public static double[,] ReadFieldData2D(string file, string dataSet)
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, dataSet);
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
double[,] data = new double[dims[0], dims[1]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <double>(data));
double[,] fieldValues = new double[dims[1], dims[0]];
for (int i = 0; i < dims[1]; i++)
{
for (int j = 0; j < dims[0]; j++)
{
fieldValues[i, j] = (double)data[j, i];
}
}
H5T.close(fDataTypeId);
H5D.close(fDataSetId);
H5F.close(fileId);
return(fieldValues);
}
//Load weights from hdf5 file. Weights must be saved as a vector per layer
public static float[] loadH5(string path, string dsname)
{
//Get file id
var h5fid = H5F.open(path, H5F.OpenMode.ACC_RDONLY);
//Get dataset id
var h5did = H5D.open(h5fid, dsname);
//Dataset size
var h5space = H5D.getSpace(h5did);
var h5size = H5S.getSimpleExtentDims(h5space);
//Dataset size to array
var S = h5size.ToArray();
//Empty double array for the data
double[] data = new double[S[0]];
//Read the dataset
var h5array = new H5Array <double>(data);
var h5dtype = H5D.getType(h5did);
H5D.read(h5did, h5dtype, h5array);
//Convert to float
float[] newarray = new float[data.Length];
Parallel.For(0, data.Length, (k) =>
{
newarray[k] = (float)data[k];
});
return(newarray);
}
public static double[, ,] ReadFieldData3D(string fileName)
{
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
H5DataSetId fDataSetId = H5D.open(fileId, "/FieldData/FD/f0");
H5DataTypeId fDataTypeId = H5D.getType(fDataSetId);
if (!H5T.equal(fDataTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
long[] dims = H5S.getSimpleExtentDims(H5D.getSpace(fDataSetId)).ToArray();
if (dims.Length != 3)
{
Console.WriteLine("Error: Invalid field data dimensions");
}
float[, ,] data = new float[dims[0], dims[1], dims[2]];
H5D.read(fDataSetId, fDataTypeId, new H5Array <float>(data));
// Reorder
double[, ,] fieldValues = new double[dims[2], dims[1], dims[0]];
for (int i = 0; i < dims[0]; i++)
{
for (int j = 0; j < dims[1]; j++)
{
for (int k = 0; k < dims[2]; k++)
{
fieldValues[k, j, i] = data[i, j, k];
}
}
}
return(fieldValues);
}
/// <summary>
/// 重写数据集的值（去条带的数据）
/// </summary>
/// <typeparam name="T">数据类型</typeparam>
/// <param name="dataSetName">数据集的名称</param>
/// <param name="dataTypeId">数据集的类型ID</param>
/// <param name="values">去条带之后数据</param>
/// <param name="BrandNo">在数据集的维度从0开始</param>
private void ReWriteDataSet <T>(string dataSetName, H5DataTypeId dataTypeId, T[] values, int BrandNo)
{
H5FileId _h5FileId = null;
H5DataSetId dataSetId = null;
H5DataSpaceId spaceid = null;
try
{
_h5FileId = H5F.open(fileName, H5F.OpenMode.ACC_RDWR);
//先找出含有指定波段的数据集
dataSetId = H5D.open(_h5FileId, dataSetName);
spaceid = H5D.getSpace(dataSetId);
long[] dims = H5S.getSimpleExtentDims(spaceid); //得到数据数组的大小，比如[3,1800,2048]
int rank = H5S.getSimpleExtentNDims(spaceid); //得到数据数组的维数，比如3
H5S.close(spaceid);
//根据数据集的名字获取数据集的ID
int size = 0;
if (rank == 0)
{
size = 1;
}
else if (rank == 1)
{
size = Convert.ToInt32(dims[0]);
}
else if (rank == 2)
{
size = Convert.ToInt32(dims[0] * dims[1]);
}
else if (rank == 3)
{
size = Convert.ToInt32(dims[0] * dims[1] * dims[2]);
}
T[] v = new T[size];
//从数据集中读取原始数据
H5D.read <T>(dataSetId, dataTypeId, new H5Array <T>(v));
//将波段校正后的数据读取赋给相应的波段
for (int i = BrandNo; i < values.Length; i++)
{
v[i] = values[i];
}
H5D.write <T>(dataSetId, dataTypeId, new H5Array <T>(v));
}
catch (Exception e)
{
throw new Exception(e.Message);
}
finally
{
H5D.close(dataSetId);
H5F.close(_h5FileId);
}
}
private void createHD5DataObject(H5GroupId h5GroupId, string pathName, ref HD5DataSetObject dataObject)
{
H5DataSetId datasetid = null;
H5DataSpaceId spaceid = null;
H5DataTypeId dataTypeid = null;
try
{
dataObject.GroupId = h5GroupId;
datasetid = H5D.open(h5GroupId, pathName);
dataObject.DatasetID = datasetid;
dataObject.DatasetName = pathName;
spaceid = H5D.getSpace(datasetid);
var dims = H5S.getSimpleExtentDims(spaceid);
dataTypeid = H5D.getType(datasetid);
dataObject.Dim = dims.Length;
HDF5DotNet.H5T.H5TClass classType = H5T.getClass(dataTypeid);
int size = H5T.getSize(dataTypeid);
H5T.Sign sign = H5T.Sign.TWOS_COMPLEMENT;
if (classType == H5T.H5TClass.INTEGER)
{
sign = H5T.getSign(dataTypeid);
}
//var rank = H5S.getSimpleExtentNDims(space);
//var statu = H5S.getSimpleExtentDims(space);
Boolean bString = H5T.isVariableString(dataTypeid);
//String name = H5T.getMemberName(dataType, 0);
// var type2 = H5T.getNativeType(dataType, H5T.Direction.DEFAULT);
Type type = getTypeof(classType, size, sign);
dataObject.DataType = type;
dataObject.Data = readData(dataObject);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
finally{
if (datasetid != null)
{
H5D.close(datasetid);
}
if (spaceid != null)
{
H5S.close(spaceid);
}
if (dataTypeid != null)
{
H5T.close(dataTypeid);
}
}
}
/// <summary>
/// 读取指定数据集，未对异常进行处理
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="datasetName"></param>
/// <param name="bandN"></param>
/// <param name="bandH"></param>
/// <param name="bandW"></param>
/// <returns></returns>
public T[] ReadDataArray <T>(String datasetName, ref int bandN, ref int bandH, ref int bandW)
{
H5DataSetId datasetId = null;
H5DataSpaceId spaceId = null;
H5DataTypeId typeId = null;
long[] dims = null;
if (!String.IsNullOrEmpty(datasetName) && _datasetNames.Contains(datasetName))
{
datasetId = H5D.open(_fileId, datasetName);
spaceId = H5D.getSpace(datasetId);
dims = H5S.getSimpleExtentDims(spaceId);
if (dims.Length == 2)
{
bandN = 1;
bandH = (int)dims[0];
bandW = (int)dims[1];
}
else if (dims.Length == 3)
{
bandN = (int)dims[0];
bandH = (int)dims[1];
bandW = (int)dims[2];
}
typeId = H5D.getType(datasetId);
typeId = H5T.getNativeType(typeId, H5T.Direction.DEFAULT);
T[] dv = new T[bandN * bandH * bandW];
H5D.read <T>(datasetId, typeId, new H5Array <T>(dv));
if (typeId != null)
{
H5T.close(typeId);
}
if (spaceId != null)
{
H5S.close(spaceId);
}
if (datasetId != null)
{
H5D.close(datasetId);
}
return(dv);
}
else
{
throw new Exception("未查到指定数据集！");
}
}
public static T[,] Read2DArray <T>(this H5FileId fileId, string dataSetName)
{
var dataset = H5D.open(fileId, dataSetName);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
// this will also need a string hack...
}
T[,] dataArray = new T[dims[0], dims[1]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
//Reading and Printing Methods
private static double[] GetDoubleDataSet(H5FileId dataFile, string path)
{
if (H5L.Exists(dataFile, path))
{
H5DataSetId dataSet = H5D.open(dataFile, path);
H5DataSpaceId space = H5D.getSpace(dataSet);
long[] size2 = H5S.getSimpleExtentDims(space);
long count = size2[0];
double[] dataArray = new double[count];
H5Array <double> wrapArray = new H5Array <double>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
return(dataArray);
}
return(null);
}
private static int[] GetInt32DataSet(H5FileId dataFile, string path)
{
if (H5L.Exists(dataFile, path))
{
var dataSet = H5D.open(dataFile, path);
var space = H5D.getSpace(dataSet);
var size2 = H5S.getSimpleExtentDims(space);
long count = size2[0];
var dataArray = new Int32[count];
var wrapArray = new H5Array <Int32>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
return(dataArray);
}
return(null);
}
public static T ReadScalar <T>(H5FileId fileId, string datasetName)
{
H5DataSetId dataset = null;
H5DataSpaceId space = null;
H5DataTypeId dataType = null;
long[] dims;
T data = default(T);
try
{
dataset = H5D.open(fileId, datasetName);
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
dataType = H5D.getType(dataset);
H5D.readScalar <T>(dataset, dataType, ref data);
if (typeof(T) == typeof(string))
{
int stringLength = H5T.getSize(dataType);
byte[] buffer = new byte[2 * stringLength];
H5D.read(dataset, dataType, new H5Array <byte>(buffer));
string stuff = System.Text.ASCIIEncoding.ASCII.GetString(buffer);
return((T)(stuff.SplitInParts(stringLength).Select(ss => (T)(object)ss)));
}
return(data);
}
catch
{
return(default(T));
}
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
}
}
public static T[] Read1DArray <T>(H5FileId fileId, string dataSetName)
{
H5DataSetId dataset = null;
H5DataSpaceId space = null;
H5DataTypeId dataType = null;
long[] dims;
try
{
dataset = H5D.open(fileId, dataSetName);
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
int stringLength = H5T.getSize(dataType);
int a = (int)dims[0];
byte[] buffer = new byte[(int)(dims[0]) * stringLength];
H5D.read(dataset, dataType, new H5Array <byte>(buffer));
string stuff = System.Text.ASCIIEncoding.ASCII.GetString(buffer);
return(stuff.SplitInParts(stringLength).Select(ss => (T)(object)ss).ToArray());
}
T[] dataArray = new T[dims[0]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
catch {
return(null);
}
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
}
}
public static T[] Read1DArray <T>(this H5FileId fileId, string dataSetName)
{
var dataset = H5D.open(fileId, dataSetName);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
int stringLength = H5T.getSize(dataType);
byte[] buffer = new byte[dims[0] * stringLength];
H5D.read(dataset, dataType, new H5Array <byte>(buffer));
string stuff = System.Text.ASCIIEncoding.ASCII.GetString(buffer);
return(stuff.SplitInParts(stringLength).Select(ss => (T)(object)ss).ToArray());
}
T[] dataArray = new T[dims[0]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
private static T[, ,] Read3DArray <T>(H5GroupId groupID, string name)
{
var dataset = H5D.open(groupID, name);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
if (typeof(T) == typeof(string))
{
// this will also need a string hack...
T[, ,] dataArray = new T[dims[0], 0, 0];
return(dataArray);
}
else
{
T[, ,] dataArray = new T[dims[0], dims[1], dims[2]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
return(dataArray);
}
}
private static T[] Read1DArray <T>(H5GroupId fileId, string dataSetName)
{
var dataset = H5D.open(fileId, dataSetName);
var space = H5D.getSpace(dataset);
var dims = H5S.getSimpleExtentDims(space);
var dataType = H5D.getType(dataset);
T[] dataArray = null;
if (typeof(T) == typeof(string))
{
// this will also need a string hack...
dataArray = new T[dims[0]];
H5D.close(dataset);
return(dataArray);
}
else
{
dataArray = new T[dims[0]];
var wrapArray = new H5Array <T>(dataArray);
H5D.read(dataset, dataType, wrapArray);
H5D.close(dataset);
return(dataArray);
}
}
private static void ReadFile(string filePath)
{
var file = H5F.open(filePath, H5F.OpenMode.ACC_RDONLY);
var dataSet = H5D.open(file, "/group/dataset");
var fileSpace = H5D.getSpace(dataSet);
var rank = H5S.getSimpleExtentNDims(fileSpace);
WriteLine("Rank: {0}", rank);
var dims = H5S.getSimpleExtentDims(fileSpace);
Write("Dims:");
foreach (var d in dims)
{
Write(" {0}", d);
}
WriteLine();
H5S.close(fileSpace);
var ints = new int[1];
var intAttribute = H5A.openName(dataSet, "int");
H5A.read(intAttribute, H5A.getType(intAttribute), new H5Array <int>(ints));
WriteLine("int: {0}", ints[0]);
H5A.close(intAttribute);
var stringAttribute = H5A.openName(dataSet, "string");
var stringType = H5A.getType(stringAttribute);
var stringSize = H5T.getSize(stringType);
WriteLine("string length: {0}", stringSize);
var buffer = new byte[stringSize];
H5A.read(stringAttribute, stringType, new H5Array <byte>(buffer));
WriteLine("string: {0}", Encoding.ASCII.GetString(buffer));
H5T.close(stringType);
H5A.close(stringAttribute);
if (rank == 2)
{
var data = new int[dims[0], dims[1]];
H5D.read(dataSet, H5D.getType(dataSet), new H5Array <int>(data));
for (int i = 0; i < data.GetLength(0); ++i)
{
for (int j = 0; j < data.GetLength(1); ++j)
{
Write(" {0}", data[i, j]);
}
WriteLine();
}
}
H5D.close(dataSet);
H5F.close(file);
}
public static int GetNumberOfDarks(string filename)
{
H5FileId zFile = null;
H5DataSetId dataset = null;
H5DataSpaceId space = null;
long[] dims;
if (!File.Exists(filename))
{
throw new Exception("File not found.");
}
try
{
zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
dataset = H5D.open(zFile, "/dark");
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
H5S.close(space);
space = null;
H5D.close(dataset);
dataset = null;
H5F.close(zFile);
zFile = null;
return((int)dims[1]);
}
catch { }
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
if (zFile != null)
{
H5F.close(zFile);
}
}
zFile = null;
try
{
zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
dataset = H5D.open(zFile, "/exchange/data_dark");
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
H5S.close(space);
space = null;
H5D.close(dataset);
dataset = null;
H5F.close(zFile);
zFile = null;
return((int)dims[1]);
}
catch
{
return(0);
}
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
if (zFile != null)
{
H5F.close(zFile);
}
}
}
private static int GetDim(string filename, int dim)
{
H5FileId zFile = null;
H5DataSetId dataset = null;
H5DataSpaceId space = null;
long[] dims;
if (!File.Exists(filename))
{
throw new Exception("File not found.");
}
try
{
zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
dataset = H5D.open(zFile, "/tomo");
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
H5S.close(space);
space = null;
H5D.close(dataset);
dataset = null;
H5F.close(zFile);
zFile = null;
return((int)dims[dim]);
}
catch { }
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
if (zFile != null)
{
H5F.close(zFile);
}
}
zFile = null;
try
{
zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
dataset = H5D.open(zFile, "/exchange/data");
space = H5D.getSpace(dataset);
dims = H5S.getSimpleExtentDims(space);
H5S.close(space);
space = null;
H5D.close(dataset);
dataset = null;
H5F.close(zFile);
zFile = null;
return((int)dims[dim]);
}
catch
{
throw new Exception("Not a valid HDF5 file.");
}
finally
{
if (space != null)
{
H5S.close(space);
}
if (dataset != null)
{
H5D.close(dataset);
}
if (zFile != null)
{
H5F.close(zFile);
}
}
}
/// <summary>
/// 得到指定属性集合中指定属性名的属性值，未对异常进行处理
/// </summary>
/// <param name="obj"></param>
/// <param name="attributeName"></param>
/// <returns></returns>
private String getAttributeValue(H5ObjectWithAttributes obj, String attributeName)
{
H5AttributeId attId = null;
attId = H5A.open(obj, attributeName);
if (attId == null)
{
return(null);
}
H5DataTypeId typeId = null;
H5DataTypeId dtId = null;
H5AttributeInfo attInfo = null;
H5DataSpaceId spaceId = null;
object attributeVal = null;
typeId = H5A.getType(attId);
attInfo = H5A.getInfo(attId);
dtId = H5A.getType(attId);
spaceId = H5A.getSpace(attId);
int dataSize = H5T.getSize(dtId);
typeId = H5T.getNativeType(typeId, H5T.Direction.DEFAULT);
H5T.H5TClass typeClass = H5T.getClass(typeId);
long[] dims = H5S.getSimpleExtentDims(spaceId);
if (dims.Length == 0)
{
dims = new long[1];
dims[0] = 1;
}
switch (typeClass)
{
case H5T.H5TClass.STRING:
long size = attInfo.dataSize;
byte[] chars = readAttribute <byte>(size, attId, typeId);
attributeVal = Encoding.ASCII.GetString(chars);
break;
case H5T.H5TClass.INTEGER:
H5T.Sign sign = H5T.Sign.TWOS_COMPLEMENT;
sign = H5T.getSign(typeId);
switch (dataSize)
{
case 1:
attributeVal = readAttribute <byte>(dims[0], attId, typeId);
break;
case 2:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
attributeVal = readAttribute <Int16>(dims[0], attId, typeId);
break;
case H5T.Sign.UNSIGNED:
attributeVal = readAttribute <UInt16>(dims[0], attId, typeId);
break;
}
break;
case 4:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
attributeVal = readAttribute <Int32>(dims[0], attId, typeId);
break;
case H5T.Sign.UNSIGNED:
attributeVal = readAttribute <UInt32>(dims[0], attId, typeId);
break;
}
break;
case 8:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
attributeVal = readAttribute <Int64>(dims[0], attId, typeId);
break;
case H5T.Sign.UNSIGNED:
attributeVal = readAttribute <UInt64>(dims[0], attId, typeId);
break;
}
break;
}
break;
case H5T.H5TClass.FLOAT:
switch (dataSize)
{
case 4:
attributeVal = readAttribute <float>(dims[0], attId, typeId);
break;
case 8:
attributeVal = readAttribute <double>(dims[0], attId, typeId);
break;
}
break;
}
if (spaceId != null)
{
H5S.close(spaceId);
}
if (attId != null)
{
H5A.close(attId);
}
if (typeId != null)
{
H5T.close(typeId);
}
if (dtId != null)
{
H5T.close(dtId);
}
return(arrayToString(attributeVal));
}
public SkimMatrix Read(string filename, int field, float scale)
{
Console.WriteLine("Reading {0}", filename);
int hdf5NameEnd = filename.IndexOf("/");
// the first part of the name in the roster file is the omx/hdf5 file
string HDFName = filename.Substring(0, hdf5NameEnd);
//rename filename to be only the name of the skim matrix inside of the skim file
//skims are stored in the "data" folder within the omx/hdf5 file
filename = filename.Substring(hdf5NameEnd);
string hdfFile = _path + "\\" + HDFName;
var dataFile = H5F.open(hdfFile, H5F.OpenMode.ACC_RDONLY);
var dataSet = H5D.open(dataFile, filename);
var space = H5D.getSpace(dataSet);
var size2 = H5S.getSimpleExtentDims(space);
long nRows = size2[0];
long nCols = size2[1];
long numZones = _mapping.Count();
// if the count in the hdf5 file is larger than the number of
// tazs in the mapping, ignore the values over the total number
//of tazs in the mapping because these are not valid zones.
_matrix = new ushort[numZones][];
for (var i = 0; i < numZones; i++)
{
_matrix[i] = new ushort[numZones];
}
//OMX is a square matrix of doubles
//In addition to the data folder for matrices, an OMX file has a lookup folder
//with a zone mapping vector. However, this is ignored since DaySim also has one.
//Therefore, it is assumed the OMX matrix does not skip rows/cols and every row/col
//corresponds to an actual zone in the DaySim zone mapping file by index
//Scaling should be set to TRUE since OMX stores doubles (not scaled integers)
var dataArray = new double[nRows, nCols];
var wrapArray = new H5Array <double>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
for (var row = 0; row < nRows; row++)
{
if (_mapping.ContainsKey(row + 1))
{
for (var col = 0; col < nCols; col++)
{
if (_mapping.ContainsKey(col + 1))
{
var value = dataArray[row, col] * scale;
if (value > 0)
{
if (value > ushort.MaxValue - 1)
{
value = ushort.MaxValue - 1;
}
_matrix[_mapping[row + 1]][_mapping[col + 1]] = (ushort)value;
}
}
}
}
}
var skimMatrix = new SkimMatrix(_matrix);
return(skimMatrix);
}
static void test_h5s_basic()
{
try
{
int rank; // Logical rank of dataspace
hssize_t[] dims1 = { SPACE1_DIM1, SPACE1_DIM2, SPACE1_DIM3 };
hssize_t[] dims2 = { SPACE2_DIM1, SPACE2_DIM2, SPACE2_DIM3, SPACE2_DIM4 };
hssize_t[] max2 = { SPACE2_MAX1, SPACE2_MAX2, SPACE2_MAX3, SPACE2_MAX4 };
hssize_t[] tmax = new hssize_t[4];
// Output message about test being performed.
Console.Write("Testing dataspace manipulation");
// Create a simple dataspace and check its rank.
H5DataSpaceId sid1 = H5S.create_simple(SPACE1_RANK, dims1);
rank = H5S.getSimpleExtentNDims(sid1);
if (rank != SPACE1_RANK)
{
Console.WriteLine("\ntest_h5s_basic: Incorrect rank {0}, should be SPACE1_RANK({1})",
rank, SPACE1_RANK);
nerrors++;
}
// Check its dims.
hssize_t[] tdims1 = new hssize_t[3];
tdims1 = H5S.getSimpleExtentDims(sid1);
int i;
for (i = 0; i < rank; i++)
{
if (tdims1[i] != dims1[i])
{
Console.WriteLine("\ntest_h5s_basic: read tdims1[{0}] = {1} differs from dims1[{0}] = {2}", i, tdims1[i], dims1[i]);
nerrors++;
}
}
// Create another simple dataspace and check its rank, dims, and maxdims.
H5DataSpaceId sid2 = H5S.create_simple(SPACE2_RANK, dims2, max2);
rank = H5S.getSimpleExtentNDims(sid2);
if (rank != SPACE2_RANK)
{
Console.WriteLine("\ntest_h5s_basic: Incorrect rank {0}, should be SPACE1_RANK({1})",
rank, SPACE1_RANK);
nerrors++;
}
hssize_t[] tdims2 = new hssize_t[3];
tdims2 = H5S.getSimpleExtentDims(sid2);
tmax = H5S.getSimpleExtentMaxDims(sid2);
for (i = 0; i < rank; i++)
{
if (tdims2[i] != dims2[i])
{
Console.WriteLine("\ntest_h5s_basic: read tdims2[{0}] = {1} differs from dims2[{0}] = {2}", i, tdims2[i], dims2[i]);
nerrors++;
}
}
for (i = 0; i < rank; i++)
{
if (tmax[i] != max2[i])
{
Console.WriteLine("\ntest_h5s_basic: read tmax[{0}] = {1} differs from max2[{0}] = {2}", i, tmax[i], max2[i]);
nerrors++;
}
}
// Close all dataspaces.
H5S.close(sid1);
H5S.close(sid2);
/*
* Try writing simple dataspaces without setting their extents.
*/
// Create the file
H5FileId fid1 = H5F.create(BASICFILE, H5F.CreateMode.ACC_TRUNC);
// Create dataspaces for testing.
dims1[0] = SPACE1_DIM1;
sid1 = H5S.create(H5S.H5SClass.SIMPLE);
sid2 = H5S.create_simple(1, dims1, dims1);
// This dataset's space has no extent; it should not be created
try
{
H5DataSetId dset1 = H5D.create(fid1, BASICDATASET, H5T.H5Type.NATIVE_INT, sid1);
// should fail, but didn't, print an error message.
Console.WriteLine("\ntest_h5s_basic: Attempting to create a dataset whose space has no extent.");
nerrors++;
}
catch (H5DcreateException) { } // does nothing, it should fail
// Create dataset with good dataspace.
H5DataSetId dataset = H5D.create(fid1, BASICDATASET2, H5T.H5Type.NATIVE_INT, sid2);
// Try some writes with the bad dataspace (sid1)
try
{
hssize_t nelems = 10; // Number of dataspace elements
H5D.writeScalar(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_INT), sid1, sid2, new H5PropertyListId(H5P.Template.DEFAULT), ref nelems);
// should fail, but didn't, print an error message.
Console.WriteLine("\ntest_h5s_basic: Attempting to write to a dataset with space that has no extent.");
nerrors++;
}
catch (H5DwriteException) { } // does nothing, it should fail
// Make sure that dataspace reads using the bad dataspace fail
try
{
hssize_t n = 10; // Number of dataspace elements
H5D.readScalar(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_INT), sid1, sid2,
new H5PropertyListId(H5P.Template.DEFAULT), ref n);
// should fail, but didn't, print an error message.
Console.WriteLine("\ntest_h5s_basic: Attempting to read a dataset with space that has no extent.");
nerrors++;
}
catch (H5DreadException) { } // does nothing, it should fail
// Close objects and file.
H5D.close(dataset);
H5S.close(sid1);
H5S.close(sid2);
H5F.close(fid1);
Console.WriteLine("\t\t\t\tPASSED");
} // end of try
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_h5s_basic
static void test_h5s_scalar()
{
try
{
hssize_t[] tdims = new hssize_t[3];
// Output message about test being performed.
Console.Write("Testing dataspace during writing");
// Create the file.
H5FileId fid1 = H5F.create(DATAFILE, H5F.CreateMode.ACC_TRUNC);
// Create scalar dataspace.
H5DataSpaceId sid1 = H5S.create_simple(SPACE3_RANK, null);
// Get the logical rank of dataspace and verify it.
int rank = H5S.getSimpleExtentNDims(sid1);
if (rank != SPACE3_RANK)
{
Console.WriteLine("\ntest_h5s_scalar: incorrect rank {0}, should be SPACE3_RANK({1})", rank, SPACE3_RANK);
nerrors++;
}
// Create and write the dataset.
uint space3_data = 65;
H5DataSetId dataset = H5D.create(fid1, "Dataset1", H5T.H5Type.NATIVE_UINT, sid1);
H5D.writeScalar(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_UINT), ref space3_data);
// Close objects and file.
H5D.close(dataset);
H5S.close(sid1);
H5F.close(fid1);
/* Open the file and verify the dataspace. */
// Open the file.
fid1 = H5F.open(DATAFILE, H5F.OpenMode.ACC_RDWR);
// Create a dataset.
dataset = H5D.open(fid1, "Dataset1");
// Get dataset's dataspace.
sid1 = H5D.getSpace(dataset);
rank = H5S.getSimpleExtentNDims(sid1);
if (rank != SPACE3_RANK)
{
Console.WriteLine("\ntest_h5s_scalar: incorrect rank {0}", rank);
}
tdims = H5S.getSimpleExtentDims(sid1);
//Console.WriteLine("tdims[0] = {0}, tdims[1] = {1}", tdims[0], tdims[1]);
if (rank != 0)
{
Console.WriteLine("\ntest_h5s_scalar: incorrect rank {0}", rank);
}
// Read the dataset.
uint rdata = 0;
H5D.readScalar(dataset, new H5DataTypeId(H5T.H5Type.NATIVE_UINT), ref rdata);
if (rdata != space3_data)
{
Console.WriteLine("\ntest_h5s_scalar: incorrect data {0}, should be {1}", rdata, space3_data);
}
// Close objects.
H5D.close(dataset);
H5S.close(sid1);
H5F.close(fid1);
Console.WriteLine("\t\t\tPASSED");
} // end of try
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_h5s_scalar_write
//private string ArrayToString<T>(T[] v)
//{
// StringBuilder sb = new StringBuilder();
// //sb.Append("[");
// foreach (T t in v)
// {
// sb.Append(t.ToString());
// sb.Append(",");
// }
// if (sb.Length > 1)
// sb.Remove(sb.Length - 1, 1);
// //sb.Append("]");
// return sb.ToString();
//}
private object GetAttributeValue(H5ObjectWithAttributes obj, string attributeName)
{
H5AttributeId attId = null;
attId = H5A.open(obj, attributeName);
if (attId == null)
{
return(null);
}
H5DataTypeId typeId = null;
H5DataTypeId dtId = null;
H5AttributeInfo attInfo = null;
H5DataSpaceId spaceId = null;
H5DataTypeId oldTypeId = null;
object retObject = null;
try
{
typeId = H5A.getType(attId);
attInfo = H5A.getInfo(attId);
dtId = H5A.getType(attId);
spaceId = H5A.getSpace(attId);
int dataSize = H5T.getSize(dtId);
//
oldTypeId = typeId;
typeId = H5T.getNativeType(typeId, H5T.Direction.DEFAULT);
H5T.H5TClass typeClass = H5T.getClass(typeId);
long[] dims = H5S.getSimpleExtentDims(spaceId);
long dimSize = 1;
if (dims.Length == 0)
{
dimSize = 1;
}
else
{
foreach (long dim in dims)
{
dimSize *= dim;
}
}
switch (typeClass)
{
case H5T.H5TClass.STRING:
long size = attInfo.dataSize;
byte[] chars = ReadArray <byte>(size, attId, typeId);
retObject = Encoding.ASCII.GetString(chars);
break;
case H5T.H5TClass.INTEGER:
H5T.Sign sign = H5T.Sign.TWOS_COMPLEMENT;
sign = H5T.getSign(oldTypeId);
switch (dataSize)
{
case 1:
retObject = ReadArray <byte>(dimSize, attId, typeId);
break;
case 2:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
retObject = ReadArray <Int16>(dimSize, attId, typeId);
break;
case H5T.Sign.UNSIGNED:
retObject = ReadArray <UInt16>(dimSize, attId, typeId);
break;
}
break;
case 4:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
retObject = ReadArray <Int32>(dimSize, attId, typeId);
break;
case H5T.Sign.UNSIGNED:
retObject = ReadArray <UInt32>(dimSize, attId, typeId);
break;
}
break;
case 8:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
retObject = ReadArray <Int64>(dimSize, attId, typeId);
break;
case H5T.Sign.UNSIGNED:
retObject = ReadArray <UInt64>(dimSize, attId, typeId);
break;
}
break;
}
break;
case H5T.H5TClass.FLOAT:
switch (dataSize)
{
case 4:
retObject = ReadArray <float>(dimSize, attId, typeId);
break;
case 8:
retObject = ReadArray <double>(dimSize, attId, typeId);
break;
}
break;
}
return(retObject);
}
finally
{
if (spaceId != null)
{
H5S.close(spaceId);
}
if (attId != null)
{
H5A.close(attId);
}
if (oldTypeId != null)
{
H5T.close(oldTypeId);
}
if (typeId != null)
{
H5T.close(typeId);
}
if (dtId != null)
{
H5T.close(dtId);
}
}
}
private void ReadOldDataSetData(string dataSetName, int bandIndex, out int bandWidth, out int bandHeight, out enumDataType dataType, out object retObject)
{
bandHeight = bandWidth = 0;
dataType = enumDataType.UInt16;
retObject = null;
H5FileId _h5FileId = null;
H5DataSpaceId spaceid = null;
H5DataSetId dataSetId = null;
try
{
_h5FileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
//先找出含有指定波段的数据集
dataSetId = H5D.open(_h5FileId, dataSetName);
spaceid = H5D.getSpace(dataSetId);
long[] dims = H5S.getSimpleExtentDims(spaceid); //得到数据数组的大小，比如[3,1800,2048]
int rank = H5S.getSimpleExtentNDims(spaceid); //得到数据数组的维数，比如3
int size = 0;
if (rank == 1)
{
bandHeight = bandWidth = 1;
size = bandWidth * bandHeight * rank;
}
else if (rank == 2)
{
bandWidth = Convert.ToInt32(dims[0]);
bandHeight = Convert.ToInt32(dims[1]);
size = bandWidth * bandHeight;
}
else if (rank == 3)
{
List <long> r = dims.ToList <long>();
r.Sort();
long[] temp = r.ToArray();
bandWidth = Convert.ToInt32(temp[1]);
bandHeight = Convert.ToInt32(temp[2]);
size = bandWidth * bandHeight * Convert.ToInt32(temp[0]);
}
int outSize = bandWidth * bandHeight;
H5DataTypeId typeId = H5D.getType(dataSetId);
H5T.H5TClass typeClass = H5T.getClass(typeId);//得到数据集的类型
int dataSize = H5T.getSize(typeId);
H5DataTypeId newTypeId = null;
switch (typeClass)
{
case H5T.H5TClass.INTEGER:
H5T.Sign sign = H5T.Sign.TWOS_COMPLEMENT;
sign = H5T.getSign(typeId);
switch (dataSize)
{
case 1:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_B8);
retObject = ReadArray <byte>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Byte;
break;
case 2:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_SHORT);
retObject = ReadArray <Int16>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Int16;
break;
case H5T.Sign.UNSIGNED:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_USHORT);
retObject = ReadArray <UInt16>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.UInt16;
break;
}
break;
case 4:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_INT);
retObject = ReadArray <Int32>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Int32;
break;
case H5T.Sign.UNSIGNED:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_UINT);
retObject = ReadArray <UInt32>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.UInt32;
break;
}
break;
case 8:
switch (sign)
{
case H5T.Sign.TWOS_COMPLEMENT:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_LONG);
retObject = ReadArray <Int64>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Int64;
break;
case H5T.Sign.UNSIGNED:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_ULONG);
retObject = ReadArray <UInt64>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.UInt64;
break;
}
break;
}
break;
case H5T.H5TClass.FLOAT:
switch (dataSize)
{
case 4:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_FLOAT);
retObject = ReadArray <float>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Float;
break;
case 8:
newTypeId = H5T.copy(H5T.H5Type.NATIVE_DOUBLE);
retObject = ReadArray <double>(size, dataSetId, newTypeId, bandIndex, outSize);
dataType = enumDataType.Double;
break;
}
break;
}
}
finally
{
H5S.close(spaceid);
H5D.close(dataSetId);
H5F.close(_h5FileId);
}
}
protected long FindNumberOfRows()
{
var num_rows_data = H5S.getSimpleExtentDims(H5D.getSpace(Id));
return(num_rows_data[0]);
}
public Dictionary <string, string> GetAttributes(string datasetName)
{
if (string.IsNullOrEmpty(datasetName) || !_datasetNames.Contains(datasetName))
{
return(null);
}
H5DataSetId datasetId = null;
H5GroupId groupId = null;
H5DataTypeId typeId = null;
H5DataSpaceId spaceId = null;
//H5PropertyListId psId = null;
try
{
int groupIndex = datasetName.LastIndexOf('/');
if (groupIndex == -1)
{
datasetId = H5D.open(_h5FileId, datasetName);
}
else
{
string groupName = datasetName.Substring(0, groupIndex + 1);
string dsName = datasetName.Substring(groupIndex + 1);
groupId = H5G.open(_h5FileId, groupName);
datasetId = H5D.open(groupId, dsName);
}
if (datasetId == null)
{
return(null);
}
Dictionary <string, string> attValues = new Dictionary <string, string>();
typeId = H5D.getType(datasetId);
H5T.H5TClass type = H5T.getClass(typeId);
int tSize = H5T.getSize(typeId);
spaceId = H5D.getSpace(datasetId);
long[] dims = H5S.getSimpleExtentDims(spaceId);
long storageSize = H5D.getStorageSize(datasetId);
attValues.Add("DataSetName", datasetName);
attValues.Add("DataType", type.ToString());
attValues.Add("DataTypeSize", tSize.ToString() + "Byte");
attValues.Add("Dims", String.Join("*", dims));
attValues.Add("StorageSize", storageSize.ToString() + "Byte");
int attrCount = H5A.getNumberOfAttributes(datasetId);
for (int i = 0; i < attrCount; i++)
{
string attName = H5A.getNameByIndex(datasetId, "/" + datasetName, H5IndexType.NAME, H5IterationOrder.NATIVE, (ulong)i);
attValues.Add(attName, ReadAttributeValue(datasetId, attName));
}
return(attValues);
}
finally
{
if (spaceId != null)
{
H5S.close(spaceId);
}
if (typeId != null)
{
H5T.close(typeId);
}
if (datasetId != null)
{
H5D.close(datasetId);
}
if (groupId != null)
{
H5G.close(groupId);
}
}
}
private Tuple <H5DataSetId, int> load_nd_datasetEx(Blob <T> blob, string strDatasetName, bool bReshape, int nMinDim = 1, int nMaxDim = int.MaxValue, H5GroupId id = null, bool bAllowSingleItems = false)
{
H5DataSetId ds = null;
int nSingleItemSize = 0;
try
{
if (id != null)
{
ds = H5D.open(id, strDatasetName);
}
else
{
ds = H5D.open(m_file, strDatasetName);
}
if (ds == null)
{
m_log.FAIL("Failed to find the dataset '" + strDatasetName + "'!");
}
// Verify that the number of dimensions are in the accepted range.
H5DataSpaceId dsSpace = H5D.getSpace(ds);
if (dsSpace == null)
{
m_log.FAIL("Failed to get the dataset space!");
}
int nDims = H5S.getSimpleExtentNDims(dsSpace);
m_log.CHECK_GE(nDims, nMinDim, "The dataset dim is out of range!");
m_log.CHECK_LE(nDims, nMaxDim, "The dataset dim is out of range!");
long[] rgDims = H5S.getSimpleExtentDims(dsSpace);
// Verify that the data format is what we expect: float or double
H5DataTypeId dsType = H5D.getType(ds);
if (dsType == null)
{
m_log.FAIL("Failed to get the dataset type!");
}
H5T.H5TClass dataClass = H5T.getClass(dsType);
switch (dataClass)
{
case H5T.H5TClass.FLOAT:
m_log.WriteLine("Datatype class: H5T_FLOAT");
break;
case H5T.H5TClass.INTEGER:
m_log.WriteLine("Datatype class: H5T_INTEGER");
break;
default:
m_log.FAIL("Unsupported datatype class: " + dataClass.ToString());
break;
}
List <int> rgBlobDims = new List <int>();
for (int i = 0; i < nDims; i++)
{
rgBlobDims.Add((int)rgDims[i]);
}
if (bReshape)
{
blob.Reshape(rgBlobDims);
}
else
{
if (!Utility.Compare <int>(rgBlobDims, blob.shape()))
{
if (!bAllowSingleItems || (rgBlobDims.Count == 1 && rgBlobDims[0] != 1))
{
string strSrcShape = Utility.ToString <int>(rgBlobDims);
m_log.FAIL("Cannot load blob from hdf5; shape mismatch. Source shape = " + strSrcShape + ", target shape = " + blob.shape_string);
}
if (rgBlobDims.Count == 1)
{
nSingleItemSize = rgBlobDims[0];
}
}
}
}
catch (Exception excpt)
{
if (ds != null)
{
H5D.close(ds);
ds = null;
}
throw excpt;
}
return(new Tuple <H5DataSetId, int>(ds, nSingleItemSize));
}
public DatasetInfo GetDatasetInfo(H5FileId fileId, string datasetName, string groupName)
{
DatasetInfo datasetInfo = new DatasetInfo();
datasetInfo.band = 1;
datasetInfo.col = 1;
datasetInfo.rank = 1;
datasetInfo.row = 1;
H5GroupId groupId = H5G.open(fileId, groupName);
H5DataSetId dataSetId = H5D.open(groupId, datasetName);
// ulong storeSize = H5D.getStorageSize(dataSetId); //得到数据数组存储大小
H5DataSpaceId spaceid = H5D.getSpace(dataSetId);
long[] dims = H5S.getSimpleExtentDims(spaceid); //得到数据数组的大小，比如[3,1800,2048]
datasetInfo.rank = H5S.getSimpleExtentNDims(spaceid); //得到数据数组的维数，比如3
int dimCount = dims.Length;
if (dimCount == 2)
{
datasetInfo.col = Convert.ToInt32(dims[1]);//宽
datasetInfo.row = Convert.ToInt32(dims[0]);
}
else if (dimCount == 3)
{
datasetInfo.band = Convert.ToInt32(dims[0]); //波段数
datasetInfo.col = Convert.ToInt32(dims[2]); //宽
datasetInfo.row = Convert.ToInt32(dims[1]); //高
}
else if (dimCount == 1)
{
datasetInfo.row = Convert.ToInt32(dims[0]);//高
}
H5DataTypeId typeId = H5D.getType(dataSetId);
H5T.H5TClass dataClass = H5T.getClass(typeId);//得到数据集的类型
string typeName = dataClass.ToString();
switch (typeName)
{
case "FLOAT":
datasetInfo.type = DataValueType.FLOAT;
break;
case "INTEGER":
datasetInfo.type = DataValueType.INT;
break;
case "COMPOUND":
datasetInfo.type = DataValueType.COMPOUND;
H5DataTypeId tid0 = H5D.getType(dataSetId);
int nMember = H5T.getNMembers(tid0);
datasetInfo.col = nMember;
break;
default:
datasetInfo.type = DataValueType.EMPTY;
break;
}
H5T.close(typeId);
H5S.close(spaceid);
H5D.close(dataSetId);
H5G.close(groupId);
return(datasetInfo);
}
public void GetDataset <T>(H5FileId fileId, string datasetName, string groupName, T[, ,] datasetOut, DataValueType type)
{
H5GroupId groupId = H5G.open(fileId, groupName);
H5DataSetId dataSetId = H5D.open(groupId, datasetName /*"EV_Emissive"*/);
switch (type)
{
case DataValueType.FLOAT:
H5DataTypeId tidfloat = new H5DataTypeId(H5T.H5Type.NATIVE_FLOAT);
// Read the array back
H5D.read(dataSetId, tidfloat,
new H5Array <T>(datasetOut));//(dataSetId, tid1, new H5Array<int>(vlReadBackArray));
// H5T.close(tidfloat);
break;
case DataValueType.INT:
H5DataTypeId tidint = new H5DataTypeId(H5T.H5Type.NATIVE_INT);
// H5T.H5TClass c = H5T.getMemberClass(tid0);
// Read the array back
H5D.read(dataSetId, tidint,
new H5Array <T>(datasetOut));//(dataSetId, tid1, new H5Array<int>(vlReadBackArray));
//H5T.close(tidint);
break;
case DataValueType.COMPOUND:
H5DataTypeId tid0 = H5D.getType(dataSetId);
int nMember = H5T.getNMembers(tid0);
H5DataSpaceId spaceid = H5D.getSpace(dataSetId);
long[] dims = H5S.getSimpleExtentDims(spaceid);//得到数据数组的大小，比如[3,1800,2048]
int length = 1;
for (int i = 0; i < dims.Length; i++)
{
length *= (int)dims[i];
}
for (int i = 0; i < nMember; i++)
{
string memberName = H5T.getMemberName(tid0, i);
H5DataTypeId memberTypeId = H5T.getMemberType(tid0, i);
H5T.H5TClass dataClass = H5T.getClass(memberTypeId); //得到数据集的类型
string typeName = dataClass.ToString();
if (typeName == "INTEGER") //目前先只支持整形的
{
H5DataTypeId tidtmp = H5T.create(H5T.CreateClass.COMPOUND, sizeof(int));
H5T.insert(tidtmp, memberName, 0, H5T.H5Type.NATIVE_INT);
int[] dataTmp = new int[length];
H5D.read(dataSetId, tidtmp, new H5Array <int>(dataTmp));
for (int j = 0; j < length; j++)
{
datasetOut[0, j, i] = (T)Convert.ChangeType(dataTmp[j], datasetOut[0, j, i].GetType());
}
}
}
H5S.close(spaceid);
break;
default:
break;
}
H5D.close(dataSetId);
H5G.close(groupId);
//H5F.close(fileId);
}
public SkimMatrix Read(string filename, int field, float scale)
{
Console.WriteLine("Reading {0}", filename);
int hdf5NameEnd = filename.IndexOf("/");
// the first part of the name in the roster file is the hdf5 file:
string HDFName = filename.Substring(0, hdf5NameEnd);
//rename filename to be only the name of the skim inside of the time period file
filename = filename.Substring(hdf5NameEnd);
string hdfFile = _path + "\\" + HDFName;
var dataFile = H5F.open(hdfFile, H5F.OpenMode.ACC_RDONLY);
var dataSet = H5D.open(dataFile, filename);
var space = H5D.getSpace(dataSet);
var size2 = H5S.getSimpleExtentDims(space);
long nRows = size2[0];
long nCols = size2[1];
long numZones = _mapping.Count();
var dataArray = new double[nRows, nCols];
var wrapArray = new H5Array <double>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
// if the count in the hdf5 file is larger than the number of
// tazs in the mapping, ignore the values over the total number
//of tazs in the mapping because these are not valid zones.
_matrix = new ushort[numZones][];
for (var i = 0; i < numZones; i++)
{
_matrix[i] = new ushort[numZones];
}
//leave as is for PSRC. Values are already scaled integers and matrices already condensed
if (Global.Configuration.PSRC)
{
for (var i = 0; i < numZones; i++)
{
for (var j = 0; j < numZones; j++)
{
_matrix[i][j] = (ushort)dataArray[i, j];
}
}
}
else
{
for (var row = 0; row < nRows; row++)
{
if (_mapping.ContainsKey(row + 1))
{
for (var col = 0; col < nCols; col++)
{
if (_mapping.ContainsKey(col + 1))
{
var value = dataArray[row, col] * scale;
if (value > 0)
{
if (value > short.MaxValue)
{
value = short.MaxValue;
}
_matrix[_mapping[row + 1]][_mapping[col + 1]] = (ushort)value;
}
}
}
}
}
}
var skimMatrix = new SkimMatrix(_matrix);
return(skimMatrix);
}
private void button1_Click(object sender, EventArgs e)
{
fileNameTextBox.Text = "";
string filename = "";
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
if ((openFileDialog1.OpenFile()) != null)
{
filename = openFileDialog1.FileName;
fileNameTextBox.Text = openFileDialog1.FileName;
Debug.WriteLine(filename);
}
H5.Open();
var h5 = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
var dataset = H5D.open(h5, "/radarData/data");
var Space = H5D.getSpace(dataset);
var size = H5S.getSimpleExtentDims(Space);
float[, , , ,] dataarray = new float[size[0], size[1], size[2], size[3], size[4] * 2];
var wrapArray = new H5Array <float>(dataarray);
NOS = (int)size[2]; //number_of_scan (X)
NOC = (int)size[3]; //Number of channel (antenna) (Y)
NOF = (int)size[4]; // Number of frequency (Z)
if (NOS < NOF)
{
m = NOS;
last = n = 50;
}
else
{
m = NOS;
last = n = 50;
}
x = new float[m][];
xb = new float[m][];
c1 = new float[m][];
y1 = new float[m][];
for (int i = 0; i < m; i++)
{
x[i] = new float[n];
xb[i] = new float[n];
c1[i] = new float[n];
y1[i] = new float[n];
for (int j = 0; j < n; j++)
{
y1[i][j] = 0;
x[i][j] = 0;
}
}
textBox1.Text = size[2].ToString();
textBox2.Text = size[4].ToString();
textBox3.Text = size[3].ToString();
var dataType = H5D.getType(dataset);
H5D.read <float>(dataset, dataType, wrapArray);
data = new float[size[2], size[3], size[4] * 2];
var xd = data.Length;
Debug.WriteLine(xd);
for (int k = 0; k < size[2]; k++)
{
for (int i = 0; i < size[3]; i++)
{
for (int j = 0; j < size[4] * 2; j++)
{
data[k, i, j] = dataarray[0, 0, k, i, j];
}
}
}
// res = 10; //10mm
res = 1; //100mm
n_o_s = NOS; //640;// 510;//number of files
n_o_c = NOC * res; //100;// NOC* res; //* res; //for outdoor =NOC * res for indoor=100; 150 for outdoor as after 15th channel readings were not proper
n_o_f = NOF;
grid = new float[NOS, NOC *res, NOF];
for (int k = 0; k < NOS; k++) //100mm
{
for (int i = 0; i < NOC; i++)
{
for (int j = 0; j < NOF; j++)
{
grid[k, i, j] = data[k, i, j * 2];
}
}
}
H5.Close();
}
hscn = 0; depth = 0; dtscn = 0; dtdep = 0; chnl = 0; dtchnl = 0;
imagescanner(0, 0, 0);
}