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constantinpape / pybdv

python tools for BigDataViewer

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data padding

martinschorb opened this issue · comments

commented

Hi,

my input data is 2024x2024. Pybvd will generate a 2048x2048 output with padded zeros.
These become obvious in linear interpolation mode as black frames
Can these be something else? NaN

Or is this a problem of BDV?

Martin

commented

I am not quite sure, but I don't actively pad the data in pybdv.
The hdf5 dataset is just created with the same shape as the input data, see https://github.com/constantinpape/pybdv/blob/master/pybdv/converter.py#L266.

What you can try is setting the fillvalue to something else in hdf5: http://docs.h5py.org/en/stable/high/dataset.html#Dataset.fillvalue. I am not sure how BDV would interpret this though.

commented

pybdv does not pad, this is most likely a BDV problem.