[ome-devel] BF exporter create big ome.tif file

[Melissa Linkert]

Hi Hadrien,

> Is that an excepted behaviour ? If it does not, should I open a ticket for it ?

The Bio-Formats exporter behavior is expected.

> Is this behaviour to add colormap to each plane a feature or a bug of
> SCIFIO ? If it is a bug should I report it to SCIFIO or you guys take
> care of it ?

I don't know if that is the expected behavior during import; as that's
not part of Bio-Formats, you would need to contact the SCIFIO developers
to find out if it should be fixed.

Regards,
-Melissa

On Tue, Jan 27, 2015 at 06:56:16PM +0100, Hadrien Mary wrote:
> Thank you Melissa. Unfortunately the trick with "Stack to Hyperstack"
> and "Hyperstack to Stack" is failing sometime (I don't know why)...
> Anyway I wrote a small python script which just load the file and save
> it while preserving the OME XML string and it seems to work pretty
> well. I paste it at the end of this mail.
> 
> Is this behaviour to add colormap to each plane a feature or a bug of
> SCIFIO ? If it is a bug should I report it to SCIFIO or you guys take
> care of it ?
> 
> -------------------------
> %load_ext autoreload
> %autoreload 2
> 
> import os
> import gc
> 
> # Just load tifffile.py from somewhere
> from sktracker.io import TiffFile, imsave
> 
> data_path = "/home/hadim/Documents/phd/data/test"
> 
> for root, dirs, files in os.walk(data_path):
>     for f in files:
>         if f.endswith('ome.tif'):
>             fname = os.path.join(root, f)
>             print(fname)
>             tf = TiffFile(fname)
>             p = tf.pages[0]
> 
>             new_path = os.path.join(os.path.dirname(fname), "fixed",
> os.path.basename(fname))
>             if not os.path.isdir(os.path.join(os.path.dirname(fname), "fixed")):
>                 os.makedirs(os.path.join(os.path.dirname(fname), "fixed"))
> 
>             imsave(new_path, tf.asarray(),
> description=p.tags['image_description'].value)
>             del p
>             del tf
>             gc.collect()
> -------------------------------