! jnl file that uses Argo data to make different vertical section salinity 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_psal_section section_direction ylo yhi time_start time_end depth_min depth_max xlo xhi depth_axis 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 
! 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=200
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



! load in first file
use RG_ArgoClim_Temp_2014.nc
let t1=ARGO_TEMPERATURE_MEAN[d=1]+ARGO_TEMPERATURE_ANOMALY[d=1]


! now set up grid for entire time range
define axis/x=20.5E:19.5E:1/unit=degree xlong
define axis/y=64.5S:79.5N:1/unit=degree ylat
define axis/t="16-Jan-2004":"16-Dec-2023":1/units=months tclim
let dyn_p=z[d=1,g=`t1, return=grid`]	

define grid/x=xlong/y=ylat/z=dyn_p/t=tclim RG_grid


! now load in second temp file
use RG_ArgoClim_Temp_2024.nc
let t2=ARGO_TEMPERATURE_MEAN[d=2]+ARGO_TEMPERATURE_ANOMALY[d=2]

! now try to put all data onto same grid
let t_b1 = t1[gt=RG_grid@asn]
let t_b2 = t2[gt=RG_grid@nrst]


! load in first salinity file
use RG_ArgoClim_Psal_2014.nc
let s1=ARGO_SALINITY_MEAN[d=3]+ARGO_SALINITY_ANOMALY[d=3]

! now load in second psal file
use RG_ArgoClim_Psal_2024.nc
let s2=ARGO_SALINITY_MEAN[d=4]+ARGO_SALINITY_ANOMALY[d=4]

! now try to put all data onto same grid
let s_b1 = s1[gt=RG_grid@asn]
let s_b2 = s2[gt=RG_grid@nrst]


! mask out the current data
let mskt1 = if t_b1 then 1 else 0 

! define new full time scale data
let dyn_t = if mskt1 eq 1 then t_b1 else t_b2
let dyn_s = if mskt1 eq 1 then s_b1 else s_b2
let dyn_p = z[d=1,g=`t1, return=grid`]

let depth_min=`$6%0%`
let depth_max=`$7%1000%`
let time_start=`$4%12%`
let time_end=`$5%36%`
set mode interpolate

! setting the default values
let xlo=`$8%130%`
let xhi=`$9%170%`
let ylo=`$2%-50%`
let yhi=`$3%-50%`
let depth_axis=`$10%0%`


! 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=`t1, 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 psal=zaxreplace(dyn_s,dep,z[gz=`t1, return=grid`])

elseif

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

let psal=dyn_s

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 psal_section = psal[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,l=`time_start`,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

else ! no averaging over x

! plotting
let psal_section = psal[x=`xlo`,y=`ylo`:`yhi`,l=`time_start`,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section
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 psal_section = psal[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,l=`time_start`,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

else ! no averaging over y

! plotting
let psal_section = psal[x=`xlo`:`xhi`,y=`ylo`,l=`time_start`,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

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 psal_section = psal[x=`xlo`:`xhi`@ave,y=`ylo`:`yhi`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

else ! no averaging over x

! plotting
let psal_section = psal[x=`xlo`,y=`ylo`:`yhi`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section
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 psal_section = psal[x=`xlo`:`xhi`,y=`ylo`:`yhi`@ave,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

else ! no averaging over y

! plotting
let psal_section = psal[x=`xlo`:`xhi`,y=`ylo`,l=`time_start`:`time_end`@ave,z=`depth_min`:`depth_max`] 

let con_lev= $11&"()"|*>"*"&
fill/nolab/set/pal=cofi_sal/lev="`con_lev`" psal_section
if `depth_axis` then 
ppl ylab Depth (meters)
elseif 
ppl ylab Pressure (dbar)
endif
ppl shakey 1,1,.08,0,5,9,,,,
ppl fill
! adding contours
con/over/nolab/lev="`con_lev`" psal_section

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_psal_section section_direction ylo yhi time_start time_end depth_min depth_max xlo xhi depth_axis con_lev