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Add script to find images #44

Merged
merged 2 commits into from
Aug 31, 2021
Merged

Add script to find images #44

merged 2 commits into from
Aug 31, 2021

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dominikl
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@dominikl dominikl commented Aug 23, 2021

Script to get a list of image IDs which names match a certain regular expression. Based on (just slightly modified): https://github.com/IDR/idr0108-sabinina-nuclearporecomplex/blob/main/scripts/find_images.py) Apart from idr0108 I used it for a few other studies. Often images which need particular rendering settings, pixel sizes, etc. set after import, can be distingushed by a common name pattern. The output can be used to successively call omero render etc. in for loop or used with parallel.

@joshmoore
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Makes sense, and we certainly don't have anything that would do this today (other than listing all and using grep). Thinking about where we might want to have this one day, two things occur to me:

  • It's probably too difficult to implement, but the FindParent and FindChildren commands could do some of this server side (see the resurrected work in Add parents and children to omero obj ome/omero-py#299); or
  • part of me wonders if search just shouldn't be made powerful enough to do something like contained-in:Project-1 type:Image name:foo

@sbesson sbesson closed this Aug 30, 2021
@sbesson sbesson reopened this Aug 30, 2021
@joshmoore
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./scripts/annotate/find_images.py:3:1: F401 'os' imported but unused

@dominikl
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Btw, I thought as well, ideally that should be done on the server side. But simply doing some regex matching on the client side for now, is just easier and quicker than going through the whole stack.

@joshmoore
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But simply doing some regex matching on the client side for now, is just easier and quicker
👍

@sbesson sbesson merged commit e54369b into IDR:master Aug 31, 2021
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3 participants