HDF5 Compatibility with STL Datatype

Hdf-forum archives
1

Hi Guys,

I am able write STL datatype using .data() function. Example vector.data().

But, That datatype is part of some compound datatype then I am not able to
write exact values(It writes some Garbage Values)

I have simplified my problem can anyone please take look on that …

Here Is my Data Structure

struct RandomData

{

               std::vector<float> values;

};

I am using HDF5 CPP library for writing above data structure to HDF file. I
am able write file but It’s writes some “Garbage Values”.

Here Is code …

#include "H5Cpp.h"

#include <vector>

using namespace std;

using namespace H5;

void main()

{

       try

       {

             struct RandomData

             {

                std::vector<float> values;

             };

             RandomData d;

             d.values.push_back(10);

             d.values.push_back(20);

             d.values.push_back(30);

             //write Dataset to File

             H5File file("file.h5",H5F_ACC_TRUNC);

             Group group = file.createGroup("group");

             int rank = 1;

             hsize_t dimesion [] = {1};

             DataSpace space(rank,dimesion);

             CompType comptype(sizeof(RandomData));

              comptype.insertMember("x"
,HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

             DataSet dataset = group.createDataSet("r1",comptype,space);

             dataset.write(&d,comptype);

             space.close();

             dataset.close();

             group.close();

             file.close();

       }

       catch(FileIException error)

       {

             error.printError();

       }

}

Am I missing something over here? If not then please guide me on
alternative solution .It’s very helpful for me.

Regards,

Shamkumar

2

A std::vector<float> will look something like this in memory:

vector<float> {
   float* buf;
   size_t size;
   size_t capactiy;
};

So that's what is getting written by your code. The data you actually want
to write is where the 'buf' pointer points (which is what vector::data()
returns).

If you want to put an array of data into a struct you can use
std::array<float> but that will have fixed size. There is no way to put a
dynamically sized array into a struct.

···

On Tue, May 3, 2016 at 12:48 AM, shamkumar rajput < shamkumar.rajput@gmail.com> wrote:

Hi Guys,

I am able write STL datatype using .data() function. Example
vector.data().

But, That datatype is part of some compound datatype then I am not able to
write exact values(It writes some Garbage Values)

I have simplified my problem can anyone please take look on that …

Here Is my Data Structure

struct RandomData

{

               std::vector<float> values;

};

I am using HDF5 CPP library for writing above data structure to HDF file.
I am able write file but It’s writes some “Garbage Values”.

Here Is code …

#include "H5Cpp.h"

#include <vector>

using namespace std;

using namespace H5;

void main()

{

       try

       {

             struct RandomData

             {

                std::vector<float> values;

             };

             RandomData d;

             d.values.push_back(10);

             d.values.push_back(20);

             d.values.push_back(30);

             //write Dataset to File

             H5File file("file.h5",H5F_ACC_TRUNC);

             Group group = file.createGroup("group");

             int rank = 1;

             hsize_t dimesion [] = {1};

             DataSpace space(rank,dimesion);

             CompType comptype(sizeof(RandomData));

              comptype.insertMember("x"
,HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

             DataSet dataset = group.createDataSet("r1",comptype,space);

             dataset.write(&d,comptype);

             space.close();

             dataset.close();

             group.close();

             file.close();

       }

       catch(FileIException error)

       {

             error.printError();

       }

}

Am I missing something over here? If not then please guide me on
alternative solution .It’s very helpful for me.

Regards,

Shamkumar

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

3

Hello Shamkumar,

The problem is that H5::PredType::NATIVE_FLOAT should only be used with a single float rather than with an array of floats.

The datatype in this statement

  comptype.insertMember("x",HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

would have to reflex the multiple values of the RandomData::values.

You would need to create an HDF5 datatype to represent the type of RandomData::values. I would guess an ArrayType, then pass that in place of H5::PredType::NATIVE_FLOAT. The length of the array would be 3.

I hope this helps.

Binh-Minh

···

________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of shamkumar rajput <shamkumar.rajput@gmail.com>
Sent: Tuesday, May 3, 2016 3:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5 Compatibility with STL Datatype

Hi Guys,

I am able write STL datatype using .data() function. Example vector.data().
But, That datatype is part of some compound datatype then I am not able to write exact values(It writes some Garbage Values)

I have simplified my problem can anyone please take look on that ...

Here Is my Data Structure

struct RandomData
{
               std::vector<float> values;
};

I am using HDF5 CPP library for writing above data structure to HDF file. I am able write file but It's writes some "Garbage Values".

Here Is code ...

#include "H5Cpp.h"
#include <vector>
using namespace std;
using namespace H5;

void main()
{
       try
       {
             struct RandomData
             {
                std::vector<float> values;
             };
             RandomData d;
             d.values.push_back(10);
             d.values.push_back(20);
             d.values.push_back(30);

             //write Dataset to File
             H5File file("file.h5",H5F_ACC_TRUNC);
             Group group = file.createGroup("group");
             int rank = 1;
             hsize_t dimesion [] = {1};
             DataSpace space(rank,dimesion);
             CompType comptype(sizeof(RandomData));

              comptype.insertMember("x",HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

             DataSet dataset = group.createDataSet("r1",comptype,space);
             dataset.write(&d,comptype);

             space.close();
             dataset.close();
             group.close();
             file.close();
       }
       catch(FileIException error)
       {
             error.printError();
       }
}

Am I missing something over here? If not then please guide me on alternative solution .It's very helpful for me.

Regards,
Shamkumar

4

Hi Guys,

Thanks you for quick reply.

Both solution are working fine for me.

Regards,
Shamkumar

···

On Tue, May 3, 2016 at 10:21 PM, David <list@aue.org> wrote:

A std::vector<float> will look something like this in memory:

vector<float> {
   float* buf;
   size_t size;
   size_t capactiy;
};

So that's what is getting written by your code. The data you actually want
to write is where the 'buf' pointer points (which is what vector::data()
returns).

If you want to put an array of data into a struct you can use
std::array<float> but that will have fixed size. There is no way to put a
dynamically sized array into a struct.

On Tue, May 3, 2016 at 12:48 AM, shamkumar rajput < > shamkumar.rajput@gmail.com> wrote:

Hi Guys,

I am able write STL datatype using .data() function. Example
vector.data().

But, That datatype is part of some compound datatype then I am not able
to write exact values(It writes some Garbage Values)

I have simplified my problem can anyone please take look on that …

Here Is my Data Structure

struct RandomData

{

               std::vector<float> values;

};

I am using HDF5 CPP library for writing above data structure to HDF file.
I am able write file but It’s writes some “Garbage Values”.

Here Is code …

#include "H5Cpp.h"

#include <vector>

using namespace std;

using namespace H5;

void main()

{

       try

       {

             struct RandomData

             {

                std::vector<float> values;

             };

             RandomData d;

             d.values.push_back(10);

             d.values.push_back(20);

             d.values.push_back(30);

             //write Dataset to File

             H5File file("file.h5",H5F_ACC_TRUNC);

             Group group = file.createGroup("group");

             int rank = 1;

             hsize_t dimesion [] = {1};

             DataSpace space(rank,dimesion);

             CompType comptype(sizeof(RandomData));

              comptype.insertMember("x"
,HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

             DataSet dataset = group.createDataSet("r1",comptype,space);

             dataset.write(&d,comptype);

             space.close();

             dataset.close();

             group.close();

             file.close();

       }

       catch(FileIException error)

       {

             error.printError();

       }

}

Am I missing something over here? If not then please guide me on
alternative solution .It’s very helpful for me.

Regards,

Shamkumar

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

5

Shamkumar, I meant "reflect", not "reflex". Sorry!

Binh-Minh

···

________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Binh-Minh Ribler <bmribler@hdfgroup.org>
Sent: Tuesday, May 3, 2016 10:58 AM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] HDF5 Compatibility with STL Datatype

Hello Shamkumar,

The problem is that H5::PredType::NATIVE_FLOAT should only be used with a single float rather than with an array of floats.

The datatype in this statement

  comptype.insertMember("x",HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

would have to reflex the multiple values of the RandomData::values.

You would need to create an HDF5 datatype to represent the type of RandomData::values. I would guess an ArrayType, then pass that in place of H5::PredType::NATIVE_FLOAT. The length of the array would be 3.

I hope this helps.

Binh-Minh

________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of shamkumar rajput <shamkumar.rajput@gmail.com>
Sent: Tuesday, May 3, 2016 3:48 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] HDF5 Compatibility with STL Datatype

Hi Guys,

I am able write STL datatype using .data() function. Example vector.data().
But, That datatype is part of some compound datatype then I am not able to write exact values(It writes some Garbage Values)

I have simplified my problem can anyone please take look on that ...

Here Is my Data Structure

struct RandomData
{
               std::vector<float> values;
};

I am using HDF5 CPP library for writing above data structure to HDF file. I am able write file but It's writes some "Garbage Values".

Here Is code ...

#include "H5Cpp.h"
#include <vector>
using namespace std;
using namespace H5;

void main()
{
       try
       {
             struct RandomData
             {
                std::vector<float> values;
             };
             RandomData d;
             d.values.push_back(10);
             d.values.push_back(20);
             d.values.push_back(30);

             //write Dataset to File
             H5File file("file.h5",H5F_ACC_TRUNC);
             Group group = file.createGroup("group");
             int rank = 1;
             hsize_t dimesion [] = {1};
             DataSpace space(rank,dimesion);
             CompType comptype(sizeof(RandomData));

              comptype.insertMember("x",HOFFSET(RandomData,values),H5::PredType::NATIVE_FLOAT);

             DataSet dataset = group.createDataSet("r1",comptype,space);
             dataset.write(&d,comptype);

             space.close();
             dataset.close();
             group.close();
             file.close();
       }
       catch(FileIException error)
       {
             error.printError();
       }
}

Am I missing something over here? If not then please guide me on alternative solution .It's very helpful for me.

Regards,
Shamkumar