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

[Curtis Rueden]

Hi Hadrien & Melissa,

> 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.

It's certainly not desirable behavior... so Hadrien, feel free to file an
issue on scifio/scifio on GitHub.

Regards,
Curtis

On Tue, Jan 27, 2015 at 7:21 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> 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()
> > -------------------------------
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