private void GetGroupDatasetNames(string groupName)
{
H5GroupId h5GroupId = H5G.open(_h5FileId, groupName);
try
{
long dscount = H5G.getNumObjects(h5GroupId);
for (int i = 0; i < dscount; i++)
{
string objname = H5G.getObjectNameByIndex(h5GroupId, (ulong)i);
ObjectInfo objInfo = H5G.getObjectInfo(h5GroupId, objname, false);
switch (objInfo.objectType)
{
case H5GType.DATASET:
if (objInfo.objectType == H5GType.DATASET)
{
if (groupName == "/")
{
_datasetNames.Add(objname);
}
else
{
_datasetNames.Add(groupName + objname);
}
}
break;
case H5GType.GROUP:
if (groupName == "/")
{
GetGroupDatasetNames(objname + "/");
}
else
{
GetGroupDatasetNames(groupName + objname + "/");
}
break;
case H5GType.LINK:
break;
case H5GType.TYPE:
break;
default:
break;
}
}
}
finally
{
if (h5GroupId != null)
{
H5G.close(h5GroupId);
}
}
}
private void createHD5GroupObject(H5GroupId id, String name, ref HDF5GroupObject hdf5Obj)
{
hdf5Obj.GroupID = id;
hdf5Obj.GroupName = name;
long num = H5G.getNumObjects(hdf5Obj.GroupID);
// the items under the group
for (ulong i = 0; i < (ulong)num; i++)
{
String objName = H5G.getObjectNameByIndex(hdf5Obj.GroupID, i);
// get the link info.
//linfo = H5L.getInfo(groupID, objName);
ObjectInfo objInfo = H5G.getObjectInfo(hdf5Obj.GroupID, objName, true);
if (objInfo.objectType == H5GType.GROUP)
{
String pathName = "/" + name + "/" + objName;
if (name.CompareTo("/") == 0)
{
pathName = "/" + objName;
}
H5GroupId groupID = null;
try
{
groupID = H5G.open(hdf5Obj.GroupID, pathName);
HDF5GroupObject subObj = new HDF5GroupObject();
subObj.ShortName = objName;
createHD5GroupObject(groupID, pathName, ref subObj);
hdf5Obj.SubGroups.Add(subObj);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
if (groupID != null)
{
H5G.close(groupID);
}
}
}
else
if (objInfo.objectType == H5GType.DATASET)
{
String pathName = "/" + name + "/" + objName;
HD5DataSetObject dataObject = new HD5DataSetObject();
dataObject.ShortName = objName;
createHD5DataObject(hdf5Obj.GroupID, pathName, ref dataObject);
hdf5Obj.Datasets.Add(dataObject);
}
}
}
/// <summary>
/// 得到所有数据集合名，未对异常进行处理
/// </summary>
private void getDatasetNames()
{
H5GroupId groupId = H5G.open(_fileId, "/");
long dscount = H5G.getNumObjects(groupId);
for (int ii = 0; ii < dscount; ++ii)
{
String v = H5G.getObjectNameByIndex(groupId, (ulong)ii);
_datasetNames.Add(v);
}
if (groupId != null)
{
H5G.close(groupId);
}
}
private bool getOMXMatrixTables()
{
// get info about the tables
this.dataGroup = H5G.open(fileId, dataGroupName);
this.NumMatrix = (int)H5G.getNumObjects(this.dataGroup);
this.MatrixNames = new List <string>();
for (int i = 0; i < NumMatrix; i++)
{
string matName = H5G.getObjectNameByIndex(this.dataGroup, (ulong)i);
MatrixNames.Add(matName);
H5DataSetId matId = H5D.open(dataGroup, matName);
tables.Add(matName, matId);
}
return(true);
}
private bool getOMXIndexMaps()
{
this.luGroup = H5G.open(fileId, luGroupName);
this.NumIndexMap = (int)H5G.getNumObjects(this.luGroup);
this.IndexMapNames = new List <string>();
for (int i = 0; i < NumIndexMap; i++)
{
string imName = H5G.getObjectNameByIndex(this.luGroup, (ulong)i);
IndexMapNames.Add(imName);
H5DataSetId imId = H5D.open(luGroup, imName);
indexMaps.Add(imName, imId);
}
return(true);
}
public static List <string> GetChildGroupNames(H5GroupId _groupId)
{
List <string> names = new List <string>();
ulong count = (ulong)H5G.getNumObjects(_groupId);;
for (ulong i = 0; i < count; i++)
{
string name = H5G.getObjectNameByIndex(_groupId, i);
ObjectInfo info = H5G.getObjectInfo(_groupId, name, false);
if (info.objectType == H5GType.GROUP)
{
names.Add(name);
}
}
return(names);
}
public void SimpleGroupCreateFind()
{
// Create an HDF5 file.
// The enumeration type H5F.CreateMode provides only the legal
// creation modes. Missing H5Fcreate parameters are provided
// with default values.
H5FileId fileId = H5F.create(TEST_FILE, H5F.CreateMode.ACC_TRUNC);
// Create a group in the file
H5GroupId groupId = H5G.create(fileId, "/simple");
// Close everything down.
H5G.close(groupId);
H5F.close(fileId);
Assert.IsTrue(System.IO.File.Exists(TEST_FILE));
fileId = H5F.open(TEST_FILE, H5F.OpenMode.ACC_RDONLY);
groupId = H5G.open(fileId, "/simple");
Assert.AreEqual(0, H5G.getNumObjects(groupId));
H5G.close(groupId);
H5F.close(fileId);
}
} // test_group_iterate
static void test_group_info()
{
try
{
Console.Write("Testing getting group information");
// Open the file.
H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
// Open the root group.
H5GroupId groupId = H5G.open(fileId, "/");
// Get number of objects in the root group.
long num_objs = H5G.getNumObjects(groupId);
if (num_objs != 3)
{
Console.WriteLine("\ntest_group_info: Root group should have 3 objects: /fromRoot, /Data, and /singleDataset, but is {0}", num_objs);
nerrors++;
}
// The root group has three objects in alphabetical order:
// intArray
// notfromRoot
// shortArray
// Note that, in order for this function to work correctly when taking the third
// parameter as H5IndexType.CRT_ORDER, the group's creation order must be tracked
// by setting the group creation property list with the C function H5Pset_link_creation_order,
// which is not included in this .NET wrappers version. - Mar, 2008
// Check object #3, should be "notfromRoot"
string obj_name = H5L.getNameByIndex(groupId, ".", H5IndexType.NAME, H5IterationOrder.INCREASING, 2);
if (obj_name != "singleDataset")
{
Console.WriteLine("\ntest_group_info: Incorrect name for 2nd objects from root group: {0}, should be {1}", obj_name, "singleDataset");
nerrors++;
}
// Close root group.
H5G.close(groupId);
// Open group "/fromRoot"
groupId = H5G.open(fileId, "/fromRoot");
H5GInfo oinfo = H5G.getInfo(groupId);
if (oinfo.nLinks != 3)
{
Console.WriteLine("\ntest_group_info: /fromRoot should have 3 objects: intArray, shortArray, notfromRoot, but is {0}", num_objs);
nerrors++;
}
// Check objects #1 and #3, should be "intArray" and "notfromRoot"
obj_name = H5L.getNameByIndex(groupId, ".", H5IndexType.NAME, H5IterationOrder.INCREASING, 0);
if (obj_name != "intArray")
{
Console.WriteLine("\ntest_group_info: Incorrect name for 1st object from group named /fromRoot: {0}, should be {1}", obj_name, "intArray");
nerrors++;
}
obj_name = H5L.getNameByIndex(groupId, ".", H5IndexType.NAME, H5IterationOrder.INCREASING, 2, new H5PropertyListId(H5P.Template.DEFAULT));
if (obj_name != "shortArray")
{
Console.WriteLine("\ntest_group_info: Incorrect name for 3rd object from group named /fromRoot: {0}, should be {1}", obj_name, "shortArray");
nerrors++;
}
// Close objects and file.
H5G.close(groupId);
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_group_info
static void test_group_basics()
{
try
{
Console.Write("Testing group basics");
// Create the file.
H5FileId fileId = H5F.create(FILE_NAME, H5F.CreateMode.ACC_TRUNC);
// Create a group.
H5GroupId groupId = H5G.create(fileId, "/fromRoot");
// Create a dataspace for common use.
hssize_t[] dims = { 1000, 20 };
H5DataSpaceId dspace = H5S.create_simple(RANK, dims);
// Create a dataset using file as location with absolute path name.
H5DataSetId dset1Id = H5D.create(fileId, "/fromRoot/intArray", H5T.H5Type.NATIVE_INT, dspace);
// Create a dataset using group as location with absolute path name.
H5DataSetId dset2Id = H5D.create(groupId, "/fromRoot/shortArray", H5T.H5Type.NATIVE_SHORT, dspace);
// Create a dataset using group as location with relative path name.
H5DataSetId dset3Id = H5D.create(groupId, "notfromRoot", H5T.H5Type.NATIVE_UCHAR, dspace);
ObjectInfo info = H5G.getObjectInfo(fileId, "/fromRoot/intArray", true);
if (info.nHardLinks != 1)
{
Console.WriteLine("\ntest_group_basics: number of hardlinks for /fromRoot/intArray should be = {0}", info.nHardLinks);
}
if (info.objectType != H5GType.DATASET)
{
Console.WriteLine("\ntest_group_basics: Object should be a dataset");
}
// Close objects and files.
H5D.close(dset1Id);
H5D.close(dset2Id);
H5D.close(dset3Id);
H5S.close(dspace);
H5G.close(groupId);
// Check various number of objects.
H5GroupId rootId = H5G.open(fileId, "/");
hssize_t num_objs = H5G.getNumObjects(rootId);
if (num_objs != 1)
{
Console.WriteLine("\ntest_group_basics: incorrect num_objs = {0} for root group\n", num_objs);
nerrors++;
}
groupId = H5G.open(fileId, "fromRoot");
num_objs = H5G.getNumObjects(groupId);
if (num_objs != 3)
{
Console.WriteLine("\ntest_group_basics: incorrect num_objs = {0} for group \"fromRoot\"\n", num_objs);
nerrors++;
}
H5G.close(rootId);
H5G.close(groupId);
H5F.close(fileId);
if (nerrors == 0)
{
Console.WriteLine("\t\t\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_group_basics
/*
* test_group_iterate -- tests that group iterating works properly.
* - opens the file created in the test_group_basics
* - creates more groups and datasets
* - iterates through root group and each sub group priting out name of each object
*/
static void test_group_iterate()
{
try
{
Console.Write("Testing group iteration");
// Open the file.
H5FileId fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
// Create a group in the file.
H5GroupId groupId = H5G.create(fileId, "/Data");
// Open first dataset.
H5DataSetId dset1Id = H5D.open(fileId, "/fromRoot/intArray");
// Get dataspace of this dataset.
H5DataSpaceId dspace = H5D.getSpace(dset1Id);
// Create a dataset in the group using absolute name.
H5DataSetId dataset = H5D.create(groupId, "/Data/IntData", H5T.H5Type.NATIVE_INT, dspace);
// Close the first dataset.
H5S.close(dspace);
H5D.close(dataset);
// Create the second dataset.
hssize_t[] dims = { 500, 20 };
dspace = H5S.create_simple(RANK, dims);
dataset = H5D.create(groupId, "/Data/FloatData", H5T.H5Type.NATIVE_FLOAT, dspace);
// Close objects and file.
H5D.close(dataset);
H5G.close(groupId);
H5F.close(fileId);
// Now reopen the file and group in the file.
fileId = H5F.open(FILE_NAME, H5F.OpenMode.ACC_RDWR);
groupId = H5G.open(fileId, "/Data");
// Access "IntData" dataset in the group.
dataset = H5D.open(groupId, "IntData");
// Create a dataset in the root group.
dataset = H5D.create(fileId, "/singleDataset", H5T.H5Type.NATIVE_INT, dspace);
// Various checks on number of objects
groupId = H5G.open(fileId, "/");
hssize_t num_objs = H5G.getNumObjects(groupId);
if (num_objs != 3)
{
Console.WriteLine("\ntest_group_iterate: / should have 3 objects: /fromRoot, /Data, and /singleDataset, but is {0}", num_objs);
}
H5G.close(groupId);
groupId = H5G.open(fileId, "/fromRoot");
num_objs = H5G.getNumObjects(groupId);
if (num_objs != 3)
{
Console.WriteLine("\ntest_group_iterate: /fromRoot should have 3 objects: intArray, shortArray, notfromRoot, but is {0}", num_objs);
}
// Use iterator to see the names of the objects in the root group and sub groups.
H5GIterateCallback myCallback;
myCallback = file_info;
int x = 0;
Console.WriteLine();
Console.WriteLine("\tRoot Group iterating:");
int index = H5G.iterate(fileId, "/", myCallback, "Object name:", ref x);
Console.WriteLine();
Console.WriteLine("\t/fromRoot iterating:");
x = 0;
index = H5G.iterate(fileId, "/fromRoot", myCallback, "Object name:", ref x);
// Close objects and file.
H5D.close(dataset);
H5G.close(groupId);
H5S.close(dspace);
H5F.close(fileId);
Console.WriteLine("\t\t\t\t\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_group_iterate
public SkimMatrix Read(string fileNameAndGroupAndDataTable, int field, float scale)
{
//mb merged these changes to local develop before pushing #210
//hdf5 filename contain "filename/group/skim"
//get the index of group
int hdf5GroupEnd = fileNameAndGroupAndDataTable.LastIndexOf("/");
string fileNameAndGroup = hdf5GroupEnd > 0 ? fileNameAndGroupAndDataTable.Substring(0, hdf5GroupEnd) : fileNameAndGroupAndDataTable;
//get the index of filename
int hdf5NameEnd = hdf5GroupEnd > 0 ? fileNameAndGroup.LastIndexOf("/") : -1;
string groupName = fileNameAndGroup.Substring(hdf5NameEnd + 1);
//get the omx/hdf5 filename
string HDFName = fileNameAndGroup.Substring(0, hdf5NameEnd);
string groupAndDataTable = fileNameAndGroupAndDataTable.Substring(hdf5NameEnd);
string hdfFile = Path.Combine(_path, HDFName);
FileInfo file = new FileInfo(hdfFile);
if (!file.Exists)
{
throw new FileNotFoundException(string.Format("The skim file {0} could not be found.", file.FullName));
}
H5FileId dataFile = H5F.open(hdfFile, H5F.OpenMode.ACC_RDONLY);
H5DataSetId dataSet = H5D.open(dataFile, groupAndDataTable);
H5DataSpaceId space = H5D.getSpace(dataSet);
long[] size2 = H5S.getSimpleExtentDims(space);
long nRows = size2[0];
long nCols = size2[1];
Debug.Assert(nRows == nCols);
long numZones = _mapping.Count();
int[] lookupMap = null;
string lookupMapName = null;
string lookupGroupName = "lookup";
H5GroupId luGroup = H5G.open(dataFile, lookupGroupName);
if (H5G.getNumObjects(luGroup) == 1L)
{
lookupMapName = H5G.getObjectNameByIndex(luGroup, 0);
H5DataSetId lookupDataSet = H5D.open(dataFile, string.Concat(lookupGroupName, "/", lookupMapName));
H5DataTypeId lookupMapType = H5D.getType(lookupDataSet);
H5DataSpaceId lookupMapSpace = H5D.getSpace(lookupDataSet);
long lookupMapSize = H5S.getSimpleExtentDims(lookupMapSpace)[0];
lookupMap = new int[lookupMapSize];
H5Array <int> lookupWrapArray = new H5Array <int>(lookupMap);
H5D.read(lookupDataSet, lookupMapType, lookupWrapArray);
}
if (lookupMap != null)
{
if (lookupMap.Length != nRows)
{
Global.PrintFile.WriteLine(string.Format("DATA WARNING: skim file: {0} has a lookup map named {1} but its length ({2}) is different than the matrix size ({3}) in group table {4}", hdfFile, lookupMapName, lookupMap.Length, nRows, groupAndDataTable));
lookupMap = null;
}
}
// 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 (int 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
double[,] dataArray = new double[nRows, nCols];
H5Array <double> wrapArray = new H5Array <double>(dataArray);
H5DataTypeId tid1 = H5D.getType(dataSet);
H5D.read(dataSet, tid1, wrapArray);
long numSuccessfuLookups = 0;
for (int row = 0; row < nRows; row++)
{
int mappingKey = (lookupMap == null) ? (row + 1) : lookupMap[row];
if (_mapping.TryGetValue(mappingKey, out int mappedRow))
{
for (int col = 0; col < nCols; col++)
{
mappingKey = (lookupMap == null) ? (col + 1) : lookupMap[col];
if (_mapping.TryGetValue(mappingKey, out int mappedCol))
{
double value = dataArray[row, col] * scale;
++numSuccessfuLookups;
if (value > 0)
{
if (value > ushort.MaxValue - 1)
{
value = ushort.MaxValue - 1;
}
_matrix[mappedRow][mappedCol] = (ushort)value; //bug #208 deferred but this will eventually changed be Convert.ToUInt16 to avoid 0.57*100=56 bug
}
}
} //for col
}
} //for row
Global.PrintFile.WriteLine(string.Format("Loaded skim file: {0} dataset: {1}, scale={6} with input matrix size={2} and DaySim matrix size={3} zones. Percentage successful mappings {4}. {5}", hdfFile, groupAndDataTable, nRows, numZones, (numSuccessfuLookups / (nRows * nCols)) * 100.0, lookupMap != null ? string.Format("Using lookupMap {0}.", lookupMapName) : "No lookupMap.", scale), true);
SkimMatrix skimMatrix = new SkimMatrix(_matrix);
return(skimMatrix);
}
public void SimpleDataReadWrite()
{
// Create an HDF5 file.
// The enumeration type H5F.CreateMode provides only the legal
// creation modes. Missing H5Fcreate parameters are provided
// with default values.
H5FileId fileId = H5F.create(TEST_FILE, H5F.CreateMode.ACC_TRUNC);
// Create a group in the file
H5GroupId groupId = H5G.create(fileId, "/simple");
// Prepare to create a data space for writing a 1-dimensional
// signed integer array.
const int RANK = 1;
long[] dims = new long[RANK];
const int SIZE = 12;
dims[0] = SIZE;
// Put descending ramp data in an array so that we can
// write it to the file.
int[] dset_data = new int[SIZE];
for (int i = 0; i < SIZE; i++)
{
dset_data[i] = SIZE - i;
}
// Create a data space to accommodate our 1-dimensional array.
// The resulting H5DataSpaceId will be used to create the
// data set.
H5DataSpaceId spaceId = H5S.create_simple(RANK, dims);
// Create the data set.
H5DataSetId dataSetId = H5D.create(fileId, "/arrayIntExample",
H5T.H5Type.NATIVE_INT, spaceId);
// Write the integer data to the data set.
H5D.write(dataSetId,
new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(dset_data));
// If we were writing a single value it might look like this.
// Create the data set.
H5DataSetId scalarId = H5D.create(fileId, "/scalarIntExample",
H5T.H5Type.NATIVE_INT, spaceId);
int singleValue = 100;
H5D.writeScalar(scalarId,
new H5DataTypeId(H5T.H5Type.NATIVE_INT),
ref singleValue);
// Close everything down.
H5D.close(dataSetId);
H5D.close(scalarId);
H5S.close(spaceId);
H5G.close(groupId);
H5F.close(fileId);
Assert.IsTrue(System.IO.File.Exists(TEST_FILE));
fileId = H5F.open(TEST_FILE, H5F.OpenMode.ACC_RDONLY);
Assert.IsTrue(fileId.Id > 0);
groupId = H5G.open(fileId, "/simple");
Assert.IsTrue(groupId.Id > 0);
Assert.AreEqual(0, H5G.getNumObjects(groupId));
// Open the data set
dataSetId = H5D.open(fileId, "/arrayIntExample");
Assert.IsTrue(dataSetId.Id > 0);
long datasetsize = H5D.getStorageSize(dataSetId);
Assert.AreEqual(SIZE * sizeof(int), datasetsize);
// Read the integer data back from the data set
int[] readDataBack = new int[SIZE];
H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
new H5Array <int>(readDataBack));
for (int i = 0; i < SIZE; i++)
{
Assert.AreEqual(SIZE - i, readDataBack[i]);
}
// Read back the single-int example
scalarId = H5D.open(fileId, "/scalarIntExample");
Assert.IsTrue(scalarId.Id > 0);
H5D.readScalar <int>(scalarId,
new H5DataTypeId(H5T.H5Type.NATIVE_INT),
ref singleValue);
Assert.AreEqual(100, singleValue);
H5D.close(dataSetId);
H5D.close(scalarId);
H5G.close(groupId);
H5F.close(fileId);
}
