Hi,
I try to implement HDF structures in C++ for using the datasets with the Boost libraries. Is there any good tutorial for using HDF with C++ class structures, because it's hard for me to translate C examples to C++. I found only the HDF API reference under http://www.hdfgroup.org/HDF5/doc/cpplus_RM/index.html
At this time I had written code to read/write numeric vector and matrix structure. I have some trouble with arrays especially string types.
Does anyone know a How-To or anything else?
Thanks
Phil
Hi Phil,
Have you looked at
http://www.hdfgroup.org/HDF5/doc/cpplus_RM/examples.html?
Binh-Minh
···
-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Kraus Philipp
Sent: Sunday, June 06, 2010 11:48 AM
To: hdf-forum@hdfgroup.org
Subject: [Hdf-forum] HDF5 with C++
Hi,
I try to implement HDF structures in C++ for using the datasets with
the Boost libraries. Is there any good tutorial for using HDF with C++
class structures, because it's hard for me to translate C examples to C
++. I found only the HDF API reference under
http://www.hdfgroup.org/HDF5/doc/cpplus_RM/index.html
At this time I had written code to read/write numeric vector and
matrix structure. I have some trouble with arrays especially string
types.
Does anyone know a How-To or anything else?
Thanks
Phil
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2:14 PM
Hi Phil,
You can take a look at the classes in casa/HDF5 of casacore
(casacore.google.com). It can read or write (hyperslabs of) N-dim arrays
of various basic numeric types (including complex) in datasets. It can
also read/write (small) arrays in attributes.
The classes also deal with exception-safe handling of hid_t variables.
Cheers,
Ger
Kraus Philipp <philipp.kraus@flashpixx.de> 6/6/2010 5:47 PM >>>
Hi,
I try to implement HDF structures in C++ for using the datasets with
the Boost libraries. Is there any good tutorial for using HDF with C++
class structures, because it's hard for me to translate C examples to
C
++. I found only the HDF API reference under
http://www.hdfgroup.org/HDF5/doc/cpplus_RM/index.html
At this time I had written code to read/write numeric vector and
matrix structure. I have some trouble with arrays especially string
types.
Does anyone know a How-To or anything else?
Thanks
Phil
···
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
I know these examples and they help me to understand the structures, but I
don't find string examples and (string) array examples. I have a hdf5 file
(created with Matlab) and I would like to read in my C++ program. My code:
std::vector<std::string> hdf::readStringVector( const std::string& p_path )
const
{
H5::DataSet l_dataset = m_file.openDataSet( p_path.c_str() );
H5::DataSpace l_dataspace = l_dataset.getSpace();
hsize_t l_size[1];
l_dataspace.getSimpleExtentDims( l_size );
l_dataspace.close();
std::vector<std::string> l_vec( l_size[0] );
*** How can I read the array data
return l_vec;
}
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Hi Phil,
You can read the string into an std::string or a char* buffer then assign it
to a vector element, or read directly to the vector element, I think. Here
is an example using the char* buffer to read a string:
char *string_ds;
dataset.read(&string_ds, vlst); // string is variable length.
or
char string_ds[size_of_your_string]; // or dynamically allocate it
dataset.read(string_ds, vlst); // string is fixed length.
I hope that helps.
Binh-Minh
···
-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Philipp Kraus
Sent: Monday, June 07, 2010 11:56 AM
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] HDF5 with C++
I know these examples and they help me to understand the structures, but I
don't find string examples and (string) array examples. I have a hdf5 file
(created with Matlab) and I would like to read in my C++ program. My code:
std::vector<std::string> hdf::readStringVector( const std::string& p_path )
const
{
H5::DataSet l_dataset = m_file.openDataSet( p_path.c_str() );
H5::DataSpace l_dataspace = l_dataset.getSpace();
hsize_t l_size[1];
l_dataspace.getSimpleExtentDims( l_size );
l_dataspace.close();
std::vector<std::string> l_vec( l_size[0] );
*** How can I read the array data
return l_vec;
}
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2:14 PM
You mix C and C++ code, but I prefere only C++.
Michael Jackson wrote:
This is what I use:
herr_t H5Lite::readStringDataset(hid_t loc_id, const std::string&
std::vector<char> buf(static_cast<int>(size+1), 0x00); //Allocate
and Zero the array
err = H5Dread(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT,
&(buf.front()) );
if (err<0) {
std::cout << "Error Reading string dataset." << std::endl;
retErr = err;
} else {
data.append( &(buf.front()) ); //Append the string to the given
string
I don't find any native C++ code to read data into the std::vector.
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/**
* @brief Reads data from the HDF5 File into an std::vector<T> object. If the dataset
* is very large this can be an expensive method to use. It is here for convenience
* using STL with hdf5.
* @param loc_id The parent location that contains the dataset to read
* @param dsetName The name of the dataset to read
* @param data A std::vector<T>. Note the vector WILL be resized to fit the data.
* The best idea is to just allocate the vector but not to size it. The method
* will size it for you.
* @return Standard HDF error condition
*/
template <typename T>
static herr_t readVectorDataset(hid_t loc_id,
const std::string& dsetName,
std::vector<T> &data)
{
hid_t did;
herr_t err = 0;
herr_t retErr = 0;
hid_t spaceId;
hid_t dataType;
T test = static_cast<T>(0x00);
dataType = H5Lite::HDFTypeForPrimitive(test);
if (dataType == -1)
{
return -1;
}
//std::cout << "HDF5 Data Type: " << H5Lite::HDFTypeForPrimitiveAsStr(test) << std::endl;
/* Open the dataset. */
// std::cout << " Opening " << dsetName << " for data Retrieval. " << std::endl;
did = H5Dopen( loc_id, dsetName.c_str() );
if ( did < 0 ) {
std::cout << " Error opening Dataset: " << did << std::endl;
return -1;
}
if ( did >= 0 ) {
spaceId = H5Dget_space(did);
if ( spaceId > 0 ) {
int32_t rank = H5Sget_simple_extent_ndims(spaceId);
if (rank > 0) {
std::vector<hsize_t> dims;
dims.resize(rank);// Allocate enough room for the dims
rank = H5Sget_simple_extent_dims(spaceId, &(dims.front()), NULL);
hsize_t numElements = 1;
for (std::vector<hsize_t>::iterator iter = dims.begin(); iter < dims.end(); ++iter ) {
numElements = numElements * (*iter);
}
// std::cout << "NumElements: " << numElements << std::endl;
//Resize the vector
data.resize( static_cast<int>(numElements) );
// for (uint32_t i = 0; i<numElements; ++i) { data[i] = 55555555; }
err = H5Dread(did, dataType, H5S_ALL, H5S_ALL, H5P_DEFAULT, &( data.front() ) );
if (err < 0) {
std::cout << "Error Reading Data." << std::endl;
retErr = err;
}
}
err = H5Sclose(spaceId);
if (err < 0 ) {
std::cout << "Error Closing Data Space" << std::endl;
retErr = err;
}
}
else
{
std::cout << "Error Opening SpaceID" << std::endl;
retErr = spaceId;
}
err = H5Dclose( did );
if (err < 0 ) {
std::cout << "Error Closing Dataset" << std::endl;
retErr = err;
}
}
return retErr;
}
What is the problem mixing C and C++. If you are using HDF5 then you are by definition mixing C and C++.
···
___________________________________________________________
Mike Jackson www.bluequartz.net
Principal Software Engineer mike.jackson@bluequartz.net
BlueQuartz Software Dayton, Ohio
On Jun 8, 2010, at 3:15 PM, Philipp Kraus wrote:
You mix C and C++ code, but I prefere only C++.
Michael Jackson wrote:
This is what I use:
herr_t H5Lite::readStringDataset(hid_t loc_id, const std::string&
std::vector<char> buf(static_cast<int>(size+1), 0x00); //Allocate
and Zero the array
err = H5Dread(did, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT,
&(buf.front()) );
if (err<0) {
std::cout << "Error Reading string dataset." << std::endl;
retErr = err;
} else {
data.append( &(buf.front()) ); //Append the string to the given
string
I don't find any native C++ code to read data into the std::vector.
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