Alignem Swift issues, ideas, items - Harris

[k34harris]

Postworkshop session ideas -- generated during Joel's visit to Harris Lab:

1. load thumbnails into the project manager in the background.
2. Delete projects from the project manager in the background. Make sure they are deleted from the TACC directories.

[alarioa]

unable to change/toggle through sections in manual alignment. track pad works but arrow keys and the scrub bar dont work

[alarioa]

not a bug: match signal 0, box is white but text is also white so you cant see it in the table unless highlighted

[alarioa]

Feature request: be able to drag 'match regions' boxes around, instead of deleting and replacing. Also be able to change the order of the match region boxes so when deleting one box, your order is messed up?

[dvee03]

Match regions are still displaying for images that I have not yet done manual alignment on. Even after hitting Ctrl+R, the issue persists.

[joelyancey]

Match regions are still displaying for images that I have not yet done manual alignment on. Even after hitting Ctrl+R, the issue persists.

Please relaunch the app. Should be fixed.

'alignem' in any Terminal on TACC to re-launch

[joelyancey]

unable to change/toggle through sections in manual alignment. track pad works but arrow keys and the scrub bar dont work

Resolved.

[joelyancey]

not a bug: match signal 0, box is white but text is also white so you cant see it in the table unless highlighted

not a bug: match signal 0, box is white but text is also white so you cant see it in the table unless highlighted

Resolved.

[lyndskirk16]

When you change the swim window size in custom grid or match regions mode, the size of the swim window is reverted back to default when you climb to the next scale. Additionally, when you go to the next scale (eg 6), if you align all and then go back to the lower scale (eg 24), the swim window sizes in custom grid and match regions have also reverted back to the original swim window size.

[lyndskirk16]

I'm having the same issue Ashley discussed in our meeting. I created a new project, but when I lost my session and logged back in, the project was no longer in the project previewer in the GUI. However, you can see it in the files to the right in my scratch folder. I would paste a screen shot in here but I'm logging this from within TACC and I'm unable. Let me know if you want it and I'll email it to you

[k34harris]

Yes *Kristen* *Kristen M. Harris, PhD * *Prof, Dept. of Neuroscience* *Univ. of Texas at Austin* *k ***@***.***>***@***.*** ***@***.***>, **synapseweb.clm.utexas.edu <http://synapseweb.clm.utexas.edu/>, *3DEM.org *Pronouns: She, Her, Hers*

…

On Wed, Jul 5, 2023 at 4:53 PM lyndskirk16 ***@***.***> wrote: I'm having the same issue Ashley discussed in our meeting. I created a new project, but when I lost my session and logged back in, the project was no longer in the project previewer in the GUI. However, you can see it in the files to the right in my scratch folder. I would paste a screen shot in here but I'm logging this from within TACC and I'm unable. Let me know if you want it and I'll email it to you — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADHOUZUNXOWFIQ7OWLALE5TXOXO3ZANCNFSM6AAAAAAY6KRLD4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[lyndskirk16]

When using the "align forward" button, new transformed images are not generated. This leads to good SNRs and match points to the right, but an unaligned image to the eye in the middle, which could be confusing to the user.

[alarioa]

Bug report: second time with same image set that it says "Something went wrong" while trying to do first alignment. Will try to upload images from scratch and start completely new, just to rule anything out.

[alarioa]

Bug report: second time with same image set that it says "Something went wrong" while trying to do first alignment. Will try to upload images from scratch and start completely new, just to rule anything out.

ok. i deleted the image set and re-uploaded from its original storage, but its still giving me some weirdness. Its like the images dont exist in the project. Ive been able to do an alignment with these images a long time ago but now unable to.

A point to make thought, is that i was able to succesfully align a newer image set (recently imaged, recently uploaded to corral) so im not sure the differences between these two sets.

the file path for the unsuccessful project is /corral-repl/projects/NeuroNex-3DEM/projects/3dem-1063/SP4B1-1-03/alignments/20230916_aa

file path to the successful project is /corral-repl/projects/NeuroNex-3DEM/projects/3dem-1063/SP3B7-1-01/alignmentrough

let me know if you need any more info. thanks!

[alarioa]

Crisis averted. Please disregard above reports. Looks like theres an issue with storage capacity 3dem, which is odd.