Installing ITK wrappers for Python (ITKv3)

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Installing ITK wrappers for Python (ITKv3)¶

This is quite some work and absolutely not fail-save. Only try it, if you must (or are bored with too much time at hand).

1. Installing ITK with Python binding on Ubuntu (>= 10.04)¶

The Ubuntu repositories provide a package which can simply be installed using:

sudo apt-get install python-insighttoolkit3

But this package wraps only a subset of ITKs functionality and therefore does not unleash MedPy s complete power. The recommendation is to follow the second or third approach.

2. Installing ITK with Python binding on Ubuntu (= 12.04)¶

If you are running Ubuntu 12.04, you can simply contact the author who will provide you with a pre-compiled Ubuntu package.

3. Compiling ITK with Python bindings on POSIX/Unix platforms¶

All descriptions are for ITK 3.20 but might also be valid for newer versions.

Getting ITK¶

Got to http://www.itk.org/ITK/resources/software.html , download the InsightToolkit-3.20.1.tar.gz resp. InsightToolkit-3.20.1.zip archive and unpack it to a folder called somthing like IKT3.20.1/src.

Configuring ITK¶

Compiling ITK requires cmake which can be found for almost all platforms. Create a new directory IKT3.20.1/build and enter it. Then run:

ccmake ../src

and subsequently hit the c key to configure the build. When finished, hit the t key to toggle the advanced mode and activate the following options:

BUILD_SHARED_LIBS ON
ITK_USE_REVIEW    ON
USE_WRAP_ITK      ON

, then c onfigure again. Ignore the warning by pressing e. Now set the following options:

WRAP_FFT            OFF
WRAP_ITK_DIMS       2;3;4 (or more, if you require)
WRAP_ITK_JAVA       OFF
WRAP_ITK_PYTHON     ON
WRAP_ITK_TCL        OFF

WRAP_double         ON
WRAP_float          ON
WRAP_signed_char    ON
WRAP_signed_long    ON
WRAP_signed_short   ON
WRAP_unsigned_char  ON
WRAP_unsigned_long  ON
WRAP_unsigned_short ON
WRAP_<datatype>   Select yourself which more to activate.

, and c onfigure another time. Finally press g to generate the make-file.

If cmake signals any errors during the configuration process, try to resolve the dependencies from which they originate.

Compiling ITK¶

Now that the configuration is done, we can compile ITK. Run:

make -j<number-of-your-porcessors>

and wait. This will take some time, depending on your computer up to 2 days are not unlikely.

If an error occurs, try to understand it and eventually re-run the previpous step with some options changed.

Installing ITK¶

Install ITK and its Python bindings simply by running:

make install (as root)

Addditional step¶

The ITK Python bindings require a third-party module called PyBuffer which is shipped with ITK but not automatically compiled. Furthermore it holds a small bug. After finishing the previous steps, create a folder called PyBuffer/src somewhere and copy all files and folders from ITK/src/Wrapping/WrapITK/ExternalProjects/PyBuffer/ into it. Now open itkPyBuffer.txx with an text editor and change the line:

int dimensions[ ImageDimension ];

to:

npy_intp dimensions[ ImageDimension ];

(see http://code.google.com/p/wrapitk/issues/detail?id=39 for patch details). Then create a folder PyBuffer/build, enter it and run:

ccmake ../src

After c onfiguring you will see some warnings. Set:

WrapITK_DIR     ITK/bin/Wrapping/WrapITK/

In some cases you will also have to set:

PYTHON_NUMARRAY_INCLUDE_DIR     /usr/include/numpy

Now c onfigure again and g enerate. To finalize run:

.. code-block:: bash

make make install (as root)

Congratulations, you are done compiling and installing ITK with Python wrappers.

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