[ome-devel] getting metadata

[Wood, Christopher]

Will,

Thanks again.

I was just wondering if something like the Blitz gateway is available for Java.

Thanks
Chris

From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
Sent: Monday, May 09, 2011 6:00 PM
To: Wood, Christopher
Cc: ome-devel at lists.openmicroscopy.org.uk
Subject: Re: [ome-devel] getting metadata

Hi Chris,

 This depends quite a bit on what OMERO version you're using and whether you're using the "Blitz Gateway" https://trac.openmicroscopy.org.uk/ome/wiki/OmeroPy/Gateway

Without using the blitz gateway, it requires a bit more knowledge of the OMERO model and how objects are linked.
http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/slice2html/omero/model.html

Image -> Pixels -> Channel -> Logical Channel.excitation wavelength
Image -> Objective Settings -> Objective

For historical reasons the model is sometimes more complex than you might expect.
E.g. Image can have several sets of Pixels.
E.g. Channel -> Logical Channel.

You can traverse the graph by writing queries with iQuery, but this is the method of last resort, since it is tricky and susceptible to model changes.

Much easier to use the Blitz gateway, which handles lazy loading, making it easier to traverse the graph.
It also 'hides' some of the complexity of the model.
However, this module is at an early stage of development and there will be some API changes with the 4.3 release.
All breaking changes are listed here: http://trac.openmicroscopy.org.uk/ome/wiki/Api/BlitzGateway
Having said all that, you can get what you want with this code

import omero
from omero.gateway import BlitzGateway
conn = BlitzGateway('root', 'omero', port=4064, host='localhost')
conn.connect()

imageId = 1234
i = conn.getImage(imageId)        # in 4.3 this will be getObject("Image", imageId)
for c in i.getChannels():
    print c.getLogicalChannel().excitationWave          # c.getExcitationWave() isn't supported - I'll fix that for 4.3

ob = i.getObjectiveSettings().getObjective()
print ob.model
print ob.nominalMagnification
print ob.lensNA
print ob.getImmersion().value                         # enumeration
print ob.getCorrection().value


Docs for the 4.2 ImageWrapper are http://hudson.openmicroscopy.org.uk/view/Beta4.2/job/OMERO-Beta4.2/javadoc/epydoc/omero.gateway._ImageWrapper-class.html
The docs are much improved for the latest code (will be 4.3 release) allowing you to follow the traversal above.
http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/epydoc/omero.gateway._ImageWrapper-class.html
Attributes of the objective can be seen http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/slice2html/omero/model/Objective.html
and are accessed 'directly' from the underlying object - instead of the methods on the ObjectiveWrapper
http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/epydoc/omero.gateway._ObjectiveWrapper-class.html

As the Blitz Gateway evolves, some things will take a little trial and error, although the documentation is improving a lot and we'll do our best not to make breaking changes - at least after 4.3 release.

Finally, you might get something out of looking at the code that displays all the image metadata in web.
This uses the Blitz Gateway, imageWrapper, channelWrapper etc.
Look under def load_metadata_acquisition()
https://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/tools/OmeroWeb/omeroweb/webclient/views.py#L947
although there is a bit more going on here with web forms etc.

 Hope that helps,

   Will.


On 9 May 2011, at 22:55, Wood, Christopher wrote:


Hi,

What is the best way to get metadata from an image using the python API?

For example, if I have a confocal image and I want to know the laser excitation wavelengths and the objective.

Thanks
Chris
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William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org





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