public void Close()
{
if (m_fileId != null)
{
H5F.close(m_fileId);
}
}
public static void UpdateCampaignInfoSet()
{
long vdsFileId = -1;
long vdsMetaFileId = -1;
long groupId = -1;
lock (_lock)
{
try
{
if (File.Exists(_options.VdsFilePath))
{
vdsFileId = H5F.open(_options.VdsFilePath, H5F.ACC_RDONLY);
vdsMetaFileId = H5F.open(_options.VdsMetaFilePath, H5F.ACC_RDONLY);
Program.CampaignInfoSet = GeneralHelper.GetCampaignInfoSet(vdsFileId, false);
}
else
{
Program.CampaignInfoSet = new List <CampaignInfo>();
}
Program.CampaignDescriptionSet = Program.CampaignInfoSet.ToDictionary(campaignInfo => campaignInfo.Name, campaignInfo =>
{
if (IOHelper.CheckLinkExists(vdsMetaFileId, campaignInfo.Name))
{
try
{
groupId = H5G.open(vdsMetaFileId, campaignInfo.Name);
if (H5A.exists(groupId, "description") > 0)
{
return(IOHelper.ReadAttribute <string>(groupId, "description").First());
}
}
finally
{
if (H5I.is_valid(groupId) > 0)
{
H5G.close(groupId);
}
}
}
return("no description available");
});
}
finally
{
if (H5I.is_valid(vdsFileId) > 0)
{
H5F.close(vdsFileId);
}
if (H5I.is_valid(vdsMetaFileId) > 0)
{
H5F.close(vdsMetaFileId);
}
}
}
}
public void H5Freset_mdc_hit_rate_statsTest1()
{
Assert.IsTrue(
H5F.reset_mdc_hit_rate_stats(m_v0_class_file) >= 0);
Assert.IsTrue(
H5F.reset_mdc_hit_rate_stats(m_v2_class_file) >= 0);
}
public void H5FunmountTest2()
{
Assert.IsFalse(
H5F.unmount(Utilities.RandomInvalidHandle(), "AA") >= 0);
Assert.IsFalse(H5F.unmount(m_v0_class_file, "") >= 0);
}
public void H5Fget_mdc_configTest2()
{
H5AC.cache_config_t conf = new H5AC.cache_config_t();
Assert.IsFalse(
H5F.get_mdc_config(Utilities.RandomInvalidHandle(),
ref conf) >= 0);
}
public void Cleanup()
{
file_.Close();
H5D.close(dataSet_);
H5F.close(h5file_);
}
public static double[][] ReadMesh(string fileName)
{
double[][] meshes = new double[3][];
string[] meshNames = { "x", "y", "z" };
H5FileId fileId = H5F.open(fileName, H5F.OpenMode.ACC_RDONLY);
for (int i = 0; i < meshNames.Length; i++)
{
H5DataSetId dsId = H5D.open(fileId, "/Mesh/" + meshNames[i]);
H5DataTypeId dtId = H5D.getType(dsId);
if (!H5T.equal(dtId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
Console.WriteLine("Error: Invalid dataset type, expected {0}", H5T.H5Type.NATIVE_FLOAT);
}
float[] mesh = new float[H5D.getStorageSize(dsId) / H5T.getSize(dtId)];
H5D.read(dsId, dtId, new H5Array <float>(mesh));
meshes[i] = mesh.Select(x => (double)x * 1000.0).ToArray(); // m -> mm
H5D.close(dsId);
H5T.close(dtId);
}
H5F.close(fileId);
return(meshes);
}
public static T GetMetadata <T>(string filename, string path)
{
H5FileId zFile = null;
if (!File.Exists(filename))
{
throw new Exception("File not found.");
}
try
{
zFile = H5F.open(filename, H5F.OpenMode.ACC_RDONLY);
return((T)HDFExtensions.ReadScalar <T>(zFile, path));
}
catch
{
throw new Exception("Path not found");
}
finally
{
if (zFile != null)
{
H5F.close(zFile);
}
}
}
/// <summary>
/// Opens an existing file and loads up the group and dataset headers in the object.
/// </summary>
/// <param name="_filename"></param>
public Hdf5File(string _filename)
{
if (!File.Exists(_filename))
{
throw new FileNotFoundException();
}
Id = H5F.open(_filename, H5F.ACC_RDWR).ToId();
if (Id.Value > 0)
{
FileId = Id;
Path = new Hdf5Path(".");
Groups = new Hdf5Groups(this);
Datasets = new Hdf5Datasets(this);
Attributes = new Hdf5Attributes(this);
AttributeHelper.LoadAttributes(Attributes);
GroupHelper.PopulateChildrenObjects(Id, this);
}
else
{
throw new Hdf5UnknownException();
}
}
//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 void H5Fget_filesizeTest2()
{
hsize_t size = 0;
Assert.IsFalse(H5F.get_filesize(Utilities.RandomInvalidHandle(),
ref size) >= 0);
}
public override void CloseDocument()
{
if (fileId != null && fileId.Id > 0 && !_fileClosed)
{
foreach (var group in EpochGroupsIDs)
{
try
{
H5G.close(group.GroupId);
H5G.close(group.SubGroupsId);
H5G.close(group.EpochsId);
}
catch (H5GcloseException ex)
{
log.DebugFormat("HDF5 group already closed: {0}", ex);
}
}
try
{
H5F.close(fileId);
}
catch (H5FcloseException ex)
{
log.DebugFormat("HDF5 file already closed: {0}", ex);
}
Interlocked.Decrement(ref _openHdf5FileCount);
_fileClosed = true;
}
}
public Hdf5Operator(string filename)
{
_fname = filename;
_h5FileId = H5F.open(filename, H5F.ACC_RDONLY);
GetAllFileAttributes();
GetAllDatasetNames();
}
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);
}
public void H5Fget_mdc_configTest1()
{
H5AC.cache_config_t conf = new H5AC.cache_config_t(
H5AC.CURR_CACHE_CONFIG_VERSION);
Assert.IsTrue(H5F.get_mdc_config(m_v0_class_file, ref conf) >= 0);
Assert.IsTrue(H5F.get_mdc_config(m_v2_class_file, ref conf) >= 0);
}
public static double ReadAttribute(string file, string dataSetOrGroup, string attribute)
{
double attr = Double.NaN;
try
{
H5FileId fileId = H5F.open(file, H5F.OpenMode.ACC_RDONLY);
H5ObjectInfo objectInfo = H5O.getInfoByName(fileId, dataSetOrGroup);
H5GroupId groupId = null;
H5DataSetId dataSetId = null;
H5AttributeId attrId;
if (objectInfo.objectType == H5ObjectType.GROUP)
{
groupId = H5G.open(fileId, dataSetOrGroup);
attrId = H5A.open(groupId, attribute);
}
else
{
dataSetId = H5D.open(fileId, dataSetOrGroup);
attrId = H5A.open(dataSetId, attribute);
}
H5DataTypeId attrTypeId = H5A.getType(attrId);
double[] dAttrs = new double[] { };
if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_FLOAT)))
{
float[] fAttrs = new float[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <float>(fAttrs));
dAttrs = (from f in fAttrs select(double) f).ToArray();
}
else if (H5T.equal(attrTypeId, H5T.copy(H5T.H5Type.NATIVE_DOUBLE)))
{
dAttrs = new double[H5S.getSimpleExtentNPoints(H5A.getSpace(attrId))];
H5A.read(attrId, attrTypeId, new H5Array <double>(dAttrs));
}
H5T.close(attrTypeId);
H5A.close(attrId);
if (groupId != null)
{
H5G.close(groupId);
}
if (dataSetId != null)
{
H5D.close(dataSetId);
}
H5F.close(fileId);
return((double)dAttrs[0]);
}
catch (HDFException e)
{
Console.WriteLine("Error: Unhandled HDF5 exception");
Console.WriteLine(e.Message);
}
return(attr);
}
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);
}
public void H5Fclear_elink_cacheTest1()
{
Assert.IsTrue(H5F.clear_elink_file_cache(m_v0_class_file) >= 0);
Assert.IsTrue(H5F.clear_elink_file_cache(m_v2_class_file) >= 0);
Assert.IsTrue(H5F.clear_elink_file_cache(m_v0_test_file) >= 0);
Assert.IsTrue(H5F.clear_elink_file_cache(m_v2_test_file) >= 0);
}
} // make_table
static void test_getting_info()
{
try
{
Console.Write("Testing getting table/field information");
// Open the file to check on the table.
H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
hssize_t nfields = 0, nrecords = 0;
string[] field_names = { "c", "i", "l" };
// Get the table info.
TableInfo table = H5TB.getTableInfo(fileId, TABLE_NAME);
if (table.nFields != N_FIELDS)
{
Console.WriteLine("\ntest_getting_info: incorrect number of fields: read {0} - should be {1}",
nfields, N_FIELDS);
nerrors++;
}
if (table.nRecords != N_RECORDS)
{
Console.WriteLine("\ntest_getting_info: incorrect number of fields: read {0} - should be {1}",
nrecords, N_RECORDS);
nerrors++;
}
// Get field info.
int [] sizes = new int[N_FIELDS];
int [] offsets = new int[N_FIELDS];
TableFieldInfo tablefield = H5TB.getFieldInfo(fileId, TABLE_NAME);
int ii;
for (ii = 0; ii < N_FIELDS; ii++)
{
if (tablefield.fieldName[ii] != field_names[ii])
{
Console.WriteLine("\ntest_getting_info: field #{0} has incorrect name: read {0} - should be {1}",
ii, field_names[ii], tablefield.fieldName[ii]);
nerrors++;
}
}
H5F.close(fileId);
Console.WriteLine("\t\t\tPASSED");
}
catch (HDFException anyHDF5E)
{
Console.WriteLine(anyHDF5E.Message);
nerrors++;
}
catch (System.Exception sysE)
{
Console.WriteLine(sysE.TargetSite);
Console.WriteLine(sysE.Message);
nerrors++;
}
} // test_getting_info
public void H5Fget_intentTest1()
{
uint intent = 4711;
Assert.IsTrue(H5F.get_intent(m_v0_class_file, ref intent) >= 0);
Assert.IsTrue(H5F.get_intent(m_v2_class_file, ref intent) >= 0);
}
private static void ConvertHdf4To5(Hdf4FileAttrs hdf4FileAttrs, string f5name,
Action <string, int, int> messageAction)
{
try
{
// Create a new file using H5F_ACC_TRUNC access,
// default file creation properties, and default file
// access properties.
H5FileId fileId = H5F.create(f5name, H5F.CreateMode.ACC_TRUNC);
int nxf5 = hdf4FileAttrs.Hdf4FileAttr.XDim;
int nyf5 = hdf4FileAttrs.Hdf4FileAttr.YDim;
int rank = 2;
//测试读取的科学数据集及其属性
int sdscount = hdf4FileAttrs.Hdf4FileAttr.DataFields.Count;
for (int k = 0; k < sdscount; k++)
{
ConvertHdf4To5BySds(hdf4FileAttrs, messageAction, k, nyf5, nxf5, rank, fileId);
}
HDFAttributeDef[] attributeDef5s = hdf4FileAttrs.GetHDFAttributeDefs();
foreach (HDFAttributeDef attributeDef5 in attributeDef5s)
{
WriteHdfAttributes.WriteHdfAttribute(fileId, attributeDef5);
}
H5F.close(fileId);
}
catch (Exception ex)
{
throw new Exception("拼接Hdf4时出错，具体信息：" + ex.Message, ex);
}
}
private static H5FileId GetFileId()
{
return
(File.Exists(Global.GetOutputPath(Global.Configuration.HDF5Path))
? H5F.open(Global.GetOutputPath(Global.Configuration.HDF5Path), H5F.OpenMode.ACC_RDWR)
: H5F.create(Global.GetOutputPath(Global.Configuration.HDF5Path), H5F.CreateMode.ACC_EXCL));
}
/// <summary>
/// Opens a Hdf-5 file
/// </summary>
/// <param name="filename"></param>
/// <param name="readOnly"></param>
/// <returns></returns>
public static long OpenFile(string filename, bool readOnly = false)
{
uint access = (readOnly) ? H5F.ACC_RDONLY : H5F.ACC_RDWR;
var fileId = H5F.open(filename, access);
return(fileId);
}
public Dictionary <string, string> TryReadDataTable(string datasetName)
{
Dictionary <string, string> result = null;
var subDsDic = ds.GetSubDatasets();
if (subDsDic.Count > 0)
{
H5ID h5FileId = H5F.open(fileName, H5F.ACC_RDONLY);
H5ID datasetId = H5D.open(h5FileId, datasetName);
H5ID typeId = H5D.get_type(datasetId);
H5ID spaceId = H5D.get_space(datasetId);
if (H5T.get_class(typeId) == H5T.class_t.COMPOUND)
{
int numCount = H5T.get_nmembers(typeId);
var size = H5T.get_size(typeId);
byte[] buffer = new byte[size.ToInt32()];
GCHandle hnd = GCHandle.Alloc(buffer, GCHandleType.Pinned);
int ndims = H5S.get_simple_extent_ndims(spaceId);
if (ndims == 1)
{
result = new Dictionary <string, string>();
H5D.read(datasetId, typeId, H5S.ALL, H5S.ALL, H5P.DEFAULT, hnd.AddrOfPinnedObject());
for (uint i = 0; i < numCount; i++)
{
string name = Marshal.PtrToStringAnsi(H5T.get_member_name(typeId, i));
int offset = H5T.get_member_offset(typeId, i).ToInt32();
H5ID subTypeId = H5T.get_member_type(typeId, i);
H5T.class_t typeClass = H5T.get_member_class(typeId, i);
string value = ReadBuffer(buffer, offset, typeClass, subTypeId);
result.Add(name, value);
H5T.close(subTypeId);
}
}
hnd.Free();
}
if (spaceId != 0)
{
H5S.close(spaceId);
}
if (typeId != 0)
{
H5T.close(typeId);
}
if (datasetId != 0)
{
H5D.close(datasetId);
}
if (h5FileId != 0)
{
H5F.close(h5FileId);
}
}
return(result);
}
public File(string filename, H5F.OpenMode mode = H5F.OpenMode.ACC_RDONLY)
{
_filename = filename;
_mode = mode;
EnsureH5Lib();
OpenFile();
}
public void H5Fset_mdc_configTest2()
{
H5AC.cache_config_t conf = new H5AC.cache_config_t(
H5AC.CURR_CACHE_CONFIG_VERSION);
Assert.IsFalse(
H5F.set_mdc_config(Utilities.RandomInvalidHandle(),
ref conf) >= 0);
}
public static void ClassCleanup()
{
// close the global test files
Assert.IsTrue(H5F.close(m_v0_class_file) >= 0);
Assert.IsTrue(H5F.close(m_v2_class_file) >= 0);
File.Delete(m_v0_class_file_name);
File.Delete(m_v2_class_file_name);
}
public bool OpenHDF(FileName file, H5F.OpenMode mode = H5F.OpenMode.ACC_RDONLY)
{
try
{
file_id = H5F.open(file.FullPath, mode);
last_exception = null;
if (file_id.Id >= 0)
return true;
else
return false;
}
catch (Exception ex)
{
last_exception = ex;
return false;
}
}
public bool CreateHDF(FileName file, H5F.CreateMode mode = H5F.CreateMode.ACC_TRUNC)
{
try
{
file_id = H5F.create(file.FullPath, mode);
last_exception = null;
if (file_id.Id >= 0)
return true;
else
return false;
}
catch (Exception ex)
{
last_exception = ex;
return false;
}
}
