def test_parameter_group_to_array():
params = """
- ["1", 1, {non-negative: false, min: -1, max: 1, vary: false}]
- ["2", 4e2, {non-negative: true, min: 10, max: 8e2, vary: true}]
- ["3", 2e4]
"""
params = ParameterGroup.from_yaml(params)
labels, values, lower_bounds, upper_bounds = params.get_label_value_and_bounds_arrays(
exclude_non_vary=False)
assert len(labels) == 3
assert len(values) == 3
assert len(lower_bounds) == 3
assert len(upper_bounds) == 3
assert labels == ["1", "2", "3"]
assert np.allclose(values, [1, np.log(4e2), 2e4])
assert np.allclose(lower_bounds, [-1, np.log(10), -np.inf])
assert np.allclose(upper_bounds, [1, np.log(8e2), np.inf])
(
labels_only_vary,
values_only_vary,
lower_bounds_only_vary,
upper_bounds_only_vary,
) = params.get_label_value_and_bounds_arrays(exclude_non_vary=True)
assert len(labels_only_vary) == 2
assert len(values_only_vary) == 2
assert len(lower_bounds_only_vary) == 2
assert len(upper_bounds_only_vary) == 2
assert labels_only_vary == ["2", "3"]
def test_parameter_to_csv(tmpdir):
csv_path = tmpdir.join("parameters.csv")
params = ParameterGroup.from_yaml("""
b:
- ["1", 0.25, {vary: false, min: 0, max: 8}]
- ["2", 0.75, {expr: '1 - $b.1', non-negative: true}]
rates:
- ["total", 2]
- ["branch1", {expr: '$rates.total * $b.1'}]
- ["branch2", {expr: '$rates.total * $b.2'}]
""")
params.to_csv(csv_path)
with open(csv_path) as f:
print(f.read())
params_from_csv = ParameterGroup.from_csv(csv_path)
for label, p in params.all():
assert params_from_csv.has(label)
p_from_csv = params_from_csv.get(label)
assert p.label == p_from_csv.label
assert p.value == p_from_csv.value
assert p.minimum == p_from_csv.minimum
assert p.maximum == p_from_csv.maximum
assert p.vary == p_from_csv.vary
assert p.non_negative == p_from_csv.non_negative
assert p.expression == p_from_csv.expression
def test_param_options():
params = """
- ["5", 1, {non-negative: false, min: -1, max: 1, vary: false}]
- ["6", 4e2, {non-negative: true, min: -7e2, max: 8e2, vary: true}]
- ["7", 2e4]
"""
params = ParameterGroup.from_yaml(params)
assert params.get("5").value == 1.0
assert not params.get("5").non_neg
assert params.get("5").min == -1
assert params.get("5").max == 1
assert not params.get("5").vary
assert params.get("6").value == 4e2
assert params.get("6").non_neg
assert params.get("6").min == -7e2
assert params.get("6").max == 8e2
assert params.get("6").vary
assert params.get("7").value == 2e4
assert not params.get("7").non_neg
assert params.get("7").min == float('-inf')
assert params.get("7").max == float('inf')
assert params.get("7").vary
def test_param_options():
params = """
- ["5", 1, {non-negative: false, min: -1, max: 1, vary: false}]
- ["6", 4e2, {non-negative: true, min: -7e2, max: 8e2, vary: true}]
- ["7", 2e4]
"""
params = ParameterGroup.from_yaml(params)
assert params.get("5").value == 1.0
assert not params.get("5").non_negative
assert params.get("5").minimum == -1
assert params.get("5").maximum == 1
assert not params.get("5").vary
assert params.get("6").value == 4e2
assert params.get("6").non_negative
assert params.get("6").minimum == -7e2
assert params.get("6").maximum == 8e2
assert params.get("6").vary
assert params.get("7").value == 2e4
assert not params.get("7").non_negative
assert params.get("7").minimum == float("-inf")
assert params.get("7").maximum == float("inf")
assert params.get("7").vary
def test_param_block_options():
params = """
block:
- 1.0
- [3.4, {vary: true}]
- {vary: false}
"""
params = ParameterGroup.from_yaml(params)
assert not params.get("block.1").vary
assert params.get("block.2").vary
def test_param_block_options():
params = """
block:
- 1.0
- [3.4, {vary: true}]
- {vary: false}
"""
params = ParameterGroup.from_yaml(params)
assert not params.get("block.1").vary
assert params.get("block.2").vary
def test_parameter_expressions():
params = """
- ["1", 2]
- ["2", 5]
- ["3", {expr: '$1 * exp($2)'}]
- ["4", {expr: '2'}]
"""
params = ParameterGroup.from_yaml(params)
assert params.get("3").expression is not None
assert not params.get("3").vary
assert params.get("3").value == params.get("1") * np.exp(params.get("2"))
assert params.get("4").value == 2
with pytest.raises(ValueError):
params_bad_expr = """
- ["3", {expr: 'None'}]
"""
ParameterGroup.from_yaml(params_bad_expr)
def test_param_label():
params = """
- ["5", 1]
- ["4", 2]
- ["3", 3]
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 3
assert [p.label for _, p in params.all()] == [f"{i}" for i in range(5, 2, -1)]
assert [p.value for _, p in params.all()] == list(range(1, 4))
def test_param_scientific():
values = [5e3, -4.2e-4, 3e-2, -2e6]
params = """
- ["1", 5e3]
- ["2", -4.2e-4]
- ["3", 3e-2]
- ["4", -2e6]
"""
params = ParameterGroup.from_yaml(params)
assert [p.value for _, p in params.all()] == values
def test_param_label():
params = """
- ["5", 1]
- ["4", 2]
- ["3", 3]
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 3
assert [p.label
for _, p in params.all()] == [f"{i}" for i in range(5, 2, -1)]
assert [p.value for _, p in params.all()] == list(range(1, 4))
def test_param_array():
params = """
- 5
- 4
- 3
- 2
- 1
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 5
assert [p.label for _, p in params.all()] == [f"{i}" for i in range(1, 6)]
assert [p.value for _, p in params.all()] == list(range(1, 6))[::-1]
def test_param_array():
params = """
- 5
- 4
- 3
- 2
- 1
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 5
assert [p.label for _, p in params.all()] == [f"{i}" for i in range(1, 6)]
assert [p.value for _, p in params.all()] == list(range(1, 6))[::-1]
def test_nested_param_group():
params = """
kinetic:
j:
- 7
- 8
- 9
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 3
group = params["kinetic"]
assert len(list(group.all())) == 3
group = group["j"]
assert len(list(group.all())) == 3
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 4)]
assert [p.value for _, p in group.all()] == list(range(7, 10))
def test_nested_param_group():
params = """
kinetic:
j:
- 7
- 8
- 9
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 3
group = params['kinetic']
assert len(list(group.all())) == 3
group = group['j']
assert len(list(group.all())) == 3
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 4)]
assert [p.value for _, p in group.all()] == list(range(7, 10))
def test_parameter_expressions_groups():
params_vary_explicit = """
b:
- [0.25, {vary: True}]
- [0.75, {expr: '1 - $b.1', vary: False}]
rates:
- ["total", 2, {vary: True}]
- ["branch1", {expr: '$rates.total * $b.1', vary: False}]
- ["branch2", {expr: '$rates.total * $b.2', vary: False}]
"""
params_vary_implicit = """
b:
- [0.25]
- [0.75, {expr: '1 - $b.1'}]
rates:
- ["total", 2]
- ["branch1", {expr: '$rates.total * $b.1'}]
- ["branch2", {expr: '$rates.total * $b.2'}]
"""
params_label_explicit = """
b:
- ["1", 0.25]
- ["2", 0.75, {expr: '1 - $b.1'}]
rates:
- ["total", 2]
- ["branch1", {expr: '$rates.total * $b.1'}]
- ["branch2", {expr: '$rates.total * $b.2'}]
"""
for params in [
params_vary_explicit, params_vary_implicit, params_label_explicit
]:
params = ParameterGroup.from_yaml(params)
assert params.get("b.1").expression is None
assert params.get("b.1").vary
assert not params.get("b.2").vary
assert params.get("b.2").expression is not None
assert params.get("rates.branch1").value == params.get(
"rates.total") * params.get("b.1")
assert params.get("rates.branch2").value == params.get(
"rates.total") * params.get("b.2")
assert params.get("rates.total").vary
assert not params.get("rates.branch1").vary
assert not params.get("rates.branch2").vary
def test_update_parameter_group_from_array():
params = """
- ["1", 1, {non-negative: false, min: -1, max: 1, vary: false}]
- ["2", 4e2, {non-negative: true, min: 10, max: 8e2, vary: true}]
- ["3", 2e4]
"""
params = ParameterGroup.from_yaml(params)
labels = ["1", "2", "3"]
values = [0, np.log(6e2), 42]
params.set_from_label_and_value_arrays(labels, values)
values[1] = np.exp(values[1])
for i in range(3):
assert params.get(f"{i+1}").value == values[i]
def test_param_group_copy():
params = """
kinetic:
- ["5", 1, {non-negative: true, min: -1, max: 1, vary: false}]
- 4
- 5
j:
- 7
- 8
"""
params = ParameterGroup.from_yaml(params)
copy = params.copy()
for label, parameter in params.all():
assert copy.has(label)
copied_parameter = copy.get(label)
assert parameter.value == copied_parameter.value
assert parameter.non_negative == copied_parameter.non_negative
assert parameter.minimum == copied_parameter.minimum
assert parameter.maximum == copied_parameter.maximum
assert parameter.vary == copied_parameter.vary
def test_nested_param_list():
params = """
kinetic:
- 3
- 4
- 5
j:
- 7
- 8
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 5
group = params['kinetic']
assert len(list(group.all())) == 3
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 4)]
assert [p.value for _, p in group.all()] == list(range(3, 6))
group = params['j']
assert len(list(group.all())) == 2
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 3)]
assert [p.value for _, p in group.all()] == list(range(7, 9))
def test_non_negative():
params = """
- ["neg", -1]
- ["negmax", -1, {max=0}]
- ["nonneg1", 1, {non-negative: True}]
- ["nonneg2", 2, {non-negative: True}]
- ["nonnegmin", 6, {non-negative: True, min: 2}]
"""
params = ParameterGroup.from_yaml(params)
result = ParameterGroup.from_parameter_dict(params.as_parameter_dict())
print(params)
params.as_parameter_dict().pretty_print()
print(result)
for label, p in params.all():
print(label)
r = result.get(label)
assert r.non_neg == p.non_neg
assert np.allclose(r.value, p.value)
assert np.allclose(r.min, p.min)
assert np.allclose(r.max, p.max)
def test_nested_param_list():
params = """
kinetic:
- 3
- 4
- 5
j:
- 7
- 8
"""
params = ParameterGroup.from_yaml(params)
assert len(list(params.all())) == 5
group = params["kinetic"]
assert len(list(group.all())) == 3
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 4)]
assert [p.value for _, p in group.all()] == list(range(3, 6))
group = params["j"]
assert len(list(group.all())) == 2
assert [p.label for _, p in group.all()] == [f"{i}" for i in range(1, 3)]
assert [p.value for _, p in group.all()] == list(range(7, 9))
def test_non_negative():
params = """
- ["neg", -1]
- ["negmax", -1, {max=0}]
- ["nonneg1", 1, {non-negative: True}]
- ["nonneg2", 2, {non-negative: True}]
- ["nonnegmin", 6, {non-negative: True, min: 2}]
"""
params = ParameterGroup.from_yaml(params)
result = ParameterGroup.from_parameter_dict(params.as_parameter_dict())
print(params)
params.as_parameter_dict().pretty_print()
print(result)
for label, p in params.all():
print(label)
r = result.get(label)
assert r.non_neg == p.non_neg
assert np.allclose(r.value, p.value)
assert np.allclose(r.min, p.min)
assert np.allclose(r.max, p.max)
