Project

General

Profile

Actions

Feature #3762

closed

upload tomography tilt series for protomo2 processing

Added by Anchi Cheng about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Start date:
11/12/2015
Due date:
% Done:

0%

Estimated time:

Description

This extends imageloader.py to do the upload


Related issues 1 (1 open0 closed)

Related to Appion - Bug #3758: uploaded signle direction tilt series causes error in preparation step for protomo2alignerIn Code ReviewAlex Noble11/11/2015

Actions
Actions #1

Updated by Anchi Cheng about 9 years ago

I have extended imageloader.py in r19363 to do this. Only thing left is to modify web help string.

One problem I did not solve is the initial guess of tilt axis orientation, called phi in the tomography prediction which is the only prediction value the tomography pipeline cares, I think. It is set to 0 now.

I can upload and protomo2aligner.py done what it can until needing to run. The cluster with protomo2 installed properly is down now so that is as far as I can get.

To test, use the method 1 in upload images (read the batch file). Add at the end tilt angle (degrees, already possible before this), and then dose (electrons per angstroms). Use group images by tilts and set the number of images per group to the number of tilts. The program will figure out the rest.

Actions #2

Updated by Anchi Cheng about 9 years ago

  • Related to Bug #3758: uploaded signle direction tilt series causes error in preparation step for protomo2aligner added
Actions #3

Updated by Alex Noble about 9 years ago

This is great, thank you Anchi. The tilt axis orientation, phi, must be the tilt azimuth. The user should definitely input this value.

I am not sure where the tilt-series uploader is on myamiweb. Could you point me to it?

Actions #4

Updated by Anchi Cheng about 9 years ago

Have you ever upload images ?

See Upload_Images_to_a_new_Project_Session

Actions #5

Updated by Alex Noble about 9 years ago

I've only ever uploaded them directly from the microscope. Haha=)

Actions #6

Updated by Alex Noble about 9 years ago

I can upload a tilt-series and with Revision 19365 the tilt-series can be processed through Appion-Protomo.

Should I work on putting places for dose and phi (azimuth) into uploadimage.php or are you working on that?

Actions #7

Updated by Anchi Cheng about 9 years ago

We only need azimuth. dose part just need modify help.js Go ahead and do it. I have other things to sort out now.

Actions #8

Updated by Alex Noble about 9 years ago

I added azimuth to the webpage (uploadimage.php) and as a parameter in uploadImages.py, but I cannot find in the image tree where I should put record azimuth in the database. This still needs to be done.

Actions #9

Updated by Anchi Cheng about 9 years ago

  • Assignee changed from Anchi Cheng to Alex Noble

It goes in the function makeTomographyPredictionData as ['predicted position']['phi'] with a conversion

according to apTomo.py, getDefaultAzimuthFromLeginon function, the conversion is

azimuth = 90.0 - (results[0]['predicted position']['phi']) * 180.0 / 3.14159
Actions #10

Updated by Alex Noble about 9 years ago

  • Assignee changed from Alex Noble to Anchi Cheng

I believe it's all working now. Le me know if I can close this issue.

Actions #11

Updated by Alex Noble about 9 years ago

  • Assignee changed from Anchi Cheng to Alex Noble
Actions #12

Updated by Anchi Cheng about 9 years ago

Go ahead

Actions #13

Updated by Alex Noble about 9 years ago

  • Status changed from Assigned to Closed
Actions

Also available in: Atom PDF