Greetings!
I've been troubleshooting a problem that exists when trying to use images
generated by Genepix 6.0/6.1 as images for spots.
Genepix generates a single, multi-image, 16 bit greyscale TIFF. It's
composition is as follows:
Index Description
1 635 preview (495x1396 pixels)
2 532 preview (495x1396 pixels)
3 635 image (1884x5472 pixels)
4 523 image (1884x5472)
The image offsets and scales are found in the .gpr file that Genepix
creates. I used those numbers to try to use the single-image tiff for spots
but most of the time it failed with an exception that I described in
previous posts:
java.lang.ClassCastException: [[B
at
com.sun.media.jai.opimage.BandMergeOpImage.shortLoop(BandMergeOpImage.java:3
41)
Once in a while, though, it would succeed but the spots would be tiny in the
images.
This is because BASE2 is using indices 1 and 2 for the images in a
multi-image tiff. In the case of GenePix 6.0/6.1 these are preview images.
If you select 'Export Images' in Genepix 6.0/6.1 it does not do what you
expect. I would expect that it would run it's own version of tiffsplit and
generate two 16-bit greyscale tiffs.
It actually creates two RGB images with 8 bits in the appropriate colour
channel - red or green. These images cannot be imported into BASE (they
provide the same exception as above).
The reason why this exception is so mysterious can be balmed on JAI. IN
core/net/sf/basedb/core/SpotImages.java the method
In private RenderedOp loadTiffImage(File file, int band)
executes this:
RenderedOp image = JAI.create("tiff", params);
For the single-image tiffs described above, this call returns the equivalent
of an empty image:
(PlanarImage[minX=0 minY=0 width=0 height=0 tileGridXOffset=0
tileGridYOffset=0 tileWidth=0 tileHeight=0 sampleModel=null
colorModel=null])
It's my opinion that this should somehow throw an exception either through
JAI or have this condition be trapped by BASE because, well, the call
CLEARLY failed.
Can a developer have this throw an exception? It would make image parsing
problems MUCH easier to find.
RIGHT! Let's return to the problem of the images.
As a user of Genepix, I cannot change it's exporting behavior. However,
when I use 'tiffsplit' on the commandline to split the GenePix multi-image
tiff and import each image (full-size, not preview) into BASE2 separately
everything works. This implies that there is not a fundamental problem with
the individual GenePix images (as found in the multi-image tiff).
BASE1 had a feature in 'Create Spot Images' that allowed you to specify:
'Index of ch1 TIFF'
'Index of ch2 TIFF'
Can you please bring back this feature in BASE2? In the meantime I will
modify our local copy to do this without prompting.
Thanks for your efforts!
Chad Matsalla
Plant Biotechnology Institute, National Research Council of Canada
Saskatoon, Saskatchewan, Canada
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