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

[donald]

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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