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.
Raw data
{
"_id": null,
"home_page": "https://github.com/australian-imaging-service/medimages4tests",
"name": "medimages4tests",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "repository analysis medical-imaging neuroimaging workflows pipelines",
"author": "Thomas G. Close",
"author_email": "tom.g.close@gmail.com",
"download_url": "",
"platform": null,
"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",
"bugtrack_url": null,
"license": "CC0",
"summary": "Generates dummy medical image data with realistic headers to be used in image handling tests",
"version": "0.3.3",
"project_urls": {
"Homepage": "https://github.com/australian-imaging-service/medimages4tests"
},
"split_keywords": [
"repository",
"analysis",
"medical-imaging",
"neuroimaging",
"workflows",
"pipelines"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "e7c5330bd7e0e6e6cdb100596193799c6b0d34ef9a009f490048183306aeb9f1",
"md5": "6e43b50406181b3ee25d058f8f296b1d",
"sha256": "8af0361fcec7e6508a5cac93bdc016021b269d7dbde0c58026055961804fd3e6"
},
"downloads": -1,
"filename": "medimages4tests-0.3.3-py3-none-any.whl",
"has_sig": false,
"md5_digest": "6e43b50406181b3ee25d058f8f296b1d",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 894399,
"upload_time": "2023-11-14T04:02:40",
"upload_time_iso_8601": "2023-11-14T04:02:40.790695Z",
"url": "https://files.pythonhosted.org/packages/e7/c5/330bd7e0e6e6cdb100596193799c6b0d34ef9a009f490048183306aeb9f1/medimages4tests-0.3.3-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-14 04:02:40",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "australian-imaging-service",
"github_project": "medimages4tests",
"travis_ci": false,
"coveralls": true,
"github_actions": true,
"lcname": "medimages4tests"
}
JSON
