public string GetVariableName(NetCdfVariable ncVariable)
{
var nameBuilder = new StringBuilder((int)NetCdfWrapper.Limits.NC_MAX_NAME);
CheckResult(NetCdfWrapper.nc_inq_varname(id, ncVariable, nameBuilder));
return(nameBuilder.ToString());
}
public NetCdfDataType GetVariableDataType(NetCdfVariable ncVariable)
{
NetCdfDataType type;
CheckResult(NetCdfWrapper.nc_inq_vartype(id, ncVariable, out type));
return(type);
}
public int GetDimensionLength(NetCdfDimension ncDimension)
{
IntPtr length;
CheckResult(NetCdfWrapper.nc_inq_dimlen(id, ncDimension, out length));
return(length.ToInt32());
}
public string GetDimensionName(NetCdfDimension ncDimension)
{
var nameBuilder = new StringBuilder((int)NetCdfWrapper.Limits.NC_MAX_NAME);
CheckResult(NetCdfWrapper.nc_inq_dimname(id, ncDimension, nameBuilder));
return(nameBuilder.ToString());
}
public NetCdfDimension AddUnlimitedDimension(string dimName)
{
int dimId;
CheckResult(NetCdfWrapper.nc_def_dim(id, dimName, new IntPtr(NetCdfWrapper.NC_UNLIMITED), out dimId));
return(new NetCdfDimension(dimId));
}
public NetCdfDimension AddDimension(string dimName, int dimSize)
{
int dimId;
CheckResult(NetCdfWrapper.nc_def_dim(id, dimName, new IntPtr(dimSize), out dimId));
return(new NetCdfDimension(dimId));
}
/// <summary>
/// Check native netcdf status code, throws when error, and displays error code and message
/// </summary>
/// <param name="result"></param>
private static void CheckResult(int result)
{
if (result != (int)NetCdfWrapper.ResultCode.NC_NOERR)
{
throw new Exception(String.Format("NetCDF error code {0}: " + NetCdfWrapper.nc_strerror(result), result));
}
}
public NetCdfDimension GetDimension(string dimName)
{
int dimId;
var status = NetCdfWrapper.nc_inq_dimid(id, dimName, out dimId);
return((status == (int)NetCdfWrapper.ResultCode.NC_NOERR) ? new NetCdfDimension(dimId) : null);
}
/// <summary>
/// Note that only char array can be higher dimensional here, it will then
/// be flattened before written
/// </summary>
public void Write(NetCdfVariable ncVariable, int[] origin, int[] shape, Array array)
{
var originPtr = NetCdfFileHelper.ConvertToIntPtr(origin);
var shapePtr = NetCdfFileHelper.ConvertToIntPtr(shape);
var ncDataType = GetNetCdfDataType(array);
switch (ncDataType)
{
case NetCdfDataType.NC_BYTE:
CheckResult(NetCdfWrapper.nc_put_vara(id, ncVariable, originPtr, shapePtr, (byte[])array));
break;
case NetCdfDataType.NC_CHAR:
var bytes = NetCdfFileHelper.FlattenCharArray(array, shape);
CheckResult(NetCdfWrapper.nc_put_vara_text(id, ncVariable, originPtr, shapePtr, bytes));
break;
case NetCdfDataType.NC_INT:
CheckResult(NetCdfWrapper.nc_put_vara_int(id, ncVariable, originPtr, shapePtr, (int[])array));
break;
case NetCdfDataType.NC_FLOAT:
CheckResult(NetCdfWrapper.nc_put_vara_float(id, ncVariable, originPtr, shapePtr, (float[])array));
break;
case NetCdfDataType.NC_DOUBLE:
CheckResult(NetCdfWrapper.nc_put_vara_double(id, ncVariable, originPtr, shapePtr, (double[])array));
break;
default:
throw new Exception(
String.Format("Unknown type for writing NetCDF variable to file: type {0} to file {1}",
ncDataType, path));
}
}
public void SetFill(bool shouldFill)
{
int oldMode;
CheckResult(NetCdfWrapper.nc_set_fill(id, shouldFill
? (int)NetCdfWrapper.CreateMode.NC_FILL
: (int)NetCdfWrapper.CreateMode.NC_NOFILL, out oldMode));
}
public IEnumerable <NetCdfDimension> GetAllDimensions()
{
int nDims;
CheckResult(NetCdfWrapper.nc_inq_ndims(id, out nDims));
// NETCDF-3: dimension has id between 0 and nDims-1:
return(Enumerable.Range(0, nDims).Select(d => new NetCdfDimension(d)));
}
/// <summary>
/// Get mapped netcdf data type for array elements, special case for char[]
/// </summary>
/// <param name="array"></param>
/// <returns></returns>
private NetCdfDataType GetNetCdfDataType(Array array)
{
var type = array.GetType().GetElementType();
if (type == typeof(char[]))
{
return(NetCdfDataType.NC_CHAR);
}
return(NetCdfWrapper.GetNetCdf3DataType(type));
}
public static NetCdfFile CreateNew(string path, bool fill = false)
{
int id;
CheckResult(NetCdfWrapper.nc_create(path, FileCreateMode, out id));
var ncFile = new NetCdfFile(path, id);
ncFile.SetFill(fill);
return(ncFile);
}
private int[] GetDimensionIds(NetCdfVariable ncVariable)
{
int nDims;
CheckResult(NetCdfWrapper.nc_inq_varndims(id, ncVariable, out nDims));
var dimIds = new int[nDims];
NetCdfWrapper.nc_inq_vardimid(id, ncVariable, dimIds);
return(dimIds);
}
public NetCdfVariable AddVariable(string varName, Type type, NetCdfDimension[] ncDimensions)
{
int varId;
CheckResult(NetCdfWrapper.nc_def_var(id, varName, NetCdfWrapper.GetNetCdf3DataType(type), ncDimensions.Length,
ncDimensions.Select(d => (int)d).ToArray(), out varId));
var ncVar = new NetCdfVariable(varId);
// variable name is unique here, guaranteed by nc_def_var call above
ncVariableLookupByName.Add(varName, ncVar);
return(ncVar);
}
public IEnumerable <string> GetVariableDimensionNames(NetCdfVariable ncVariable)
{
var dimensions = GetDimensionIds(ncVariable);
foreach (var dimId in dimensions)
{
var nameBuilder = new StringBuilder((int)NetCdfWrapper.Limits.NC_MAX_NAME);
CheckResult(NetCdfWrapper.nc_inq_dimname(id, dimId, nameBuilder));
yield return(nameBuilder.ToString());
}
}
/// <summary>
///
/// </summary>
/// <param name="path"></param>
/// <param name="writeAccess">opens readonly when true</param>
/// <returns></returns>
public static NetCdfFile OpenExisting(string path, bool writeAccess = false)
{
int id;
var mode = writeAccess ? NetCdfWrapper.CreateMode.NC_WRITE : NetCdfWrapper.CreateMode.NC_NOWRITE;
CheckResult(NetCdfWrapper.nc_open(path, mode, out id));
var netcdf = new NetCdfFile(path, id);
netcdf.BuildVariableLookup();
return(netcdf);
}
/// <summary>
/// Read a part of the variable from file, given a certain stride
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="origin"></param>
/// <param name="shape">When shape is -1, this corresponds to reading that entire dimension</param>
/// <param name="stride"></param>
/// <returns></returns>
public Array Read(NetCdfVariable ncVariable, int[] origin, int[] shape, int[] stride)
{
CreateShapeForFullRange(ncVariable, ref shape);
var count = Enumerable.Range(0, origin.Length).Select(i => (shape[i] - origin[i]) / stride[i]).ToArray();
var size = NetCdfFileHelper.GetSize(count);
var originPtr = NetCdfFileHelper.ConvertToIntPtr(origin);
var stridePtr = NetCdfFileHelper.ConvertToIntPtr(stride);
var countPtr = NetCdfFileHelper.ConvertToIntPtr(count);
var type = GetDataType(ncVariable);
switch (type)
{
case NetCdfDataType.NC_BYTE:
var byteArray = new byte[size];
CheckResult(NetCdfWrapper.nc_get_vars(id, ncVariable, originPtr, countPtr, stridePtr, byteArray));
return(NetCdfFileHelper.CreateArrayFromShape(byteArray, count));
case NetCdfDataType.NC_CHAR:
if (shape.Length != 2)
{
throw new NotSupportedException(
"NetCdf: only char arrays for independent string variables supported");
}
var charArray = new byte[size];
CheckResult(NetCdfWrapper.nc_get_vars_text(id, ncVariable, originPtr, countPtr, stridePtr, charArray));
return(NetCdfFileHelper.CreateCharArrayFromShape(charArray, count));
case NetCdfDataType.NC_INT:
var intArray = new int[size];
CheckResult(NetCdfWrapper.nc_get_vars_int(id, ncVariable, originPtr, countPtr, stridePtr, intArray));
return(NetCdfFileHelper.CreateArrayFromShape(intArray, count));
case NetCdfDataType.NC_FLOAT:
var floatArray = new float[size];
CheckResult(NetCdfWrapper.nc_get_vars_float(id, ncVariable, originPtr, countPtr, stridePtr, floatArray));
return(NetCdfFileHelper.CreateArrayFromShape(floatArray, count));
case NetCdfDataType.NC_DOUBLE:
var doubleArray = new double[size];
CheckResult(NetCdfWrapper.nc_get_vars_double(id, ncVariable, originPtr, countPtr, stridePtr, doubleArray));
return(NetCdfFileHelper.CreateArrayFromShape(doubleArray, count));
default:
throw new Exception(
String.Format("Unknown type for reading NetCDF variable from file: type {0} from file {1}",
type, path));
}
}
public int[] GetShape(NetCdfVariable ncVariable)
{
var dimIds = GetDimensionIds(ncVariable);
var nDims = dimIds.Length;
var shape = new int[nDims];
for (int i = 0; i < nDims; ++i)
{
IntPtr len;
CheckResult(NetCdfWrapper.nc_inq_dimlen(id, dimIds[i], out len));
shape[i] = len.ToInt32();
}
return(shape);
}
public bool IsCharArray(NetCdfVariable ncVariable)
{
int nDims;
NetCdfWrapper.nc_inq_varndims(id, ncVariable, out nDims);
if (nDims < 2)
{
return(false);
}
NetCdfDataType ncType;
CheckResult(NetCdfWrapper.nc_inq_vartype(id, ncVariable, out ncType));
return(ncType == NetCdfDataType.NC_CHAR);
}
/// <summary>
/// Reads the variables from the netcdf file, needed when opening a new file
/// </summary>
/// <returns></returns>
private void UpdateVariableLookup(ref IDictionary <string, NetCdfVariable> lookup)
{
lookup.Clear();
int nVars;
CheckResult(NetCdfWrapper.nc_inq_nvars(id, out nVars));
var variables = Enumerable.Range(0, nVars).Select(vi => new NetCdfVariable(vi)).ToList();
foreach (var ncVar in variables)
{
lookup.Add(GetVariableName(ncVar), ncVar);
}
}
public bool IsVariableUnlimited(NetCdfVariable ncVariable)
{
int nDims;
CheckResult(NetCdfWrapper.nc_inq_varndims(id, ncVariable, out nDims));
var dimIds = new int[nDims];
CheckResult(NetCdfWrapper.nc_inq_vardimid(id, ncVariable, dimIds));
int unlimitedDimId;
CheckResult(NetCdfWrapper.nc_inq_unlimdim(id, out unlimitedDimId));
return(dimIds.Contains(unlimitedDimId));
}
/// <summary>
///
/// </summary>
/// <param name="varId"></param>
/// <param name="attributeName"></param>
/// <returns>null when attribute does not exist</returns>
private NetCdfAttribute GetAttribute(int varId, string attributeName)
{
NetCdfDataType type;
IntPtr lengthPtr;
var status = NetCdfWrapper.nc_inq_att(id, varId, attributeName, out type, out lengthPtr);
int length = lengthPtr.ToInt32();
if (status == (int)NetCdfWrapper.ResultCode.NC_ENOTATT)
{
return(null);
}
CheckResult(status);
switch (type)
{
case NetCdfDataType.NC_CHAR:
var charArray = new byte[length + 1];
IntPtr ptr = UTF8Marshal.BytesUTF8ToPtr(charArray);
CheckResult(NetCdfWrapper.nc_get_att_text(id, varId, attributeName, ptr));
charArray[length] = 0;
return(new NetCdfAttribute(attributeName, UTF8Marshal.PtrToStringUTF8(ptr)));
case NetCdfDataType.NC_INT:
var intArray = new int[length];
CheckResult(NetCdfWrapper.nc_get_att_int(id, varId, attributeName, intArray));
return(new NetCdfAttribute(attributeName, intArray[0]));
case NetCdfDataType.NC_FLOAT:
var floatArray = new float[length];
CheckResult(NetCdfWrapper.nc_get_att_float(id, varId, attributeName, floatArray));
return(new NetCdfAttribute(attributeName, floatArray[0]));
case NetCdfDataType.NC_DOUBLE:
var doubleArray = new double[length];
CheckResult(NetCdfWrapper.nc_get_att_double(id, varId, attributeName, doubleArray));
return(new NetCdfAttribute(attributeName, doubleArray[0]));
default:
throw new Exception(
String.Format("Unknown type {0} for reading NetCDF attribute {1} from file {2}",
type, attributeName, path));
}
}
public Dictionary <string, object> GetAttributes(NetCdfVariable ncVariable)
{
var nameValueDictionary = new Dictionary <string, object>();
int nAtts;
CheckResult(NetCdfWrapper.nc_inq_varnatts(id, ncVariable, out nAtts));
for (int i = 0; i < nAtts; ++i)
{
var nameBuilder = new StringBuilder((int)NetCdfWrapper.Limits.NC_MAX_NAME);
NetCdfWrapper.nc_inq_attname(id, ncVariable, i, nameBuilder);
var name = nameBuilder.ToString();
var attribute = GetAttribute(ncVariable, name);
nameValueDictionary.Add(attribute.Name, attribute.Value);
}
return(nameValueDictionary);
}
/// <summary>
/// Read out the entire variable from the file
/// </summary>
/// <param name="ncVariable"></param>
/// <returns></returns>
public Array Read(NetCdfVariable ncVariable)
{
var type = GetDataType(ncVariable);
var size = GetSize(ncVariable);
var shape = GetShape(ncVariable);
switch (type)
{
case NetCdfDataType.NC_BYTE:
var byteArray = new byte[size];
CheckResult(NetCdfWrapper.nc_get_var(id, ncVariable, byteArray));
return(NetCdfFileHelper.CreateArrayFromShape(byteArray, shape));
case NetCdfDataType.NC_CHAR:
var charArray = new byte[size];
CheckResult(NetCdfWrapper.nc_get_var_text(id, ncVariable, charArray));
return(NetCdfFileHelper.CreateCharArrayFromShape(charArray, shape));
case NetCdfDataType.NC_INT:
var intArray = new int[size];
CheckResult(NetCdfWrapper.nc_get_var_int(id, ncVariable, intArray));
return(NetCdfFileHelper.CreateArrayFromShape(intArray, shape));
case NetCdfDataType.NC_FLOAT:
var floatArray = new float[size];
CheckResult(NetCdfWrapper.nc_get_var_float(id, ncVariable, floatArray));
return(NetCdfFileHelper.CreateArrayFromShape(floatArray, shape));
case NetCdfDataType.NC_DOUBLE:
var doubleArray = new double[size];
CheckResult(NetCdfWrapper.nc_get_var_double(id, ncVariable, doubleArray));
return(NetCdfFileHelper.CreateArrayFromShape(doubleArray, shape));
default:
throw new Exception(
String.Format("Unknown type for reading NetCDF variable from file: type {0} from file {1}",
type, path));
}
}
private void WriteAttribute(int varId, NetCdfAttribute ncAttribute)
{
var value = ncAttribute.Value;
if (value is string)
{
var str = (string)value;
CheckResult(NetCdfWrapper.nc_put_att_text(id, varId, ncAttribute.Name,
new IntPtr(str.Length), UTF8Marshal.StringUTF8ToPtr(str)));
}
else if (value is double)
{
var d = (double)value;
CheckResult(NetCdfWrapper.nc_put_att_double(id, varId, ncAttribute.Name,
NetCdfDataType.NC_DOUBLE, new IntPtr(1),
new[] { d }));
}
else if (value is float)
{
var i = (float)value;
CheckResult(NetCdfWrapper.nc_put_att_float(id, varId, ncAttribute.Name,
NetCdfDataType.NC_FLOAT, new IntPtr(1),
new[] { i }));
}
else if (value is int)
{
var i = (int)value;
CheckResult(NetCdfWrapper.nc_put_att_int(id, varId, ncAttribute.Name,
NetCdfDataType.NC_INT, new IntPtr(1),
new[] { i }));
}
else
{
throw new NotImplementedException(string.Format("NetCdf Attribute type '{0}' not implemented",
value != null ? value.GetType().ToString() : "<null>"));
}
}
public static extern int nc_create(string path, NetCdfWrapper.CreateMode mode, out int ncidp);
public void Flush()
{
CheckResult(NetCdfWrapper.nc_sync(id));
}
public void Close()
{
ncVariableLookupByName.Clear();
CheckResult(NetCdfWrapper.nc_close(id));
}
public void EndDefine()
{
CheckResult(NetCdfWrapper.nc_enddef(id));
}
public void ReDefine()
{
CheckResult(NetCdfWrapper.nc_redef(id));
}
