[ome-devel] File conversion with RGB separation into multiple files does not work

[Simon Blanchoud]

Hi all,

For the purpose of my work, I'd need to convert a sequence of JPEG 
images into an OME-TIFF stack using the command line tools. Despite the 
original recording being in gray levels, I thus end-up with a sequence 
of RGB files. I thus wanted to use the -separate option of bfconvert to 
do the job (along with -stitch and -expand) but I've noticed the 
following bug (I've uploaded a test RGB tiff stack under QA 11043 that 
reproduces it):

So, if I run : "./bfconvert -stitch -expand -separate RGB_test.tif 
RGB.ome.tiff", I get what I would expect (i.e. a 3xN stack with R,G&B 
splitted, N here being the number of planes).

If I run : "./bfconvert -stitch -expand -separate -channel 0 
RGB_test.tif RGB_R.ome.tiff", I also do get the N stack of only the red 
channel that I would expect (or G or B if specified).

However, if I run : "./bfconvert -stitch -expand -separate RGB_test.tif 
RGB_%c.ome.tiff", I do not get 3 separated N stacks (as I would have 
expected, at least personally), but I get 3 times the same 3xN stack as 
in my first example.

Finally, if I run : "./bfconvert -stitch -expand -separate RGB_test.tif 
RGB_%w.ome.tiff", I end up with the exact same issue as above (plus, 
personally, I would think that the channels could be named RGB or some 
such, instead of 0,1,2).

I've been digging in the java code for a few days but could not find a 
fix yet. The only interesting point I could sort out is that it has to 
come from quite a low level as writing only one of the 3 channels does 
produce the expected output for that channel, and the writing of the 
plane data is called only the required amount of times. So there must be 
some cross-writing between the various files.

I'm working on a Mac OS X 10.10.2 with the latest Bio-Formats from the 
GitHub repository.

Cheers,
Simon Blanchoud
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