A setup script to generate ITK Python Wheels

Related tags

Deep Learningpythoncmakecross-platformreproducible-researchimage-processingregistrationitkpython-wrappingsscikit-build
Overview

ITK Python Package

This project provides a setup.py script to build ITK Python binary packages and infrastructure to build ITK external module Python packages.

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.

Installation

To install the ITK Python package:

    $ pip install itk

Usage

Simple example script

    import itk
    import sys

    input_filename = sys.argv[1]
    output_filename = sys.argv[2]

    image = itk.imread(input_filename)

    median = itk.median_image_filter(image, radius=2)

    itk.imwrite(median, output_filename)

See also the ITK Python Quick Start Guide. There are also many downloadable examples documented in Sphinx.

For more information on ITK's Python wrapping, an introduction is provided in the ITK Software Guide.

Comments
  • Add support for shared libraries dependencies in remote modules

    Add support for shared libraries dependencies in remote modules

    We want to package the OpenCL ICD loader in particular in dependent remote modules.

    We can build on the shared library support in 5.3rc1 for TBB.

    For the platform-specific wheel fix-up tools, auditwheel (Linux), delocate (macOS), delvewheel (Windows) we need to add support for additional shared libraries. Mostly, this should be making the scripts that expose the path to local libraries with environmental variables allow appending to that variable, then set this variable to the path to the OpenCL ICD loader library in the remote module GitHub CI configuration.

    E.g.:

    https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/ad3f8d0c3dcb0e1b959924b4ceea8e832d612758/scripts/internal/manylinux-build-module-wheels.sh#L14

    ->

    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/work/oneTBB-prefix/lib64

    For Windows:

    https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/ad3f8d0c3dcb0e1b959924b4ceea8e832d612758/scripts/windows_build_wheels.py#L225-L228

    We may need to change this script to enable passing addition paths as a CLI argument. Also, we will likely need to adjust the strategy since delvewheel patches itk/__init__.py.

    For macOS:

    https://github.com/InsightSoftwareConsortium/ITKPythonPackage/blob/ad3f8d0c3dcb0e1b959924b4ceea8e832d612758/scripts/macpython-build-module-wheels.sh#L29

    opened by thewtex 17
  • Source path directory too long

    Source path directory too long

    When attempting to install via the pip: pip install itk

    I receive the following error:

    ITK source code directory path length is too long (${n} > 50).
Please move the ITK source code directory to a directory with a shorter path.

    According to this article (https://public.kitware.com/pipermail/community/2013-December/004475.html), the check is due to Visual Studio and truncation of commands.

    Is there a way to specify the build and install directory? In addition, the build files in skbuild are fairly long as it is so I could only place the ITKPythonPackage directory in my D: drive for it to work.

    If there is not a way to specify the build and install directory, I propose this option be added and documentation be added to the front page.

    opened by addisonElliott 14
  • COMP: Ensure tbb library is built with the expected deployment target

    COMP: Ensure tbb library is built with the expected deployment target

    This commit is a follow-up of these commits:

    • a5f774ba5 (ENH: Add TBB support to Linux wheels)
    • 374c744a1 (ENH: Add macOS wheel TBB support)
    • 037a326c1 (ENH: Build macOS module wheels with TBB support)

    It ensures that oneTBB is built specifying the non-default options expected by oneTBB ^1 and it should ensure the library can be loaded on macOS >= 10.9.

    See https://discourse.itk.org/t/itk-5-3rc4-post3-failure-to-load-libtbb-library-observed-on-macos-10-13/5405/1#suggested-path-forward-3

    opened by jcfr 13
  • delocate is failing on Python files

    delocate is failing on Python files

    Interestingly, delocate-listdeps has recently started to fail when building module packages:

    +/Users/Kitware/Dashboards/ITK/ITKPythonPackage/scripts/../venvs/2.7/bin/delocate-listdeps /Users/travis/build/InsightSoftwareConsortium/ITKRingArtifact/dist/itk_ringartifact-0.1.0-cp27-cp27m-macosx_10_6_x86_64.whl /Users/travis/build/InsightSoftwareConsortium/ITKRingArtifact/dist/itk_ringartifact-0.1.0-cp34-cp34m-macosx_10_6_x86_64.whl /Users/travis/build/InsightSoftwareConsortium/ITKRingArtifact/dist/itk_ringartifact-0.1.0-cp35-cp35m-macosx_10_6_x86_64.whl /Users/travis/build/InsightSoftwareConsortium/ITKRingArtifact/dist/itk_ringartifact-0.1.0-cp36-cp36m-macosx_10_6_x86_64.whl
/Users/travis/build/InsightSoftwareConsortium/ITKRingArtifact/dist/itk_ringartifact-0.1.0-cp27-cp27m-macosx_10_6_x86_64.whl:
Traceback (most recent call last):
  File "/Users/Kitware/Dashboards/ITK/ITKPythonPackage/scripts/../venvs/2.7/bin/delocate-listdeps", line 61, in <module>
    main()
  File "/Users/Kitware/Dashboards/ITK/ITKPythonPackage/scripts/../venvs/2.7/bin/delocate-listdeps", line 44, in main
    lib_dict = wheel_libs(path)
  File "/Users/kitware/Dashboards/ITK/ITKPythonPackage/venvs/2.7/lib/python2.7/site-packages/delocate/libsana.py", line 161, in wheel_libs
    lib_dict = tree_libs(tmpdir, filt_func)
  File "/Users/kitware/Dashboards/ITK/ITKPythonPackage/venvs/2.7/lib/python2.7/site-packages/delocate/libsana.py", line 54, in tree_libs
    for install_name in get_install_names(depending_libpath):
  File "/Users/kitware/Dashboards/ITK/ITKPythonPackage/venvs/2.7/lib/python2.7/site-packages/delocate/tools.py", line 173, in get_install_names
    if not _line0_says_object(lines[0], filename):
  File "/Users/kitware/Dashboards/ITK/ITKPythonPackage/venvs/2.7/lib/python2.7/site-packages/delocate/tools.py", line 143, in _line0_says_object
    raise InstallNameError('Unexpected first line: ' + line0)
delocate.tools.InstallNameError: Unexpected first line: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump: '/private/var/folders/bb/n7t3rs157850byt_jfdcq9k80000gn/T/tmp_NF5m6/itk/itkFourierStripeArtifactImageFilterPython.py': The file was not recognized as a valid object file

    CC: @jcfr @matthew-brett

    opened by thewtex 10
  • Add support for multiple manylinux versions

    Add support for multiple manylinux versions

    Motivation for this change is to build wheels with C++ ABI compatible with Slicer built using newer g++ having _GLIBCXX_USE_CXX11_ABI defaulting to 1.

    See https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html

    Note that the latest Slicer release (5.0) is built using centos7 based ^1 environment having _GLIBCXX_USE_CXX11_ABI set to 0.

    We should likely build wheels using both manylinux2014 and manylinux_2_28.

    As of 2022.06.22, this pull-request uses 2_24, as commented ^2 by @henryiii, I will instead update dockcross ^3 to add 2_28 based image (instead of 2_24).

    References:

    • https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_dual_abi.html
    • https://discuss.python.org/t/how-to-set-glibcxx-use-cxx11-abi-for-manylinux2014-and-manylinux2010-wheels/10551
    • https://github.com/pytorch/pytorch/issues/51039
    • https://github.com/pypa/manylinux/issues/1012
    • https://github.com/dockcross/dockcross/pull/705
    opened by jcfr 9
  • itkHelpers.py missing in itk python 5.2.0

    itkHelpers.py missing in itk python 5.2.0

    Unable to find itkHelpers.py in the installation and got python error: ModuleNotFoundError: No module named 'itkHelpers'

    itk python 5.2.0 installed via pip install itk

    opened by yliu7366 8
  • import _ITKPyBasePython failed

    import _ITKPyBasePython failed

    my Env: win10 64 bits python 3.6 itk 5.1.0

    my err: File "C:\Users\haoch\AppData\Local\Programs\Python\Python36\lib\site-packages\itk\Configuration..\ITKPyBasePython.py", line 15, in import _ITKPyBasePython ImportError: DLL load failed:

    when I use itk.imread(path),then the error occured what can I do?

    opened by xiaoxifei1223 8
  • Latest manylinux images missing `sudo`

    Latest manylinux images missing `sudo`

    Summary

    Local and CI tests in relation to https://github.com/InsightSoftwareConsortium/ITKPythonPackage/pull/233 fail to build on Linux. The issue appears to originate from the dockcross manylinux image.

    Observed behavior

    Building wheels for x64 using manylinux_2_28
++ type ninja
++ MANYLINUX_VERSION=_2_28
++ echo 'Building wheels for x64 using manylinux_2_28'
+ sudo ldconfig
/opt/rh/gcc-toolset-12/root/usr/bin/sudo: line 41: /usr/bin/sudo: No such file or directory
Error: Process completed with exit code 127.

    See log: https://github.com/InsightSoftwareConsortium/ITKSplitComponents/actions/runs/3583756532/jobs/6029570633

    Expected behavior

    Build succeeds.

    Steps to Reproduce

    > MANYLINUX_VERSION=_2_28
> IMAGE_TAG=20221128-2024e4b

# Generate dockcross scripts
> docker run --rm dockcross/manylinux${MANYLINUX_VERSION}-x64:${IMAGE_TAG} > /tmp/dockcross-manylinux-x64
> chmod u+x /tmp/dockcross-manylinux-x64

# Launch container
> /tmp/dockcross-manylinux-x64 bash

# Try to run any command with sudo
>> sudo ldconfig
/opt/rh/gcc-toolset-12/root/usr/bin/sudo: line 41: /usr/bin/sudo: No such file or directory

# Try to find sudo in /usr/bin
>> ls /usr/bin | grep sudo
# no results

    Other Notes

    Possibly related to the most recent image tag update: https://github.com/InsightSoftwareConsortium/ITKPythonPackage/pull/230

    Investigation shows that sudo works in the previous dockcross image:

    > IMAGE_TAG=20221108-102ebcc
> docker run --rm dockcross/manylinux${MANYLINUX_VERSION}-x64:${IMAGE_TAG} > /tmp/dockcross-manylinux-x64
> chmod u+x /tmp/dockcross-manylinux-x64
> /tmp/dockcross-manylinux-x64 bash
>> sudo ldconfig
>> sudo echo "sudo works"
sudo works
    opened by tbirdso 6
  • ENH: Add build script update step to download script

    ENH: Add build script update step to download script

    Several related updates:

    • Adds update step to apply build script patches to ITKPythonBuilds packages
    • Exposes manylinux parameters and resolves issue where wrong image was used with specialized tarballs
    • Reverts manylinux image tag while awaiting fix for sudo issue tracked in https://github.com/InsightSoftwareConsortium/ITKPythonPackage/issues/235 and https://github.com/dockcross/dockcross/issues/746

    These changes are tested at https://github.com/InsightSoftwareConsortium/ITKSplitComponents/actions/runs/3586129456

    opened by tbirdso 6
  • CMake version ignored

    CMake version ignored

    Despite explicitly getting CMake 3.24 in the CI, an older version is used during some stage resulting in insufficient version error:

    -- Configuring done
-- Generating done
-- Build files have been written to: /work/_cmake_test_compile/build
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
  CMake 3.24 or higher is required.  You are running version 3.23.1


-- Configuring incomplete, errors occurred!
  File "/opt/python/cp38-cp38/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 544, in setup
    env = cmkr.configure(cmake_args,
  File "/opt/python/cp38-cp38/lib/python3.8/site-packages/skbuild/cmaker.py", line 221, in configure
    raise SKBuildError(
An error occurred while configuring with CMake.
  Command:

    "cmake" "/work" "-G" "Ninja" "-DCMAKE_INSTALL_PREFIX:PATH=/work/_skbuild/linux-x86_64-3.8/cmake-install" "-DPYTHON_EXECUTABLE:FILEPATH=/opt/python/cp38-cp38/bin/python" "-DPYTHON_VERSION_STRING:STRING=3.8.13" "-DPYTHON_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.8.13/include/python3.8" "-DPYTHON_LIBRARY:FILEPATH=libpython3.8.a" "-DSKBUILD:BOOL=TRUE" "-DCMAKE_MODULE_PATH:PATH=/opt/python/cp38-cp38/lib/python3.8/site-packages/skbuild/resources/cmake" "-DITK_DIR:PATH=/work/ITK-cp38-cp38-manylinux_2_28_x64" "-DITK_USE_SYSTEM_SWIG:BOOL=ON" "-DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel" "-DSWIG_EXECUTABLE:FILEPATH=/work/ITK-cp38-cp38-manylinux_2_28_x64/Wrapping/Generators/SwigInterface/swig/bin/swig" "-DCMAKE_CXX_COMPILER_TARGET:STRING=x86_64-linux-gnu" "-DCMAKE_INSTALL_LIBDIR:STRING=lib" "-DBUILD_TESTING:BOOL=OFF" "-DPython3_EXECUTABLE:FILEPATH=/opt/python/cp38-cp38/bin/python" "-DPython3_INCLUDE_DIR:PATH=/opt/python/cp38-cp38/bin/../include/python3.8" "-DCMAKE_BUILD_TYPE:STRING=Release"

    This might be a problem in https://github.com/python-cmake-buildsystem/python-cmake-buildsystem.

    opened by dzenanz 6
  • TimeVaryingDiffeomorphisms in ITKPythonPackage

    TimeVaryingDiffeomorphisms in ITKPythonPackage

    Hello I wanted to know if the itkpythonpackage provides bindings for the deformable registration components of itk. So far i havent found this using google search.

    Thansk

    opened by cakeinspace 6
  • COMP: Consolidate Linux ARM build script

    COMP: Consolidate Linux ARM build script

    Several quality-of-life fixes and updates for ARM support:

    • Consolidates ARM module script with x86_64 module script for easier maintenance and comparison between procedures. Internal ARM script is preserved as a wrapper around generic internal build script.
    • Splits MANYLINUX_VERSION variable into MANYLINUX_VERSION prefix and TARGET_ARCH postfix to better reflect available images.
    • Uses sudo to avoid permissions failure when running docker or cleaning up files on ARM systems

    Applies changes introduced by @thewtex in https://github.com/InsightSoftwareConsortium/ITKPythonPackage/pull/234.

    Tests have passed at https://github.com/InsightSoftwareConsortium/ITKSplitComponents/actions/runs/3736106376/jobs/6340059855. Note that ARM builds on Github Actions runners are significantly slower than x86/x64 builds due to emulation. ITKSplitComponents Linux jobs previously completed in ~10 minutes and now complete in ~30 minutes with the addition of ARM wheels.

    co-authored-by: Matt McCormick [email protected]

    opened by tbirdso 9
  • fail to build release 5.2rc03 on ArchLinux

    fail to build release 5.2rc03 on ArchLinux

    Error log:

    CMake Error at Wrapping/CMakeUtilityFunctions.cmake:40 (math):
  math cannot parse the expression: ")

  set(ITK_WRAP_VECTOR_COMPONENTS + 1": syntax error, unexpected
  exp_CLOSEPARENT (1).
Call Stack (most recent call first):
  Wrapping/WrapBasicTypes.cmake:55 (INCREMENT)
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)


CMake Warning (dev) at Wrapping/CMakeUtilityFunctions.cmake:40 (math):
  Unexpected character in expression at position 1: "

Call Stack (most recent call first):
  Wrapping/WrapBasicTypes.cmake:63 (INCREMENT)
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Error at Wrapping/WrapBasicTypes.cmake:73 (message):
  ITK_WRAP_VECTOR_COMPONENTS must include ITK_WRAP_IMAGE_DIMS
Call Stack (most recent call first):
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)

    See the complete build log here

    opened by hubutui 20
Releases(v5.3.0)
Owner
Insight Software Consortium
Community development of the Insight Toolkit (ITK)
Insight Software Consortium
GitHub Repository https://itkpythonpackage.readthedocs.io
Official code for our ICCV paper: "From Continuity to Editability: Inverting GANs with Consecutive Images"

GANInversion_with_ConsecutiveImgs Official code for our ICCV paper: "From Continuity to Editability: Inverting GANs with Consecutive Images" https://a

QingyangXu 38 Dec 07, 2022
Deepface is a lightweight face recognition and facial attribute analysis (age, gender, emotion and race) framework for python

deepface Deepface is a lightweight face recognition and facial attribute analysis (age, gender, emotion and race) framework for python. It is a hybrid

Kushal Shingote 2 Feb 10, 2022
An elaborate and exhaustive paper list for Named Entity Recognition (NER)

Named-Entity-Recognition-NER-Papers by Pengfei Liu, Jinlan Fu and other contributors. An elaborate and exhaustive paper list for Named Entity Recognit

Pengfei Liu 388 Dec 18, 2022
Audio Domain Adaptation for Acoustic Scene Classification using Disentanglement Learning

Audio Domain Adaptation for Acoustic Scene Classification using Disentanglement Learning Reference Abeßer, J. & Müller, M. Towards Audio Domain Adapt

Jakob Abeßer 2 Jul 06, 2022
PERIN is Permutation-Invariant Semantic Parser developed for MRP 2020

PERIN: Permutation-invariant Semantic Parsing David Samuel & Milan Straka Charles University Faculty of Mathematics and Physics Institute of Formal an

ÚFAL 40 Jan 04, 2023
Principled Detection of Out-of-Distribution Examples in Neural Networks

ODIN: Out-of-Distribution Detector for Neural Networks This is a PyTorch implementation for detecting out-of-distribution examples in neural networks.

189 Nov 29, 2022
Background Matting: The World is Your Green Screen

Background Matting: The World is Your Green Screen By Soumyadip Sengupta, Vivek Jayaram, Brian Curless, Steve Seitz, and Ira Kemelmacher-Shlizerman Th

Soumyadip Sengupta 4.6k Jan 04, 2023
ViViT: Curvature access through the generalized Gauss-Newton's low-rank structure

ViViT is a collection of numerical tricks to efficiently access curvature from the generalized Gauss-Newton (GGN) matrix based on its low-rank structure. Provided functionality includes computing

Felix Dangel 12 Dec 08, 2022
ZEBRA: Zero Evidence Biometric Recognition Assessment

ZEBRA: Zero Evidence Biometric Recognition Assessment license: LGPLv3 - please reference our paper version: 2020-06-11 author: Andreas Nautsch (EURECO

Voice Privacy Challenge 2 Dec 12, 2021
Agent-based model simulator for air quality and pandemic risk assessment in architectural spaces

Agent-based model simulation for air quality and pandemic risk assessment in architectural spaces. User Guide archABM is a fast and open source agent-

Vicomtech 10 Dec 05, 2022
This repository contains the implementations related to the experiments of a set of publicly available datasets that are used in the time series forecasting research space.

TSForecasting This repository contains the implementations related to the experiments of a set of publicly available datasets that are used in the tim

Rakshitha Godahewa 80 Dec 30, 2022
DvD-TD3: Diversity via Determinants for TD3 version

DvD-TD3: Diversity via Determinants for TD3 version The implementation of paper Effective Diversity in Population Based Reinforcement Learning. Instal

3 Feb 11, 2022
SeisComP/SeisBench interface to enable deep-learning (re)picking in SeisComP

scdlpicker SeisComP/SeisBench interface to enable deep-learning (re)picking in SeisComP Objective This is a simple deep learning (DL) repicker module

Joachim Saul 6 May 13, 2022
[ ICCV 2021 Oral ] Our method can estimate camera poses and neural radiance fields jointly when the cameras are initialized at random poses in complex scenarios (outside-in scenes, even with less texture or intense noise )

GNeRF This repository contains official code for the ICCV 2021 paper: GNeRF: GAN-based Neural Radiance Field without Posed Camera. This implementation

Quan Meng 191 Dec 26, 2022
TransFGU: A Top-down Approach to Fine-Grained Unsupervised Semantic Segmentation

TransFGU: A Top-down Approach to Fine-Grained Unsupervised Semantic Segmentation Zhaoyun Yin, Pichao Wang, Fan Wang, Xianzhe Xu, Hanling Zhang, Hao Li

DamoCV 25 Dec 16, 2022
(ICCV 2021 Oral) Re-distributing Biased Pseudo Labels for Semi-supervised Semantic Segmentation: A Baseline Investigation.

DARS Code release for the paper "Re-distributing Biased Pseudo Labels for Semi-supervised Semantic Segmentation: A Baseline Investigation", ICCV 2021

CVMI Lab 58 Jan 01, 2023
Code repository for the paper: Hierarchical Kinematic Probability Distributions for 3D Human Shape and Pose Estimation from Images in the Wild (ICCV 2021)

Hierarchical Kinematic Probability Distributions for 3D Human Shape and Pose Estimation from Images in the Wild Akash Sengupta, Ignas Budvytis, Robert

Akash Sengupta 149 Dec 14, 2022
A PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing"

A PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf 2021). Abstract In this work we propose Pathfind

Benedek Rozemberczki 49 Dec 01, 2022
Hitters Linear Regression - Hitters Linear Regression With Python

Hitters_Linear_Regression Kullanacağımız veri seti Carnegie Mellon Üniversitesi'

AyseBuyukcelik 2 Jan 26, 2022
Learning to Identify Top Elo Ratings with A Dueling Bandits Approach

Learning to Identify Top Elo Ratings We propose two algorithms MaxIn-Elo and MaxIn-mElo to solve the top players identification on the transitive and

2 Jan 14, 2022