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Convention of Ellipse angles and CTF astigmatism angles #2406

Open leginonbot opened 6 months ago

leginonbot commented 6 months ago

Author Name: Neil Voss (@vosslab) Original Redmine Issue: 2406, https://emg.nysbc.org/redmine/issues/2406 Original Date: 2013-06-26 Original Assignee: Neil Voss

create new bug, so slow migration of our incorrect CTF astigmatism angle convention, this should probably wait until the end of the CTF Estimation Challenge.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-08-05T17:22:28Z

Neil,

I am going to work on this this week. First thing I found is your change in r17701. The comment in line 82 to line 84 defines a as the major axis of the ellipse, alpha is measure from x-axis to a (major axis. Then in r17701, you reverse axis when a > b, which makes alpha measured from x-axis to minor axis.

What is it really?

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2013-08-07T11:01:04Z

Yeah, I think the ellipse angle (which is based on a list of x and y values) is opposite my CTF angle (which is based on image data).

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-08-07T15:36:30Z

Neil,

Your r17800 broke Appion. Until the astigmation angle input to that is changed, the sign change in the display should not be done, yet. I reverted it back in r17804, but will use your change to get the conversion ready. What is coded in r17701 worked with the old code of ctfdisplay. I was just asking a question, mainly wonder if you want to change the comment in the code.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-10-28T23:06:07Z

I've made the sign changes in my sandbox and created a separate aptest database to test the ctfchallenge dataset 1. Amber ran ace, ace2,ctffind, phasor, and ctfRefine on them last week.

I looked at them today. Apart from ctfRefine, all the other seems to give the expected sign in the result plot, myamiweb, and database. I fixed the bug regarding ctfRefine and re-ran ctfRefine6 which gave similar results as others. The best image to look at is

zz13jul08z-ctfchal_set1_set_001_challenge_mic_006.mrc

It has a visually detectable astigmatism at -58 degrees.

makestack2.py result was checked with --fliptype=ace2image and --keepall. Keepall flag leaves the ctf-corrected image undeleted when the run is finished. Therefore, I could calculate from it the power spectrum and examine the astg_angle applied in the correction. It looks good, too (-58)

The use of astig_angle in apFrealign.py was checked by preparing single model reconstruction for Frealign and examining its parameter files. It looks good, too (-58).

Also checked parameter output for stack in myamiweb such as

/myamiweb/processing/listCTFvalues.php?expId=11956&sId=5

Remaining tasks:

  1. Is there anything need changing for ctftilt? Neil?
  2. Selection of bestCtfValue. Is it consistent with the display in image viewer? Amber?
  3. Write dbschema update script. Anchi
  4. Do we have xmipp result? Amber?
leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-10-28T23:08:22Z

More question:

Amber, is there changes I might need to do for relion preparation?

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-10-28T23:12:47Z

One more for Neil,

Is inteactiveCTF ready for testing? We did not include it in the testing this.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-11-06T21:43:27Z

r17982 changes all the signes r17983 is the schema update related files for this change.

scan-ctfdata.py can be used to find if a user is still adding ctf values to the database or using the table within 1 day, so that its update need to be delayed.

Database must be updated if appion python/php codes are updated.

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-12-16T16:00:47Z

The schema change was applied to NRAMM database 1 month ago and there is no report on problem resulting from it. Looks like a success.