Account for integer MetaData/stationIdentification (#206)

* integer MetaData/stationIdentification * remove output * add new files
MetOffice · May 20, 2024 · bcd0f03 · bcd0f03
1 parent b30d912
commit bcd0f03
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Showing 7 changed files with 100 additions and 8 deletions.
diff --git a/src/opsinputs/VarObsWriterParameters.h b/src/opsinputs/VarObsWriterParameters.h
@@ -76,6 +76,9 @@ class VarObsWriterParameters : public oops::ObsFilterParametersBase {
   /// length of each output profile is set to the length of the profiles in the ObsSpace.
   oops::Parameter<bool> varobsLengthIsIC_PLevels{"varobs_length_is_IC_PLevels", false, this};
 
+  /// Set to true if MetaData/stationIdentification is an integer instead of a string.
+  oops::Parameter<bool> StationIDIntToString{"station_ID_int_to_string", false, this};
+
   /// Update OPS flag to output the varbc predictors
   oops::Parameter<bool> outputVarBCPredictors{"output_varbc_predictors", false, this};
 

diff --git a/src/opsinputs/opsinputs_fill_mod.F90 b/src/opsinputs/opsinputs_fill_mod.F90
@@ -1837,12 +1837,14 @@ end subroutine opsinputs_fill_fillinteger
 !>   Name of the JEDI variable used to populate \p String1.
 !> \param[in] JediGroup
 !>   Group of the JEDI variable used to populate \p String1.
-!>
+!> \param[in] ConvertIntToSTring
+!>   Convert an integer-valued ObsSpace vector to a string.
 !> \note This function returns early (without a warning) if the specified JEDI variable is not found.
 !> We rely on warnings printed by the OPS code whenever data needed to output a requested varfield
 !> are not found.
 subroutine opsinputs_fill_fillstring( &
-  Hdr, OpsVarName, JediToOpsLayoutMapping, StringLen, String1, ObsSpace, JediVarName, JediVarGroup)
+  Hdr, OpsVarName, JediToOpsLayoutMapping, StringLen, String1, ObsSpace, JediVarName, JediVarGroup, &
+  ConvertIntToSTring)
 implicit none
 
 ! Subroutine arguments:
@@ -1854,29 +1856,57 @@ subroutine opsinputs_fill_fillstring( &
 type(c_ptr), value, intent(in)                     :: ObsSpace
 character(len=*), intent(in)                       :: JediVarName
 character(len=*), intent(in)                       :: JediVarGroup
+logical, optional, intent(in)                      :: ConvertIntToString
 
 ! Local declarations:
 character(len=StringLen)                           :: VarValue(JediToOpsLayoutMapping % NumJediObs)
+integer(integer64)                                 :: IntVarValue(JediToOpsLayoutMapping % NumJediObs)
 integer                                            :: i
+logical                                            :: IntToString
+character(len=20)                                  :: IntAsString
 
 ! Body:
 
+
+
 if (obsspace_has(ObsSpace, JediVarGroup, JediVarName)) then
+  if (present(ConvertIntToString)) then
+    IntToString = ConvertIntToString
+  else
+    IntToString = .false.
+  end if
+
   ! Retrieve data from JEDI
-  call opsinputs_obsspace_get_db_string(ObsSpace, JediVarGroup, JediVarName, &
-                                        int(StringLen, kind=c_int), VarValue)
+  if (IntToString) then
+    call obsspace_get_db(ObsSpace, JediVarGroup, JediVarName, IntVarValue)
+  else
+    call opsinputs_obsspace_get_db_string(ObsSpace, JediVarGroup, JediVarName, &
+         int(StringLen, kind=c_int), VarValue)
+  end if
 
   ! Fill the OPS data structures
   call Ops_Alloc(Hdr, OpsVarName, JediToOpsLayoutMapping % NumOpsObs, String1)
   do i = 1, JediToOpsLayoutMapping % NumOpsObs
     if (JediToOpsLayoutMapping % ConvertRecordsToMultilevelObs) then
       if (JediToOpsLayoutMapping % RecordStarts(i + 1) > JediToOpsLayoutMapping % RecordStarts(i)) then
         ! This record is non-empty. Use the first location from that record.
-        String1(i) = VarValue(JediToOpsLayoutMapping % LocationsOrderedByRecord( &
-                                JediToOpsLayoutMapping % RecordStarts(i)))
+        if (IntToString) then
+           write(IntAsString,"(I0)") &
+             IntVarValue(JediToOpsLayoutMapping % LocationsOrderedByRecord( &
+             JediToOpsLayoutMapping % RecordStarts(i)))
+          String1(i) = IntAsString
+        else
+          String1(i) = VarValue(JediToOpsLayoutMapping % LocationsOrderedByRecord( &
+               JediToOpsLayoutMapping % RecordStarts(i)))
+        end if
       end if
     else
-      String1(i) = VarValue(i)
+      if (IntToString) then
+        write(IntAsString,"(I0)") IntVarValue(i)
+        String1(i) = IntAsString
+      else
+        String1(i) = VarValue(i)
+      end if
     end if
   end do
 end if

diff --git a/src/opsinputs/opsinputs_varobswriter_mod.F90 b/src/opsinputs/opsinputs_varobswriter_mod.F90
@@ -155,6 +155,7 @@ module opsinputs_varobswriter_mod
   logical            :: RequireTForTheta
   logical            :: FillObsTypeFromOpsSubType
   logical            :: VarobsLengthIsIC_PLevels
+  logical            :: StationIDIntToString
 
   character(len=100) :: latitudeName
   character(len=100) :: longitudeName
@@ -313,6 +314,8 @@ function opsinputs_varobswriter_create(self, f_conf, comm_is_valid, comm, channe
 
 call f_conf % get_or_die("varobs_length_is_IC_PLevels", self % VarobsLengthIsIC_PLevels)
 
+call f_conf % get_or_die("station_ID_int_to_string", self % StationIDIntToString)
+
 call f_conf % get_or_die("size_of_varobs_array", self % size_of_varobs_array)
 
 call f_conf % get_or_die("compress_var_channels", self % compressVarChannels)
@@ -738,7 +741,8 @@ subroutine opsinputs_varobswriter_populateobservations( &
 
 if (obsspace_has(ObsSpace, "MetaData", "stationIdentification")) then
   call opsinputs_fill_fillstring(Ob % Header % Callsign, "Callsign", JediToOpsLayoutMapping, &
-    LenCallSign, Ob % Callsign, ObsSpace, "stationIdentification", "MetaData")
+    LenCallSign, Ob % Callsign, ObsSpace, "stationIdentification", "MetaData", &
+    self % StationIDIntToString)
 else if (obsspace_has(ObsSpace, "MetaData", "satelliteIdentifier")) then
   call opsinputs_varobswriter_fillsatid(Ob, ObsSpace, JediToOpsLayoutMapping)
   call Ops_Alloc(Ob % Header % Callsign, "Callsign", JediToOpsLayoutMapping % NumOpsObs, Ob % Callsign)

diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
@@ -106,6 +106,9 @@ set_tests_properties(test_opsinputs_varobswriter_setup PROPERTIES FIXTURES_SETUP
 ADD_WRITER_TEST(NAME     varobswriter_001_VarField_pstar
                 YAML     001_VarField_pstar.yaml
                 DATA     001_VarField_pstar.nc4)
+ADD_WRITER_TEST(NAME     varobswriter_001_VarField_pstar_stationID_integer
+                YAML     001_VarField_pstar_stationID_integer.yaml
+                DATA     001_VarField_pstar_stationID_integer.nc4)
 ADD_WRITER_TEST(NAME     varobswriter_002_VarField_temperature_Surface
                 YAML     002_VarField_temperature_Surface.yaml
                 DATA     002_VarField_temperature_Surface.nc4)

diff --git a/test/generate_unittest_netcdfs.py b/test/generate_unittest_netcdfs.py
@@ -69,6 +69,30 @@ def output_1d_simulated_var_to_netcdf(var_name, file_name, with_bias=False):
     f.close()
 
 
+def output_1d_simulated_var_to_netcdf_stationID_integer(var_name, file_name):
+    f = nc4.Dataset(file_name, 'w', format="NETCDF4")
+
+    nlocs = 4
+    f.createDimension('Location', nlocs)
+
+    var = f.createVariable('MetaData/latitude', 'f', ('Location',))
+    var[:] = [21, 22, -23, 24]
+    var = f.createVariable('MetaData/longitude', 'f', ('Location',))
+    var[:] = [31, 32, 33, 34]
+    var = f.createVariable('MetaData/time', 'f', ('Location',))
+    minute = 1 / 60.
+    var[:] = [1 * minute, 2 * minute, 3 * minute, 4 * minute]
+    var = f.createVariable('MetaData/stationIdentification', 'i', ('Location',))
+    var[:] = [1, 2, 3, 4]
+    var = f.createVariable('ObsValue/' + var_name, 'f', ('Location',))
+    obsVal = [1.1, missing_float, 1.3, 1.4]
+    var[:] = obsVal
+    var = f.createVariable('ObsError/' + var_name, 'f', ('Location',))
+    var[:] = [0.1, missing_float, 0.3, 0.4]
+    f.date_time = 2018010100
+
+    f.close()
+
 def output_1d_simulated_vars_to_netcdf(var_name_1, var_name_2, file_name):
     f = nc4.Dataset(file_name, 'w', format="NETCDF4")
 
@@ -640,6 +664,7 @@ def copy_var_to_var(Group, invarname, outvarname, filename):
 if __name__ == "__main__":
     # VarObs
     output_1d_simulated_var_to_netcdf('surfacePressure',             'testinput/001_VarField_pstar.nc4') # Surface
+    output_1d_simulated_var_to_netcdf_stationID_integer('surfacePressure', 'testinput/001_VarField_pstar_stationID_integer.nc4')
     output_1d_simulated_var_to_netcdf('airTemperatureAt2M',           'testinput/002_VarField_temperature_Surface.nc4')
     output_2d_simulated_var_to_netcdf('airTemperature',               'testinput/002_VarField_temperature_RadarZ.nc4')
     output_1d_simulated_var_to_netcdf('relativeHumidityAt2M',         'testinput/003_VarField_rh_Surface.nc4')

diff --git a/test/testinput/001_VarField_pstar_stationID_integer.nc4 b/test/testinput/001_VarField_pstar_stationID_integer.nc4
diff --git a/test/testinput/001_VarField_pstar_stationID_integer.yaml b/test/testinput/001_VarField_pstar_stationID_integer.yaml
@@ -0,0 +1,27 @@
+time window:
+  begin: 2018-01-01T00:00:00Z
+  end: 2018-01-01T02:00:00Z
+
+observations:
+  - obs space:
+      name: Surface
+      obsdatain:
+        engine:
+          type: H5File
+          obsfile: Data/001_VarField_pstar_stationID_integer.nc4
+      simulated variables: [surfacePressure]
+    obs filters:
+    # Set the flag of observations with missing values to "pass": we want to check if these
+    # values are encoded correctly in the VarObsFile.
+    - filter: Reset Flags to Pass
+      flags_to_reset: [10, 15]  # missing, Hfailed
+    - filter: VarObs Writer
+      # Convert integer station ID to string.
+      station_ID_int_to_string: true
+      general_mode: debug
+    - filter: VarObs Checker
+      expected_main_table_columns:
+        Callsign: ["1", "2", "3", "4"]
+    HofX: ObsValue # just a placeholder -- not used, but needed to force calls to postFilter.
+    benchmarkFlag: 1000 # just to keep the ObsFilters test happy
+    flaggedBenchmark: 0