// creates the NetCDF file following nc structure.
//func WriteNetcdf(any interface{}) error {
func WriteNetcdf(nc *lib.Nc, m *config.Map, cfg toml.Configtoml, ncType string, prefixAll string) {
// build filename
filename := fmt.Sprintf(cfg.Outputfile+"OS_%s%s_%s.nc",
strings.ToUpper(nc.Attributes["cycle_mesure"]),
strings.ToUpper(prefixAll),
ncType)
//fmt.Println(filename)
// get roscop definition file for variables attributes
var roscop = nc.Roscop
fmt.Fprintf(echo, "writing netCDF: %s\n", filename)
// get variables_1D size
len_1D := nc.Dimensions["TIME"]
len_2D := nc.Dimensions["DEPTH"]
// Create a new NetCDF 3 file. The dataset is returned.
ds, err := netcdf.CreateFile(filename, netcdf.CLOBBER)
if err != nil {
log.Fatal(err)
}
defer ds.Close()
// Add the dimensions for our data to the dataset
dim_1D := make([]netcdf.Dim, 1)
dim_2D := make([]netcdf.Dim, 2)
// dimensions for ROSCOP paremeters as DEPTH, PRES, TEMP, PSAL, etc
dim_2D[0], err = ds.AddDim("TIME", uint64(len_1D))
if err != nil {
log.Fatal(err)
}
dim_2D[1], err = ds.AddDim("DEPTH", uint64(len_2D))
if err != nil {
log.Fatal(err)
}
// dimension for PROFILE, LATITUDE, LONGITUDE and BATH
dim_1D[0] = dim_2D[0]
// Add the variable to the dataset that will store our data
map_1D := make(map[string]netcdf.Var)
for key, _ := range nc.Variables_1D {
// convert types from code_roscop structure to native netcdf types
var netcdfType netcdf.Type
/*//remove LATITUDE and LONGITUDE from the key list if thermo file
if ncType=="THERMO"{
if key == "LATITUDE" {
continue
}
if key == "LONGITUDE" {
continue
}
}*/
pa := roscop.GetAttributesStringValue(key, "types")
switch pa {
case "int32":
netcdfType = netcdf.INT
case "float32":
netcdfType = netcdf.FLOAT
case "float64":
netcdfType = netcdf.DOUBLE
default:
log.Fatal(fmt.Sprintf("Error: key: %s, Value: [%s], check roscop file\n", key, pa)) // wrong type, check code_roscop file
}
// add variables
v, err := ds.AddVar(key, netcdfType, dim_1D)
if err != nil {
log.Fatal(err)
}
map_1D[key] = v
// define variable attributes with the right type
// for an physical parameter, get a slice of attributes name
for _, name := range roscop.GetAttributes(key) {
// for each attribute, get the value
value := roscop.GetAttributesValue(key, name)
// add new attribute to the variable v
a := v.Attr(name)
// value is an interface{}, need type assertion
switch value.(type) {
case string:
err = a.WriteBytes([]byte(value.(string)))
case int32:
err = a.WriteInt32s([]int32{value.(int32)})
case float32:
err = a.WriteFloat32s([]float32{value.(float32)})
case float64:
err = a.WriteFloat64s([]float64{value.(float64)})
default:
log.Fatal(fmt.Sprintf("netcdf: create 1D attribute error, %v=%v:%v (%T)",
key, name, value, value)) // wrong type, check code_roscop file
}
if err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, v, v))
}
fmt.Fprintf(debug, "%s: %s=%v (%T)\n", key, name, value, value)
}
}
// Add the variable to the dataset that will store our data
map_2D := make(map[string]netcdf.Var)
// use the order list gave by split or splitAll (config file) because
// the iteration order is not specified and is not guaranteed to be
// the same from one iteration to the next in golang
// for key, _ := range nc.Variables_2D {
for _, key := range config.GetPhysicalParametersList(m) {
// remove PRFL from the key list
if key == "PRFL" {
continue
}
/*if key == "SSJT" {
continue
}*/
// convert types from code_roscop structure to native netcdf types
var netcdfType netcdf.Type
pa := roscop.GetAttributesStringValue(key, "types")
switch pa {
case "int32":
netcdfType = netcdf.INT
case "float32":
netcdfType = netcdf.FLOAT
case "float64":
netcdfType = netcdf.DOUBLE
default:
log.Fatal(fmt.Sprintf("Error: key: %s, Value: [%s], check roscop file\n", key, pa)) // wrong type, check code_roscop file
}
v, err := ds.AddVar(key, netcdfType, dim_2D)
if err != nil {
log.Fatal(err)
}
map_2D[key] = v
// define variable attributes with the right type
// for an physical parameter, get a slice of attributes name
for _, name := range roscop.GetAttributes(key) {
// for each attribute, get the value
value := roscop.GetAttributesValue(key, name)
// add new attribute to the variable v
a := v.Attr(name)
// value is an interface{}, need type assertion
switch value.(type) {
case string:
err = a.WriteBytes([]byte(value.(string)))
case int32:
err = a.WriteInt32s([]int32{value.(int32)})
case float32:
err = a.WriteFloat32s([]float32{value.(float32)})
case float64:
err = a.WriteFloat64s([]float64{value.(float64)})
default:
log.Fatal(fmt.Sprintf("netcdf: create 1D attribute error: key: %s, Value: [%s], \n", key, value))
}
if err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, v, v))
}
fmt.Fprintf(debug, "%s: %s=%v (%T)\n", key, name, value, value)
}
}
// defines global attributes
for key, value := range nc.Attributes {
a := ds.Attr(key)
err = a.WriteBytes([]byte(value))
if err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, value, value))
}
}
// leave define mode in NetCDF3
ds.EndDef()
// Create the data with the above dimensions and type,
// write them to the file.
for key, value := range nc.Variables_1D {
// convert types from code_roscop structure to native netcdf types
switch roscop.GetAttributesStringValue(key, "types") {
case "int32":
length := len(value.([]float64))
v := make([]int32, length)
fmt.Fprintf(echo, "writing %s: %d\n", key, len(v))
fmt.Fprintf(debug, "writing %s: %d\n", key, len(v))
for i := 0; i < length; i++ {
v[i] = int32(value.([]float64)[i])
}
if err := map_1D[key].WriteInt32s(v); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, v, v))
}
case "float32":
length := len(value.([]float64))
v := make([]float32, length)
fmt.Fprintf(echo, "writing %s: %d\n", key, len(v))
fmt.Fprintf(debug, "writing %s: %d\n", key, len(v))
for i := 0; i < length; i++ {
v[i] = float32(value.([]float64)[i])
}
if err := map_1D[key].WriteFloat32s(v); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, v, v))
}
case "float64":
length := len(value.([]float64))
v := make([]float64, length)
fmt.Fprintf(echo, "writing %s: %d\n", key, len(v))
fmt.Fprintf(debug, "writing %s: %d\n", key, len(v))
for i := 0; i < length; i++ {
v[i] = float64(value.([]float64)[i])
}
if err := map_1D[key].WriteFloat64s(v); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: %v (%T)", err, key, v, v))
}
default:
log.Fatal(fmt.Sprintf("%s, %v", err, key))
}
}
// write data 2D (value.data) to netcdf variables
// for key, value := range nc.Variables_2D {
for _, key := range config.GetPhysicalParametersList(m) {
// remove PRFL from the key list
if key == "PRFL" {
continue
}
value := nc.Variables_2D[key]
i := 0
ht := len(lib.GetData(value))
wd := len(lib.GetData(value)[0])
fmt.Fprintf(echo, "writing %s: %d x %d\n", key, ht, wd)
fmt.Fprintf(debug, "writing %s: %d x %d\n", key, ht, wd)
// Write<type> netcdf methods need []<type>, [][]data will be flatten
gopher := make([]float64, ht*wd)
for x := 0; x < ht; x++ {
for y := 0; y < wd; y++ {
gopher[i] = lib.GetData(value)[x][y]
i++
}
}
switch roscop.GetAttributesStringValue(key, "types") {
case "int32":
v := make([]int32, ht*wd)
for i := 0; i < ht*wd; i++ {
v[i] = int32(gopher[i])
}
if err := map_2D[key].WriteInt32s(v); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: (%T)", err, key, v))
}
case "float32":
v := make([]float32, ht*wd)
for i := 0; i < ht*wd; i++ {
v[i] = float32(gopher[i])
}
if err := map_2D[key].WriteFloat32s(v); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: (%T)", err, key, v))
}
case "float64":
if err := map_2D[key].WriteFloat64s(gopher); err != nil {
log.Fatal(fmt.Sprintf("%s, %v: (%T)", err, key, gopher))
}
default:
log.Fatal(fmt.Sprintf("%s, %v", err, key))
}
}
fmt.Fprintf(echo, "writing %s done ...\n", filename)
}
func WriteAscii(nc *lib.Nc, cfg toml.Configtoml, map_format map[string]string, hdr []string, inst string, prefixAll string) {
// define 2 files, profiles header and data
var asciiFilename string
// build filenames
str := nc.Attributes["cycle_mesure"]
str = strings.Replace(str, "\r", "", -1)
headerFilename := fmt.Sprintf(cfg.Outputfile+"%s."+inst, strings.ToLower(str))
asciiFilename = fmt.Sprintf(cfg.Outputfile+"%s%s_"+inst, strings.ToLower(str), prefixAll)
//fmt.Println(headerFilename)
//fmt.Println(asciiFilename)
// open header file for writing result
fid_hdr, err := os.Create(headerFilename)
if err != nil {
log.Fatal(err)
}
defer fid_hdr.Close()
// use buffered mode for writing
fbuf_hdr := bufio.NewWriter(fid_hdr)
// open ASCII file for writing result
fid_ascii, err := os.Create(asciiFilename)
if err != nil {
log.Fatal(err)
}
defer fid_ascii.Close()
// use buffered mode for writing
fbuf_ascii := bufio.NewWriter(fid_ascii)
// write header to string
str = fmt.Sprintf("%s %s %s %s %s %s\n",
nc.Attributes["cycle_mesure"],
nc.Attributes["plateforme"],
nc.Attributes["institute"],
nc.Attributes["type_instrument"],
nc.Attributes["instrument_number"],
nc.Attributes["pi"])
// write first line header on header file and ascii file
fmt.Fprintf(fbuf_hdr, str)
fmt.Fprintf(fbuf_ascii, str)
// display on screen
fmt.Printf("%s", str)
// write physical parameters in second line
str = ""
for _, key := range hdr {
fmt.Fprintf(fbuf_ascii, "%s ", key)
fmt.Fprintf(lib.Debug, "%s ", key)
}
// append new line
fmt.Fprintln(fbuf_ascii, "\n")
// write second line header on ascii file
fmt.Fprintln(fbuf_ascii, str)
// display on screen
fmt.Printf("%s", str)
// get data (slices) from nc struct
len_1D := nc.Dimensions["TIME"]
len_2D := nc.Dimensions["DEPTH"]
time := nc.Variables_1D["TIME"].([]float64)
lat := nc.Variables_1D["LATITUDE"].([]float64)
lon := nc.Variables_1D["LONGITUDE"].([]float64)
profile := nc.Variables_1D["PROFILE"].([]float64)
// loop over each profile
for x := 0; x < len_1D; x++ {
str = ""
t1 := lib.NewTimeFromJulian(time[x])
// write profile informations to ASCII data file with DEPTH = -1
// TODOS: adapt profile format to stationPrefixLength
fmt.Fprintf(fbuf_ascii, "%05.0f %f %f %f %s",
profile[x],
t1.JulianDayOfYear(),
lat[x],
lon[x],
t1.Format("20060102150405"))
// write profile informations to header file
str = fmt.Sprintf("%05.0f %s %s %s %4.4g %4.4g %s %s\n",
profile[x],
t1.Format("02/01/2006 15:04:05"),
lib.DecimalPosition2String(lat[x], 0),
lib.DecimalPosition2String(lon[x], 0),
nc.Extras_f[fmt.Sprintf("MINPRES:%d", int(profile[x]))],
nc.Extras_f[fmt.Sprintf("PRES:%d", int(profile[x]))],
nc.Extras_s[fmt.Sprintf("TYPECAST:%s", int(profile[x]))],
cfg.Ladcp.CruisePrefix+nc.Extras_s[fmt.Sprintf("PRFL_NAME:%d", int(profile[x]))])
// write profile information to header file
fmt.Fprintf(fbuf_hdr, str)
// display on screen
fmt.Printf("%s", str)
// fill last header columns with 1e36
for i := 0; i < len(hdr)-6; i++ {
fmt.Fprintf(fbuf_ascii, " %g", 1e36)
}
fmt.Fprintln(fbuf_ascii) // add newline
// loop over each level
for y := 0; y < len_2D; y++ {
fmt.Fprintf(fbuf_ascii, "%05.0f ", profile[x])
// loop over each physical parameter (key) in the rigth order
for _, key := range hdr {
// if key not in map, goto next key
if _, ok := nc.Variables_2D[key]; ok {
// fill 2D slice
data := lib.GetData(nc.Variables_2D[key])[x][y]
// print data with it's format, change format for FillValue
if data == 1e36 {
fmt.Fprintf(fbuf_ascii, "%g ", data)
} else {
if strings.ContainsAny(map_format[key], "lf") {
res := strings.Split(map_format[key], "l")
map_format[key] = strings.Join(res, "")
}
fmt.Fprintf(fbuf_ascii, map_format[key]+" ", data)
}
}
}
fmt.Fprintf(fbuf_ascii, "\n")
}
fbuf_ascii.Flush()
fbuf_hdr.Flush()
}
}