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Fix an issue with imageh5 #191

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Jul 5, 2023
Merged

Fix an issue with imageh5 #191

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49 changes: 26 additions & 23 deletions src/Image.C
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Original file line number Diff line number Diff line change
Expand Up @@ -1347,25 +1347,28 @@ void Image::writeImagePlane_2(int cycle, std::string &path, float_sw4 t )
H5Sclose(dset_space);
H5Dclose(dset);

if( mGridinfo == 1 )
char grid_name[16];
if( mGridinfo >= 1 )
{
int g=mEW->mNumberOfGrids-1;
int globalSizes[3] = {mEW->m_global_nx[g], mEW->m_global_ny[g], mEW->m_global_nz[g]} ;
if(mLocationType == Image::X)
globalSizes[0] = 1;
if (mLocationType == Image::Y)
globalSizes[1] = 1;
if (mLocationType == Image::Z)
globalSizes[2] = 1;

dims = globalSizes[0]*globalSizes[1]*globalSizes[2];
dset_space = H5Screate_simple(1, &dims, NULL);
/* cout << "Rank " << mEW->getRank() << " creating grid array with length " << dims << endl; */
dset = H5Dcreate(h5_fid, "grid", dtype, dset_space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if( dset < 0 )
cout << "ERROR: Image::writeImagePlane_2 could not create HDF5 grid dataset" << endl;
H5Sclose(dset_space);
H5Dclose(dset);
for (int g = mEW->mNumberOfCartesianGrids; g < mEW->mNumberOfGrids; g++) {
int globalSizes[3] = {mEW->m_global_nx[g], mEW->m_global_ny[g], mEW->m_global_nz[g]} ;
if(mLocationType == Image::X)
globalSizes[0] = 1;
if (mLocationType == Image::Y)
globalSizes[1] = 1;
if (mLocationType == Image::Z)
globalSizes[2] = 1;

dims = globalSizes[0]*globalSizes[1]*globalSizes[2];
dset_space = H5Screate_simple(1, &dims, NULL);
/* cout << "Rank " << mEW->getRank() << " creating grid array with length " << dims << endl; */
sprintf(grid_name, "grid%d", g);
dset = H5Dcreate(h5_fid, grid_name, dtype, dset_space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if( dset < 0 )
cout << "ERROR: Image::writeImagePlane_2 could not create HDF5 grid dataset" << endl;
H5Sclose(dset_space);
H5Dclose(dset);
}
}

delete [] grid_size;
Expand Down Expand Up @@ -1481,7 +1484,7 @@ void Image::writeImagePlane_2(int cycle, std::string &path, float_sw4 t )
}
} // End if ihavearray

if( mGridinfo == 1 )
if( mGridinfo >= 1 )
add_grid_to_file_hdf5( s.str().c_str(), iwrite, 0);
/* if( mGridinfo == 2 ) */
/* add_grid_filenames_to_file( s.str().c_str() ); */
Expand All @@ -1495,6 +1498,7 @@ void Image::writeImagePlane_2(int cycle, std::string &path, float_sw4 t )
void Image::add_grid_to_file_hdf5( const char* fname, bool iwrite, size_t offset )
{
bool ihavearray = plane_in_proc(m_gridPtIndex[0]);
char grid_name[16];
if( ihavearray )
{
#ifdef USE_HDF5
Expand All @@ -1512,17 +1516,16 @@ void Image::add_grid_to_file_hdf5( const char* fname, bool iwrite, size_t offset
if( mEW->usingParallelFS() )
MPI_Barrier( m_mpiComm_writers );

sprintf(grid_name, "grid%d", g);
if( m_double )
{
char dblStr[]="double";
m_pio[g]->write_array_hdf5(fname, NULL, "grid", 1, m_gridimage->m_doubleField[g], offset, dblStr );
offset += (globalSizes[0]*globalSizes[1]*globalSizes[2]*sizeof(double));
m_pio[g]->write_array_hdf5(fname, NULL, grid_name, 1, m_gridimage->m_doubleField[g], 0, dblStr );
}
else
{
char fltStr[]="float";
m_pio[g]->write_array_hdf5(fname, NULL, "grid", 1, m_gridimage->m_floatField[g], offset, fltStr );
offset += (globalSizes[0]*globalSizes[1]*globalSizes[2]*sizeof(float));
m_pio[g]->write_array_hdf5(fname, NULL, grid_name, 1, m_gridimage->m_floatField[g], 0, fltStr );
}
}
#endif
Expand Down
90 changes: 22 additions & 68 deletions tools/plotimageh5.ipynb
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