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

[Hadrien Mary]

Thanks all. Discussion is moved to https://github.com/scifio/scifio/issues/255.

--
Hadrien Mary

Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088

Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse


On Tue, Jan 27, 2015 at 7:32 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> 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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>
>