Python NiftiMasker.transform方法代码示例

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
def test_mask_4d():
    # Dummy mask
    mask = np.zeros((10, 10, 10), dtype=int)
    mask[3:7, 3:7, 3:7] = 1
    mask_bool = mask.astype(bool)
    mask_img = Nifti1Image(mask, np.eye(4))

    # Dummy data
    data = np.zeros((10, 10, 10, 3), dtype=int)
    data[..., 0] = 1
    data[..., 1] = 2
    data[..., 2] = 3
    data_img_4d = Nifti1Image(data, np.eye(4))
    data_imgs = [index_img(data_img_4d, 0), index_img(data_img_4d, 1),
                 index_img(data_img_4d, 2)]

    # check whether transform is indeed selecting niimgs subset
    sample_mask = np.array([0, 2])
    masker = NiftiMasker(mask_img=mask_img, sample_mask=sample_mask)
    masker.fit()
    data_trans = masker.transform(data_imgs)
    data_trans_img = index_img(data_img_4d, sample_mask)
    data_trans_direct = data_trans_img.get_data()[mask_bool, :]
    data_trans_direct = np.swapaxes(data_trans_direct, 0, 1)
    assert_array_equal(data_trans, data_trans_direct)

    masker = NiftiMasker(mask_img=mask_img, sample_mask=sample_mask)
    masker.fit()
    data_trans2 = masker.transform(data_img_4d)
    assert_array_equal(data_trans2, data_trans_direct)

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
def test_with_files():
    # Standard masking
    data = np.zeros((40, 40, 40, 2))
    data[20, 20, 20] = 1
    data_img = Nifti1Image(data, np.eye(4))

    with testing.write_tmp_imgs(data_img) as filename:
        masker = NiftiMasker()
        masker.fit(filename)
        masker.transform(filename)

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
def test_joblib_cache():
    if not LooseVersion(nibabel.__version__) > LooseVersion('1.1.0'):
        # Old nibabel do not pickle
        raise SkipTest
    from sklearn.externals.joblib import hash, Memory
    mask = np.zeros((40, 40, 40))
    mask[20, 20, 20] = 1
    mask_img = Nifti1Image(mask, np.eye(4))

    with testing.write_tmp_imgs(mask_img, create_files=True)\
            as filename:
        masker = NiftiMasker(mask_img=filename)
        masker.fit()
        mask_hash = hash(masker.mask_img_)
        masker.mask_img_.get_data()
        assert_true(mask_hash == hash(masker.mask_img_))

    # Test a tricky issue with memmapped joblib.memory that makes
    # imgs return by inverse_transform impossible to save
    cachedir = mkdtemp()
    try:
        masker.memory = Memory(cachedir=cachedir, mmap_mode='r',
                               verbose=0)
        X = masker.transform(mask_img)
        # inverse_transform a first time, so that the result is cached
        out_img = masker.inverse_transform(X)
        out_img = masker.inverse_transform(X)
        out_img.to_filename(os.path.join(cachedir, 'test.nii'))
    finally:
        shutil.rmtree(cachedir, ignore_errors=True)

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
def test_auto_mask():
    # This mostly a smoke test
    data = np.zeros((9, 9, 9))
    data[3:-3, 3:-3, 3:-3] = 10
    img = Nifti1Image(data, np.eye(4))
    masker = NiftiMasker()
    # Smoke test the fit
    masker.fit(img)
    # Smoke test the transform
    # With a 4D img
    masker.transform([img, ])
    # With a 3D img
    masker.transform(img)

    # check exception when transform() called without prior fit()
    masker2 = NiftiMasker(mask_img=img)
    testing.assert_raises_regex(
        ValueError,
        'has not been fitted. ', masker2.transform, img)

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
def test_4d_single_scan():
    mask = np.zeros((10, 10, 10))
    mask[3:7, 3:7, 3:7] = 1
    mask_img = Nifti1Image(mask, np.eye(4))

    data_5d = [np.random.random((10, 10, 10, 1)) for i in range(5)]
    data_4d = [d[..., 0] for d in data_5d]
    data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
    data_4d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_4d]

    masker = NiftiMasker(mask_img=mask_img)
    masker.fit()
    data_trans_5d = masker.transform(data_5d)
    data_trans_4d = masker.transform(data_4d)

    assert_array_equal(data_trans_4d, data_trans_5d)

# 需要导入模块: from nilearn.input_data.nifti_masker import NiftiMasker [as 别名]
# 或者: from nilearn.input_data.nifti_masker.NiftiMasker import transform [as 别名]
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())