Cs value for uploaded images

Added by Jason van Rooyen about 9 years ago

Hi guys,

Can anyone help me find and change the Cs values for an uploaded dataset, please? These data were recorded off-site and uploaded separately.

I would like to change the value (from 2.7 to 2.3) without having to upload all the images for the session.

I tried searching the ap% processing database in phpMyAdmin but I can only find the script values "--cs=".

Any thoughts?

Thanks,
Jason

Replies (2)

RE: Cs value for uploaded images - Added by Anchi Cheng about 9 years ago

Cs value is part of InstrumentData in leginondb. During importing images, a special pair of tem and camera instruments are created to give a single pointer for things like cs values.

Use python script to find id for the instrument (Do this in the same environment as Leginon running to access database through sinedon.

from leginon import leginondata
a = leginondata.AcquisitionImageData(filename='your_uploaded_image.mrc').query()[0]
temdata = a['scope']['tem']
temdata.dbid

"your_uploaded_image.mrc" is the filename of any image that you need cs changed.

After this, you can use phpMyAdmin or equivalent to change cs at that row of leginondb.InstrumentData. One important thing to do is to retain the same `DEF_timestamp` so that the change will be applied to the images already uploaded. The default would update `DEF_timestamp`.

One problem for this retro change is that all images uploaded with 2.7 cs value as "AppionTEM" name will all be changed to 2.3 since the database only records one tem InstrumentData with the name match. Is this o.k ?

RE: Cs value for uploaded images - Added by Jason van Rooyen about 9 years ago

Thanks Anchi! What you say makes sense.

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