Task #11912 (closed)
Opened 10 years ago
Closed 10 years ago
PIL on nightshade
Reported by: | wmoore | Owned by: | spli |
---|---|---|---|
Priority: | critical | Milestone: | 5.0.0 |
Component: | Deployment | Version: | n.a. |
Keywords: | n.a. | Cc: | ux@…, analysis@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
We demo'd the Kymograph script on nightshade today and realised that something is not right.
It works fine on my machine (and I think it has worked nicely on nightshade before now), but
what we saw today was that the rotation of image slices using PIL is looking awful.
I don't know if it's missing some dependencies, or is a version that is using a different
resampling algorithm by default or what?
Or maybe some numpy issue in converting images to/from PIL.
I'm using the basic rotate function of a PIL image
image.rotate(toRotate, expand=True)
Anyone got any ideas about what could be causing this problem?
Here's an couple of screenshots of the script working on my local server and not on nightshade.
I'll see if I can find out any more info...
Change History (12)
comment:1 Changed 10 years ago by wmoore
comment:2 Changed 10 years ago by wmoore
Simon: These are 16-bit images
comment:3 Changed 10 years ago by spli
OK, Chris Coletta had similar problems with PIL and 16bit images in PyCHRM/WND-CHRM, I'll talk to him.
comment:4 Changed 10 years ago by wmoore
This is actually working OK on my machine with 16-bit images
$ python Python 2.7.6 (default, Dec 11 2013, 12:35:35) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin $ pip freeze ... PIL==1.1.7 numpy==1.8.0 ...
comment:5 Changed 10 years ago by spli
- Cc ux@… analysis@… added
comment:6 Changed 10 years ago by pwalczysko
Also on trout it was 16-bit image which I tested. See screenshots on https://trac.openmicroscopy.org.uk/ome/ticket/11916.
comment:7 Changed 10 years ago by wmoore
Simon - any progress on this? I just got an e-mail from the user I spoke to last week asking about progress. She would like to come to next Thursdays drop-in session and 'check in'. Cheers,
comment:8 Changed 10 years ago by spli
I'll see if there's a workaround on Monday that works with python-imaging/PIL 1.1.6. If that fails I guess installing a later version of PIL is one option. Problem is nightshade isn't setup to use pip/virtualenv, though compiling a new RPM is another option.
comment:9 Changed 10 years ago by wmoore
Simon - since trout has the same issue as nightshade, could we see if upgrading to latest PIL/pillow helps there?
Also just tried howe, and there's no problem there - Kymographs look fine.
comment:10 Changed 10 years ago by spli
I think I've got a workaround that'll work on older PIL versions.
comment:11 Changed 10 years ago by spli
Use this to check whether your version of PIL is affected: https://gist.github.com/manics/8648955
PR opened: https://github.com/ome/scripts/pull/62
comment:12 Changed 10 years ago by spli
- Resolution set to fixed
- Status changed from new to closed
Open a ticket and put me on it.
Are these 8/16 bit images?
Simon
On 17 Jan 2014, at 13:24, Petr Walczysko wrote:
Hi Simon
Thank you. Unfortunately, I think we have the same problem on trout as well.
See below.
Cheers
Petr
<Screen Shot 2014-01-17 at 13.23.39.png>
On 16 Jan 2014, at 16:30, Simon Li wrote:
Petr mentioned it in devteam earlier. Trout has the same version of PIL (though a different version of numpy) installed, can you replicate it there?
[spli@nightshade2 ~]$ rpm -q python-imaging numpy
python-imaging-1.1.6-19.el6.x86_64
numpy-1.3.0-6.2.el6.x86_64
If that doesn't work then I think we'll need to redo the python dependencies on Nightshade, which could be non-trivial. For instance it's also also missing pytables (which has other dependencies, with particular version requirements), so it might be worth setting up a virtualenv incorporating (or not) the system packages. I've just tried installing tables from scratch in a CentOS VM (verifying the OMERO.searcher install instructions) and it's a bit of a pain at the moment. Or rebuild and push out our own RPMs (I've got some).
Simon
On 16 Jan 2014, at 16:15, Will Moore wrote:
Hi Kenny (or anyone who might have an idea....)