Posted by
Peter Haub on
Mar 09, 2015; 12:24pm
URL: http://imagej.273.s1.nabble.com/TrakEM2-Stitching-overlapping-images-from-coordinates-tp5011918p5011920.html
Hi Andre
and everybody who may concerned,
we are also facing a memory problem stitching 4000 images using the
Grid/Collection stitching plugin.
Our 8bit image has a size of more then 12 GByte (or > 12 GPixel).
I wonder if this could have something to do with the integer type
definition of the 'index' variable in the ByteArray.setValue function:
public void setValue( final int index, final byte value )
The error message is:
(Fiji Is Just) ImageJ 2.0.0-rc-23/1.49m; Java 1.6.0_24 [64-bit]; Windows
7 6.1; 16857MB of 20000MB (84%)
java.lang.ArrayIndexOutOfBoundsException: -1741201634
at
net.imglib2.img.basictypeaccess.array.ByteArray.setValue(ByteArray.java:68)
at
net.imglib2.type.numeric.integer.GenericByteType.setValue(GenericByteType.java:101)
at
net.imglib2.type.numeric.integer.UnsignedByteType.set(UnsignedByteType.java:161)
at
net.imglib2.type.numeric.integer.UnsignedByteType.setInteger(UnsignedByteType.java:179)
at
net.imglib2.type.numeric.integer.AbstractIntegerType.setReal(AbstractIntegerType.java:67)
at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:1017)
at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:972)
at mpicbg.stitching.fusion.Fusion.writeTile(Fusion.java:977)
at mpicbg.stitching.fusion.Fusion.writeBlock(Fusion.java:916)
at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:224)
at plugin.Stitching_Grid.run(Stitching_Grid.java:590)
Regards,
Peter
On 09.03.2015 04:26, Andre Pereira wrote:
> Hi everybody,
>
> We are trying to stitch a very large dataset (~90GB) of overlapping images. We used the Grid/collection stitching plugin, which was able to stitch the images correctly in smaller datasets, but we ran into memory problems with the larger ones. We then switched to TrakEM2 which is doing a great job at handling the large ones.
>
> We are, however, facing a problem with the positioning of the tiles. After importing the images using a text file with the coordinates, the tiles are not positioned in the exact position. There is a small, but important shift. We verified our coordinates in the text file and they are correct. Our reconstructions with the Grid/collection stitching plugin, for instance, are accurate.
>
> Has anyone had this problem before?
>
> Thanks for your help!
>
> Kind regards,
> Andre Pereira
>
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