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Representative row approach for non-inactivation titer change #12

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Merged
dylanhmorris merged 1 commit into from
Nov 3, 2025
Merged

Representative row approach for non-inactivation titer change #12

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9 changes: 7 additions & 2 deletions pyter/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -290,7 +290,7 @@ class HalfLifeData(AbstractData):
log_base: np.ndarray = attrs.Factory(lambda: np.array([10]))
well_volume: np.ndarray = attrs.Factory(lambda: np.array([1.0]))
false_hit_rate: np.ndarray = attrs.Factory(lambda: np.array([0]))
log_titer_change_other: np.ndarray = attrs.Factory(lambda: np.array([0]))
log_well_change_other: np.ndarray = attrs.Factory(lambda: np.array([0]))

well_internal_id_values: dict = attrs.Factory(dict)
titer_internal_id_values: dict = attrs.Factory(dict)
Expand All @@ -302,7 +302,8 @@ class HalfLifeData(AbstractData):
id_representative_rows: dict = attrs.Factory(dict)
n_values: dict = attrs.Factory(dict)

titer_time: np.ndarray = None
titer_time: np.ndarray | None = None
log_titer_change_other: np.ndarray | None = None

def update_internal_ids(self):
"""
Expand Down Expand Up @@ -360,6 +361,10 @@ def update_internal_ids(self):
)

self.titer_time = self.well_time[self.id_representative_rows["titer"]]
self.log_titer_change_other = np.broadcast_to(
self.log_well_change_other,
self.well_internal_id_values["titer"].shape,
)[self.id_representative_rows["titer"]]

def index_prior_parameters(self):
"""
Expand Down
21 changes: 11 additions & 10 deletions test/test_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,11 @@
)
@pytest.mark.parametrize(
"known_change_vec",
[np.array([-1.5, 15.5, 2.6431]), np.array([-0.352]), 0, None],
[np.array([-1.5, 1.5, 2.6431, -3.322]), np.array([-0.352]), 0, None],
)
def test_non_inactivation_change(data, known_change_vec):
"""
Test that the log_titer_change_other argument
Test that the log_well_change_other argument
works as expected for modeling known change in
titers due to factors other than inactivation.
"""
Expand All @@ -57,19 +57,20 @@ def test_non_inactivation_change(data, known_change_vec):
with seed(rng_seed=5):
if known_change_vec is not None:
data_change = copy.deepcopy(data)
data_change.log_titer_change_other = known_change_vec
data_change.log_well_change_other = known_change_vec
else:
data_change = data
sim_titers_change, sim_wells_change = model.model(
data=data_change.freeze()
)
assert all((sim_wells == 0) | (sim_wells == 1))
assert all((sim_wells_change == 0) | (sim_wells_change == 1))
if known_change_vec is not None:
assert all(sim_titers + known_change_vec == sim_titers_change)
assert not any(
sim_titers + known_change_vec + 0.52 == sim_titers_change
)
if known_change_vec is None:
expected_change = 0
else:
assert all(sim_titers == sim_titers_change)
assert not any(sim_titers + 0.52 == sim_titers_change)
expected_change = np.broadcast_to(
known_change_vec,
data_change.well_internal_id_values["titer"].shape,
)[data_change.id_representative_rows["titer"]]
assert all(sim_titers + expected_change == sim_titers_change)
assert not any(sim_titers + expected_change + 0.52 == sim_titers_change)