[ome-users] Change in API

[Sebastien Besson (Staff)]

Hi Sebastian,

you are correct. This API was modified between 5.0.x and 5.1.x as part of the
changes to support units in the model.

On 5.0.x, getPixelsPhysicalSizeX() was returning an PrimitiveType object
which was unwrapped via getValue().
http://downloads.openmicroscopy.org/latest/bio-formats5.0/api/ome/xml/meta/MetadataRetrieve.html#getPixelsPhysicalSizeX(int)
http://downloads.openmicroscopy.org/latest/bio-formats5.0/api/ome/xml/model/primitives/PositiveFloat.html

On 5.1.x, the same method now returns a Length object, i.e a combination of a
value and a length unit.
http://downloads.openmicroscopy.org/latest/bio-formats5.1/api/ome/xml/meta/MetadataRetrieve.html#getPixelsPhysicalSizeX(int)
http://downloads.openmicroscopy.org/latest/bio-formats5.1/api/ome/units/quantity/Length.html

Other examples showing how to retrieve the unit or how to retrieve the length value
in a specific unit are given in:
https://www.openmicroscopy.org/site/support/bio-formats5.1/developers/matlab-dev.html#ome-metadata
These are MATLAB examples but the same semantics should be portable to python-bioformats.

Best,
Sebastien

On 2 May 2015, at 11:04, Sebastian Rhode <sebrhode at gmail.com<mailto:sebrhode at gmail.com>> wrote:

Hi,

I am using the BioFormats package 5.1.1 from python (via python-bioformats) and noticed, that my old code does not work any more.

To get the scaling I used before:

getPixelsPhysicalSizeX(0).getValue().floatValue()

but this seems to be now:

getPixelsPhysicalSizeX(0).value().floatValue()

Is this correct and why was it changed? I am just curious? Or is the a issue of the python-bioformats wrapper?

Cheers,

Sebastian
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