Added example utility using OOPS and IODA (#553)

* Move soca utils to subdirectory

utils/CMakeLists.txt

@@ -1,18 +1,20 @@
 project(gdas-utils LANGUAGES C CXX )
 
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_C_STANDARD 11)
+set(CMAKE_C_STANDARD_REQUIRED ON)
+set(CMAKE_C_EXTENSIONS OFF)
+set(CMAKE_FORTRAN_STANDARD 08)
+set(CMAKE_FORTRAN_STANDARD_REQUIRED ON)
+set(CMAKE_FORTRAN_EXTENSIONS OFF)
+
 find_package(NetCDF REQUIRED COMPONENTS CXX)
 find_package(oops REQUIRED)
 find_package(atlas REQUIRED)
 find_package(soca REQUIRED)
 
-# Increment post processing
-ecbuild_add_executable( TARGET gdas_incr_handler.x
-                        SOURCES gdas_incr_handler.cc gdas_postprocincr.h)
-target_compile_features( gdas_incr_handler.x PUBLIC cxx_std_17)
-target_link_libraries( gdas_incr_handler.x PUBLIC NetCDF::NetCDF_CXX oops atlas soca)
-
-# Hybrid-Weight
-ecbuild_add_executable( TARGET gdas_socahybridweights.x
-                        SOURCES gdas_socahybridweights.cc )
-target_compile_features( gdas_socahybridweights.x PUBLIC cxx_std_17)
-target_link_libraries( gdas_socahybridweights.x PUBLIC NetCDF::NetCDF_CXX oops atlas soca)
+add_subdirectory(soca)
+add_subdirectory(ioda_example)
+add_subdirectory(test)

utils/ioda_example/CMakeLists.txt

@@ -0,0 +1,6 @@
+ecbuild_add_executable( TARGET gdas_meanioda.x
+                        SOURCES gdas_meanioda.cc )
+
+target_compile_features( gdas_meanioda.x PUBLIC cxx_std_17)
+target_link_libraries( gdas_meanioda.x PUBLIC oops ioda)
+

utils/ioda_example/gdas_meanioda.cc

@@ -0,0 +1,14 @@
+#include "gdas_meanioda.h"
+#include "oops/runs/Run.h"
+
+// this is an example application that
+// will use IODA to read a file and print something
+// it is intended to be very bare bones
+// you will note the .cc file is very empty
+// the .h file is where the action is!
+
+int main(int argc, char ** argv) {
+  oops::Run run(argc, argv);
+  gdasapp::IodaExample iodaexample;
+  return run.execute(iodaexample);
+}

utils/ioda_example/gdas_meanioda.h

@@ -0,0 +1,86 @@
+#include <iostream>
+#include <numeric>
+#include "eckit/config/LocalConfiguration.h"
+#include "ioda/Group.h"
+#include "ioda/ObsSpace.h"
+#include "ioda/ObsVector.h"
+#include "oops/base/PostProcessor.h"
+#include "oops/mpi/mpi.h"
+#include "oops/runs/Application.h"
+#include "oops/util/DateTime.h"
+#include "oops/util/Duration.h"
+#include "oops/util/Logger.h"
+
+namespace gdasapp {
+  // this is an example of how one can use OOPS and IODA to do something
+  // in this code, we will read in configuration from YAML
+  // and then use that configuration to read in a IODA formatted file,
+  // read one group/variable (with optional channel)
+  // and compute and print out the mean of the variable.
+  // Nothing fancy, but you can see how this could be expanded!
+
+  class IodaExample : public oops::Application {
+   public:
+    explicit IodaExample(const eckit::mpi::Comm & comm = oops::mpi::world())
+      : Application(comm) {}
+    static const std::string classname() {return "gdasapp::IodaExample";}
+
+    int execute(const eckit::Configuration & fullConfig, bool /*validate*/) const {
+
+      // get the obs space configuration
+      const eckit::LocalConfiguration obsConfig(fullConfig, "obs space");
+      ioda::ObsTopLevelParameters obsparams;
+      obsparams.validateAndDeserialize(obsConfig);  // TODO CRM, can I remove this and then the simulated vars junk??
+      oops::Log::info() << "obs space: " << std::endl << obsConfig << std::endl;
+
+      // time window stuff
+      std::string winbegin;
+      std::string winend;
+      fullConfig.get("window begin", winbegin);
+      fullConfig.get("window end", winend);
+
+      // what variable to get the mean of
+      std::string group;
+      std::string variable;
+      fullConfig.get("group", group);
+      fullConfig.get("variable", variable);
+      int chan = 0;
+      if (fullConfig.has("channel")) {
+        fullConfig.get("channel", chan);
+      }
+
+      // read the obs space
+      // Note, the below line does a lot of heavy lifting
+      // we can probably go to a lower level function (and more of them) to accomplish the same thing
+      ioda::ObsSpace ospace(obsparams, oops::mpi::world(), util::DateTime(winbegin), util::DateTime(winend), oops::mpi::myself());
+      const size_t nlocs = ospace.nlocs();
+      oops::Log::info() << "nlocs =" << nlocs << std::endl;
+      std::vector<float> buffer(nlocs);
+
+      // below is grabbing from the IODA obs space the specified group/variable and putting it into the buffer
+      if (chan == 0) {
+        // no channel is selected
+        ospace.get_db(group, variable, buffer);
+      } else {
+        // give it the channel as a single item list
+        ospace.get_db(group, variable, buffer, {chan});
+      }
+
+      // the below line computes the mean, aka sum divided by count
+      const float mean = std::accumulate(buffer.begin(), buffer.end(), 0) / float(nlocs);
+
+      // write the mean out to the stdout
+      oops::Log::info() << "mean value for " << group << "/" << variable << "=" << mean << std::endl;
+
+      // a better program should return a real exit code depending on result, but this is just an example!
+      return 0;
+    }
+    // -----------------------------------------------------------------------------
+   private:
+    std::string appname() const {
+      return "gdasapp::IodaExample";
+    }
+    // -----------------------------------------------------------------------------
+  };
+
+}  // namespace gdasapp

utils/soca/CMakeLists.txt

@@ -0,0 +1,11 @@
+# Increment post processing
+ecbuild_add_executable( TARGET gdas_incr_handler.x
+                        SOURCES gdas_incr_handler.cc gdas_postprocincr.h)
+target_compile_features( gdas_incr_handler.x PUBLIC cxx_std_17)
+target_link_libraries( gdas_incr_handler.x PUBLIC NetCDF::NetCDF_CXX oops atlas soca)
+
+# Hybrid-Weight
+ecbuild_add_executable( TARGET gdas_socahybridweights.x
+                        SOURCES gdas_socahybridweights.cc )
+target_compile_features( gdas_socahybridweights.x PUBLIC cxx_std_17)
+target_link_libraries( gdas_socahybridweights.x PUBLIC NetCDF::NetCDF_CXX oops atlas soca)

utils/test/CMakeLists.txt

@@ -0,0 +1,13 @@
+# Create Data directory for test input config and symlink all files
+list( APPEND utils_test_input
+  testinput/gdas_meanioda.yaml
+)
+
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/testinput)
+CREATE_SYMLINK( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ${utils_test_input} )
+
+# Test example IODA utility that computes the mean of a variable
+ecbuild_add_test( TARGET  test_gdasapp_util_ioda_example
+                  COMMAND ${CMAKE_BINARY_DIR}/bin/gdas_meanioda.x
+                  ARGS    "testinput/gdas_meanioda.yaml"
+                  LIBS    gdas-utils)

utils/test/testinput/gdas_meanioda.yaml

@@ -0,0 +1,16 @@
+# the window is 30 years long to capture anything we can throw at it in this input file
+window begin: 2000-11-01T09:00:00Z
+window end: 2030-11-01T15:00:00Z
+obs space:
+  name: gmi_gpm_test_mean
+  obsdatain:
+    engine:
+      type: H5File
+      obsfile: ../../../soca/test/Data/obs/gmi_gpm_obs.nc
+  # the below 2 lines are not used but needed by the IODA obsspace it seems...
+  simulated variables: [brightnessTemperature]
+  observed variables: [brightnessTemperature]
+group: ObsValue
+variable: brightnessTemperature
+# channel is optional, depends on what variable you are reading
+channel: 6