hdf5: reader can now read FD data & other improvements
Thorsten Liebig
parent
5c721e4704
commit
8dc581a314
|
|
@ -54,7 +54,139 @@ bool HDF5_File_Reader::IsValid()
|
|||
return true;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::OpenGroup(hid_t &file, hid_t &group, string groupName)
|
||||
{
|
||||
file = H5Fopen( m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
|
||||
if (file==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::OpenGroup: opening the given file """ << m_filename << """ failed" << endl;
|
||||
return 0;
|
||||
}
|
||||
if (H5Lexists(file, groupName.c_str(), H5P_DEFAULT)<=0)
|
||||
{
|
||||
H5Fclose(file);
|
||||
return 0;
|
||||
}
|
||||
|
||||
group = H5Gopen(file, groupName.c_str() );
|
||||
if (group<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::OpenGroup: can't open group """ << groupName << """" << endl;
|
||||
H5Fclose(file);
|
||||
return 0;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::ReadAttribute(string grp_name, string attr_name, vector<float> &attr_values)
|
||||
{
|
||||
vector<double> d_attr_values;
|
||||
if (ReadAttribute(grp_name, attr_name, d_attr_values)==false)
|
||||
return false;
|
||||
attr_values.resize(d_attr_values.size(),0);
|
||||
for (size_t n=0;n<d_attr_values.size();++n)
|
||||
attr_values.at(n)=d_attr_values.at(n);
|
||||
return true;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::ReadAttribute(string grp_name, string attr_name, vector<double> &attr_values)
|
||||
{
|
||||
attr_values.clear();
|
||||
|
||||
hid_t hdf5_file = H5Fopen( m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
|
||||
if (hdf5_file==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::OpenGroup: opening the given file """ << m_filename << """ failed" << endl;
|
||||
return 0;
|
||||
}
|
||||
|
||||
if (H5Lexists(hdf5_file, grp_name.c_str(), H5P_DEFAULT)<=0)
|
||||
{
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
|
||||
hid_t attr = H5Aopen_by_name(hdf5_file, grp_name.c_str(), attr_name.c_str(), H5P_DEFAULT, H5P_DEFAULT);
|
||||
if (attr==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadAttribute: Opening the given Attribute: """ << attr_name << """ failed" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
|
||||
hid_t type = H5Aget_type(attr);
|
||||
if (type<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadAttribute: Dataset type error" << endl;
|
||||
H5Aclose(attr);
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
|
||||
attr_values.clear();
|
||||
if (H5Tget_class(type)==H5T_FLOAT)
|
||||
{
|
||||
size_t numVal = H5Aget_storage_size(attr)/H5Tget_size(type);
|
||||
hid_t datatype=-1;
|
||||
void *value=NULL;
|
||||
float *f_value=NULL;
|
||||
double *d_value=NULL;
|
||||
if (H5Tget_size(type)==sizeof(float))
|
||||
{
|
||||
f_value = new float[numVal];
|
||||
value = f_value;
|
||||
datatype = H5T_NATIVE_FLOAT;
|
||||
}
|
||||
if (H5Tget_size(type)==sizeof(double))
|
||||
{
|
||||
d_value = new double[numVal];
|
||||
value = d_value;
|
||||
datatype = H5T_NATIVE_DOUBLE;
|
||||
}
|
||||
if (H5Aread(attr, datatype, value)<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadAttribute: Reading the given Attribute failed" << endl;
|
||||
H5Aclose(attr);
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
if (f_value)
|
||||
for (size_t n=0;n<numVal;++n)
|
||||
attr_values.push_back(f_value[n]);
|
||||
if (d_value)
|
||||
for (size_t n=0;n<numVal;++n)
|
||||
attr_values.push_back(d_value[n]);
|
||||
delete[] f_value;
|
||||
delete[] d_value;
|
||||
}
|
||||
else
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadAttribute: Attribute type not supported" << endl;
|
||||
H5Aclose(attr);
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
H5Aclose(attr);
|
||||
H5Fclose(hdf5_file);
|
||||
return true;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::ReadDataSet(string ds_name, hsize_t &nDim, hsize_t* &dims, float* &data)
|
||||
{
|
||||
double* d_data;
|
||||
if (ReadDataSet(ds_name, nDim, dims, d_data)==false)
|
||||
return false;
|
||||
hsize_t data_size = 1;
|
||||
for (unsigned int d=0;d<nDim;++d)
|
||||
data_size*=dims[d];
|
||||
data = new float[data_size];
|
||||
for (size_t n=0;n<data_size;++n)
|
||||
data[n]=d_data[n];
|
||||
delete[] d_data;
|
||||
return true;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::ReadDataSet(string ds_name, hsize_t &nDim, hsize_t* &dims, double* &data)
|
||||
{
|
||||
if (IsValid()==false)
|
||||
return false;
|
||||
|
|
@ -96,16 +228,32 @@ bool HDF5_File_Reader::ReadDataSet(string ds_name, hsize_t &nDim, hsize_t* &dims
|
|||
hsize_t data_size = 1;
|
||||
for (unsigned int d=0;d<nDim;++d)
|
||||
data_size*=dims[d];
|
||||
data = new float[data_size];
|
||||
if (H5Dread(dataset,type,H5S_ALL,H5S_ALL,H5P_DEFAULT,data)<0)
|
||||
|
||||
void *value=NULL;
|
||||
float *f_value=NULL;
|
||||
data = new double[data_size];
|
||||
if (H5Tget_size(type)==sizeof(float))
|
||||
{
|
||||
f_value = new float[data_size];
|
||||
value = f_value;
|
||||
}
|
||||
else
|
||||
value = data;
|
||||
|
||||
if (H5Dread(dataset,type,H5S_ALL,H5S_ALL,H5P_DEFAULT,value)<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadDataSet: error reading data" << endl;
|
||||
H5Dclose(dataset);
|
||||
H5Fclose(hdf5_file);
|
||||
delete[] data;
|
||||
delete[] f_value;
|
||||
data=NULL;
|
||||
return false;
|
||||
}
|
||||
if (f_value)
|
||||
for (size_t n=0;n<data_size;++n)
|
||||
data[n]=f_value[n];
|
||||
delete[] f_value;
|
||||
H5Dclose(dataset);
|
||||
H5Fclose(hdf5_file);
|
||||
return true;
|
||||
|
|
@ -144,6 +292,7 @@ bool HDF5_File_Reader::ReadMesh(float** lines, unsigned int* numLines, int &mesh
|
|||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
|
||||
for (int n=0;n<3;++n)
|
||||
{
|
||||
hsize_t nDim;
|
||||
|
|
@ -171,26 +320,11 @@ unsigned int HDF5_File_Reader::GetNumTimeSteps()
|
|||
if (IsValid()==false)
|
||||
return false;
|
||||
|
||||
hid_t hdf5_file = H5Fopen( m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
|
||||
if (hdf5_file==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetNumTimeSteps: opening the given file """ << m_filename << """ failed" << endl;
|
||||
hid_t hdf5_file;
|
||||
hid_t TD_grp;
|
||||
if (OpenGroup(hdf5_file, TD_grp, "/FieldData/TD")==false)
|
||||
return false;
|
||||
}
|
||||
|
||||
if (H5Lexists(hdf5_file, "/FieldData/TD", H5P_DEFAULT)<=0)
|
||||
{
|
||||
H5Fclose(hdf5_file);
|
||||
return 0;
|
||||
}
|
||||
|
||||
hid_t TD_grp = H5Gopen(hdf5_file, "/FieldData/TD" );
|
||||
if (TD_grp<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetNumTimeSteps: can't open group ""/FieldData/TD""" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return 0;
|
||||
}
|
||||
hsize_t numObj;
|
||||
if (H5Gget_num_objs(TD_grp,&numObj)<0)
|
||||
{
|
||||
|
|
@ -209,26 +343,11 @@ bool HDF5_File_Reader::ReadTimeSteps(vector<unsigned int> ×tep, vector<stri
|
|||
if (IsValid()==false)
|
||||
return false;
|
||||
|
||||
hid_t hdf5_file = H5Fopen( m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
|
||||
if (hdf5_file==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadTimeSteps: opening the given file """ << m_filename << """ failed" << endl;
|
||||
hid_t hdf5_file;
|
||||
hid_t TD_grp;
|
||||
if (OpenGroup(hdf5_file, TD_grp, "/FieldData/TD")==false)
|
||||
return false;
|
||||
}
|
||||
|
||||
if (H5Lexists(hdf5_file, "/FieldData/TD", H5P_DEFAULT)<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadTimeSteps: can't open ""/FieldData/TD""" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
hid_t TD_grp = H5Gopen(hdf5_file, "/FieldData/TD" );
|
||||
if (TD_grp<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadTimeSteps: can't open ""/FieldData/TD""" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return false;
|
||||
}
|
||||
hsize_t numObj;
|
||||
if (H5Gget_num_objs(TD_grp,&numObj)<0)
|
||||
{
|
||||
|
|
@ -277,27 +396,10 @@ float**** HDF5_File_Reader::GetTDVectorData(size_t idx, float &time, unsigned in
|
|||
if (IsValid()==false)
|
||||
return false;
|
||||
|
||||
hid_t hdf5_file = H5Fopen( m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
|
||||
if (hdf5_file==-1)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetTDVectorData: opening the given file """ << m_filename << """ failed" << endl;
|
||||
hid_t hdf5_file;
|
||||
hid_t TD_grp;
|
||||
if (OpenGroup(hdf5_file, TD_grp, "/FieldData/TD")==false)
|
||||
return false;
|
||||
}
|
||||
|
||||
time = 0;
|
||||
if (H5Lexists(hdf5_file, "/FieldData/TD", H5P_DEFAULT)<=0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetTDVectorData: can't open ""/FieldData/TD""" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return NULL;
|
||||
}
|
||||
hid_t TD_grp = H5Gopen(hdf5_file, "/FieldData/TD" );
|
||||
if (TD_grp<0)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetTDVectorData: can't open ""/FieldData/TD""" << endl;
|
||||
H5Fclose(hdf5_file);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
hsize_t numObj;
|
||||
if (H5Gget_num_objs(TD_grp,&numObj)<0)
|
||||
|
|
@ -345,7 +447,7 @@ float**** HDF5_File_Reader::GetTDVectorData(size_t idx, float &time, unsigned in
|
|||
|
||||
hsize_t nDim;
|
||||
hsize_t* dims=NULL;
|
||||
float* data=NULL;
|
||||
double* data=NULL;
|
||||
ReadDataSet(ds_name, nDim, dims, data);
|
||||
if (nDim!=4)
|
||||
{
|
||||
|
|
@ -388,20 +490,107 @@ float**** HDF5_File_Reader::GetTDVectorData(size_t idx, float &time, unsigned in
|
|||
|
||||
unsigned int HDF5_File_Reader::GetNumFrequencies()
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetNumFrequencies(): not implemented yet!" << endl;
|
||||
return 0;
|
||||
vector<float> frequencies;
|
||||
if (ReadFrequencies(frequencies)==false)
|
||||
return 0;
|
||||
return frequencies.size();
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::ReadFrequencies(vector<float> &frequencies)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::ReadFrequencies(): not implemented yet!" << endl;
|
||||
return false;
|
||||
if (IsValid()==false)
|
||||
return false;
|
||||
|
||||
return ReadAttribute("/FieldData/FD","frequency",frequencies);
|
||||
}
|
||||
|
||||
complex<float>**** HDF5_File_Reader::GetFDVectorData(size_t idx, float &frequency, unsigned int data_size[])
|
||||
complex<float>**** HDF5_File_Reader::GetFDVectorData(size_t idx, unsigned int data_size[])
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData(): not implemented yet!" << endl;
|
||||
return NULL;
|
||||
hsize_t nDim;
|
||||
hsize_t* dims=NULL;
|
||||
double* data=NULL;
|
||||
stringstream ds_name;
|
||||
|
||||
// read real values
|
||||
ds_name << "/FieldData/FD/f" << idx << "_real";
|
||||
if (ReadDataSet(ds_name.str(), nDim, dims, data) == false)
|
||||
return NULL;
|
||||
if (nDim!=4)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData: data dimension invalid" << endl;
|
||||
delete[] dims;
|
||||
delete[] data;
|
||||
return NULL;
|
||||
}
|
||||
if (dims[0]!=3)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData: vector data dimension invalid" << endl;
|
||||
delete[] dims;
|
||||
delete[] data;
|
||||
return NULL;
|
||||
}
|
||||
data_size[0]=dims[3];
|
||||
data_size[1]=dims[2];
|
||||
data_size[2]=dims[1];
|
||||
delete[] dims;
|
||||
data_size[3]=3;
|
||||
size_t pos = 0;
|
||||
complex<float>**** field = Create_N_3DArray<complex<float> >(data_size);
|
||||
for (unsigned int d=0;d<3;++d)
|
||||
for (unsigned int k=0;k<data_size[2];++k)
|
||||
for (unsigned int j=0;j<data_size[1];++j)
|
||||
for (unsigned int i=0;i<data_size[0];++i)
|
||||
{
|
||||
field[d][i][j][k]=data[pos++];
|
||||
}
|
||||
delete[] data;
|
||||
|
||||
// read imaginary values
|
||||
ds_name.str("");
|
||||
ds_name << "/FieldData/FD/f" << idx << "_imag";
|
||||
if (ReadDataSet(ds_name.str(), nDim, dims, data) == false)
|
||||
{
|
||||
Delete_N_3DArray<complex<float> >(field, data_size);
|
||||
return NULL;
|
||||
}
|
||||
if (nDim!=4)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData: data dimension invalid" << endl;
|
||||
delete[] dims;
|
||||
delete[] data;
|
||||
Delete_N_3DArray<complex<float> >(field, data_size);
|
||||
return NULL;
|
||||
}
|
||||
if (dims[0]!=3)
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData: vector data dimension invalid" << endl;
|
||||
delete[] dims;
|
||||
delete[] data;
|
||||
Delete_N_3DArray<complex<float> >(field, data_size);
|
||||
return NULL;
|
||||
}
|
||||
if ((data_size[0]!=dims[3]) || (data_size[1]!=dims[2]) || (data_size[2]!=dims[1]))
|
||||
{
|
||||
cerr << "HDF5_File_Reader::GetFDVectorData: data dimension mismatch" << endl;
|
||||
delete[] dims;
|
||||
delete[] data;
|
||||
Delete_N_3DArray<complex<float> >(field, data_size);
|
||||
return NULL;
|
||||
}
|
||||
delete[] dims;
|
||||
|
||||
pos = 0;
|
||||
complex<double> I(0,1);
|
||||
for (unsigned int d=0;d<3;++d)
|
||||
for (unsigned int k=0;k<data_size[2];++k)
|
||||
for (unsigned int j=0;j<data_size[1];++j)
|
||||
for (unsigned int i=0;i<data_size[0];++i)
|
||||
{
|
||||
field[d][i][j][k]+= I*data[pos++];
|
||||
}
|
||||
delete[] data;
|
||||
|
||||
return field;
|
||||
}
|
||||
|
||||
bool HDF5_File_Reader::CalcFDVectorData(vector<float> &frequencies, vector<complex<float>****> &FD_data, unsigned int data_size[4])
|
||||
|
|
|
|||
|
|
@ -46,19 +46,25 @@ public:
|
|||
|
||||
unsigned int GetNumFrequencies();
|
||||
bool ReadFrequencies(std::vector<float> &frequencies);
|
||||
std::complex<float>**** GetFDVectorData(size_t idx, float &frequency, unsigned int data_size[4]);
|
||||
std::complex<float>**** GetFDVectorData(size_t idx, unsigned int data_size[4]);
|
||||
|
||||
/*!
|
||||
Calculate
|
||||
*/
|
||||
bool CalcFDVectorData(std::vector<float> &frequencies, std::vector<std::complex<float>****> &FD_data, unsigned int data_size[4]);
|
||||
|
||||
bool ReadAttribute(std::string grp_name, std::string attr_name, std::vector<double> &attr_values);
|
||||
bool ReadAttribute(std::string grp_name, std::string attr_name, std::vector<float> &attr_values);
|
||||
|
||||
bool IsValid();
|
||||
|
||||
protected:
|
||||
std::string m_filename;
|
||||
|
||||
bool ReadDataSet(std::string ds_name, hsize_t &nDim, hsize_t* &dims, double* &data);
|
||||
bool ReadDataSet(std::string ds_name, hsize_t &nDim, hsize_t* &dims, float* &data);
|
||||
|
||||
bool OpenGroup(hid_t &file, hid_t &group, std::string groupName);
|
||||
};
|
||||
|
||||
#endif // HDF5_FILE_READER_H
|
||||
|
|
|
|||
Loading…
Reference in New Issue