problem writing a dataset to a .h5 file

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1

Hi everybody,
I have problems writing a .h5 file. I want to write Coordinates of a 3D-Mesh to the .h5 file, believing that I have to arrange the points in an array with 3 columns and rows as much as I have points. As I don´t know before how many points there are gonna be, I have to allocate my coordinate array dynamically. The code looks like this (it´s C++):

float** Coordinates;
Coordinates = new float*[3];
for(int l=0; l<3; l++)
    {Coordinates[l] = new float[xdims];
    }

for(int i=0; i<ydims; i++)
        { Coordinates[0][i] = xPoints[i]; //xPoints, yPoints are vectors, so I know how many points I´ve read in from a file
          Coordinates[1][i] = yPoints[i];
          Coordinates[2][i] = 0;
        }//for(int i

Now I try to write that to an .h5 file:

hsize_t dims[2];
dims[0] = 3;
dims[1] = xdims;
hid_t datatype, dataspace;
hid_t file, dataset;
herr_t status;

//create H5File
file = H5Fcreate(H5FileName.c_str(), H5F_ACC_TRUNC , H5P_DEFAULT, H5P_DEFAULT);
dataspace = H5Screate_simple(RANK1, dims, NULL); // RANK1 = 2
datatype = H5Tcopy(H5T_NATIVE_FLOAT);
status = H5Tset_order(datatype,H5T_ORDER_LE);
dataset = H5Dcreate2(file,DATASETNAME1,datatype,dataspace,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, Coordinates); //!!! the problem is here !!!!
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);

Well, the problem occurs in the function H5Dwrite, and as I have successfully writen files with an 1D-array, I believe that the problem is that my CoordinatesArray is 2D and dynamically allocated (looking at the declaration, it´s a double pointer).
How can I write my coordinates array? Should I just write it as a 1D-array where the points are coded like
x1,y1,z1,x2,y2,z2,x3,.... ?
Is it possible for my visualization programm (in my case ParaView) to read this?

Thx for any help,
NH

···

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2

Natalie,

H5Dwrite expects a pointer to the first element of a write buffer which is contiguous in memory. The way the array is declared in memory here can result in non-contiguous data. If you wish to keep the same array in memory you will have to write the dataset using hyperslabs. In order to declare a contiguous array you could do something like:

float** Coordinates;
Coordinates = new float*[3];
Coordinates[0] = new float[xdims*3];
for(int l=1; l<3; l++)
     {Coordinates[l] = Coordinates[l-1] + xdims;
     }

Also, H5Dwrite expects a pointer to the first element in the write buffer, while Coordinates is a pointer to a pointer to the first element, so the H5Dwrite call should be changed to something like:

status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, Coordinates[0]);

Finally, only Coordinates[0] and Coordinates need to be deleted. I hope this is helpful.

Neil Fortner
The HDF Group

Quoting Natalie Happenhofer <nataliehapp@hotmail.com>:

···

Hi everybody,
I have problems writing a .h5 file. I want to write Coordinates of a 3D-Mesh to the .h5 file, believing that I have to arrange the points in an array with 3 columns and rows as much as I have points. As I don´t know before how many points there are gonna be, I have to allocate my coordinate array dynamically. The code looks like this (it´s C++):

float** Coordinates;
Coordinates = new float*[3];
for(int l=0; l<3; l++)
    {Coordinates[l] = new float[xdims];
    }

for(int i=0; i<ydims; i++)
        { Coordinates[0][i] = xPoints[i]; //xPoints, yPoints are vectors, so I know how many points I´ve read in from a file
          Coordinates[1][i] = yPoints[i];
          Coordinates[2][i] = 0;
        }//for(int i

Now I try to write that to an .h5 file:

hsize_t dims[2];
dims[0] = 3;
dims[1] = xdims;
hid_t datatype, dataspace;
hid_t file, dataset;
herr_t status;

//create H5File
file = H5Fcreate(H5FileName.c_str(), H5F_ACC_TRUNC , H5P_DEFAULT, H5P_DEFAULT);
dataspace = H5Screate_simple(RANK1, dims, NULL); // RANK1 = 2
datatype = H5Tcopy(H5T_NATIVE_FLOAT);
status = H5Tset_order(datatype,H5T_ORDER_LE);
dataset = H5Dcreate2(file,DATASETNAME1,datatype,dataspace,H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
status = H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, Coordinates); //!!! the problem is here !!!!
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);

Well, the problem occurs in the function H5Dwrite, and as I have successfully writen files with an 1D-array, I believe that the problem is that my CoordinatesArray is 2D and dynamically allocated (looking at the declaration, it´s a double pointer).
How can I write my coordinates array? Should I just write it as a 1D-array where the points are coded like
x1,y1,z1,x2,y2,z2,x3,.... ?
Is it possible for my visualization programm (in my case ParaView) to read this?

Thx for any help,
NH

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

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