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hdf5: reader can now read FD data & other improvements

pull/1/head
Thorsten Liebig 2012-07-31 14:24:11 +02:00
parent 5c721e4704
commit 8dc581a314
2 changed files with 262 additions and 67 deletions
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315
tools/hdf5_file_reader.cpp
View File

@ -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> &timestep, 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;
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;
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;
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])

8
tools/hdf5_file_reader.h
View File

@ -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