from collections import OrderedDict
import numpy as np
from . import model_conical_indenter # noqa: F401
from . import model_hertz_paraboloidal # noqa: F401
from . import model_hertz_three_sided_pyramid # noqa: F401
from . import model_sneddon_spherical # noqa: F401
from . import model_sneddon_spherical_approximation # noqa: F401
#: Common ancillary parameters
ANCILLARY_COMMON = OrderedDict()
ANCILLARY_COMMON["max_indent"] = ("Maximum indentation", "m")
[docs]class ModelIncompleteError(BaseException):
pass
[docs]def get_anc_parms(idnt, model_key):
"""Compute ancillary parameters for a force-distance dataset
Ancillary parameters include parameters that:
- are unrelated to fitting: They may just be important parameters
to the user.
- require the entire dataset: They cannot be extracted during
fitting, because they require more than just the approach xor
retract curve to compute (e.g. hysteresis, jump of retract curve
at maximum indentation). They may, additionally, depend on
initial fit parameters set by the user.
- require a fit: They are dependent on fitting parameters but
are not required during fitting.
Notes
-----
If an ancillary parameter name matches that of a fitting parameter,
then it is assumed that it can be used for fitting. Please see
:func:`nanite.indent.Indentation.get_initial_fit_parameters`
and :func:`nanite.fit.guess_initial_parameters`.
Ancillary parameters are set to `np.nan` if they cannot be
computed.
Parameters
----------
idnt: nanite.indent.Indentation
The force-distance data for which to compute the ancillary
parameters
model_key: str
Name of the model
Returns
-------
ancillaries: collections.OrderedDict
key-value dictionary of ancillary parameters
"""
# TODO:
# - ancillaries are not cached yet (some ancillaries might depend on
# fitting interval or other initial parameters - take that into account)
# - "max_indent" actually belongs to "common_ancillaries" (see fit.py)
anc_ord = OrderedDict()
# compute maximal indentation
if ("tip position" in idnt
and "params_fitted" in idnt.fit_properties
and "contact_point" in idnt.fit_properties["params_fitted"]):
cp = idnt.fit_properties["params_fitted"]["contact_point"].value
idmax = idnt.data.appr["fit"].argmax()
mi = idnt.data.appr["tip position"][idmax]
mival = (cp-mi)
else:
mival = np.nan
anc_ord["max_indent"] = mival
# Model ancillaries
md = models_available[model_key]
if hasattr(md, "compute_ancillaries"):
anc_par = md.compute_ancillaries(idnt)
for kk in md.parameter_anc_keys:
anc_ord[kk] = anc_par[kk]
return anc_ord
[docs]def get_anc_parm_keys(model_key):
"""Return the key names of a model's ancillary parameters"""
akeys = list(ANCILLARY_COMMON.keys())
md = models_available[model_key]
if hasattr(md, "parameter_anc_keys"):
akeys += md.parameter_anc_keys
return akeys
[docs]def get_init_parms(model_key):
"""Get initial fit parameters for a model"""
md = models_available[model_key]
parms = md.get_parameter_defaults()
return parms
[docs]def get_model_by_name(name):
"""Convenience function to obtain a model by name instead of by key"""
for key in models_available:
if models_available[key].model_name == name:
return models_available[key]
else:
raise KeyError("No model with name '{}'!".format(name))
[docs]def get_parm_name(model_key, parm_key):
"""Return parameter label
Parameters
----------
model_key: str
The model key (e.g. "hertz_cone")
parm_key: str
The parameter key (e.g. "E")
Returns
-------
parm_name: str
The parameter label (e.g. "Young's Modulus")
"""
md = models_available[model_key]
if parm_key in md.parameter_keys:
idx = md.parameter_keys.index(parm_key)
return md.parameter_names[idx]
elif (hasattr(md, "compute_ancillaries")
and parm_key in md.parameter_anc_keys):
idx = md.parameter_anc_keys.index(parm_key)
return md.parameter_anc_names[idx]
elif parm_key in ANCILLARY_COMMON:
return ANCILLARY_COMMON[parm_key][0]
[docs]def get_parm_unit(model_key, parm_key):
"""Return parameter unit
Parameters
----------
model_key: str
The model key (e.g. "hertz_cone")
parm_key: str
The parameter key (e.g. "E")
Returns
-------
parm_unit: str
The parameter unit (e.g. "Pa")
"""
md = models_available[model_key]
if parm_key in md.parameter_keys:
idx = md.parameter_keys.index(parm_key)
return md.parameter_units[idx]
elif (hasattr(md, "compute_ancillaries")
and parm_key in md.parameter_anc_keys):
idx = md.parameter_anc_keys.index(parm_key)
return md.parameter_anc_units[idx]
elif parm_key in ANCILLARY_COMMON:
return ANCILLARY_COMMON[parm_key][1]
[docs]def register_model(module, module_name):
"""Register a fitting model"""
global models_available # this is not necessary, but clarifies things
# sanity checks
missing = []
for attr in ["get_parameter_defaults",
"model",
"residual",
"model_doc",
"model_key",
"model_name",
"parameter_keys",
"parameter_names",
"parameter_units",
"valid_axes_x",
"valid_axes_y",
]:
if not hasattr(module, attr):
missing.append(attr)
if missing:
raise ModelIncompleteError(
"Model `{}` is missing the following ".format(module_name)
+ "attributes: {}".format(", ".join(missing)))
# check for completeness of ancillary parameter recipe
if hasattr(module, "compute_ancillaries"):
missing_anc = []
for attr in ["parameter_anc_keys",
"parameter_anc_names",
"parameter_anc_units",
]:
if not hasattr(module, attr):
missing_anc.append(attr)
if missing_anc:
raise ModelIncompleteError(
"Model `{}` is missing the following ".format(module_name)
+ "attributes: {}".format(", ".join(missing_anc)))
# add model
models_available[module.model_key] = module
models_available = {}
# Populate list of available fit models
_loc = locals().copy()
for _item in _loc:
if _item.startswith("model_"):
register_model(_loc[_item], _item)