Help! I've been beating my head on this for a while now and I can't figure
out what's wrong!
I'm trying to read from an HDF5 file using the C++ API with the code below,
but I keep getting an Access Violation error in the read command, within
H5D_scatter_mem's while loop. I've tried reading the entire data set and
hyperslabs, but the only successful read I've done is if I read one element
from the set. The HDF5 file and the library I built seems fine as I can use
the h5dump tool to read the dataset in question
I'd appreciate any help anyone can give me. Thanks!
-John
···
--------------
John Kua
Research Scientist
Electrical Engineering and Computer Science Department
University of California, Berkeley
email: jkua@eecs.berkeley.edu
int fileReader::readHdf5File(string fileName){
/*
* Try block to detect exceptions raised by any of the calls inside it
*/
try
{
/*
* Turn off the auto-printing when failure occurs so that we can
* handle the errors appropriately
*/
Exception::dontPrint();
/*
* Open the specified file and the specified dataset in the file.
*/
H5File file( fileName.c_str(), H5F_ACC_RDONLY );
Group group = file.openGroup("/Lidar");
DataSet dataset = group.openDataSet("range1");
/*
* Get the class of the datatype that is used by the dataset.
*/
H5T_class_t type_class = dataset.getTypeClass();
/*
* Get class of datatype and print message if it's an integer.
*/
if( type_class == H5T_INTEGER )
{
cout << "Data set has INTEGER type" << endl;
/*
* Get the integer datatype
*/
IntType intype = dataset.getIntType();
/*
* Get order of datatype and print message if it's a little endian.
*/
H5std_string order_string;
H5T_order_t order = intype.getOrder( order_string );
cout << order_string << endl;
/*
* Get size of the data element stored in file and print it.
*/
size_t size = intype.getSize();
cout << "Data size is " << size << endl;
}
/*
* Get dataspace of the dataset.
*/
DataSpace dataspace = dataset.getSpace();
/*
* Get the number of dimensions in the dataspace.
*/
int rank = dataspace.getSimpleExtentNdims();
/*
* Get the dimension size of each dimension in the dataspace and
* display them.
*/
hsize_t dims_out[2];
int ndims = dataspace.getSimpleExtentDims( dims_out, NULL);
cout << "rank " << rank << ", dimensions " <<
(unsigned long)(dims_out[0]) << " x " <<
(unsigned long)(dims_out[1]) << endl;
//dataspace.selectAll();
hsize_t offset[2]; // hyperslab offset in the file
hsize_t count[2]; // size of the hyperslab in the file
offset[0] = 0;
offset[1] = 0;
count[0] = 5;
count[1] = 5;
dataspace.selectHyperslab( H5S_SELECT_SET, count, offset );
/*
* Define the memory dataspace.
*/
hsize_t dimsm[2]; /* memory space dimensions */
dimsm[0] = dims_out[0];
dimsm[1] = dims_out[1];
DataSpace memspace( rank, dimsm );
//memspace.selectAll();
memspace.selectHyperslab( H5S_SELECT_SET, count, offset );
int ** data_out = new int*[dims_out[0]];
for ( int i = 0; i < dims_out[0]; i++ ){
data_out[i] = new int[dims_out[1]];
for ( int j = 0; j < dims_out[1]; j++ ){
data_out[i][j] = 0;
}
}
cout << "Finished init" << endl;
for (int j = 0; j < dims_out[0]; j++)
{
cout << j << ": ";
for (int i = 0; i < 10; i++)
cout << data_out[j][i] << " ";
cout << endl;
}
dataset.read( data_out, PredType::NATIVE_INT, memspace, dataspace );
//dataset.read( data_out, PredType::NATIVE_INT);
for (int j = 0; j < dims_out[0]; j++)
{
for (int i = 0; i < 10; i++)
cout << data_out[j][i] << " ";
cout << endl;
}
} // end of try block
// catch failure caused by the H5File operations
catch( FileIException error )
{
error.printError();
return -1;
}
// catch failure caused by the DataSet operations
catch( DataSetIException error )
{
error.printError();
return -1;
}
// catch failure caused by the DataSpace operations
catch( DataSpaceIException error )
{
error.printError();
return -1;
}
// catch failure caused by the DataSpace operations
catch( DataTypeIException error )
{
error.printError();
return -1;
}
return 0; // successfully terminated
}