Missing getValue() method for OME metadata import in Matlab

[Ajaxel]

Hello,
the following code from http://www.openmicroscopy.org/site/supp ... b-dev.html
gives error due to missing getValue method:

Code: Select all

data = bfopen('/path/to/data/file');
omeMeta = data{1, 4};

voxelSizeX = omeMeta.getPixelsPhysicalSizeX(0).getValue(); % in µm
voxelSizeY = omeMeta.getPixelsPhysicalSizeY(0).getValue(); % in µm
voxelSizeZ = omeMeta.getPixelsPhysicalSizeZ(0).getValue(); % in µm



tested with bioformats_package.jar 5.1.0

[sbesson]

Hi,

you are absolutely correct, the MATLAB documentation had not been updated as part of 5.1.0 to cover the new methods to retrieve physical pixel size with the new units. A Pull Request had been opened to fix the documentation but we did not update it. The documentation has just been re-released live with this change so the MATLAB documentation page should be up-to-date now.

Thanks for notifying us and let us know if you anything is unclear or not working.

Best,
Sebastien

[Ajaxel]

Good work, thanks!

[Ajaxel]

ohh, one other thing:
the class returned with the .value(ome.units.UNITS.MICROM) method is java.lang.Double.
I guess it should be converted to matlab double?

Best regards,
Ilya

[sbesson]

Hi Ilya,

yes absolutely, you should be able to use conversion methods like `doubleValue` e.g.

Code: Select all

pixelSixeX = physicalSizeX.value(ome.units.UNITS.NM).doubleValue();


This is definitely worth adding to the code snippets.

Thanks,
Sebastien