def test_assert_objectarray_equal():
    if versions['numpy'] < '1.4':
        raise SkipTest("Skipping because of known segfaults with numpy < 1.4")
    # explicit dtype so we could test with numpy < 1.6
    a = np.array([np.array([0, 1]), np.array(1)], dtype=object)
    b = np.array([np.array([0, 1]), np.array(1)], dtype=object)

    # they should be ok for both types of comparison
    for strict in True, False:
        # good with self
        assert_objectarray_equal(a, a, strict=strict)
        # good with a copy
        assert_objectarray_equal(a, a.copy(), strict=strict)
        # good while operating with an identical one
        # see http://projects.scipy.org/numpy/ticket/2117
        assert_objectarray_equal(a, b, strict=strict)

    # now check if we still fail for a good reason
    for value_equal, b in (
            (False, np.array(1)),
            (False, np.array([1])),
            (False, np.array([np.array([0, 1]), np.array((1, 2))], dtype=object)),
            (False, np.array([np.array([0, 1]), np.array(1.1)], dtype=object)),
            (True, np.array([np.array([0, 1]), np.array(1.0)], dtype=object)),
            (True, np.array([np.array([0, 1]), np.array(1, dtype=object)], dtype=object)),
    ):
        assert_raises(AssertionError, assert_objectarray_equal, a, b)
        if value_equal:
            # but should not raise for non-default strict=False
            assert_objectarray_equal(a, b, strict=False)
        else:
            assert_raises(AssertionError, assert_objectarray_equal, a, b, strict=False)

def test_mapper_vs_zscore():
    """Test by comparing to results of elderly z-score function
    """
    # data: 40 sample feature line in 20d space (40x20; samples x features)
    dss = [
        dataset_wizard(np.concatenate(
            [np.arange(40) for i in range(20)]).reshape(20,-1).T,
                targets=1, chunks=1),
        ] + datasets.values()

    for ds in dss:
        ds1 = deepcopy(ds)
        ds2 = deepcopy(ds)

        zsm = ZScoreMapper(chunks_attr=None)
        assert_raises(RuntimeError, zsm.forward, ds1.samples)
        idhashes = (idhash(ds1), idhash(ds1.samples))
        zsm.train(ds1)
        idhashes_train = (idhash(ds1), idhash(ds1.samples))
        assert_equal(idhashes, idhashes_train)

        # forward dataset
        ds1z_ds = zsm.forward(ds1)
        idhashes_forwardds = (idhash(ds1), idhash(ds1.samples))
        # must not modify samples in place!
        assert_equal(idhashes, idhashes_forwardds)

        # forward samples explicitly
        ds1z = zsm.forward(ds1.samples)
        idhashes_forward = (idhash(ds1), idhash(ds1.samples))
        assert_equal(idhashes, idhashes_forward)

        zscore(ds2, chunks_attr=None)
        assert_array_almost_equal(ds1z, ds2.samples)
        assert_array_equal(ds1.samples, ds.samples)

def test_sphere_scaled():
    s1 = ne.Sphere(3)
    s = ne.Sphere(3, element_sizes=(1, 1))

    # Should give exactly the same results since element_sizes are 1s
    for p in ((0, 0), (-23, 1)):
        assert_array_equal(s1(p), s(p))
        ok_(len(s(p)) == len(set(s(p))))

    # Raise exception if query dimensionality does not match element_sizes
    assert_raises(ValueError, s, (1,))

    s = ne.Sphere(3, element_sizes=(1.5, 2))
    assert_array_equal(s((0, 0)),
                       [(-2, 0), (-1, -1), (-1, 0), (-1, 1),
                        (0, -1), (0, 0), (0, 1),
                        (1, -1), (1, 0), (1, 1), (2, 0)])

    s = ne.Sphere(1.5, element_sizes=(1.5, 1.5, 1.5))
    res = s((0, 0, 0))
    ok_(np.all([np.sqrt(np.sum(np.array(x)**2)) <= 1.5 for x in res]))
    ok_(len(res) == 7)

    # all neighbors so no more than 1 voxel away -- just a cube, for
    # some "sphere" effect radius had to be 3.0 ;)
    td = np.sqrt(3*1.5**2)
    s = ne.Sphere(td, element_sizes=(1.5, 1.5, 1.5))
    res = s((0, 0, 0))
    ok_(np.all([np.sqrt(np.sum(np.array(x)**2)) <= td for x in res]))
    ok_(np.all([np.sum(np.abs(x) > 1) == 0 for x in res]))
    ok_(len(res) == 27)

def test_basic_collectable():
    c = Collectable()

    # empty by default
    assert_equal(c.name, None)
    assert_equal(c.value, None)
    assert_equal(c.__doc__, None)

    # late assignment
    c.name = 'somename'
    c.value = 12345
    assert_equal(c.name, 'somename')
    assert_equal(c.value, 12345)

    # immediate content
    c = Collectable('value', 'myname', "This is a test")
    assert_equal(c.name, 'myname')
    assert_equal(c.value, 'value')
    assert_equal(c.__doc__, "This is a test")
    assert_equal(str(c), 'myname')

    # repr
    e = eval(repr(c))
    assert_equal(e.name, 'myname')
    assert_equal(e.value, 'value')
    assert_equal(e.__doc__, "This is a test")

    # shallow copy does not create a view of value array
    c.value = np.arange(5)
    d = copy.copy(c)
    assert_false(d.value.base is c.value)

    # names starting with _ are not allowed
    assert_raises(ValueError, c._set_name, "_underscore")

def test_corrstability_smoketest(ds):
    if not 'chunks' in ds.sa:
        return
    if len(ds.sa['targets'].unique) > 30:
        # was regression dataset
        return
    # very basic testing since
    cs = CorrStability()
    #ds = datasets['uni2small']
    out = cs(ds)
    assert_equal(out.shape, (ds.nfeatures,))
    ok_(np.all(out >= -1.001))  # it should be a correlation after all
    ok_(np.all(out <= 1.001))

    # and theoretically those nonbogus features should have higher values
    if 'nonbogus_targets' in ds.fa:
        bogus_features = np.array([x==None for x in  ds.fa.nonbogus_targets])
        assert_array_less(np.mean(out[bogus_features]), np.mean(out[~bogus_features]))
    # and if we move targets to alternative location
    ds = ds.copy(deep=True)
    ds.sa['alt'] = ds.T
    ds.sa.pop('targets')
    assert_raises(KeyError, cs, ds)
    cs = CorrStability('alt')
    out_ = cs(ds)
    assert_array_equal(out, out_)

def test_sifter_with_balancing():
    # extended previous test which was already
    # "... somewhat duplicating the doctest"
    ds = Dataset(samples=np.arange(12).reshape((-1, 2)),
                 sa={'chunks':   [ 0 ,  1 ,  2 ,  3 ,  4,   5 ],
                     'targets':  ['c', 'c', 'c', 'p', 'p', 'p']})

    # Without sifter -- just to assure that we do get all of them
    # i.e. 6*5*4*3/(4!) = 15
    par = ChainNode([NFoldPartitioner(cvtype=4, attr='chunks')])
    assert_equal(len(list(par.generate(ds))), 15)

    # so we will take 4 chunks out of available 7, but would care only
    # about those partitions where we have balanced number of 'c' and 'p'
    # entries
    assert_raises(ValueError,
                  lambda x: list(Sifter([('targets', dict(wrong=1))]).generate(x)),
                  ds)

    par = ChainNode([NFoldPartitioner(cvtype=4, attr='chunks'),
                     Sifter([('partitions', 2),
                             ('targets',
                              dict(uvalues=['c', 'p'],
                                   balanced=True))])
                     ])
    dss = list(par.generate(ds))
    # print [ x[x.sa.partitions==2].sa.targets for x in dss ]
    assert_equal(len(dss), 9)
    for ds_ in dss:
        testing = ds[ds_.sa.partitions == 2]
        assert_array_equal(np.unique(testing.sa.targets), ['c', 'p'])
        # and we still have both targets  present in training
        training = ds[ds_.sa.partitions == 1]
        assert_array_equal(np.unique(training.sa.targets), ['c', 'p'])

def test_permute_chunks():

    def is_sorted(x):
        return np.array_equal(np.sort(x), x)

    ds = give_data()
    # change targets labels
    # there is no target labels permuting within chunks,
    # assure = True would be error
    ds.sa['targets'] = range(len(ds.sa.targets))
    permutation = AttributePermutator(attr='targets',
                                      chunk_attr='chunks',
                                      strategy='chunks',
                                      assure=True)

    pds = permutation(ds)

    assert_false(is_sorted(pds.sa.targets))
    assert_true(np.array_equal(pds.samples, ds.samples))
    for chunk_id in np.unique(pds.sa.chunks):
        chunk_ds = pds[pds.sa.chunks == chunk_id]
        assert_true(is_sorted(chunk_ds.sa.targets))
        
    permutation = AttributePermutator(attr='targets',
                                      strategy='chunks')
    assert_raises(ValueError, permutation, ds)

def test_product_flatten():
    nsamples = 17
    product_name_values = [('chan', ['C1', 'C2']),
                         ('freq', np.arange(4, 20, 6)),
                         ('time', np.arange(-200, 800, 200))]

    shape = (nsamples,) + tuple(len(v) for _, v in product_name_values)

    sample_names = ['samp%d' % i for i in xrange(nsamples)]

    # generate random data in four dimensions
    data = np.random.normal(size=shape)
    ds = Dataset(data, sa=dict(sample_names=sample_names))

    # apply flattening to ds
    flattener = ProductFlattenMapper(product_name_values)

    # test I/O (only if h5py is available)
    if externals.exists('h5py'):
        from mvpa2.base.hdf5 import h5save, h5load
        import tempfile
        import os

        _, testfn = tempfile.mkstemp('mapper.h5py', 'test_product')
        h5save(testfn, flattener)
        flattener = h5load(testfn)
        os.unlink(testfn)

    mds = flattener(ds)

    prod = lambda x:reduce(operator.mul, x)

    # ensure the size is ok
    assert_equal(mds.shape, (nsamples,) + (prod(shape[1:]),))

    ndim = len(product_name_values)

    idxs = [range(len(v)) for _, v in product_name_values]
    for si in xrange(nsamples):
        for fi, p in enumerate(itertools.product(*idxs)):
            data_tup = (si,) + p

            x = mds[si, fi]

            # value should match
            assert_equal(data[data_tup], x.samples[0, 0])

            # indices should match as well
            all_idxs = tuple(x.fa['chan_freq_time_indices'].value.ravel())
            assert_equal(p, all_idxs)

            # values and indices in each dimension should match
            for i, (name, value) in enumerate(product_name_values):
                assert_equal(x.fa[name].value, value[p[i]])
                assert_equal(x.fa[name + '_indices'].value, p[i])

    product_name_values += [('foo', [1, 2, 3])]
    flattener = ProductFlattenMapper(product_name_values)
    assert_raises(ValueError, flattener, ds)

    def test_vector_alignment_find_rotation_illegal_inputs(self):
        arr = np.asarray
        illegal_args = [
            [arr([1, 2]), arr([1, 3])],
            [arr([1, 2, 3]), arr([1, 3])],
            [arr([1, 2, 3]), np.random.normal(size=(3, 3))]
        ]

        for illegal_arg in illegal_args:
            assert_raises((ValueError, IndexError),
                          vector_alignment_find_rotation, *illegal_arg)

def test_attrmap_conflicts():
    am_n = AttributeMap({'a':1, 'b':2, 'c':1})
    am_t = AttributeMap({'a':1, 'b':2, 'c':1}, collisions_resolution='tuple')
    am_l = AttributeMap({'a':1, 'b':2, 'c':1}, collisions_resolution='lucky')
    q_f = ['a', 'b', 'a', 'c']
    # should have no effect on forward mapping
    ok_(np.all(am_n.to_numeric(q_f) == am_t.to_numeric(q_f)))
    ok_(np.all(am_t.to_numeric(q_f) == am_l.to_numeric(q_f)))

    assert_raises(ValueError, am_n.to_literal, [2])
    r_t = am_t.to_literal([2, 1])
    r_l = am_l.to_literal([2, 1])

def test_mean_tpr():
    # Let's test now on some disbalanced sets
    assert_raises(ValueError, mean_tpr, [1], [])
    assert_raises(ValueError, mean_tpr, [], [1])
    assert_raises(ValueError, mean_tpr, [], [])

    # now interesting one where there were no target when it was in predicted
    assert_raises(ValueError, mean_tpr, [1], [0])
    assert_raises(ValueError, mean_tpr, [0, 1], [0, 0])
    # but it should be ok to have some targets not present in prediction
    assert_equal(mean_tpr([0, 0], [0, 1]), .5)
    # the same regardless how many samples in 0-class, if all misclassified
    # (winner by # of samples takes all)
    assert_equal(mean_tpr([0, 0, 0], [0, 0, 1]), .5)
    # whenever mean-accuracy would be different
    assert_almost_equal(mean_match_accuracy([0, 0, 0], [0, 0, 1]), 2/3.)

def test_splitter():
    ds = give_data()
    # split with defaults
    spl1 = Splitter('chunks')
    assert_raises(NotImplementedError, spl1, ds)

    splits = list(spl1.generate(ds))
    assert_equal(len(splits), len(ds.sa['chunks'].unique))

    for split in splits:
        # it should have perform basic slicing!
        assert_true(split.samples.base is ds.samples)
        assert_equal(len(split.sa['chunks'].unique), 1)
        assert_true('lastsplit' in split.a)
    assert_true(splits[-1].a.lastsplit)

    # now again, more customized
    spl2 = Splitter('targets', attr_values = [0,1,1,2,3,3,3], count=4,
                   noslicing=True)
    splits = list(spl2.generate(ds))
    assert_equal(len(splits), 4)
    for split in splits:
        # it should NOT have perform basic slicing!
        assert_false(split.samples.base is ds.samples)
        assert_equal(len(split.sa['targets'].unique), 1)
        assert_equal(len(split.sa['chunks'].unique), 10)
    assert_true(splits[-1].a.lastsplit)

    # two should be identical
    assert_array_equal(splits[1].samples, splits[2].samples)

    # now go wild and split by feature attribute
    ds.fa['roi'] = np.repeat([0,1], 5)
    # splitter should auto-detect that this is a feature attribute
    spl3 = Splitter('roi')
    splits = list(spl3.generate(ds))
    assert_equal(len(splits), 2)
    for split in splits:
        assert_true(split.samples.base is ds.samples)
        assert_equal(len(split.fa['roi'].unique), 1)
        assert_equal(split.shape, (100, 5))

    # and finally test chained splitters
    cspl = ChainNode([spl2, spl3, spl1])
    splits = list(cspl.generate(ds))
    # 4 target splits and 2 roi splits each and 10 chunks each
    assert_equal(len(splits), 80)

def test_collections():
    sa = SampleAttributesCollection()
    assert_equal(len(sa), 0)

    assert_raises(ValueError, sa.__setitem__, 'test', 0)
    l = range(5)
    sa['test'] = l
    # auto-wrapped
    assert_true(isinstance(sa['test'], ArrayCollectable))
    assert_equal(len(sa), 1)

    # names which are already present in dict interface
    assert_raises(ValueError, sa.__setitem__, 'values', range(5))

    sa_c = copy.deepcopy(sa)
    assert_equal(len(sa), len(sa_c))
    assert_array_equal(sa.test, sa_c.test)

def test_cached_query_engine():
    """Test cached query engine
    """
    sphere = ne.Sphere(1)
    # dataset with just one "space"
    ds = datasets['3dlarge']
    qe0 = ne.IndexQueryEngine(myspace=sphere)
    qec = ne.CachedQueryEngine(qe0)

    # and ground truth one
    qe = ne.IndexQueryEngine(myspace=sphere)
    results_ind = []
    results_kw = []

    def cmp_res(res1, res2):
        comp = [x == y for x, y in zip(res1, res2)]
        ok_(np.all(comp))

    for iq, q in enumerate((qe, qec)):
        q.train(ds)
        # sequential train on the same should be ok in both cases
        q.train(ds)
        res_ind = [q[fid] for fid in xrange(ds.nfeatures)]
        res_kw = [q(myspace=x) for x in ds.fa.myspace]
        # test if results match
        cmp_res(res_ind, res_kw)

        results_ind.append(res_ind)
        results_kw.append(res_kw)

    # now check if results of cached were the same as of regular run
    cmp_res(results_ind[0], results_ind[1])

    # Now do sanity checks
    assert_raises(ValueError, qec.train, ds[:, :-1])
    assert_raises(ValueError, qec.train, ds.copy())
    ds2 = ds.copy()
    qec.untrain()
    qec.train(ds2)
    # should be the same results on the copy
    cmp_res(results_ind[0], [qec[fid] for fid in xrange(ds.nfeatures)])
    cmp_res(results_kw[0], [qec(myspace=x) for x in ds.fa.myspace])
    ok_(qec.train(ds2) is None)

def test_query_engine():
    data = np.arange(54)
    # indices in 3D
    ind = np.transpose((np.ones((3, 3, 3)).nonzero()))
    # sphere generator for 3 elements diameter
    sphere = ne.Sphere(1)
    # dataset with just one "space"
    ds = Dataset([data, data], fa={'s_ind': np.concatenate((ind, ind))})
    # and the query engine attaching the generator to the "index-space"
    qe = ne.IndexQueryEngine(s_ind=sphere)
    # cannot train since the engine does not know about the second space
    assert_raises(ValueError, qe.train, ds)
    # now do it again with a full spec
    ds = Dataset([data, data], fa={'s_ind': np.concatenate((ind, ind)),
                                   't_ind': np.repeat([0,1], 27)})
    qe = ne.IndexQueryEngine(s_ind=sphere, t_ind=None)
    qe.train(ds)
    # internal representation check
    # YOH: invalid for new implementation with lookup tables (dictionaries)
    #assert_array_equal(qe._searcharray,
    #                   np.arange(54).reshape(qe._searcharray.shape) + 1)
    # should give us one corner, collapsing the 't_ind'
    assert_array_equal(qe(s_ind=(0, 0, 0)),
                       [0, 1, 3, 9, 27, 28, 30, 36])
    # directly specifying an index for 't_ind' without having an ROI
    # generator, should give the same corner, but just once
    assert_array_equal(qe(s_ind=(0, 0, 0), t_ind=0), [0, 1, 3, 9])
    # just out of the mask -- no match
    assert_array_equal(qe(s_ind=(3, 3, 3)), [])
    # also out of the mask -- but single match
    assert_array_equal(qe(s_ind=(2, 2, 3), t_ind=1), [53])
    # query by id
    assert_array_equal(qe(s_ind=(0, 0, 0), t_ind=0), qe[0])
    assert_array_equal(qe(s_ind=(0, 0, 0), t_ind=[0, 1]),
                       qe(s_ind=(0, 0, 0)))
    # should not fail if t_ind is outside
    assert_array_equal(qe(s_ind=(0, 0, 0), t_ind=[0, 1, 10]),
                       qe(s_ind=(0, 0, 0)))

    # should fail if asked about some unknown thing
    assert_raises(ValueError, qe.__call__, s_ind=(0, 0, 0), buga=0)

    # Test by using some literal feature atttribute
    ds.fa['lit'] =  ['roi1', 'ro2', 'r3']*18
    # should work as well as before
    assert_array_equal(qe(s_ind=(0, 0, 0)), [0, 1, 3, 9, 27, 28, 30, 36])
    # should fail if asked about some unknown (yet) thing
    assert_raises(ValueError, qe.__call__, s_ind=(0,0,0), lit='roi1')

    # Create qe which can query literals as well
    qe_lit = ne.IndexQueryEngine(s_ind=sphere, t_ind=None, lit=None)
    qe_lit.train(ds)
    # should work as well as before
    assert_array_equal(qe_lit(s_ind=(0, 0, 0)), [0, 1, 3, 9, 27, 28, 30, 36])
    # and subselect nicely -- only /3 ones
    assert_array_equal(qe_lit(s_ind=(0, 0, 0), lit='roi1'),
                       [0, 3, 9, 27, 30, 36])
    assert_array_equal(qe_lit(s_ind=(0, 0, 0), lit=['roi1', 'ro2']),
                       [0, 1, 3, 9, 27, 28, 30, 36])

def test_sphere():
    # test sphere initialization
    s = ne.Sphere(1)
    center0 = (0, 0, 0)
    center1 = (1, 1, 1)
    assert_equal(len(s(center0)), 7)
    target = array([array([-1,  0,  0]),
              array([ 0, -1,  0]),
              array([ 0,  0, -1]),
              array([0, 0, 0]),
              array([0, 0, 1]),
              array([0, 1, 0]),
              array([1, 0, 0])])
    # test of internals -- no recomputation of increments should be done
    prev_increments = s._increments
    assert_array_equal(s(center0), target)
    ok_(prev_increments is s._increments)
    # query lower dimensionality
    _ = s((0, 0))
    ok_(not prev_increments is s._increments)

    # test Sphere call
    target = [array([0, 1, 1]),
              array([1, 0, 1]),
              array([1, 1, 0]),
              array([1, 1, 1]),
              array([1, 1, 2]),
              array([1, 2, 1]),
              array([2, 1, 1])]
    res = s(center1)
    assert_array_equal(array(res), target)
    # They all should be tuples
    ok_(np.all([isinstance(x, tuple) for x in res]))

    # test for larger diameter
    s = ne.Sphere(4)
    assert_equal(len(s(center1)), 257)

    # test extent keyword
    #s = ne.Sphere(4,extent=(1,1,1))
    #assert_array_equal(array(s((0,0,0))), array([[0,0,0]]))

    # test Errors during initialisation and call
    #assert_raises(ValueError, ne.Sphere, 2)
    #assert_raises(ValueError, ne.Sphere, 1.0)

    # no longer extent available
    assert_raises(TypeError, ne.Sphere, 1, extent=(1))
    assert_raises(TypeError, ne.Sphere, 1, extent=(1.0, 1.0, 1.0))

    s = ne.Sphere(1)
    #assert_raises(ValueError, s, (1))
    if __debug__:
        # No float coordinates allowed for now...
        # XXX might like to change that ;)
        # 
        assert_raises(ValueError, s, (1.0, 1.0, 1.0))

def test_gifti_dataset(fn, format_, include_nodes):
    expected_ds = _get_test_dataset(include_nodes)

    expected_ds_sa = expected_ds.copy(deep=True)
    expected_ds_sa.sa['chunks'] = [4, 3, 2, 1, 3, 2]
    expected_ds_sa.sa['targets'] = ['t%d' % i for i in xrange(6)]


    # build GIFTI file from scratch
    gifti_string = _build_gifti_string(format_, include_nodes)
    with open(fn, 'w') as f:
        f.write(gifti_string)

    # reading GIFTI file
    ds = gifti_dataset(fn)
    assert_datasets_almost_equal(ds, expected_ds)

    # test GiftiImage input
    img = nb_giftiio.read(fn)
    ds2 = gifti_dataset(img)
    assert_datasets_almost_equal(ds2, expected_ds)

    # test using Nibabel's output from write
    nb_giftiio.write(img, fn)
    ds3 = gifti_dataset(fn)
    assert_datasets_almost_equal(ds3, expected_ds)

    # test targets and chunks arguments
    ds3_sa = gifti_dataset(fn, targets=expected_ds_sa.targets,
                           chunks=expected_ds_sa.chunks)
    assert_datasets_almost_equal(ds3_sa, expected_ds_sa)

    # test map2gifti
    img2 = map2gifti(ds)
    ds4 = gifti_dataset(img2)
    assert_datasets_almost_equal(ds4, expected_ds)

    map2gifti(ds, fn, encoding=format_)
    ds5 = gifti_dataset(fn)
    assert_datasets_almost_equal(ds5, expected_ds)

    # test map2gifti with array input; nodes are not stored
    map2gifti(ds.samples, fn)
    ds6 = gifti_dataset(fn)
    if include_nodes:
        assert_raises(AssertionError, assert_datasets_almost_equal,
                      ds6, expected_ds)
    else:
        assert_datasets_almost_equal(ds6, expected_ds)

    assert_raises(TypeError, gifti_dataset, ds3_sa)
    assert_raises(TypeError, map2gifti, img, fn)

def test_array_collectable():
    c = ArrayCollectable()

    # empty by default
    assert_equal(c.name, None)
    assert_equal(c.value, None)

    # late assignment
    c.name = 'somename'
    assert_raises(ValueError, c._set, 12345)
    assert_equal(c.value, None)
    c.value = np.arange(5)
    assert_equal(c.name, 'somename')
    assert_array_equal(c.value, np.arange(5))

    # immediate content
    data = np.random.random(size=(3,10))
    c = ArrayCollectable(data.copy(), 'myname',
                         "This is a test", length=3)
    assert_equal(c.name, 'myname')
    assert_array_equal(c.value, data)
    assert_equal(c.__doc__, "This is a test")
    assert_equal(str(c), 'myname')

    # repr
    from numpy import array
    e = eval(repr(c))
    assert_equal(e.name, 'myname')
    assert_array_almost_equal(e.value, data)
    assert_equal(e.__doc__, "This is a test")

    # cannot assign array of wrong length
    assert_raises(ValueError, c._set, np.arange(5))
    assert_equal(len(c), 3)

    # shallow copy DOES create a view of value array
    c.value = np.arange(3)
    d = copy.copy(c)
    assert_true(d.value.base is c.value)

    # names starting with _ are not allowed
    assert_raises(ValueError, c._set_name, "_underscore")

def test_rfe_sensmap():
    # http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2013q3/002538.html
    # just a smoke test. fails with
    from mvpa2.clfs.svm import LinearCSVMC
    from mvpa2.clfs.meta import FeatureSelectionClassifier
    from mvpa2.measures.base import CrossValidation, RepeatedMeasure
    from mvpa2.generators.splitters import Splitter
    from mvpa2.generators.partition import NFoldPartitioner
    from mvpa2.misc.errorfx import mean_mismatch_error
    from mvpa2.mappers.fx import mean_sample
    from mvpa2.mappers.fx import maxofabs_sample
    from mvpa2.generators.base import Repeater
    from mvpa2.featsel.rfe import RFE
    from mvpa2.featsel.helpers import FractionTailSelector, BestDetector
    from mvpa2.featsel.helpers import NBackHistoryStopCrit
    from mvpa2.datasets import vstack

    from mvpa2.misc.data_generators import normal_feature_dataset

    # Let's simulate the beast -- 6 categories total groupped into 3
    # super-ordinate, and actually without any 'superordinate' effect
    # since subordinate categories independent
    fds = normal_feature_dataset(nlabels=3,
                                 snr=1, # 100,   # pure signal! ;)
                                 perlabel=9,
                                 nfeatures=6,
                                 nonbogus_features=range(3),
                                 nchunks=3)
    clfsvm = LinearCSVMC()

    rfesvm = RFE(clfsvm.get_sensitivity_analyzer(postproc=maxofabs_sample()),
                 CrossValidation(
                     clfsvm,
                     NFoldPartitioner(),
                     errorfx=mean_mismatch_error, postproc=mean_sample()),
                 Repeater(2),
                 fselector=FractionTailSelector(0.70, mode='select', tail='upper'),
                 stopping_criterion=NBackHistoryStopCrit(BestDetector(), 10),
                 update_sensitivity=True)

    fclfsvm = FeatureSelectionClassifier(clfsvm, rfesvm)

    sensanasvm = fclfsvm.get_sensitivity_analyzer(postproc=maxofabs_sample())


    # manually repeating/splitting so we do both RFE sensitivity and classification
    senses, errors = [], []
    for i, pset in enumerate(NFoldPartitioner().generate(fds)):
        # split partitioned dataset
        split = [d for d in Splitter('partitions').generate(pset)]
        senses.append(sensanasvm(split[0])) # and it also should train the classifier so we would ask it about error
        errors.append(mean_mismatch_error(fclfsvm.predict(split[1]), split[1].targets))

    senses = vstack(senses)
    errors = vstack(errors)

    # Let's compare against rerunning the beast simply for classification with CV
    errors_cv = CrossValidation(fclfsvm, NFoldPartitioner(), errorfx=mean_mismatch_error)(fds)
    # and they should match
    assert_array_equal(errors, errors_cv)

    # buggy!
    cv_sensana_svm = RepeatedMeasure(sensanasvm, NFoldPartitioner())
    senses_rm = cv_sensana_svm(fds)

    #print senses.samples, senses_rm.samples
    #print errors, errors_cv.samples
    assert_raises(AssertionError,
                  assert_array_almost_equal,
                  senses.samples, senses_rm.samples)
    raise SkipTest("Known failure for repeated measures: https://github.com/PyMVPA/PyMVPA/issues/117")

def test_gnbsearchlight_permutations():
    import mvpa2
    from mvpa2.base.node import ChainNode
    from mvpa2.clfs.gnb import GNB
    from mvpa2.generators.base import  Repeater
    from mvpa2.generators.partition import NFoldPartitioner, OddEvenPartitioner
    #import mvpa2.generators.permutation
    #reload(mvpa2.generators.permutation)
    from mvpa2.generators.permutation import AttributePermutator
    from mvpa2.testing.datasets import datasets
    from mvpa2.measures.base import CrossValidation
    from mvpa2.measures.gnbsearchlight import sphere_gnbsearchlight
    from mvpa2.measures.searchlight import sphere_searchlight
    from mvpa2.mappers.fx import mean_sample
    from mvpa2.misc.errorfx import mean_mismatch_error
    from mvpa2.clfs.stats import MCNullDist
    from mvpa2.testing.tools import assert_raises, ok_, assert_array_less

    # mvpa2.debug.active = ['APERM', 'SLC'] #, 'REPM']
    # mvpa2.debug.metrics += ['pid']
    count = 10
    nproc = 1 + int(mvpa2.externals.exists('pprocess'))
    ds = datasets['3dsmall'].copy()
    ds.fa['voxel_indices'] = ds.fa.myspace

    slkwargs = dict(radius=3, space='voxel_indices',  enable_ca=['roi_sizes'],
                    center_ids=[1, 10, 70, 100])

    mvpa2.seed(mvpa2._random_seed)
    clf  = GNB()
    splt = NFoldPartitioner(cvtype=2, attr='chunks')

    repeater   = Repeater(count=count)
    permutator = AttributePermutator('targets', limit={'partitions': 1}, count=1)

    null_sl = sphere_gnbsearchlight(clf, ChainNode([splt, permutator], space=splt.get_space()),
                                    postproc=mean_sample(), errorfx=mean_mismatch_error,
                                    **slkwargs)

    distr_est = MCNullDist(repeater, tail='left', measure=null_sl,
                           enable_ca=['dist_samples'])
    sl = sphere_gnbsearchlight(clf, splt,
                               reuse_neighbors=True,
                               null_dist=distr_est, postproc=mean_sample(),
                               errorfx=mean_mismatch_error,
                               **slkwargs)
    if __debug__:                         # assert is done only without -O mode
        assert_raises(NotImplementedError, sl, ds)

    # "ad-hoc searchlights can't handle yet varying targets across partitions"
    if False:
        # after above limitation is removed -- enable
        sl_map = sl(ds)
        sl_null_prob = sl.ca.null_prob.samples.copy()

    mvpa2.seed(mvpa2._random_seed)
    ### 'normal' Searchlight
    clf  = GNB()
    splt = NFoldPartitioner(cvtype=2, attr='chunks')
    repeater   = Repeater(count=count)
    permutator = AttributePermutator('targets', limit={'partitions': 1}, count=1)
    # rng=np.random.RandomState(0)) # to trigger failure since the same np.random state
    # would be reused across all pprocesses
    null_cv = CrossValidation(clf, ChainNode([splt, permutator], space=splt.get_space()),
                              postproc=mean_sample())
    null_sl_normal = sphere_searchlight(null_cv, nproc=nproc, **slkwargs)
    distr_est_normal = MCNullDist(repeater, tail='left', measure=null_sl_normal,
                           enable_ca=['dist_samples'])

    cv = CrossValidation(clf, splt, errorfx=mean_mismatch_error,
                         enable_ca=['stats'], postproc=mean_sample() )
    sl = sphere_searchlight(cv, nproc=nproc, null_dist=distr_est_normal, **slkwargs)
    sl_map_normal = sl(ds)
    sl_null_prob_normal = sl.ca.null_prob.samples.copy()

    # For every feature -- we should get some variance in estimates In
    # case of failure they are all really close to each other (up to
    # numerical precision), so variance will be close to 0
    assert_array_less(-np.var(distr_est_normal.ca.dist_samples.samples[0],
                              axis=1), -1e-5)
    for s in distr_est_normal.ca.dist_samples.samples[0]:
        ok_(len(np.unique(s)) > 1)