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

[Bill Lorensen]

>From the zlib FAQ:
http://www.zlib.net/zlib_faq.html#faq32


On Wed, Jun 25, 2014 at 9:52 AM, Dr. Roman Grothausmann
<grothausmann.roman at mh-hannover.de> wrote:
> 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
>>>>>> _____________________________________
>>>>>> 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
>>
>>
>
> --
> 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



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