Open Microscopy Environment

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 :

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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

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

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

Dear Philippe,

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

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


Cheers,
Mark

mtbc wrote: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