Bug: mias One MNU plate

[jburel]

Import One MNU plate

[mlinkert]

Appears to be a duplicate of #9077.

[jburel]

Oops
I pasted the wrong error. The error occurred while parsing the ROI.More details tomorrow I used another computer to import

[jburel]

This time with correct error

java.lang.IndexOutOfBoundsException: Index: 61, Size: 60
	at java.util.ArrayList.RangeCheck(Unknown Source)
	at java.util.ArrayList.get(Unknown Source)
	at ome.formats.OverlayMetadataStore.setImageROIRef(OverlayMetadataStore.java:145)
	at loci.formats.meta.FilterMetadata.setImageROIRef(FilterMetadata.java:1272)
	at loci.formats.in.MIASReader.parseMasks(MIASReader.java:1080)
	at loci.formats.in.MIASReader.initFile(MIASReader.java:833)
	at loci.formats.FormatReader.setId(FormatReader.java:1092)
	at ome.formats.importer.ImportLibrary.importOverlays(ImportLibrary.java:384)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:706)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6253)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:200)
	at

[mlinkert]

I couldn't duplicate this exception using the latest build (OMERO.insight-4.3.3-2997-d4ecc78-ice33-b80), and comparing ome.formats.OverlayMetadataStore? on sprint17-bugfixes with the line numbers here it looks like you shouldn't be able to get that stack trace at all with sprint17-bugfixes merged into develop.

Is there any chance that an older version of Insight was used here? If not, is there anything special that needs to be done to reproduce the problem? I was just importing One MNU Plate/001/Well0014/mode1_z000_t000_im1_1.tif into a screen.

[jburel]

I tried again with today's build (OMERO.insight-4.3.3-3023-3bbdef2-ice33-b171-win) still the same error
I selected the folder 001 under One MNU Plate and started the import.

[jburel]

info found in the log

2012-06-08 13:52:48,498 INFO  [              loci.formats.FormatHandler] ( Thread-24) Building list of TIFF files
2012-06-08 13:52:57,330 INFO  [              loci.formats.FormatHandler] ( Thread-24) Populating core metadata
2012-06-08 13:52:57,446 INFO  [       loci.formats.in.MinimalTiffReader] ( Thread-24) Reading IFDs
2012-06-08 13:52:57,456 INFO  [       loci.formats.in.MinimalTiffReader] ( Thread-24) Populating metadata
2012-06-08 13:52:57,474 INFO  [              loci.formats.FormatHandler] ( Thread-24) Populating metadata hashtable
2012-06-08 13:52:57,474 INFO  [              loci.formats.FormatHandler] ( Thread-24) Populating MetadataStore
2012-06-08 13:52:57,767 WARN  [              loci.formats.FormatHandler] ( Thread-24) Could not determine the plate dimensions.

[mlinkert]

Fixed with: ​https://github.com/melissalinkert/bioformats/commit/3f3738f2cc6d3b8a8746e08b65cd2fb47bbfb1cb