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 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);
}
