[ITK-users] compressing MetaImages bigger than 4GB leads to data loss

[Bradley Lowekamp]

Please try compiling with ITK_USE_64BITS_IDS OFF, this flag is only needed for windows 64.

Brad

On Jun 25, 2014, at 8:59 AM, Dr. Roman Grothausmann <grothausmann.roman at mh-hannover.de> wrote:

> On 25/06/14 14:51, Dr. Roman Grothausmann wrote:
>> Dear Brad,
>> 
>> On 25/06/14 14:24, Bradley Lowekamp wrote:
>>> That sounds like a bug to me. What OS? version of ITK? Are you using ITK's zlib?
>> 
>> Linux, Debian 7.2, self compiled itk-4.5.1 (problem also exists with itk-4.4.0),
>> I tried both ITK's zlib and system zlib, same problem for both.
> 
> Forgot:
> uname -a
> Linux imgserv0 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3+deb7u2 x86_64 GNU/Linux
> 
> itk configured with:
> ITK_USE_64BITS_IDS               ON
> 
> So files bigger than 4GB can be handled, just the compression seems to be affected.
> 
> 
>> 
>> I also tested system libtiff. In that case the ITKwriter/libtiff throws an error
>> that the file is too large for the TIFF-Standard, just as it should be.
>> 
>> Many thanks for looking into this.
>> Roman
>> 
>>> On Jun 25, 2014, at 8:16 AM, Dr. Roman Grothausmann
>>> <grothausmann.roman at mh-hannover.de> wrote:
>>> 
>>>> Dear mailing list members,
>>>> 
>>>> 
>>>> Working with a labelled tomogram that is larger than 4GB made me realize that
>>>> when saving the data as a compressed MetaImage (mhd) leads to a complete data
>>>> loss. It seems the way libz is used that files bigger than 4GB are compressed
>>>> incorrectly. If that's not possible the itkFileWriter should issue an error
>>>> in case an image is bigger than 4GB. So far it just goes on as if nothing
>>>> would be wrong and only when opening the image again the reader reports that
>>>> "Uncompress failed".
>>>> Is this a bug?
>>>> 
>>>> Just as a side node: writing the same file as a compressed TIFF works fine,
>>>> though e.g. imagej/fiji opens the file with MSB swapped.
>>>> 
>>>> Any help or hints are very much appreciated
>>>> Roman
>>>> 
>>>> --
>>>> Dr. Roman Grothausmann
>>>> 
>>>> Tomographie und Digitale Bildverarbeitung
>>>> Tomography and Digital Image Analysis
>>>> 
>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover
>>>> Carl-Neuberg-Str. 1
>>>> D-30625 Hannover
>>>> 
>>>> Tel. +49 511 532-9574
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>> 
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>> 
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> 
>> 
> 
> -- 
> Dr. Roman Grothausmann
> 
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
> 
> Institut für Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
> 
> Tel. +49 511 532-9574