Open Microscopy Environment

Hello,
I am trying to use getHypercube from Matlab. In general it works, but it returns the images as the int8, rather than uint8 class. Is it feature or bug?

Thank you!

ok it was similar case with getTile,
got it fixed with:

Code: Select all

tile = store.getTile(z, c, t, minX, minY, width, height);
tPlane = typecast(tile, 'uint8');
tPlane = reshape(tPlane, [width, height])';
tPlane = swapbytes(tPlane);


Happy to see you fixed it. For information, all the getTile(), getHyperCube()... methods of the raw pixel store return linear java.langByte[] arrays which are automatically casted to int8 in Matlab. They need to be reshaped and casted into the appropriate format as you did.

See also the toMatrix() utility function of the OMERO.matlab toolbox.

Best,
Sebastien

Hi Sebastien,
right, however the problem with the toMatrix() function is that it probably can't properly reshape the results from getTile function, because it does not know dimensions of the output dataset and takes width/height from the pixels object which may be trimmed.
Or I just did something wrong

You're absolutely right.

Note that improvements have been brought to the toMatrix.m function to pass tile size as an optional argument. These changes will be included in OMERO.matlab 4.4.7 which should be released later on this week.

Sebastien