def it_never_requires_deprecated():
test_s = s(s.is_kws_r(a=s.is_deprecated()))
test_s.validate(dict())
class ErrorModel(Params):
schema = s(
s.is_kws_r(
p_dud=s.is_deprecated(),
p_edman_failure=s.is_float(bounds=(0, 1)),
p_detach=s.is_float(bounds=(0, 1)),
dyes=s.is_list(elems=s.is_kws_r(
dye_name=s.is_str(),
p_bleach_per_cycle=s.is_float(bounds=(0, 1)),
p_non_fluorescent=s.is_float(bounds=(0, 1)),
# gain and vpd are the new parameters and beta, sigma are the legacy
gain=s.is_float(required=False, bounds=(0, None)),
vpd=s.is_float(required=False, bounds=(0, None)),
beta=s.is_float(required=False, bounds=(0, None)),
sigma=s.is_float(required=False, bounds=(0, None)),
)),
labels=s.is_list(elems=s.is_kws_r(
label_name=s.is_str(),
p_failure_to_bind_amino_acid=s.is_float(bounds=(0, 1)),
p_failure_to_attach_to_dye=s.is_float(bounds=(0, 1)),
)),
))
defaults = Munch(p_edman_failure=0.06, p_detach=0.05, dyes=[], labels=[])
def __init__(self, **kwargs):
dyes = kwargs["dyes"] = kwargs.pop("dyes", [])
for dye in dyes:
dye.p_bleach_per_cycle = dye.get(
"p_bleach_per_cycle", kwargs.pop("p_bleach_per_cycle", 0.05))
dye.p_non_fluorescent = dye.get(
"p_non_fluorescent", kwargs.pop("p_non_fluorescent", 0.07))
labels = kwargs["labels"] = kwargs.pop("labels", [])
for label in labels:
label.p_failure_to_bind_amino_acid = label.get(
"p_failure_to_bind_amino_acid",
kwargs.pop("p_failure_to_bind_amino_acid", 0.0),
)
label.p_failure_to_attach_to_dye = label.get(
"p_failure_to_attach_to_dye",
kwargs.pop("p_failure_to_attach_to_dye", 0.0),
)
super().__init__(**kwargs)
@classmethod
def no_errors(cls, n_channels, **kwargs):
beta = kwargs.pop("beta", 7500.0)
sigma = kwargs.pop("sigma", 0.0)
gain = kwargs.pop("gain", 10.0)
vpd = kwargs.pop("vpd", 0.1)
return cls(
p_edman_failure=0.0,
p_detach=0.0,
dyes=[
Munch(
dye_name=f"dye_{ch}",
p_bleach_per_cycle=0.0,
p_non_fluorescent=0.0,
sigma=sigma,
beta=beta,
gain=gain,
vpd=vpd,
) for ch in range(n_channels)
],
labels=[
Munch(
label_name=f"label_{ch}",
p_failure_to_bind_amino_acid=0.0,
p_failure_to_attach_to_dye=0.0,
) for ch in range(n_channels)
],
**kwargs,
)
@classmethod
def from_err_set(cls, err_set, **kwargs):
"""err_set is a construct used by the error iterators in pgen"""
n_channels = len(err_set.p_non_fluorescent)
return cls(
p_edman_failure=err_set.p_edman_failure[0],
p_detach=err_set.p_detach[0],
dyes=[
Munch(
dye_name=f"dye_{ch}",
p_bleach_per_cycle=p_bleach_per_cycle,
p_non_fluorescent=p_non_fluorescent,
sigma=dye_sigma,
beta=dye_beta,
gain=dye_gain,
vpd=dye_vpd,
) for ch, dye_beta, dye_sigma, dye_gain, dye_vpd,
p_bleach_per_cycle, p_non_fluorescent in zip(
range(n_channels),
err_set.dye_beta,
err_set.dye_sigma,
err_set.dye_gain,
err_set.dye_vpd,
err_set.p_bleach_per_cycle,
err_set.p_non_fluorescent,
)
],
labels=[
Munch(
label_name=f"label_{ch}",
p_failure_to_bind_amino_acid=0.0,
p_failure_to_attach_to_dye=0.0,
) for ch in range(n_channels)
],
**kwargs,
)
@classmethod
def from_defaults(cls, n_channels):
return cls(
p_edman_failure=cls.defaults.p_edman_failure,
p_detach=cls.defaults.p_detach,
dyes=[
Munch(
dye_name=f"dye_{ch}",
p_bleach_per_cycle=0.05,
p_non_fluorescent=0.07,
sigma=0.16,
beta=7500.0,
gain=7500.0,
vpd=0.10,
) for ch in range(n_channels)
],
labels=[
Munch(
label_name=f"label_{ch}",
p_failure_to_bind_amino_acid=0.0,
p_failure_to_attach_to_dye=0.0,
) for ch in range(n_channels)
],
)
def scale_dyes(self, key, scalar):
for dye in self.dyes:
dye[key] *= scalar
def set_dye_param(self, key, val):
for dye in self.dyes:
dye[key] = val
def it_validates_any_usage():
test_s = s(s.is_deprecated())
with zest.raises(SchemaValidationFailed):
test_s.validate(1)
