From 3e8c0ddf4a034067500d00352f0910dc8800c322 Mon Sep 17 00:00:00 2001
From: Cheng Da <cheng.da@nasa.gov>
Date: Wed, 18 Oct 2023 09:41:59 -0400
Subject: [PATCH] update SSS processing & obsop

---
 src/obs/obsop_sss.f90 |  4 ++++
 src/obs/read_smap.f90 |  7 ++++++-
 src/obs/superob.f90   | 14 ++++++++++++++
 3 files changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/obs/obsop_sss.f90 b/src/obs/obsop_sss.f90
index 2872f69..5b2925e 100644
--- a/src/obs/obsop_sss.f90
+++ b/src/obs/obsop_sss.f90
@@ -488,6 +488,10 @@ SUBROUTINE process_command_line
       CALL GET_COMMAND_ARGUMENT(i+1,arg2)
       PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
       read (arg2,*) DO_SUPEROBS
+    case('-binary')
+      CALL GET_COMMAND_ARGUMENT(i+1,arg2)
+      PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
+      read (arg2,*) BINARY_INPUT
     case('-thin')
       CALL GET_COMMAND_ARGUMENT(i+1,arg2)
       PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
diff --git a/src/obs/read_smap.f90 b/src/obs/read_smap.f90
index ea1ad47..f529094 100644
--- a/src/obs/read_smap.f90
+++ b/src/obs/read_smap.f90
@@ -253,6 +253,8 @@ SUBROUTINE read_jpl_smap_l2_sss_h5(obsinfile, obs_data, nobs, Syyyymmddhh, delta
   INTEGER,PARAMETER :: QUAL_FLAG_SSS_USABLE_BAD  = 1
   INTEGER,PARAMETER :: QUAL_FLAG_SSS_HAS_LAND    = 1
   INTEGER,PARAMETER :: QUAL_FLAG_SSS_HAS_ICE     = 1
+  REAL(r_size),PARAMETER :: oerr_qc_user  = 2.0 ! psu, obs with JPL > oerr_qc_user removed
+  REAL(r_size),PARAMETER :: oerr_min_user = 0.2 ! psu, obs with JPL oerr < oerr_min_user has err oerr_min_user 
 
 !-------------------------------------------------------------------------------
 ! Open the hdf5 file 
@@ -393,6 +395,9 @@ SUBROUTINE read_jpl_smap_l2_sss_h5(obsinfile, obs_data, nobs, Syyyymmddhh, delta
    where(stde < r4FillValue)
       valid = .false.
    end where
+   where(stde > oerr_qc_user) ! User QC based on read-in oerr
+      valid = .false.
+   end where
    WRITE(6,*) "[msg] read_jpl_smap_l2_sss_h5::smap_sss_uncertainty: min, max=", &
               minval(stde, mask=valid), maxval(stde, mask=valid)
  
@@ -481,7 +486,7 @@ SUBROUTINE read_jpl_smap_l2_sss_h5(obsinfile, obs_data, nobs, Syyyymmddhh, delta
            obs_data(n)%x_grd(2) = alat2d(i,j)
            obs_data(n)%hour     = sss_time_in_seconds_since19780101(i)/3600.
            obs_data(n)%value    = sea_surface_salinity(i,j)
-           obs_data(n)%oerr     = stde(i,j)
+           obs_data(n)%oerr     = max(stde(i,j), oerr_min_user) ! set a limit bound for error
         end if
      end do
   end do
diff --git a/src/obs/superob.f90 b/src/obs/superob.f90
index 519e5bf..6d75835 100644
--- a/src/obs/superob.f90
+++ b/src/obs/superob.f90
@@ -64,6 +64,8 @@ PROGRAM superob
   INTEGER, DIMENSION(:,:), ALLOCATABLE :: supercnt
   INTEGER :: idx
   REAL(r_size) :: min_oerr = 0.2 !(K)
+  REAL(r_size) :: input_oerr = 0.75 ! (K)
+  LOGICAL :: HAS_INPUT_OERR = .false.
 
   !-----------------------------------------------------------------------------
   ! Initialize the common_oceanmodel module, and process command line options
@@ -181,6 +183,10 @@ PROGRAM superob
         nobs = idx
       endif
 
+      if (HAS_INPUT_OERR) then
+         oerr(:) = input_oerr
+      endif
+
       call write_obs3(trim(obsoutfile),nobs,elem(1:nobs), &
                                             rlon(1:nobs), &
                                             rlat(1:nobs), &
@@ -243,6 +249,14 @@ SUBROUTINE process_command_line
       CALL GET_COMMAND_ARGUMENT(i+1,arg2)
       PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
       read (arg2,*) min_quality_level
+    case('-inputoerr')
+      CALL GET_COMMAND_ARGUMENT(i+1,arg2)
+      PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
+      read (arg2,*) HAS_INPUT_OERR
+    case('-useroerr')
+      CALL GET_COMMAND_ARGUMENT(i+1,arg2)
+      PRINT *, "Argument ", i+1, " = ",TRIM(arg2)
+      read (arg2,*) input_oerr
     case('-debug')
       CALL GET_COMMAND_ARGUMENT(i+1,arg2)
       PRINT *, "Argument ", i+1, " = ",TRIM(arg2)