[ITK] [ITK-users] Big tiff file

[Dženan Zukić]

Perhaps the condition
<https://github.com/InsightSoftwareConsortium/ITK/blob/4456e0431b0d35f55eb1eadc5ca8a7c3fe2c8af9/Modules/IO/TIFF/src/itkTIFFImageIO.cxx#L595>
should be greater or equal? Because the equal case already wraps around
using signed arithmetic.

On Mon, Oct 23, 2017 at 9:15 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Hello,
>
> You have correctly figured this out. Technically the regular tiff format
> can support up to 4GB, but  in ITK we made the determination to switch to
> the BigTiff format at 2GB [1]. This is does to ensure that we can properly
> do signed integer arithmetic for the file format.
>
> I have also used ImageJ/FIJI and a program call IMOD [2] (another electron
> microscopy viewer) for viewing these big tiff files.
>
> HTH,
> Brad
>
> [1] https://github.com/InsightSoftwareConsortium/ITK/blob/
> 4456e0431b0d35f55eb1eadc5ca8a7c3fe2c8af9/Modules/IO/TIFF/
> src/itkTIFFImageIO.cxx#L595
> [2] http://bio3d.colorado.edu/imod/
>
> On 10/21/17, 8:40 PM, "Gib Bogle" <g.bogle at auckland.ac.nz> wrote:
>
>     I've managed to find the answer to one of my questions, by looking at
> the file header values.  A TIFF file less than 2GB has these 4 header bytes:
>     49 49 2A 00
>     and over 2GB (BigTIFF) has
>     49 49 2B 00
>     ITK handles this automatically.
>
>     I can view the big TIFFs with Fiji (ImageJ), so this is not a bad
> option for displaying the slices.  What I like about Irfanview is that it's
> very light-weight.  ImageJ loads the whole file into memory, which can take
> some time, while Irfanview loads one slice at a time.
>
>     I am not keen about Slicer - it is a real heavy-weight - and Tomviz is
> very specialised, designed for viewing tomography data, i.e. images in a
> tilt series.
>     ________________________________________
>     From: Matt McCormick <matt.mccormick at kitware.com>
>     Sent: Sunday, 22 October 2017 4:48 a.m.
>     To: Dženan Zukić
>     Cc: Gib Bogle; Insight-users
>     Subject: Re: [ITK-users] Big tiff file
>
>     Hi,
>
>     Since ITKv4, support for "BigTiff" was added, so ITK can support TIFF
>     files larger than 4GB.
>
>     One possible limitation may be the filesystem -- avoid FAT32 formatted
>     filesystem that will run into size limits.
>
>     The file could be viewed with a number of ITK-supported viewers, e.g.
>
>     - 3D-Slicer: https://www.slicer.org/
>     - ITK-SNAP: http://www.itksnap.org/
>     - Tomviz: http://www.tomviz.org/
>
>     HTH,
>     Matt
>
>     On Sat, Oct 21, 2017 at 11:40 AM, Dženan Zukić <dzenanz at gmail.com>
> wrote:
>     > Hi Gib,
>     >
>     > TIFF is limited to 4GiB. Unless you must use TIFF, better switch to
>     > MetaImage or NRRD.
>     >
>     > Regards,
>     > Dženan
>     >
>     > On Sat, Oct 21, 2017 at 12:08 AM, Gib Bogle <g.bogle at auckland.ac.nz>
> wrote:
>     >>
>     >> Hi,
>     >>
>     >>
>     >> I am joining a stack of 2D tiffs into a 3D tiff, and have run into a
>     >> problem with big files.  When the uncompressed size of the 3D file
> is more
>     >> than 2GB I get an error when I try to view it with Irfanview.  At
> first I
>     >> thought maybe I needed to upgrade from ITK4.8.0, but after
> installing and
>     >> using ITK4.12.2 I see that I have the same issue.  Irfanview says:
>     >>
>     >> "Invalid or unsupported TIF file"
>     >>
>     >> I now suspect that the problem is not ITK-related, rather it is a
>     >> limitation of Irfanview.
>     >>
>     >> I have two questions:
>     >>
>     >>
>     >> Is there a limit on the allowed size of a tiff file?
>     >>
>     >> Is there another program (preferably free) that can open for
> viewing tiff
>     >> files bigger than 2GB?
>     >>
>     >>
>     >> It is useful but not essential for me to be able to view these big
> 3D
>     >> files.  I will use ITK functions to process the 3D files, and I'm
> assuming
>     >> that any file that ITK can create it can also read.
>     >>
>     >>
>     >> Thanks
>     >>
>     >> Gib
>     >>
>     >>
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