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saving original date + testing #24

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Merged
guillaumevernieres merged 3 commits into from
Mar 25, 2025
Merged

saving original date + testing #24

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e9237cc
saving original date + testing
Mar 23, 2025
0074b34
added originaldate to iodavars; passed tests
Mar 24, 2025
539a5a8
Update NetCDFToIodaConverter.h and util.h
Mar 24, 2025
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15 changes: 13 additions & 2 deletions utils/preproc/NetCDFToIodaConverter.h
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,6 @@ namespace obsforge {
// Read the provider's netcdf file
obsforge::preproc::iodavars::IodaVars iodaVars = providerToIodaVars(inputFilenames_[myrank]);


for (int i = myrank + comm_.size(); i < inputFilenames_.size(); i += comm_.size()) {
iodaVars.append(providerToIodaVars(inputFilenames_[i]));
oops::Log::info() << " appending: " << inputFilenames_[i] << std::endl;
Expand All @@ -73,6 +72,7 @@ namespace obsforge {
}
nobs = iodaVars.location_;


// Get the total number of obs across pe's
int nobsAll(0);
comm_.allReduce(nobs, nobsAll, eckit::mpi::sum());
Expand All @@ -88,6 +88,7 @@ namespace obsforge {
gatherObs(iodaVars.obsError_, iodaVarsAll.obsError_);
gatherObs(iodaVars.preQc_, iodaVarsAll.preQc_);


// Create empty group backed by HDF file
if (oops::mpi::world().rank() == 0) {
ioda::Group group =
Expand Down Expand Up @@ -122,7 +123,7 @@ namespace obsforge {
ioda::VariableCreationParameters int_params = createVariableParams<int>();
ioda::VariableCreationParameters long_params = createVariableParams<int64_t>();

// Create the mendatory IODA variables
// Create the mandatory IODA variables
ioda::Variable iodaDatetime =
ogrp.vars.createWithScales<int64_t>("MetaData/dateTime",
{ogrp.vars["Location"]}, long_params);
Expand Down Expand Up @@ -178,6 +179,8 @@ namespace obsforge {
}
}
tmpIntMeta.writeWithEigenRegular(iodaVars.intMetadata_.col(count));


count++;
}

Expand All @@ -191,6 +194,14 @@ namespace obsforge {
count++;
}

if (iodaVars.originalDatetime_.size() != 0) {
ioda::Variable iodaOriginalDatetime =
ogrp.vars.createWithScales<int64_t>("MetaData/originalDateTime",
{ogrp.vars["Location"]}, long_params);
iodaOriginalDatetime.writeWithEigenRegular(iodaVars.originalDatetime_);
}


// Test output
iodaVars.testOutput();

Expand Down
21 changes: 19 additions & 2 deletions utils/preproc/util.h
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Expand Up @@ -116,6 +116,7 @@ namespace obsforge {
std::vector<std::string> floatMetadataName_; // String descriptor of the float metadata
Eigen::ArrayXXi intMetadata_; // Optional array of integer metadata
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std::vector<std::string> intMetadataName_; // String descriptor of the integer metadata
Eigen::Array<int64_t, Eigen::Dynamic, 1> originalDatetime_; // Epoch date in seconds

// Optional global attributes
std::map<std::string, std::string> strGlobalAttr_;
Expand All @@ -133,6 +134,7 @@ namespace obsforge {
floatMetadataName_(fmnames),
intMetadata_(location_, imnames.size()),
intMetadataName_(imnames),
originalDatetime_(), // initialized as empty
channel_(1),
channelValues_(Eigen::ArrayXi::Constant(channel_, -1))
{
Expand All @@ -145,8 +147,6 @@ namespace obsforge {
ASSERT(nVars_ == other.nVars_);
ASSERT(nfMetadata_ == other.nfMetadata_);
ASSERT(niMetadata_ == other.niMetadata_);
ASSERT(floatMetadataName_ == floatMetadataName_);
ASSERT(intMetadataName_ == intMetadataName_);
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// Concatenate Eigen arrays and vectors
longitude_.conservativeResize(location_ + other.location_);
Expand All @@ -157,6 +157,9 @@ namespace obsforge {
preQc_.conservativeResize(location_ * channel_ + other.location_ * other.channel_);
floatMetadata_.conservativeResize(location_ + other.location_, nfMetadata_);
intMetadata_.conservativeResize(location_ + other.location_, niMetadata_);
if (originalDatetime_.size() != 0) {
originalDatetime_.conservativeResize(location_ + other.location_);
}

// Copy data from the 'other' object to this object
longitude_.tail(other.location_) = other.longitude_;
Expand All @@ -167,6 +170,9 @@ namespace obsforge {
preQc_.tail(other.location_) = other.preQc_;
floatMetadata_.bottomRows(other.location_) = other.floatMetadata_;
intMetadata_.bottomRows(other.location_) = other.intMetadata_;
if (originalDatetime_.size() != 0) {
originalDatetime_.tail(other.location_) = other.originalDatetime_;
}

// Update obs count
location_ += other.location_;
Expand Down Expand Up @@ -194,6 +200,10 @@ namespace obsforge {
for (int k = 0; k < niMetadata_; k++) {
iodaVarsMasked.intMetadata_(j, k) = intMetadata_(i, k);
}
// ugly, may be unnecessary; just to be safe
if (originalDatetime_.size() != 0) {
iodaVarsMasked.originalDatetime_(j) = originalDatetime_(i);
}
j++;
} // end if (mask(i))
}
Expand All @@ -206,6 +216,7 @@ namespace obsforge {
preQc_ = iodaVarsMasked.preQc_;
floatMetadata_ = iodaVarsMasked.floatMetadata_;
intMetadata_ = iodaVarsMasked.intMetadata_;
originalDatetime_ = iodaVarsMasked.originalDatetime_;

// Update obs count
location_ = iodaVarsMasked.location_;
Expand All @@ -221,11 +232,17 @@ namespace obsforge {
oops::Log::test() << checksum(longitude_, "longitude") << std::endl;
oops::Log::test() << checksum(latitude_, "latitude") << std::endl;
oops::Log::test() << checksum(datetime_, "datetime") << std::endl;
if (originalDatetime_.size() != 0) {
oops::Log::test() << checksum(originalDatetime_, "originalDatetime") << std::endl;
}
}

// Changing the date and Adjusting Errors
void reDate(const util::DateTime & windowBegin, const util::DateTime & windowEnd,
const std::string &epochDate, float errRatio) {
// save the original
originalDatetime_ = datetime_;

// windowBegin and End into DAwindowTimes
std::vector<util::DateTime> DAwindowTimes = {windowBegin, windowEnd};
// Epoch DateTime from Provider
Expand Down
4 changes: 4 additions & 0 deletions utils/test/testref/insituall2ioda.test
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Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,7 @@ datetime:
Min: 1616619601
Max: 1616641199
Sum: 51732172800
originalDatetime:
Min: 1616598720
Max: 1616645340
Sum: 51731904960
4 changes: 4 additions & 0 deletions utils/test/testref/rads2ioda.test
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Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,7 @@ datetime:
Min: 5131805184
Max: 5131807744
Sum: 112899742208
originalDatetime:
Min: 5131805184
Max: 5131807744
Sum: 112899742208