Add null check for image.getFormat() #9
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Under some conditions, an Image might have no associated format. This will be the case for ROMIO pixel buffer e.g. created by scripts or OMERO pyramid pixel buffer created by the PixelService for large images without resolutions.
chris-allan
reviewed
May 20, 2024
| @@ -325,7 +325,7 @@ protected ZarrPixelBuffer createOmeNgffPixelBuffer(Pixels pixels) { | |||
| String uri = getUri(image); | |||
| if (uri == null) { | |||
| // Quick exit if we think we're OME-NGFF but there is no URI | |||
| if ("OMEXML".equals(image.getFormat().getValue())) { | |||
| if (image.getFormat() != null && "OMEXML".equals(image.getFormat().getValue())) { | |||
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Should probably just be:
"OMEXML".equals(unwrap(image.getFormat()))
With a static import of omero.rtypes.unwrap. Similar examples can be see in com.glencoesoftware.omero.ms.image.region.ImageDataRequestHandler.
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Unfortunately, this does not work out of the box since image.getFormat() returns an ome.model.core.Format object and I get
/Users/sbesson/Documents/GitHub/omero-zarr-pixel-buffer/src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java:330: error: incompatible types: Format cannot be converted to RType
if ("OMEXML".equals(unwrap(image.getFormat()))) {
Could look into using the OriginalFileFormatEnumHandler to find the proper enumeration and return the IObject but I wonder if it's overkill.
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Scratch what I said. Since it's an instance of ome.model.Image (server side object) what you have currently is all we can really do.
chris-allan
approved these changes
May 20, 2024
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Under some conditions, an Image might have no associated format. This will be the case for ROMIO pixel buffer e.g. created by scripts or OMERO pyramid pixel buffer created by the PixelService for large images without resolutions.
To test this PR, use an OMERO.server with the https://github.com/glencoesoftware/omero-zarr-pixel-buffer extension and create a ROMIO image e.g. using the
Images from ROIsscript.Without this PR a call to
RenderingSettings.resetDefaultswill cause a NPE of typeand the image will end up in a broken state.
With this PR, the
PixelsService.getPixelBuffershould return aRomioPixelBufferas expected and the server logic should complete the creation of a rendering definition and thumbnail