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

[Dr. Roman Grothausmann]

On 25/06/14 15:16, Bradley Lowekamp wrote:
> Please try compiling with ITK_USE_64BITS_IDS OFF, this flag is only needed for windows 64.

I just did, sadly the problem is still there.
I chose ITK_USE_64BITS_IDS ON because vtk needs it to be able to cope with files 
bigger than 4GB. How comes linux doesn't need it?

> 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
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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
>

-- 
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