[ome-users] 5.0.0-rc1 on NDPI file: ImageConverter renders black bar in the right area of the image

[Kristian Kjærgaard]

Using loci_tools.jar from 5.0.0-rc1 to extract a 8192^2 pixel squared area
in the top right of AH09.ndpi (linked below), I see a black area in the
right part of the image. I'm sure its supposed to render the rest of the
image and not just a black rectangle.

My command:
java -mx2048m -cp loci_tools-5.0.0-rc1.jar
loci.formats.tools.ImageConverter -series 0 -crop 10240,0,8192,8192
AH09.ndpi tile.jpg

Response:
AH09.ndpi
NDPIReader initializing AH09.ndpi
Reading IFDs
Populating metadata
Populating OME metadata
[Hamamatsu NDPI] -> exports/tile.jpg [JPEG]
        Converted 1/1 planes (100%)
[done]
8.907s elapsed (1320.0+6361.0ms per plane, 1224ms overhead)
java -mx2048m -cp  loci.formats.tools.ImageConverter -series 0 -crop
9,78s user 0,86s system 84% cpu 12,529 total

I'm on Kubuntu 13.10 and java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.12) (7u25-2.3.12-4ubuntu3)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

I also tried using Oracle's java implementation: java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) 64-Bit Server VM (build 24.45-b08, mixed mode)

Both java VMs produce the same black area to the right.

Attached are: Link to original file and link to extracted tile.

I hope this information is useful and provided through the proper channels.
If not, please let me know.

--
Merry Christmas

 AH09.ndpi<https://docs.google.com/file/d/0B4ijDc1V08E3MlpvWTFKSG0tWEE/edit?usp=drive_web>

 tile.jpg<https://docs.google.com/file/d/0B4ijDc1V08E3ZC1HRFE4U2JsSEU/edit?usp=drive_web>

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