Add SMOS SSS to IODA converter with test data (NOAA-EMC#653)

* working stub

* seems to work with the current develop

* rewrote smos ioda converter to match new parent class

* added datetime to smos ioda file

* tweaked cdl files to make it past netcdf converter

* clean up todos

* clean up todos

* removed variable from ioda conversion yaml

* addition iodaVars.referenceDate

* from arrays to vectors

* note for Eigen Maps

utils/obsproc/Smos2Ioda.h

@@ -0,0 +1,87 @@
+#pragma once
+
+#include <iostream>
+#include <netcdf>    // NOLINT (using C API)
+#include <string>
+#include <vector>
+
+#include "eckit/config/LocalConfiguration.h"
+
+#include <Eigen/Dense>    // NOLINT
+
+#include "ioda/Group.h"
+#include "ioda/ObsGroup.h"
+
+#include "NetCDFToIodaConverter.h"
+
+namespace gdasapp {
+
+  class Smos2Ioda : public NetCDFToIodaConverter {
+   public:
+    explicit Smos2Ioda(const eckit::Configuration & fullConfig)
+    : NetCDFToIodaConverter(fullConfig) {
+      variable_ = "Salinity";
+    }
+
+    // Read netcdf file and populate iodaVars
+    gdasapp::IodaVars providerToIodaVars(const std::string fileName) final {
+      oops::Log::info() << "Processing files provided by SMOS" << std::endl;
+
+      // Open the NetCDF file in read-only mode
+      netCDF::NcFile ncFile(fileName, netCDF::NcFile::read);
+
+      // Get number of obs
+      int nobs = ncFile.getDim("n_grid_points").getSize();
+
+      // Set the int metadata names
+      // TODO(AFE): add other metadata in form of
+      // std::vector<std::string> intMetadataNames = {"pass", "cycle", "mission"};
+      std::vector<std::string> intMetadataNames = {};
+
+      // Set the float metadata name
+      // TODO(AFE): add other metadata in form of
+      // std::vector<std::string> floatMetadataNames = {"mdt"};
+      std::vector<std::string> floatMetadataNames = {};
+      // Create instance of iodaVars object
+      gdasapp::IodaVars iodaVars(nobs, floatMetadataNames, intMetadataNames);
+
+      std::vector<float> lat(iodaVars.location);
+      ncFile.getVar("Latitude").getVar(lat.data());
+
+      std::vector<float> lon(iodaVars.location);
+      ncFile.getVar("Longitude").getVar(lon.data());
+
+      std::vector<float> sss(iodaVars.location);
+      ncFile.getVar("SSS_corr").getVar(sss.data());
+
+      std::vector<float> sss_error(iodaVars.location);
+      ncFile.getVar("Sigma_SSS_corr").getVar(sss_error.data());
+
+      std::vector< uint16_t > sss_qc(iodaVars.location);
+      ncFile.getVar("Dg_quality_SSS_corr").getVar(sss_qc.data());
+
+      // according to https://earth.esa.int/eogateway/documents/20142/0/SMOS-L2-Aux-Data-Product-Specification.pdf,
+      // this is UTC decimal days after MJD2000 which is
+      // Jan 01 2000 00:00:00 GMT+0000
+      std::vector<float> datetime(iodaVars.location);
+      ncFile.getVar("Mean_acq_time").getVar(datetime.data());
+
+      iodaVars.referenceDate = "seconds since 1970-01-01T00:00:00Z";
+
+      // unix epoch (seconds after iodaVars.referenceDate) at
+      // Jan 01 2000 00:00:00 GMT+0000
+      const int mjd2000 = 946684800;
+
+      // TODO(AFE) maybe use Eigen Maps here
+      for (int i = 0; i < iodaVars.location; i++) {
+        iodaVars.longitude(i) = lon[i];
+        iodaVars.latitude(i) = lat[i];
+        iodaVars.obsVal(i) = sss[i];
+        iodaVars.obsError(i) = sss_error[i];
+        iodaVars.preQc(i) = sss_qc[i];
+        iodaVars.datetime(i) =  static_cast<int64_t>(datetime[i]*86400.0f) + mjd2000;
+      }
+      return iodaVars;
+    };
+  };  // class Smos2Ioda
+}  // namespace gdasapp

utils/obsproc/applications/gdas_obsprovider2ioda.h

@@ -7,6 +7,7 @@
 #include "oops/runs/Application.h"
 
 #include "../Rads2Ioda.h"
+#include "../Smos2Ioda.h"
 
 namespace gdasapp {
   class ObsProvider2IodaApp : public oops::Application {
@@ -25,6 +26,9 @@ namespace gdasapp {
         conv2ioda.writeToIoda();
       } else if (provider == "GHRSST") {
         oops::Log::info() << "Comming soon!" << std::endl;
+      } else if (provider == "SMOS") {
+        Smos2Ioda conv2ioda(fullConfig);
+        conv2ioda.writeToIoda();
       } else {
         oops::Log::info() << "Provider not implemented" << std::endl;
         return 1;

utils/test/CMakeLists.txt

@@ -2,6 +2,7 @@
 list( APPEND utils_test_input
   testinput/gdas_meanioda.yaml
   testinput/gdas_rads2ioda.yaml
+  testinput/gdas_smos2ioda.yaml
 )
 
 file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/testinput)
@@ -37,3 +38,10 @@ ecbuild_add_test( TARGET  test_gdasapp_util_rads2ioda
                   ARGS    "../testinput/gdas_rads2ioda.yaml"
                   LIBS    gdas-utils
                   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/obsproc)
+
+# Test the SMOS to IODA converter
+ecbuild_add_test( TARGET  test_gdasapp_util_smos2ioda
+                  COMMAND ${CMAKE_BINARY_DIR}/bin/gdas_obsprovider2ioda.x
+                  ARGS    "../testinput/gdas_smos2ioda.yaml"
+                  LIBS    gdas-utils
+                  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/obsproc)

utils/test/prepdata.sh

@@ -22,7 +22,7 @@ cdl2nc4 icec_amsr2_south_2.nc4 ${project_source_dir}/testdata/icec_amsr2_south_2
 # TODO(Andy): Fix the corrupted cdl files below
 #cdl2nc4 sss_smap_1.nc4 ${project_source_dir}/testdata/sss_smap_1.cdl
 #cdl2nc4 sss_smap_2.nc4 ${project_source_dir}/testdata/sss_smap_2.cdl
-#cdl2nc4 sss_smos_1.nc4 ${project_source_dir}/testdata/sss_smos_1.cdl
-#cdl2nc4 sss_smos_2.nc4 ${project_source_dir}/testdata/sss_smos_2.cdl
+cdl2nc4 sss_smos_1.nc4 ${project_source_dir}/testdata/sss_smos_1.cdl
+cdl2nc4 sss_smos_2.nc4 ${project_source_dir}/testdata/sss_smos_2.cdl
 cdl2nc4 ghrsst_sst_mb_202107010000.nc4 ${project_source_dir}/testdata/ghrsst_sst_mb_202107010000.cdl
 cdl2nc4 ghrsst_sst_mb_202107010100.nc4 ${project_source_dir}/testdata/ghrsst_sst_mb_202107010100.cdl