Variables for IODA format added after cleanup of the ioda converter

NOAA-EMC · Sep 21, 2023 · 1f2fc4e · 1f2fc4e
1 parent 945c359
commit 1f2fc4e
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Showing 2 changed files with 70 additions and 5 deletions.
diff --git a/utils/obsproc/NetCDFToIodaConverter.h b/utils/obsproc/NetCDFToIodaConverter.h
@@ -25,6 +25,11 @@ namespace gdasapp {
     Eigen::ArrayXf obsVal;
     Eigen::ArrayXf obsError;
     Eigen::ArrayXi preQc;
+    Eigen::ArrayXi dateVal;
+    Eigen::ArrayXf latVal;
+    Eigen::ArrayXf lonVal;
+    Eigen::ArrayXi cycleVal;
+    Eigen::ArrayXi passVal;
     std::string units;  // reference date for epoch time
   };
 
@@ -84,24 +89,48 @@ namespace gdasapp {
       float_params.setFillValue<float>(missing_value);
 
       // Create the IODA variables
+      // TODO(Mindo): Get the date info from the netcdf file
       ioda::Variable adtIodaDatetime =
-        ogrp.vars.createWithScales<float>("Metadata/dateTime",
+        ogrp.vars.createWithScales<int>("MetaData/dateTime",
+                                          {ogrp.vars["Location"]}, float_params);
+      adtIodaDatetime.atts.add<std::string>("units",
+                                          {"seconds since 1858-11-17 00:00:00 UTC"}, {1});
+      ioda::Variable cycleIodaVal =
+        ogrp.vars.createWithScales<int>("MetaData/cycle",
+                                          {ogrp.vars["Location"]}, float_params);
+      ioda::Variable passIodaVal =
+        ogrp.vars.createWithScales<int>("MetaData/pass",
+                                          {ogrp.vars["Location"]}, float_params);
+      ioda::Variable latIodaVal =
+        ogrp.vars.createWithScales<float>("MetaData/latitude",
+                                          {ogrp.vars["Location"]}, float_params);
+      ioda::Variable lonIodaVal =
+        ogrp.vars.createWithScales<float>("MetaData/longitude",
                                           {ogrp.vars["Location"]}, float_params);
-      // TODO(Mindo): Get the date info from the netcdf file
-      adtIodaDatetime.atts.add<std::string>("units", {"seconds since 9999-04-15T12:00:00Z"}, {1});
-
       ioda::Variable adtIodaObsVal =
         ogrp.vars.createWithScales<float>("ObsValue/"+variable_,
                                           {ogrp.vars["Location"]}, float_params);
       ioda::Variable adtIodaObsErr =
         ogrp.vars.createWithScales<float>("ObsError/"+variable_,
                                           {ogrp.vars["Location"]}, float_params);
+      ioda::Variable adtIodaPreQCVal =
+        ogrp.vars.createWithScales<int>("PreQC/absoluteDynamicTopography",
+                                          {ogrp.vars["Location"]}, float_params);
+      // Write metadata value to group
+      adtIodaDatetime.writeWithEigenRegular(iodaVars.dateVal);
+      cycleIodaVal.writeWithEigenRegular(iodaVars.cycleVal);
+      passIodaVal.writeWithEigenRegular(iodaVars.passVal);
+      latIodaVal.writeWithEigenRegular(iodaVars.latVal);
+      lonIodaVal.writeWithEigenRegular(iodaVars.lonVal);
 
       // Write adt obs value to group
       adtIodaObsVal.writeWithEigenRegular(iodaVars.obsVal);
 
       // Write adt obs error to group
       adtIodaObsErr.writeWithEigenRegular(iodaVars.obsError);
+
+      // Write PreQC
+      adtIodaPreQCVal.writeWithEigenRegular(iodaVars.preQc);
     }
 
    private:

diff --git a/utils/obsproc/Rads2Ioda.h b/utils/obsproc/Rads2Ioda.h
@@ -39,6 +39,36 @@ namespace gdasapp {
       iodaVars.obsVal = Eigen::ArrayXf(iodaVars.location);
       iodaVars.obsError = Eigen::ArrayXf(iodaVars.location);
       iodaVars.preQc = Eigen::ArrayXi(iodaVars.location);
+      iodaVars.dateVal = Eigen::ArrayXi(iodaVars.location);
+      iodaVars.latVal = Eigen::ArrayXf(iodaVars.location);
+      iodaVars.lonVal = Eigen::ArrayXf(iodaVars.location);
+      iodaVars.cycleVal = Eigen::ArrayXi(iodaVars.location);
+      iodaVars.passVal = Eigen::ArrayXi(iodaVars.location);
+
+      // Get dateTime
+      netCDF::NcVar dateTimeNcVar = ncFile.getVar("time_mjd");
+      int dateTimeVal[iodaVars.location];  // NOLINT (can't pass vector to getVar below)
+      dateTimeNcVar.getVar(dateTimeVal);   // units is controlled at NetcdfConverter.h
+
+      // Get other metadatas
+      netCDF::NcVar cycleNcVar = ncFile.getVar("cycle");
+      int cycleVal[iodaVars.location];  // NOLINT (can't pass vector to getVar below)
+      cycleNcVar.getVar(cycleVal);
+      netCDF::NcVar passNcVar = ncFile.getVar("pass");
+      int passVal[iodaVars.location];  // NOLINT (can't pass vector to getVar below)
+      passNcVar.getVar(passVal);
+
+      netCDF::NcVar latNcVar = ncFile.getVar("lat");
+      int latVal[iodaVars.location];  // NOLINT (can't pass vector to getVar below)
+      latNcVar.getVar(latVal);
+
+      netCDF::NcVar lonNcVar = ncFile.getVar("lon");
+      int lonVal[iodaVars.location];  // NOLINT (can't pass vector to getVar below)
+      lonNcVar.getVar(lonVal);
+      std::string geounits;
+      lonNcVar.getAtt("units").getValues(geounits);
+      float geoscaleFactor;
+      lonNcVar.getAtt("scale_factor").getValues(&geoscaleFactor);
 
       // Get adt_egm2008 obs values and attributes
       netCDF::NcVar adtNcVar = ncFile.getVar("adt_egm2008");
@@ -50,11 +80,17 @@ namespace gdasapp {
       adtNcVar.getAtt("scale_factor").getValues(&scaleFactor);
       for (int i = 0; i <= iodaVars.location; i++) {
         iodaVars.obsVal(i) = static_cast<float>(adtObsVal[i])*scaleFactor;
+        iodaVars.dateVal(i) = static_cast<int>(dateTimeVal[i])*24*60*60;
+        iodaVars.cycleVal(i) = static_cast<int>(cycleVal[i]);
+        iodaVars.passVal(i) = static_cast<int>(passVal[i]);
+        iodaVars.latVal(i) = static_cast<int>(latVal[i])*geoscaleFactor;
+        iodaVars.lonVal(i) = static_cast<int>(lonVal[i])*geoscaleFactor;
       }
 
-      // Do something for obs error
+      // Do something for obs error and PreQC
       for (int i = 0; i <= iodaVars.location; i++) {
         iodaVars.obsError(i) = 0.1;
+        iodaVars.preQc(i) = 0.0;
       }
     };
   };  // class Rads2Ioda