test_dicom.py

#!/usr/bin/env python
#
# test_dicom.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#

import os.path as op
import            tarfile

import mock
import pytest

import fsl.data.dicom    as fsldcm
import fsl.utils.tempdir as tempdir


datadir = op.join(op.dirname(__file__), 'testdata')


pytestmark = pytest.mark.dicomtest


def setup_module():

    if not fsldcm.enabled():
        raise RuntimeError('dcm2niix is not present - tests cannot be run')


def test_disabled():

    with mock.patch('fsl.data.dicom.enabled', return_value=False):
        with pytest.raises(RuntimeError):
            fsldcm.scanDir('.')
        with pytest.raises(RuntimeError):
            fsldcm.loadSeries({})


def test_enabled():

    try:
        fsldcm.enabled.invalidate()
        assert fsldcm.enabled()
        fsldcm.enabled.invalidate()
        # test dcm2niix not present
        with mock.patch('subprocess.check_output',
                        side_effect=Exception()):
            assert not fsldcm.enabled()


        # test presence of different versions
        tests = [(b'version v2.1.20191212', True),
                 (b'version v1.0.20171216', True),
                 (b'version v1.0.20171215', True),
                 (b'version v1.0.20171214', False),
                 (b'version v1.0.20160930', False),
                 (b'version v1.0.20160929', False),
                 (b'version v0.0.00000000', False),
                 (b'version blurgh',        False)]

        for verstr, expected in tests:
            fsldcm.enabled.invalidate()
            with mock.patch('subprocess.check_output', return_value=verstr):
                assert fsldcm.enabled() == expected

    finally:
        fsldcm.enabled.invalidate()


def test_scanDir():

    with tempdir.tempdir() as td:

        series = fsldcm.scanDir(td)
        assert len(series) == 0

        datafile = op.join(datadir, 'example_dicom.tbz2')

        with tarfile.open(datafile) as f:
            f.extractall()

        series = fsldcm.scanDir(td)
        assert len(series) == 3

        for s in series:
            assert (s['PatientName'] == 'MCCARTHY_PAUL' or
                    s['PatientName'] == 'MCCARTHY_PAUL_2')


def test_loadSeries():

    with tempdir.tempdir() as td:

        datafile = op.join(datadir, 'example_dicom.tbz2')

        with tarfile.open(datafile) as f:
            f.extractall()

        series   = fsldcm.scanDir(td)
        expShape = (512, 512, 1)
        explens  = [1, 2]

        for s, explen in zip(series, explens):

            imgs = fsldcm.loadSeries(s)

            assert len(imgs) == explen

            for img in imgs:

                assert img.dicomDir               == td
                assert img.shape                  == expShape
                assert img[:].shape               == expShape
                assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
                       img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
                assert 'PatientName'                      in img.metaKeys()
                assert 'MCCARTHY_PAUL'                    in img.metaValues() or \
                       'MCCARTHY_PAUL_2'                  in img.metaValues()
                assert ('PatientName', 'MCCARTHY_PAUL')   in img.metaItems() or \
                       ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()