Medimages4tests

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

$ 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

# 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

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

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.