[ome-devel] connecting to omero via python

[Adam Fraser]

Thanks Will,

This is great! It works for me and should keep me busy for a while.

One suggestion for the API would be to add a getPlane() method to
omero.model.Pixels and/or omero.model.ImageI ...it's confusing that I can
get these objects that tell me all all about an image yet they won't let me
at the raw pixel data.

Again, thanks very much,
-Adam

On Mon, Feb 7, 2011 at 6:21 PM, Will Moore <will at lifesci.dundee.ac.uk>wrote:

> Hi Adam,
>
> I should warn you that the whole python API is a bit ad hoc at the moment,
> since it's been developed experimentally for a number of different use cases
> (E.g. scripts, web-client) and we're in the process of rationalising this to
> some extent.
> At the moment you have to look in a bunch of different places to find the
> functionality you need (as you've seen).
>
> The solution I've attached uses the latest trunk code, although the methods
> may have been unchanged since the 4.2.2 release?
>
> I wasn't sure what you meant by
> project = 'xxx'
> dataset = 'xxx'
>
> I imagine you want to let users connect to OMERO, browse their Projects
> (choose one) browse it's Datasets and select one with images to process.
> The only bit that is missing from the attached script is getting the user's
> choice.
>
> Hope that gets you going, and that any changes in the API don't cause too
> much pain!
>
>   Will.
>
>
>
>
>
> On 7 Feb 2011, at 21:43, Adam Fraser wrote:
>
> Hi Will,
>
> Thanks for your response, I would have gotten back to you sooner but I was
> traveling.
>
> On Sat, Feb 5, 2011 at 3:04 AM, Will Moore <will at lifesci.dundee.ac.uk>wrote:
>
>> Hi Adam,
>>
>> Sorry for the confusion, but the connection you're using for most stuff is
>> the 'blitzcon' connection?
>>
>
> No, I was primarily connecting via:
> c = omero.client('ome2-copy.fzk.de')
> s = c.createSession('afraser', '****')
> g = s.createGateway()
>
>
>> Or is 'blitzcon' the "second" connection you're using to get Dataset ID?
>>
>
> yup.
>
>
>> Confusingly, we have a 'gateway' service in the createSession()
>> connection, but we also refer to the 'blitzcon' connection as omero.gateway
>>
>
> hrm, I'm definitely confused then because I can do g.getPlane(ID, 0,0,0)
> with the above gateway, but there's no such getPlane method in what we're
> calling blitzcon.
>
> Also confusingly, I can get a session from blitzcon, but it's apparently
> not the same as the type of session I get from
> omero.clients.BaseClient.createSession(user, password)
>
> blitzcon = client_wrapper("afraser", "****", host="ome2-copy.fzk.de",
> port=4064)
> blitzcon.connect()
> s = blitzcon.getSession()
> s.getGateway() #fails
>
> ... of course the only reason I'm trying to get the gateway here is because
> I need getPlane().
>
>
>>
>> You want to allow the user to browse their Projects and Datasets by name,
>> to get Dataset ID?
>> You can use the container service to list Projects and Datasets...
>>
>
>
> >>> projects = cs.loadContainerHierarchy("Project", None, None)
>> >>> for p in projects:
>> >>>        print p.getName().getValue()
>> >>>        for d in p.linkedDatasetList():
>> >>>             print d.getName().getValue()
>>
>
> Ok, this would prevent me from having to connect via the blitzcon thing
> but...
>
>
>> But if you know the name of the Dataset from the start, and you simply
>> want the ID, you CAN use the query service.
>>
>
> Hrm, I know _nothing_ about the db schema, so I'd like to avoid this unless
> it's going to give me a serious performance improvement.
>
>
>> Generally you will find it much easier to work with the blitzcon
>> connection.
>>
>
> Ok, so I should use blitzcon = omero.client_wrapper(...), that's fine.
> Thanks for clearing this up. I don't want to use the gateway if it's going
> to change on me, I had the impression it was the right thing to use after
> reading this page<http://trac.openmicroscopy.org.uk/omero/wiki/OmeroPy/Gateway>
> .
>
> So here's where this puts me in terms of code:
>
> import omero
> from omero import client_wrapper
> import numpy as np
>
> user = 'xxx'
> pw = 'xxx'
> host = 'xxx'
> project = 'xxx'
> dataset = 'xxx'
>
> blitzcon = client_wrapper(user, pw, host, port=4064)
> blitzcon.connect()
>
> # get all image ids from dataset:
> *image_ids = #???*
>
> for image_id in image_ids:
>     im = blitzcon.getImage(image_id)
>     # Get raw image plane.
>     #    previously: plane = g.getPlane(image_id, 0, 0, 0)
>     *plane = #???*
>     px = im.getPixels(0)
>     h = px.getSizeY().getValue()
>     w = px.getSizeX().getValue()
>     imdata = np.array(list(plane))
>     imdata.shape = (h,w)
>     # now I can do stuff with imdata
>
> Any chance you can help me fill in those 2 blanks?
>
> Thanks again,
> Adam
>
>
>   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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