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

[Hadrien Mary]

PS: I have many files like this. If you know a quick script which
could clean up theses files, it would be awesome !

--
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 3:41 PM, Hadrien Mary <hadrien.mary at gmail.com> wrote:
> Ok I get it. I was drag and droping my file to Fiji menu bar. So I
> guess this bug happens only when an OME TIFF file is opened with
> SCIFIO. I confirm it works if I open the file with BF importer.
>
> In case it helps I attached to this mail the result of a tiffdump.
>
> --
> 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 3:32 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>> Hi Hadrien,
>>
>>> Are you sure your BF version in Fiji is 5.0 and not 5.1 ? Version
>>> provided by BF update site is 5.0.6-DEV.
>>
>> 5.0.6-DEV, 2fdc56c, built 2015-Jan-22.
>>
>> run("Bio-Formats Importer", "open=/Users/curtis/Desktop/test.ome.tif
>> autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
>> run("Bio-Formats Exporter", "save=/Users/curtis/Desktop/bf-exporter.ome.tif
>> compression=Uncompressed");
>>
>> Both test and bf-exporter files are 28MB.
>>
>> OS X 10.10.1, Java 1.6.0_65 [64-bit]
>>
>> Maybe try dumping the output file using tiffdump (part of the libtiff CLI)
>> to see what's bloating the file so much?
>>
>> Regards,
>> Curtis
>>
>> On Tue, Jan 27, 2015 at 3:17 PM, Hadrien Mary <hadrien.mary at gmail.com>
>> wrote:
>>>
>>> Thank you both for the answer.
>>>
>>> It's weird because the filesize is correct if I use bfconvert (coming
>>> from OME 5.1.0-m1, 3 October 2014). But I just reinstalled Fiji and
>>> enable BF update site but I still have an oversized file using BF
>>> exporter... I didn't check any options when exporting (single file and
>>> uncompressed).
>>>
>>> Are you sure your BF version in Fiji is 5.0 and not 5.1 ? Version
>>> provided by BF update site is 5.0.6-DEV.
>>>
>>> --
>>> 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 3:01 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>> > Hi Hadrien,
>>> >
>>> >> I use BF exporter to save it, the created file is exactly the same
>>> >> (dimensions and OME XML string) but the size is really huge (654.8MB).
>>> >
>>> > I cannot reproduce this problem with the latest version of Bio-Formats
>>> > from
>>> > the Bio-Formats update site.
>>> >
>>> > I tried saving your file using the Bio-Formats Exporter, as well as
>>> > "converting" it to another OME-TIFF using the bfconvert command line
>>> > tool.
>>> > Here are my results:
>>> >
>>> > 29592020 test.ome.tif
>>> > 29560221 bf-exporter.ome.tif
>>> > 29558724 bfconvert.ome.tif
>>> >
>>> > The bfconvert used was a 2014-Dec-5 build of the develop branch. The
>>> > Bio-Formats version in ImageJ was updated from the BF update site within
>>> > the
>>> > past few days.
>>> >
>>> > Is your installation fully up to date? Which options did you have
>>> > checked
>>> > when exporting? Etc.
>>> >
>>> > Regards,
>>> > Curtis
>>> >
>>> > On Tue, Jan 27, 2015 at 10:56 AM, Hadrien Mary <hadrien.mary at gmail.com>
>>> > wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> I have an OME TIFF file (generated by Micro-Manager). It's original
>>> >> size is 29.6MB. Now if I use BF exporter to save it, the created file
>>> >> is exactly the same (dimensions and OME XML string) but the size is
>>> >> really huge (654.8MB).
>>> >>
>>> >> The file can be found here:
>>> >>
>>> >>
>>> >> https://arwen.hadim.fr/public.php?service=files&t=80e1586f55c8795c0c1c86e96aac7281
>>> >>
>>> >> This issue happens with other files as well.
>>> >>
>>> >> Thanks
>>> >>
>>> >> --
>>> >> 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
>>> >> _______________________________________________
>>> >> ome-devel mailing list
>>> >> ome-devel at lists.openmicroscopy.org.uk
>>> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>> >
>>> >
>>> >
>>> > _______________________________________________
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>>> > ome-devel at lists.openmicroscopy.org.uk
>>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>> >
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>>
>>
>>
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