#################################
Image registration with imagedata
#################################
|Docs Badge| |buildstatus| |coverage| |pypi|
Helper modules to do
image registration for `Imagedata` **Series** objects.
Available modules
#################
NPreg
-----
`NPreg` by Erlend Hodneland is implemented in Python,
and available as a self-supported PyPi package.
There are three implementations of `NPreg`:
* Pure Python/NumPy code. Source code will run on any Python platform.
* Cython code. Binary code compiled for supported platforms.
* CuPy/CUDA code. Source code which will run on platforms with a working `CuPy` and CUDA Toolkit.
FSL
---
`FSL`
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)
has several methods for image registration.
Using `FSL` image registration from Python requires the `FSL` interface from
nipype, as well as a the `FSL` executables.
Each `FSL` method may have different requirements.
The common factor is that `FSL` methods will read and write NIfTI image files.
A function `register_fsl` is provided here.
This function will register a moving Series to a fixed Series.
The default registration method is fsl.MCFLIRT.
The function will accept other registration methods.
ITK-Elastix
-----------
The popular `Elastix` GUI is based on the C++ `ITK` image registration routines.
Like the `FSL` methods, there are numerous `Elastix` methods available, all with
different requirements.
The `itk-elastix`
(https://github.com/InsightSoftwareConsortium/ITKElastix)
Python library is one particular interface to the `Elastix/ITK` routines.
Prerequisites
#############
NPreg on CUDA GPU
-----------------
imagedata-registration will benefit from a CUDA GPU. If this is available,
install `CuPy` (https://docs.cupy.dev).
* First, install the `CUDA Toolkit`: see https://developer.nvidia.com/cuda-toolkit.
* There are different options for installing `CuPy`. See:
https://docs.cupy.dev/en/stable/install.html
FSL
---
The imagedata-registration FSL module is a wrapper around the official FSL tools.
A native FSL installation is required on the host computer.
ITK-Elastix
-------------
`ITK-Elastix` is installed automatically as a dependency for this package.
Installation
############
.. code-block::
pip install imagedata-registration
Examples
########
`NPreg examples <docs/NPreg.rst>`_
`FSL examples <docs/FSL.rst>`_
`ITK-Elastix examples <docs/ITKElastix.rst>`_
.. |Docs Badge| image:: https://readthedocs.org/projects/imagedata_registration/badge/
:alt: Documentation Status
:target: https://imagedata_registration.readthedocs.io
.. |buildstatus| image:: https://github.com/erling6232/imagedata_registration/actions/workflows/build_wheels.yml/badge.svg
:target: https://github.com/erling6232/imagedata_registration/actions?query=branch%3Amain
:alt: Build Status
.. _buildstatus: https://github.com/erling6232/imagedata_registration/actions
.. |coverage| image:: https://codecov.io/gh/erling6232/imagedata_registration/branch/main/graph/badge.svg?token=1OPGNXJ8Z3
:alt: Coverage
:target: https://codecov.io/gh/erling6232/imagedata_registration
.. |pypi| image:: https://img.shields.io/pypi/v/imagedata-registration.svg
:target: https://pypi.python.org/pypi/imagedata-registration
:alt: PyPI Version
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"description": "#################################\nImage registration with imagedata\n#################################\n\n|Docs Badge| |buildstatus| |coverage| |pypi|\n\n\nHelper modules to do\nimage registration for `Imagedata` **Series** objects.\n\nAvailable modules\n#################\n\nNPreg\n-----\n\n`NPreg` by Erlend Hodneland is implemented in Python,\nand available as a self-supported PyPi package.\nThere are three implementations of `NPreg`:\n\n* Pure Python/NumPy code. Source code will run on any Python platform.\n* Cython code. Binary code compiled for supported platforms.\n* CuPy/CUDA code. Source code which will run on platforms with a working `CuPy` and CUDA Toolkit.\n\nFSL\n---\n\n`FSL`\n(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL)\nhas several methods for image registration.\nUsing `FSL` image registration from Python requires the `FSL` interface from\nnipype, as well as a the `FSL` executables.\nEach `FSL` method may have different requirements.\nThe common factor is that `FSL` methods will read and write NIfTI image files.\n\nA function `register_fsl` is provided here.\nThis function will register a moving Series to a fixed Series.\nThe default registration method is fsl.MCFLIRT.\nThe function will accept other registration methods.\n\nITK-Elastix\n-----------\n\nThe popular `Elastix` GUI is based on the C++ `ITK` image registration routines.\nLike the `FSL` methods, there are numerous `Elastix` methods available, all with\ndifferent requirements.\nThe `itk-elastix`\n(https://github.com/InsightSoftwareConsortium/ITKElastix)\nPython library is one particular interface to the `Elastix/ITK` routines.\n\nPrerequisites\n#############\n\nNPreg on CUDA GPU\n-----------------\n\nimagedata-registration will benefit from a CUDA GPU. If this is available,\ninstall `CuPy` (https://docs.cupy.dev).\n\n* First, install the `CUDA Toolkit`: see https://developer.nvidia.com/cuda-toolkit.\n\n* There are different options for installing `CuPy`. See:\n https://docs.cupy.dev/en/stable/install.html\n\nFSL\n---\n\nThe imagedata-registration FSL module is a wrapper around the official FSL tools.\nA native FSL installation is required on the host computer.\n\nITK-Elastix\n-------------\n\n`ITK-Elastix` is installed automatically as a dependency for this package.\n\nInstallation\n############\n\n.. code-block::\n\n pip install imagedata-registration\n\nExamples\n########\n\n`NPreg examples <docs/NPreg.rst>`_\n\n`FSL examples <docs/FSL.rst>`_\n\n`ITK-Elastix examples <docs/ITKElastix.rst>`_\n\n\n.. |Docs Badge| image:: https://readthedocs.org/projects/imagedata_registration/badge/\n :alt: Documentation Status\n :target: https://imagedata_registration.readthedocs.io\n\n.. |buildstatus| image:: https://github.com/erling6232/imagedata_registration/actions/workflows/build_wheels.yml/badge.svg\n :target: https://github.com/erling6232/imagedata_registration/actions?query=branch%3Amain\n :alt: Build Status\n\n.. _buildstatus: https://github.com/erling6232/imagedata_registration/actions\n\n.. |coverage| image:: https://codecov.io/gh/erling6232/imagedata_registration/branch/main/graph/badge.svg?token=1OPGNXJ8Z3\n :alt: Coverage\n :target: https://codecov.io/gh/erling6232/imagedata_registration\n\n.. |pypi| image:: https://img.shields.io/pypi/v/imagedata-registration.svg\n :target: https://pypi.python.org/pypi/imagedata-registration\n :alt: PyPI Version\n\n",
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