[Insight-users] ITK image to Numpy matrix and viceversa

[Bradley Lowekamp]

Paolo,

You are correct with the command line: 

git://github.com/tobiasmaier/itkPyBuffer.git Modules/External/itkPyBuffer


When you place an ITK module into the ITK External or Remote subdirectory, it become just like the build-in ITK modules. It gets built along side of the rest of ITK, and also will get wrapped for this case.


After running the above command, I re-ran ccmake and it informed me that PYTHON_NUMARRAY_INCLUDE_DIR, needed to be defined.

The variable that needs to be set is Module_ITKBufferConvertion. This should be enabled. I thought this use to come up in the CMake GUI, but it did not for me. I had to go into the CMakeCache.txt file and manually change the variable to ON to enable it.

Hope that helps,
Brad

On Jan 30, 2013, at 8:57 AM, Paolo Zaffino <p.zaffino at yahoo.it> wrote:

> Dear Brad,
> thanks for your answer but I'm not yet able to get working that module.
> First I think that the command is git clone git://github.com/tobiasmaier/itkPyBuffer.git Modules/External/itkPyBuffer, right?
> Anyway I didn't understand how compile it, if I have to compile it before ITK or if it will be compiled during the itk building.
> The problem is that I don't see the option to enable itkPyBuffer in the cmake step for ITK.
> 
> Yes, I know of simpleITK, but in this case I need of ITK...anyway thanks for the advice.
> 
> Thanks a lot.
> Paolo
> 
> 
> 
> 
> Il 29/01/2013 15:20, Bradley Lowekamp ha scritto:
>> Hello Paolo,
>> 
>> I have used the the following external module for get numpy support for WrapITK:
>> 
>> https://github.com/tobiasmaier/itkPyBuffer
>> 
>> 
>> From the root ITK source dir just clone the repo into the Modules/External directory:
>> 
>> git clone git://github.com/tobiasmaier/itkPyBuffer.git Modules/External/
>> 
>> Rerun ccmake, and turn on this module. And recompile.
>> 
>> 
>> While you are waiting you can check to see if SimpleITK has the functionality you need.
>> I'd like to point out that SimpleITK has built in support for numpy, and has binary eggs available for download. 
>> http://www.itk.org/Wiki/ITK/Release_4/SimpleITK
>> 
>> Brad
>> 
>> On Jan 29, 2013, at 8:46 AM, Paolo Zaffino <p.zaffino at yahoo.it> wrote:
>> 
>>> Dear ITK community,
>>> 
>>> I compiled ITK 4.3.1 with the Python support and all went fine.
>>> I am able to run ITK functions from Python, but I'm also interested in converting an ITK image into a Numpy matrix and viceversa.
>>> How can I do this?
>>> 
>>> Thank you very much.
>>> Regards.
>>> Paolo
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