Read and manipulate cs files

Import and Export
1

Hi,

in the 3D Variability analysis tutorial video you mention that there is a simple way to read and manipulate cs files such that the content could be plotted elsewhere. @apunjani in the video mentioned that there is a tutorial on this available. Sadly I was not able to find this. I only found that there are details forthcoming in the data management tutorial. Could you give a rough intro in how this is achieved?

Thank you and Best,

David

2

This is all I can find right now, a detailed tutorial would be very helpful:

3

Thanks @olibclarke , yes this I also found but it is hardly specific enough to be useful.

4

Did anyone manage to read the file somehow?

5

They are just numpy structured arrays (recarrays). It’s easy to do whatever you want in an ipython session or notebook.

import numpy as np
cs = np.load("file.cs")
print(cs.dtype.names)
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6

thanks a lot! This works.

7

Cool. Make sure cs['uid'] always agrees between any particle sets you are comparing!

(If you have pyem, you can also use pyem.metadata and pyem.star libraries for relational operations, correlating to Relion, cisTEM/FREALIGN, etc.)

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8

Hi @david.haselbach, @olibclarke,

Please see our new tutorial on reading and manipulating .cs files!

3 Likes
9

Hi @stephan,

this looks great I am looking forward to trying. Thanks a lot!

Best,

David

1 Like