// 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
}