Bug: Big image reads broken in OMERO

[jburel]

I imported the image png/8kx8k from test_image_good. Sometimes The "clock" icon is displayed post import in Importer tab
Black thumbnail in browser
See error from Blitz.log

[omero.createMissingThumbnailMetadata]
2012-11-07 21:53:19,311 INFO  [             ome.io.nio.FilePathResolver] (l.Server-6) Metadata only file, resulting path: /OMERO/Files/357
2012-11-07 21:53:19,312 INFO  [                ome.io.nio.PixelsService] (l.Server-6) Using Pyramid BfPixelBuffer: /OMERO/Pixels/951_pyramid
2012-11-07 21:53:19,312 ERROR [                ome.io.nio.PixelsService] (l.Server-6) Error instantiating pixel buffer: /OMERO/Pixels/951_pyramid
ome.conditions.ResourceError: FormatException: /OMERO/Pixels/951_pyramid
Invalid TIFF file
	at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:73)
	at ome.io.bioformats.BfPixelBuffer.isLittleEndian(BfPixelBuffer.java:92)
	at ome.io.bioformats.BfPyramidPixelBuffer.initializeReader(BfPyramidPixelBuffer.java:192)
	at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:171)
	at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:141)
	at ome.io.nio.PixelsService.createPyramidPixelBuffer(PixelsService.java:636)
	at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:410)
	at ome.services.ThumbnailBean.retrieveThumbnailSet(ThumbnailBean.java:927)
	at ome.services.ThumbnailBean.getThumbnailByLongestSideSet(ThumbnailBean.java:901)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)

[jburel]

see #9757

[jburel]

actually the size of the /OMERO/Pixels/951_pyramid is 0.

[jburel]

Starting the rendering engine to generate the bird eye view

omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Invalid T size: -1
                        	at loci.formats.FormatTools.getIndex(FormatTools.java:330)
                        	at loci.formats.FormatTools.getIndex(FormatTools.java:278)
                        	at loci.formats.FormatReader.getIndex(FormatReader.java:976)
                        	at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:360)
                        	at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:462)
                        	at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:450)
                        	at ome.io.bioformats.BfPyramidPixelBuffer.getTile(BfPyramidPixelBuffer.java:992)
                        	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216)

[jburel]

I wrote a little script to check the problems.
Using directly the MinimalTiffReader works fine i.e. sizeT=1, using OmeroPixelsPyramidReader returns sizeT=-1

[jburel]

OmeroPixelsPyramidReader class is the one I have been using.

[jmoore]

With the introduction of the subresolution API in bioformats 4.4.4, the OmeroPyramid subclass is now doing things incorrectly leading to the negative T=-1. Passing to Melissa for a possible fix.

[mlinkert]

Should be fixed with these two PRs:

​https://github.com/openmicroscopy/bioformats/pull/211

​https://github.com/openmicroscopy/openmicroscopy/pull/478