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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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SetOfCtfs is not created upon selecting a subset from SetOfCtfs #510

Closed azazellochg closed 8 years ago

azazellochg commented 8 years ago

I think this issue was raised before but I cant find it anymore. The problem is when I analyze results of CTF estimation and select a subset, click on +Micrographs, only a SetOfMics is created that does not show any CTF info anymore (I know that this SetOfMics has relation to input SetOfCtfs). This means I can select mics with good CTF only once after CTF estimation and this is really annoying.

I usually select micrographs with good CTF, creating a new subset. But I would like to split the data into defocus groups for picking (e.g., pick mics with high defocus first). The problem is that subset of good mics have no more CTF info displayed.

I've tried the following workaround: use scipion - create subset by intersecting a full CTF set with good SetOfMics, and it produces a new SetOfCtfs, however the latter one can't be used later for a micrograph subset selection (error - no SetOfMics associated was found). UPDATE: I guess I could assign this new ctfset to good mics and use it further.

So, my overall request would be to create both SetOfCtfs and SetOfMics upon selecting mics with good CTF (in Analyze results for ctffind4, for example)

delarosatrevin commented 8 years ago

You are totally right and this request is completely reasonable. We had (back in time) also the option to create also SetOfCTFs button, but after some discussion was removed. I guess that creating both, as you suggest is a good approach. I think we should fix the subset problem, but anyway the subset workaround is annoying for following this methology.

josuegbl commented 8 years ago

@azazellochg, you can use ctf -assign to select the micrographs that belongs to your SetOfCTFs. In any case, I'm agree with @delarosatrevin.

azazellochg commented 8 years ago

@josuegbl ctf assign does not seem to work for me (see attached image). The workflow was: import mics and ctfs, select good ctf1 (produced outputMics), assign ctf (input is good ctf1 mics + full setof CTFs). Last step fails.

error1

josuegbl commented 8 years ago

@azazellochg ctf assign has not been tested in scipion-box branch. I fixed the error, at least no fail for me. Just update.

josuegbl commented 8 years ago

Thank you very much for you feedback

azazellochg commented 8 years ago

@josuegbl thanks! you are right, I should have checked this in 1.0.1 branch.

azazellochg commented 8 years ago

@delarosatrevin I have started to look into this and would like to ask you whether this line is ever reached? I cant remember anywhere creating subset of ctf from ctfs

delarosatrevin commented 8 years ago

This is related to your original request. In showj GUI in Java we had a button to create a subset of ctfs...and this probably ends in this part of the python code. I think the best option is what you proposed, when creating the subset of micrographs, we can also create the subset of ctfs associated.

azazellochg commented 8 years ago

Fixed in 75fb437, however we should recheck this after closing #565