Python testing.generate_fake_fmri函数代码示例

def test_generate_fake_fmri():
    shapes = [(6, 6, 7), (10, 11, 12)]
    lengths = [16, 20]
    kinds = ['noise', 'step']
    n_blocks = [None, 1, 4]
    block_size = [None, 4]
    block_type = ['classification', 'regression']

    rand_gen = np.random.RandomState(3)

    for shape, length, kind, n_block, bsize, btype in itertools.product(
            shapes, lengths, kinds, n_blocks, block_size, block_type):

        if n_block is None:
            fmri, mask = generate_fake_fmri(
                shape=shape, length=length, kind=kind,
                n_blocks=n_block, block_size=bsize,
                block_type=btype,
                rand_gen=rand_gen)
        else:
            fmri, mask, target = generate_fake_fmri(
                shape=shape, length=length, kind=kind,
                n_blocks=n_block, block_size=bsize,
                block_type=btype,
                rand_gen=rand_gen)

        assert_equal(fmri.shape[:-1], shape)
        assert_equal(fmri.shape[-1], length)

        if n_block is not None:
            assert_equal(target.size, length)

    assert_raises(ValueError, generate_fake_fmri, length=10, n_blocks=10,
                  block_size=None, rand_gen=rand_gen)

def test_smooth_img():
    # This function only checks added functionalities compared
    # to _smooth_array()
    shapes = ((10, 11, 12), (13, 14, 15))
    lengths = (17, 18)
    fwhm = (1., 2., 3.)

    img1, mask1 = testing.generate_fake_fmri(shape=shapes[0],
                                             length=lengths[0])
    img2, mask2 = testing.generate_fake_fmri(shape=shapes[1],
                                             length=lengths[1])

    for create_files in (False, True):
        with testing.write_tmp_imgs(img1, img2,
                                    create_files=create_files) as imgs:
            # List of images as input
            out = image.smooth_img(imgs, fwhm)
            assert_true(isinstance(out, list))
            assert_true(len(out) == 2)
            for o, s, l in zip(out, shapes, lengths):
                assert_true(o.shape == (s + (l,)))

            # Single image as input
            out = image.smooth_img(imgs[0], fwhm)
            assert_true(isinstance(out, nibabel.Nifti1Image))
            assert_true(out.shape == (shapes[0] + (lengths[0],)))

def test_index_img():
    img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
    testing.assert_raises_regex(TypeError, '4D Niimg-like',
                                image.index_img, img_3d, 0)

    affine = np.array([[1., 2., 3., 4.],
                       [5., 6., 7., 8.],
                       [9., 10., 11., 12.],
                       [0., 0., 0., 1.]])
    img_4d, _ = testing.generate_fake_fmri(affine=affine)

    fourth_dim_size = img_4d.shape[3]
    tested_indices = (list(range(fourth_dim_size)) +
                      [slice(2, 8, 2), [1, 2, 3, 2], [],
                       (np.arange(fourth_dim_size) % 3) == 1])
    for i in tested_indices:
        this_img = image.index_img(img_4d, i)
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(this_img.get_data(),
                           expected_data_3d)
        assert_array_equal(this_img.get_affine(),
                           img_4d.get_affine())

    for i in [fourth_dim_size, - fourth_dim_size - 1,
              [0, fourth_dim_size],
              np.repeat(True, fourth_dim_size + 1)]:
        testing.assert_raises_regex(
            IndexError,
            'out of bounds|invalid index|out of range',
            image.index_img, img_4d, i)

def test_index_img():
    img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
    testing.assert_raises_regex(TypeError,
                                "Input data has incompatible dimensionality: "
                                "Expected dimension is 4D and you provided "
                                "a 3D image.",
                                image.index_img, img_3d, 0)

    affine = np.array([[1., 2., 3., 4.],
                       [5., 6., 7., 8.],
                       [9., 10., 11., 12.],
                       [0., 0., 0., 1.]])
    img_4d, _ = testing.generate_fake_fmri(affine=affine)

    fourth_dim_size = img_4d.shape[3]
    tested_indices = (list(range(fourth_dim_size)) +
                      [slice(2, 8, 2), [1, 2, 3, 2], [],
                       (np.arange(fourth_dim_size) % 3) == 1])
    for i in tested_indices:
        this_img = image.index_img(img_4d, i)
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(this_img.get_data(),
                           expected_data_3d)
        assert_array_equal(compat.get_affine(this_img),
                           compat.get_affine(img_4d))

    for i in [fourth_dim_size, - fourth_dim_size - 1,
              [0, fourth_dim_size],
              np.repeat(True, fourth_dim_size + 1)]:
        testing.assert_raises_regex(
            IndexError,
            'out of bounds|invalid index|out of range|boolean index',
            image.index_img, img_4d, i)

def test_smooth_img():
    # This function only checks added functionalities compared
    # to _smooth_array()
    shapes = ((10, 11, 12), (13, 14, 15))
    lengths = (17, 18)
    fwhm = (1., 2., 3.)

    img1, mask1 = testing.generate_fake_fmri(shape=shapes[0],
                                             length=lengths[0])
    img2, mask2 = testing.generate_fake_fmri(shape=shapes[1],
                                             length=lengths[1])

    for create_files in (False, True):
        with testing.write_tmp_imgs(img1, img2,
                                    create_files=create_files) as imgs:
            # List of images as input
            out = image.smooth_img(imgs, fwhm)
            assert_true(isinstance(out, list))
            assert_true(len(out) == 2)
            for o, s, l in zip(out, shapes, lengths):
                assert_true(o.shape == (s + (l,)))

            # Single image as input
            out = image.smooth_img(imgs[0], fwhm)
            assert_true(isinstance(out, nibabel.Nifti1Image))
            assert_true(out.shape == (shapes[0] + (lengths[0],)))

    # Check corner case situations when fwhm=0, See issue #1537
    # Test whether function smooth_img raises a warning when fwhm=0.
    assert_warns(UserWarning, image.smooth_img, img1, fwhm=0.)

    # Test output equal when fwhm=None and fwhm=0
    out_fwhm_none = image.smooth_img(img1, fwhm=None)
    out_fwhm_zero = image.smooth_img(img1, fwhm=0.)
    assert_array_equal(out_fwhm_none.get_data(), out_fwhm_zero.get_data())

    data1 = np.zeros((10, 11, 12))
    data1[2:4, 1:5, 3:6] = 1
    data2 = np.zeros((13, 14, 15))
    data2[2:4, 1:5, 3:6] = 9
    img1_nifti2 = nibabel.Nifti2Image(data1, affine=np.eye(4))
    img2_nifti2 = nibabel.Nifti2Image(data2, affine=np.eye(4))
    out = image.smooth_img([img1_nifti2, img2_nifti2], fwhm=1.)

def test_iter_img():
    img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
    testing.assert_raises_regex(TypeError,
                                "Input data has incompatible dimensionality: "
                                "Expected dimension is 4D and you provided "
                                "a 3D image.",
                                image.iter_img, img_3d)

    affine = np.array([[1., 2., 3., 4.],
                       [5., 6., 7., 8.],
                       [9., 10., 11., 12.],
                       [0., 0., 0., 1.]])
    img_4d, _ = testing.generate_fake_fmri(affine=affine)

    for i, img in enumerate(image.iter_img(img_4d)):
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(img.get_data(),
                           expected_data_3d)
        assert_array_equal(compat.get_affine(img),
                           compat.get_affine(img_4d))

    with testing.write_tmp_imgs(img_4d) as img_4d_filename:
        for i, img in enumerate(image.iter_img(img_4d_filename)):
            expected_data_3d = img_4d.get_data()[..., i]
            assert_array_equal(img.get_data(),
                               expected_data_3d)
            assert_array_equal(compat.get_affine(img),
                               compat.get_affine(img_4d))
        # enables to delete "img_4d_filename" on windows
        del img

    img_3d_list = list(image.iter_img(img_4d))
    for i, img in enumerate(image.iter_img(img_3d_list)):
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(img.get_data(),
                           expected_data_3d)
        assert_array_equal(compat.get_affine(img),
                           compat.get_affine(img_4d))

    with testing.write_tmp_imgs(*img_3d_list) as img_3d_filenames:
        for i, img in enumerate(image.iter_img(img_3d_filenames)):
            expected_data_3d = img_4d.get_data()[..., i]
            assert_array_equal(img.get_data(),
                               expected_data_3d)
            assert_array_equal(compat.get_affine(img),
                               compat.get_affine(img_4d))
        # enables to delete "img_3d_filename" on windows
        del img

def test_iter_img():
    img_3d = nibabel.Nifti1Image(np.ones((3, 4, 5)), np.eye(4))
    testing.assert_raises_regex(TypeError, '4D Niimg-like',
                                image.iter_img, img_3d)

    affine = np.array([[1., 2., 3., 4.],
                       [5., 6., 7., 8.],
                       [9., 10., 11., 12.],
                       [0., 0., 0., 1.]])
    img_4d, _ = testing.generate_fake_fmri(affine=affine)

    for i, img in enumerate(image.iter_img(img_4d)):
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(img.get_data(),
                           expected_data_3d)
        assert_array_equal(img.get_affine(),
                           img_4d.get_affine())

    with testing.write_tmp_imgs(img_4d) as img_4d_filename:
        for i, img in enumerate(image.iter_img(img_4d_filename)):
            expected_data_3d = img_4d.get_data()[..., i]
            assert_array_equal(img.get_data(),
                               expected_data_3d)
            assert_array_equal(img.get_affine(),
                               img_4d.get_affine())
        # enables to delete "img_4d_filename" on windows
        del img

    img_3d_list = list(image.iter_img(img_4d))
    for i, img in enumerate(image.iter_img(img_3d_list)):
        expected_data_3d = img_4d.get_data()[..., i]
        assert_array_equal(img.get_data(),
                           expected_data_3d)
        assert_array_equal(img.get_affine(),
                           img_4d.get_affine())

    with testing.write_tmp_imgs(*img_3d_list) as img_3d_filenames:
        for i, img in enumerate(image.iter_img(img_3d_filenames)):
            expected_data_3d = img_4d.get_data()[..., i]
            assert_array_equal(img.get_data(),
                               expected_data_3d)
            assert_array_equal(img.get_affine(),
                               img_4d.get_affine())
        # enables to delete "img_3d_filename" on windows
        del img

def test_high_variance_confounds():
    # See also test_signals.test_high_variance_confounds()
    # There is only tests on what is added by image.high_variance_confounds()
    # compared to signal.high_variance_confounds()

    shape = (40, 41, 42)
    length = 17
    n_confounds = 10

    img, mask_img = testing.generate_fake_fmri(shape=shape, length=length)

    confounds1 = image.high_variance_confounds(img, mask_img=mask_img,
                                               percentile=10.,
                                               n_confounds=n_confounds)
    assert_true(confounds1.shape == (length, n_confounds))

    # No mask.
    confounds2 = image.high_variance_confounds(img, percentile=10.,
                                               n_confounds=n_confounds)
    assert_true(confounds2.shape == (length, n_confounds))

def test_matrix_orientation():
    """Test if processing is performed along the correct axis."""

    # the "step" kind generate heavyside-like signals for each voxel.
    # all signals being identical, standardizing along the wrong axis
    # would leave a null signal. Along the correct axis, the step remains.
    fmri, mask = testing.generate_fake_fmri(shape=(40, 41, 42), kind="step")
    masker = NiftiMasker(mask_img=mask, standardize=True, detrend=True)
    timeseries = masker.fit_transform(fmri)
    assert(timeseries.shape[0] == fmri.shape[3])
    assert(timeseries.shape[1] == mask.get_data().sum())
    std = timeseries.std(axis=0)
    assert(std.shape[0] == timeseries.shape[1])  # paranoid
    assert(not np.any(std < 0.1))

    # Test inverse transform
    masker = NiftiMasker(mask_img=mask, standardize=False, detrend=False)
    masker.fit()
    timeseries = masker.transform(fmri)
    recovered = masker.inverse_transform(timeseries)
    np.testing.assert_array_almost_equal(recovered.get_data(), fmri.get_data())

def test_pd_index_img():
    # confirm indices from pandas dataframes are handled correctly
    if 'pandas' not in sys.modules:
        raise SkipTest

    affine = np.array([[1., 2., 3., 4.],
                       [5., 6., 7., 8.],
                       [9., 10., 11., 12.],
                       [0., 0., 0., 1.]])
    img_4d, _ = testing.generate_fake_fmri(affine=affine)

    fourth_dim_size = img_4d.shape[3]

    rng = np.random.RandomState(0)

    arr = rng.rand(fourth_dim_size) > 0.5
    df = pd.DataFrame({"arr": arr})

    np_index_img = image.index_img(img_4d, arr)
    pd_index_img = image.index_img(img_4d, df)
    assert_array_equal(np_index_img.get_data(),
                       pd_index_img.get_data())

def test_nifti_maps_masker_2():
    # Test resampling in NiftiMapsMasker
    affine = np.eye(4)

    shape1 = (10, 11, 12)  # fmri
    shape2 = (13, 14, 15)  # mask
    shape3 = (16, 17, 18)  # maps

    n_regions = 9
    length = 3

    fmri11_img, _ = generate_random_img(shape1, affine=affine,
                                        length=length)
    _, mask22_img = generate_random_img(shape2, affine=affine,
                                        length=length)

    maps33_img, _ = \
        testing.generate_maps(shape3, n_regions, affine=affine)

    mask_img_4d = nibabel.Nifti1Image(np.ones((2, 2, 2, 2), dtype=np.int8),
                                      affine=np.diag((4, 4, 4, 1)))

    # verify that 4D mask arguments are refused
    masker = NiftiMapsMasker(maps33_img, mask_img=mask_img_4d)
    testing.assert_raises_regex(DimensionError,
                                "Input data has incompatible dimensionality: "
                                "Expected dimension is 3D and you provided "
                                "a 4D image.",
                                masker.fit)

    # Test error checking
    assert_raises(ValueError, NiftiMapsMasker, maps33_img,
                  resampling_target="mask")
    assert_raises(ValueError, NiftiMapsMasker, maps33_img,
                  resampling_target="invalid")

    # Target: mask
    masker = NiftiMapsMasker(maps33_img, mask_img=mask22_img,
                             resampling_target="mask")

    masker.fit()
    np.testing.assert_almost_equal(get_affine(masker.mask_img_),
                                   get_affine(mask22_img))
    assert_equal(masker.mask_img_.shape, mask22_img.shape)

    np.testing.assert_almost_equal(get_affine(masker.mask_img_),
                                   get_affine(masker.maps_img_))
    assert_equal(masker.mask_img_.shape, masker.maps_img_.shape[:3])

    transformed = masker.transform(fmri11_img)
    assert_equal(transformed.shape, (length, n_regions))

    fmri11_img_r = masker.inverse_transform(transformed)
    np.testing.assert_almost_equal(get_affine(fmri11_img_r),
                                   get_affine(masker.maps_img_))
    assert_equal(fmri11_img_r.shape, (masker.maps_img_.shape[:3] + (length,)))

    # Target: maps
    masker = NiftiMapsMasker(maps33_img, mask_img=mask22_img,
                             resampling_target="maps")

    masker.fit()
    np.testing.assert_almost_equal(get_affine(masker.maps_img_),
                                   get_affine(maps33_img))
    assert_equal(masker.maps_img_.shape, maps33_img.shape)

    np.testing.assert_almost_equal(get_affine(masker.mask_img_),
                                   get_affine(masker.maps_img_))
    assert_equal(masker.mask_img_.shape, masker.maps_img_.shape[:3])

    transformed = masker.transform(fmri11_img)
    assert_equal(transformed.shape, (length, n_regions))

    fmri11_img_r = masker.inverse_transform(transformed)
    np.testing.assert_almost_equal(get_affine(fmri11_img_r),
                                   get_affine(masker.maps_img_))
    assert_equal(fmri11_img_r.shape, (masker.maps_img_.shape[:3] + (length,)))

    # Test with clipped maps: mask does not contain all maps.
    # Shapes do matter in that case
    affine1 = np.eye(4)
    shape1 = (10, 11, 12)
    shape2 = (8, 9, 10)  # mask
    affine2 = np.diag((2, 2, 2, 1))  # just for mask
    shape3 = (16, 18, 20)  # maps

    n_regions = 9
    length = 21

    fmri11_img, _ = generate_random_img(shape1, affine=affine1, length=length)
    _, mask22_img = testing.generate_fake_fmri(shape2, length=1,
                                               affine=affine2)
    # Target: maps
    maps33_img, _ = \
        testing.generate_maps(shape3, n_regions, affine=affine1)

    masker = NiftiMapsMasker(maps33_img, mask_img=mask22_img,
                             resampling_target="maps")

    masker.fit()
#.........这里部分代码省略.........

def test_signal_extraction_with_maps_and_labels():
    shape = (4, 5, 6)
    n_regions = 7
    length = 8

    # Generate labels
    labels = list(range(n_regions + 1))  # 0 is background
    labels_img = generate_labeled_regions(shape, n_regions, labels=labels)
    labels_data = labels_img.get_data()
    # Convert to maps
    maps_data = np.zeros(shape + (n_regions,))
    for n, l in enumerate(labels):
        if n == 0:
            continue

        maps_data[labels_data == l, n - 1] = 1

    maps_img = nibabel.Nifti1Image(maps_data, labels_img.affine)

    # Generate fake data
    fmri_img, _ = generate_fake_fmri(shape=shape, length=length,
                                     affine=labels_img.affine)

    # Extract signals from maps and labels: results must be identical.
    maps_signals, maps_labels = signal_extraction.img_to_signals_maps(
        fmri_img, maps_img)
    labels_signals, labels_labels = signal_extraction.img_to_signals_labels(
        fmri_img, labels_img)

    np.testing.assert_almost_equal(maps_signals, labels_signals)

    # Same thing with a mask, containing only 3 regions.
    mask_data = (labels_data == 1) + (labels_data == 2) + (labels_data == 5)
    mask_img = nibabel.Nifti1Image(mask_data.astype(np.int8),
                                   labels_img.affine)
    labels_signals, labels_labels = signal_extraction.img_to_signals_labels(
        fmri_img, labels_img, mask_img=mask_img)

    maps_signals, maps_labels = signal_extraction.img_to_signals_maps(
        fmri_img, maps_img, mask_img=mask_img)

    np.testing.assert_almost_equal(maps_signals, labels_signals)
    assert_true(maps_signals.shape[1] == n_regions)
    assert_true(maps_labels == list(range(len(maps_labels))))
    assert_true(labels_signals.shape == (length, n_regions))
    assert_true(labels_labels == labels[1:])

    # Inverse operation (mostly smoke test)
    labels_img_r = signal_extraction.signals_to_img_labels(
        labels_signals, labels_img, mask_img=mask_img)
    assert_true(labels_img_r.shape == shape + (length,))

    maps_img_r = signal_extraction.signals_to_img_maps(
        maps_signals, maps_img, mask_img=mask_img)
    assert_true(maps_img_r.shape == shape + (length,))

    # Check that NaNs in regions inside mask are preserved
    region1 = labels_data == 2
    indices = [ind[:1] for ind in np.where(region1)]
    fmri_img.get_data()[indices + [slice(None)]] = float('nan')
    labels_signals, labels_labels = signal_extraction.img_to_signals_labels(
        fmri_img, labels_img, mask_img=mask_img)
    assert_true(np.all(np.isnan(labels_signals[:, labels_labels.index(2)])))

def test_largest_cc_img():
    """ Check the extraction of the largest connected component, for niftis

    Similiar to smooth_img tests for largest connected_component_img, here also
    only the added features for largest_connected_component are tested.
    """

    # Test whether dimension of 3Dimg and list of 3Dimgs are kept.
    shapes = ((10, 11, 12), (13, 14, 15))
    regions = [1, 3]

    img1 = testing.generate_labeled_regions(shape=shapes[0],
                                            n_regions=regions[0])
    img2 = testing.generate_labeled_regions(shape=shapes[1],
                                            n_regions=regions[1])

    for create_files in (False, True):
        with testing.write_tmp_imgs(img1, img2,
                                    create_files=create_files) as imgs:
            # List of images as input
            out = largest_connected_component_img(imgs)
            assert_true(isinstance(out, list))
            assert_true(len(out) == 2)
            for o, s in zip(out, shapes):
                assert_true(o.shape == (s))

            # Single image as input
            out = largest_connected_component_img(imgs[0])
            assert_true(isinstance(out, Nifti1Image))
            assert_true(out.shape == (shapes[0]))

        # Test whether 4D Nifti throws the right error.
        img_4D = testing.generate_fake_fmri(shapes[0], length=17)
        assert_raises(DimensionError, largest_connected_component_img, img_4D)

    # tests adapted to non-native endian data dtype
    img1_change_dtype = nibabel.Nifti1Image(img1.get_data().astype('>f8'),
                                            affine=img1.affine)
    img2_change_dtype = nibabel.Nifti1Image(img2.get_data().astype('>f8'),
                                            affine=img2.affine)

    for create_files in (False, True):
        with testing.write_tmp_imgs(img1_change_dtype, img2_change_dtype,
                                    create_files=create_files) as imgs:
            # List of images as input
            out = largest_connected_component_img(imgs)
            assert_true(isinstance(out, list))
            assert_true(len(out) == 2)
            for o, s in zip(out, shapes):
                assert_true(o.shape == (s))

            # Single image as input
            out = largest_connected_component_img(imgs[0])
            assert_true(isinstance(out, Nifti1Image))
            assert_true(out.shape == (shapes[0]))

    # Test the output with native and without native
    out_native = largest_connected_component_img(img1)

    out_non_native = largest_connected_component_img(img1_change_dtype)
    np.testing.assert_equal(out_native.get_data(), out_non_native.get_data())