reading metadata

[phm]

Hi,
I trying to get the value of overlap metadata in ome.tif Lavision image. Opening image in Fiji with Bioformats and metadata actived shown the field :

Code: Select all

xyz-Table_XY_Overlap   10.000000


However, using java code as :

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ServiceFactory factory;
factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata meta = service.createOMEXMLMetadata();
ImageProcessorReader reader = new ImageProcessorReader();
reader.setMetadataStore(meta);
reader.setId(imageDir+imageFile[0]);
int series = 0;
reader.setSeries(series);
double sx = meta.getPixelsPhysicalSizeX(series).value().doubleValue();
double sy = meta.getPixelsPhysicalSizeY(series).value().doubleValue();
double sz = meta.getPixelsPhysicalSizeZ(series).value().doubleValue();
cal.pixelWidth = sx;
cal.pixelHeight = sy;
cal.pixelDepth = sz;
cal.setUnit("microns");
String overlapMetadata = "xyz-Table_XY_Overlap";
String overlap =reader.getSeriesMetadataValue(overlapMetadata).toString());


return a null pointer exception for overlap but not sx, sy or sz ????
Philippe

[mtbc]

Dear Philippe,

Perhaps that key is among the global rather than the series metadata? You can check using showinf -nopix as at https://docs.openmicroscopy.org/latest/ ... splay.html

If you still have trouble, please do feel free to paste to us the output of showinf applied to your file or even just upload the image to http://qa.openmicroscopy.org.uk/qa/upload/ with a covering comment and we should be glad to take a look.

Cheers,
Mark

[phm]

Hi Mark,
I uploaded the file 11-30-56_140218E17-5netpattehomo4 x 3-2_UltraII[00 x 00]_C00_xyz-Table Z0000.ome.tif
on your server.
Thanks
Philippe

[mtbc]

Dear Philippe,

Yes, showinf shows that the overlay's in the global metadata, not the series metadata. Try instead something like,

Code: Select all

String overlap = reader.getGlobalMetadata().get(overlapMetadata).toString();


Cheers,
Mark

[phm]

Dear Philippe,

Yes, showinf shows that the overlay's in the global metadata, not the series metadata. Try instead something like,

Code: Select all

String overlap = reader.getGlobalMetadata().get(overlapMetadata).toString();


Cheers,
Mark

Solved !
Thanks Mark,

Philippe