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#3007 Renamed ioda_file to ioda_reader
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Howard Soh committed Dec 21, 2024
1 parent 587dd70 commit d8467bf
Showing 1 changed file with 28 additions and 26 deletions.
54 changes: 28 additions & 26 deletions src/tools/other/ioda2nc/ioda2nc.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,8 @@ static constexpr char program_name[] = "ioda2nc";
// Variables for command line arguments
//

static iodaReader ioda_reader;

// StringArray to store IODA file name
static StringArray ioda_files;

Expand Down Expand Up @@ -124,7 +126,6 @@ static vector<Observation> observations;
// Output NetCDF file, dimensions, and variables
//
static NcFile *f_out = (NcFile *) nullptr;
static iodaFile ioda_file;

////////////////////////////////////////////////////////////////////////

Expand Down Expand Up @@ -298,6 +299,8 @@ static void process_command_line(int argc, char **argv) {
// Process the configuration
conf_info.process_config();

ioda_reader.set_data_config(default_config_file.c_str(), config_file.c_str());

// Check that valid_end_ut >= valid_beg_ut
if(valid_beg_ut != (unixtime) 0 && valid_end_ut != (unixtime) 0
&& valid_beg_ut > valid_end_ut) {
Expand All @@ -312,7 +315,6 @@ static void process_command_line(int argc, char **argv) {
if(do_summary) save_summary_only = !conf_info.getSummaryInfo().raw_data;
else save_summary_only = false;

ioda_file.set_data_config(&conf_info);
return;
}

Expand Down Expand Up @@ -427,13 +429,13 @@ static void process_ioda_file(int i_pb) {
exit(1);
}

ioda_file.read_ioda(f_in);
ioda_reader.read_ioda(f_in);

e_ioda_format ioda_format_ver = ioda_file.get_format_ver();
bool has_msg_type = ioda_file.msg_type_name.nonempty();
bool has_station_id = ioda_file.station_id_name.nonempty();
e_ioda_format ioda_format_ver = ioda_reader.get_format_ver();
bool has_msg_type = ioda_reader.msg_type_name.nonempty();
bool has_station_id = ioda_reader.station_id_name.nonempty();
bool is_netcdf_ready = check_core_data(has_msg_type, has_station_id,
ioda_file.dim_names, ioda_file.metadata_vars,
ioda_reader.dim_names, ioda_reader.metadata_vars,
ioda_format_ver);
if(!is_netcdf_ready) {
mlog << Error << "\n" << method_name
Expand All @@ -453,8 +455,8 @@ static void process_ioda_file(int i_pb) {
max_time_str[0] = 0;
modified_hdr_typ[0] = 0;

int nlocs = ioda_file.nlocs;
int nstring = ioda_file.nstring;
int nlocs = ioda_reader.nlocs;
int nstring = ioda_reader.nstring;

// Compute the number of IODA records in the current file.

Expand All @@ -471,7 +473,7 @@ static void process_ioda_file(int i_pb) {
vector<float *> v_obs_data;

StringArray raw_var_names;
if(do_all_vars || obs_var_names.n() == 0) raw_var_names = ioda_file.obs_value_vars;
if(do_all_vars || obs_var_names.n() == 0) raw_var_names = ioda_reader.obs_value_vars;
else raw_var_names = obs_var_names;

NcVar obs_var;
Expand Down Expand Up @@ -553,7 +555,7 @@ static void process_ioda_file(int i_pb) {
}
}

msg_ut = ioda_file.vld_arr[i_read];
msg_ut = ioda_reader.vld_arr[i_read];

// Check to make sure that the message time hasn't changed
// from one IODA message to the next
Expand Down Expand Up @@ -599,7 +601,7 @@ static void process_ioda_file(int i_pb) {
}

if(has_msg_type) {
m_strncpy(hdr_typ, ioda_file.msg_types[i_read].c_str(),
m_strncpy(hdr_typ, ioda_reader.msg_types[i_read].c_str(),
nstring, method_name_s, "hdr_typ");

// If the message type is not listed in the configuration
Expand All @@ -625,7 +627,7 @@ static void process_ioda_file(int i_pb) {

if(has_station_id) {
char tmp_sid[nstring+1];
m_strncpy(tmp_sid, ioda_file.station_ids[i_read].c_str(),
m_strncpy(tmp_sid, ioda_reader.station_ids[i_read].c_str(),
nstring, method_name_s, "tmp_sid");
m_replace_char(tmp_sid, ' ', '_');
hdr_sid = tmp_sid;
Expand All @@ -644,13 +646,13 @@ static void process_ioda_file(int i_pb) {
// LON LAT DHR ELV TYP T29 ITP

// Longitude
hdr_lon = ioda_file.lon_arr[i_read];
hdr_lon = ioda_reader.lon_arr[i_read];

// Latitude
hdr_lat = ioda_file.lat_arr[i_read];
hdr_lat = ioda_reader.lat_arr[i_read];

// Elevation
hdr_elv = ioda_file.elv_arr[i_read];
hdr_elv = ioda_reader.elv_arr[i_read];

// Compute the valid time and check if it is within the
// specified valid range
Expand Down Expand Up @@ -700,7 +702,7 @@ static void process_ioda_file(int i_pb) {

// Check if the message elevation is within the specified range.
// Missing data values for elevation are retained.
if(!ioda_file.check_missing_thresh(hdr_elv) &&
if(!ioda_reader.check_missing_thresh(hdr_elv) &&
(hdr_elv < conf_info.beg_elev || hdr_elv > conf_info.end_elev) ) {
rej_elv++;
continue;
Expand All @@ -718,8 +720,8 @@ static void process_ioda_file(int i_pb) {
continue;
}
obs_arr[1] = var_idx;
obs_arr[2] = ioda_file.obs_pres_arr[i_read];
obs_arr[3] = ioda_file.obs_hght_arr[i_read];
obs_arr[2] = ioda_reader.obs_pres_arr[i_read];
obs_arr[3] = ioda_reader.obs_hght_arr[i_read];
obs_arr[4] = v_obs_data[idx][i_read];
addObservation(obs_arr, (string)hdr_typ, (string)hdr_sid, hdr_vld_ut,
hdr_lat, hdr_lon, hdr_elv, (float)v_qc_data[idx][i_read]);
Expand Down Expand Up @@ -800,7 +802,7 @@ static void process_ioda_file(int i_pb) {
}
}

ioda_file.clear();
ioda_reader.clear();

for(idx=0; idx<v_obs_data.size(); idx++ ) delete [] v_obs_data[idx];
for(idx=0; idx<v_qc_data.size(); idx++ ) delete [] v_qc_data[idx];
Expand Down Expand Up @@ -885,7 +887,7 @@ static void addObservation(const float *obs_arr, const ConcatString &hdr_typ,
{
// Write the quality flag to the netCDF file
ConcatString obs_qty;
if(ioda_file.check_missing_thresh(quality_mark))
if(ioda_reader.check_missing_thresh(quality_mark))
obs_qty.add("NA");
else obs_qty.format("%d", nint(quality_mark));

Expand Down Expand Up @@ -986,23 +988,23 @@ static bool check_core_data(const bool has_msg_type, const bool has_station_id,
StringArray &t_core_dims = (ioda_format_ver == e_ioda_format::v2)
? core_dims : core_dims_v1;
for(int idx=0; idx<t_core_dims.n(); idx++) {
if (!ioda_file.is_in_metadata_map(t_core_dims[idx], dim_names)) {
if (!ioda_reader.is_in_metadata_map(t_core_dims[idx], dim_names)) {
mlog << Error << "\n" << method_name << "-> "
<< "core dimension \"" << t_core_dims[idx] << "\" is missing.\n\n";
is_netcdf_ready = false;
}
}

if ((ioda_format_ver == e_ioda_format::v1) && (has_msg_type || has_station_id)) {
if (!ioda_file.is_in_metadata_map("nstring", dim_names)) {
if (!ioda_reader.is_in_metadata_map("nstring", dim_names)) {
mlog << Error << "\n" << method_name << "-> "
<< "core dimension \"nstring\" is missing.\n\n";
is_netcdf_ready = false;
}
}

for(int idx=0; idx<core_meta_vars.n(); idx++) {
if(!ioda_file.is_in_metadata_map(core_meta_vars[idx], metadata_vars)) {
if(!ioda_reader.is_in_metadata_map(core_meta_vars[idx], metadata_vars)) {
mlog << Error << "\n" << method_name << "-> "
<< "core variable \"" << core_meta_vars[idx] << "\" is missing.\n\n";
is_netcdf_ready = false;
Expand Down Expand Up @@ -1040,7 +1042,7 @@ static bool get_obs_data_float(NcFile *f_in, const ConcatString &var_name,
status = get_nc_data(obs_var, obs_buf, nlocs);
if(status) {
for(int idx=0; idx<nlocs; idx++)
if(ioda_file.check_missing_thresh(obs_buf[idx])) obs_buf[idx] = bad_data_float;
if(ioda_reader.check_missing_thresh(obs_buf[idx])) obs_buf[idx] = bad_data_float;
}
else mlog << Error << "\n" << method_name
<< "trouble getting " << var_name << "\n\n";
Expand Down Expand Up @@ -1080,7 +1082,7 @@ static bool get_obs_data_float(NcFile *f_in, const ConcatString &var_name,
}
if(status) {
for(int idx=0; idx<nlocs; idx++)
if(ioda_file.check_missing_thresh(qc_buf[idx])) qc_buf[idx] = bad_data_float;
if(ioda_reader.check_missing_thresh(qc_buf[idx])) qc_buf[idx] = bad_data_float;
}
else {
for(int idx=0; idx<nlocs; idx++)
Expand Down

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