Bug: IMS thumbnail fails on z-out-of-bounds

[jamoore]

As "Niko", ​http://demo.openmicroscopy.org/webclient/?show=image-162695

-15 13:10:02,900 INFO  [                 org.perf4j.TimingLogger] (Server-469) start[1397563802899] time[1] tag[omero.loadMetadataByDimensionPool]
2014-04-15 13:10:02,900 INFO  [                 org.perf4j.TimingLogger] (Server-469) start[1397563802898] time[2] tag[omero.createMissingThumbnailMetadata]
2014-04-15 13:10:02,910 INFO  [             ome.io.nio.FilePathResolver] (Server-469) Metadata only file, resulting path: /repositories/demo/ManagedRepository/Niko_2560/2014-
03/25/23-36-01.860/XY_point_2.ims
2014-04-15 13:10:02,993 DEBUG [                   loci.formats.Memoizer] (Server-469) loaded memo file: /repositories/demo/BioFormatsCache/repositories/demo/ManagedRepository
/Niko_2560/2014-03/25/23-36-01.860/.XY_point_2.ims.bfmemo (818521 bytes)
2014-04-15 13:10:02,993 DEBUG [                   loci.formats.Memoizer] (Server-469) start[1397563802911] time[81] tag[loci.formats.Memoizer.loadMemo]
2014-04-15 13:10:02,993 DEBUG [                   loci.formats.Memoizer] (Server-469) start[1397563802911] time[81] tag[loci.formats.Memoizer.setId]
2014-04-15 13:10:02,993 INFO  [                ome.io.nio.PixelsService] (Server-469) Creating BfPixelBuffer: /repositories/demo/ManagedRepository/Niko_2560/2014-03/25/23-36-
01.860/XY_point_2.ims Series: 0
2014-04-15 13:10:02,998 INFO  [             omeis.providers.re.Renderer] (Server-469) Enabling alphaless rendering.
2014-04-15 13:10:02,998 INFO  [             omeis.providers.re.Renderer] (Server-469) Disabling PriColor rendering, channel color not primary.
2014-04-15 13:10:02,998 INFO  [             omeis.providers.re.Renderer] (Server-469) Using: 'omeis.providers.re.HSBStrategy' rendering strategy.
2014-04-15 13:10:03,000 INFO  [                 org.perf4j.TimingLogger] (Server-469) start[1397563802891] time[108] tag[omero.call.exception]
2014-04-15 13:10:03,001 WARN  [        ome.services.util.ServiceHandler] (Server-469) Unknown exception thrown.

java.lang.RuntimeException: ome.io.nio.DimensionsOutOfBoundsException: Z '26' greater than sizeZ '26'.
        at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:248) ~[rendering.jar:na]
        at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105) ~[rendering.jar:na]
        at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) ~[rendering.jar:na]
        at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) ~[rendering.jar:na]
        at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) ~[rendering.jar:na]
        at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) ~[rendering.jar:na]
        at ome.services.ThumbnailBean.createScaledImage(ThumbnailBean.java:610) ~[server.jar:na]
        at ome.services.ThumbnailBean._createThumbnail(ThumbnailBean.java:818) ~[server.jar:na]
        at ome.services.ThumbnailBean.retrieveThumbnail(ThumbnailBean.java:1061) ~[server.jar:na]
        at ome.services.ThumbnailBean.retrieveThumbnailAndUpdateMetadata(ThumbnailBean.java:1016) ~[server.jar:na]

[jamoore]

Melissa, do you have any initial ideas on this?

[mlinkert]

Only thing I can think of here is that there is a mismatch between the ZCT dimensions in the DB and the dimensions provided by the reader/memo file. Current dev_5_0 shows SizeZ = 53 when calling setId, and that seems to match what I see in the memo file. I'm having difficulty logging in to the web client or postgres to verify that the DB values are different, though.

[jamoore]

From web:

Owner:	Niko Surname
Acquisition Date:	2014-01-20 16:17:41
Imported Date:	2014-03-25 19:00:04
Dimensions (XY):	993 x 992
Pixels Type:	uint16
Pixels Size (XYZ) (µm):	
0.11 x 0.11 x 0.75
Z-sections/Timepoints:	53 x 204
Channels:	
0, 1

[mlinkert]

PR opened: ​https://github.com/openmicroscopy/bioformats/pull/1094