[0d99a6a] | 1 | """ |
---|
| 2 | Model Info and Parameter Tables |
---|
| 3 | =============================== |
---|
| 4 | |
---|
| 5 | Defines :class:`ModelInfo` and :class:`ParameterTable` and the routines for |
---|
| 6 | manipulating them. In particular, :func:`make_model_info` converts a kernel |
---|
| 7 | module into the model info block as seen by the rest of the sasmodels library. |
---|
| 8 | """ |
---|
[04045f4] | 9 | from __future__ import print_function |
---|
| 10 | |
---|
[6d6508e] | 11 | from copy import copy |
---|
| 12 | from os.path import abspath, basename, splitext |
---|
[da63656] | 13 | import inspect |
---|
[db03406] | 14 | import logging |
---|
[69aa451] | 15 | |
---|
[7ae2b7f] | 16 | import numpy as np # type: ignore |
---|
[69aa451] | 17 | |
---|
[db03406] | 18 | from . import autoc |
---|
| 19 | |
---|
[a86f6c0] | 20 | # Optional typing |
---|
[2d81cfe] | 21 | # pylint: disable=unused-import |
---|
[a86f6c0] | 22 | try: |
---|
[04045f4] | 23 | from typing import Tuple, List, Union, Dict, Optional, Any, Callable, Sequence, Set |
---|
[e65c3ba] | 24 | from types import ModuleType |
---|
[a86f6c0] | 25 | except ImportError: |
---|
| 26 | pass |
---|
| 27 | else: |
---|
| 28 | Limits = Tuple[float, float] |
---|
[04dc697] | 29 | #LimitsOrChoice = Union[Limits, Tuple[Sequence[str]]] |
---|
[9a943d0] | 30 | ParameterDef = Tuple[str, str, float, Limits, str, str] |
---|
[a86f6c0] | 31 | ParameterSetUser = Dict[str, Union[float, List[float]]] |
---|
| 32 | ParameterSet = Dict[str, float] |
---|
| 33 | TestInput = Union[str, float, List[float], Tuple[float, float], List[Tuple[float, float]]] |
---|
| 34 | TestValue = Union[float, List[float]] |
---|
| 35 | TestCondition = Tuple[ParameterSetUser, TestInput, TestValue] |
---|
[2d81cfe] | 36 | # pylint: enable=unused-import |
---|
[a86f6c0] | 37 | |
---|
[db03406] | 38 | logger = logging.getLogger(__name__) |
---|
| 39 | |
---|
[6aee3ab] | 40 | # If MAX_PD changes, need to change the loop macros in kernel_iq.c |
---|
| 41 | MAX_PD = 5 #: Maximum number of simultaneously polydisperse parameters |
---|
[d19962c] | 42 | |
---|
[69aa451] | 43 | # assumptions about common parameters exist throughout the code, such as: |
---|
[108e70e] | 44 | # (1) kernel functions Iq, Iqxy, Iqac, Iqabc, form_volume, ... don't see them |
---|
[69aa451] | 45 | # (2) kernel drivers assume scale is par[0] and background is par[1] |
---|
| 46 | # (3) mixture models drop the background on components and replace the scale |
---|
| 47 | # with a scale that varies from [-inf, inf] |
---|
| 48 | # (4) product models drop the background and reassign scale |
---|
| 49 | # and maybe other places. |
---|
| 50 | # Note that scale and background cannot be coordinated parameters whose value |
---|
| 51 | # depends on the some polydisperse parameter with the current implementation |
---|
[7b9e4dd] | 52 | DEFAULT_BACKGROUND = 1e-3 |
---|
[7edce22] | 53 | COMMON_PARAMETERS = [ |
---|
[9a943d0] | 54 | ("scale", "", 1, (0.0, np.inf), "", "Source intensity"), |
---|
[7b9e4dd] | 55 | ("background", "1/cm", DEFAULT_BACKGROUND, (-np.inf, np.inf), "", "Source background"), |
---|
[7edce22] | 56 | ] |
---|
| 57 | assert (len(COMMON_PARAMETERS) == 2 |
---|
[40a87fa] | 58 | and COMMON_PARAMETERS[0][0] == "scale" |
---|
| 59 | and COMMON_PARAMETERS[1][0] == "background"), "don't change common parameters" |
---|
[69aa451] | 60 | |
---|
[a86f6c0] | 61 | |
---|
[69aa451] | 62 | def make_parameter_table(pars): |
---|
[f6029fd] | 63 | # type: (List[ParameterDef]) -> ParameterTable |
---|
[7edce22] | 64 | """ |
---|
| 65 | Construct a parameter table from a list of parameter definitions. |
---|
| 66 | |
---|
| 67 | This is used by the module processor to convert the parameter block into |
---|
| 68 | the parameter table seen in the :class:`ModelInfo` for the module. |
---|
| 69 | """ |
---|
[69aa451] | 70 | processed = [] |
---|
| 71 | for p in pars: |
---|
[a86f6c0] | 72 | if not isinstance(p, (list, tuple)) or len(p) != 6: |
---|
[69aa451] | 73 | raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r" |
---|
| 74 | %str(p)) |
---|
| 75 | processed.append(parse_parameter(*p)) |
---|
| 76 | partable = ParameterTable(processed) |
---|
[95498a3] | 77 | partable.check_angles() |
---|
[69aa451] | 78 | return partable |
---|
| 79 | |
---|
[a86f6c0] | 80 | def parse_parameter(name, units='', default=np.NaN, |
---|
[04045f4] | 81 | user_limits=None, ptype='', description=''): |
---|
[60f03de] | 82 | # type: (str, str, float, Sequence[Any], str, str) -> Parameter |
---|
[7edce22] | 83 | """ |
---|
| 84 | Parse an individual parameter from the parameter definition block. |
---|
| 85 | |
---|
| 86 | This does type and value checking on the definition, leading |
---|
| 87 | to early failure in the model loading process and easier debugging. |
---|
| 88 | """ |
---|
[69aa451] | 89 | # Parameter is a user facing class. Do robust type checking. |
---|
| 90 | if not isstr(name): |
---|
| 91 | raise ValueError("expected string for parameter name %r"%name) |
---|
| 92 | if not isstr(units): |
---|
| 93 | raise ValueError("expected units to be a string for %s"%name) |
---|
[04045f4] | 94 | |
---|
| 95 | # Process limits as [float, float] or [[str, str, ...]] |
---|
[c1a888b] | 96 | choices = [] # type: List[str] |
---|
[04045f4] | 97 | if user_limits is None: |
---|
| 98 | limits = (-np.inf, np.inf) |
---|
| 99 | elif not isinstance(user_limits, (tuple, list)): |
---|
| 100 | raise ValueError("invalid limits for %s"%name) |
---|
| 101 | else: |
---|
| 102 | # if limits is [[str,...]], then this is a choice list field, |
---|
| 103 | # and limits are 1 to length of string list |
---|
| 104 | if isinstance(user_limits[0], (tuple, list)): |
---|
| 105 | choices = user_limits[0] |
---|
| 106 | limits = (0., len(choices)-1.) |
---|
| 107 | if not all(isstr(k) for k in choices): |
---|
| 108 | raise ValueError("choices must be strings for %s"%name) |
---|
| 109 | else: |
---|
| 110 | try: |
---|
| 111 | low, high = user_limits |
---|
| 112 | limits = (float(low), float(high)) |
---|
| 113 | except Exception: |
---|
[bb4b509] | 114 | raise ValueError("invalid limits for %s: %r"%(name, user_limits)) |
---|
[50ec515] | 115 | if low >= high: |
---|
| 116 | raise ValueError("require lower limit < upper limit") |
---|
[69aa451] | 117 | |
---|
[04045f4] | 118 | # Process default value as float, making sure it is in range |
---|
[69aa451] | 119 | if not isinstance(default, (int, float)): |
---|
| 120 | raise ValueError("expected default %r to be a number for %s" |
---|
| 121 | % (default, name)) |
---|
[04045f4] | 122 | if default < limits[0] or default > limits[1]: |
---|
[69aa451] | 123 | raise ValueError("default value %r not in range for %s" |
---|
| 124 | % (default, name)) |
---|
| 125 | |
---|
[04045f4] | 126 | # Check for valid parameter type |
---|
[a86f6c0] | 127 | if ptype not in ("volume", "orientation", "sld", "magnetic", ""): |
---|
| 128 | raise ValueError("unexpected type %r for %s" % (ptype, name)) |
---|
[69aa451] | 129 | |
---|
[04045f4] | 130 | # Check for valid parameter description |
---|
[69aa451] | 131 | if not isstr(description): |
---|
| 132 | raise ValueError("expected description to be a string") |
---|
| 133 | |
---|
| 134 | # Parameter id for name[n] does not include [n] |
---|
| 135 | if "[" in name: |
---|
| 136 | if not name.endswith(']'): |
---|
| 137 | raise ValueError("Expected name[len] for vector parameter %s"%name) |
---|
| 138 | pid, ref = name[:-1].split('[', 1) |
---|
| 139 | ref = ref.strip() |
---|
| 140 | else: |
---|
| 141 | pid, ref = name, None |
---|
| 142 | |
---|
| 143 | # automatically identify sld types |
---|
[40a87fa] | 144 | if ptype == '' and (pid.startswith('sld') or pid.endswith('sld')): |
---|
[a86f6c0] | 145 | ptype = 'sld' |
---|
[69aa451] | 146 | |
---|
| 147 | # Check if using a vector definition, name[k], as the parameter name |
---|
| 148 | if ref: |
---|
| 149 | if ref == '': |
---|
| 150 | raise ValueError("Need to specify vector length for %s"%name) |
---|
| 151 | try: |
---|
| 152 | length = int(ref) |
---|
| 153 | control = None |
---|
[a86f6c0] | 154 | except ValueError: |
---|
[69aa451] | 155 | length = None |
---|
| 156 | control = ref |
---|
| 157 | else: |
---|
| 158 | length = 1 |
---|
| 159 | control = None |
---|
| 160 | |
---|
| 161 | # Build the parameter |
---|
| 162 | parameter = Parameter(name=name, units=units, default=default, |
---|
[a86f6c0] | 163 | limits=limits, ptype=ptype, description=description) |
---|
[69aa451] | 164 | |
---|
| 165 | # TODO: need better control over whether a parameter is polydisperse |
---|
[a86f6c0] | 166 | parameter.polydisperse = ptype in ('orientation', 'volume') |
---|
| 167 | parameter.relative_pd = ptype == 'volume' |
---|
[69aa451] | 168 | parameter.choices = choices |
---|
| 169 | parameter.length = length |
---|
| 170 | parameter.length_control = control |
---|
| 171 | return parameter |
---|
| 172 | |
---|
[ce896fd] | 173 | |
---|
[4bfd277] | 174 | def expand_pars(partable, pars): |
---|
[a86f6c0] | 175 | # type: (ParameterTable, ParameterSetUser) -> ParameterSet |
---|
[ce896fd] | 176 | """ |
---|
[6d6508e] | 177 | Create demo parameter set from key-value pairs. |
---|
[ce896fd] | 178 | |
---|
[4bfd277] | 179 | *pars* are the key-value pairs to use for the parameters. Any |
---|
| 180 | parameters not specified in *pars* are set from the *partable* defaults. |
---|
[ce896fd] | 181 | |
---|
[4bfd277] | 182 | If *pars* references vector fields, such as thickness[n], then support |
---|
[ce896fd] | 183 | different ways of assigning the demo values, including assigning a |
---|
| 184 | specific value (e.g., thickness3=50.0), assigning a new value to all |
---|
| 185 | (e.g., thickness=50.0) or assigning values using list notation. |
---|
| 186 | """ |
---|
[4bfd277] | 187 | if pars is None: |
---|
[ce896fd] | 188 | result = partable.defaults |
---|
| 189 | else: |
---|
[4bfd277] | 190 | lookup = dict((p.id, p) for p in partable.kernel_parameters) |
---|
[ce896fd] | 191 | result = partable.defaults.copy() |
---|
[9a943d0] | 192 | scalars = dict((name, value) for name, value in pars.items() |
---|
| 193 | if name not in lookup or lookup[name].length == 1) |
---|
[40a87fa] | 194 | vectors = dict((name, value) for name, value in pars.items() |
---|
[4bfd277] | 195 | if name in lookup and lookup[name].length > 1) |
---|
[256dfe1] | 196 | #print("lookup", lookup) |
---|
| 197 | #print("scalars", scalars) |
---|
| 198 | #print("vectors", vectors) |
---|
[ce896fd] | 199 | if vectors: |
---|
| 200 | for name, value in vectors.items(): |
---|
| 201 | if np.isscalar(value): |
---|
| 202 | # support for the form |
---|
[4bfd277] | 203 | # dict(thickness=0, thickness2=50) |
---|
| 204 | for k in range(1, lookup[name].length+1): |
---|
[ce896fd] | 205 | key = name+str(k) |
---|
| 206 | if key not in scalars: |
---|
[256dfe1] | 207 | scalars[key] = value |
---|
[ce896fd] | 208 | else: |
---|
| 209 | # supoprt for the form |
---|
[4bfd277] | 210 | # dict(thickness=[20,10,3]) |
---|
[40a87fa] | 211 | for (k, v) in enumerate(value): |
---|
[256dfe1] | 212 | scalars[name+str(k+1)] = v |
---|
[9a943d0] | 213 | result.update(scalars) |
---|
[256dfe1] | 214 | #print("expanded", result) |
---|
[ce896fd] | 215 | |
---|
[6d6508e] | 216 | return result |
---|
| 217 | |
---|
| 218 | def prefix_parameter(par, prefix): |
---|
[a86f6c0] | 219 | # type: (Parameter, str) -> Parameter |
---|
[6d6508e] | 220 | """ |
---|
| 221 | Return a copy of the parameter with its name prefixed. |
---|
| 222 | """ |
---|
| 223 | new_par = copy(par) |
---|
| 224 | new_par.name = prefix + par.name |
---|
| 225 | new_par.id = prefix + par.id |
---|
| 226 | |
---|
| 227 | def suffix_parameter(par, suffix): |
---|
[a86f6c0] | 228 | # type: (Parameter, str) -> Parameter |
---|
[6d6508e] | 229 | """ |
---|
| 230 | Return a copy of the parameter with its name prefixed. |
---|
| 231 | """ |
---|
| 232 | new_par = copy(par) |
---|
| 233 | # If name has the form x[n], replace with x_suffix[n] |
---|
| 234 | new_par.name = par.id + suffix + par.name[len(par.id):] |
---|
| 235 | new_par.id = par.id + suffix |
---|
[ce896fd] | 236 | |
---|
[69aa451] | 237 | class Parameter(object): |
---|
| 238 | """ |
---|
| 239 | The available kernel parameters are defined as a list, with each parameter |
---|
| 240 | defined as a sublist with the following elements: |
---|
| 241 | |
---|
[f88e248] | 242 | *name* is the name that will be displayed to the user. Names |
---|
[69aa451] | 243 | should be lower case, with words separated by underscore. If |
---|
[f88e248] | 244 | acronyms are used, the whole acronym should be upper case. For vector |
---|
| 245 | parameters, the name will be followed by *[len]* where *len* is an |
---|
| 246 | integer length of the vector, or the name of the parameter which |
---|
| 247 | controls the length. The attribute *id* will be created from name |
---|
| 248 | without the length. |
---|
[69aa451] | 249 | |
---|
| 250 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
---|
| 251 | *1e-6/Ang^2* for SLDs. |
---|
| 252 | |
---|
| 253 | *default value* will be the initial value for the model when it |
---|
| 254 | is selected, or when an initial value is not otherwise specified. |
---|
| 255 | |
---|
| 256 | *limits = [lb, ub]* are the hard limits on the parameter value, used to |
---|
| 257 | limit the polydispersity density function. In the fit, the parameter limits |
---|
| 258 | given to the fit are the limits on the central value of the parameter. |
---|
| 259 | If there is polydispersity, it will evaluate parameter values outside |
---|
| 260 | the fit limits, but not outside the hard limits specified in the model. |
---|
| 261 | If there are no limits, use +/-inf imported from numpy. |
---|
| 262 | |
---|
| 263 | *type* indicates how the parameter will be used. "volume" parameters |
---|
[108e70e] | 264 | will be used in all functions. "orientation" parameters are not passed, |
---|
| 265 | but will be used to convert from *qx*, *qy* to *qa*, *qb*, *qc* in calls to |
---|
| 266 | *Iqxy* and *Imagnetic*. If *type* is the empty string, the parameter will |
---|
[69aa451] | 267 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. "sld" parameters |
---|
| 268 | can automatically be promoted to magnetic parameters, each of which |
---|
| 269 | will have a magnitude and a direction, which may be different from |
---|
[6e7ff6d] | 270 | other sld parameters. The volume parameters are used for calls |
---|
[39a06c9] | 271 | to form_volume within the kernel (required for volume normalization), |
---|
| 272 | to shell_volume (for hollow shapes), and to effective_radius (for |
---|
| 273 | structure factor interactions) respectively. |
---|
[69aa451] | 274 | |
---|
| 275 | *description* is a short description of the parameter. This will |
---|
| 276 | be displayed in the parameter table and used as a tool tip for the |
---|
| 277 | parameter value in the user interface. |
---|
| 278 | |
---|
| 279 | Additional values can be set after the parameter is created: |
---|
| 280 | |
---|
[6e7ff6d] | 281 | * *length* is the length of the field if it is a vector field |
---|
| 282 | |
---|
| 283 | * *length_control* is the parameter which sets the vector length |
---|
| 284 | |
---|
| 285 | * *is_control* is True if the parameter is a control parameter for a vector |
---|
| 286 | |
---|
| 287 | * *polydisperse* is true if the parameter accepts a polydispersity |
---|
| 288 | |
---|
| 289 | * *relative_pd* is true if that polydispersity is a portion of the |
---|
[40a87fa] | 290 | value (so a 10% length dipsersity would use a polydispersity value |
---|
| 291 | of 0.1) rather than absolute dispersisity (such as an angle plus or |
---|
| 292 | minus 15 degrees). |
---|
[69aa451] | 293 | |
---|
[50ec515] | 294 | *choices* is the option names for a drop down list of options, as for |
---|
| 295 | example, might be used to set the value of a shape parameter. |
---|
| 296 | |
---|
[b171acd] | 297 | Control parameters are used for variant models such as :ref:`rpa` which |
---|
| 298 | have different cases with different parameters, as well as models |
---|
| 299 | like :ref:`spherical_sld` with its user defined number of shells. |
---|
| 300 | The control parameter should appear in the parameter table along with the |
---|
| 301 | parameters it is is controlling. For variant models, use *[CASES]* in |
---|
| 302 | place of the parameter limits Within the parameter definition table, |
---|
| 303 | with case names such as:: |
---|
| 304 | |
---|
| 305 | CASES = ["diblock copolymer", "triblock copolymer", ...] |
---|
| 306 | |
---|
| 307 | This should give *limits=[[case1, case2, ...]]*, but the model loader |
---|
| 308 | translates it to *limits=[0, len(CASES)-1]*, and adds *choices=CASES* to |
---|
| 309 | the :class:`Parameter` definition. Note that models can use a list of |
---|
| 310 | cases as a parameter without it being a control parameter. Either way, |
---|
| 311 | the parameter is sent to the model evaluator as *float(choice_num)*, |
---|
| 312 | where choices are numbered from 0. :meth:`ModelInfo.get_hidden_parameters` |
---|
| 313 | will determine which parameers to display. |
---|
| 314 | |
---|
| 315 | The class contructor should not be called directly, but instead the |
---|
| 316 | parameter table is built using :func:`make_parameter_table` and |
---|
[a5b8477] | 317 | :func:`parse_parameter` therein. |
---|
[69aa451] | 318 | """ |
---|
| 319 | def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf), |
---|
[a86f6c0] | 320 | ptype='', description=''): |
---|
[c1a888b] | 321 | # type: (str, str, float, Limits, str, str) -> None |
---|
[a86f6c0] | 322 | self.id = name.split('[')[0].strip() # type: str |
---|
| 323 | self.name = name # type: str |
---|
| 324 | self.units = units # type: str |
---|
| 325 | self.default = default # type: float |
---|
| 326 | self.limits = limits # type: Limits |
---|
| 327 | self.type = ptype # type: str |
---|
| 328 | self.description = description # type: str |
---|
[69aa451] | 329 | |
---|
[d19962c] | 330 | # Length and length_control will be filled in once the complete |
---|
[69aa451] | 331 | # parameter table is available. |
---|
[a86f6c0] | 332 | self.length = 1 # type: int |
---|
| 333 | self.length_control = None # type: Optional[str] |
---|
| 334 | self.is_control = False # type: bool |
---|
[69aa451] | 335 | |
---|
| 336 | # TODO: need better control over whether a parameter is polydisperse |
---|
[a86f6c0] | 337 | self.polydisperse = False # type: bool |
---|
| 338 | self.relative_pd = False # type: bool |
---|
[69aa451] | 339 | |
---|
[ce896fd] | 340 | # choices are also set externally. |
---|
[a86f6c0] | 341 | self.choices = [] # type: List[str] |
---|
[ce896fd] | 342 | |
---|
[69aa451] | 343 | def as_definition(self): |
---|
[a86f6c0] | 344 | # type: () -> str |
---|
[69aa451] | 345 | """ |
---|
| 346 | Declare space for the variable in a parameter structure. |
---|
| 347 | |
---|
| 348 | For example, the parameter thickness with length 3 will |
---|
| 349 | return "double thickness[3];", with no spaces before and |
---|
| 350 | no new line character afterward. |
---|
| 351 | """ |
---|
| 352 | if self.length == 1: |
---|
| 353 | return "double %s;"%self.id |
---|
| 354 | else: |
---|
| 355 | return "double %s[%d];"%(self.id, self.length) |
---|
| 356 | |
---|
| 357 | def as_function_argument(self): |
---|
[a86f6c0] | 358 | # type: () -> str |
---|
[40a87fa] | 359 | r""" |
---|
[69aa451] | 360 | Declare the variable as a function argument. |
---|
| 361 | |
---|
| 362 | For example, the parameter thickness with length 3 will |
---|
[40a87fa] | 363 | return "double \*thickness", with no spaces before and |
---|
[69aa451] | 364 | no comma afterward. |
---|
| 365 | """ |
---|
| 366 | if self.length == 1: |
---|
| 367 | return "double %s"%self.id |
---|
| 368 | else: |
---|
| 369 | return "double *%s"%self.id |
---|
| 370 | |
---|
| 371 | def as_call_reference(self, prefix=""): |
---|
[c1a888b] | 372 | # type: (str) -> str |
---|
[bb4b509] | 373 | """ |
---|
| 374 | Return *prefix* + parameter name. For struct references, use "v." |
---|
| 375 | as the prefix. |
---|
| 376 | """ |
---|
[69aa451] | 377 | # Note: if the parameter is a struct type, then we will need to use |
---|
| 378 | # &prefix+id. For scalars and vectors we can just use prefix+id. |
---|
| 379 | return prefix + self.id |
---|
| 380 | |
---|
| 381 | def __str__(self): |
---|
[a86f6c0] | 382 | # type: () -> str |
---|
[69aa451] | 383 | return "<%s>"%self.name |
---|
| 384 | |
---|
| 385 | def __repr__(self): |
---|
[a86f6c0] | 386 | # type: () -> str |
---|
[69aa451] | 387 | return "P<%s>"%self.name |
---|
| 388 | |
---|
[d19962c] | 389 | |
---|
[69aa451] | 390 | class ParameterTable(object): |
---|
[d19962c] | 391 | """ |
---|
| 392 | ParameterTable manages the list of available parameters. |
---|
| 393 | |
---|
| 394 | There are a couple of complications which mean that the list of parameters |
---|
| 395 | for the kernel differs from the list of parameters that the user sees. |
---|
| 396 | |
---|
| 397 | (1) Common parameters. Scale and background are implicit to every model, |
---|
| 398 | but are not passed to the kernel. |
---|
| 399 | |
---|
| 400 | (2) Vector parameters. Vector parameters are passed to the kernel as a |
---|
| 401 | pointer to an array, e.g., thick[], but they are seen by the user as n |
---|
| 402 | separate parameters thick1, thick2, ... |
---|
| 403 | |
---|
| 404 | Therefore, the parameter table is organized by how it is expected to be |
---|
| 405 | used. The following information is needed to set up the kernel functions: |
---|
| 406 | |
---|
| 407 | * *kernel_parameters* is the list of parameters in the kernel parameter |
---|
[40a87fa] | 408 | table, with vector parameter p declared as p[]. |
---|
[d19962c] | 409 | |
---|
| 410 | * *iq_parameters* is the list of parameters to the Iq(q, ...) function, |
---|
[40a87fa] | 411 | with vector parameter p sent as p[]. |
---|
[d19962c] | 412 | |
---|
| 413 | * *form_volume_parameters* is the list of parameters to the form_volume(...) |
---|
[40a87fa] | 414 | function, with vector parameter p sent as p[]. |
---|
[d19962c] | 415 | |
---|
| 416 | Problem details, which sets up the polydispersity loops, requires the |
---|
| 417 | following: |
---|
| 418 | |
---|
| 419 | * *theta_offset* is the offset of the theta parameter in the kernel parameter |
---|
[40a87fa] | 420 | table, with vector parameters counted as n individual parameters |
---|
| 421 | p1, p2, ..., or offset is -1 if there is no theta parameter. |
---|
[d19962c] | 422 | |
---|
| 423 | * *max_pd* is the maximum number of polydisperse parameters, with vector |
---|
[40a87fa] | 424 | parameters counted as n individual parameters p1, p2, ... Note that |
---|
| 425 | this number is limited to sasmodels.modelinfo.MAX_PD. |
---|
[d19962c] | 426 | |
---|
| 427 | * *npars* is the total number of parameters to the kernel, with vector |
---|
[40a87fa] | 428 | parameters counted as n individual parameters p1, p2, ... |
---|
[d19962c] | 429 | |
---|
[b6dab59] | 430 | * *common_parameters* is the list of common parameters, with a unique |
---|
| 431 | copy for each model so that structure factors can have a default |
---|
| 432 | background of 0.0. |
---|
| 433 | |
---|
[d19962c] | 434 | * *call_parameters* is the complete list of parameters to the kernel, |
---|
[40a87fa] | 435 | including scale and background, with vector parameters recorded as |
---|
| 436 | individual parameters p1, p2, ... |
---|
[d19962c] | 437 | |
---|
| 438 | * *active_1d* is the set of names that may be polydisperse for 1d data |
---|
| 439 | |
---|
| 440 | * *active_2d* is the set of names that may be polydisperse for 2d data |
---|
| 441 | |
---|
| 442 | User parameters are the set of parameters visible to the user, including |
---|
| 443 | the scale and background parameters that the kernel does not see. User |
---|
| 444 | parameters don't use vector notation, and instead use p1, p2, ... |
---|
| 445 | """ |
---|
[69aa451] | 446 | def __init__(self, parameters): |
---|
[a86f6c0] | 447 | # type: (List[Parameter]) -> None |
---|
[b6dab59] | 448 | |
---|
| 449 | # scale and background are implicit parameters |
---|
| 450 | # Need them to be unique to each model in case they have different |
---|
| 451 | # properties, such as default=0.0 for structure factor backgrounds. |
---|
| 452 | self.common_parameters = [Parameter(*p) for p in COMMON_PARAMETERS] |
---|
| 453 | |
---|
[d19962c] | 454 | self.kernel_parameters = parameters |
---|
[60eab2a] | 455 | self._set_vector_lengths() |
---|
[32e3c9b] | 456 | self.npars = sum(p.length for p in self.kernel_parameters) |
---|
[9eb3632] | 457 | self.nmagnetic = sum(p.length for p in self.kernel_parameters |
---|
[bb4b509] | 458 | if p.type == 'sld') |
---|
[9eb3632] | 459 | self.nvalues = 2 + self.npars |
---|
| 460 | if self.nmagnetic: |
---|
| 461 | self.nvalues += 3 + 3*self.nmagnetic |
---|
[a86f6c0] | 462 | self.call_parameters = self._get_call_parameters() |
---|
| 463 | self.defaults = self._get_defaults() |
---|
[d19962c] | 464 | #self._name_table= dict((p.id, p) for p in parameters) |
---|
[60eab2a] | 465 | |
---|
[d19962c] | 466 | # Set the kernel parameters. Assumes background and scale are the |
---|
| 467 | # first two parameters in the parameter list, but these are not sent |
---|
| 468 | # to the underlying kernel functions. |
---|
| 469 | self.iq_parameters = [p for p in self.kernel_parameters |
---|
| 470 | if p.type not in ('orientation', 'magnetic')] |
---|
[108e70e] | 471 | self.orientation_parameters = [p for p in self.kernel_parameters |
---|
| 472 | if p.type == 'orientation'] |
---|
[d19962c] | 473 | self.form_volume_parameters = [p for p in self.kernel_parameters |
---|
| 474 | if p.type == 'volume'] |
---|
| 475 | |
---|
| 476 | # Theta offset |
---|
| 477 | offset = 0 |
---|
| 478 | for p in self.kernel_parameters: |
---|
| 479 | if p.name == 'theta': |
---|
| 480 | self.theta_offset = offset |
---|
| 481 | break |
---|
| 482 | offset += p.length |
---|
| 483 | else: |
---|
| 484 | self.theta_offset = -1 |
---|
[69aa451] | 485 | |
---|
[d19962c] | 486 | # number of polydisperse parameters |
---|
| 487 | num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse) |
---|
| 488 | # Don't use more polydisperse parameters than are available in the model |
---|
| 489 | self.max_pd = min(num_pd, MAX_PD) |
---|
[69aa451] | 490 | |
---|
[d19962c] | 491 | # true if has 2D parameters |
---|
| 492 | self.has_2d = any(p.type in ('orientation', 'magnetic') |
---|
| 493 | for p in self.kernel_parameters) |
---|
[8698a0d] | 494 | self.is_asymmetric = any(p.name == 'psi' for p in self.kernel_parameters) |
---|
[bb4b509] | 495 | self.magnetism_index = [k for k, p in enumerate(self.call_parameters) |
---|
[610ef23] | 496 | if p.id.endswith('_M0')] |
---|
[69aa451] | 497 | |
---|
[d19962c] | 498 | self.pd_1d = set(p.name for p in self.call_parameters |
---|
[a86f6c0] | 499 | if p.polydisperse and p.type not in ('orientation', 'magnetic')) |
---|
[32e3c9b] | 500 | self.pd_2d = set(p.name for p in self.call_parameters if p.polydisperse) |
---|
[69aa451] | 501 | |
---|
[0535624] | 502 | def set_zero_background(self): |
---|
| 503 | """ |
---|
| 504 | Set the default background to zero for this model. This is done for |
---|
| 505 | structure factor models. |
---|
| 506 | """ |
---|
| 507 | # type: () -> None |
---|
| 508 | # Make sure background is the second common parameter. |
---|
| 509 | assert self.common_parameters[1].id == "background" |
---|
| 510 | self.common_parameters[1].default = 0.0 |
---|
| 511 | self.defaults = self._get_defaults() |
---|
| 512 | |
---|
[95498a3] | 513 | def check_angles(self): |
---|
| 514 | """ |
---|
| 515 | Check that orientation angles are theta, phi and possibly psi. |
---|
| 516 | """ |
---|
[8698a0d] | 517 | theta = phi = psi = -1 |
---|
| 518 | for k, p in enumerate(self.kernel_parameters): |
---|
| 519 | if p.name == 'theta': |
---|
| 520 | theta = k |
---|
| 521 | if p.type != 'orientation': |
---|
| 522 | raise TypeError("theta must be an orientation parameter") |
---|
| 523 | elif p.name == 'phi': |
---|
| 524 | phi = k |
---|
| 525 | if p.type != 'orientation': |
---|
| 526 | raise TypeError("phi must be an orientation parameter") |
---|
| 527 | elif p.name == 'psi': |
---|
| 528 | psi = k |
---|
| 529 | if p.type != 'orientation': |
---|
| 530 | raise TypeError("psi must be an orientation parameter") |
---|
[108e70e] | 531 | elif p.type == 'orientation': |
---|
| 532 | raise TypeError("only theta, phi and psi can be orientation parameters") |
---|
[8698a0d] | 533 | if theta >= 0 and phi >= 0: |
---|
[108e70e] | 534 | last_par = len(self.kernel_parameters) - 1 |
---|
[8698a0d] | 535 | if phi != theta+1: |
---|
| 536 | raise TypeError("phi must follow theta") |
---|
| 537 | if psi >= 0 and psi != phi+1: |
---|
| 538 | raise TypeError("psi must follow phi") |
---|
[95498a3] | 539 | if (psi >= 0 and psi != last_par) or (psi < 0 and phi != last_par): |
---|
| 540 | raise TypeError("orientation parameters must appear at the " |
---|
| 541 | "end of the parameter table") |
---|
[8698a0d] | 542 | elif theta >= 0 or phi >= 0 or psi >= 0: |
---|
| 543 | raise TypeError("oriented shapes must have both theta and phi and maybe psi") |
---|
| 544 | |
---|
[0bdddc2] | 545 | def __getitem__(self, key): |
---|
| 546 | # Find the parameter definition |
---|
| 547 | for par in self.call_parameters: |
---|
| 548 | if par.name == key: |
---|
[e65c3ba] | 549 | return par |
---|
| 550 | raise KeyError("unknown parameter %r"%key) |
---|
[0bdddc2] | 551 | |
---|
[e3571cb] | 552 | def __contains__(self, key): |
---|
| 553 | for par in self.call_parameters: |
---|
| 554 | if par.name == key: |
---|
| 555 | return True |
---|
[e65c3ba] | 556 | return False |
---|
[e3571cb] | 557 | |
---|
[a86f6c0] | 558 | def _set_vector_lengths(self): |
---|
[256dfe1] | 559 | # type: () -> List[str] |
---|
[a86f6c0] | 560 | """ |
---|
| 561 | Walk the list of kernel parameters, setting the length field of the |
---|
| 562 | vector parameters from the upper limit of the reference parameter. |
---|
| 563 | |
---|
| 564 | This needs to be done once the entire parameter table is available |
---|
| 565 | since the reference may still be undefined when the parameter is |
---|
| 566 | initially created. |
---|
| 567 | |
---|
[256dfe1] | 568 | Returns the list of control parameter names. |
---|
| 569 | |
---|
[a86f6c0] | 570 | Note: This modifies the underlying parameter object. |
---|
| 571 | """ |
---|
| 572 | # Sort out the length of the vector parameters such as thickness[n] |
---|
| 573 | for p in self.kernel_parameters: |
---|
| 574 | if p.length_control: |
---|
[e65c3ba] | 575 | ref = self._get_ref(p) |
---|
[a86f6c0] | 576 | ref.is_control = True |
---|
[256dfe1] | 577 | ref.polydisperse = False |
---|
[a86f6c0] | 578 | low, high = ref.limits |
---|
| 579 | if int(low) != low or int(high) != high or low < 0 or high > 20: |
---|
| 580 | raise ValueError("expected limits on %s to be within [0, 20]" |
---|
| 581 | % ref.name) |
---|
[04045f4] | 582 | p.length = int(high) |
---|
[a86f6c0] | 583 | |
---|
[e65c3ba] | 584 | def _get_ref(self, p): |
---|
| 585 | # type: (Parameter) -> Parameter |
---|
| 586 | for ref in self.kernel_parameters: |
---|
| 587 | if ref.id == p.length_control: |
---|
| 588 | return ref |
---|
| 589 | raise ValueError("no reference variable %r for %s" |
---|
| 590 | % (p.length_control, p.name)) |
---|
| 591 | |
---|
[a86f6c0] | 592 | def _get_defaults(self): |
---|
| 593 | # type: () -> ParameterSet |
---|
| 594 | """ |
---|
| 595 | Get a list of parameter defaults from the parameters. |
---|
| 596 | |
---|
| 597 | Expands vector parameters into parameter id+number. |
---|
| 598 | """ |
---|
| 599 | # Construct default values, including vector defaults |
---|
| 600 | defaults = {} |
---|
| 601 | for p in self.call_parameters: |
---|
| 602 | if p.length == 1: |
---|
| 603 | defaults[p.id] = p.default |
---|
| 604 | else: |
---|
| 605 | for k in range(1, p.length+1): |
---|
| 606 | defaults["%s%d"%(p.id, k)] = p.default |
---|
| 607 | return defaults |
---|
| 608 | |
---|
| 609 | def _get_call_parameters(self): |
---|
| 610 | # type: () -> List[Parameter] |
---|
[b6dab59] | 611 | full_list = self.common_parameters[:] |
---|
[a86f6c0] | 612 | for p in self.kernel_parameters: |
---|
| 613 | if p.length == 1: |
---|
| 614 | full_list.append(p) |
---|
| 615 | else: |
---|
| 616 | for k in range(1, p.length+1): |
---|
| 617 | pk = Parameter(p.id+str(k), p.units, p.default, |
---|
| 618 | p.limits, p.type, p.description) |
---|
| 619 | pk.polydisperse = p.polydisperse |
---|
| 620 | pk.relative_pd = p.relative_pd |
---|
[50ec515] | 621 | pk.choices = p.choices |
---|
[a86f6c0] | 622 | full_list.append(pk) |
---|
[32e3c9b] | 623 | |
---|
| 624 | # Add the magnetic parameters to the end of the call parameter list. |
---|
[9eb3632] | 625 | if self.nmagnetic > 0: |
---|
[32e3c9b] | 626 | full_list.extend([ |
---|
[610ef23] | 627 | Parameter('up_frac_i', '', 0., [0., 1.], |
---|
[32e3c9b] | 628 | 'magnetic', 'fraction of spin up incident'), |
---|
[610ef23] | 629 | Parameter('up_frac_f', '', 0., [0., 1.], |
---|
[32e3c9b] | 630 | 'magnetic', 'fraction of spin up final'), |
---|
[610ef23] | 631 | Parameter('up_angle', 'degrees', 0., [0., 360.], |
---|
[32e3c9b] | 632 | 'magnetic', 'spin up angle'), |
---|
| 633 | ]) |
---|
| 634 | slds = [p for p in full_list if p.type == 'sld'] |
---|
| 635 | for p in slds: |
---|
| 636 | full_list.extend([ |
---|
[610ef23] | 637 | Parameter(p.id+'_M0', '1e-6/Ang^2', 0., [-np.inf, np.inf], |
---|
[32e3c9b] | 638 | 'magnetic', 'magnetic amplitude for '+p.description), |
---|
[610ef23] | 639 | Parameter(p.id+'_mtheta', 'degrees', 0., [-90., 90.], |
---|
[bb4b509] | 640 | 'magnetic', 'magnetic latitude for '+p.description), |
---|
[610ef23] | 641 | Parameter(p.id+'_mphi', 'degrees', 0., [-180., 180.], |
---|
[bb4b509] | 642 | 'magnetic', 'magnetic longitude for '+p.description), |
---|
[32e3c9b] | 643 | ]) |
---|
| 644 | #print("call parameters", full_list) |
---|
[a86f6c0] | 645 | return full_list |
---|
| 646 | |
---|
[85fe7f8] | 647 | def user_parameters(self, pars, is2d=True): |
---|
[0d99a6a] | 648 | # type: (Dict[str, float], bool) -> List[Parameter] |
---|
[69aa451] | 649 | """ |
---|
[d19962c] | 650 | Return the list of parameters for the given data type. |
---|
| 651 | |
---|
[c5ac2b2] | 652 | Vector parameters are expanded in place. If multiple parameters |
---|
[d19962c] | 653 | share the same vector length, then the parameters will be interleaved |
---|
| 654 | in the result. The control parameters come first. For example, |
---|
| 655 | if the parameter table is ordered as:: |
---|
| 656 | |
---|
| 657 | sld_core |
---|
| 658 | sld_shell[num_shells] |
---|
| 659 | sld_solvent |
---|
| 660 | thickness[num_shells] |
---|
| 661 | num_shells |
---|
| 662 | |
---|
| 663 | and *pars[num_shells]=2* then the returned list will be:: |
---|
| 664 | |
---|
| 665 | num_shells |
---|
| 666 | scale |
---|
| 667 | background |
---|
| 668 | sld_core |
---|
| 669 | sld_shell1 |
---|
| 670 | thickness1 |
---|
| 671 | sld_shell2 |
---|
| 672 | thickness2 |
---|
| 673 | sld_solvent |
---|
| 674 | |
---|
| 675 | Note that shell/thickness pairs are grouped together in the result |
---|
| 676 | even though they were not grouped in the incoming table. The control |
---|
| 677 | parameter is always returned first since the GUI will want to set it |
---|
| 678 | early, and rerender the table when it is changed. |
---|
[32e3c9b] | 679 | |
---|
| 680 | Parameters marked as sld will automatically have a set of associated |
---|
[610ef23] | 681 | magnetic parameters (p_M0, p_mtheta, p_mphi), as well as polarization |
---|
| 682 | information (up_theta, up_frac_i, up_frac_f). |
---|
[69aa451] | 683 | """ |
---|
[04045f4] | 684 | # control parameters go first |
---|
[d19962c] | 685 | control = [p for p in self.kernel_parameters if p.is_control] |
---|
| 686 | |
---|
| 687 | # Gather entries such as name[n] into groups of the same n |
---|
[04045f4] | 688 | dependent = {} # type: Dict[str, List[Parameter]] |
---|
| 689 | dependent.update((p.id, []) for p in control) |
---|
[d19962c] | 690 | for p in self.kernel_parameters: |
---|
| 691 | if p.length_control is not None: |
---|
| 692 | dependent[p.length_control].append(p) |
---|
| 693 | |
---|
| 694 | # Gather entries such as name[4] into groups of the same length |
---|
[32e3c9b] | 695 | fixed_length = {} # type: Dict[int, List[Parameter]] |
---|
[d19962c] | 696 | for p in self.kernel_parameters: |
---|
| 697 | if p.length > 1 and p.length_control is None: |
---|
[32e3c9b] | 698 | fixed_length.setdefault(p.length, []).append(p) |
---|
[d19962c] | 699 | |
---|
| 700 | # Using the call_parameters table, we already have expanded forms |
---|
| 701 | # for each of the vector parameters; put them in a lookup table |
---|
[f88e248] | 702 | # Note: p.id and p.name are currently identical for the call parameters |
---|
| 703 | expanded_pars = dict((p.id, p) for p in self.call_parameters) |
---|
[d19962c] | 704 | |
---|
[32e3c9b] | 705 | def append_group(name): |
---|
| 706 | """add the named parameter, and related magnetic parameters if any""" |
---|
| 707 | result.append(expanded_pars[name]) |
---|
| 708 | if is2d: |
---|
[610ef23] | 709 | for tag in '_M0', '_mtheta', '_mphi': |
---|
| 710 | if name+tag in expanded_pars: |
---|
| 711 | result.append(expanded_pars[name+tag]) |
---|
[32e3c9b] | 712 | |
---|
[d19962c] | 713 | # Gather the user parameters in order |
---|
[b6dab59] | 714 | result = control + self.common_parameters |
---|
[d19962c] | 715 | for p in self.kernel_parameters: |
---|
| 716 | if not is2d and p.type in ('orientation', 'magnetic'): |
---|
| 717 | pass |
---|
| 718 | elif p.is_control: |
---|
| 719 | pass # already added |
---|
| 720 | elif p.length_control is not None: |
---|
| 721 | table = dependent.get(p.length_control, []) |
---|
| 722 | if table: |
---|
| 723 | # look up length from incoming parameters |
---|
[fb5914f] | 724 | table_length = int(pars.get(p.length_control, p.length)) |
---|
[d19962c] | 725 | del dependent[p.length_control] # first entry seen |
---|
| 726 | for k in range(1, table_length+1): |
---|
| 727 | for entry in table: |
---|
[32e3c9b] | 728 | append_group(entry.id+str(k)) |
---|
[d19962c] | 729 | else: |
---|
| 730 | pass # already processed all entries |
---|
| 731 | elif p.length > 1: |
---|
[32e3c9b] | 732 | table = fixed_length.get(p.length, []) |
---|
[d19962c] | 733 | if table: |
---|
| 734 | table_length = p.length |
---|
[32e3c9b] | 735 | del fixed_length[p.length] |
---|
[d19962c] | 736 | for k in range(1, table_length+1): |
---|
| 737 | for entry in table: |
---|
[32e3c9b] | 738 | append_group(entry.id+str(k)) |
---|
[d19962c] | 739 | else: |
---|
| 740 | pass # already processed all entries |
---|
| 741 | else: |
---|
[32e3c9b] | 742 | append_group(p.id) |
---|
| 743 | |
---|
[610ef23] | 744 | if is2d and 'up_angle' in expanded_pars: |
---|
[32e3c9b] | 745 | result.extend([ |
---|
[610ef23] | 746 | expanded_pars['up_frac_i'], |
---|
| 747 | expanded_pars['up_frac_f'], |
---|
| 748 | expanded_pars['up_angle'], |
---|
[32e3c9b] | 749 | ]) |
---|
[d19962c] | 750 | |
---|
| 751 | return result |
---|
[69aa451] | 752 | |
---|
| 753 | def isstr(x): |
---|
[a86f6c0] | 754 | # type: (Any) -> bool |
---|
[7edce22] | 755 | """ |
---|
| 756 | Return True if the object is a string. |
---|
| 757 | """ |
---|
[69aa451] | 758 | # TODO: 2-3 compatible tests for str, including unicode strings |
---|
| 759 | return isinstance(x, str) |
---|
| 760 | |
---|
[da63656] | 761 | |
---|
[108e70e] | 762 | #: Set of variables defined in the model that might contain C code |
---|
[e44432d] | 763 | C_SYMBOLS = ['Imagnetic', 'Iq', 'Iqxy', 'Iqac', 'Iqabc', 'form_volume', 'shell_volume', 'c_code'] |
---|
[108e70e] | 764 | |
---|
[da63656] | 765 | def _find_source_lines(model_info, kernel_module): |
---|
[e65c3ba] | 766 | # type: (ModelInfo, ModuleType) -> None |
---|
[da63656] | 767 | """ |
---|
| 768 | Identify the location of the C source inside the model definition file. |
---|
| 769 | |
---|
[108e70e] | 770 | This code runs through the source of the kernel module looking for lines |
---|
| 771 | that contain C code (because it is a c function definition). Clearly |
---|
| 772 | there are all sorts of reasons why this might not work (e.g., code |
---|
| 773 | commented out in a triple-quoted line block, code built using string |
---|
| 774 | concatenation, code defined in the branch of an 'if' block, code imported |
---|
| 775 | from another file), but it should work properly in the 95% case, and for |
---|
| 776 | the remainder, getting the incorrect line number will merely be |
---|
| 777 | inconvenient. |
---|
[da63656] | 778 | """ |
---|
[108e70e] | 779 | # Only need line numbers if we are creating a C module and the C symbols |
---|
| 780 | # are defined. |
---|
| 781 | if (callable(model_info.Iq) |
---|
| 782 | or not any(hasattr(model_info, s) for s in C_SYMBOLS)): |
---|
[da63656] | 783 | return |
---|
| 784 | |
---|
[108e70e] | 785 | # load the module source if we can |
---|
[98ba1fc] | 786 | try: |
---|
| 787 | source = inspect.getsource(kernel_module) |
---|
| 788 | except IOError: |
---|
| 789 | return |
---|
[da63656] | 790 | |
---|
[108e70e] | 791 | # look for symbol at the start of the line |
---|
| 792 | for lineno, line in enumerate(source.split('\n')): |
---|
| 793 | for name in C_SYMBOLS: |
---|
| 794 | if line.startswith(name): |
---|
| 795 | # Add 1 since some compilers complain about "#line 0" |
---|
| 796 | model_info.lineno[name] = lineno + 1 |
---|
| 797 | break |
---|
[da63656] | 798 | |
---|
[6d6508e] | 799 | def make_model_info(kernel_module): |
---|
[7edce22] | 800 | # type: (module) -> ModelInfo |
---|
| 801 | """ |
---|
| 802 | Extract the model definition from the loaded kernel module. |
---|
| 803 | |
---|
| 804 | Fill in default values for parts of the module that are not provided. |
---|
| 805 | |
---|
[108e70e] | 806 | Note: vectorized Iq and Iqac/Iqabc functions will be created for python |
---|
[7edce22] | 807 | models when the model is first called, not when the model is loaded. |
---|
| 808 | """ |
---|
[65314f7] | 809 | if hasattr(kernel_module, "model_info"): |
---|
| 810 | # Custom sum/multi models |
---|
| 811 | return kernel_module.model_info |
---|
[01c8d9e] | 812 | |
---|
[6d6508e] | 813 | info = ModelInfo() |
---|
[b6dab59] | 814 | |
---|
| 815 | # Build the parameter table |
---|
[6d6508e] | 816 | #print("make parameter table", kernel_module.parameters) |
---|
[c1a888b] | 817 | parameters = make_parameter_table(getattr(kernel_module, 'parameters', [])) |
---|
[b6dab59] | 818 | |
---|
| 819 | # background defaults to zero for structure factor models |
---|
| 820 | structure_factor = getattr(kernel_module, 'structure_factor', False) |
---|
| 821 | if structure_factor: |
---|
[0535624] | 822 | parameters.set_zero_background() |
---|
[b6dab59] | 823 | |
---|
| 824 | # TODO: remove demo parameters |
---|
| 825 | # The plots in the docs are generated from the model default values. |
---|
| 826 | # Sascomp set parameters from the command line, and so doesn't need |
---|
| 827 | # demo values for testing. |
---|
[4bfd277] | 828 | demo = expand_pars(parameters, getattr(kernel_module, 'demo', None)) |
---|
[b6dab59] | 829 | |
---|
[724257c] | 830 | filename = abspath(kernel_module.__file__).replace('.pyc', '.py') |
---|
[6d6508e] | 831 | kernel_id = splitext(basename(filename))[0] |
---|
| 832 | name = getattr(kernel_module, 'name', None) |
---|
| 833 | if name is None: |
---|
| 834 | name = " ".join(w.capitalize() for w in kernel_id.split('_')) |
---|
| 835 | |
---|
| 836 | info.id = kernel_id # string used to load the kernel |
---|
[724257c] | 837 | info.filename = filename |
---|
[6d6508e] | 838 | info.name = name |
---|
| 839 | info.title = getattr(kernel_module, 'title', name+" model") |
---|
| 840 | info.description = getattr(kernel_module, 'description', 'no description') |
---|
| 841 | info.parameters = parameters |
---|
| 842 | info.demo = demo |
---|
| 843 | info.composition = None |
---|
| 844 | info.docs = kernel_module.__doc__ |
---|
| 845 | info.category = getattr(kernel_module, 'category', None) |
---|
| 846 | info.structure_factor = getattr(kernel_module, 'structure_factor', False) |
---|
[c036ddb] | 847 | # TODO: find Fq by inspection |
---|
[6e7ba14] | 848 | info.effective_radius_type = getattr(kernel_module, 'effective_radius_type', None) |
---|
[c036ddb] | 849 | info.have_Fq = getattr(kernel_module, 'have_Fq', False) |
---|
[04045f4] | 850 | info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y']) |
---|
[d321747] | 851 | # Note: custom.load_custom_kernel_module assumes the C sources are defined |
---|
| 852 | # by this attribute. |
---|
[6d6508e] | 853 | info.source = getattr(kernel_module, 'source', []) |
---|
[108e70e] | 854 | info.c_code = getattr(kernel_module, 'c_code', None) |
---|
[5399809] | 855 | info.effective_radius = getattr(kernel_module, 'effective_radius', None) |
---|
[e62a134] | 856 | # TODO: check the structure of the tests |
---|
[6d6508e] | 857 | info.tests = getattr(kernel_module, 'tests', []) |
---|
[9a943d0] | 858 | info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore |
---|
[e44432d] | 859 | info.shell_volume = getattr(kernel_module, 'shell_volume', None) # type: ignore |
---|
[9a943d0] | 860 | info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore |
---|
| 861 | info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore |
---|
[108e70e] | 862 | info.Iqac = getattr(kernel_module, 'Iqac', None) # type: ignore |
---|
| 863 | info.Iqabc = getattr(kernel_module, 'Iqabc', None) # type: ignore |
---|
[32e3c9b] | 864 | info.Imagnetic = getattr(kernel_module, 'Imagnetic', None) # type: ignore |
---|
[9a943d0] | 865 | info.profile = getattr(kernel_module, 'profile', None) # type: ignore |
---|
| 866 | info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore |
---|
[0bdddc2] | 867 | info.random = getattr(kernel_module, 'random', None) |
---|
[04045f4] | 868 | info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore |
---|
[6d6508e] | 869 | |
---|
[108e70e] | 870 | info.lineno = {} |
---|
[da63656] | 871 | _find_source_lines(info, kernel_module) |
---|
[67cc0ff] | 872 | if getattr(kernel_module, 'py2c', False): |
---|
| 873 | try: |
---|
[765d025] | 874 | warnings = autoc.convert(info, kernel_module) |
---|
[67cc0ff] | 875 | except Exception as exc: |
---|
[765d025] | 876 | warnings = [str(exc)] |
---|
| 877 | if warnings: |
---|
| 878 | warnings.append("while converting %s from C to python"%name) |
---|
| 879 | if len(warnings) > 2: |
---|
| 880 | warnings = "\n".join(warnings) |
---|
| 881 | else: |
---|
| 882 | warnings = " ".join(warnings) |
---|
| 883 | logger.warn(warnings) |
---|
[67cc0ff] | 884 | |
---|
[765d025] | 885 | # Default single and opencl to True for C models. Python models have callable Iq. |
---|
[c01ed3e] | 886 | # Needs to come after autoc.convert since the Iq symbol may have been |
---|
| 887 | # converted from python to C |
---|
| 888 | info.opencl = getattr(kernel_module, 'opencl', not callable(info.Iq)) |
---|
| 889 | info.single = getattr(kernel_module, 'single', not callable(info.Iq)) |
---|
[225bf94] | 890 | |
---|
[4f4d3e3] | 891 | # Set control flag for explicitly set parameters, e.g., in the RPA model. |
---|
| 892 | control = getattr(kernel_module, 'control', None) |
---|
| 893 | if control is not None: |
---|
| 894 | parameters[control].is_control = True |
---|
[c01ed3e] | 895 | |
---|
[67cc0ff] | 896 | if callable(info.Iq) and parameters.has_2d: |
---|
| 897 | raise ValueError("oriented python models not supported") |
---|
[da63656] | 898 | |
---|
[6d6508e] | 899 | return info |
---|
| 900 | |
---|
| 901 | class ModelInfo(object): |
---|
| 902 | """ |
---|
| 903 | Interpret the model definition file, categorizing the parameters. |
---|
| 904 | |
---|
| 905 | The module can be loaded with a normal python import statement if you |
---|
| 906 | know which module you need, or with __import__('sasmodels.model.'+name) |
---|
| 907 | if the name is in a string. |
---|
| 908 | |
---|
[7edce22] | 909 | The structure should be mostly static, other than the delayed definition |
---|
[108e70e] | 910 | of *Iq*, *Iqac* and *Iqabc* if they need to be defined. |
---|
[6d6508e] | 911 | """ |
---|
[a5b8477] | 912 | #: Full path to the file defining the kernel, if any. |
---|
[340428e] | 913 | filename = None # type: Optional[str] |
---|
[a5b8477] | 914 | #: Id of the kernel used to load it from the filesystem. |
---|
[a86f6c0] | 915 | id = None # type: str |
---|
[a5b8477] | 916 | #: Display name of the model, which defaults to the model id but with |
---|
| 917 | #: capitalization of the parts so for example core_shell defaults to |
---|
| 918 | #: "Core Shell". |
---|
[a86f6c0] | 919 | name = None # type: str |
---|
[a5b8477] | 920 | #: Short description of the model. |
---|
[a86f6c0] | 921 | title = None # type: str |
---|
[a5b8477] | 922 | #: Long description of the model. |
---|
[a86f6c0] | 923 | description = None # type: str |
---|
[a5b8477] | 924 | #: Model parameter table. Parameters are defined using a list of parameter |
---|
| 925 | #: definitions, each of which is contains parameter name, units, |
---|
| 926 | #: default value, limits, type and description. See :class:`Parameter` |
---|
| 927 | #: for details on the individual parameters. The parameters are gathered |
---|
| 928 | #: into a :class:`ParameterTable`, which provides various views into the |
---|
| 929 | #: parameter list. |
---|
[a86f6c0] | 930 | parameters = None # type: ParameterTable |
---|
[a5b8477] | 931 | #: Demo parameters as a *parameter:value* map used as the default values |
---|
| 932 | #: for :mod:`compare`. Any parameters not set in *demo* will use the |
---|
| 933 | #: defaults from the parameter table. That means no polydispersity, and |
---|
| 934 | #: in the case of multiplicity models, a minimal model with no interesting |
---|
| 935 | #: scattering. |
---|
[a86f6c0] | 936 | demo = None # type: Dict[str, float] |
---|
[a5b8477] | 937 | #: Composition is None if this is an independent model, or it is a |
---|
| 938 | #: tuple with comoposition type ('product' or 'misture') and a list of |
---|
| 939 | #: :class:`ModelInfo` blocks for the composed objects. This allows us |
---|
| 940 | #: to rebuild a complete mixture or product model from the info block. |
---|
| 941 | #: *composition* is not given in the model definition file, but instead |
---|
| 942 | #: arises when the model is constructed using names such as |
---|
| 943 | #: *sphere*hardsphere* or *cylinder+sphere*. |
---|
[a86f6c0] | 944 | composition = None # type: Optional[Tuple[str, List[ModelInfo]]] |
---|
[a5b8477] | 945 | #: Different variants require different parameters. In order to show |
---|
| 946 | #: just the parameters needed for the variant selected by :attr:`control`, |
---|
| 947 | #: you should provide a function *hidden(control) -> set(['a', 'b', ...])* |
---|
| 948 | #: indicating which parameters need to be hidden. For multiplicity |
---|
| 949 | #: models, you need to use the complete name of the parameter, including |
---|
| 950 | #: its number. So for example, if variant "a" uses only *sld1* and *sld2*, |
---|
| 951 | #: then *sld3*, *sld4* and *sld5* of multiplicity parameter *sld[5]* |
---|
| 952 | #: should be in the hidden set. |
---|
| 953 | hidden = None # type: Optional[Callable[[int], Set[str]]] |
---|
| 954 | #: Doc string from the top of the model file. This should be formatted |
---|
| 955 | #: using ReStructuredText format, with latex markup in ".. math" |
---|
| 956 | #: environments, or in dollar signs. This will be automatically |
---|
| 957 | #: extracted to a .rst file by :func:`generate.make_docs`, then |
---|
| 958 | #: converted to HTML or PDF by Sphinx. |
---|
[a86f6c0] | 959 | docs = None # type: str |
---|
[a5b8477] | 960 | #: Location of the model description in the documentation. This takes the |
---|
| 961 | #: form of "section" or "section:subsection". So for example, |
---|
| 962 | #: :ref:`porod` uses *category="shape-independent"* so it is in the |
---|
[40a87fa] | 963 | #: :ref:`shape-independent` section whereas |
---|
| 964 | #: :ref:`capped-cylinder` uses: *category="shape:cylinder"*, which puts |
---|
[a5b8477] | 965 | #: it in the :ref:`shape-cylinder` section. |
---|
[a86f6c0] | 966 | category = None # type: Optional[str] |
---|
[a5b8477] | 967 | #: True if the model can be computed accurately with single precision. |
---|
[40a87fa] | 968 | #: This is True by default, but models such as :ref:`bcc-paracrystal` set |
---|
[a5b8477] | 969 | #: it to False because they require double precision calculations. |
---|
[a86f6c0] | 970 | single = None # type: bool |
---|
[bb4b509] | 971 | #: True if the model can be run as an opencl model. If for some reason |
---|
| 972 | #: the model cannot be run in opencl (e.g., because the model passes |
---|
| 973 | #: functions by reference), then set this to false. |
---|
| 974 | opencl = None # type: bool |
---|
[a5b8477] | 975 | #: True if the model is a structure factor used to model the interaction |
---|
| 976 | #: between form factor models. This will default to False if it is not |
---|
| 977 | #: provided in the file. |
---|
[a86f6c0] | 978 | structure_factor = None # type: bool |
---|
[c036ddb] | 979 | #: True if the model defines an Fq function with signature |
---|
| 980 | #: void Fq(double q, double *F1, double *F2, ...) |
---|
| 981 | have_Fq = False |
---|
[e44432d] | 982 | #: List of options for computing the effective radius of the shape, |
---|
| 983 | #: or None if the model is not usable as a form factor model. |
---|
| 984 | effective_radius_type = None # type: List[str] |
---|
[a5b8477] | 985 | #: List of C source files used to define the model. The source files |
---|
[108e70e] | 986 | #: should define the *Iq* function, and possibly *Iqac* or *Iqabc* if the |
---|
| 987 | #: model defines orientation parameters. Files containing the most basic |
---|
| 988 | #: functions must appear first in the list, followed by the files that |
---|
[e44432d] | 989 | #: use those functions. |
---|
[a86f6c0] | 990 | source = None # type: List[str] |
---|
[39a06c9] | 991 | #: inline source code, added after all elements of source |
---|
| 992 | c_code = None # type: Optional[str] |
---|
[a5b8477] | 993 | #: Returns the form volume for python-based models. Form volume is needed |
---|
| 994 | #: for volume normalization in the polydispersity integral. If no |
---|
| 995 | #: parameters are *volume* parameters, then form volume is not needed. |
---|
| 996 | #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq` |
---|
| 997 | #: defined using a string containing C code), form_volume must also be |
---|
| 998 | #: C code, either defined as a string, or in the sources. |
---|
[f619de7] | 999 | form_volume = None # type: Union[None, str, Callable[[np.ndarray], float]] |
---|
[e44432d] | 1000 | #: Returns the shell volume for python-based models. Form volume and |
---|
| 1001 | #: shell volume are needed for volume normalization in the polydispersity |
---|
| 1002 | #: integral and structure interactions for hollow shapes. If no |
---|
| 1003 | #: parameters are *volume* parameters, then shell volume is not needed. |
---|
| 1004 | #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq` |
---|
| 1005 | #: defined using a string containing C code), shell_volume must also be |
---|
| 1006 | #: C code, either defined as a string, or in the sources. |
---|
| 1007 | shell_volume = None # type: Union[None, str, Callable[[np.ndarray], float]] |
---|
[d92182f] | 1008 | #: Computes the effective radius of the shape given the volume parameters. |
---|
| 1009 | #: Only needed for models defined in python that can be used for |
---|
| 1010 | #: monodisperse approximation for non-dilute solutions, P@S. The first |
---|
| 1011 | #: argument is the integer effective radius mode, with default 0. |
---|
| 1012 | effective_radius = None # type: Union[None, Callable[[int, np.ndarray], float]] |
---|
[a5b8477] | 1013 | #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined |
---|
| 1014 | #: by the parameter table. *Iq* can be defined as a python function, or |
---|
| 1015 | #: as a C function. If it is defined in C, then set *Iq* to the body of |
---|
| 1016 | #: the C function, including the return statement. This function takes |
---|
| 1017 | #: values for *q* and each of the parameters as separate *double* values |
---|
| 1018 | #: (which may be converted to float or long double by sasmodels). All |
---|
| 1019 | #: source code files listed in :attr:`sources` will be loaded before the |
---|
| 1020 | #: *Iq* function is defined. If *Iq* is not present, then sources should |
---|
| 1021 | #: define *static double Iq(double q, double a, double b, ...)* which |
---|
| 1022 | #: will return *I(q, a, b, ...)*. Multiplicity parameters are sent as |
---|
| 1023 | #: pointers to doubles. Constants in floating point expressions should |
---|
[d92182f] | 1024 | #: include the decimal point. See :mod:`generate` for more details. If |
---|
[d8eaa3d] | 1025 | #: *have_Fq* is True, then Iq should return an interleaved array of |
---|
[d92182f] | 1026 | #: $[\sum F(q_1), \sum F^2(q_1), \ldots, \sum F(q_n), \sum F^2(q_n)]$. |
---|
[f619de7] | 1027 | Iq = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
---|
[108e70e] | 1028 | #: Returns *I(qab, qc, a, b, ...)*. The interface follows :attr:`Iq`. |
---|
| 1029 | Iqac = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
---|
| 1030 | #: Returns *I(qa, qb, qc, a, b, ...)*. The interface follows :attr:`Iq`. |
---|
| 1031 | Iqabc = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
---|
[32e3c9b] | 1032 | #: Returns *I(qx, qy, a, b, ...)*. The interface follows :attr:`Iq`. |
---|
| 1033 | Imagnetic = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
---|
[a5b8477] | 1034 | #: Returns a model profile curve *x, y*. If *profile* is defined, this |
---|
| 1035 | #: curve will appear in response to the *Show* button in SasView. Use |
---|
| 1036 | #: :attr:`profile_axes` to set the axis labels. Note that *y* values |
---|
| 1037 | #: will be scaled by 1e6 before plotting. |
---|
[c1a888b] | 1038 | profile = None # type: Optional[Callable[[np.ndarray], None]] |
---|
[a5b8477] | 1039 | #: Axis labels for the :attr:`profile` plot. The default is *['x', 'y']*. |
---|
| 1040 | #: Only the *x* component is used for now. |
---|
| 1041 | profile_axes = None # type: Tuple[str, str] |
---|
| 1042 | #: Returns *sesans(z, a, b, ...)* for models which can directly compute |
---|
| 1043 | #: the SESANS correlation function. Note: not currently implemented. |
---|
[c1a888b] | 1044 | sesans = None # type: Optional[Callable[[np.ndarray], np.ndarray]] |
---|
[e65c3ba] | 1045 | #: Returns a random parameter set for the model |
---|
| 1046 | random = None # type: Optional[Callable[[], Dict[str, float]]] |
---|
[108e70e] | 1047 | #: Line numbers for symbols defining C code |
---|
| 1048 | lineno = None # type: Dict[str, int] |
---|
[39a06c9] | 1049 | #: The set of tests that must pass. The format of the tests is described |
---|
| 1050 | #: in :mod:`model_test`. |
---|
| 1051 | tests = None # type: List[TestCondition] |
---|
[da63656] | 1052 | |
---|
[6d6508e] | 1053 | def __init__(self): |
---|
[a86f6c0] | 1054 | # type: () -> None |
---|
[6d6508e] | 1055 | pass |
---|
| 1056 | |
---|
[04045f4] | 1057 | def get_hidden_parameters(self, control): |
---|
[a5b8477] | 1058 | """ |
---|
| 1059 | Returns the set of hidden parameters for the model. *control* is the |
---|
| 1060 | value of the control parameter. Note that multiplicity models have |
---|
| 1061 | an implicit control parameter, which is the parameter that controls |
---|
| 1062 | the multiplicity. |
---|
| 1063 | """ |
---|
[04045f4] | 1064 | if self.hidden is not None: |
---|
| 1065 | hidden = self.hidden(control) |
---|
| 1066 | else: |
---|
[ce176ca] | 1067 | controls = [p for p in self.parameters.kernel_parameters |
---|
| 1068 | if p.is_control] |
---|
[04045f4] | 1069 | if len(controls) != 1: |
---|
| 1070 | raise ValueError("more than one control parameter") |
---|
| 1071 | hidden = set(p.id+str(k) |
---|
| 1072 | for p in self.parameters.kernel_parameters |
---|
| 1073 | for k in range(control+1, p.length+1) |
---|
| 1074 | if p.length > 1) |
---|
[bd547d0] | 1075 | for p in self.parameters.kernel_parameters: |
---|
| 1076 | if p.length > 1 and p.type == "sld": |
---|
| 1077 | for k in range(control+1, p.length+1): |
---|
| 1078 | base = p.id+str(k) |
---|
| 1079 | hidden.update((base+"_M0", base+"_mtheta", base+"_mphi")) |
---|
[04045f4] | 1080 | return hidden |
---|