def test_to_and_from_ascii(self, sans_benchmark):
sans_prop_ref = ps.SansProperty()
sans_prop_ref.from_cryson_int(sans_benchmark['cryson_int'])
sans_prop = ps.SansProperty()
with tempfile.NamedTemporaryFile() as f:
sans_prop_ref.to_ascii(f.name)
sans_prop.from_ascii(f.name)
np.testing.assert_array_almost_equal(
sans_prop.qvalues, sans_prop_ref.qvalues)
def test_from_cryson_pdb(self, sans_benchmark):
sans_prop = ps.SansProperty()
sans_prop.from_cryson_pdb(sans_benchmark['cryson_pdb'], args='')
sans_prop_ref = ps.SansProperty()
sans_prop_ref.from_cryson_int(sans_benchmark['cryson_int'])
np.testing.assert_array_almost_equal(
sans_prop.qvalues, sans_prop_ref.qvalues)
np.testing.assert_array_almost_equal(
sans_prop.profile, sans_prop_ref.profile)
def sans_benchmark(request):
r"""Sassena output containing 1000 I(Q) profiles for the hiAPP centroids.
Yields
------
dict
'profiles' : HDF5 handle to the file containing the I(Q) profiles
'property_list' : list of SansProperty instances, one for each leaf
'tree_with_no_property' : cnextend.Tree with random distances among
leafs and without included properties.
"""
# setup or initialization
handle = h5py.File(os.path.join(data_dir, 'sans', 'profiles.h5'), 'r')
profiles = handle['fqt']
n_leafs = len(profiles)
# Create a node tree.
# m is a 1D compressed matrix of distances between leafs
m = np.random.random(int(n_leafs * (n_leafs - 1) / 2))
z = linkage(m)
tree = cnextend.Tree(z)
# values is a list of SansProperty instances, one for each tree leaf
values = list()
for i in range(tree.nleafs):
sans_property = idprop.SansProperty()
sans_property.from_sassena(handle, index=i)
values.append(sans_property)
def teardown():
handle.close()
request.addfinalizer(teardown)
return dict(profiles=handle, property_list=values,
tree_with_no_property=tree)
def sans_fit(sans_benchmark):
r"""
Parameters
----------
sans_benchmark : :function:`~pytest.fixture`
Returns
-------
dict
A dictionary containing the following key, value pairs:
tree: :class:`~idpflex.cnextend.Tree`
A hiearchical tree with random distances among leafs, and endowed
with a :class:`~idpflex.properties.SansProperty`.
property_name: str
Just the name of the property
depth: int
Tree depth resulting in the best fit to experiment_property
coefficients: :py:`dict`
weights of each node at Tree depth resulting in best fit. (key, val)
pair is (node ID, weight).
background : float
Flat background added to the profile at depth for optimal fit
experiment_property: :class:`~idpflex.properties.SansProperty`
Experimental profile from a linear combination of the profiles
at depth for optimal fit using `coefficients` and `background`.
"""
tree = deepcopy(sans_benchmark['tree_with_no_property'])
values = sans_benchmark['property_list']
name = values[0].name # property name
idprop.propagator_size_weighted_sum(values, tree)
# create a SANS profile as a linear combination of the clusters at a
# particular depth
depth = 4
coeffs = (0.45, 0.00, 0.07, 0.25, 0.23) # they must add to one
coefficients = dict()
nodes = tree.nodes_at_depth(depth)
n_nodes = 1 + depth # depth=0 corresponds to the root node (nclusters=1)
q_values = (tree.root[name].x[:-1] + tree.root[name].x[1:]) / 2 # midpoint
profile = np.zeros(len(q_values))
for i in range(n_nodes):
coefficients[nodes[i].id] = coeffs[i]
p = nodes[i][name]
profile += coeffs[i] * (p.y[:-1] + p.y[1:]) / 2
background = 0.05 * max(profile) # flat background
profile += background
experiment_property = idprop.SansProperty(name=name,
qvalues=q_values,
profile=profile,
errors=0.1 * profile)
return {
'tree': tree,
'property_name': name,
'depth': depth,
'coefficients': coefficients,
'background': background,
'experiment_property': experiment_property
}
def test_from_sassena(self, sans_benchmark):
sans_prop = ps.SansProperty()
sans_prop.from_sassena(sans_benchmark['profiles'], index=666)
assert sans_prop.qvalues[13].item() - 0.0656565651298 < 0.000000001
assert sans_prop.profile[13].item() - 741970.84461578 < 0.000001
def test_default_name(self):
sans_prop = ps.SansProperty()
assert sans_prop.name == 'sans'
def test_from_cryson_int(self, sans_benchmark):
sans_prop = ps.SansProperty()
sans_prop.from_cryson_int(sans_benchmark['cryson_int'])
assert sans_prop.qvalues[8] == 0.08
assert sans_prop.profile[8] == 0.229457E+06
assert sans_prop.errors[8] == 0.0