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ascii2nc.cc
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ascii2nc.cc
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// *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
// ** Copyright UCAR (c) 1992 - 2021
// ** University Corporation for Atmospheric Research (UCAR)
// ** National Center for Atmospheric Research (NCAR)
// ** Research Applications Lab (RAL)
// ** P.O.Box 3000, Boulder, Colorado, 80307-3000, USA
// *=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
////////////////////////////////////////////////////////////////////////
//
// Filename: ascii2nc.cc
//
// Description:
// Parse ASCII observations and convert them to NetCDF.
//
// Mod# Date Name Description
// ---- ---- ---- -----------
// 000 01-22-08 Halley Gotway New
// 001 09-16-08 Halley Gotway Keep track of the header values and
// only write out a header record when they change.
// 002 07-15-10 Halley Gotway Store accumulation intervals in
// seconds rather than hours.
// 003 01-06-12 Holmes Added use of command line class to
// parse the command line arguments.
// 005 08-01-12 Oldenburg Added support for obs quality flag.
// 006 09-13-12 Halley Gotway Added support for Little_r and
// factored out common code.
// 007 02-06-13 Rehak Added support for surfrad data.
// 008 03-13-13 Rehak Added optional summarization of obs.
// 009 03-26-13 Rehak Updated configuration file
// specification, changed how the
// summary width is specified in the
// netCDF file and added summary info
// to the netCDF global attributes.
// 010 05-21-14 Halley Gotway Print usage for fewer than 2 files
// on the command line.
// 011 07-07-14 Halley Gotway Added the mask_grid and mask_poly
// options to filter spatially.
// 012 07-23-14 Halley Gotway Add message_type_map configuration
// file option.
// 013 09-21-15 Prestopnik Add Aeronet observations.
// 014 07-23-18 Halley Gotway Support masks defined by gen_vx_mask.
// 015 03-20-19 Fillmore Add aeronetv2 and aeronetv3 options.
// 016 01-30-20 Bullock Add python option.
// 017 01-25-21 Halley Gotway MET #1630 Handle zero obs.
// 018 03-01-21 Fillmore Replace pickle files for temporary
// ascii.
//
////////////////////////////////////////////////////////////////////////
using namespace std;
#include <cstdio>
#include <cstdlib>
#include <ctime>
#include <ctype.h>
#include <dirent.h>
#include <iostream>
#include <fstream>
#include <math.h>
#include <regex.h>
#include <string.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include <vector>
#include <netcdf>
using namespace netCDF;
#include "data2d_factory.h"
#include "mask_poly.h"
#include "apply_mask.h"
#include "vx_grid.h"
#include "vx_nc_util.h"
#include "vx_util.h"
#include "vx_math.h"
#include "vx_log.h"
#include "ascii2nc_conf_info.h"
#include "file_handler.h"
#include "little_r_handler.h"
#include "met_handler.h"
#include "surfrad_handler.h"
#include "wwsis_handler.h"
#include "aeronet_handler.h"
#ifdef ENABLE_PYTHON
#include "global_python.h"
#include "python_handler.h"
#endif
////////////////////////////////////////////////////////////////////////
// Constants
static const char *program_name = "ascii2nc";
static const char *DEFAULT_CONFIG_FILENAME =
"MET_BASE/config/Ascii2NcConfig_default";
////////////////////////////////////////////////////////////////////////
// Supported input ASCII formats
enum ASCIIFormat {
ASCIIFormat_None,
ASCIIFormat_MET,
ASCIIFormat_Little_R,
ASCIIFormat_SurfRad,
ASCIIFormat_WWSIS,
ASCIIFormat_Aeronet_v2,
ASCIIFormat_Aeronet_v3,
ASCIIFormat_Python,
};
static ASCIIFormat ascii_format = ASCIIFormat_None;
////////////////////////////////////////////////////////////////////////
// Variables for command line arguments
static vector< ConcatString > asfile_list;
static ConcatString ncfile;
static ConcatString config_filename(replace_path(DEFAULT_CONFIG_FILENAME));
static Ascii2NcConfInfo config_info;
static Grid mask_grid;
static MaskPlane mask_area;
static MaskPoly mask_poly;
static StringArray mask_sid;
static int compress_level = -1;
////////////////////////////////////////////////////////////////////////
static FileHandler *create_file_handler(const ASCIIFormat,
const ConcatString &);
static FileHandler *determine_ascii_format(const ConcatString &);
static void usage();
static void set_format(const StringArray &);
static void set_config(const StringArray &);
static void set_mask_grid(const StringArray &);
static void set_mask_poly(const StringArray &);
static void set_mask_sid(const StringArray &);
static void set_compress(const StringArray &);
static void setup_wrapper_path();
////////////////////////////////////////////////////////////////////////
int main(int argc, char *argv[]) {
CommandLine cline;
//
// Set handler to be called for memory allocation error
//
set_new_handler(oom);
//
// Check for zero arguments
//
if(argc == 1) usage();
//
// Parse the command line into tokens
//
cline.set(argc, argv);
//
// Set the usage function
//
cline.set_usage(usage);
//
// Add the options function calls
//
cline.add(set_format, "-format", 1);
cline.add(set_config, "-config", 1);
cline.add(set_mask_grid, "-mask_grid", 1);
cline.add(set_mask_poly, "-mask_poly", 1);
cline.add(set_mask_sid, "-mask_sid", 1);
cline.add(set_compress, "-compress", 1);
//
// Parse the command line
//
cline.parse();
//
// Check for error. There should be at least two arguments left:
// the ascii input filenames and the netCDF output filename
//
if(cline.n() < 2) usage();
//
// Store the input ASCII file name and the output NetCDF file name
//
for (int i = 0; i < cline.n() - 1; ++i)
asfile_list.push_back((string)cline[i]);
ncfile = cline[cline.n() - 1];
//
// Read the config file
//
mlog << Debug(1)
<< "Config File: " << config_filename << "\n";
config_info.read_config(DEFAULT_CONFIG_FILENAME, config_filename.text());
//
// Create the file handler based on the ascii format specified on
// the command line. If one wasn't specified, we'll look in the
// first file to guess the format.
//
FileHandler *file_handler = create_file_handler(ascii_format, asfile_list[0]);
if(file_handler == 0) return(0);
int deflate_level = compress_level;
if(deflate_level < 0) deflate_level = config_info.get_compression_level();
if(deflate_level > 9) deflate_level = config_info.get_compression_level();
file_handler->setCompressionLevel(deflate_level);
file_handler->setSummaryInfo(config_info.getSummaryInfo());
//
// Set the masking grid and polyline, if specified.
//
if(mask_grid.nx() > 0 || mask_grid.ny() > 0) file_handler->setGridMask(mask_grid);
if(!mask_area.is_empty()) file_handler->setAreaMask(mask_area);
if(mask_poly.n_points() > 0) file_handler->setPolyMask(mask_poly);
if(mask_sid.n_elements() > 0) file_handler->setSIDMask(mask_sid);
//
// Load the message type map
//
file_handler->setMessageTypeMap(config_info.getMessageTypeMap());
//
// Process the files. If a configuration file was specified, do any
// extra processing specified.
//
file_handler->readAsciiFiles(asfile_list);
//
// Summarize the observations, if directed. We need to use a different
// call to writeNetcdfFile in this case so that we can include the
// summarization details.
//
if(config_info.getSummaryInfo().flag) {
file_handler->summarizeObs(config_info.getSummaryInfo());
}
int status = file_handler->writeNetcdfFile(ncfile.text());
delete file_handler;
if(!status) return(1);
return(0);
}
////////////////////////////////////////////////////////////////////////
FileHandler *create_file_handler(const ASCIIFormat format, const ConcatString &ascii_filename) {
#ifdef ENABLE_PYTHON
PythonHandler * ph = 0;
#endif
//
// If the ASCII format was specified, just create the appropriate
// object and return it. If it wasn't specified, look in the
// file to guess the format.
//
switch(format) {
case ASCIIFormat_MET: {
return((FileHandler *) new MetHandler(program_name));
}
case ASCIIFormat_Little_R: {
return((FileHandler *) new LittleRHandler(program_name));
}
case ASCIIFormat_SurfRad: {
return((FileHandler *) new SurfradHandler(program_name));
}
case ASCIIFormat_WWSIS: {
return((FileHandler *) new WwsisHandler(program_name));
}
case ASCIIFormat_Aeronet_v2: {
AeronetHandler *handler = new AeronetHandler(program_name);
handler->setFormatVersion(2);
return((FileHandler *) handler);
}
case ASCIIFormat_Aeronet_v3: {
AeronetHandler *handler = new AeronetHandler(program_name);
handler->setFormatVersion(3);
return((FileHandler *) handler);
}
#ifdef ENABLE_PYTHON
case ASCIIFormat_Python: {
setup_wrapper_path();
ph = new PythonHandler(program_name, ascii_filename.text());
return((FileHandler *) ph);
}
#endif
default: {
return(determine_ascii_format(ascii_filename));
}
}
return(0);
}
////////////////////////////////////////////////////////////////////////
FileHandler *determine_ascii_format(const ConcatString &ascii_filename) {
//
// Use the contents of the file to try to guess its format.
//
//
// Open the input ASCII observation file
//
LineDataFile f_in;
if(!f_in.open(ascii_filename.c_str())) {
mlog << Error << "\ndetermine_ascii_format() -> "
<< "can't open input ASCII file \"" << ascii_filename
<< "\" for reading\n\n";
exit(1);
}
//
// See if this is a MET file.
//
f_in.rewind();
MetHandler *met_file = new MetHandler(program_name);
if (met_file->isFileType(f_in)) {
f_in.close();
return((FileHandler *) met_file);
}
delete met_file;
//
// See if this is a Little R file.
//
f_in.rewind();
LittleRHandler *little_r_file = new LittleRHandler(program_name);
if (little_r_file->isFileType(f_in)) {
f_in.close();
return((FileHandler *) little_r_file);
}
delete little_r_file;
//
// See if this is a SURFRAD file.
//
f_in.rewind();
SurfradHandler *surfrad_file = new SurfradHandler(program_name);
if (surfrad_file->isFileType(f_in)) {
f_in.close();
return((FileHandler *) surfrad_file);
}
delete surfrad_file;
//
// See if this is a WWSIS file.
//
f_in.rewind();
WwsisHandler *wwsis_file = new WwsisHandler(program_name);
if(wwsis_file->isFileType(f_in)) {
f_in.close();
return((FileHandler *) wwsis_file);
}
delete wwsis_file;
//
// See if this is a Aeronet file.
//
f_in.rewind();
AeronetHandler *aeronet_file = new AeronetHandler(program_name);
if(aeronet_file->isFileType(f_in)) {
f_in.close();
return((FileHandler *) aeronet_file);
}
delete aeronet_file;
//
// If we get here, we didn't recognize the file contents.
//
mlog << Error << "\ndetermine_ascii_format() -> "
<< "could not determine file format based on file contents\n\n";
f_in.close();
exit(1);
return(0);
}
////////////////////////////////////////////////////////////////////////
void usage() {
cout << "\nUsage: "
<< program_name << "\n"
<< "\tascii_file1 [ascii_file2 ... ascii_filen]\n"
<< "\tnetcdf_file\n"
<< "\t[-format ASCII_format]\n"
<< "\t[-config file]\n"
<< "\t[-mask_grid string]\n"
<< "\t[-mask_poly file]\n"
<< "\t[-mask_sid file|list]\n"
<< "\t[-log file]\n"
<< "\t[-v level]\n"
<< "\t[-compress level]\n\n"
<< "\twhere\t\"ascii_file\" is the formatted ASCII "
<< "observation file to be converted to NetCDF format "
<< "(required).\n"
<< "\t\t\"netcdf_file\" indicates the name of the output "
<< "NetCDF file to be written (required).\n"
<< "\t\t\"-format ASCII_format\" may be set to \""
<< MetHandler::getFormatString() << "\", \""
<< LittleRHandler::getFormatString() << "\", \""
<< SurfradHandler::getFormatString() << "\", \""
<< WwsisHandler::getFormatString() << "\", \""
<< AeronetHandler::getFormatString() << "\", \""
<< AeronetHandler::getFormatString_v2() << "\", \""
<< AeronetHandler::getFormatString_v3() << "\"";
#ifdef ENABLE_PYTHON
cout << ", \"" << PythonHandler::getFormatString() << "\"";
#endif
cout << " (optional).\n"
<< "\t\t\"-config file\" uses the specified configuration file "
<< "to generate summaries of the fields in the ASCII files (optional).\n"
<< "\t\t\"-mask_grid string\" is a named grid or a data file defining "
<< "the grid for filtering the point observations spatially (optional).\n"
<< "\t\t\"-mask_poly file\" is a polyline file, the output of gen_vx_mask, "
<< "or a gridded data file with field information for filtering "
<< "the point observations spatially (optional).\n"
<< "\t\t\"-mask_sid file|list\" is a station ID masking file or a "
<< "comma-separated list of station ID's for filtering the point "
<< "observations spatially (optional).\n"
<< "\t\t For a list of length greater than one, the first element is "
<< "stored as the mask name (optional).\n"
<< "\t\t\"-log file\" outputs log messages to the specified "
<< "file (optional).\n"
<< "\t\t\"-v level\" overrides the default level of logging ("
<< mlog.verbosity_level() << ") (optional).\n"
<< "\t\t\"-compress level\" overrides the compression level of NetCDF variable ("
<< config_info.get_compression_level() << ") (optional).\n\n"
<< "\tThe \"" << MetHandler::getFormatString()
<< "\" ASCII format consists of 11 columns:\n"
<< "\t\tMessage_Type Station_ID Valid_Time(YYYYMMDD_HHMMSS)\n"
<< "\t\tLat(Deg North) Lon(Deg East) Elevation(msl)\n"
<< "\t\tVar_Name(or GRIB_Code) Level Height(msl or agl)\n"
<< "\t\tQC_String Observation_Value\n\n"
<< "\t\twhere\t\"Level\" is the pressure level (hPa) or "
<< "accumulation interval (HH[MMSS]).\n"
<< "\t\t\t\"Height\" is meters above sea level or above ground level for the "
<< "observation (msl or agl).\n\n"
<< "\t\t\tUse a value of \"" << bad_data_int
<< "\" or \"" << na_str << "\" to indicate missing data.\n\n"
<< flush;
exit (1);
}
////////////////////////////////////////////////////////////////////////
void set_format(const StringArray & a) {
if(MetHandler::getFormatString() == a[0]) {
ascii_format = ASCIIFormat_MET;
}
else if(LittleRHandler::getFormatString() == a[0]) {
ascii_format = ASCIIFormat_Little_R;
}
else if(SurfradHandler::getFormatString() == a[0]) {
ascii_format = ASCIIFormat_SurfRad;
}
else if(WwsisHandler::getFormatString() == a[0]) {
ascii_format = ASCIIFormat_WWSIS;
}
else if(AeronetHandler::getFormatString() == a[0]
|| AeronetHandler::getFormatString_v2() == a[0]) {
ascii_format = ASCIIFormat_Aeronet_v2;
}
else if(AeronetHandler::getFormatString_v3() == a[0]) {
ascii_format = ASCIIFormat_Aeronet_v3;
}
#ifdef ENABLE_PYTHON
else if(PythonHandler::getFormatString() == a[0]) {
ascii_format = ASCIIFormat_Python;
}
#endif
else {
mlog << Error << "\nset_format() -> "
<< "unsupported ASCII observation format \""
<< a[0] << "\".\n\n";
exit(1);
}
}
////////////////////////////////////////////////////////////////////////
void set_config(const StringArray & a) {
config_filename = a[0];
}
////////////////////////////////////////////////////////////////////////
void set_mask_grid(const StringArray & a) {
// List the grid masking file
mlog << Debug(1)
<< "Grid Masking: " << a[0] << "\n";
parse_grid_mask(a[0], mask_grid);
// List the grid mask
mlog << Debug(2)
<< "Parsed Masking Grid: " << mask_grid.name() << " ("
<< mask_grid.nx() << " x " << mask_grid.ny() << ")\n";
}
////////////////////////////////////////////////////////////////////////
void set_mask_poly(const StringArray & a) {
ConcatString mask_name;
// List the poly masking file
mlog << Debug(1)
<< "Polyline Masking File: " << a[0] << "\n";
parse_poly_mask(a[0], mask_poly, mask_grid, mask_area, mask_name);
// List the mask information
if(mask_poly.n_points() > 0) {
mlog << Debug(2)
<< "Parsed Masking Polyline: " << mask_poly.name()
<< " containing " << mask_poly.n_points() << " points\n";
}
// List the area mask information
if(mask_area.nx() > 0 || mask_area.ny() > 0) {
mlog << Debug(2)
<< "Parsed Masking Area: " << mask_name
<< " for (" << mask_grid.nx() << " x " << mask_grid.ny()
<< ") grid\n";
}
return;
}
////////////////////////////////////////////////////////////////////////
void set_mask_sid(const StringArray & a) {
ConcatString mask_name;
// List the station ID mask
mlog << Debug(1)
<< "Station ID Mask: " << a[0] << "\n";
parse_sid_mask(a[0], mask_sid, mask_name);
// List the length of the station ID mask
mlog << Debug(2)
<< "Parsed Station ID Mask: " << mask_name
<< " containing " << mask_sid.n_elements() << " points\n";
}
////////////////////////////////////////////////////////////////////////
void set_compress(const StringArray & a) {
compress_level = atoi(a[0].c_str());
}
////////////////////////////////////////////////////////////////////////
void setup_wrapper_path() {
#ifdef ENABLE_PYTHON
ConcatString command;
GP.initialize();
run_python_string("import sys");
command << cs_erase
<< "sys.path.append(\""
<< replace_path(wrappers_dir)
<< "\")";
run_python_string(command.text());
#endif
return;
}
////////////////////////////////////////////////////////////////////////