[ome-devel] CLI render - and a philosophic question re: rendering settings

[Damir Sudar]

Hi Josh and whoever is interested,

I'm finally gearing up to upgrade to 5.3.3 for all its great new 
capabilities and was trying some stuff on my 5.3.3 test server. One of 
those was the render.py script that, per below, wasn't really usable in 
vanilla 5.2.x. Unfortunately I get the exact same exceptions with 5.3.3 
so I guess I should wait for 5.4? Or is the situation with 5.3 more 
solvable?

Now the philosophical question: as in IDR, we have a very large image 
dataset that we are quantitatively analyzing and also want to show 
visually. This is part of a large project to asses the effects of a set 
of perturbing agents (perturbagens) on a panel cell lines, where in our 
case a large panel of different microenvironment components and drugs 
are used as the perturbagens. During import into OMERO each image gets 
its rendering settings from the min/max values in the image itself so 
all images have different settings and the unsuspecting viewer may see 
all kinds of interesting intensity effects that are mostly fake while 
real effects may be masked. So I'm looking for a general way to set the 
rendering settings across the entire experiment to something that allows 
comparing images but doesn't generate loads of black and 
over-exposed-looking images. I was thinking that you guys encountered 
this same issue with many of the IDR datasets so was hoping for some 
wise thoughts.

Anyway, this is why I'm so interested in the render.py utility and thus 
my hope it will make it to production-level soon.

One thought to be able to display the larger dynamic range needed for 
the above (and which is not really possible with the current linear 
scaling between min and max values), is the idea of supporting 
non-linear colormaps for the rendering. I saw some mentions of a 
CodomainMap in the RenderingEngine docs. Would that be a future way to 
support non-linear scale transforms such as gamma curves and such?

Cheers,
- Damir

On 7/10/2017 6:45, Josh Moore wrote:
>
>> Next I tried a few of the basic commands of the render plugin:
>> 1 ---
> ...
>>    File "/home/omero_user/OMERO.server/lib/python/omero/plugins/render.py",
>> line 117, in init_from_channel
>>      self.min = channel.getWindowMin()
> ...
>> omero.UnloadedEntityException: Object unloaded:object #0
> Vanilla 5.2 is not loading the necessary metadata for the plugin to
> work. Unfortunately, solving this isn't as simple as copying a new
> file into your installation. In fact, I haven't yet found a smoking
> gun between the versions.
>
>
>> 2---
>> AttributeError: 'ImageI' object has no attribute '_closeRE'
>> ---
> Here again, changes from 5.3 are not available in your version, though
> at least these I know where they come from.
>
>
>> Rather than trying more of this, I thought to check with you first whether
>> I'm missing something fundamental.
> 5.3 :) (or the upcoming 5.4)
>
> Fundamentally, the plugin is not production quality and has only been
> used in isolated situations. We certainly intend to get it into the
> testing pipeline for 5.4 but that's not likely to uncover what's going
> on with 5.2. If you or anyone on your side wants to continue digging,
> we're happy to evaluate your changes, but there's a question of how
> far you want to go in modifying your local installation.
>
> Cheers,
> ~Josh.
>
>
>
>> Thanks,
>> - Damir
>>
>> On 6/2/2017 2:35, Simon Li wrote:
>>
>> The render plugin (not tested on 5.3):
>> https://github.com/openmicroscopy/openmicroscopy/blob/metadata53/components/tools/OmeroPy/src/omero/plugins/render.py
>> Try dropping this into OMERO.server/lib/python/omero/plugins/
>>
>> Example YAML render settings file:
>> https://github.com/IDR/idr-metadata/blob/master/idr0015-UNKNOWN-taraoceans/screenA/idr0015-screenA-renderdef.yml
>>
>> omero render edit --help
>> omero render edit --copy Plate:1 renderdef.yml
>> omero render copy Image:SrcID Plate:TargetID
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-- 
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
http://biosciences.lbl.gov/profiles/damir-sudar-2/

Visiting Scientist, Oregon Health & Science University