[ome-devel] connecting to omero via python

[Adam Fraser]

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
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