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Moved where zeros are filtered to next to where this is needed (when applying nested sampling) #127

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Moved where zeros are filtered to next to where this is needed (when applying nested sampling) #127

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Moved where zeros are filtered to next to where this is needed (neste…
jfkcooper Nov 12, 2024
41a0963
linting
jfkcooper Nov 12, 2024
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2 changes: 2 additions & 0 deletions hogben/models/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -420,6 +420,8 @@ def nested_sampling(self,
model.bkg = background_level
model.dq = 2
data = SimulateReflectivity(model, angle_times).simulate()
# filter zeros as nested sampling doesn't deal with these well
data = data[:, (data[1] != 0)]

dataset = refnx.dataset.ReflectDataset(
[data[0], data[1], data[2]]
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2 changes: 2 additions & 0 deletions hogben/models/samples.py
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Expand Up @@ -410,6 +410,8 @@ def nested_sampling(self,
for structure in self.structures:
model = refnx.reflect.ReflectModel(structure)
data = SimulateReflectivity(model, angle_times).simulate()
# filter zeros as nested sampling doesn't deal with these well
data = data[:, (data[1] != 0)]
objective = Objective(model, data)
objectives.append(objective)
global_objective = GlobalObjective(objectives)
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3 changes: 0 additions & 3 deletions hogben/simulate.py
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Expand Up @@ -103,9 +103,6 @@ def simulate(self, polarised: bool = False) -> \
self._run_experiment(*condition, polarised) for condition in self.angle_times
])

# filter zeros
simulation = simulation[:, (simulation[1] != 0)]

# order by q
simulation = simulation[:, np.argsort(simulation[0])]

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19 changes: 19 additions & 0 deletions hogben/tests/test_simulation.py
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Expand Up @@ -107,6 +107,25 @@ def test_incident_flux_data(self):

sim_not_in_pol._incident_flux_data(polarised=True)

def test_number_of_points(self, refnx_model):
"""
Tests that the number of points generated in the
simulation is what we define (even when many are zero)
"""
NPOINTS = 100
angle_times = [(0.3, NPOINTS, 10000)]
sim = SimulateReflectivity(refnx_model,
angle_times=angle_times).simulate()
assert len(sim[0]) == NPOINTS
angle_times = [(0.3, NPOINTS, 5)]
sim = SimulateReflectivity(refnx_model,
angle_times=angle_times).simulate()
assert len(sim[0]) == NPOINTS
angle_times = [(0.3, NPOINTS, 5), (2.0, NPOINTS, 50)]
sim = SimulateReflectivity(refnx_model,
angle_times=angle_times).simulate()
assert len(sim[0]) == NPOINTS * 2

def test_reflectivity(self, refnx_model):
"""
Checks that a refnx model reflectivity generated through
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