issue with star file reading? about blik

[brisvag]

Hey @McHaillet, nice to see you here! :) I've been making several changes lately and haven't pushed a new version yet. Unfortunately I also need to bump the cryohub version and maybe something else, so it's not quite ready to go out.

However, you might be able to install everything you need with:

pip install "git+git://github.com/gutsche-lab/blik.git#egg=blik[all]"
pip install "napari[all]==0.4.18"
pip install "git+git://github.com/brisvag/cryohub.git@fix/io-star#egg=cryohub"

And this should work. I'm in the process of cleaning up and fixing bugs, so please tell me anything that goes wrong!

[McHaillet]

I made a new issue with the video attached!

Not a bug, just a napari weirdness that I've been fighting to change but people disagree with :P those options refer to either the "selected points" and the points created from now on.

Hmm, that seems a bit counter-intuitive. Now you also need to first switch to 3D viewing to efficiently select all the points.

[McHaillet]

Had to switch from git+git: to git+https: to do the pip install directly from the repo, but now its working.

The command to open the starfile and tomogram now works and the visualization looks very nice!

Some things I noticed at first glance:

1. when changing the opacity of the coordinate points and particle orientation vectors they become black dots on my tomographic volume, instead of becoming translucent.
2. changing the slider of the coordinate point size or symbol does not appear to do anything. For the orientation vectors it works fine.

I can also make a github issue of these things if you want, let me know ;)

[McHaillet]

About the second point, just noticed I had to first select all the coordinate points before I could change size and shape.

[brisvag]

when changing the opacity of the coordinate points and particle orientation vectors they become black dots on my tomographic volume, instead of becoming translucent.

Does not happen for me :/ can you send a small video of it, and record exactly which steps you took from loading to the bug? And yes, would be best to make a new issue :)

About the second point, just noticed I had to first select all the coordinate points before I could change size and shape.

Not a bug, just a napari weirdness that I've been fighting to change but people disagree with :P those options refer to either the "selected points" and the points created from now on.

[brisvag]

Yup, I agree. Relevant discussion: napari/napari#5748; feel free to add weigh in there so maybe we can convince folks :P

Now you also need to first switch to 3D viewing to efficiently select all the points.

You can actually select all points in the points layer with shift+a. Take a look at all the shortucts in File->preferences->shortcuts, there's some useful stuff there!

[brisvag]

I just released a new version (0.5.0), so all the workarounds above are no longer needed!