big volumes chunking

[martinschorb]

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 use a reasonable chunk size (default would be 64, right?) and then read in this amount of slices as a volume and then convert with make_bdv.

Now, I could assign each slice group a new ViewSetup, but in the end, it will all be one volume and thus one ViewSetup...

Any ideas?

Would it make sense to have a dedicated converter function for a set of slices?
Maybe directly from a list of tif files into one volume?

[constantinpape]

Would it make sense to have a dedicated converter function for a set of slices?
Maybe directly from a list of tif files into one volume?

Yes, makes sense.
I have something similar implemented already for another project:
https://github.com/constantinpape/z5/blob/master/src/python/module/z5py/converter.py#L154
So should be easy to port this to pybdv.

What would you call the function?

[martinschorb]

Hi,

what is the status of consolidating the slice-based conversion from MoBIE and the generic pybdv?
I would like to look into tiff slices at some point.

[constantinpape]

what is the status of consolidating the slice-based conversion from MoBIE and the generic pybdv?
I would like to look into tiff slices at some point.

This is in principle possible already, but you will need elf in your environment.
I will check if it actually works and then post an example.

To properly consolidate everything I will need some time for proper software work; as I am focusing on finishing my thesis right now this will only happen in a few months.

[constantinpape]

Yes, it is possible, I added a paragraph to the readme:
https://github.com/constantinpape/pybdv#advanced-io-options

Note that you need the very latest elf commit for the tif stack to work:
constantinpape/elf@f0e1d69