I have a .h5 file of size 128x128x64, hdf5read or h5read command is reading 64x128x128, I want MATLAB to read original size of the file, can you please help me?

data = h5read( 'Soln_700.00279.h5','/T')

or

file = hdf5info('Soln_700.00279.h5')
data_P = hdf5read(file.GroupHierarchy.Datasets(1))

I have tried above both commands, but MATLAB is reading the size in reverse I guess, but I do not know which column is x and y, except z that I know is of size 64. I would appreciate any help.

Thank you

Answer 1

[Walter Roberson]

You need to examine the hdf5info that is returned, looking at the dimensions information for file.GroupHierarchy.Datasets(1) to try to figure out which is x and which is y.

The most common arrangement in hdf5 files is x, y, z -- which is not the same as what MATLAB uses. MATLAB uses y, x, z so it is common to see something like

data_P = permute(data_P, [2 1 3]);

[Vinay Tripathi]

Hi, thank you for responding.

But here, I have 64 grids in z direction that is how I know 64 dimension is in z direction. but x and y I don't understand, given same number of grids in both the directions. Matlab is showing either z, x, y or z, y, x, that I still need help with!

here is the hdf5 info -

info =

struct with fields:

Filename: '\Soln_700.00279.h5'

Name: '/'

Groups: []

Datasets: [8×1 struct]

Datatypes: []

Links: []

Attributes: []

HDF5 Soln_700.00279.h5

Group '/'

Dataset 'P'

Size: 64x128x128

MaxSize: 64x128x128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'T'

Size: 64x128x128

MaxSize: 64x128x128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'Vx'

Size: 64x128x128

MaxSize: 64x128x128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'Vy'

Size: 64x128x128

MaxSize: 64x128x128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'Vz'

Size: 64x128x128

MaxSize: 64x128x128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'X'

Size: 128

MaxSize: 128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'Y'

Size: 128

MaxSize: 128

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000

Dataset 'Z'

Size: 64

MaxSize: 64

Datatype: H5T_IEEE_F64LE (double)

ChunkSize: []

Filters: none

FillValue: 0.000000