# -*- coding: utf-8 -*-
# Author: Tommy Clausner <Tommy.Clausner@gmail.com>
#
# License: BSD (3-clause)
import os.path as op

import pytest
import numpy as np
from numpy.testing import (assert_array_less, assert_allclose,
                           assert_array_equal)
from scipy.spatial.distance import cdist

import mne
from mne import (SourceEstimate, VolSourceEstimate, VectorSourceEstimate,
                 read_evokeds, SourceMorph, compute_source_morph,
                 read_source_morph, read_source_estimate,
                 read_forward_solution, grade_to_vertices, morph_data,
                 setup_volume_source_space, make_forward_solution,
                 make_sphere_model, make_ad_hoc_cov)
from mne.datasets import testing
from mne.minimum_norm import (apply_inverse, read_inverse_operator,
                              make_inverse_operator)
from mne.source_space import get_volume_labels_from_aseg
from mne.utils import (run_tests_if_main, requires_nibabel, _TempDir,
                       requires_dipy, requires_h5py, requires_version)
from mne.fixes import _get_args

# Setup paths

data_path = testing.data_path(download=False)
sample_dir = op.join(data_path, 'MEG', 'sample')
subjects_dir = op.join(data_path, 'subjects')
fname_evoked = op.join(sample_dir, 'sample_audvis-ave.fif')
fname_trans = op.join(sample_dir, 'sample_audvis_trunc-trans.fif')
fname_inv_vol = op.join(sample_dir,
                        'sample_audvis_trunc-meg-vol-7-meg-inv.fif')
fname_fwd_vol = op.join(sample_dir,
                        'sample_audvis_trunc-meg-vol-7-fwd.fif')
fname_vol = op.join(sample_dir,
                    'sample_audvis_trunc-grad-vol-7-fwd-sensmap-vol.w')
fname_inv_surf = op.join(sample_dir,
                         'sample_audvis_trunc-meg-eeg-oct-6-meg-inv.fif')
fname_fmorph = op.join(data_path, 'MEG', 'sample',
                       'fsaverage_audvis_trunc-meg')
fname_smorph = op.join(sample_dir, 'sample_audvis_trunc-meg')
fname_t1 = op.join(subjects_dir, 'sample', 'mri', 'T1.mgz')
fname_brain = op.join(subjects_dir, 'sample', 'mri', 'brain.mgz')
fname_stc = op.join(sample_dir, 'fsaverage_audvis_trunc-meg')


def _real_vec_stc():
    inv = read_inverse_operator(fname_inv_surf)
    evoked = read_evokeds(fname_evoked, baseline=(None, 0))[0].crop(0, 0.01)
    return apply_inverse(evoked, inv, pick_ori='vector')


def test_sourcemorph_consistency():
    """Test SourceMorph class consistency."""
    assert _get_args(SourceMorph.__init__)[1:] == \
        mne.morph._SOURCE_MORPH_ATTRIBUTES


@requires_version('scipy', '0.13')  # SciPy 0.13 reduction bug
@testing.requires_testing_data
def test_sparse_morph():
    """Test sparse morphing."""
    rng = np.random.RandomState(0)
    vertices_fs = [np.sort(rng.permutation(np.arange(10242))[:4]),
                   np.sort(rng.permutation(np.arange(10242))[:6])]
    data = rng.randn(10, 1)
    stc_fs = SourceEstimate(data, vertices_fs, 1, 1, 'fsaverage')
    spheres_fs = [mne.read_surface(op.join(
        subjects_dir, 'fsaverage', 'surf', '%s.sphere.reg' % hemi))[0]
        for hemi in ('lh', 'rh')]
    spheres_sample = [mne.read_surface(op.join(
        subjects_dir, 'sample', 'surf', '%s.sphere.reg' % hemi))[0]
        for hemi in ('lh', 'rh')]
    morph_fs_sample = compute_source_morph(
        stc_fs, 'fsaverage', 'sample', sparse=True, spacing=None,
        subjects_dir=subjects_dir)
    stc_sample = morph_fs_sample.apply(stc_fs)
    offset = 0
    orders = list()
    for v1, s1, v2, s2 in zip(stc_fs.vertices, spheres_fs,
                              stc_sample.vertices, spheres_sample):
        dists = cdist(s1[v1], s2[v2])
        order = np.argmin(dists, axis=-1)
        assert_array_less(dists[np.arange(len(order)), order], 1.5)  # mm
        orders.append(order + offset)
        offset += len(order)
    assert_allclose(stc_fs.data, stc_sample.data[np.concatenate(orders)])
    # Return
    morph_sample_fs = compute_source_morph(
        stc_sample, 'sample', 'fsaverage', sparse=True, spacing=None,
        subjects_dir=subjects_dir)
    stc_fs_return = morph_sample_fs.apply(stc_sample)
    offset = 0
    orders = list()
    for v1, s, v2 in zip(stc_fs.vertices, spheres_fs, stc_fs_return.vertices):
        dists = cdist(s[v1], s[v2])
        order = np.argmin(dists, axis=-1)
        assert_array_less(dists[np.arange(len(order)), order], 1.5)  # mm
        orders.append(order + offset)
        offset += len(order)
    assert_allclose(stc_fs.data, stc_fs_return.data[np.concatenate(orders)])


@requires_version('scipy', '0.13')  # SciPy 0.12 zero-length reduction bug
@testing.requires_testing_data
def test_xhemi_morph():
    """Test cross-hemisphere morphing."""
    stc = read_source_estimate(fname_stc, subject='sample')
    # smooth 1 for speed where possible
    smooth = 4
    spacing = 4
    n_grade_verts = 2562
    stc = compute_source_morph(
        stc, 'sample', 'fsaverage_sym', smooth=smooth, warn=False,
        spacing=spacing, subjects_dir=subjects_dir).apply(stc)
    morph = compute_source_morph(
        stc, 'fsaverage_sym', 'fsaverage_sym', smooth=1, xhemi=True,
        warn=False, spacing=[stc.vertices[0], []],
        subjects_dir=subjects_dir)
    stc_xhemi = morph.apply(stc)
    assert stc_xhemi.data.shape[0] == n_grade_verts
    assert stc_xhemi.rh_data.shape[0] == 0
    assert len(stc_xhemi.vertices[1]) == 0
    assert stc_xhemi.lh_data.shape[0] == n_grade_verts
    assert len(stc_xhemi.vertices[0]) == n_grade_verts
    # complete reversal mapping
    morph = compute_source_morph(
        stc, 'fsaverage_sym', 'fsaverage_sym', smooth=smooth, xhemi=True,
        warn=False, spacing=stc.vertices, subjects_dir=subjects_dir)
    mm = morph.morph_mat
    assert mm.shape == (n_grade_verts * 2,) * 2
    assert mm.size > n_grade_verts * 2
    assert mm[:n_grade_verts, :n_grade_verts].size == 0  # L to L
    assert mm[n_grade_verts:, n_grade_verts:].size == 0  # R to L
    assert mm[n_grade_verts:, :n_grade_verts].size > n_grade_verts  # L to R
    assert mm[:n_grade_verts, n_grade_verts:].size > n_grade_verts  # R to L
    # more complicated reversal mapping
    vertices_use = [stc.vertices[0], np.arange(10242)]
    n_src_verts = len(vertices_use[1])
    assert vertices_use[0].shape == (n_grade_verts,)
    assert vertices_use[1].shape == (n_src_verts,)
    # ensure it's sufficiently diffirent to manifest round-trip errors
    assert np.in1d(vertices_use[1], stc.vertices[1]).mean() < 0.3
    morph = compute_source_morph(
        stc, 'fsaverage_sym', 'fsaverage_sym', smooth=smooth, xhemi=True,
        warn=False, spacing=vertices_use, subjects_dir=subjects_dir)
    mm = morph.morph_mat
    assert mm.shape == (n_grade_verts + n_src_verts, n_grade_verts * 2)
    assert mm[:n_grade_verts, :n_grade_verts].size == 0
    assert mm[n_grade_verts:, n_grade_verts:].size == 0
    assert mm[:n_grade_verts, n_grade_verts:].size > n_grade_verts
    assert mm[n_grade_verts:, :n_grade_verts].size > n_src_verts
    # morph forward then back
    stc_xhemi = morph.apply(stc)
    morph = compute_source_morph(
        stc_xhemi, 'fsaverage_sym', 'fsaverage_sym', smooth=smooth,
        xhemi=True, warn=False, spacing=stc.vertices,
        subjects_dir=subjects_dir)
    stc_return = morph.apply(stc_xhemi)
    for hi in range(2):
        assert_array_equal(stc_return.vertices[hi], stc.vertices[hi])
    correlation = np.corrcoef(stc.data.ravel(), stc_return.data.ravel())[0, 1]
    assert correlation > 0.9  # not great b/c of sparse grade + small smooth


@requires_h5py
@testing.requires_testing_data
def test_surface_vector_source_morph():
    """Test surface and vector source estimate morph."""
    tempdir = _TempDir()

    inverse_operator_surf = read_inverse_operator(fname_inv_surf)

    stc_surf = read_source_estimate(fname_smorph, subject='sample')
    stc_surf.crop(0.09, 0.1)  # for faster computation

    stc_vec = _real_vec_stc()

    source_morph_surf = compute_source_morph(
        inverse_operator_surf['src'], subjects_dir=subjects_dir,
        smooth=1, warn=False)  # smooth 1 for speed
    assert source_morph_surf.subject_from == 'sample'
    assert source_morph_surf.subject_to == 'fsaverage'
    assert source_morph_surf.kind == 'surface'
    assert isinstance(source_morph_surf.src_data, dict)
    assert isinstance(source_morph_surf.src_data['vertices_from'], list)
    assert isinstance(source_morph_surf, SourceMorph)
    stc_surf_morphed = source_morph_surf.apply(stc_surf)
    assert isinstance(stc_surf_morphed, SourceEstimate)
    stc_vec_morphed = source_morph_surf.apply(stc_vec)
    with pytest.raises(ValueError, match='Only volume source estimates'):
        source_morph_surf.apply(stc_surf, output='nifti1')

    # check if correct class after morphing
    assert isinstance(stc_surf_morphed, SourceEstimate)
    assert isinstance(stc_vec_morphed, VectorSourceEstimate)

    # check __repr__
    assert 'surface' in repr(source_morph_surf)

    # check loading and saving for surf
    source_morph_surf.save(op.join(tempdir, '42.h5'))

    source_morph_surf_r = read_source_morph(op.join(tempdir, '42.h5'))

    assert (all([read == saved for read, saved in
                 zip(sorted(source_morph_surf_r.__dict__),
                     sorted(source_morph_surf.__dict__))]))

    # check wrong subject correction
    stc_surf.subject = None
    assert isinstance(source_morph_surf.apply(stc_surf), SourceEstimate)


@requires_h5py
@requires_nibabel()
@requires_dipy()
@pytest.mark.slowtest
@testing.requires_testing_data
def test_volume_source_morph():
    """Test volume source estimate morph, special cases and exceptions."""
    import nibabel as nib
    tempdir = _TempDir()
    inverse_operator_vol = read_inverse_operator(fname_inv_vol)
    stc_vol = read_source_estimate(fname_vol, 'sample')

    # check for invalid input type
    with pytest.raises(TypeError, match='src must be an instance of'):
        compute_source_morph(src=42)

    # check for raising an error if neither
    # inverse_operator_vol['src'][0]['subject_his_id'] nor subject_from is set,
    # but attempting to perform a volume morph
    src = inverse_operator_vol['src']
    src[0]['subject_his_id'] = None

    with pytest.raises(ValueError, match='subject_from could not be inferred'):
        compute_source_morph(src=src, subjects_dir=subjects_dir)

    # check infer subject_from from src[0]['subject_his_id']
    src[0]['subject_his_id'] = 'sample'

    with pytest.raises(ValueError, match='Inter-hemispheric morphing'):
        compute_source_morph(src=src, subjects_dir=subjects_dir, xhemi=True)

    with pytest.raises(ValueError, match='Only surface.*sparse morph'):
        compute_source_morph(src=src, sparse=True, subjects_dir=subjects_dir)

    # terrible quality buts fast
    zooms = 20
    kwargs = dict(zooms=zooms, niter_sdr=(1,), niter_affine=(1,))
    source_morph_vol = compute_source_morph(
        subjects_dir=subjects_dir, src=inverse_operator_vol['src'], **kwargs)
    shape = (13,) * 3  # for the given zooms

    assert source_morph_vol.subject_from == 'sample'

    # the brain used in sample data has shape (255, 255, 255)
    assert tuple(source_morph_vol.sdr_morph.domain_shape) == shape

    assert tuple(source_morph_vol.pre_affine.domain_shape) == shape

    # proofs the above
    assert_array_equal(source_morph_vol.zooms, (zooms,) * 3)

    # assure proper src shape
    mri_size = (src[0]['mri_height'], src[0]['mri_depth'], src[0]['mri_width'])
    assert source_morph_vol.src_data['src_shape_full'] == mri_size

    fwd = read_forward_solution(fname_fwd_vol)
    source_morph_vol = compute_source_morph(
        fwd['src'], 'sample', 'sample', subjects_dir=subjects_dir,
        **kwargs)

    # check wrong subject_to
    with pytest.raises(IOError, match='cannot read file'):
        compute_source_morph(fwd['src'], 'sample', '42',
                             subjects_dir=subjects_dir)

    # two different ways of saving
    source_morph_vol.save(op.join(tempdir, 'vol'))

    # check loading
    source_morph_vol_r = read_source_morph(
        op.join(tempdir, 'vol-morph.h5'))

    # check for invalid file name handling ()
    with pytest.raises(IOError, match='not found'):
        read_source_morph(op.join(tempdir, '42'))

    # check morph
    stc_vol_morphed = source_morph_vol.apply(stc_vol)

    # check output as NIfTI
    assert isinstance(source_morph_vol.apply(stc_vol, output='nifti2'),
                      nib.Nifti2Image)

    # check for subject_from mismatch
    source_morph_vol_r.subject_from = '42'
    with pytest.raises(ValueError, match='subject_from must match'):
        source_morph_vol_r.apply(stc_vol_morphed)

    # check if nifti is in grid morph space with voxel_size == spacing
    img_morph_res = source_morph_vol.apply(stc_vol, output='nifti1')

    # assure morph spacing
    assert isinstance(img_morph_res, nib.Nifti1Image)
    assert img_morph_res.header.get_zooms()[:3] == (zooms,) * 3

    # assure src shape
    img_mri_res = source_morph_vol.apply(stc_vol, output='nifti1',
                                         mri_resolution=True)
    assert isinstance(img_mri_res, nib.Nifti1Image)
    assert (img_mri_res.shape == (src[0]['mri_height'], src[0]['mri_depth'],
                                  src[0]['mri_width']) +
            (img_mri_res.shape[3],))

    # check if nifti is defined resolution with voxel_size == (5., 5., 5.)
    img_any_res = source_morph_vol.apply(stc_vol, output='nifti1',
                                         mri_resolution=(5., 5., 5.))
    assert isinstance(img_any_res, nib.Nifti1Image)
    assert img_any_res.header.get_zooms()[:3] == (5., 5., 5.)

    # check if morph outputs correct data
    assert isinstance(stc_vol_morphed, VolSourceEstimate)

    # check if loaded and saved objects contain the same
    assert (all([read == saved for read, saved in
                 zip(sorted(source_morph_vol_r.__dict__),
                     sorted(source_morph_vol.__dict__))]))

    # check __repr__
    assert 'volume' in repr(source_morph_vol)

    # check Nifti2Image
    assert isinstance(
        source_morph_vol.apply(stc_vol, mri_resolution=True,
                               mri_space=True, output='nifti2'),
        nib.Nifti2Image)

    # Degenerate conditions
    with pytest.raises(TypeError, match='output must be'):
        source_morph_vol.apply(stc_vol, output=1)
    with pytest.raises(ValueError, match='subject_from does not match'):
        compute_source_morph(src=src, subject_from='42')
    with pytest.raises(ValueError, match='output must be one of'):
        source_morph_vol.apply(stc_vol, output='42')
    with pytest.raises(TypeError, match='subject_to must'):
        compute_source_morph(src, 'sample', None,
                             subjects_dir=subjects_dir)
    # Check if not morphed, but voxel size not boolean, raise ValueError.
    # Note that this check requires dipy to not raise the dipy ImportError
    # before checking if the actual voxel size error will raise.
    with pytest.raises(ValueError, match='Cannot infer original voxel size'):
        stc_vol.as_volume(inverse_operator_vol['src'], mri_resolution=4)


@pytest.mark.slowtest
@testing.requires_testing_data
def test_morph_stc_dense():
    """Test morphing stc."""
    subject_from = 'sample'
    subject_to = 'fsaverage'
    stc_from = read_source_estimate(fname_smorph, subject='sample')
    stc_to = read_source_estimate(fname_fmorph)
    # make sure we can specify grade
    stc_from.crop(0.09, 0.1)  # for faster computation
    stc_to.crop(0.09, 0.1)  # for faster computation
    assert_array_equal(stc_to.time_as_index([0.09, 0.1], use_rounding=True),
                       [0, len(stc_to.times) - 1])

    # After dep change this to:
    # stc_to1 = compute_source_morph(
    #     subject_to=subject_to, spacing=3, smooth=12, src=stc_from,
    #     subjects_dir=subjects_dir).apply(stc_from)
    with pytest.deprecated_call():
        stc_to1 = stc_from.morph(
            subject_to=subject_to, grade=3, smooth=12,
            subjects_dir=subjects_dir)
    assert_allclose(stc_to.data, stc_to1.data, atol=1e-5)

    mean_from = stc_from.data.mean(axis=0)
    mean_to = stc_to1.data.mean(axis=0)
    assert np.corrcoef(mean_to, mean_from).min() > 0.999

    vertices_to = grade_to_vertices(subject_to, grade=3,
                                    subjects_dir=subjects_dir)

    # make sure we can fill by morphing
    with pytest.warns(RuntimeWarning, match='consider increasing'):
        morph = compute_source_morph(
            stc_from, subject_from, subject_to, spacing=None, smooth=1,
            subjects_dir=subjects_dir)
    # after deprecation change this to:
    # stc_to5 = morph.apply(stc_from)
    with pytest.deprecated_call():
        stc_to5 = stc_from.morph_precomputed(
            morph_mat=morph.morph_mat, subject_to=subject_to,
            vertices_to=morph.vertices_to)
    assert stc_to5.data.shape[0] == 163842 + 163842
    # after deprecation delete this
    with pytest.deprecated_call():
        stc_to6 = morph_data(
            subject_from, subject_to, stc_from, grade=None, smooth=1,
            subjects_dir=subjects_dir)
    assert_allclose(stc_to6.data, stc_to5.data)

    # Morph vector data
    stc_vec = _real_vec_stc()
    stc_vec_to1 = compute_source_morph(
        stc_vec, subject_from, subject_to, subjects_dir=subjects_dir,
        spacing=vertices_to, smooth=1, warn=False).apply(stc_vec)
    assert stc_vec_to1.subject == subject_to
    assert stc_vec_to1.tmin == stc_vec.tmin
    assert stc_vec_to1.tstep == stc_vec.tstep
    assert len(stc_vec_to1.lh_vertno) == 642
    assert len(stc_vec_to1.rh_vertno) == 642

    # Degenerate conditions

    # Morphing to a density that is too high should raise an informative error
    # (here we need to push to grade=6, but for some subjects even grade=5
    # will break)
    with pytest.raises(ValueError, match='Cannot use icosahedral grade 6 '):
        compute_source_morph(
            stc_to1, subject_from=subject_to, subject_to=subject_from,
            spacing=6, subjects_dir=subjects_dir)
    del stc_to1

    with pytest.raises(ValueError, match='smooth.* has to be at least 1'):
        compute_source_morph(
            stc_from, subject_from, subject_to, spacing=5, smooth=-1,
            subjects_dir=subjects_dir)

    # subject from mismatch
    with pytest.raises(ValueError, match="does not match source space subj"):
        compute_source_morph(stc_from, subject_from='foo',
                             subjects_dir=subjects_dir)

    # only one set of vertices
    with pytest.raises(ValueError, match="grade.*list must have two elements"):
        compute_source_morph(
            stc_from, subject_from=subject_from, spacing=[vertices_to[0]],
            subjects_dir=subjects_dir)


@requires_version('scipy', '0.13')
@testing.requires_testing_data
def test_morph_stc_sparse():
    """Test morphing stc with sparse=True."""
    subject_from = 'sample'
    subject_to = 'fsaverage'
    # Morph sparse data
    # Make a sparse stc
    stc_from = read_source_estimate(fname_smorph, subject='sample')
    stc_from.vertices[0] = stc_from.vertices[0][[100, 500]]
    stc_from.vertices[1] = stc_from.vertices[1][[200]]
    stc_from._data = stc_from._data[:3]

    stc_to_sparse = compute_source_morph(
        stc_from, subject_from=subject_from, subject_to=subject_to,
        spacing=None, sparse=True, subjects_dir=subjects_dir).apply(stc_from)

    assert_allclose(np.sort(stc_from.data.sum(axis=1)),
                    np.sort(stc_to_sparse.data.sum(axis=1)))
    assert len(stc_from.rh_vertno) == len(stc_to_sparse.rh_vertno)
    assert len(stc_from.lh_vertno) == len(stc_to_sparse.lh_vertno)
    assert stc_to_sparse.subject == subject_to
    assert stc_from.tmin == stc_from.tmin
    assert stc_from.tstep == stc_from.tstep

    stc_from.vertices[0] = np.array([], dtype=np.int64)
    stc_from._data = stc_from._data[:1]

    stc_to_sparse = compute_source_morph(
        stc_from, subject_from, subject_to, spacing=None, sparse=True,
        subjects_dir=subjects_dir).apply(stc_from)

    assert_allclose(np.sort(stc_from.data.sum(axis=1)),
                    np.sort(stc_to_sparse.data.sum(axis=1)))
    assert len(stc_from.rh_vertno) == len(stc_to_sparse.rh_vertno)
    assert len(stc_from.lh_vertno) == len(stc_to_sparse.lh_vertno)
    assert stc_to_sparse.subject == subject_to
    assert stc_from.tmin == stc_from.tmin
    assert stc_from.tstep == stc_from.tstep

    # Degenerate cases
    with pytest.raises(ValueError, match='spacing must be set to None'):
        compute_source_morph(
            stc_from, subject_from=subject_from, subject_to=subject_to,
            spacing=5, sparse=True, subjects_dir=subjects_dir)
    with pytest.raises(ValueError, match='xhemi=True can only be used with'):
        compute_source_morph(
            stc_from, subject_from=subject_from, subject_to=subject_to,
            spacing=None, sparse=True, xhemi=True, subjects_dir=subjects_dir)


@requires_nibabel()
@testing.requires_testing_data
def test_volume_labels_morph(tmpdir):
    """Test generating a source space from volume label."""
    # see gh-5224
    evoked = mne.read_evokeds(fname_evoked)[0].crop(0, 0)
    evoked.pick_channels(evoked.ch_names[:306:8])
    evoked.info.normalize_proj()
    n_ch = len(evoked.ch_names)
    aseg_fname = op.join(subjects_dir, 'sample', 'mri', 'aseg.mgz')
    label_names = get_volume_labels_from_aseg(aseg_fname)
    src = setup_volume_source_space(
        'sample', subjects_dir=subjects_dir, volume_label=label_names[:2],
        mri=aseg_fname)
    assert len(src) == 2
    assert src.kind == 'volume'
    n_src = sum(s['nuse'] for s in src)
    sphere = make_sphere_model('auto', 'auto', evoked.info)
    fwd = make_forward_solution(evoked.info, fname_trans, src, sphere)
    assert fwd['sol']['data'].shape == (n_ch, n_src * 3)
    inv = make_inverse_operator(evoked.info, fwd, make_ad_hoc_cov(evoked.info),
                                loose=1.)
    stc = apply_inverse(evoked, inv)
    assert stc.data.shape == (n_src, 1)
    img = stc.as_volume(src, mri_resolution=True)
    n_on = np.array(img.dataobj).astype(bool).sum()
    assert n_on == 291  # was 291 on `master` before gh-5590
    img = stc.as_volume(src, mri_resolution=False)
    n_on = np.array(img.dataobj).astype(bool).sum()
    assert n_on == 44  # was 20 on `master` before gh-5590


run_tests_if_main()