From vladimir.fonov at gmail.com  Wed Nov 27 13:07:37 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 27 Nov 2013 13:07:37 -0500
Subject: [MINC-development] large attributes in MINC2 and upgrading to HDF5
	version 1.8
Message-ID: <529634E9.7040609@gmail.com>

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 , 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


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

From sorench at gmail.com  Wed Nov 27 13:15:46 2013
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 27 Nov 2013 10:15:46 -0800
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <529634E9.7040609@gmail.com>
References: <529634E9.7040609@gmail.com>
Message-ID: <CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>

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> 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 , 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
>
>
> 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
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
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From vladimir.fonov at gmail.com  Wed Nov 27 13:19:41 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 27 Nov 2013 13:19:41 -0500
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>
References: <529634E9.7040609@gmail.com>
	<CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>
Message-ID: <529637BD.5010004@gmail.com>

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>
>     _________________________________________________
>     MINC-development mailing list
>     MINC-development at bic.mni.__mcgill.ca
>     <mailto:MINC-development at bic.mni.mcgill.ca>
>     http://www.bic.mni.mcgill.ca/__mailman/listinfo/minc-__development
>     <http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>
>
>
>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com

From sorench at gmail.com  Wed Nov 27 13:39:17 2013
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 27 Nov 2013 10:39:17 -0800
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <529637BD.5010004@gmail.com>
References: <529634E9.7040609@gmail.com>
	<CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>
	<529637BD.5010004@gmail.com>
Message-ID: <CAHfsrRbb8Uut2uDhK-JTepwkaTNRa9bYq+ef7Pw5wVn3U=i5mg@mail.gmail.com>

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
>> >
>>     _________________________________________________
>>     MINC-development mailing list
>>     MINC-development at bic.mni.__mcgill.ca
>>     <mailto:MINC-development at bic.mni.mcgill.ca>
>>     http://www.bic.mni.mcgill.ca/__mailman/listinfo/minc-__development
>>     <http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development>
>>
>>
>>
>>
>>
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>
>>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>
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From vladimir.fonov at gmail.com  Wed Nov 27 15:13:30 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Wed, 27 Nov 2013 15:13:30 -0500
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <CAHfsrRbb8Uut2uDhK-JTepwkaTNRa9bYq+ef7Pw5wVn3U=i5mg@mail.gmail.com>
References: <529634E9.7040609@gmail.com>	<CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>	<529637BD.5010004@gmail.com>
	<CAHfsrRbb8Uut2uDhK-JTepwkaTNRa9bYq+ef7Pw5wVn3U=i5mg@mail.gmail.com>
Message-ID: <5296526A.80503@gmail.com>

Yes, it is easier to compile hdf5 separately in this case and tell itk 
to use it


On 13-11-27 01:39 PM, Soren Christensen wrote:
> 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 <mailto: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>
>         <mailto: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>
>
>              <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>
>
>
>         <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

From a.janke at gmail.com  Wed Nov 27 15:56:59 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 28 Nov 2013 06:56:59 +1000
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <529637BD.5010004@gmail.com>
References: <529634E9.7040609@gmail.com>
	<CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>
	<529637BD.5010004@gmail.com>
Message-ID: <CAG0CB20xD4i8eXsPjBAaS6Y0nN+xxNnKt1RpimYOgRdAEtLwNw@mail.gmail.com>

On 28 November 2013 04:19, 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.

I have no objections, This sort of change should also be pushed across
to the master branch along with all the other commits you have done as
of late so that we can tag and release a new version with all this in.
I am increasingly using the develop branch of libminc/minc-tools in
production now.



a

From vladimir.fonov at gmail.com  Thu Nov 28 13:36:33 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 28 Nov 2013 13:36:33 -0500
Subject: [MINC-development] large attributes in MINC2 and upgrading to
 HDF5 version 1.8
In-Reply-To: <CAG0CB20xD4i8eXsPjBAaS6Y0nN+xxNnKt1RpimYOgRdAEtLwNw@mail.gmail.com>
References: <529634E9.7040609@gmail.com>	<CAHfsrRYZ9DKh+yf7R1fy3Z1mdunWkVDXi3AhXzMpUD_6cTEaKg@mail.gmail.com>	<529637BD.5010004@gmail.com>
	<CAG0CB20xD4i8eXsPjBAaS6Y0nN+xxNnKt1RpimYOgRdAEtLwNw@mail.gmail.com>
Message-ID: <52978D31.9060009@gmail.com>

Hello,


ok, I merged changes into develop branch. Also I finally implemented an 
on-the-fly file format converter to be able to read MINC1 files using 
MINC2 API (by converting MINC1 file into MINC2 in /tmp first).

On 13-11-27 03:56 PM, Andrew Janke wrote:
> On 28 November 2013 04:19, 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.
>
> I have no objections, This sort of change should also be pushed across
> to the master branch along with all the other commits you have done as
> of late so that we can tag and release a new version with all this in.
> I am increasingly using the develop branch of libminc/minc-tools in
> production now.


-- 
Best regards,

  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com