"""Test the nifti_region module

Functions in this file only test features added by the NiftiLabelsMasker class,
not the underlying functions (clean(), img_to_signals_labels(), etc.). See
test_masking.py and test_signal.py for details.
"""

from nose.tools import assert_raises, assert_equal
import numpy as np

import nibabel

from nilearn.input_data.nifti_labels_masker import NiftiLabelsMasker
from nilearn._utils import testing, as_ndarray
from nilearn._utils.exceptions import DimensionError
from nilearn._utils.testing import assert_less


def generate_random_img(shape, length=1, affine=np.eye(4),
                        rand_gen=np.random.RandomState(0)):
    data = rand_gen.randn(*(shape + (length,)))
    return nibabel.Nifti1Image(data, affine), nibabel.Nifti1Image(
        as_ndarray(data[..., 0] > 0.2, dtype=np.int8), affine)


def test_nifti_labels_masker():
    # Check working of shape/affine checks
    shape1 = (13, 11, 12)
    affine1 = np.eye(4)

    shape2 = (12, 10, 14)
    affine2 = np.diag((1, 2, 3, 1))

    n_regions = 9
    length = 3

    fmri11_img, mask11_img = generate_random_img(shape1, affine=affine1,
                                                 length=length)
    fmri12_img, mask12_img = generate_random_img(shape1, affine=affine2,
                                                 length=length)
    fmri21_img, mask21_img = generate_random_img(shape2, affine=affine1,
                                                 length=length)

    labels11_img = testing.generate_labeled_regions(shape1, affine=affine1,
                                                    n_regions=n_regions)

    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 = NiftiLabelsMasker(labels11_img, mask_img=mask_img_4d)
    testing.assert_raises_regex(DimensionError, "Data must be a 3D",
                                masker.fit)

    # check exception when transform() called without prior fit()
    masker11 = NiftiLabelsMasker(labels11_img, resampling_target=None)
    testing.assert_raises_regex(
        ValueError, 'has not been fitted. ', masker11.transform, fmri11_img)

    # No exception raised here
    signals11 = masker11.fit().transform(fmri11_img)
    assert_equal(signals11.shape, (length, n_regions))

    masker11 = NiftiLabelsMasker(labels11_img, mask_img=mask11_img,
                                 resampling_target=None)
    signals11 = masker11.fit().transform(fmri11_img)
    assert_equal(signals11.shape, (length, n_regions))

    # Test all kinds of mismatch between shapes and between affines
    masker11 = NiftiLabelsMasker(labels11_img, resampling_target=None)
    masker11.fit()
    assert_raises(ValueError, masker11.transform, fmri12_img)
    assert_raises(ValueError, masker11.transform, fmri21_img)

    masker11 = NiftiLabelsMasker(labels11_img, mask_img=mask12_img,
                                 resampling_target=None)
    assert_raises(ValueError, masker11.fit)

    masker11 = NiftiLabelsMasker(labels11_img, mask_img=mask21_img,
                                 resampling_target=None)
    assert_raises(ValueError, masker11.fit)

    # Transform, with smoothing (smoke test)
    masker11 = NiftiLabelsMasker(labels11_img, smoothing_fwhm=3,
                                 resampling_target=None)
    signals11 = masker11.fit().transform(fmri11_img)
    assert_equal(signals11.shape, (length, n_regions))

    masker11 = NiftiLabelsMasker(labels11_img, smoothing_fwhm=3,
                                 resampling_target=None)
    signals11 = masker11.fit_transform(fmri11_img)
    assert_equal(signals11.shape, (length, n_regions))

    testing.assert_raises_regex(
        ValueError, 'has not been fitted. ',
        NiftiLabelsMasker(labels11_img).inverse_transform, signals11)

    # Call inverse transform (smoke test)
    fmri11_img_r = masker11.inverse_transform(signals11)
    assert_equal(fmri11_img_r.shape, fmri11_img.shape)
    np.testing.assert_almost_equal(fmri11_img_r.get_affine(),
                                   fmri11_img.get_affine())


def test_nifti_labels_masker_resampling():
    # Test resampling in NiftiLabelsMasker
    shape1 = (10, 11, 12)
    affine = np.eye(4)

    # mask
    shape2 = (16, 17, 18)

    # labels
    shape3 = (13, 14, 15)

    n_regions = 9
    length = 3

    # With data of the same affine
    fmri11_img, _ = generate_random_img(shape1, affine=affine,
                                        length=length)
    _, mask22_img = generate_random_img(shape2, affine=affine,
                                        length=length)

    labels33_img = testing.generate_labeled_regions(shape3, n_regions,
                                                    affine=affine)

    # Test error checking
    assert_raises(ValueError, NiftiLabelsMasker, labels33_img,
                  resampling_target="mask")
    assert_raises(ValueError, NiftiLabelsMasker, labels33_img,
                  resampling_target="invalid")

    # Target: labels
    masker = NiftiLabelsMasker(labels33_img, mask_img=mask22_img,
                               resampling_target="labels")

    masker.fit()
    np.testing.assert_almost_equal(masker.labels_img_.get_affine(),
                                   labels33_img.get_affine())
    assert_equal(masker.labels_img_.shape, labels33_img.shape)

    np.testing.assert_almost_equal(masker.mask_img_.get_affine(),
                                   masker.labels_img_.get_affine())
    assert_equal(masker.mask_img_.shape, masker.labels_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(fmri11_img_r.get_affine(),
                                   masker.labels_img_.get_affine())
    assert_equal(fmri11_img_r.shape,
                 (masker.labels_img_.shape[:3] + (length,)))

    # Test with clipped labels: mask does not contain all labels.
    # Shapes do matter in that case, because there is some resampling
    # taking place.
    shape1 = (10, 11, 12)  # fmri
    shape2 = (8, 9, 10)  # mask
    shape3 = (16, 18, 20)  # maps

    n_regions = 9
    length = 21

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

    # Target: labels
    labels33_img = testing.generate_labeled_regions(shape3, n_regions,
                                                    affine=affine)

    masker = NiftiLabelsMasker(labels33_img, mask_img=mask22_img,
                               resampling_target="labels")

    masker.fit()
    np.testing.assert_almost_equal(masker.labels_img_.get_affine(),
                                   labels33_img.get_affine())
    assert_equal(masker.labels_img_.shape, labels33_img.shape)

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

    uniq_labels = np.unique(masker.labels_img_.get_data())
    assert_equal(uniq_labels[0], 0)
    assert_equal(len(uniq_labels) - 1, n_regions)

    transformed = masker.transform(fmri11_img)
    assert_equal(transformed.shape, (length, n_regions))
    # Some regions have been clipped. Resulting signal must be zero
    assert_less((transformed.var(axis=0) == 0).sum(), n_regions)

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

    # Test with data and atlas of different shape: the atlas should be
    # resampled to the data
    shape22 = (5, 5, 6)
    affine2 = 2 * np.eye(4)
    affine2[-1, -1] = 1

    fmri22_img, _ = generate_random_img(shape22, affine=affine2,
                                        length=length)
    masker = NiftiLabelsMasker(labels33_img, mask_img=mask22_img)

    masker.fit_transform(fmri22_img)
    np.testing.assert_array_equal(
        masker._resampled_labels_img_.get_affine(),
        affine2)

    # Test with filenames
    with testing.write_tmp_imgs(fmri22_img) as filename:
        masker = NiftiLabelsMasker(labels33_img, resampling_target='data')
        masker.fit_transform(filename)
