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Change data format to only use structured arrays #42

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merged 6 commits into from
Jul 25, 2023
Merged

Change data format to only use structured arrays #42

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71ed76b
Change data format to only use structured arrays to avoid data loader…
kdund Jul 14, 2023
130047e
add .flake8 file to ignore assert errors
kdund Jul 14, 2023
1d05fb2
Merge branch 'main' into nt_likelihood_dataformat
kdund Jul 24, 2023
47fd90f
Merge remote-tracking branch 'origin/main' into nt_likelihood_dataformat
dachengx Jul 25, 2023
d56a1e0
flake ignore in setup.cfg
dachengx Jul 25, 2023
93fc829
Remove unused import
dachengx Jul 25, 2023
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2 changes: 2 additions & 0 deletions .flake8
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
[flake8]
extend-ignore = S101
9 changes: 5 additions & 4 deletions alea/blueice_extended_model.py
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Expand Up @@ -6,6 +6,7 @@
import scipy.stats as stats
from blueice.likelihood import LogAncillaryLikelihood
from blueice.likelihood import LogLikelihoodSum
from inference_interface import dict_to_structured_array, structured_array_to_dict
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from alea.statistical_model import StatisticalModel
from alea.simulators import BlueiceDataGenerator
Expand Down Expand Up @@ -187,7 +188,7 @@ def _generate_data(self, **generate_values) -> list:
generate_values_anc = {k: v for k, v in generate_values.items() if k in ancillary_keys}
ancillary_measurements = self._generate_ancillary_measurements(
**generate_values_anc)
return science_data + [ancillary_measurements] + [generate_values]
return science_data + [ancillary_measurements] + [dict_to_structured_array(generate_values)]

def _generate_science_data(self, **generate_values) -> list:
science_data = [
Expand All @@ -209,7 +210,7 @@ def _generate_ancillary_measurements(self, **generate_values) -> dict:
parameter_meas = param.fit_limits[1]
ancillary_measurements[name] = parameter_meas

return ancillary_measurements
return dict_to_structured_array(ancillary_measurements)

def _set_efficiency(self, source, ll):
if "efficiency_name" not in source:
Expand Down Expand Up @@ -275,12 +276,12 @@ def constraint_terms(self) -> dict:
"""
return {name: func.logpdf for name, func in self.constraint_functions.items()}

def set_data(self, d: dict):
def set_data(self, d: np.array):
"""
Set the data of the ancillary likelihood (ancillary measurements).

Args:
d (dict): Data in this case is a dict of ancillary measurements.
d (np.array): Data of ancillary measurements, stored as numpy array
"""
# This results in shifted constraint terms.
if set(d.keys()) != set(self.parameters.names):
Expand Down