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nvladimus / npy2bdv

Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.
GNU General Public License v3.0
34 stars 11 forks source link

affine options to save a view #1

Closed VolkerH closed 5 years ago

VolkerH commented 5 years ago

Hi, thanks for making this public. I think this will be quite useful to me. I'm after creating BigStitcher datasets files directly from python. I know the tiling pattern and the approximate overlap of multiple tiles from a SPIM, would you consider adding the option to optionally pass in the affine transform parameters for each view (currently you pass in the dx,dy,dz as far as I could see?

nvladimus commented 5 years ago

Hi! Yes, I will add this, it's a good feature to have. Stay tuned!

nvladimus commented 5 years ago

Added along with simple example (shearing along X axis), check it out.

VolkerH commented 4 years ago

Hi,

thanks. I just found some time to play with the library and test the affine transform. For a single dataset in the .xml it works fine.

However, when I add several dataset there is no option to associate a separate affine transform for each. All datasets are assigned the same affine transform. To make it useable for generating moasics or something that is already coarsely aligned (e.g. from stage position metadata) to then refine in BigStitcher, one would have to be able to specify a separate affine transform for each dataset.

I'm just reading through the code to see how that could be done in an elegant way.