HDF5 transpose data?

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Nycholas Maia
Nycholas Maia 2019-10-23
回答： Anudeep Kumar 2025-6-3
I have a HDF5 file called "output.h5" and it have a dataset called "density" which is a matrix with 21 rows and 2 cols.
I read this HDF5 dataset, but I got the transposed version of my density matrix (2 rows, 21 cols). Why? How can I solve it?
matlab.jpg
Here is my HDF5 dump of this file:
h5dump output.h5
HDF5 "output.h5" {
GROUP "/" {
GROUP "my" {
GROUP "path" {
GROUP "to" {
DATASET "density" {
DATATYPE H5T_IEEE_F64LE
DATASPACE SIMPLE { ( 21, 2 ) / ( 21, 2 ) }
DATA {
(0,0): 0, 2,
(1,0): 1, 2,
(2,0): 2, 4,
(3,0): 3, 8,
(4,0): 4, 14,
(5,0): 5, 22,
(6,0): 6, 32,
(7,0): 7, 44,
(8,0): 8, 58,
(9,0): 9, 74,
(10,0): 10, 92,
(11,0): 11, 112,
(12,0): 12, 134,
(13,0): 13, 158,
(14,0): 14, 184,
(15,0): 15, 212,
(16,0): 16, 242,
(17,0): 17, 274,
(18,0): 18, 308,
(19,0): 19, 344,
(20,0): 20, 382
}
}
}
}
}
}
}
Thanks

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回答（1 个）

Anudeep Kumar
Anudeep Kumar 2025-6-3
Hey Nycholas,
I believe this maybe due to the difference in the way different languages store data. C uses row-major and MATLAB uses column-major to store data. So when you read a dataset from an HDF5 file in MATLAB, the dimensions may appear transposed.
There is a detailed discussion on the same in the following MATLAB Answer link :
https://www.mathworks.com/matlabcentral/answers/308303-why-does-matlab-transpose-hdf5-data
You can use the transpose operator to obtain data in your intended shape as follows
data = h5read('output.h5', '/my/path/to/density')';

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