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2D input data #16
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Yes, that would be the best option! |
minimal example ;-) |
However, I see that this one still comes "3D".
The output that I get from IMOD (from reconstructing/blending TEM tiled montages) has an image:
Would this be a problem? |
Yes, this is still 3d, so I think whichever program writes to bdv is also adding the z axis.
No I don't think this is a problem. I can just add something to
I am not quite sure what you mean by this. I also create all the downsampling in python, but it works with this kind of data already. |
We discussed this and this is not really relevant for Martin's current use case. BUT I think it would actually be nice to properly support 2d data, because this is a very important use-case. Unfortunately, there is no 'native' support for 2d in the BigDataViewer File Format yet, so the trick one has to do is to add a singleton z-axis. @martinschorb, let me know what you think. |
perfect. |
as I did for the type conversions to unsigned int ;-) |
Ok, great. I will let you know once I had time too implement it :). |
It's not in yet, correct? Just to be sure I run the newest version... |
Yes, it's not in yet. |
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 to now use pybdv's
convert_to_bdv
to convert an existing hdf5 file and this is written as 2D. Could you apply something similar within the hdf5 file as well? Or could you add support for 2D data? BDV can somehow deal with it. Should I send you a 2D hdf5 file that is compatible with the BDV universe?Thanks...
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