Python fixes.in1d函数代码示例

def test_label_in_src():
    """Test label in src"""
    src = read_source_spaces(src_fname)
    label = read_label(v1_label_fname)

    # construct label from source space vertices
    vert_in_src = np.intersect1d(label.vertices, src[0]['vertno'], True)
    where = in1d(label.vertices, vert_in_src)
    pos_in_src = label.pos[where]
    values_in_src = label.values[where]
    label_src = Label(vert_in_src, pos_in_src, values_in_src,
                      hemi='lh').fill(src)

    # check label vertices
    vertices_status = in1d(src[0]['nearest'], label.vertices)
    vertices_in = np.nonzero(vertices_status)[0]
    vertices_out = np.nonzero(np.logical_not(vertices_status))[0]
    assert_array_equal(label_src.vertices, vertices_in)
    assert_array_equal(in1d(vertices_out, label_src.vertices), False)

    # check values
    value_idx = digitize(src[0]['nearest'][vertices_in], vert_in_src, True)
    assert_array_equal(label_src.values, values_in_src[value_idx])

    # test exception
    vertices = np.append([-1], vert_in_src)
    assert_raises(ValueError, Label(vertices, hemi='lh').fill, src)

def test_morph():
    """Test inter-subject label morphing
    """
    label_orig = read_label(real_label_fname)
    label_orig.subject = 'sample'
    # should work for specifying vertices for both hemis, or just the
    # hemi of the given label
    vals = list()
    for grade in [5, [np.arange(10242), np.arange(10242)], np.arange(10242)]:
        label = label_orig.copy()
        # this should throw an error because the label has all zero values
        assert_raises(ValueError, label.morph, 'sample', 'fsaverage')
        label.values.fill(1)
        label = label.morph(None, 'fsaverage', 5, grade, subjects_dir, 1)
        label = label.morph('fsaverage', 'sample', 5, None, subjects_dir, 2)
        assert_true(np.mean(in1d(label_orig.vertices, label.vertices)) == 1.0)
        assert_true(len(label.vertices) < 3 * len(label_orig.vertices))
        vals.append(label.vertices)
    assert_array_equal(vals[0], vals[1])
    # make sure label smoothing can run
    assert_equal(label.subject, 'sample')
    verts = [np.arange(10242), np.arange(10242)]
    for hemi in ['lh', 'rh']:
        label.hemi = hemi
        label.morph(None, 'fsaverage', 5, verts, subjects_dir, 2)
    assert_raises(TypeError, label.morph, None, 1, 5, verts,
                  subjects_dir, 2)
    assert_raises(TypeError, label.morph, None, 'fsaverage', 5.5, verts,
                  subjects_dir, 2)
    with warnings.catch_warnings(record=True):  # morph map could be missing
        label.smooth(subjects_dir=subjects_dir)  # make sure this runs

def test_morph():
    """Test inter-subject label morphing
    """
    label_orig = read_label(real_label_fname)
    label_orig.subject = 'sample'
    # should work for specifying vertices for both hemis, or just the
    # hemi of the given label
    vals = list()
    for grade in [5, [np.arange(10242), np.arange(10242)], np.arange(10242)]:
        label = label_orig.copy()
        # this should throw an error because the label has all zero values
        assert_raises(ValueError, label.morph, 'sample', 'fsaverage')
        label.values.fill(1)
        label.morph(None, 'fsaverage', 5, grade, subjects_dir, 2,
                    copy=False)
        label.morph('fsaverage', 'sample', 5, None, subjects_dir, 2,
                    copy=False)
        assert_true(np.mean(in1d(label_orig.vertices, label.vertices)) == 1.0)
        assert_true(len(label.vertices) < 3 * len(label_orig.vertices))
        vals.append(label.vertices)
    assert_array_equal(vals[0], vals[1])
    # make sure label smoothing can run
    label.morph(label.subject, 'fsaverage', 5,
                [np.arange(10242), np.arange(10242)], subjects_dir, 2,
                copy=False)
    # subject name should be inferred now
    label.smooth(subjects_dir=subjects_dir)

def test_morph():
    """Test inter-subject label morphing
    """
    label_orig = read_label(real_label_fname)
    label_orig.subject = "sample"
    # should work for specifying vertices for both hemis, or just the
    # hemi of the given label
    vals = list()
    for grade in [5, [np.arange(10242), np.arange(10242)], np.arange(10242)]:
        label = label_orig.copy()
        # this should throw an error because the label has all zero values
        assert_raises(ValueError, label.morph, "sample", "fsaverage")
        label.values.fill(1)
        label.morph(None, "fsaverage", 5, grade, subjects_dir, 1, copy=False)
        label.morph("fsaverage", "sample", 5, None, subjects_dir, 2, copy=False)
        assert_true(np.mean(in1d(label_orig.vertices, label.vertices)) == 1.0)
        assert_true(len(label.vertices) < 3 * len(label_orig.vertices))
        vals.append(label.vertices)
    assert_array_equal(vals[0], vals[1])
    # make sure label smoothing can run
    assert_equal(label.subject, "sample")
    verts = [np.arange(10242), np.arange(10242)]
    for hemi in ["lh", "rh"]:
        label.hemi = hemi
        label.morph(None, "fsaverage", 5, verts, subjects_dir, 2)
    assert_raises(TypeError, label.morph, None, 1, 5, verts, subjects_dir, 2)
    assert_raises(TypeError, label.morph, None, "fsaverage", 5.5, verts, subjects_dir, 2)
    label.smooth(subjects_dir=subjects_dir)  # make sure this runs

def test_grow_labels():
    """Test generation of circular source labels"""
    seeds = [0, 50000]
    # these were chosen manually in mne_analyze
    should_be_in = [[49, 227], [51207, 48794]]
    hemis = [0, 1]
    labels = grow_labels('sample', seeds, 3, hemis, subjects_dir, n_jobs=2)

    for label, seed, hemi, sh in zip(labels, seeds, hemis, should_be_in):
        assert_true(np.any(label.vertices == seed))
        assert_true(np.all(in1d(sh, label.vertices)))
        if hemi == 0:
            assert_equal(label.hemi, 'lh')
        else:
            assert_equal(label.hemi, 'rh')

def test_grow_labels():
    """Test generation of circular source labels"""
    seeds = [0, 50000]
    # these were chosen manually in mne_analyze
    should_be_in = [[49, 227], [51207, 48794]]
    hemis = [0, 1]
    names = ['aneurism', 'tumor']
    labels = grow_labels('sample', seeds, 3, hemis, subjects_dir, n_jobs=2,
                         names=names)

    tgt_names = ['aneurism-lh', 'tumor-rh']
    tgt_hemis = ['lh', 'rh']
    for label, seed, hemi, sh, name in zip(labels, seeds, tgt_hemis,
                                           should_be_in, tgt_names):
        assert_true(np.any(label.vertices == seed))
        assert_true(np.all(in1d(sh, label.vertices)))
        assert_equal(label.hemi, hemi)
        assert_equal(label.name, name)

    # grow labels with and without overlap
    seeds = [57532, [58887, 6304]]
    l01, l02 = grow_labels('fsaverage', seeds, 20, [0, 0], subjects_dir)
    seeds = [57532, [58887, 6304]]
    l11, l12 = grow_labels('fsaverage', seeds, 20, [0, 0], subjects_dir,
                           overlap=False)

    # test label naming
    assert_equal(l01.name, 'Label_0-lh')
    assert_equal(l02.name, 'Label_1-lh')
    assert_equal(l11.name, 'Label_0-lh')
    assert_equal(l12.name, 'Label_1-lh')

    # make sure set 1 does not overlap
    overlap = np.intersect1d(l11.vertices, l12.vertices, True)
    assert_array_equal(overlap, [])

    # make sure both sets cover the same vertices
    l0 = l01 + l02
    l1 = l11 + l12
    assert_array_equal(l1.vertices, l0.vertices)

#.........这里部分代码省略.........
    write_labels_to_annot([label], 'sample', 'test2', subjects_dir=tempdir)
    assert_true(op.exists(dst % ('lh', 'test2')))
    assert_true(op.exists(dst % ('rh', 'test2')))
    # rh only
    for label in labels:
        if label.hemi == 'rh':
            break
    write_labels_to_annot([label], 'sample', 'test3', subjects_dir=tempdir)
    assert_true(op.exists(dst % ('lh', 'test3')))
    assert_true(op.exists(dst % ('rh', 'test3')))
    # label alone
    assert_raises(TypeError, write_labels_to_annot, labels[0], 'sample',
                  'test4', subjects_dir=tempdir)

    # write left and right hemi labels with filenames:
    fnames = [op.join(tempdir, hemi + '-myparc') for hemi in ['lh', 'rh']]
    with warnings.catch_warnings(record=True):  # specify subject_dir param
        for fname in fnames:
                write_labels_to_annot(labels, annot_fname=fname)

    # read it back
    labels2 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                     annot_fname=fnames[0])
    labels22 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                      annot_fname=fnames[1])
    labels2.extend(labels22)

    names = [label.name for label in labels2]

    for label in labels:
        idx = names.index(label.name)
        assert_labels_equal(label, labels2[idx])

    # same with label-internal colors
    for fname in fnames:
        write_labels_to_annot(labels, 'sample', annot_fname=fname,
                              overwrite=True, subjects_dir=subjects_dir)
    labels3 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                     annot_fname=fnames[0])
    labels33 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                      annot_fname=fnames[1])
    labels3.extend(labels33)
    names3 = [label.name for label in labels3]
    for label in labels:
        idx = names3.index(label.name)
        assert_labels_equal(label, labels3[idx])

    # make sure we can't overwrite things
    assert_raises(ValueError, write_labels_to_annot, labels, 'sample',
                  annot_fname=fnames[0], subjects_dir=subjects_dir)

    # however, this works
    write_labels_to_annot(labels, 'sample', annot_fname=fnames[0],
                          overwrite=True, subjects_dir=subjects_dir)

    # label without color
    labels_ = labels[:]
    labels_[0] = labels_[0].copy()
    labels_[0].color = None
    write_labels_to_annot(labels_, 'sample', annot_fname=fnames[0],
                          overwrite=True, subjects_dir=subjects_dir)

    # duplicate color
    labels_[0].color = labels_[2].color
    assert_raises(ValueError, write_labels_to_annot, labels_, 'sample',
                  annot_fname=fnames[0], overwrite=True,
                  subjects_dir=subjects_dir)

    # invalid color inputs
    labels_[0].color = (1.1, 1., 1., 1.)
    assert_raises(ValueError, write_labels_to_annot, labels_, 'sample',
                  annot_fname=fnames[0], overwrite=True,
                  subjects_dir=subjects_dir)

    # overlapping labels
    labels_ = labels[:]
    cuneus_lh = labels[6]
    precuneus_lh = labels[50]
    labels_.append(precuneus_lh + cuneus_lh)
    assert_raises(ValueError, write_labels_to_annot, labels_, 'sample',
                  annot_fname=fnames[0], overwrite=True,
                  subjects_dir=subjects_dir)

    # unlabeled vertices
    labels_lh = [label for label in labels if label.name.endswith('lh')]
    write_labels_to_annot(labels_lh[1:], 'sample', annot_fname=fnames[0],
                          overwrite=True, subjects_dir=subjects_dir)
    labels_reloaded = read_labels_from_annot('sample', annot_fname=fnames[0],
                                             subjects_dir=subjects_dir)
    assert_equal(len(labels_lh), len(labels_reloaded))
    label0 = labels_lh[0]
    label1 = labels_reloaded[-1]
    assert_equal(label1.name, "unknown-lh")
    assert_true(np.all(in1d(label0.vertices, label1.vertices)))

    # unnamed labels
    labels4 = labels[:]
    labels4[0].name = None
    assert_raises(ValueError, write_labels_to_annot, labels4,
                  annot_fname=fnames[0])

def test_write_labels_to_annot():
    """Test writing FreeSurfer parcellation from labels"""
    tempdir = _TempDir()

    labels = read_labels_from_annot('sample', subjects_dir=subjects_dir)

    # write left and right hemi labels:
    fnames = ['%s/%s-myparc' % (tempdir, hemi) for hemi in ['lh', 'rh']]

    for fname in fnames:
        write_labels_to_annot(labels, annot_fname=fname)

    # read it back
    labels2 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                     annot_fname=fnames[0])
    labels22 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                      annot_fname=fnames[1])
    labels2.extend(labels22)

    names = [label.name for label in labels2]

    for label in labels:
        idx = names.index(label.name)
        assert_labels_equal(label, labels2[idx])

    # same with label-internal colors
    for fname in fnames:
        write_labels_to_annot(labels, annot_fname=fname, overwrite=True)
    labels3 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                     annot_fname=fnames[0])
    labels33 = read_labels_from_annot('sample', subjects_dir=subjects_dir,
                                      annot_fname=fnames[1])
    labels3.extend(labels33)
    names3 = [label.name for label in labels3]
    for label in labels:
        idx = names3.index(label.name)
        assert_labels_equal(label, labels3[idx])

    # make sure we can't overwrite things
    assert_raises(ValueError, write_labels_to_annot, labels,
                  annot_fname=fnames[0])

    # however, this works
    write_labels_to_annot(labels, annot_fname=fnames[0], overwrite=True)

    # label without color
    labels_ = labels[:]
    labels_[0] = labels_[0].copy()
    labels_[0].color = None
    write_labels_to_annot(labels_, annot_fname=fnames[0], overwrite=True)

    # duplicate color
    labels_[0].color = labels_[2].color
    assert_raises(ValueError, write_labels_to_annot, labels_,
                  annot_fname=fnames[0], overwrite=True)

    # invalid color inputs
    labels_[0].color = (1.1, 1., 1., 1.)
    assert_raises(ValueError, write_labels_to_annot, labels_,
                  annot_fname=fnames[0], overwrite=True)

    # overlapping labels
    labels_ = labels[:]
    cuneus_lh = labels[6]
    precuneus_lh = labels[50]
    labels_.append(precuneus_lh + cuneus_lh)
    assert_raises(ValueError, write_labels_to_annot, labels_,
                  annot_fname=fnames[0], overwrite=True)

    # unlabeled vertices
    labels_lh = [label for label in labels if label.name.endswith('lh')]
    write_labels_to_annot(labels_lh[1:], 'sample', annot_fname=fnames[0],
                          overwrite=True, subjects_dir=subjects_dir)
    labels_reloaded = read_labels_from_annot('sample', annot_fname=fnames[0],
                                             subjects_dir=subjects_dir)
    assert_equal(len(labels_lh), len(labels_reloaded))
    label0 = labels_lh[0]
    label1 = labels_reloaded[-1]
    assert_equal(label1.name, "unknown-lh")
    assert_true(np.all(in1d(label0.vertices, label1.vertices)))

def test_write_labels_to_annot():
    """Test writing FreeSurfer parcellation from labels"""
    tempdir = _TempDir()

    labels = read_labels_from_annot("sample", subjects_dir=subjects_dir)

    # create temporary subjects-dir skeleton
    surf_dir = op.join(subjects_dir, "sample", "surf")
    temp_surf_dir = op.join(tempdir, "sample", "surf")
    os.makedirs(temp_surf_dir)
    shutil.copy(op.join(surf_dir, "lh.white"), temp_surf_dir)
    shutil.copy(op.join(surf_dir, "rh.white"), temp_surf_dir)
    os.makedirs(op.join(tempdir, "sample", "label"))

    # test automatic filenames
    dst = op.join(tempdir, "sample", "label", "%s.%s.annot")
    write_labels_to_annot(labels, "sample", "test1", subjects_dir=tempdir)
    assert_true(op.exists(dst % ("lh", "test1")))
    assert_true(op.exists(dst % ("rh", "test1")))
    # lh only
    for label in labels:
        if label.hemi == "lh":
            break
    write_labels_to_annot([label], "sample", "test2", subjects_dir=tempdir)
    assert_true(op.exists(dst % ("lh", "test2")))
    assert_true(op.exists(dst % ("rh", "test2")))
    # rh only
    for label in labels:
        if label.hemi == "rh":
            break
    write_labels_to_annot([label], "sample", "test3", subjects_dir=tempdir)
    assert_true(op.exists(dst % ("lh", "test3")))
    assert_true(op.exists(dst % ("rh", "test3")))
    # label alone
    assert_raises(TypeError, write_labels_to_annot, labels[0], "sample", "test4", subjects_dir=tempdir)

    # write left and right hemi labels with filenames:
    fnames = ["%s/%s-myparc" % (tempdir, hemi) for hemi in ["lh", "rh"]]
    for fname in fnames:
        write_labels_to_annot(labels, annot_fname=fname)

    # read it back
    labels2 = read_labels_from_annot("sample", subjects_dir=subjects_dir, annot_fname=fnames[0])
    labels22 = read_labels_from_annot("sample", subjects_dir=subjects_dir, annot_fname=fnames[1])
    labels2.extend(labels22)

    names = [label.name for label in labels2]

    for label in labels:
        idx = names.index(label.name)
        assert_labels_equal(label, labels2[idx])

    # same with label-internal colors
    for fname in fnames:
        write_labels_to_annot(labels, annot_fname=fname, overwrite=True)
    labels3 = read_labels_from_annot("sample", subjects_dir=subjects_dir, annot_fname=fnames[0])
    labels33 = read_labels_from_annot("sample", subjects_dir=subjects_dir, annot_fname=fnames[1])
    labels3.extend(labels33)
    names3 = [label.name for label in labels3]
    for label in labels:
        idx = names3.index(label.name)
        assert_labels_equal(label, labels3[idx])

    # make sure we can't overwrite things
    assert_raises(ValueError, write_labels_to_annot, labels, annot_fname=fnames[0])

    # however, this works
    write_labels_to_annot(labels, annot_fname=fnames[0], overwrite=True)

    # label without color
    labels_ = labels[:]
    labels_[0] = labels_[0].copy()
    labels_[0].color = None
    write_labels_to_annot(labels_, annot_fname=fnames[0], overwrite=True)

    # duplicate color
    labels_[0].color = labels_[2].color
    assert_raises(ValueError, write_labels_to_annot, labels_, annot_fname=fnames[0], overwrite=True)

    # invalid color inputs
    labels_[0].color = (1.1, 1.0, 1.0, 1.0)
    assert_raises(ValueError, write_labels_to_annot, labels_, annot_fname=fnames[0], overwrite=True)

    # overlapping labels
    labels_ = labels[:]
    cuneus_lh = labels[6]
    precuneus_lh = labels[50]
    labels_.append(precuneus_lh + cuneus_lh)
    assert_raises(ValueError, write_labels_to_annot, labels_, annot_fname=fnames[0], overwrite=True)

    # unlabeled vertices
    labels_lh = [label for label in labels if label.name.endswith("lh")]
    write_labels_to_annot(labels_lh[1:], "sample", annot_fname=fnames[0], overwrite=True, subjects_dir=subjects_dir)
    labels_reloaded = read_labels_from_annot("sample", annot_fname=fnames[0], subjects_dir=subjects_dir)
    assert_equal(len(labels_lh), len(labels_reloaded))
    label0 = labels_lh[0]
    label1 = labels_reloaded[-1]
    assert_equal(label1.name, "unknown-lh")
    assert_true(np.all(in1d(label0.vertices, label1.vertices)))