[ome-users] omero Beta4: Displaying an image from omero in matlab

[dzmacdonald]

Hi Bram,

it also looks like I forgot to commit some code to convert byte arrays  
to matlab double arrays, and stacks.

I'll fix that now.

Regards

D.

On Feb 17, 2009, at 2:20 PM, donald wrote:

> Hi Bram,
>
> Sorry, the Gateway methods are in the middle of being changed. I'm
> going to write doc for them in a couple of days.
>
> When we moved the Gateway from the client to the server as a service
> some of the methods became inappropriate for a server side call (too
> much data being sent, or just nor correct). There are methods now in
> the OMEROJava directory under the util part the class is called
> GatewayUtils and it should do a lot of that for you.
>
> http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroJava/src/omerojava/util/GatewayUtils.java
>
> client = omero.client('localhost');
> session = client.createSession('root','ome');
> gateway = session.createGateway();
> p = gateway.getPixels(57);
> renderedImage = omerojava.util.GatewayUtils.toBufferedImage(p, image)
>
> If you find any errors or wish new methods added please don't hesitate
> to ask.
>
> If you have code you wish to add please feel free, that would be
> excellent. :-)
>
> Regards
>
> Donald
>
> On Feb 17, 2009, at 12:50 PM, <b.gerritsen at nki.nl> wrote:
>
>> Dear all,
>>
>> Some of the omero matlab scripts in the trunk do not work for me.
>> Displaying an image from omero in matlab failed for me. After
>> checking out the api it looks like the getPlane() function was to
>> blame as it has changed from the previous version:
>>
>> (copied directly from the docs for beta4 )
>> ---
>>
>> byte[]   getPlane(long pixelsId, int z, int c, int t, Ice.Current
>> current)
>>       Get the raw plane for the pixels pixelsId, this returns a 2d
>> array representing the plane, it returns doubles but will not lose
>> data.
>>
>> ---
>>
>> The returned array is one-dimensional and not two as the comment
>> states. Although I'm new to both omero and matlab, I wrote a matlab
>> function (see below) that displays images from omero. It works for
>> the tiff files that I'm uploading into omero. If there are better
>> ways to do it, please let me know!
>>
>> Thanks!
>> Bram Gerritsen
>>
>>
>> ------------------------------------------
>>
>> function drawImage(hostname, username, password, pixelsId)
>> omeroGateway = createOmeroJavaService(hostname, username, password);
>> pixels = omeroGateway.getPixels(pixelsId);
>> pixelType = pixels.getPixelsType.getValue.getValue.toCharArray;
>>
>> plane = swapbytes (typecast (omeroGateway.getPlane(pixelsId, 0, 0,
>> 0), pixelType)); % OMERO uses Big Endian whereas intel systems use
>> Little Endian
>>
>> sizeX = pixels.getSizeX.getValue;
>> sizeY = pixels.getSizeY.getValue;
>> total = sizeX*sizeY;
>>
>> rgbImage = zeros (sizeX, sizeY, 3, pixelType);
>> for j=1:sizeY,
>>     for i=1:sizeX,
>>             rgbImage(i, j, 1)=plane ( (j-1)*sizeX + i);
>>             rgbImage(i, j, 2)=plane ( (j-1)*sizeX + i);
>>             rgbImage(i, j, 3)=plane ( (j-1)*sizeX + i);
>>     end
>> end
>>
>> figure(1);
>> image (rgbImage);
>> drawnow;
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>
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