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aarpon / hrm

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.
http://huygens-rm.org
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[BUG REPORT] SNR estimator broken? #21

Closed lacan closed 1 year ago

lacan commented 1 year ago

Describe the bug Due to how long the SNR estimator runs now, we had stopped using it. I tried it with a single channel dataset and have much trouble interpreting what it written... It just says Original 3 times and no links to help are displayed

To Reproduce Request an SNR estimation from a single channel image. I do not know the behaviour for multichannel images as of this writing

Expected behavior The classic Estimated SNR value, a lowest estimation and a highest estimation. Or something like on the documentation here https://svi.nl/HuygensRemoteManagerHelpSnrEstimator

Screenshots image

Environment Server-side Huygens Remote Manager  
HRM version 3.9
HRM required database version 20
HRM current database version 20
HuCore minimum required version 21.10.1
HuCore current version 23.4.0-p6
HuCore server type medium
Licenses in use  
Detailed license information  
HuCore license file valid
HRM-OMERO Connector  
Version  
System  
Operating system Linux x86_64
Kernel release 3.10.0-1160.99.1.el7.x86_64
LAMP versions  
Apache version 2.4.6
Database type and version mysqli 5.7.43
PHP (Apache mod) version 8.2.11
Configuration  
Send test e-mail to HRM admin  
Memory limit 128MB
Max execution time 30s
File downloads  
HRM configuration disabled
Maximum post size  
php.ini 8MB
HRM configuration limited by php.ini.
in use 8MB
File uploads  
php.ini enabled
HRM configuration enabled
in use enabled
Maximum upload file size  
php.ini 2MB
HRM configuration limited by php.ini.
in use 2MB

Client-side FireFox 118.0.1 (64-bit)

KevinNamink commented 1 year ago

I agree it is a bit slow for larger images.

I've tried a few images but I cannot reproduce this undecipherable output. What type of image are you using? What are the image dimensions?

lacan commented 1 year ago

Dear @KevinNamink,

Thanks for looking into it. It is a lif file with 2048x2048x231 z slices

https://drive.switch.ch/index.php/s/Wip2HmXnHoxppg2 Password is hrm and the link will expire on friday.

Best Oli

KevinNamink commented 1 year ago

Thanks for the file. I can now reproduce it. I've found and fixed the issue. The cause was in Huygens. In Huygens 23.10 this particular issue will be fixed.

I've also found a bug with the "legacy" SNR estimation mode. That should also work again with Huygens 23.10. This might be a faster method if that is important.

I think these problems are specific to Huygens 23.04, I'll try to put these fixes in a patch for that version as well. (I cannot 100% guarantee this patch will come.)