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HDF5 - reading part of dataset

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Pavel Inchin
Pavel Inchin on 28 Jan 2019
Edited: Sunson29 on 15 Apr 2019
I'd like to read only part of the dataset of HDF5 file using h5read function in Matlab . Particularly in 1 of the dimensions I want to read only every 4th value.
I can read the whole dataset as:
tempp = hdf5read(nameCur,namedataset);
its size: 160x100x200x10.
Next, when I want to read the whole dataset using "start" and "count" attributes, it works fine:
tempp = h5read(nameCur,namedataset,[1 1 1 1],[160 100 200 10]);
Then I want to read all dataset using "stride" attribute too:
tempp = h5read(nameCur,namedataset,[1 1 1 1],[160 100 200 10],[1 1 1 1]);
works nice!
But when I want finally to read every 4th value from second dimension
tempp = h5read(nameCur,namedataset,[1 1 1 1],[160 100 200 10],[1 4 1 1]);
it gives me error:
Error using h5readc
The index arguments exceed the size of the dataset.
I don't understand what is the reason for that. Thanks

  1 Comment

Pavel Inchin
Pavel Inchin on 15 Apr 2019
Just in case someone stucked with this, the solution is simply:
tempp = h5read(nameCur,namedataset,[1 1 1 1],[160 25 200 10],[1 4 1 1]);

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Answers (2)

Sunson29
Sunson29 on 15 Apr 2019
Edited: Sunson29 on 15 Apr 2019
Dear friend, I hope I could answer your question. But I guess I am more "beginer " than you.
May I ask a very quick question ?
I am trying to open just one portion of HDF5 file, because it's way too big (20G). In that files, there are 3 dataset, X,Y,Z, X is the 20G, others are small, can be open directly.
I can run the code "dset = hdf5read('GOLD_XYZ_OSC.0001_1024.hdf5','/Z');";
but why I cannot run the code like you do dset = hdf5read('GOLD_XYZ_OSC.0001_1024.hdf5','/Z', [1 1], [1 3]);
Error: Expected a string scalar or character vector for the parameter name.
Z is a big row, one row, many column. I tried to put just few elements (i=1:3) in dset. Thank you!!!!

  1 Comment

Pavel Inchin
Pavel Inchin on 15 Apr 2019
what is a size of "Z" you'd like to read?

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Sunson29
Sunson29 on 15 Apr 2019
Edited: Sunson29 on 15 Apr 2019
my friend, you reply so fast!
Could you go to this link plz? It's easier to see.
I got very very similiar index issue, like you had before. Thank you!!!!

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