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| #pragma once | ||
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| #include <ctime> | ||
| #include <iomanip> | ||
| #include <iostream> | ||
| #include <map> | ||
| #include <netcdf> // NOLINT (using C API) | ||
| #include <sstream> | ||
| #include <string> | ||
| #include <vector> | ||
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| #include "eckit/config/LocalConfiguration.h" | ||
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| #include <Eigen/Dense> // NOLINT | ||
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| #include "ioda/../../../../core/IodaUtils.h" | ||
| #include "ioda/Group.h" | ||
| #include "ioda/ObsGroup.h" | ||
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| #include "oops/util/dateFunctions.h" | ||
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| #include "NetCDFToIodaConverter.h" | ||
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| namespace gdasapp { | ||
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| class IcecJpssrr2Ioda : public NetCDFToIodaConverter { | ||
| public: | ||
| explicit IcecJpssrr2Ioda(const eckit::Configuration & fullConfig, const eckit::mpi::Comm & comm) | ||
| : NetCDFToIodaConverter(fullConfig, comm) { | ||
| variable_ = "seaIceFraction"; | ||
| } | ||
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| // Read netcdf file and populate iodaVars | ||
| gdasapp::obsproc::iodavars::IodaVars providerToIodaVars(const std::string fileName) final { | ||
| oops::Log::info() << "Processing files provided by the JPSSRR" << std::endl; | ||
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| // Open the NetCDF file in read-only mode | ||
| netCDF::NcFile ncFile(fileName, netCDF::NcFile::read); | ||
| oops::Log::info() << "Reading... " << fileName << std::endl; | ||
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| // Get the number of obs in the file | ||
| int dimxSize = ncFile.getDim("Columns").getSize(); | ||
| int dimySize = ncFile.getDim("Rows").getSize(); | ||
| int nobs = dimxSize * dimySize; | ||
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| // Set the int metadata names | ||
| std::vector<std::string> intMetadataNames = {"oceanBasin"}; | ||
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| // Set the float metadata name | ||
| std::vector<std::string> floatMetadataNames = {}; | ||
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| // Create instance of iodaVars object | ||
| gdasapp::obsproc::iodavars::IodaVars iodaVars(nobs, floatMetadataNames, intMetadataNames); | ||
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| oops::Log::debug() << "--- iodaVars.location_: " << iodaVars.location_ << std::endl; | ||
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| // Read non-optional metadata: longitude and latitude | ||
| std::vector<float> oneDimLatVal(iodaVars.location_); | ||
| ncFile.getVar("Latitude").getVar(oneDimLatVal.data()); | ||
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| std::vector<float> oneDimLonVal(iodaVars.location_); | ||
| ncFile.getVar("Longitude").getVar(oneDimLonVal.data()); | ||
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| // Create a vector to hold the Summary Qc variable | ||
| // User-level summary QC: 0=Normal, 1=Uncertain | ||
| std::vector<signed char> oneDimFlagsVal(iodaVars.location_); | ||
| ncFile.getVar("SummaryQC_Ice_Concentration").getVar(oneDimFlagsVal.data()); | ||
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| // Get Ice_Concentration obs values | ||
| std::vector<float> oneDimObsVal(iodaVars.location_); | ||
| ncFile.getVar("IceConc").getVar(oneDimObsVal.data()); | ||
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| // Read and process the starting and ending of dateTime | ||
| auto timeStartAttr = ncFile.getAtt("time_coverage_start"); | ||
| auto timeEndAttr = ncFile.getAtt("time_coverage_end"); | ||
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| // Extract attribute values as strings | ||
| std::string timeStartStr, timeEndStr; | ||
| timeStartAttr.getValues(timeStartStr); | ||
| timeEndAttr.getValues(timeEndStr); | ||
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| // Convert the extracted strings to util::DateTime objects | ||
| util::DateTime timeStartDtime(timeStartStr); | ||
| util::DateTime timeEndDtime(timeEndStr); | ||
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| // Create vectors of util::DateTime | ||
| std::vector<util::DateTime> timeStartVector = {timeStartDtime}; | ||
| std::vector<util::DateTime> timeEndVector = {timeEndDtime}; | ||
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| // Set epoch time for JPSSRR ICEC | ||
| util::DateTime epochDtime("1970-01-01T00:00:00Z"); | ||
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| // Convert Obs DateTime objects to epoch time offsets in seconds | ||
| int64_t timeStartOffsets | ||
| = ioda::convertDtimeToTimeOffsets(epochDtime, timeStartVector)[0]; | ||
| int64_t timeEndOffsets | ||
| = ioda::convertDtimeToTimeOffsets(epochDtime, timeEndVector)[0]; | ||
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| iodaVars.referenceDate_ = "seconds since 1970-01-01T00:00:00Z"; | ||
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| // Update non-optional Eigen arrays | ||
| for (int i = 0; i < iodaVars.location_; i++) { | ||
| iodaVars.longitude_(i) = oneDimLonVal[i]; | ||
| iodaVars.latitude_(i) = oneDimLatVal[i]; | ||
| iodaVars.obsVal_(i) = static_cast<float>(oneDimObsVal[i]*0.01); | ||
| iodaVars.obsError_(i) = 0.1; // Do something for obs error | ||
| iodaVars.preQc_(i) = oneDimFlagsVal[i]; | ||
| iodaVars.datetime_(i) = | ||
| timeStartOffsets + (timeEndOffsets - timeStartOffsets) * 0.5; | ||
| // Store optional metadata, set ocean basins to -999 for now | ||
| iodaVars.intMetadata_.row(i) << -999; | ||
| } | ||
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| // basic test for iodaVars.trim | ||
| Eigen::Array<bool, Eigen::Dynamic, 1> mask = | ||
| ((iodaVars.obsVal_ >= 0.0 && iodaVars.obsVal_ <= 1.0) && | ||
| iodaVars.datetime_ > 0.0 && | ||
| (iodaVars.latitude_ <= -40.0 || iodaVars.latitude_ >= 40.0)); | ||
| iodaVars.trim(mask); | ||
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| return iodaVars; | ||
| }; | ||
| }; // class IcecMirs2Ioda | ||
| } // namespace gdasapp | ||
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