pro makeHDFdata, gas, year, site
close,/all

; 2012 new gather does not reverse altitudes - edit covariances here


;you need to enter the percentage errors as determined by error calcncar and listed in Error_summary for your gas
;these will be multiplied by the total column to get the error in molecules/cm2

if site eq 'TAB' then begin
srandcolper=0.0
sspectcolper=0.0

 if gas eq 'hno3' then begin
  srandcolper=0.7233 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=6.0234; spectral error
 endif

 if gas eq 'hcl' then begin
  srandcolper=2.0036 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=7.8468; spectral error
 endif

 if gas eq 'hf' then begin
  srandcolper=1.07434 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=2.0513; spectral error
 endif

 if gas eq 'clono2' then begin
  srandcolper=24.8 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=3.7; spectral error
 endif

 if gas eq 'o3' then begin
  srandcolper=0.5121;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=1.8144; spectral error
 endif

 if gas eq 'c2h6' then begin
  srandcolper=1.2078;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=10.7629; spectral error
 endif

 if gas eq 'n2o' then begin
  srandcolper=0.4842;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=3.5734; spectral error
 endif

 if gas eq 'co' then begin
  srandcolper=0.6280;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=1.1707; spectral error
 endif

 if srandcolper eq 0 then begin
  print, 'random and systematic error percentages not yet entered in makeHDFdata for this gas. Using fill value'
  stop
 endif
endif ;close TAB


if site eq 'MLO' then begin
srandcolper=0.0
sspectcolper=0.0

 if gas eq 'hno3' then begin
  srandcolper=1.7993 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=6.1783; spectral error
 endif

 if gas eq 'hcl' then begin
  srandcolper=1.1229 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=3.4154; spectral error
 endif

 if gas eq 'hf' then begin
  srandcolper=1.05456 ;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=0.61739; spectral error
 endif

 if gas eq 'o3' then begin
  srandcolper=0.49616;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=1.6240; spectral error
 endif

 if gas eq 'c2h6' then begin
  srandcolper=1.3058;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=13.5258; spectral error
 endif

 if gas eq 'co' then begin
  srandcolper=0.5026;random error percentages calculated by errorcalcncar, listed in Error_summary
  sspectcolper=1.5615; spectral error
 endif

 if srandcolper eq 0 then begin
  print, 'random and systematic error percentages not yet entered in makeHDFdata for this gas. Using fill value'
  stop
 endif
endif ;close MLO

if srandcolper eq 0 then begin
  print, 'random and systematic error percentages not yet entered in makeHDFdata for this site. Using fill value'
  stop
 endif

capgas=strupcase(gas)

savfilename='../'+gas+'.sav'
;savfilename='../'+gas+'.housefiltered_all.sav'
restore,savfilename

il=where(data.year eq year, nil)
if nil eq 0 then goto, next
temp=data(il)
data=temp

;add a bit to remove any MLO measurements from 19961029 or 19961102)
if site eq 'MLO' then begin
 furtherfilter=where(temp.year eq 1996 and temp.day eq 29 and temp.month eq 10, complement=others)
 datat=temp(others)
 furtherfilter2=where(datat.year eq 1996 and datat.day eq 2 and datat.month eq 11, complement=others)
 data=datat(others)
endif

n=n_elements(data.datetime)
if site eq 'TAB' then nlayers=47
if site eq 'MLO' then nlayers=41

Srandomfile=capgas+'_Srandom.covariance'
Srandom=fltarr(nlayers, nlayers)
Ssystfile=capgas+'_Ssystematic.covariance'
Ssyst=fltarr(nlayers, nlayers)
junk=''
;read the covariance matrices in
openr,1,Srandomfile
readf,1,junk
readf,1,Srandom
close,1
openr,1,Ssystfile
readf,1,junk
readf,1,Ssyst
close,1

;reverse both of these matrices because everything else is altitude bottom-top!
;temp=reverse(reverse(Srandom,1),2)
;Srandom=temp
;temp=reverse(reverse(Ssyst,1),2)
;Ssyst=temp

inputfilename=gas+'_'+year+'_input.txt'
openw,1,inputfilename
printf,1, 'DATETIME'
for i=0, n-1 do printf,1, data(i).datetime
printf,1,'LATITUDE.INSTRUMENT'
printf,1, data(0).latitude
printf,1,'LONGITUDE.INSTRUMENT'
printf,1, data(0).longitude
printf,1,'ALTITUDE.INSTRUMENT'
printf,1, data(0).alt_instrument

printf,1,'ALTITUDE.BOUNDARIES'
;for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
 printf,1,data(0).alt_boundaries(0,j)
 endfor
 for j=0, nlayers-1 do begin
 printf,1,data(0).alt_boundaries(1,j)
 endfor
;endfor

;printf,1,'ALTITUDE.LAYER.INDEX'
;;for i=0, n-1 do begin
; for j=0, nlayers-1 do printf,1, data(0).alt_index(j)
;;endfor

printf,1,'SURFACE.PRESSURE_INDEPENDENT'
for i=0, n-1 do begin
 if data(i).surface_pressure eq -999.0000 then begin
  printf,1,'      -90000.000'
 endif else printf,1, data(i).surface_pressure
endfor

printf,1,'SURFACE.TEMPERATURE_INDEPENDENT'
for i=0, n-1 do printf,1, data(i).surface_temperature

printf,1,'ALTITUDE'
for j=0, nlayers-1 do printf,1,data(0).altitude(j)

printf,1,'PRESSURE_INDEPENDENT'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).p(j)
 endfor
endfor

printf,1,'TEMPERATURE_INDEPENDENT'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).t(j)
 endfor
endfor

printf,1,capgas+'.MIXING.RATIO_ABSORPTION.SOLAR'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).retvmr(j)
 endfor
endfor

printf,1, capgas+'.MIXING.RATIO_ABSORPTION.SOLAR_APRIORI'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).aprvmr(j)
 endfor
endfor

printf,1,capgas+'.MIXING.RATIO_ABSORPTION.SOLAR_AVK'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  for k=0, nlayers-1 do begin
   printf,1,data(i).AK(j,k)
  endfor
 endfor
endfor

printf,1, 'INTEGRATION.TIME'; capgas+'.MIXING.RATIO_ABSORPTION.SOLAR_INTEGRATION.TIME'
for i=0, n-1 do printf,1,data(i).int_time

printf,1,capgas+'.MIXING.RATIO_ABSORPTION.SOLAR_UNCERTAINTY.RANDOM'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  for k=0, nlayers-1 do begin
   printf,1,Srandom(j,k)
  endfor
 endfor
endfor

printf,1, capgas+'.MIXING.RATIO_ABSORPTION.SOLAR_UNCERTAINTY.SYSTEMATIC'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  for k=0, nlayers-1 do begin
   printf,1,Ssyst(j,k)
  endfor
 endfor
endfor

printf,1,capgas+'.COLUMN.PARTIAL_ABSORPTION.SOLAR'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).retlaycol(j)
 endfor
endfor

printf,1,capgas+'.COLUMN.PARTIAL_ABSORPTION.SOLAR_APRIORI'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).aprlaycol(j)
 endfor
endfor

printf,1,capgas+'.COLUMN_ABSORPTION.SOLAR'
for i=0, n-1 do printf,1,data(i).rettc
printf,1,capgas+'.COLUMN_ABSORPTION.SOLAR_APRIORI'
for i=0, n-1 do printf,1,data(i).aprtc

printf,1,capgas+'.COLUMN_ABSORPTION.SOLAR_AVK'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
   printf,1,data(i).aktc(j)
 endfor
endfor

printf,1,capgas+'.COLUMN_ABSORPTION.SOLAR_UNCERTAINTY.RANDOM'
if srandcolper ne 0. then begin
 for i=0, n-1 do printf,1, (srandcolper/100.)*data(i).rettc
endif else begin
 for i=0, n-1 do printf,1, '-9.0000E+004'
endelse

printf,1,capgas+'.COLUMN_ABSORPTION.SOLAR_UNCERTAINTY.SYSTEMATIC'
if sspectcolper ne 0 then begin
 for i=0, n-1 do printf,1, (sspectcolper/100.)*data(i).rettc
endif else begin
 for i=0L, 572-1 do printf,1, '-9.0000E+004'
endelse

printf,1,'ANGLE.SOLAR_ZENITH.ASTRONOMICAL'
for i=0, n-1 do printf,1,data(i).sza

printf,1,'ANGLE.SOLAR_AZIMUTH'
for i=0, n-1 do begin
 if data(i).azi le 180 then printf,1, data(i).azi ;azi is 360 from S, converting to description in meta, +/- S
 if data(i).azi gt 180 then printf,1, (360.-data(i).azi)*(-1)
endfor

printf,1,'H2O.MIXING.RATIO_ABSORPTION.SOLAR'
for i=0, n-1 do begin
 for j=0, nlayers-1 do begin
  printf,1,data(i).aprh2ovmr(j)
 endfor
endfor

printf,1,'H2O.COLUMN_ABSORPTION.SOLAR'
for i=0, n-1 do printf,1,data(i).aprh2otc
close,1

next:

end