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

[Dr. Roman Grothausmann]

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
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>

-- 
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