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

[Curtis Rueden]

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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