[MINC-development] large attributes in MINC2 and upgrading to HDF5 version 1.8

[Soren Christensen]

Thanks. I have previously run into problems with this, when MINC2 was
compiled against a different HDF version from that of ITK. Is there a good
way to deal with that then?  Libminc in it's current form cannot build with
the HDF in ITK can it?
I suppose one can try to build both ITK and libMINC against the same system
HDF, but the less one can leave ITK to it's default set up the better I
guess, less problems.
Sorry for the many questions - just exited about that fix as it will save
me a lot of headaches.

Thanks
Soren


On Wed, Nov 27, 2013 at 10:19 AM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:

> Hello,
>
> you will have to compile latest version of libminc and then specify
> ITK_USE_SYSTEM_MINC and LIBMINC_DIR when building ITK.
>
> I can also try to include this version of libminc in next release of ITK
> ,if nobody objects.
>
>
> On 13-11-27 01:15 PM, Soren Christensen wrote:
>
>> Hi Vladimir,
>>   That sounds great. I've had that problem too. What is the easiest way
>> to propagate your changes to ITK?  Is it to somehow merge locally with
>> the ITK release branch or is there a better way?
>>
>> Thanks
>> Soren
>>
>>
>> On Wed, Nov 27, 2013 at 10:07 AM, Vladimir S. FONOV
>> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
>>
>>     Hello Everybody,
>>
>>     I came across a problem in MINC2 , that total size of attributes for
>>     group was limited to 64k , which was creating problems in storing
>>     some dicom tags, for example dicom_0x0029:el_0x1020 is sometimes
>>     quite big, so together with other tags it would overfill 64k limit
>>     and cause problems.
>>
>>     The problem didn't happen with MINC1 which didn't seem to have this
>>     limitation.
>>
>>     The solution for this problem is explained in
>>     http://www.hdfgroup.org/HDF5/__doc/UG/13_Attributes.html
>>
>>     <http://www.hdfgroup.org/HDF5/doc/UG/13_Attributes.html> , see
>>     "Large Attributes Stored in Dense Attribute Storage ". Unfortunately
>>     it creates a minc file which requires one to use HDF5 version 1.8 ,
>>     so potentially files with such large attributes will not be readable
>>     by minc compiled with HDF5 version 1.6 ( minc 2.0, I suppose).
>>
>>     I made changes and also created a couple of new test cases in
>>     HDF5_large_attribute  branch of libminc:
>>     https://github.com/BIC-MNI/__libminc/tree/HDF5_large___attribute
>>
>>     <https://github.com/BIC-MNI/libminc/tree/HDF5_large_attribute>
>>
>>
>>     Unless there are some objections, I will merge it into the develop
>>     branch of libminc (which is supposed to become libminc release
>>     2.3.00 sometime soon).
>>
>>     --
>>     Best regards,
>>
>>       Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com <http://gmail.com
>> >
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>>
>>
>>
>>
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>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
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