Пример #1
0
def test_shuffled_edges():

    d = copy.deepcopy(d_original)
    original_dwell = json.loads(arbplf_dwell(json.dumps(d)))

    d = copy.deepcopy(d_original)
    original_ll = json.loads(arbplf_ll(json.dumps(d)))

    d = copy.deepcopy(d_original)
    d['site_reduction'] = {'aggregation' : 'sum'}
    original_em_update = json.loads(arbplf_em_update(json.dumps(d)))

    iter_count = 10
    for i in range(iter_count):
        d_shuffled, perm = _shuffle_edges(d_original)

        # the ll output does not have an edge column
        d = copy.deepcopy(d_shuffled)
        ll = json.loads(arbplf_ll(json.dumps(d)))
        assert_equal(ll, original_ll)

        d = copy.deepcopy(d_shuffled)
        dwell = json.loads(arbplf_dwell(json.dumps(d)))
        dwell_prime = _perm_output_edges(dwell, perm)
        dwell_prime['data'].sort()
        assert_equal(dwell_prime, original_dwell)

        d = copy.deepcopy(d_shuffled)
        d['site_reduction'] = {'aggregation' : 'sum'}
        em_update = json.loads(arbplf_em_update(json.dumps(d)))
        em_update_prime = _perm_output_edges(em_update, perm)
        em_update_prime['data'].sort()
        assert_equal(em_update_prime, original_em_update)
Пример #2
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def test_shuffled_nodes():

    d = copy.deepcopy(d_original)
    original_dwell = json.loads(arbplf_dwell(json.dumps(d)))

    d = copy.deepcopy(d_original)
    original_ll = json.loads(arbplf_ll(json.dumps(d)))

    d = copy.deepcopy(d_original)
    d['site_reduction'] = {'aggregation' : 'sum'}
    original_em_update = json.loads(arbplf_em_update(json.dumps(d)))

    iter_count = 10
    for i in range(iter_count):
        d_shuffled = _shuffle_nodes(d_original)

        d = copy.deepcopy(d_shuffled)
        dwell = json.loads(arbplf_dwell(json.dumps(d)))
        assert_equal(dwell, original_dwell)

        d = copy.deepcopy(d_shuffled)
        ll = json.loads(arbplf_ll(json.dumps(d)))
        assert_equal(ll, original_ll)

        d = copy.deepcopy(d_shuffled)
        d['site_reduction'] = {'aggregation' : 'sum'}
        em_update = json.loads(arbplf_em_update(json.dumps(d)))
        assert_equal(em_update, original_em_update)
Пример #3
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def mydwell(d):
    """
    Provides a dict -> pandas.DataFrame wrapper of the pure JSON arbplf_dwell.
    """
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    return df
Пример #4
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def test_heterogeneous_edge_rates():
    # try changing one of the edge rate coefficients
    d = {
        "model_and_data": {
            "edges": [[0, 1], [1, 2]],
            "edge_rate_coefficients": [1, 2],
            "rate_matrix": [[0, 1], [0, 0]],
            "probability_array": [[[1, 0], [1, 1], [1, 0]]]
        },
        "site_reduction": {
            "aggregation": "only"
        }
    }

    actual_marginal = json.loads(arbplf_marginal(json.dumps(d)))
    assert_equal(actual_marginal, desired_marginal)

    g = copy.deepcopy(d)
    g['trans_reduction'] = dict(selection=[[0, 1], [1, 0]])
    actual_trans = json.loads(arbplf_trans(json.dumps(g)))
    assert_equal(actual_trans, desired_trans)

    actual_ll = json.loads(arbplf_ll(json.dumps(d)))
    desired_ll = {"columns": ["value"], "data": [[-3.0]]}
    assert_equal(actual_ll, desired_ll)

    actual_em_update = json.loads(arbplf_em_update(json.dumps(d)))
    assert_equal(actual_em_update, desired_em_update)

    actual_dwell = json.loads(arbplf_dwell(json.dumps(d)))
    assert_equal(actual_dwell, desired_dwell)
Пример #5
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def test_edges_are_not_preordered():
    # Try switching the order of the edges in the input
    # and increasing the birth rate in the rate matrix.
    d = {
        "model_and_data": {
            "edges": [[1, 2], [0, 1]],
            "edge_rate_coefficients": [1, 2],
            "rate_matrix": [[0, 2], [0, 0]],
            "probability_array": [[[1, 0], [1, 1], [1, 0]]]
        },
        "site_reduction": {
            "aggregation": "only"
        }
    }

    actual_marginal = json.loads(arbplf_marginal(json.dumps(d)))
    assert_equal(actual_marginal, desired_marginal)

    g = copy.deepcopy(d)
    g['trans_reduction'] = dict(selection=[[0, 1], [1, 0]])
    actual_trans = json.loads(arbplf_trans(json.dumps(g)))
    assert_equal(actual_trans, desired_trans)

    actual_ll = json.loads(arbplf_ll(json.dumps(d)))
    desired_ll = {"columns": ["value"], "data": [[-6.0]]}
    assert_equal(actual_ll, desired_ll)

    actual_em_update = json.loads(arbplf_em_update(json.dumps(d)))
    assert_equal(actual_em_update, desired_em_update)

    actual_dwell = json.loads(arbplf_dwell(json.dumps(d)))
    assert_equal(actual_dwell, desired_dwell)
Пример #6
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def mydwell(d):
    """
    Provides a dict -> pandas.DataFrame wrapper of the pure JSON arbplf_dwell.
    """
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    return df
def test_dwell():
    d = copy.deepcopy(D)
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    actual = df.pivot('edge', 'state', 'value').values
    # compute the desired closed form solution
    u = np.cumsum([0] + rates)
    a, b = u[:-1], u[1:]
    v = exprel(b - a) * exp(-b)
    desired = np.vstack([v, 1-v]).T
    # compare actual and desired result
    assert_allclose(actual, desired)
def test_truncated_dwell():
    d = copy.deepcopy(D)
    d['model_and_data']['probability_array'][0][-1] = [0, 1]
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    actual = df.pivot('edge', 'state', 'value').values
    # compute the desired closed form solution
    u = np.cumsum([0] + rates)
    a, b = u[:-1], u[1:]
    T = u[-1]
    # this way is not robust when a == b.
    def F(x):
        return -(exp(T - x) + x) / expm1(T)
    v = (F(b) - F(a)) / (b - a)
    desired = np.vstack([v, 1-v]).T
    # this way is better
    v = (exprel(b-a)*exp(T-b) - 1) / expm1(T)
    desired = np.vstack([v, 1-v]).T
    # compare actual and desired result
    assert_allclose(actual, desired)
Пример #9
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def mydwell(d):
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    return df
Пример #10
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def mydwell(d):
    s = arbplf_dwell(json.dumps(d))
    df = pd.read_json(StringIO(s), orient='split', precise_float=True)
    return df