pybdv

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constantinpape

Hi Constantin I reinstalled conda env and pybdv recently. Was processing a file as usual and got an error. ``` (/das/work/p15/p15889/Maxim_LCT) [polikarpov_m@ra-gpu-001 scripts_batch]$ Downsample scale 1 / 5 /das/work/p15/p15889/Maxim_LCT/lib/python3.6/site-packages/pybdv/downsample.py:51: UserWarning:...

maximka48

metadata - auto-fill scales from N5 attributes

1

auto-fill scales from N5 attributes

martinschorb

Halo computation in downsample function does not work correctly

3

fortunately it is only necessary for the `interpolate` mode, for the others the 'natural' halo that results from upscaling the bounding box is sufficient.

constantinpape

on the fly example 3D, multi channels, multi timepoints

1

Hi @constantinpape, Thank you for this package, is there any chance you will upgrade "soon" your [ on the fly 2D example](https://github.com/constantinpape/pybdv/blob/master/examples/on_the_fly.py) with a minimal 3D, multi channels, multi timepoints?...

romainGuiet

big volumes chunking

4

Hi, I was wondering what would be a good way of using pybdv to convert a large stack of individual slices (usually tif). I think what I would do is...

martinschorb

dealing with absolute paths

4

Hi, what can we do to make pybdv applicable to the following scenario: - 2 large datasets in some common storage location (maybe even separate group shares) - no write...

martinschorb

2D input data

10

Hi, currently pybdv only supports 3D input data. This is fine as long as I use make_bdv. I will just fake the third dimension by using ```np.expand_dims(data.copy(),axis=0)```. However, I like...

martinschorb

Add update_metadata convenience function

10

cc @martinschorb

constantinpape

adding 2D data to hdf5 container

13

Hi, it seems that with the current 2D implementation something goes wrong when I add multiple 2D datasets into one hdf5. In this case this is tiles of a mosaic....

martinschorb