Kymograph script & analysis_utils

[will-moore]

Demo movie on #8206.

[jburel]

@will-moore:

• add support for permissions
• version need to be updated

[sbesson]

Support for permissions proposed in PR will-moore#1

[will-moore]

@joshmoore @sbesson I'm still not happy about our solution for sharing 'util' code between scripts (using "analysis_utils.py" above - as discussed on https://trac.openmicroscopy.org.uk/ome/ticket/9368). This requires you to have dist/lib/scripts/ on your PYTHONPATH and it creates an invalid 'script' to appear in the client UIs. Although we can find workarounds for these, it makes it too inconvenient for admins to install these scripts.

[joshmoore]

@will-moore, definitely still a problem. Concrete suggestion?

[will-moore]

My preference for now is to simply duplicate the code in the 2 scripts that need it. Until the scripting framework supports a "proper" solution, an alternative solution is more pain than having one method in two places.

[joshmoore]

For the moment, that's probably the best we can do (unless we add a "scripts-common.git").

[joshmoore]

NB: Interestingly, I wonder if fs-lite provides a solution, in that scripts get uploaded to an importable directory.

[joshmoore]

@will-moore, can you accept @sbesson's pr now?

[will-moore]

@sbesson PR can't be merged automatically, No.

[joshmoore]

@will-moore, can you recheck @sbesson's PR?

[ximenesuk]

Kymograph and Kymograph Analysis both worked as expected. The former took a long time but this was on an fslite imported image so may be an fslite performance issue. Plot Profile worked okay if I left the Channel blank but it gave an error if I entered a Channel (full exception available if needed):

WARNING:omero.gateway:ApiUsageException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to 86:24:41:e3:-592b8985:13a208e041e:-614aomero.api.RawPixelsStore getTile((0, -1, 2, 275, 221, 11, 43), {})
Traceback (most recent call last):
File "/home/omero/slave/workspace/OMERO-merge-green/src/dist/lib/python/omero/gateway/init.py", line 3324, in call
return self.f(_args, *_kwargs)
File "/home/omero/slave/workspace/OMERO-merge-green/src/dist/lib/python/omero_api_RawPixelsStore_ice.py", line 189, in getTile
return _M_omero.api.RawPixelsStore._op_getTile.invoke(self, ((z, c, t, x, y, w, h), _ctx))
ApiUsageException: exception ::omero::ApiUsageException
{
serverStackTrace = ome.conditions.ApiUsageException: Invalid C index: -1/2
at loci.formats.FormatTools.getIndex(FormatTools.java:325)
at loci.formats.FormatTools.getIndex(FormatTools.java:278)
at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:258)
at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:356)
at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:480)
at ome.services.RawPixelsBean.getTile(RawPixelsBean.java:777)
...

[will-moore]

This will be rebased onto dev_4_4 as a new branch