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Michael Ebner edited this page Oct 30, 2018 · 61 revisions

ITK_NiftyMIC:

This repository contains numerous additional filters and functions to extend the standard WrapITK Release 4.13. Its installation is a necessary requirement in order to use NiftyMIC and related research-focused toolkits within the GIFT-Surg project.

The installation as described here was tested for Python 2 and 3 on

  • Ubuntu 16.04

using

  • CMake 3.11.0 and 3.12.3

Compilation

Clone this repository and prepare for an out-of-source build by executing

  • git clone [email protected]:gift-surg/ITK_NiftyMIC.git
  • mkdir ITK_NiftyMIC-build
  • cd ITK_NiftyMIC-build

In case you want to use a Python environment, activate it first before you proceed. Additionally, make sure that NumPy is installed (pip install numpy --upgrade).

Then compile ITK_NiftyMIC -- including Python wrapping -- by running

cmake \
  -D CMAKE_BUILD_TYPE=Release \
  -D BUILD_TESTING=OFF \
  -D BUILD_EXAMPLES=OFF \
  -D BUILD_SHARED_LIBS=ON \
  -D ITK_WRAP_PYTHON=ON \
  -D ITK_LEGACY_SILENT=ON \
  -D ITK_WRAP_float=ON \
  -D ITK_WRAP_double=ON \
  -D ITK_WRAP_signed_char=ON \
  -D ITK_WRAP_signed_long=ON \
  -D ITK_WRAP_signed_short=ON \
  -D ITK_WRAP_unsigned_char=ON \
  -D ITK_WRAP_unsigned_long=ON \
  -D ITK_WRAP_unsigned_short=ON \
  -D ITK_WRAP_vector_float=ON \
  -D ITK_WRAP_vector_double=ON \
  -D ITK_WRAP_covariant_vector_double=ON \
  -D Module_ITKReview=ON \
  -D Module_SmoothingRecursiveYvvGaussianFilter=ON \
  -D Module_BridgeNumPy=ON \
  ../ITK_NiftyMIC/

make -j8

Once the compilation is finished (which can take a couple of hours), the ITK path file needs to be linked so that Python can access it.

Linking

  • Link Python libraries:

    • Virtual environment is used:
      • cp Wrapping/Generators/Python/WrapITK.pth path-to-venv/lib/python*/site-packages/
    • No virtual environment:
      • SITEDIR=$(python -m site --user-site)
      • mkdir -p "$SITEDIR"
      • cp Wrapping/Generators/Python/WrapITK.pth $SITEDIR

  • If NiftyMIC is to be installed:

    • export NIFTYMIC_ITK_DIR=absolute-path-to-ITK_NiftyMIC-build

Usage

ITK_NiftyMIC should now be available in Python. Check it by opening Python and run

  • import itk
  • print(itk.Image.D3.New())
  • print(itk.OrientedGaussianInterpolateImageFilter.ID3ID3.New())

In case everything went fine without any error you are ready to go to use ITK_NiftyMIC within Python now.

Funding

This work is partially funded by the UCL Engineering and Physical Sciences Research Council (EPSRC) Centre for Doctoral Training in Medical Imaging (EP/L016478/1), the Innovative Engineering for Health award (Wellcome Trust [WT101957] and EPSRC [NS/A000027/1]), and supported by researchers at the National Institute for Health Research University College London Hospitals (UCLH) Biomedical Research Centre.

Known issues

ITK_NiftyMIC currently is based on ITK 4.13 code. Given the very active development of ITK some of the previously used download links during compilation time were outdated. Associated problems should now have been fixed. Plans to upgrade to the current ITK version are made but this might take some more time.

Error: Protocol "https" not supported or disabled in libcurl

If this error occurs please reinstall curl with https functionality as described, e.g., here

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