"""
Model Info and Parameter Tables
===============================
Defines :class:`ModelInfo` and :class:`ParameterTable` and the routines for
manipulating them. In particular, :func:`make_model_info` converts a kernel
module into the model info block as seen by the rest of the sasmodels library.
"""
from __future__ import print_function
from copy import copy
from os.path import abspath, basename, splitext
import inspect
import logging
import numpy as np # type: ignore
# Optional typing
# pylint: disable=unused-import
try:
from typing import (
Tuple, List, Union, Dict, Optional, Any, Callable, Sequence, Set,
Mapping)
from types import ModuleType
Limits = Tuple[float, float]
#LimitsOrChoice = Union[Limits, Tuple[Sequence[str]]]
ParameterDef = Tuple[str, str, float, Limits, str, str]
ParameterSetUser = Mapping[str, Union[float, List[float]]]
ParameterSet = Mapping[str, float]
TestInput = Union[str, float, List[float], Tuple[float, float], List[Tuple[float, float]]]
TestValue = Union[float, List[float]]
TestCondition = Tuple[ParameterSetUser, TestInput, TestValue]
except ImportError:
pass
# pylint: enable=unused-import
logger = logging.getLogger(__name__)
# If MAX_PD changes, need to change the loop macros in kernel_iq.c
MAX_PD = 5 #: Maximum number of simultaneously polydisperse parameters
# assumptions about common parameters exist throughout the code, such as:
# (1) kernel functions Iq, Iqxy, Iqac, Iqabc, form_volume, ... don't see them
# (2) kernel drivers assume scale is par[0] and background is par[1]
# (3) mixture models drop the background on components and replace the scale
# with a scale that varies from [-inf, inf]
# (4) product models drop the background and reassign scale
# and maybe other places.
# Note that scale and background cannot be coordinated parameters whose value
# depends on the some polydisperse parameter with the current implementation
DEFAULT_BACKGROUND = 1e-3
COMMON_PARAMETERS = [
("scale", "", 1, (0.0, np.inf), "", "Scale factor or Volume fraction"),
("background", "1/cm", DEFAULT_BACKGROUND, (-np.inf, np.inf), "", "Source background"),
]
assert (len(COMMON_PARAMETERS) == 2
and COMMON_PARAMETERS[0][0] == "scale"
and COMMON_PARAMETERS[1][0] == "background"), "don't change common parameters"
[docs]def make_parameter_table(pars):
# type: (List[ParameterDef]) -> ParameterTable
"""
Construct a parameter table from a list of parameter definitions.
This is used by the module processor to convert the parameter block into
the parameter table seen in the :class:`ModelInfo` for the module.
"""
processed = []
for p in pars:
if not isinstance(p, (list, tuple)) or len(p) != 6:
raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r"
%str(p))
processed.append(parse_parameter(*p))
partable = ParameterTable(processed)
partable.check_angles(strict=True)
return partable
[docs]def parse_parameter(name, units='', default=np.NaN,
user_limits=None, ptype='', description=''):
# type: (str, str, float, Sequence[Any], str, str) -> Parameter
"""
Parse an individual parameter from the parameter definition block.
This does type and value checking on the definition, leading
to early failure in the model loading process and easier debugging.
"""
# Parameter is a user facing class. Do robust type checking.
if not isstr(name):
raise ValueError("expected string for parameter name %r"%name)
if not isstr(units):
raise ValueError("expected units to be a string for %s"%name)
# Process limits as [float, float] or [[str, str, ...]]
choices = [] # type: List[str]
if user_limits is None:
limits = (-np.inf, np.inf)
elif not isinstance(user_limits, (tuple, list)):
raise ValueError("invalid limits for %s"%name)
else:
# if limits is [[str,...]], then this is a choice list field,
# and limits are 1 to length of string list
if isinstance(user_limits[0], (tuple, list)):
choices = user_limits[0]
limits = (0., len(choices)-1.)
if not all(isstr(k) for k in choices):
raise ValueError("choices must be strings for %s"%name)
else:
try:
low, high = user_limits
limits = (float(low), float(high))
except Exception:
raise ValueError("invalid limits for %s: %r"%(name, user_limits))
if low >= high:
raise ValueError("require lower limit < upper limit")
# Process default value as float, making sure it is in range
if not isinstance(default, (int, float)):
raise ValueError("expected default %r to be a number for %s"
% (default, name))
if default < limits[0] or default > limits[1]:
raise ValueError("default value %r not in range for %s"
% (default, name))
# Check for valid parameter type
if ptype not in ("volume", "orientation", "sld", "magnetic", ""):
raise ValueError("unexpected type %r for %s" % (ptype, name))
# Check for valid parameter description
if not isstr(description):
raise ValueError("expected description to be a string")
# Parameter id for name[n] does not include [n]
ref = None # type: Optional[str]
if "[" in name:
if not name.endswith(']'):
raise ValueError("Expected name[len] for vector parameter %s"%name)
pid, ref = name[:-1].split('[', 1)
ref = ref.strip()
else:
pid, ref = name, None
# automatically identify sld types
if ptype == '' and (pid.startswith('sld') or pid.endswith('sld')):
ptype = 'sld'
# Check if using a vector definition, name[k], as the parameter name
if ref:
if ref == '':
raise ValueError("Need to specify vector length for %s"%name)
try:
length = int(ref)
control = None
except ValueError:
length = None
control = ref
else:
length = 1
control = None
# Build the parameter
parameter = Parameter(name=name, units=units, default=default,
limits=limits, ptype=ptype, description=description)
# TODO: need better control over whether a parameter is polydisperse
parameter.polydisperse = ptype in ('orientation', 'volume')
parameter.relative_pd = ptype == 'volume'
parameter.choices = choices
parameter.length = length
parameter.length_control = control
return parameter
[docs]def expand_pars(partable, pars=None):
# type: (ParameterTable, ParameterSetUser) -> ParameterSet
"""
Create a parameter set from key-value pairs.
*pars* are the key-value pairs to use for the parameters. Any
parameters not specified in *pars* are set from the *partable* defaults.
If *pars* references vector fields, such as thickness[n], then support
different ways of assigning the parameter values, including assigning a
specific value (e.g., thickness3=50.0), assigning a new value to all
(e.g., thickness=50.0) or assigning values using list notation.
"""
if pars is None:
result = partable.defaults
else:
lookup = dict((p.id, p) for p in partable.kernel_parameters)
result = dict(partable.defaults)
scalars = dict((name, value) for name, value in pars.items()
if name not in lookup or lookup[name].length == 1)
vectors = dict((name, value) for name, value in pars.items()
if name in lookup and lookup[name].length > 1)
#print("lookup", lookup)
#print("scalars", scalars)
#print("vectors", vectors)
for name, value in vectors.items():
if np.isscalar(value):
# support for the form
# dict(thickness=0, thickness2=50)
for k in range(1, lookup[name].length+1):
key = name+str(k)
if key not in scalars:
scalars[key] = value
else:
# supoprt for the form
# dict(thickness=[20,10,3])
for (k, v) in enumerate(value):
scalars[name+str(k+1)] = v
result.update(scalars)
#print("expanded", result)
return result
[docs]def prefix_parameter(par, prefix):
# type: (Parameter, str) -> Parameter
"""
Return a copy of the parameter with its name prefixed.
"""
new_par = copy(par)
new_par.name = prefix + par.name
new_par.id = prefix + par.id
return new_par
[docs]def suffix_parameter(par, suffix):
# type: (Parameter, str) -> Parameter
"""
Return a copy of the parameter with its name prefixed.
"""
new_par = copy(par)
# If name has the form x[n], replace with x_suffix[n]
new_par.name = par.id + suffix + par.name[len(par.id):]
new_par.id = par.id + suffix
return new_par
[docs]class Parameter(object):
"""
The available kernel parameters are defined as a list, with each parameter
defined as a sublist with the following elements:
*name* is the name that will be displayed to the user. Names
should be lower case, with words separated by underscore. If
acronyms are used, the whole acronym should be upper case. For vector
parameters, the name will be followed by *[len]* where *len* is an
integer length of the vector, or the name of the parameter which
controls the length. The attribute *id* will be created from name
without the length.
*units* should be one of *degrees* for angles, *Ang* for lengths,
*1e-6/Ang^2* for SLDs.
*default* will be the initial value for the model when it
is selected, or when an initial value is not otherwise specified.
*limits ([lb, ub])* are the hard limits on the parameter value, used to
limit the polydispersity density function. In the fit, the parameter limits
given to the fit are the limits on the central value of the parameter.
If there is polydispersity, it will evaluate parameter values outside
the fit limits, but not outside the hard limits specified in the model.
If there are no limits, use +/-inf imported from numpy.
*type* indicates how the parameter will be used. "volume" parameters
will be used in all functions. "orientation" parameters are not passed,
but will be used to convert from *qx*, *qy* to *qa*, *qb*, *qc* in calls to
*Iqxy* and *Imagnetic*. If *type* is the empty string, the parameter will
be used in all of *Iq*, *Iqxy* and *Imagnetic*. "sld" parameters
can automatically be promoted to magnetic parameters, each of which
will have a magnitude and a direction, which may be different from
other sld parameters. The volume parameters are used for calls
to form_volume within the kernel (required for volume normalization),
to shell_volume (for hollow shapes), and to radius_effective (for
structure factor interactions) respectively.
*description* is a short description of the parameter. This will
be displayed in the parameter table and used as a tool tip for the
parameter value in the user interface.
Additional values can be set after the parameter is created:
* *length* is the length of the field if it is a vector field
* *length_control* is the parameter which sets the vector length
* *is_control* is True if the parameter is a control parameter for a vector
* *polydisperse* is true if the parameter accepts a polydispersity
* *relative_pd* is true if that polydispersity is a portion of the
value (so a 10% length dipsersity would use a polydispersity value
of 0.1) rather than absolute dispersisity (such as an angle plus or
minus 15 degrees).
*choices* is the option names for a drop down list of options, as for
example, might be used to set the value of a shape parameter.
Control parameters are used for variant models such as :ref:`rpa` which
have different cases with different parameters, as well as models
like *spherical_sld* with its user defined number of shells.
The control parameter should appear in the parameter table along with the
parameters it is is controlling. For variant models, use *[CASES]* in
place of the parameter limits Within the parameter definition table,
with case names such as::
CASES = ["diblock copolymer", "triblock copolymer", ...]
This should give *limits=[[case1, case2, ...]]*, but the model loader
translates it to *limits=[0, len(CASES)-1]*, and adds *choices=CASES* to
the :class:`Parameter` definition. Note that models can use a list of
cases as a parameter without it being a control parameter. Either way,
the parameter is sent to the model evaluator as *float(choice_num)*,
where choices are numbered from 0. :meth:`ModelInfo.get_hidden_parameters`
will determine which parameers to display.
The class contructor should not be called directly, but instead the
parameter table is built using :func:`make_parameter_table` and
:func:`parse_parameter` therein.
"""
def __init__(self, name, units='', default=np.NaN, limits=(-np.inf, np.inf),
ptype='', description=''):
# type: (str, str, float, Limits, str, str) -> None
self.id = name.split('[')[0].strip() # type: str
self.name = name # type: str
self.units = units # type: str
self.default = default # type: float
self.limits = limits # type: Limits
self.type = ptype # type: str
self.description = description # type: str
# Length and length_control will be filled in once the complete
# parameter table is available.
self.length = 1 # type: int
self.length_control = None # type: Optional[str]
self.is_control = False # type: bool
# TODO: need better control over whether a parameter is polydisperse
self.polydisperse = False # type: bool
self.relative_pd = False # type: bool
# choices are also set externally.
self.choices = [] # type: List[str]
[docs] def as_definition(self):
# type: () -> str
"""
Declare space for the variable in a parameter structure.
For example, the parameter thickness with length 3 will
return "double thickness[3];", with no spaces before and
no new line character afterward.
"""
if self.length == 1:
return "double %s;"%self.id
else:
return "double %s[%d];"%(self.id, self.length)
[docs] def as_function_argument(self):
# type: () -> str
r"""
Declare the variable as a function argument.
For example, the parameter thickness with length 3 will
return "double \*thickness", with no spaces before and
no comma afterward.
"""
if self.length == 1:
return "double %s"%self.id
else:
return "double *%s"%self.id
def __str__(self):
# type: () -> str
return "<%s>"%self.name
def __repr__(self):
# type: () -> str
return "P<%s>"%self.name
[docs]class ParameterTable(object):
"""
ParameterTable manages the list of available parameters.
There are a couple of complications which mean that the list of parameters
for the kernel differs from the list of parameters that the user sees.
(1) Common parameters. Scale and background are implicit to every model,
but are not passed to the kernel.
(2) Vector parameters. Vector parameters are passed to the kernel as a
pointer to an array, e.g., thick[], but they are seen by the user as n
separate parameters thick1, thick2, ...
Therefore, the parameter table is organized by how it is expected to be
used. The following information is needed to set up the kernel functions:
* *kernel_parameters* is the list of parameters in the kernel parameter
table, with vector parameter p declared as p[].
* *iq_parameters* is the list of parameters to the Iq(q, ...) function,
with vector parameter p sent as p[].
* *form_volume_parameters* is the list of parameters to the form_volume(...)
function, with vector parameter p sent as p[].
Problem details, which sets up the polydispersity loops, requires the
following:
* *theta_offset* is the offset of the theta parameter in the kernel parameter
table, with vector parameters counted as n individual parameters
p1, p2, ..., or offset is -1 if there is no theta parameter.
* *max_pd* is the maximum number of polydisperse parameters, with vector
parameters counted as n individual parameters p1, p2, ... Note that
this number is limited to sasmodels.modelinfo.MAX_PD.
* *npars* is the total number of parameters to the kernel, with vector
parameters counted as n individual parameters p1, p2, ...
* *common_parameters* is the list of common parameters, with a unique
copy for each model so that structure factors can have a default
background of 0.0.
* *call_parameters* is the complete list of parameters to the kernel,
including scale and background, with vector parameters recorded as
individual parameters p1, p2, ...
* *active_1d* is the set of names that may be polydisperse for 1d data
* *active_2d* is the set of names that may be polydisperse for 2d data
User parameters are the set of parameters visible to the user, including
the scale and background parameters that the kernel does not see. User
parameters don't use vector notation, and instead use p1, p2, ...
"""
def __init__(self, parameters):
# type: (List[Parameter]) -> None
# scale and background are implicit parameters
# Need them to be unique to each model in case they have different
# properties, such as default=0.0 for structure factor backgrounds.
self.common_parameters = [Parameter(*p) for p in COMMON_PARAMETERS]
self.kernel_parameters = parameters
self._set_vector_lengths()
self.npars = sum(p.length for p in self.kernel_parameters)
self.nmagnetic = sum(p.length for p in self.kernel_parameters
if p.type == 'sld')
self.nvalues = 2 + self.npars
if self.nmagnetic:
self.nvalues += 3 + 3*self.nmagnetic
self.call_parameters = self._get_call_parameters()
self.defaults = self._get_defaults()
#self._name_table= dict((p.id, p) for p in parameters)
# Set the kernel parameters. Assumes background and scale are the
# first two parameters in the parameter list, but these are not sent
# to the underlying kernel functions.
self.iq_parameters = [p for p in self.kernel_parameters
if p.type not in ('orientation', 'magnetic')]
self.orientation_parameters = [p for p in self.kernel_parameters
if p.type == 'orientation']
self.form_volume_parameters = [p for p in self.kernel_parameters
if p.type == 'volume']
# Theta offset
offset = 0
for p in self.kernel_parameters:
if p.name == 'theta':
self.theta_offset = offset
break
offset += p.length
else:
self.theta_offset = -1
# number of polydisperse parameters
num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse)
# Don't use more polydisperse parameters than are available in the model
self.max_pd = min(num_pd, MAX_PD)
# true if has 2D parameters
self.has_2d = any(p.type in ('orientation', 'magnetic')
for p in self.kernel_parameters)
self.is_asymmetric = any(p.name == 'psi' for p in self.kernel_parameters)
self.magnetism_index = [k for k, p in enumerate(self.call_parameters)
if p.id.endswith('_M0')]
self.pd_1d = set(p.name for p in self.call_parameters
if p.polydisperse and p.type not in ('orientation', 'magnetic'))
self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse)
# Final checks
self.check_duplicates()
self.check_angles()
[docs] def set_zero_background(self):
# type: () -> None
"""
Set the default background to zero for this model. This is done for
structure factor models.
"""
# Make sure background is the second common parameter.
assert self.common_parameters[1].id == "background"
self.common_parameters[1].default = 0.0
self.defaults = self._get_defaults()
[docs] def check_angles(self, strict=False):
"""
Check that orientation angles are theta, phi and possibly psi.
*strict* should be True when checking a parameter table defined
in a model file, but False when checking from mixture models, etc.,
where the parameters aren't being passed to a calculator directly.
"""
theta = phi = psi = -1
for k, p in enumerate(self.kernel_parameters):
if p.name == 'theta':
theta = k
if p.type != 'orientation':
raise TypeError("theta must be an orientation parameter")
elif p.name == 'phi':
phi = k
if p.type != 'orientation':
raise TypeError("phi must be an orientation parameter")
elif p.name == 'psi':
psi = k
if p.type != 'orientation':
raise TypeError("psi must be an orientation parameter")
elif strict and p.type == 'orientation':
raise TypeError("only theta, phi and psi can be orientation parameters")
if theta >= 0 and phi >= 0:
last_par = len(self.kernel_parameters) - 1
if phi != theta+1:
raise TypeError("phi must follow theta")
if psi >= 0 and psi != phi+1:
raise TypeError("psi must follow phi")
# TODO: Why must theta/phi/psi be at the end? Consistency only?
if strict and phi != last_par and psi != last_par:
raise TypeError("orientation parameters must appear at the "
"end of the parameter table")
elif theta >= 0 or phi >= 0 or psi >= 0:
raise TypeError("oriented shapes must have both theta and phi and maybe psi")
[docs] def check_duplicates(self):
"""
Check for duplicate parameter names
"""
checked, dups = set(), set()
for p in self.call_parameters:
if p.id in checked:
dups.add(p.id)
else:
checked.add(p.id)
if dups:
raise TypeError("Duplicate parameters: {}"
.format(", ".join(sorted(dups))))
def __getitem__(self, key):
# Find the parameter definition
for par in self.call_parameters:
if par.name == key:
return par
raise KeyError("unknown parameter %r"%key)
def __contains__(self, key):
for par in self.call_parameters:
if par.name == key:
return True
return False
def _set_vector_lengths(self):
# type: () -> None
"""
Walk the list of kernel parameters, setting the length field of the
vector parameters from the upper limit of the reference parameter.
This needs to be done once the entire parameter table is available
since the reference may still be undefined when the parameter is
initially created.
Returns the list of control parameter names.
Note: This modifies the underlying parameter object.
"""
# Sort out the length of the vector parameters such as thickness[n]
for p in self.kernel_parameters:
if p.length_control:
ref = self._get_ref(p)
ref.is_control = True
ref.polydisperse = False
low, high = ref.limits
if int(low) != low or int(high) != high or low < 0 or high > 20:
raise ValueError("expected limits on %s to be within [0, 20]"
% ref.name)
p.length = int(high)
def _get_ref(self, p):
# type: (Parameter) -> Parameter
for ref in self.kernel_parameters:
if ref.id == p.length_control:
return ref
raise ValueError("no reference variable %r for %s"
% (p.length_control, p.name))
def _get_defaults(self):
# type: () -> ParameterSet
"""
Get a list of parameter defaults from the parameters.
Expands vector parameters into parameter id+number.
"""
# Construct default values, including vector defaults
defaults = {}
for p in self.call_parameters:
if p.length == 1:
defaults[p.id] = p.default
else:
for k in range(1, p.length+1):
defaults["%s%d"%(p.id, k)] = p.default
return defaults
def _get_call_parameters(self):
# type: () -> List[Parameter]
full_list = self.common_parameters[:]
for p in self.kernel_parameters:
if p.length == 1:
full_list.append(p)
else:
for k in range(1, p.length+1):
pk = Parameter(p.id+str(k), p.units, p.default,
p.limits, p.type, p.description)
pk.polydisperse = p.polydisperse
pk.relative_pd = p.relative_pd
pk.choices = p.choices
full_list.append(pk)
# Add the magnetic parameters to the end of the call parameter list.
if self.nmagnetic > 0:
full_list.extend([
Parameter('up_frac_i', '', 0., [0., 1.],
'magnetic', 'fraction of spin up incident'),
Parameter('up_frac_f', '', 0., [0., 1.],
'magnetic', 'fraction of spin up final'),
Parameter('up_angle', 'degrees', 0., [0., 360.],
'magnetic', 'spin up angle'),
])
slds = [p for p in full_list if p.type == 'sld']
for p in slds:
full_list.extend([
Parameter(p.id+'_M0', '1e-6/Ang^2', 0., [-np.inf, np.inf],
'magnetic', 'magnetic amplitude for '+p.description),
Parameter(p.id+'_mtheta', 'degrees', 0., [-90., 90.],
'magnetic', 'magnetic latitude for '+p.description),
Parameter(p.id+'_mphi', 'degrees', 0., [-180., 180.],
'magnetic', 'magnetic longitude for '+p.description),
])
#print("call parameters", full_list)
return full_list
[docs] def user_parameters(self, pars, is2d=True):
# type: (Dict[str, float], bool) -> List[Parameter]
"""
Return the list of parameters for the given data type.
Vector parameters are expanded in place. If multiple parameters
share the same vector length, then the parameters will be interleaved
in the result. The control parameters come first. For example,
if the parameter table is ordered as::
sld_core
sld_shell[num_shells]
sld_solvent
thickness[num_shells]
num_shells
and *pars[num_shells]=2* then the returned list will be::
num_shells
scale
background
sld_core
sld_shell1
thickness1
sld_shell2
thickness2
sld_solvent
Note that shell/thickness pairs are grouped together in the result
even though they were not grouped in the incoming table. The control
parameter is always returned first since the GUI will want to set it
early, and rerender the table when it is changed.
Parameters marked as sld will automatically have a set of associated
magnetic parameters (p_M0, p_mtheta, p_mphi), as well as polarization
information (up_theta, up_frac_i, up_frac_f).
"""
# control parameters go first
control = [p for p in self.kernel_parameters if p.is_control]
# Gather entries such as name[n] into groups of the same n
dependent = {} # type: Dict[str, List[Parameter]]
dependent.update((p.id, []) for p in control)
for p in self.kernel_parameters:
if p.length_control is not None:
dependent[p.length_control].append(p)
# Gather entries such as name[4] into groups of the same length
fixed_length = {} # type: Dict[int, List[Parameter]]
for p in self.kernel_parameters:
if p.length > 1 and p.length_control is None:
fixed_length.setdefault(p.length, []).append(p)
# Using the call_parameters table, we already have expanded forms
# for each of the vector parameters; put them in a lookup table
# Note: p.id and p.name are currently identical for the call parameters
expanded_pars = dict((p.id, p) for p in self.call_parameters)
def append_group(name):
"""add the named parameter, and related magnetic parameters if any"""
result.append(expanded_pars[name])
if is2d:
for tag in '_M0', '_mtheta', '_mphi':
if name+tag in expanded_pars:
result.append(expanded_pars[name+tag])
# Gather the user parameters in order
result = control + self.common_parameters
for p in self.kernel_parameters:
if not is2d and p.type in ('orientation', 'magnetic'):
pass
elif p.is_control:
pass # already added
elif p.length_control is not None:
table = dependent.get(p.length_control, [])
if table:
# look up length from incoming parameters
table_length = int(pars.get(p.length_control, p.length))
del dependent[p.length_control] # first entry seen
for k in range(1, table_length+1):
for entry in table:
append_group(entry.id+str(k))
else:
pass # already processed all entries
elif p.length > 1:
table = fixed_length.get(p.length, [])
if table:
table_length = p.length
del fixed_length[p.length]
for k in range(1, table_length+1):
for entry in table:
append_group(entry.id+str(k))
else:
pass # already processed all entries
else:
append_group(p.id)
if is2d and 'up_angle' in expanded_pars:
result.extend([
expanded_pars['up_frac_i'],
expanded_pars['up_frac_f'],
expanded_pars['up_angle'],
])
return result
def _simple_insert(parameters, insert, remove):
"""
Build new parameters from old with insertion locations specified.
*parameters* is the existing parameter list.
*insert* is list of parameters to insert.
*remove* is list of parameter names to remove.
The new parameters are inserted as a block replacing the first removed
parameter.
"""
remove = set(remove)
new_list = []
for par in parameters:
if par.id not in remove:
new_list.append(par)
if par.id in remove and insert:
new_list.extend(insert)
insert = []
return new_list
def _insert_after(parameters, insert, remove, insert_after):
"""
Build new parameters from old with insertion locations specified.
*parameters* is the existing parameter list.
*insert* is list of parameters to insert.
*remove* is list of parameter names to remove.
*insert_after* where to insert names, as {"old": "new,new,..."}
"""
remove = set(remove)
new_list = []
lookup = {p.id: p for p in insert}
def _process_group(key):
items = insert_after.get(key, None)
if items is None:
return
for name in items.split(','):
# Make sure par is available
if name not in lookup:
raise ValueError("variable %s not in new parameters"
" when inserting %s after %r"
% (name, items, key))
# Make sure par hasn't be used
if lookup[name] is None:
raise ValueError("variable %s already processed"
" when inserting %s after %r"
% (name, items, key))
# Append par
new_list.append(lookup[name])
# Mark par as used
lookup[name] = None
_process_group("")
for par in parameters:
if par.id not in remove:
new_list.append(par)
_process_group(par.id)
for name, par in lookup.items():
if par is not None:
raise ValueError("parameter %s not listed in insert_after", name)
return new_list
[docs]def derive_table(table, insert, remove, insert_after=None):
# type: (ParameterTable, List[str], List[Parameter], Optional[Dict[str, str]]) -> ParameterTable
"""
Create a derived parameter table.
Parameters given in *insert* are added to the table and parameters
named in *remove* are deleted from the table. If *insert_after* is
provided, then it indicates where in the new parameter table the
parameters are inserted.
"""
old = table.kernel_parameters
if insert_after is None:
new = _simple_insert(old, insert, remove)
else:
new = _insert_after(old, insert, remove, insert_after)
return ParameterTable(new)
[docs]def isstr(x):
# type: (Any) -> bool
"""
Return True if the object is a string.
"""
# TODO: 2-3 compatible tests for str, including unicode strings
return isinstance(x, str)
#: Set of variables defined in the model that might contain C code
C_SYMBOLS = ['Imagnetic', 'Iq', 'Iqxy', 'Iqac', 'Iqabc',
'form_volume', 'shell_volume', 'c_code', 'valid']
def _find_source_lines(model_info, kernel_module):
# type: (ModelInfo, ModuleType) -> None
"""
Identify the location of the C source inside the model definition file.
This code runs through the source of the kernel module looking for lines
that contain C code (because it is a c function definition). Clearly
there are all sorts of reasons why this might not work (e.g., code
commented out in a triple-quoted line block, code built using string
concatenation, code defined in the branch of an 'if' block, code imported
from another file), but it should work properly in the 95% case, and for
the remainder, getting the incorrect line number will merely be
inconvenient.
"""
# Only need line numbers if we are creating a C module and the C symbols
# are defined.
if (callable(model_info.Iq)
or not any(hasattr(model_info, s) for s in C_SYMBOLS)):
return
# load the module source if we can
try:
source = inspect.getsource(kernel_module)
except IOError:
return
# look for symbol at the start of the line
for lineno, line in enumerate(source.split('\n')):
for name in C_SYMBOLS:
if line.startswith(name):
# Add 1 since some compilers complain about "#line 0"
model_info.lineno[name] = lineno + 1
break
[docs]def make_model_info(kernel_module):
# type: (ModuleType) -> ModelInfo
"""
Extract the model definition from the loaded kernel module.
Fill in default values for parts of the module that are not provided.
Note: vectorized Iq and Iqac/Iqabc functions will be created for python
models when the model is first called, not when the model is loaded.
"""
if hasattr(kernel_module, "model_info"):
# Custom sum/multi models
return kernel_module.model_info
info = ModelInfo()
# Build the parameter table
#print("make parameter table", kernel_module.parameters)
parameters = make_parameter_table(getattr(kernel_module, 'parameters', []))
# background defaults to zero for structure factor models
structure_factor = getattr(kernel_module, 'structure_factor', False)
if structure_factor:
parameters.set_zero_background()
filename = abspath(kernel_module.__file__).replace('.pyc', '.py')
kernel_id = splitext(basename(filename))[0]
name = getattr(kernel_module, 'name', None)
if name is None:
name = " ".join(w.capitalize() for w in kernel_id.split('_'))
info.id = kernel_id # string used to load the kernel
info.basefile = info.filename = filename
info.name = name
info.title = getattr(kernel_module, 'title', name+" model")
info.description = getattr(kernel_module, 'description', 'no description')
info.base = info.parameters = parameters
info.translation = None
info.composition = None
info.docs = kernel_module.__doc__
info.category = getattr(kernel_module, 'category', None)
info.structure_factor = getattr(kernel_module, 'structure_factor', False)
# TODO: find Fq by inspection
info.radius_effective_modes = getattr(kernel_module, 'radius_effective_modes', None)
info.have_Fq = getattr(kernel_module, 'have_Fq', False)
info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y'])
# Note: custom.load_custom_kernel_module assumes the C sources are defined
# by this attribute.
info.source = getattr(kernel_module, 'source', [])
info.c_code = getattr(kernel_module, 'c_code', None)
info.radius_effective = getattr(kernel_module, 'radius_effective', None)
# TODO: check the structure of the tests
info.tests = getattr(kernel_module, 'tests', [])
info.valid = getattr(kernel_module, 'valid', '')
info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore
info.shell_volume = getattr(kernel_module, 'shell_volume', None) # type: ignore
info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore
info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore
info.Iqac = getattr(kernel_module, 'Iqac', None) # type: ignore
info.Iqabc = getattr(kernel_module, 'Iqabc', None) # type: ignore
info.Imagnetic = getattr(kernel_module, 'Imagnetic', None) # type: ignore
info.profile = getattr(kernel_module, 'profile', None) # type: ignore
info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore
# Default single and opencl to True for C models. Python models have callable Iq.
info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq))
info.single = getattr(kernel_module, 'single', not callable(info.Iq))
info.random = getattr(kernel_module, 'random', None)
info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore
# Set control flag for explicitly set parameters, e.g., in the RPA model.
control = getattr(kernel_module, 'control', None)
if control is not None:
parameters[control].is_control = True
if callable(info.Iq) and parameters.has_2d:
raise ValueError("oriented python models not supported")
# CRUFT: support old-style ER() for effective radius
# radius_effective(mode, ...), if it is present, should be a callable
# python function accepting the shape parameters, and have a corresponding
# Iq function in python (Fq in python is not suported at this time).
# If ER() is present, it might represent a 4.2 model that hasn't been
# converted, or it might represent a 4.2+5.0 model with both ER and
# radius_effective defined. Unfortunately we can't easily tell whether
# radius_effective is defined in the C sources without loading them,
# so just issue a warning if we see ER in a C model.
ER = getattr(kernel_module, 'ER', None)
if ER is not None:
if callable(info.Iq) and info.radius_effective is None:
info.radius_effective_modes = ['ER']
info.radius_effective = lambda mode, *args: ER(*args)
# TODO: uncomment the following for the sasview 4.3 release
#logger.warning(
# "ER(...) deprecated. Replace with radius_effective(mode, ...)."
# " See plugin model docs for details."
#)
else:
logger.warning(
"ER(...) function ignored. Using radius_effective(mode, ...)"
" instead if it exists.")
## --- untested, so left unsupported for now ---
## CRUFT: support old-style VR for form/shell ratio
#if info.shell_volume is None:
# VR = getattr(kernel_module, 'VR')
# if VR is not None:
# info.shell_volume = lambda *args: info.form_volume(*args)*VR(*args)
info.lineno = {}
_find_source_lines(info, kernel_module)
return info
[docs]class ModelInfo(object):
"""
Interpret the model definition file, categorizing the parameters.
The module can be loaded with a normal python import statement if you
know which module you need, or with __import__('sasmodels.model.'+name)
if the name is in a string.
The structure should be mostly static, other than the delayed definition
of *Iq*, *Iqac* and *Iqabc* if they need to be defined.
"""
#: Full path to the file defining the kernel, if any.
filename = None # type: Optional[str]
#: Base file is usually filename, but not when a model has been
#: reparameterized, in which case it is the file containing the original
#: model definition. This is needed to signal an additional dependency for
#: the model time stamp, and so that the compiler reports correct file
#: for syntax errors.
basefile = None # type: Optional[str]
#: Id of the kernel used to load it from the filesystem.
id = None # type: str
#: Display name of the model, which defaults to the model id but with
#: capitalization of the parts so for example core_shell defaults to
#: "Core Shell".
name = None # type: str
#: Short description of the model.
title = None # type: str
#: Long description of the model.
description = None # type: str
#: Model parameter table. Parameters are defined using a list of parameter
#: definitions, each of which is contains parameter name, units,
#: default value, limits, type and description. See :class:`Parameter`
#: for details on the individual parameters. The parameters are gathered
#: into a :class:`ParameterTable`, which provides various views into the
#: parameter list.
parameters = None # type: ParameterTable
#: For reparameterized systems, *base* is the base parameter table. For
#: normal systems it is simply a copy of *parameters*.
base = None # type: ParameterTable
#: Parameter translation code to convert from *parameters* table from
#: caller to the *base* table used to evaluate the model.
translation = None # type: Optional[str]
#: Composition is None if this is an independent model, or it is a
#: tuple with comoposition type ('product' or 'misture') and a list of
#: :class:`ModelInfo` blocks for the composed objects. This allows us
#: to rebuild a complete mixture or product model from the info block.
#: *composition* is not given in the model definition file, but instead
#: arises when the model is constructed using names such as
#: *sphere*hardsphere* or *cylinder+sphere*.
composition = None # type: Optional[Tuple[str, List[ModelInfo]]]
#: Different variants require different parameters. In order to show
#: just the parameters needed for the variant selected,
#: you should provide a function *hidden(control) -> set(['a', 'b', ...])*
#: indicating which parameters need to be hidden. For multiplicity
#: models, you need to use the complete name of the parameter, including
#: its number. So for example, if variant "a" uses only *sld1* and *sld2*,
#: then *sld3*, *sld4* and *sld5* of multiplicity parameter *sld[5]*
#: should be in the hidden set.
hidden = None # type: Optional[Callable[[int], Set[str]]]
#: Doc string from the top of the model file. This should be formatted
#: using ReStructuredText format, with latex markup in ".. math"
#: environments, or in dollar signs. This will be automatically
#: extracted to a .rst file by :func:`.generate.make_doc`, then
#: converted to HTML or PDF by Sphinx.
docs = None # type: str
#: Location of the model description in the documentation. This takes the
#: form of "section" or "section:subsection". So for example,
#: :ref:`porod` uses *category="shape-independent"* so it is in the
#: :ref:`shape-independent` section whereas
#: :ref:`capped-cylinder` uses: *category="shape:cylinder"*, which puts
#: it in the :ref:`shape-cylinder` section.
category = None # type: Optional[str]
#: True if the model can be computed accurately with single precision.
#: This is True by default, but models such as :ref:`bcc-paracrystal` set
#: it to False because they require double precision calculations.
single = None # type: bool
#: True if the model can be run as an opencl model. If for some reason
#: the model cannot be run in opencl (e.g., because the model passes
#: functions by reference), then set this to false.
opencl = None # type: bool
#: True if the model is a structure factor used to model the interaction
#: between form factor models. This will default to False if it is not
#: provided in the file.
structure_factor = None # type: bool
#: True if the model defines an Fq function with signature
#: ``void Fq(double q, double *F1, double *F2, ...)``
have_Fq = False
#: List of options for computing the effective radius of the shape,
#: or None if the model is not usable as a form factor model.
radius_effective_modes = None # type: List[str]
#: List of C source files used to define the model. The source files
#: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the
#: model defines orientation parameters. Files containing the most basic
#: functions must appear first in the list, followed by the files that
#: use those functions.
source = None # type: List[str]
#: inline source code, added after all elements of source
c_code = None # type: Optional[str]
#: Expression which evaluates to True if the input parameters are valid
#: and the model can be computed, or False otherwise. Invalid parameter
#: sets will not be included in the weighted $I(Q)$ calculation or its
#: volume normalization. Use C syntax for the expressions, with || for or
#: && for and and ! for not. Any non-magnetic parameter can be used.
valid = None # type: str
#: Returns the form volume for python-based models. Form volume is needed
#: for volume normalization in the polydispersity integral. If no
#: parameters are *volume* parameters, then form volume is not needed.
#: For C-based models, (with :attr:`source` defined, or with :attr:`Iq`
#: defined using a string containing C code), form_volume must also be
#: C code, either defined as a string, or in the sources.
form_volume = None # type: Union[None, str, Callable[[np.ndarray], float]]
#: Returns the shell volume for python-based models. Form volume and
#: shell volume are needed for volume normalization in the polydispersity
#: integral and structure interactions for hollow shapes. If no
#: parameters are *volume* parameters, then shell volume is not needed.
#: For C-based models, (with :attr:`source` defined, or with :attr:`Iq`
#: defined using a string containing C code), shell_volume must also be
#: C code, either defined as a string, or in the sources.
shell_volume = None # type: Union[None, str, Callable[[np.ndarray], float]]
#: Computes the effective radius of the shape given the volume parameters.
#: Only needed for models defined in python that can be used for
#: monodisperse approximation for non-dilute solutions, P@S. The first
#: argument is the integer effective radius mode, with default 0.
radius_effective = None # type: Union[None, Callable[[int, np.ndarray], float]]
#: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined
#: by the parameter table. *Iq* can be defined as a python function, or
#: as a C function. If it is defined in C, then set *Iq* to the body of
#: the C function, including the return statement. This function takes
#: values for *q* and each of the parameters as separate *double* values
#: (which may be converted to float or long double by sasmodels). All
#: source code files listed in :attr:`source` will be loaded before the
#: *Iq* function is defined. If *Iq* is not present, then sources should
#: define *static double Iq(double q, double a, double b, ...)* which
#: will return *I(q, a, b, ...)*. Multiplicity parameters are sent as
#: pointers to doubles. Constants in floating point expressions should
#: include the decimal point. See :mod:`.generate` for more details. If
#: *have_Fq* is True, then Iq should return an interleaved array of
#: $[\sum F(q_1), \sum F^2(q_1), \ldots, \sum F(q_n), \sum F^2(q_n)]$.
Iq = None # type: Union[None, str, Callable[[...], np.ndarray]]
#: Returns *I(qx, qy, a, b, ...)*. The interface follows :attr:`Iq`.
Iqxy = None # type: Union[None, str, Callable[[...], np.ndarray]]
#: Returns *I(qab, qc, a, b, ...)*. The interface follows :attr:`Iq`.
Iqac = None # type: Union[None, str, Callable[[...], np.ndarray]]
#: Returns *I(qa, qb, qc, a, b, ...)*. The interface follows :attr:`Iq`.
Iqabc = None # type: Union[None, str, Callable[[...], np.ndarray]]
#: Returns *I(qx, qy, a, b, ...)*. The interface follows :attr:`Iq`.
Imagnetic = None # type: Union[None, str, Callable[[...], np.ndarray]]
#: Returns a model profile curve *x, y*. If *profile* is defined, this
#: curve will appear in response to the *Show* button in SasView. Use
#: :attr:`profile_axes` to set the axis labels. Note that *y* values
#: will be scaled by 1e6 before plotting.
profile = None # type: Optional[Callable[[np.ndarray], None]]
#: Axis labels for the :attr:`profile` plot. The default is *['x', 'y']*.
#: Only the *x* component is used for now.
profile_axes = None # type: Tuple[str, str]
#: Returns *sesans(z, a, b, ...)* for models which can directly compute
#: the SESANS correlation function. Note: not currently implemented.
sesans = None # type: Optional[Callable[[np.ndarray], np.ndarray]]
#: Returns a random parameter set for the model
random = None # type: Optional[Callable[[], Dict[str, float]]]
#: Line numbers for symbols defining C code
lineno = None # type: Dict[str, int]
#: The set of tests that must pass. The format of the tests is described
#: in :mod:`.model_test`.
tests = None # type: List[TestCondition]
def __init__(self):
# type: () -> None
pass
[docs] def get_hidden_parameters(self, control):
"""
Returns the set of hidden parameters for the model. *control* is the
value of the control parameter. Note that multiplicity models have
an implicit control parameter, which is the parameter that controls
the multiplicity.
"""
if self.hidden is not None:
hidden = self.hidden(control)
else:
controls = [p for p in self.parameters.kernel_parameters
if p.is_control]
if len(controls) != 1:
raise ValueError("more than one control parameter")
hidden = set(p.id+str(k)
for p in self.parameters.kernel_parameters
for k in range(control+1, p.length+1)
if p.length > 1)
for p in self.parameters.kernel_parameters:
if p.length > 1 and p.type == "sld":
for k in range(control+1, p.length+1):
base = p.id+str(k)
hidden.update((base+"_M0", base+"_mtheta", base+"_mphi"))
return hidden