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imageloader.py and uploadImages.py insert image into the database before saving the image #2285

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 2285, https://emg.nysbc.org/redmine/issues/2285 Original Date: 2013-03-06 Original Assignee: Saikat Chowdhury

This causes problem to imcached that query images in the database and want to cache the image for web image viewers. Often that the file is not completely saved before the read starts by imcached.

Jim wants to make it a rule that the image should be saved to Leginon image path before database insertion.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-03-06T23:18:13Z

r17443 read mrc in as num array and save to destination through imagedata.insert() Since these programs are not used for stack uploading, it should be o.k. to load into memory. Otherwise, the fake image in the imagedata would overwrite the copied mrc image if done before the imagedta.insert()

This need to be merged into myami-2.2-redux

Neil I hope you don't recall a case where reading the image into memory is not possible in upload.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2013-03-07T21:39:05Z

Hi Anchi,

My only worry about this is that if numpy or sinedon goes buggy again and does not properly clear the memory then you could have a memory leak, which is why we did it in the first place (????). If it works though I cannot argue against it.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-03-08T00:31:10Z

Neil,

If numpy causes memory leak, Leginon won't be stable any way. I did the copy in the first place because copy is faster read and then write.

Saikat, Please test this for me. Just upload some image as you have been doing and see if it runs. Update the issue with whether it is successful. If so, the issue can be closed.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Saikat Chowdhury (Saikat Chowdhury) Original Date: 2013-03-08T01:58:46Z

Hi Anchi, I just uploaded 10 micrographs in the project "13mar07z - test upload". It seems to have worked fine. I can view the micrographs in the image viewer do FFT etc. It seems to work fine. For some reason I can't see this project/session in the project/session list page in appion.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-03-08T02:08:11Z

If you click on the 'show all' button, it should show. I didn't know about this feature until now, neat.