[ome-devel] getting metadata

[Will Moore]

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
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

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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