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Merged
Chris Thomas (ctgh) merged 3 commits into from
May 1, 2026
Merged

Changes needed for ufo pr 4112 #283

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1e4fd0c
Version that builds
mikecooke77 Apr 22, 2026
9e59861
MOve unneccessary prossibly problematic brackets
mikecooke77 Apr 23, 2026
62f9995
Fix the passing by reference rather than a copy
mikecooke77 Apr 23, 2026
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12 changes: 6 additions & 6 deletions src/opsinputs/CxWriter.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,9 @@
namespace opsinputs {

CxWriter::CxWriter(ioda::ObsSpace & obsdb, const Parameters_ & params,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors)
: obsdb_(obsdb), geovars_(), flags_(std::move(flags)), obsErrors_(std::move(obsErrors)),
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors)
: obsdb_(obsdb), geovars_(), extradiagvars_(), flags_(flags), obsErrors_(obsErrors),
parameters_(params)
{
oops::Log::trace() << "CxWriter constructor starting" << std::endl;
Expand Down Expand Up @@ -93,14 +93,14 @@ void CxWriter::postFilter(const ufo::GeoVaLs & gv,
for (const ufo::Variable &var : parameters_.variables_for_qc.value().get())
filtervars += var;
ioda::ObsDataVector<int> flags(obsdb_, filtervars.toOopsObsVariables());
for (int ivar = 0; ivar < flags.nvars(); ivar++) {
for (size_t ivar = 0; ivar < flags.nvars(); ivar++) {
const std::string varname = flags.varnames()[ivar];
flags[varname] = flags_->operator[](varname);
flags[varname] = flags_.operator[](varname);
}
opsinputs_cxwriter_post_f90(key_, obsdb_, gv.toFortran(), flags,
hofx.nvars(), hofx.nlocs(), hofx.varnames(), &hofx.toFortran());
} else {
opsinputs_cxwriter_post_f90(key_, obsdb_, gv.toFortran(), *flags_,
opsinputs_cxwriter_post_f90(key_, obsdb_, gv.toFortran(), flags_,
hofx.nvars(), hofx.nlocs(), hofx.varnames(), &hofx.toFortran());
}
}
Expand Down
8 changes: 4 additions & 4 deletions src/opsinputs/CxWriter.h
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Expand Up @@ -51,8 +51,8 @@ class CxWriter : public ufo::ObsFilterBase,
typedef CxWriterParameters Parameters_;

CxWriter(ioda::ObsSpace &, const Parameters_ &,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors);
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors);
~CxWriter();

void preProcess() override {}
Expand All @@ -78,8 +78,8 @@ class CxWriter : public ufo::ObsFilterBase,
ioda::ObsSpace & obsdb_;
oops::Variables geovars_;
oops::ObsVariables extradiagvars_;
std::shared_ptr<ioda::ObsDataVector<int>> flags_;
std::shared_ptr<ioda::ObsDataVector<float>> obsErrors_;
ioda::ObsDataVector<int> & flags_;
ioda::ObsDataVector<float> & obsErrors_;

CxWriterParameters parameters_;
};
Expand Down
16 changes: 8 additions & 8 deletions src/opsinputs/VarObsWriter.cc
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Expand Up @@ -29,10 +29,10 @@
namespace opsinputs {

VarObsWriter::VarObsWriter(ioda::ObsSpace & obsdb, const Parameters_ & params,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors)
: obsdb_(obsdb), geovars_(), extradiagvars_(), flags_(std::move(flags)),
obsErrors_(std::move(obsErrors)), parameters_(params)
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors)
: obsdb_(obsdb), geovars_(), extradiagvars_(), flags_(flags),
obsErrors_(obsErrors), parameters_(params)
{
oops::Log::trace() << "VarObsWriter constructor starting" << std::endl;

Expand Down Expand Up @@ -121,15 +121,15 @@ void VarObsWriter::postFilter(const ufo::GeoVaLs & gv,
for (const ufo::Variable &var : parameters_.variables_for_qc.value().get())
filtervars += var;
ioda::ObsDataVector<int> flags(obsdb_, filtervars.toOopsObsVariables());
for (int ivar = 0; ivar < flags.nvars(); ivar++) {
for (size_t ivar = 0; ivar < flags.nvars(); ivar++) {
std::string varname = flags.varnames()[ivar];
flags[varname] = flags_->operator[](varname);
flags[varname] = flags_.operator[](varname);
}
opsinputs_varobswriter_post_f90(key_, obsdb_, flags, *obsErrors_,
opsinputs_varobswriter_post_f90(key_, obsdb_, flags, obsErrors_,
hofx.nvars(), hofx.nlocs(), hofx.toFortran(),
obsdiags.toFortran());
} else {
opsinputs_varobswriter_post_f90(key_, obsdb_, *flags_, *obsErrors_,
opsinputs_varobswriter_post_f90(key_, obsdb_, flags_, obsErrors_,
hofx.nvars(), hofx.nlocs(), hofx.toFortran(),
obsdiags.toFortran());
}
Expand Down
8 changes: 4 additions & 4 deletions src/opsinputs/VarObsWriter.h
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Original file line number Diff line number Diff line change
Expand Up @@ -60,8 +60,8 @@ class VarObsWriter : public ufo::ObsFilterBase,
typedef VarObsWriterParameters Parameters_;

VarObsWriter(ioda::ObsSpace &, const Parameters_ &,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors);
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors);
~VarObsWriter();

void preProcess() override {}
Expand All @@ -87,8 +87,8 @@ class VarObsWriter : public ufo::ObsFilterBase,
ioda::ObsSpace & obsdb_;
oops::Variables geovars_;
oops::ObsVariables extradiagvars_;
std::shared_ptr<ioda::ObsDataVector<int>> flags_;
std::shared_ptr<ioda::ObsDataVector<float>> obsErrors_;
ioda::ObsDataVector<int> & flags_;
ioda::ObsDataVector<float> & obsErrors_;
std::vector<int> varchannels_;

VarObsWriterParameters parameters_;
Expand Down
6 changes: 3 additions & 3 deletions test/opsinputs/CxChecker.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,9 @@ struct CxChecker::PrintCxFileOutput {


CxChecker::CxChecker(ioda::ObsSpace & obsdb, const Parameters_ & params,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors)
: obsdb_(obsdb), geovars_(), flags_(std::move(flags)), obsErrors_(std::move(obsErrors)),
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors)
: obsdb_(obsdb), geovars_(), flags_(flags), obsErrors_(obsErrors),
parameters_(params)
{
oops::Log::trace() << "CxChecker constructor starting" << std::endl;
Expand Down
8 changes: 4 additions & 4 deletions test/opsinputs/CxChecker.h
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Expand Up @@ -58,8 +58,8 @@ class CxChecker : public ufo::ObsFilterBase,
typedef CxCheckerParameters Parameters_;

CxChecker(ioda::ObsSpace &, const Parameters_ &,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors);
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors);
~CxChecker();

void preProcess() override {}
Expand Down Expand Up @@ -96,8 +96,8 @@ class CxChecker : public ufo::ObsFilterBase,
ioda::ObsSpace & obsdb_;
oops::Variables geovars_;
oops::ObsVariables extradiagvars_;
std::shared_ptr<ioda::ObsDataVector<int>> flags_;
std::shared_ptr<ioda::ObsDataVector<float>> obsErrors_;
ioda::ObsDataVector<int> & flags_;
ioda::ObsDataVector<float> & obsErrors_;

CxCheckerParameters parameters_;
};
Expand Down
12 changes: 6 additions & 6 deletions test/opsinputs/ResetFlagsToPass.cc
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Expand Up @@ -17,9 +17,9 @@ namespace opsinputs {
namespace test {

ResetFlagsToPass::ResetFlagsToPass(ioda::ObsSpace & obsdb, const Parameters_ & params,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > /*obsErrors*/)
: obsdb_(obsdb), geovars_(), flags_(std::move(flags)), parameters_(params)
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & /*obsErrors*/)
: obsdb_(obsdb), geovars_(), flags_(flags), parameters_(params)
{
oops::Log::trace() << "ResetFlagsToPass constructor starting" << std::endl;

Expand All @@ -36,9 +36,9 @@ void ResetFlagsToPass::postFilter(const ufo::GeoVaLs &,
const ioda::ObsVector &/*bias*/,
const ufo::ObsDiagnostics &) {
oops::Log::trace() << "ResetFlagsToPass postFilter" << std::endl;
for (size_t v = 0; v < flags_->nvars(); ++v) {
ioda::ObsDataRow<int> &varflags = (*flags_)[v];
for (size_t i = 0; i < flags_->nlocs(); ++i)
for (size_t v = 0; v < flags_.nvars(); ++v) {
ioda::ObsDataRow<int> &varflags = flags_[v];
for (size_t i = 0; i < flags_.nlocs(); ++i)
if (oops::contains(flagsToReset_, varflags[i]))
varflags[i] = ufo::QCflags::pass;
}
Expand Down
6 changes: 3 additions & 3 deletions test/opsinputs/ResetFlagsToPass.h
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Expand Up @@ -50,8 +50,8 @@ class ResetFlagsToPass : public ufo::ObsFilterBase,
typedef ResetFlagsToPassParameters Parameters_;

ResetFlagsToPass(ioda::ObsSpace &, const Parameters_ &,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors);
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors);
~ResetFlagsToPass();

void preProcess() override {}
Expand All @@ -71,7 +71,7 @@ class ResetFlagsToPass : public ufo::ObsFilterBase,
ioda::ObsSpace & obsdb_;
oops::Variables geovars_;
oops::ObsVariables extradiagvars_;
std::shared_ptr<ioda::ObsDataVector<int>> flags_;
ioda::ObsDataVector<int> & flags_;

ResetFlagsToPassParameters parameters_;

Expand Down
6 changes: 3 additions & 3 deletions test/opsinputs/VarObsChecker.cc
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Expand Up @@ -75,9 +75,9 @@ struct VarObsChecker::PrintVarObsOutput {


VarObsChecker::VarObsChecker(ioda::ObsSpace & obsdb, const Parameters_ & params,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors)
: obsdb_(obsdb), geovars_(), flags_(std::move(flags)), obsErrors_(std::move(obsErrors)),
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors)
: obsdb_(obsdb), geovars_(), flags_(flags), obsErrors_(obsErrors),
parameters_(params)
{
oops::Log::trace() << "VarObsChecker constructor starting" << std::endl;
Expand Down
8 changes: 4 additions & 4 deletions test/opsinputs/VarObsChecker.h
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Expand Up @@ -57,8 +57,8 @@ class VarObsChecker : public ufo::ObsFilterBase,
typedef VarObsCheckerParameters Parameters_;

VarObsChecker(ioda::ObsSpace &, const Parameters_ &,
std::shared_ptr<ioda::ObsDataVector<int> > flags,
std::shared_ptr<ioda::ObsDataVector<float> > obsErrors);
ioda::ObsDataVector<int> & flags,
ioda::ObsDataVector<float> & obsErrors);
~VarObsChecker();

void preProcess() override {}
Expand Down Expand Up @@ -89,8 +89,8 @@ class VarObsChecker : public ufo::ObsFilterBase,
ioda::ObsSpace & obsdb_;
oops::Variables geovars_;
oops::ObsVariables extradiagvars_;
std::shared_ptr<ioda::ObsDataVector<int>> flags_;
std::shared_ptr<ioda::ObsDataVector<float>> obsErrors_;
ioda::ObsDataVector<int> & flags_;
ioda::ObsDataVector<float> & obsErrors_;

VarObsCheckerParameters parameters_;
};
Expand Down
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