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fiji / Stitching

Fiji's Stitching plugins reconstruct big images from tiled input images.
http://imagej.net/Stitching
GNU General Public License v2.0
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Odd File not Found Error #43

Open lacan opened 7 years ago

lacan commented 7 years ago

Hi

I have files that have a particular name r02c02f01p01-ch1sk1fk1fl1.tiff Which I feed into the stitcher with r02c02f{ii}p01-ch1sk1fk1fl1.tiff because I have 9 fields and they are a 3x3 stitch.

However when it tries to load the first tile, I get this error

OperettaReader initializing X:\Joao\PE\assay1__2017-07-27T14_54_29-Measurement 1\Images\r02c02f01p01-ch1sk1fk1fl1.tiff
java.io.FileNotFoundException: X:\Joao\PE\assay1__2017-07-27T14_54_29-Measurement 1\Images\r07c02f02p01-ch1sk1fk1fl1.tiff (The system cannot find the file specified)

Why is it trying to load r07c02f02p01-ch1sk1fk1fl1.tiff when I never specified this as being a variable?

These images are on a share that is mounted on a windows machine...

If I copy the files locally, it works...

this is very odd and cannot make heads or tails of it. Any help is greatly appreciated.

Oli

imagejan commented 7 years ago

That's very odd indeed. I'd say this seems to be more likely a Bio-Formats issue (and I know that bio-formats tries to load group files when used with the standard BF.openImagePlus call that is used in the stitching plugin). Did you try what happens if you load the file manually using the loci.plugins.BF class?