[ome-users] bfconvert of .r3d file

[Melissa Linkert]

Hi Alex,

Thank you for reporting this.

> We run bfconvert to convert .r3d files, (Deltavision, 32-bit floats) into tiff slices, as in
>
>     bfconvert -separate file.r3d slice.%c.%z.tiff
>
> for further processing. It works well under Ubuntu 14.04 but it chokes under Red Hat Enterprise Linux Server release 6.7 producing faulty tiff slices (pixel values are incorrect, e.g. all pixels have 65535). In my tests I use bfconvert versions 5.0.2 and 5.1.8 on both systems.

We're trying a few things to duplicate the problem now, but in the
meantime could you please confirm that the output of 'md5sum file.r3d'
is the same on both systems?  It would also be useful to know which
software is being used to validate the converted TIFF files, as that
may help to point us in the right direction.

Regards,
-Melissa

On Mon, Mar 7, 2016 at 7:01 PM, Alexandre Cunha <cunha at caltech.edu> wrote:
>
> Hi,
>
> We run bfconvert to convert .r3d files, (Deltavision, 32-bit floats) into tiff slices, as in
>
>     bfconvert -separate file.r3d slice.%c.%z.tiff
>
> for further processing. It works well under Ubuntu 14.04 but it chokes under Red Hat Enterprise Linux Server release 6.7 producing faulty tiff slices (pixel values are incorrect, e.g. all pixels have 65535). In my tests I use bfconvert versions 5.0.2 and 5.1.8 on both systems.
>
> I was wondering if this is a known problem on RedHat machines and/or .r3d files. Any advice?
>
> Many thanks,
> - Alex
>
> ---
>
> [607] : bfconvert -version
> Version: 5.1.8
> VCS revision: 9eb8da31c1f01989f439963b9cc215b4398bedd8
> Build date: 12 February 2016
>
> OR
>
> (bfconvert -version
> Version: 5.0.2
> VCS revision: 0c4215a
> Build date: 27 May 2014)
>
>
> lsb_release -a
>
> LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
> Distributor ID: RedHatEnterpriseServer
> Description:    Red Hat Enterprise Linux Server release 6.7 (Santiago)
> Release:        6.7
> Codename:       Santiago
>
> Distributor ID: Ubuntu
> Description:    Ubuntu 14.04.4 LTS
> Release:        14.04
> Codename:       trusty
>
>
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