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());
}
/// <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 NetCdfDataType GetVariableDataType(NetCdfVariable ncVariable)
{
NetCdfDataType type;
CheckResult(NetCdfWrapper.nc_inq_vartype(id, ncVariable, out type));
return(type);
}
/// <summary>
/// write array to file, origin is assumed at 0, and shape is taken from array
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="array"></param>
public void Write(NetCdfVariable ncVariable, Array array)
{
var shape = array.GetShape();
var origin = new int[array.Rank];
Write(ncVariable, origin, shape, array);
}
/// <summary>
/// Use this when the attribute might not exist
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="attributeName"></param>
/// <returns>The attribute value as a string, or null</returns>
public string GetAttributeValue(NetCdfVariable ncVariable, string attributeName)
{
var attribute = GetAttribute(ncVariable, attributeName);
if (attribute != null)
{
return(attribute.Value.ToString());
}
return(null);
}
/// <summary>
/// When shape = -1, this is replaced by the size of the dimension
/// as read from the netcdf file
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="shape"></param>
private void CreateShapeForFullRange(NetCdfVariable ncVariable, ref int[] shape)
{
for (int i = 0; i < shape.Length; ++i)
{
if (shape[i] != -1)
{
continue;
}
shape[i] = GetShape(ncVariable)[i];
}
}
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 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());
}
}
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);
}
/// <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);
}
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));
}
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));
}
}
public int GetSize(NetCdfVariable ncVariable)
{
var shape = GetShape(ncVariable);
return NetCdfFileHelper.GetSize(shape);
}
/// <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 GetSize(NetCdfVariable ncVariable)
{
var shape = GetShape(ncVariable);
return(NetCdfFileHelper.GetSize(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);
}
public void SetCaching(NetCdfVariable ncVariable, bool caching)
{
// todo: what should we do here?
}
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 NetCdfDataType GetVariableDataType(NetCdfVariable ncVariable)
{
NetCdfDataType type;
CheckResult(NetCdfWrapper.nc_inq_vartype(id, ncVariable, out type));
return type;
}
public void AddAttribute(NetCdfVariable ncVariable, NetCdfAttribute ncAttribute)
{
WriteAttribute(ncVariable, ncAttribute);
}
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);
}
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;
}
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 IEnumerable<NetCdfDimension> GetDimensions(NetCdfVariable ncVariable)
{
return GetVariableDimensionNames(ncVariable).Select(GetDimension);
}
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));
}
}
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();
}
/// <summary>
/// Use this when the attribute might not exist
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="attributeName"></param>
/// <returns>The attribute value as a string, or null</returns>
public string GetAttributeValue(NetCdfVariable ncVariable, string attributeName)
{
var attribute = GetAttribute(ncVariable, attributeName);
if (attribute != null) return attribute.Value.ToString();
return null;
}
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();
}
}
public IEnumerable <NetCdfDimension> GetDimensions(NetCdfVariable ncVariable)
{
return(GetVariableDimensionNames(ncVariable).Select(GetDimension));
}
/// <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 AddAttribute(NetCdfVariable ncVariable, NetCdfAttribute ncAttribute)
{
WriteAttribute(ncVariable, ncAttribute);
}
/// <summary>
/// When shape = -1, this is replaced by the size of the dimension
/// as read from the netcdf file
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="shape"></param>
private void CreateShapeForFullRange(NetCdfVariable ncVariable, ref int[] shape)
{
for (int i = 0; i < shape.Length; ++i)
{
if (shape[i] != -1) continue;
shape[i] = GetShape(ncVariable)[i];
}
}
/// <summary>
/// write array to file, origin is assumed at 0, and shape is taken from array
/// </summary>
/// <param name="ncVariable"></param>
/// <param name="array"></param>
public void Write(NetCdfVariable ncVariable, Array array)
{
var shape = array.GetShape();
var origin = new int[array.Rank];
Write(ncVariable, origin, shape, array);
}
public void SetCaching(NetCdfVariable ncVariable, bool caching)
{
// todo: what should we do here?
}
