid,hi,delta2).  See the Ferret Users Manual for more information.



cancel/all data
cancel/all var
cancel/all sym
set window/clear
go set_pixel_size 1024 768
set mem/size=60
define viewport/xlim=.0,.95/ylim=0,1 top

PPL DFLTFNT DR
ppl conpre @P1@DR
ppl axlsze 0.15,.15
ppl axset 1,1,1,1
ppl pen 0,7
ppl pen 1,7
ppl labset .15,.15,.15



use RG_ArgoClim_Full.nc
let dyn_t=ARGO_TEMPERATURE_MEAN[d=1]+ARGO_TEMPERATURE_ANOMALY[d=1]
let dyn_p=ARGO_SALINITY_MEAN[d=1]+ARGO_SALINITY_ANOMALY[d=1]
let dyn_p=z[d=1,g=`dyn_t, return=grid`]

let depth_min=`$6%1000%`
let depth_max=`$7%2000%`
let time_start=`$4%37%`
let time_end=`$5%37%`

! setting the default values
let xlo=`$8%180%`
let xhi=`$9%180%`
let ylo=`$2%-50%`
let yhi=`$3%10%`
let depth_axis=`$1%1%`
set mode interpolate

! start of plotting section. 


if `depth_axis` then

! you want meters instead of db as the depth axis unit

! first need to change to depth from pressure
let xo=sin(y[g=`dyn_t, return=grid`]*3.1415926/180)
let xxo=xo*xo
let bot_line=9.780318*(1.0+(5.2788*10^-3+2.36*10^-5*xxo)*xxo) + 1.092*10^-6*dyn_p
let top_line=(((-1.82*10^-15*dyn_p+2.279*10^-10)*dyn_p-2.2512*10^-5)*dyn_p+9.72659)*dyn_p
let dep=top_line/bot_line
! then regrid onto original pressure grid spacing
let temp=zaxreplace(dyn_t,dep,z[gz=`dyn_p, return=grid`])

elseif

! you want db instead of m as the depth axis unit

let temp=dyn_t

endif 

! setting depth region
set region/z=`depth_min`:`depth_max`

! a vertical section can only be made if the depths are different. 
! depth is the same
let a=if `depth_max` eq `depth_min` then 1 else 0
if `a` then say "depth is the same - cannot graph a section"

! time is the same - do not average


let b=if `time_start` eq `time_end` then 1 else 0 
let c=if (`xlo`) ne (`xhi`) then 1 else 0
let d=if (`ylo`) ne (`yhi`) then 1 else 0
let boundb=if (`xlo`) gt (`xhi`) then 1 else 0


if `b` then 
if ($1%TRUE|N>TRUE|E>FALSE|>TRUE%) then 	!checking whether it is a N-S or E-W section & assigning N-S as default
if `c` then

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,l=`time_start`,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`,l=`time_start`]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

else ! no averaging over x

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`,y=`ylo`:`yhi`,l=`time_start`,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`,l=`time_start`]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay
endif	! c loop

else ! E-W section

! Ensuring longitudes are properly plotted
if `boundb` then
let xhi=`xhi`+360
endif 



if `d` then 

! plotting

let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,l=`time_start`,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,z=`depth_min`:`depth_max`,l=`time_start`]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

else ! no averaging over y

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`,l=`time_start`,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`,z=`depth_min`:`depth_max`,l=`time_start`]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

endif	! d loop

endif	!b
endif !n-s

! time is different

let e=if `time_start` ne `time_end` then 1 else 0 
if `e` then 
if ($1%TRUE|N>TRUE|E>FALSE|>TRUE%) then 	!checking whether it is a N-S or E-W section & assigning N-S as default

if `c` then

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`,l=`time_start`:`time_end`@ave]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

else ! no averaging over x

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`,y=`ylo`:`yhi`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`,l=`time_start`:`time_end`@ave]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay
endif	! c loop

else ! E-W section
if `boundb` then
let xhi=`xhi`+360
endif

if `d` then 

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,z=`depth_min`:`depth_max`,l=`time_start`:`time_end`@ave]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

else ! no averaging over y

! plotting
let con_lev= $10&"()"|*>"*"&
fill/nolab/set/pal=cofi_pot/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 
ppl ylab Pressure (dbar)
ppl shakey 1,,.08,,5,,,,,,
ppl fill
! adding contours
con/over/nolab/set/lev="`con_lev`" temp[x=`xlo`:`xhi`,y=`ylo`,z=`depth_min`:`depth_max`,l=`time_start`:`time_end`@ave]
 ppl conset .11,,,,,,,5.7,1.,1
 ppl contour/overlay

endif	! d loop

endif	!b
endif !n-s

! adding in etopo6 to give bathymetry
use etopo6_grid.nc

if ($1%TRUE|N>TRUE|E>FALSE|>TRUE%) then 	! N-S section

! making a mask to put in bathymetry only where there is land
!let msk= if temp[y=-50:25,x=130:250,z=0:2000,l=1:36@ave] then 0 else 1
!shade/pal=grey/over/lev=(1)/nolab/nokey msk[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`]
if `c` then
let mskb if btdata*(-1) lt dyn_p then 1
repeat/x=`xlo`:`xhi` shad/over/nolab/nokey/pal=black mskb[y=`ylo`:`yhi`,z=`depth_min`:`depth_max`]

else
let mskb if btdata*(-1) lt dyn_p then 1
shad/over/nolab/nokey/pal=black mskb[x=`xlo`,y=`ylo`:`yhi`,z=`depth_min`:`depth_max`]
endif

else	! E-W section

! making a mask to put in bathymetry only where there is land
!let msk= if temp[y=-50:25,x=130:250,z=0:2000,l=1:36@ave] then 0 else 1
!shade/pal=grey/over/lev=(1)/nolab/nokey msk[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,z=`depth_min`:`depth_max`]
if `d` then
let mskb if btdata*(-1) lt dyn_p then 1
repeat/y=`ylo`:`yhi` shad/over/nolab/nokey/pal=black mskb[x=`xlo`:`xhi`,z=`depth_min`:`depth_max`]

else
let mskb if btdata*(-1) lt dyn_p then 1
shad/over/nolab/nokey/pal=black mskb[y=`ylo`,x=`xlo`:`xhi`,z=`depth_min`:`depth_max`]
endif
say Plot is finished
say To adjust parameters, use the command line to pass arguments
say For this file, the form to pass arguments is
say go fer_temp_section section_direction ylo yhi time_start time_end depth_min depth_max xlo xhi con_lev