// read cnv files in two pass, the first to get dimensions
// second to get data
func ReadSeabird(nc *lib.Nc, m *config.Map, files []string, optCfgfile string) {
switch {
case filestruct.Instrument == cfg.Instrument.Type[0]:
config.GetConfigCTD(nc, m, cfg, optCfgfile, filestruct.TypeInstrument, optAll)
// first pass, return dimensions fron cnv files
nc.Dimensions["TIME"], nc.Dimensions["DEPTH"] = firstPassCTD(nc, files)
// initialize 2D data
nc.Variables_2D = make(lib.AllData_2D)
for i, _ := range m.Map_var {
nc.Variables_2D.NewData_2D(i, nc.Dimensions["TIME"], nc.Dimensions["DEPTH"])
}
// second pass, read files again, extract data and fill slices
secondPassCTD(nc, files)
// write ASCII file
WriteAsciiCTD(nc, m.Map_format, m.Hdr, filestruct.Instrument)
// write netcdf file
//if err := nc.WriteNetcdf(); err != nil {
//log.Fatal(err)
//}
WriteNetcdf(nc, m, filestruct.Instrument)
case filestruct.Instrument == cfg.Instrument.Type[1]:
config.GetConfigBTL(nc, m, cfg, optCfgfile, filestruct.TypeInstrument)
// first pass, return dimensions fron btl files
nc.Dimensions["TIME"], nc.Dimensions["DEPTH"] = firstPassBTL(nc, m, files)
// // initialize 2D data
// nc.Variables_2D = make(AllData_2D)
// for i, _ := range map_var {
// nc.Variables_2D.NewData_2D(i, nc.Dimensions["TIME"], nc.Dimensions["DEPTH"])
// }
// second pass, read files again, extract data and fill slices
secondPassBTL(nc, m, files)
// write ASCII file
WriteAsciiBTL2(nc, m.Map_format, m.Hdr, filestruct.Instrument)
// write netcdf file
//if err := nc.WriteNetcdf(); err != nil {
//log.Fatal(err)
//}
WriteNetcdf(nc, m, filestruct.Instrument)
}
}
func GetConfigCTD(nc *lib.Nc, m *Map, cfg toml.Configtoml, configFile string, Type string, optAll *bool) {
// var split, header, format string
var split, splitAll []string
// define map from netcdf structure
nc.Dimensions = make(map[string]int)
nc.Attributes = make(map[string]string)
nc.Extras_f = make(map[string]float64)
nc.Extras_s = make(map[string]string)
nc.Variables_1D = make(map[string]interface{})
// initialize map entry from nil interface to empty slice of float64
nc.Variables_1D["PROFILE"] = []float64{}
nc.Variables_1D["TIME"] = []float64{}
nc.Variables_1D["LATITUDE"] = []float64{}
nc.Variables_1D["LONGITUDE"] = []float64{}
nc.Variables_1D["BATH"] = []float64{}
nc.Variables_1D["TYPECAST"] = []float64{}
nc.Variables_1D["TYPECAST"] = append(nc.Variables_1D["TYPECAST"].([]float64), -1)
nc.Roscop = roscop.CodeRoscopFromCsv(cfg.Roscopfile)
// add some global attributes for profile, change in future
nc.Attributes["data_type"] = Type
split = cfg.Ctd.Split
splitAll = cfg.Ctd.SplitAll
// stationPrefixLength = cfg.Ctd.StationPrefixLength
// TODOS: complete
nc.Attributes["cycle_mesure"] = cfg.Cruise.CycleMesure
nc.Attributes["plateforme"] = cfg.Cruise.Plateforme
nc.Attributes["institute"] = cfg.Cruise.Institute
nc.Attributes["pi"] = cfg.Cruise.Pi
nc.Attributes["timezone"] = cfg.Cruise.Timezone
nc.Attributes["begin_date"] = cfg.Cruise.BeginDate
nc.Attributes["end_date"] = cfg.Cruise.EndDate
nc.Attributes["creator"] = cfg.Cruise.Creator
nc.Attributes["type_instrument"] = cfg.Ctd.TypeInstrument
nc.Attributes["instrument_number"] = cfg.Ctd.InstrumentNumber
// add specific column(s) to the first header line in ascii file
// First column should be PRFL
m.Hdr = append(m.Hdr, "PRFL")
// fill map_var from split (read in .ini configuration file)
// store the position (column) of each physical parameter
var fields []string
if *optAll {
fields = splitAll
} else {
fields = split
}
fmt.Fprintln(debug, "getConfig: ", fields)
// construct header slice from split
for i := 0; i < len(fields); i += 2 {
if v, err := strconv.Atoi(fields[i+1]); err == nil {
m.Map_var[fields[i]] = v - 1
m.Hdr = append(m.Hdr, fields[i])
}
}
fmt.Fprintln(debug, "getConfig: ", m.Hdr)
// fill map_format from code_roscop
for _, key := range m.Hdr {
m.Map_format[key] = roscop.GetRoscopformat(nc.Roscop[key])
}
//return nc
}