Medimages4tests
===============
.. image:: https://github.com/australian-imaging-service/medimages4tests/actions/workflows/test.yml/badge.svg
:target: https://github.com/australian-imaging-service/medimages4tests/actions/workflows/test.yml
.. image:: https://codecov.io/gh/australian-imaging-service/medimages4tests/branch/main/graph/badge.svg?token=UIS0OGPST7
:target: https://codecov.io/gh/australian-imaging-service/medimages4tests
.. image:: https://img.shields.io/pypi/pyversions/medimages4tests.svg
:target: https://pypi.python.org/pypi/medimages4tests/
:alt: Supported Python versions
.. image:: https://img.shields.io/pypi/v/medimages4tests.svg
:target: https://pypi.python.org/pypi/medimages4tests/
:alt: Latest Version
Generates dummy medical images, with junk image data but realistic headers,
to test imaging handling pipelines
Installation
------------
Medimage4tests is available on PyPI so to install, simply use pip
.. code-block:: bash
$ pip3 install medimages4tests
or include in your package's ``test_requires``.
Usage
-----
Create a pytest fixture consisting of a dummy image with field-map metadata in DICOM format
.. code-block:: python
# Import medimages4tests generator functions
from medimages4tests.dummy.dicom.mri.fmap.ge.discovery_mr888.dv26_0_r05_2008a import get_image
# Return generated images in pytest fixtures (or alternative test framework)
@pytest.fixture()
def ge_dicom_fmap():
return get_image()
Create a dummy NIfTI image
.. code-block:: python
import numpy
# Import `get_image` function
from medimages4tests.dummy.nifti import get_image
# Create dummy nifti image of 10x10x10 containing all ones
@pytest.fixture()
def ones_nifti():
return get_image(
data=numpy.ones((10, 10, 10))
)
Access real T1-weighted from OpenNeuro.org
.. code-block:: python
from medimages4tests.mri.neuro.t1w import get_image
@pytest.fixture()
def t1w_nifti():
return get_image(sample="ds004130-ON01016")
Acknowledgements
~~~~~~~~~~~~~~~~
The authors acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy (NCRIS) capability.
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"description": "Medimages4tests\n===============\n\n.. image:: https://github.com/australian-imaging-service/medimages4tests/actions/workflows/test.yml/badge.svg\n :target: https://github.com/australian-imaging-service/medimages4tests/actions/workflows/test.yml\n.. image:: https://codecov.io/gh/australian-imaging-service/medimages4tests/branch/main/graph/badge.svg?token=UIS0OGPST7\n :target: https://codecov.io/gh/australian-imaging-service/medimages4tests\n.. image:: https://img.shields.io/pypi/pyversions/medimages4tests.svg\n :target: https://pypi.python.org/pypi/medimages4tests/\n :alt: Supported Python versions\n.. image:: https://img.shields.io/pypi/v/medimages4tests.svg\n :target: https://pypi.python.org/pypi/medimages4tests/\n :alt: Latest Version\n\nGenerates dummy medical images, with junk image data but realistic headers,\nto test imaging handling pipelines\n\nInstallation\n------------\n\nMedimage4tests is available on PyPI so to install, simply use pip\n\n.. code-block:: bash\n\n $ pip3 install medimages4tests\n \nor include in your package's ``test_requires``.\n\n\nUsage\n-----\n\nCreate a pytest fixture consisting of a dummy image with field-map metadata in DICOM format\n\n.. code-block:: python\n\n # Import medimages4tests generator functions\n from medimages4tests.dummy.dicom.mri.fmap.ge.discovery_mr888.dv26_0_r05_2008a import get_image\n\n # Return generated images in pytest fixtures (or alternative test framework)\n @pytest.fixture()\n def ge_dicom_fmap():\n return get_image()\n\nCreate a dummy NIfTI image\n\n.. code-block:: python\n\n import numpy\n # Import `get_image` function\n from medimages4tests.dummy.nifti import get_image\n\n # Create dummy nifti image of 10x10x10 containing all ones\n @pytest.fixture()\n def ones_nifti():\n return get_image(\n data=numpy.ones((10, 10, 10))\n )\n \nAccess real T1-weighted from OpenNeuro.org\n\n.. code-block:: python\n\n\n from medimages4tests.mri.neuro.t1w import get_image\n\n @pytest.fixture()\n def t1w_nifti():\n return get_image(sample=\"ds004130-ON01016\")\n\n\nAcknowledgements\n~~~~~~~~~~~~~~~~\nThe authors acknowledge the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy (NCRIS) capability.\n",
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