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Merge pull request InsightSoftwareConsortium#297 from InsightSoftwareConsortium/strip-trailing-whitespace
strip trailing whitespace
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‎CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.16.3 FATAL_ERROR)
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cmake_minimum_required(VERSION 3.26.6 FATAL_ERROR)
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# NOTE: 3.26.6 is the first cmake vesion to support Development.SABIModule
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project(ITKPythonPackage CXX)
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‎README.md‎

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# ITK Python Package
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This project provides a `setup.py` script to build ITK Python binary
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packages and infrastructure to build ITK external module Python
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packages.
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This project configures pyproject.toml files and manages environmental
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variables needed to build ITK Python binary wheels on MacOS, Linux, and Windows platforms.
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Scripts are available for both [ITK infrastructure](https://github.com/insightSoftwareConsortium/ITK) and
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ITK external module Python packages.
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The Insight Toolkit (ITK) is an open-source, cross-platform system that provides developers
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with an extensive suite of software tools for image analysis.
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- [Frequently Asked Questions](#frequently-asked-questions)
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- [Additional Information](#additional-information)
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## Using ITK Python Packages
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## Using ITK Python Packages (pre-built, or locally built)
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ITKPythonPackage scripts can be used to produce [Python](https://www.python.org/) packages
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for ITK and ITK external modules. The resulting packages can be
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hosted on the [Python Package Index (PyPI)](https://pypi.org/)
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for easy distribution.
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### Installation
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### Installation of pre-built packages
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To install baseline ITK Python packages:
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‎docs/Build_ITK_Module_Python_packages.rst‎

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python -m pip install itk-<your-short-module-name>
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where `itk-<your-short-module-name>` is the short name for your module that is
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specified in your setup.py file.
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specified in the configured `pyproject.toml` file.
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Automate PyPI Package Uploads
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-----------------------------
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itk-<your-short-module-name>
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where `<your-short-module-name>` is the short name for your module that is
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specified in your setup.py file. That scope will be available if you have
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specified in your configured `pyproject.toml` file. That scope will be available if you have
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already uploaded a first set of wheels via twine as described above; and that
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is the recommended approach. Otherwise, if you are creating the project at
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this time, choose an unlimited scope, but be careful with the created token.
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:alt: GitHub PyPI token secret
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To push packages to PyPI, first, make sure to update the `version` for your
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package in the *setup.py* file. The initial version might be `0.1.0` or
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package in the *pyproject.toml* file. The initial version might be `0.1.0` or
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`1.0.0`. Subsequent versions should follow
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`semantic versioning <https://semver.org/>`_.
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‎docs/Build_ITK_Python_packages.rst‎

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Linux
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-----
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On any linux distribution with docker and bash installed, running the script dockcross-manylinux-build-wheels.sh will create 64-bit wheels for both python 2.x and python 3.x in the dist directory.
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On any linux distribution with docker and bash installed, running the script dockcross-manylinux-build-wheels.sh will create 64-bit wheels for python 3.9+ in the dist directory.
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For example::
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errors. Windows 10 ships with an antivirus application, Windows Defender, that
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is enabled by default.
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sdist
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-----
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To create source distributions, sdist's, that will be used by pip to compile a wheel for installation if a binary wheel is not available for the current Python version or platform::
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$ python setup.py sdist --formats=gztar,zip
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[...]
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$ ls -1 dist/
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itk-4.11.0.dev20170216.tar.gz
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itk-4.11.0.dev20170216.zip
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Manual builds
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=============
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Building ITK Python wheels
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--------------------------
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Build the ITK Python wheel with the following command::
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python3 -m venv build-itk
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./build-itk/bin/pip install --upgrade pip
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./build-itk/bin/pip install -r requirements-dev.txt numpy
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./build-itk/bin/python setup.py bdist_wheel
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Build a wheel for a custom version of ITK
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-----------------------------------------
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To build a wheel for a custom version of ITK, point to your ITK git repository
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with the `ITK_SOURCE_DIR` CMake variable::
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./build-itk/bin/python setup.py bdist_wheel -- \
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-DITK_SOURCE_DIR:PATH=/path/to/ITKPythonPackage-core-build/ITK
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Other CMake variables can also be passed with `-D` after the double dash.
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.. The below instructions are outdated and need to be re-written
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.. sdist
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.. -----
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..
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.. To create source distributions, sdist's, that will be used by pip to compile a wheel for installation if a binary wheel is not available for the current Python version or platform::
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..
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.. $ python setup.py sdist --formats=gztar,zip
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.. [...]
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..
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.. $ ls -1 dist/
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.. itk-4.11.0.dev20170216.tar.gz
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.. itk-4.11.0.dev20170216.zip
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..
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.. Manual builds
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.. =============
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..
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.. Building ITK Python wheels
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.. --------------------------
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..
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.. Build the ITK Python wheel with the following command::
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..
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.. python3 -m venv build-itk
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.. ./build-itk/bin/pip install --upgrade pip
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.. ./build-itk/bin/pip install -r requirements-dev.txt numpy
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.. ./build-itk/bin/python setup.py bdist_wheel
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..
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.. Build a wheel for a custom version of ITK
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.. -----------------------------------------
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..
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.. To build a wheel for a custom version of ITK, point to your ITK git repository
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.. with the `ITK_SOURCE_DIR` CMake variable::
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..
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.. ./build-itk/bin/python setup.py bdist_wheel -- \
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.. -DITK_SOURCE_DIR:PATH=/path/to/ITKPythonPackage-core-build/ITK
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..
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.. Other CMake variables can also be passed with `-D` after the double dash.

‎docs/code/CompareITKTypes.py‎

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import itk
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itk.F == itk.ctype('float') # True
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itk.F == itk.ctype("float") # True

‎docs/code/CreateBaseline.py‎

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import itk
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import sys
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image = itk.Image[itk.UC,2].New()
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image.SetRegions([10,10])
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image.SetOrigin([0,0])
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image.SetSpacing([0.5,0.5])
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image = itk.Image[itk.UC, 2].New()
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image.SetRegions([10, 10])
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image.SetOrigin([0, 0])
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image.SetSpacing([0.5, 0.5])
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image.Allocate()
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image.FillBuffer(1)
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itk.imwrite(image, sys.argv[1])

‎docs/code/ExplicitInstantiation.py‎

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# An apriori ImageType
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PixelType = itk.F
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ImageType = itk.Image[PixelType,2]
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ImageType = itk.Image[PixelType, 2]
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image = itk.imread(input_filename, PixelType)
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# An image type dynamically determined from the type on disk

‎docs/code/InstantiateITKObjects.py‎

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import itk
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# Instantiate SmartPointer objects
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InputType = itk.Image[itk.F,3]
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OutputType = itk.Image[itk.F,3]
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InputType = itk.Image[itk.F, 3]
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OutputType = itk.Image[itk.F, 3]
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median = itk.MedianImageFilter[InputType, OutputType].New()
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# Instantiate non-SmartPointer objects

‎docs/code/MixingITKAndNumPy.py‎

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import sys
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from pathlib import Path
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data_dir = Path(__file__).parent.resolve() / '..' / 'data'
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data_dir = Path(__file__).parent.resolve() / ".." / "data"
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input_image_filename = sys.argv[1]
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temp_dir = Path(input_image_filename).parent
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output_image_filename = sys.argv[2]
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input_mesh_filename = data_dir / 'cow.vtk'
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output_mesh_filename = temp_dir / 'cow.vtk'
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input_transform_filename = data_dir / 'rigid.tfm'
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output_transform_filename = temp_dir / 'rigid.tfm'
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input_mesh_filename = data_dir / "cow.vtk"
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output_mesh_filename = temp_dir / "cow.vtk"
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input_transform_filename = data_dir / "rigid.tfm"
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output_transform_filename = temp_dir / "rigid.tfm"
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import itk
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arr = np.zeros([3, 3], np.uint8)
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matrix = itk.vnl_matrix_from_array(arr)
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# Array from VNL matrix

‎docs/code/test.py‎

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import tempfile
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def add_test(cmd):
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cmd.insert(0, sys.executable)
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subprocess.check_call(cmd)
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def cleanup(files):
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for f in files:
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if os.path.isdir(f):
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shutil.rmtree(f)
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# Create temporary folder to save output images
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temp_folder = tempfile.mkdtemp()
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# Change current working directory to find scripts

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