[0d99a6a] | 1 | """ |
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| 2 | Model Info and Parameter Tables |
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| 3 | =============================== |
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| 4 | |
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| 5 | Defines :class:`ModelInfo` and :class:`ParameterTable` and the routines for |
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| 6 | manipulating them. In particular, :func:`make_model_info` converts a kernel |
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| 7 | module into the model info block as seen by the rest of the sasmodels library. |
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| 8 | """ |
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[04045f4] | 9 | from __future__ import print_function |
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| 10 | |
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[6d6508e] | 11 | from copy import copy |
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| 12 | from os.path import abspath, basename, splitext |
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[69aa451] | 13 | |
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[7ae2b7f] | 14 | import numpy as np # type: ignore |
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[69aa451] | 15 | |
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[6d6508e] | 16 | from .details import mono_details |
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[69aa451] | 17 | |
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[a86f6c0] | 18 | # Optional typing |
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| 19 | try: |
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[04045f4] | 20 | from typing import Tuple, List, Union, Dict, Optional, Any, Callable, Sequence, Set |
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[a86f6c0] | 21 | except ImportError: |
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| 22 | pass |
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| 23 | else: |
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| 24 | from .details import CallDetails |
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| 25 | Limits = Tuple[float, float] |
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[04dc697] | 26 | #LimitsOrChoice = Union[Limits, Tuple[Sequence[str]]] |
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[9a943d0] | 27 | ParameterDef = Tuple[str, str, float, Limits, str, str] |
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[a86f6c0] | 28 | ParameterSetUser = Dict[str, Union[float, List[float]]] |
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| 29 | ParameterSet = Dict[str, float] |
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| 30 | TestInput = Union[str, float, List[float], Tuple[float, float], List[Tuple[float, float]]] |
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| 31 | TestValue = Union[float, List[float]] |
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| 32 | TestCondition = Tuple[ParameterSetUser, TestInput, TestValue] |
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| 33 | |
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[7edce22] | 34 | MAX_PD = 4 #: Maximum number of simultaneously polydisperse parameters |
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[d19962c] | 35 | |
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[69aa451] | 36 | # assumptions about common parameters exist throughout the code, such as: |
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| 37 | # (1) kernel functions Iq, Iqxy, form_volume, ... don't see them |
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| 38 | # (2) kernel drivers assume scale is par[0] and background is par[1] |
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| 39 | # (3) mixture models drop the background on components and replace the scale |
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| 40 | # with a scale that varies from [-inf, inf] |
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| 41 | # (4) product models drop the background and reassign scale |
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| 42 | # and maybe other places. |
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| 43 | # Note that scale and background cannot be coordinated parameters whose value |
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| 44 | # depends on the some polydisperse parameter with the current implementation |
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[7edce22] | 45 | COMMON_PARAMETERS = [ |
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[9a943d0] | 46 | ("scale", "", 1, (0.0, np.inf), "", "Source intensity"), |
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| 47 | ("background", "1/cm", 1e-3, (0.0, np.inf), "", "Source background"), |
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[7edce22] | 48 | ] |
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| 49 | assert (len(COMMON_PARAMETERS) == 2 |
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| 50 | and COMMON_PARAMETERS[0][0]=="scale" |
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| 51 | and COMMON_PARAMETERS[1][0]=="background"), "don't change common parameters" |
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[69aa451] | 52 | |
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[a86f6c0] | 53 | |
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[69aa451] | 54 | def make_parameter_table(pars): |
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[f6029fd] | 55 | # type: (List[ParameterDef]) -> ParameterTable |
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[7edce22] | 56 | """ |
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| 57 | Construct a parameter table from a list of parameter definitions. |
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| 58 | |
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| 59 | This is used by the module processor to convert the parameter block into |
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| 60 | the parameter table seen in the :class:`ModelInfo` for the module. |
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| 61 | """ |
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[69aa451] | 62 | processed = [] |
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| 63 | for p in pars: |
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[a86f6c0] | 64 | if not isinstance(p, (list, tuple)) or len(p) != 6: |
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[69aa451] | 65 | raise ValueError("Parameter should be [name, units, default, limits, type, desc], but got %r" |
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| 66 | %str(p)) |
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| 67 | processed.append(parse_parameter(*p)) |
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| 68 | partable = ParameterTable(processed) |
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| 69 | return partable |
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| 70 | |
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[a86f6c0] | 71 | def parse_parameter(name, units='', default=np.NaN, |
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[04045f4] | 72 | user_limits=None, ptype='', description=''): |
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[60f03de] | 73 | # type: (str, str, float, Sequence[Any], str, str) -> Parameter |
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[7edce22] | 74 | """ |
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| 75 | Parse an individual parameter from the parameter definition block. |
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| 76 | |
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| 77 | This does type and value checking on the definition, leading |
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| 78 | to early failure in the model loading process and easier debugging. |
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| 79 | """ |
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[69aa451] | 80 | # Parameter is a user facing class. Do robust type checking. |
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| 81 | if not isstr(name): |
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| 82 | raise ValueError("expected string for parameter name %r"%name) |
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| 83 | if not isstr(units): |
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| 84 | raise ValueError("expected units to be a string for %s"%name) |
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[04045f4] | 85 | |
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| 86 | # Process limits as [float, float] or [[str, str, ...]] |
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[c1a888b] | 87 | choices = [] # type: List[str] |
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[04045f4] | 88 | if user_limits is None: |
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| 89 | limits = (-np.inf, np.inf) |
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| 90 | elif not isinstance(user_limits, (tuple, list)): |
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| 91 | raise ValueError("invalid limits for %s"%name) |
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| 92 | else: |
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| 93 | # if limits is [[str,...]], then this is a choice list field, |
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| 94 | # and limits are 1 to length of string list |
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| 95 | if isinstance(user_limits[0], (tuple, list)): |
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| 96 | choices = user_limits[0] |
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| 97 | limits = (0., len(choices)-1.) |
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| 98 | if not all(isstr(k) for k in choices): |
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| 99 | raise ValueError("choices must be strings for %s"%name) |
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| 100 | else: |
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| 101 | try: |
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| 102 | low, high = user_limits |
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| 103 | limits = (float(low), float(high)) |
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| 104 | except Exception: |
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[a5b8477] | 105 | print("user_limits",user_limits) |
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[04045f4] | 106 | raise ValueError("invalid limits for %s"%name) |
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| 107 | else: |
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| 108 | if low >= high: |
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| 109 | raise ValueError("require lower limit < upper limit") |
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[69aa451] | 110 | |
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[04045f4] | 111 | # Process default value as float, making sure it is in range |
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[69aa451] | 112 | if not isinstance(default, (int, float)): |
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| 113 | raise ValueError("expected default %r to be a number for %s" |
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| 114 | % (default, name)) |
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[04045f4] | 115 | if default < limits[0] or default > limits[1]: |
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[69aa451] | 116 | raise ValueError("default value %r not in range for %s" |
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| 117 | % (default, name)) |
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| 118 | |
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[04045f4] | 119 | # Check for valid parameter type |
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[a86f6c0] | 120 | if ptype not in ("volume", "orientation", "sld", "magnetic", ""): |
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| 121 | raise ValueError("unexpected type %r for %s" % (ptype, name)) |
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[69aa451] | 122 | |
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[04045f4] | 123 | # Check for valid parameter description |
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[69aa451] | 124 | if not isstr(description): |
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| 125 | raise ValueError("expected description to be a string") |
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| 126 | |
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| 127 | # Parameter id for name[n] does not include [n] |
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| 128 | if "[" in name: |
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| 129 | if not name.endswith(']'): |
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| 130 | raise ValueError("Expected name[len] for vector parameter %s"%name) |
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| 131 | pid, ref = name[:-1].split('[', 1) |
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| 132 | ref = ref.strip() |
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| 133 | else: |
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| 134 | pid, ref = name, None |
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| 135 | |
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| 136 | # automatically identify sld types |
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[a86f6c0] | 137 | if ptype== '' and (pid.startswith('sld') or pid.endswith('sld')): |
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| 138 | ptype = 'sld' |
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[69aa451] | 139 | |
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| 140 | # Check if using a vector definition, name[k], as the parameter name |
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| 141 | if ref: |
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| 142 | if ref == '': |
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| 143 | raise ValueError("Need to specify vector length for %s"%name) |
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| 144 | try: |
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| 145 | length = int(ref) |
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| 146 | control = None |
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[a86f6c0] | 147 | except ValueError: |
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[69aa451] | 148 | length = None |
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| 149 | control = ref |
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| 150 | else: |
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| 151 | length = 1 |
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| 152 | control = None |
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| 153 | |
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| 154 | # Build the parameter |
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| 155 | parameter = Parameter(name=name, units=units, default=default, |
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[a86f6c0] | 156 | limits=limits, ptype=ptype, description=description) |
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[69aa451] | 157 | |
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| 158 | # TODO: need better control over whether a parameter is polydisperse |
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[a86f6c0] | 159 | parameter.polydisperse = ptype in ('orientation', 'volume') |
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| 160 | parameter.relative_pd = ptype == 'volume' |
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[69aa451] | 161 | parameter.choices = choices |
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| 162 | parameter.length = length |
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| 163 | parameter.length_control = control |
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| 164 | |
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| 165 | return parameter |
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| 166 | |
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[ce896fd] | 167 | |
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[4bfd277] | 168 | def expand_pars(partable, pars): |
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[a86f6c0] | 169 | # type: (ParameterTable, ParameterSetUser) -> ParameterSet |
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[ce896fd] | 170 | """ |
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[6d6508e] | 171 | Create demo parameter set from key-value pairs. |
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[ce896fd] | 172 | |
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[4bfd277] | 173 | *pars* are the key-value pairs to use for the parameters. Any |
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| 174 | parameters not specified in *pars* are set from the *partable* defaults. |
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[ce896fd] | 175 | |
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[4bfd277] | 176 | If *pars* references vector fields, such as thickness[n], then support |
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[ce896fd] | 177 | different ways of assigning the demo values, including assigning a |
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| 178 | specific value (e.g., thickness3=50.0), assigning a new value to all |
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| 179 | (e.g., thickness=50.0) or assigning values using list notation. |
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| 180 | """ |
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[4bfd277] | 181 | if pars is None: |
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[ce896fd] | 182 | result = partable.defaults |
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| 183 | else: |
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[4bfd277] | 184 | lookup = dict((p.id, p) for p in partable.kernel_parameters) |
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[ce896fd] | 185 | result = partable.defaults.copy() |
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[9a943d0] | 186 | scalars = dict((name, value) for name, value in pars.items() |
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| 187 | if name not in lookup or lookup[name].length == 1) |
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[4bfd277] | 188 | vectors = dict((name,value) for name,value in pars.items() |
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| 189 | if name in lookup and lookup[name].length > 1) |
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[ce896fd] | 190 | if vectors: |
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| 191 | for name, value in vectors.items(): |
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| 192 | if np.isscalar(value): |
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| 193 | # support for the form |
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[4bfd277] | 194 | # dict(thickness=0, thickness2=50) |
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| 195 | for k in range(1, lookup[name].length+1): |
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[ce896fd] | 196 | key = name+str(k) |
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| 197 | if key not in scalars: |
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| 198 | scalars[key] = vectors |
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| 199 | else: |
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| 200 | # supoprt for the form |
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[4bfd277] | 201 | # dict(thickness=[20,10,3]) |
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[ce896fd] | 202 | for (k,v) in enumerate(value): |
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| 203 | scalars[name+str(k)] = v |
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[9a943d0] | 204 | result.update(scalars) |
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[ce896fd] | 205 | |
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[6d6508e] | 206 | return result |
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| 207 | |
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| 208 | def prefix_parameter(par, prefix): |
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[a86f6c0] | 209 | # type: (Parameter, str) -> Parameter |
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[6d6508e] | 210 | """ |
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| 211 | Return a copy of the parameter with its name prefixed. |
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| 212 | """ |
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| 213 | new_par = copy(par) |
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| 214 | new_par.name = prefix + par.name |
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| 215 | new_par.id = prefix + par.id |
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| 216 | |
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| 217 | def suffix_parameter(par, suffix): |
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[a86f6c0] | 218 | # type: (Parameter, str) -> Parameter |
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[6d6508e] | 219 | """ |
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| 220 | Return a copy of the parameter with its name prefixed. |
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| 221 | """ |
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| 222 | new_par = copy(par) |
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| 223 | # If name has the form x[n], replace with x_suffix[n] |
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| 224 | new_par.name = par.id + suffix + par.name[len(par.id):] |
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| 225 | new_par.id = par.id + suffix |
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[ce896fd] | 226 | |
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[69aa451] | 227 | class Parameter(object): |
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| 228 | """ |
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| 229 | The available kernel parameters are defined as a list, with each parameter |
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| 230 | defined as a sublist with the following elements: |
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| 231 | |
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| 232 | *name* is the name that will be used in the call to the kernel |
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| 233 | function and the name that will be displayed to the user. Names |
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| 234 | should be lower case, with words separated by underscore. If |
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| 235 | acronyms are used, the whole acronym should be upper case. |
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| 236 | |
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| 237 | *units* should be one of *degrees* for angles, *Ang* for lengths, |
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| 238 | *1e-6/Ang^2* for SLDs. |
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| 239 | |
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| 240 | *default value* will be the initial value for the model when it |
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| 241 | is selected, or when an initial value is not otherwise specified. |
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| 242 | |
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| 243 | *limits = [lb, ub]* are the hard limits on the parameter value, used to |
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| 244 | limit the polydispersity density function. In the fit, the parameter limits |
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| 245 | given to the fit are the limits on the central value of the parameter. |
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| 246 | If there is polydispersity, it will evaluate parameter values outside |
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| 247 | the fit limits, but not outside the hard limits specified in the model. |
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| 248 | If there are no limits, use +/-inf imported from numpy. |
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| 249 | |
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| 250 | *type* indicates how the parameter will be used. "volume" parameters |
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| 251 | will be used in all functions. "orientation" parameters will be used |
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| 252 | in *Iqxy* and *Imagnetic*. "magnetic* parameters will be used in |
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| 253 | *Imagnetic* only. If *type* is the empty string, the parameter will |
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| 254 | be used in all of *Iq*, *Iqxy* and *Imagnetic*. "sld" parameters |
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| 255 | can automatically be promoted to magnetic parameters, each of which |
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| 256 | will have a magnitude and a direction, which may be different from |
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[6e7ff6d] | 257 | other sld parameters. The volume parameters are used for calls |
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| 258 | to form_volume within the kernel (required for volume normalization) |
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| 259 | and for calls to ER and VR for effective radius and volume ratio |
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| 260 | respectively. |
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[69aa451] | 261 | |
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| 262 | *description* is a short description of the parameter. This will |
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| 263 | be displayed in the parameter table and used as a tool tip for the |
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| 264 | parameter value in the user interface. |
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| 265 | |
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| 266 | Additional values can be set after the parameter is created: |
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| 267 | |
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[6e7ff6d] | 268 | * *length* is the length of the field if it is a vector field |
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| 269 | |
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| 270 | * *length_control* is the parameter which sets the vector length |
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| 271 | |
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| 272 | * *is_control* is True if the parameter is a control parameter for a vector |
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| 273 | |
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| 274 | * *polydisperse* is true if the parameter accepts a polydispersity |
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| 275 | |
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| 276 | * *relative_pd* is true if that polydispersity is a portion of the |
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| 277 | value (so a 10% length dipsersity would use a polydispersity value of 0.1) |
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| 278 | rather than absolute dispersisity (such as an angle plus or minus |
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| 279 | 15 degrees). |
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[69aa451] | 280 | |
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[a5b8477] | 281 | These values are set by :func:`make_parameter_table` and |
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| 282 | :func:`parse_parameter` therein. |
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[69aa451] | 283 | """ |
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| 284 | def __init__(self, name, units='', default=None, limits=(-np.inf, np.inf), |
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[a86f6c0] | 285 | ptype='', description=''): |
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[c1a888b] | 286 | # type: (str, str, float, Limits, str, str) -> None |
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[a86f6c0] | 287 | self.id = name.split('[')[0].strip() # type: str |
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| 288 | self.name = name # type: str |
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| 289 | self.units = units # type: str |
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| 290 | self.default = default # type: float |
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| 291 | self.limits = limits # type: Limits |
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| 292 | self.type = ptype # type: str |
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| 293 | self.description = description # type: str |
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[69aa451] | 294 | |
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[d19962c] | 295 | # Length and length_control will be filled in once the complete |
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[69aa451] | 296 | # parameter table is available. |
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[a86f6c0] | 297 | self.length = 1 # type: int |
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| 298 | self.length_control = None # type: Optional[str] |
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| 299 | self.is_control = False # type: bool |
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[69aa451] | 300 | |
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| 301 | # TODO: need better control over whether a parameter is polydisperse |
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[a86f6c0] | 302 | self.polydisperse = False # type: bool |
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| 303 | self.relative_pd = False # type: bool |
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[69aa451] | 304 | |
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[ce896fd] | 305 | # choices are also set externally. |
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[a86f6c0] | 306 | self.choices = [] # type: List[str] |
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[ce896fd] | 307 | |
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[69aa451] | 308 | def as_definition(self): |
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[a86f6c0] | 309 | # type: () -> str |
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[69aa451] | 310 | """ |
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| 311 | Declare space for the variable in a parameter structure. |
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| 312 | |
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| 313 | For example, the parameter thickness with length 3 will |
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| 314 | return "double thickness[3];", with no spaces before and |
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| 315 | no new line character afterward. |
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| 316 | """ |
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| 317 | if self.length == 1: |
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| 318 | return "double %s;"%self.id |
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| 319 | else: |
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| 320 | return "double %s[%d];"%(self.id, self.length) |
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| 321 | |
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| 322 | def as_function_argument(self): |
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[a86f6c0] | 323 | # type: () -> str |
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[69aa451] | 324 | """ |
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| 325 | Declare the variable as a function argument. |
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| 326 | |
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| 327 | For example, the parameter thickness with length 3 will |
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| 328 | return "double *thickness", with no spaces before and |
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| 329 | no comma afterward. |
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| 330 | """ |
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| 331 | if self.length == 1: |
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| 332 | return "double %s"%self.id |
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| 333 | else: |
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| 334 | return "double *%s"%self.id |
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| 335 | |
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| 336 | def as_call_reference(self, prefix=""): |
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[c1a888b] | 337 | # type: (str) -> str |
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[69aa451] | 338 | # Note: if the parameter is a struct type, then we will need to use |
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| 339 | # &prefix+id. For scalars and vectors we can just use prefix+id. |
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| 340 | return prefix + self.id |
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| 341 | |
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| 342 | def __str__(self): |
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[a86f6c0] | 343 | # type: () -> str |
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[69aa451] | 344 | return "<%s>"%self.name |
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| 345 | |
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| 346 | def __repr__(self): |
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[a86f6c0] | 347 | # type: () -> str |
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[69aa451] | 348 | return "P<%s>"%self.name |
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| 349 | |
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[d19962c] | 350 | |
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[69aa451] | 351 | class ParameterTable(object): |
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[d19962c] | 352 | """ |
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| 353 | ParameterTable manages the list of available parameters. |
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| 354 | |
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| 355 | There are a couple of complications which mean that the list of parameters |
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| 356 | for the kernel differs from the list of parameters that the user sees. |
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| 357 | |
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| 358 | (1) Common parameters. Scale and background are implicit to every model, |
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| 359 | but are not passed to the kernel. |
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| 360 | |
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| 361 | (2) Vector parameters. Vector parameters are passed to the kernel as a |
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| 362 | pointer to an array, e.g., thick[], but they are seen by the user as n |
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| 363 | separate parameters thick1, thick2, ... |
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| 364 | |
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| 365 | Therefore, the parameter table is organized by how it is expected to be |
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| 366 | used. The following information is needed to set up the kernel functions: |
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| 367 | |
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| 368 | * *kernel_parameters* is the list of parameters in the kernel parameter |
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| 369 | table, with vector parameter p declared as p[]. |
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| 370 | |
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| 371 | * *iq_parameters* is the list of parameters to the Iq(q, ...) function, |
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| 372 | with vector parameter p sent as p[]. |
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| 373 | |
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| 374 | * *iqxy_parameters* is the list of parameters to the Iqxy(qx, qy, ...) |
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| 375 | function, with vector parameter p sent as p[]. |
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| 376 | |
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| 377 | * *form_volume_parameters* is the list of parameters to the form_volume(...) |
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| 378 | function, with vector parameter p sent as p[]. |
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| 379 | |
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| 380 | Problem details, which sets up the polydispersity loops, requires the |
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| 381 | following: |
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| 382 | |
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| 383 | * *theta_offset* is the offset of the theta parameter in the kernel parameter |
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| 384 | table, with vector parameters counted as n individual parameters |
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| 385 | p1, p2, ..., or offset is -1 if there is no theta parameter. |
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| 386 | |
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| 387 | * *max_pd* is the maximum number of polydisperse parameters, with vector |
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| 388 | parameters counted as n individual parameters p1, p2, ... Note that |
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| 389 | this number is limited to sasmodels.modelinfo.MAX_PD. |
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| 390 | |
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| 391 | * *npars* is the total number of parameters to the kernel, with vector |
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| 392 | parameters counted as n individual parameters p1, p2, ... |
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| 393 | |
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| 394 | * *call_parameters* is the complete list of parameters to the kernel, |
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| 395 | including scale and background, with vector parameters recorded as |
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| 396 | individual parameters p1, p2, ... |
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| 397 | |
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| 398 | * *active_1d* is the set of names that may be polydisperse for 1d data |
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| 399 | |
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| 400 | * *active_2d* is the set of names that may be polydisperse for 2d data |
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| 401 | |
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| 402 | User parameters are the set of parameters visible to the user, including |
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| 403 | the scale and background parameters that the kernel does not see. User |
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| 404 | parameters don't use vector notation, and instead use p1, p2, ... |
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| 405 | |
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| 406 | * *control_parameters* is the |
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| 407 | |
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| 408 | """ |
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[69aa451] | 409 | # scale and background are implicit parameters |
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| 410 | COMMON = [Parameter(*p) for p in COMMON_PARAMETERS] |
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| 411 | |
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| 412 | def __init__(self, parameters): |
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[a86f6c0] | 413 | # type: (List[Parameter]) -> None |
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[d19962c] | 414 | self.kernel_parameters = parameters |
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[60eab2a] | 415 | self._set_vector_lengths() |
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[a86f6c0] | 416 | self.call_parameters = self._get_call_parameters() |
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| 417 | self.defaults = self._get_defaults() |
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[d19962c] | 418 | #self._name_table= dict((p.id, p) for p in parameters) |
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[60eab2a] | 419 | |
---|
[d19962c] | 420 | # Set the kernel parameters. Assumes background and scale are the |
---|
| 421 | # first two parameters in the parameter list, but these are not sent |
---|
| 422 | # to the underlying kernel functions. |
---|
| 423 | self.iq_parameters = [p for p in self.kernel_parameters |
---|
| 424 | if p.type not in ('orientation', 'magnetic')] |
---|
| 425 | self.iqxy_parameters = [p for p in self.kernel_parameters |
---|
| 426 | if p.type != 'magnetic'] |
---|
| 427 | self.form_volume_parameters = [p for p in self.kernel_parameters |
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| 428 | if p.type == 'volume'] |
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| 429 | |
---|
| 430 | # Theta offset |
---|
| 431 | offset = 0 |
---|
| 432 | for p in self.kernel_parameters: |
---|
| 433 | if p.name == 'theta': |
---|
| 434 | self.theta_offset = offset |
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| 435 | break |
---|
| 436 | offset += p.length |
---|
| 437 | else: |
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| 438 | self.theta_offset = -1 |
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[69aa451] | 439 | |
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[d19962c] | 440 | # number of polydisperse parameters |
---|
| 441 | num_pd = sum(p.length for p in self.kernel_parameters if p.polydisperse) |
---|
| 442 | # Don't use more polydisperse parameters than are available in the model |
---|
| 443 | # Note: we can do polydispersity on arbitrary parameters, so it is not |
---|
| 444 | # clear that this is a good idea; it does however make the poly_details |
---|
| 445 | # code easier to write, so we will leave it in for now. |
---|
| 446 | self.max_pd = min(num_pd, MAX_PD) |
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[69aa451] | 447 | |
---|
[d19962c] | 448 | self.npars = sum(p.length for p in self.kernel_parameters) |
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[69aa451] | 449 | |
---|
[d19962c] | 450 | # true if has 2D parameters |
---|
| 451 | self.has_2d = any(p.type in ('orientation', 'magnetic') |
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| 452 | for p in self.kernel_parameters) |
---|
[69aa451] | 453 | |
---|
[d19962c] | 454 | self.pd_1d = set(p.name for p in self.call_parameters |
---|
[a86f6c0] | 455 | if p.polydisperse and p.type not in ('orientation', 'magnetic')) |
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[d19962c] | 456 | self.pd_2d = set(p.name for p in self.call_parameters |
---|
| 457 | if p.polydisperse and p.type != 'magnetic') |
---|
[69aa451] | 458 | |
---|
[a86f6c0] | 459 | |
---|
| 460 | def _set_vector_lengths(self): |
---|
| 461 | # type: () -> None |
---|
| 462 | """ |
---|
| 463 | Walk the list of kernel parameters, setting the length field of the |
---|
| 464 | vector parameters from the upper limit of the reference parameter. |
---|
| 465 | |
---|
| 466 | This needs to be done once the entire parameter table is available |
---|
| 467 | since the reference may still be undefined when the parameter is |
---|
| 468 | initially created. |
---|
| 469 | |
---|
| 470 | Note: This modifies the underlying parameter object. |
---|
| 471 | """ |
---|
| 472 | # Sort out the length of the vector parameters such as thickness[n] |
---|
| 473 | for p in self.kernel_parameters: |
---|
| 474 | if p.length_control: |
---|
| 475 | for ref in self.kernel_parameters: |
---|
| 476 | if ref.id == p.length_control: |
---|
| 477 | break |
---|
| 478 | else: |
---|
| 479 | raise ValueError("no reference variable %r for %s" |
---|
| 480 | % (p.length_control, p.name)) |
---|
| 481 | ref.is_control = True |
---|
| 482 | low, high = ref.limits |
---|
| 483 | if int(low) != low or int(high) != high or low < 0 or high > 20: |
---|
| 484 | raise ValueError("expected limits on %s to be within [0, 20]" |
---|
| 485 | % ref.name) |
---|
[04045f4] | 486 | p.length = int(high) |
---|
[a86f6c0] | 487 | |
---|
| 488 | def _get_defaults(self): |
---|
| 489 | # type: () -> ParameterSet |
---|
| 490 | """ |
---|
| 491 | Get a list of parameter defaults from the parameters. |
---|
| 492 | |
---|
| 493 | Expands vector parameters into parameter id+number. |
---|
| 494 | """ |
---|
| 495 | # Construct default values, including vector defaults |
---|
| 496 | defaults = {} |
---|
| 497 | for p in self.call_parameters: |
---|
| 498 | if p.length == 1: |
---|
| 499 | defaults[p.id] = p.default |
---|
| 500 | else: |
---|
| 501 | for k in range(1, p.length+1): |
---|
| 502 | defaults["%s%d"%(p.id, k)] = p.default |
---|
| 503 | return defaults |
---|
| 504 | |
---|
| 505 | def _get_call_parameters(self): |
---|
| 506 | # type: () -> List[Parameter] |
---|
| 507 | full_list = self.COMMON[:] |
---|
| 508 | for p in self.kernel_parameters: |
---|
| 509 | if p.length == 1: |
---|
| 510 | full_list.append(p) |
---|
| 511 | else: |
---|
| 512 | for k in range(1, p.length+1): |
---|
| 513 | pk = Parameter(p.id+str(k), p.units, p.default, |
---|
| 514 | p.limits, p.type, p.description) |
---|
| 515 | pk.polydisperse = p.polydisperse |
---|
| 516 | pk.relative_pd = p.relative_pd |
---|
| 517 | full_list.append(pk) |
---|
| 518 | return full_list |
---|
| 519 | |
---|
[fb5914f] | 520 | def user_parameters(self, pars={}, is2d=True): |
---|
[0d99a6a] | 521 | # type: (Dict[str, float], bool) -> List[Parameter] |
---|
[69aa451] | 522 | """ |
---|
[d19962c] | 523 | Return the list of parameters for the given data type. |
---|
| 524 | |
---|
| 525 | Vector parameters are expanded as in place. If multiple parameters |
---|
| 526 | share the same vector length, then the parameters will be interleaved |
---|
| 527 | in the result. The control parameters come first. For example, |
---|
| 528 | if the parameter table is ordered as:: |
---|
| 529 | |
---|
| 530 | sld_core |
---|
| 531 | sld_shell[num_shells] |
---|
| 532 | sld_solvent |
---|
| 533 | thickness[num_shells] |
---|
| 534 | num_shells |
---|
| 535 | |
---|
| 536 | and *pars[num_shells]=2* then the returned list will be:: |
---|
| 537 | |
---|
| 538 | num_shells |
---|
| 539 | scale |
---|
| 540 | background |
---|
| 541 | sld_core |
---|
| 542 | sld_shell1 |
---|
| 543 | thickness1 |
---|
| 544 | sld_shell2 |
---|
| 545 | thickness2 |
---|
| 546 | sld_solvent |
---|
| 547 | |
---|
| 548 | Note that shell/thickness pairs are grouped together in the result |
---|
| 549 | even though they were not grouped in the incoming table. The control |
---|
| 550 | parameter is always returned first since the GUI will want to set it |
---|
| 551 | early, and rerender the table when it is changed. |
---|
[69aa451] | 552 | """ |
---|
[04045f4] | 553 | # control parameters go first |
---|
[d19962c] | 554 | control = [p for p in self.kernel_parameters if p.is_control] |
---|
| 555 | |
---|
| 556 | # Gather entries such as name[n] into groups of the same n |
---|
[04045f4] | 557 | dependent = {} # type: Dict[str, List[Parameter]] |
---|
| 558 | dependent.update((p.id, []) for p in control) |
---|
[d19962c] | 559 | for p in self.kernel_parameters: |
---|
| 560 | if p.length_control is not None: |
---|
| 561 | dependent[p.length_control].append(p) |
---|
| 562 | |
---|
| 563 | # Gather entries such as name[4] into groups of the same length |
---|
[c1a888b] | 564 | fixed = {} # type: Dict[int, List[Parameter]] |
---|
[d19962c] | 565 | for p in self.kernel_parameters: |
---|
| 566 | if p.length > 1 and p.length_control is None: |
---|
| 567 | fixed.setdefault(p.length, []).append(p) |
---|
| 568 | |
---|
| 569 | # Using the call_parameters table, we already have expanded forms |
---|
| 570 | # for each of the vector parameters; put them in a lookup table |
---|
| 571 | expanded_pars = dict((p.name, p) for p in self.call_parameters) |
---|
| 572 | |
---|
| 573 | # Gather the user parameters in order |
---|
| 574 | result = control + self.COMMON |
---|
| 575 | for p in self.kernel_parameters: |
---|
| 576 | if not is2d and p.type in ('orientation', 'magnetic'): |
---|
| 577 | pass |
---|
| 578 | elif p.is_control: |
---|
| 579 | pass # already added |
---|
| 580 | elif p.length_control is not None: |
---|
| 581 | table = dependent.get(p.length_control, []) |
---|
| 582 | if table: |
---|
| 583 | # look up length from incoming parameters |
---|
[fb5914f] | 584 | table_length = int(pars.get(p.length_control, p.length)) |
---|
[d19962c] | 585 | del dependent[p.length_control] # first entry seen |
---|
| 586 | for k in range(1, table_length+1): |
---|
| 587 | for entry in table: |
---|
| 588 | result.append(expanded_pars[entry.id+str(k)]) |
---|
| 589 | else: |
---|
| 590 | pass # already processed all entries |
---|
| 591 | elif p.length > 1: |
---|
| 592 | table = fixed.get(p.length, []) |
---|
| 593 | if table: |
---|
| 594 | table_length = p.length |
---|
| 595 | del fixed[p.length] |
---|
| 596 | for k in range(1, table_length+1): |
---|
| 597 | for entry in table: |
---|
| 598 | result.append(expanded_pars[entry.id+str(k)]) |
---|
| 599 | else: |
---|
| 600 | pass # already processed all entries |
---|
| 601 | else: |
---|
| 602 | result.append(p) |
---|
| 603 | |
---|
| 604 | return result |
---|
[69aa451] | 605 | |
---|
| 606 | def isstr(x): |
---|
[a86f6c0] | 607 | # type: (Any) -> bool |
---|
[7edce22] | 608 | """ |
---|
| 609 | Return True if the object is a string. |
---|
| 610 | """ |
---|
[69aa451] | 611 | # TODO: 2-3 compatible tests for str, including unicode strings |
---|
| 612 | return isinstance(x, str) |
---|
| 613 | |
---|
[6d6508e] | 614 | def make_model_info(kernel_module): |
---|
[7edce22] | 615 | # type: (module) -> ModelInfo |
---|
| 616 | """ |
---|
| 617 | Extract the model definition from the loaded kernel module. |
---|
| 618 | |
---|
| 619 | Fill in default values for parts of the module that are not provided. |
---|
| 620 | |
---|
| 621 | Note: vectorized Iq and Iqxy functions will be created for python |
---|
| 622 | models when the model is first called, not when the model is loaded. |
---|
| 623 | """ |
---|
[6d6508e] | 624 | info = ModelInfo() |
---|
| 625 | #print("make parameter table", kernel_module.parameters) |
---|
[c1a888b] | 626 | parameters = make_parameter_table(getattr(kernel_module, 'parameters', [])) |
---|
[4bfd277] | 627 | demo = expand_pars(parameters, getattr(kernel_module, 'demo', None)) |
---|
[6d6508e] | 628 | filename = abspath(kernel_module.__file__) |
---|
| 629 | kernel_id = splitext(basename(filename))[0] |
---|
| 630 | name = getattr(kernel_module, 'name', None) |
---|
| 631 | if name is None: |
---|
| 632 | name = " ".join(w.capitalize() for w in kernel_id.split('_')) |
---|
| 633 | |
---|
| 634 | info.id = kernel_id # string used to load the kernel |
---|
| 635 | info.filename = abspath(kernel_module.__file__) |
---|
| 636 | info.name = name |
---|
| 637 | info.title = getattr(kernel_module, 'title', name+" model") |
---|
| 638 | info.description = getattr(kernel_module, 'description', 'no description') |
---|
| 639 | info.parameters = parameters |
---|
| 640 | info.demo = demo |
---|
| 641 | info.composition = None |
---|
| 642 | info.docs = kernel_module.__doc__ |
---|
| 643 | info.category = getattr(kernel_module, 'category', None) |
---|
| 644 | info.single = getattr(kernel_module, 'single', True) |
---|
| 645 | info.structure_factor = getattr(kernel_module, 'structure_factor', False) |
---|
[04045f4] | 646 | info.profile_axes = getattr(kernel_module, 'profile_axes', ['x', 'y']) |
---|
[6d6508e] | 647 | info.source = getattr(kernel_module, 'source', []) |
---|
[e62a134] | 648 | # TODO: check the structure of the tests |
---|
[6d6508e] | 649 | info.tests = getattr(kernel_module, 'tests', []) |
---|
[9a943d0] | 650 | info.ER = getattr(kernel_module, 'ER', None) # type: ignore |
---|
| 651 | info.VR = getattr(kernel_module, 'VR', None) # type: ignore |
---|
| 652 | info.form_volume = getattr(kernel_module, 'form_volume', None) # type: ignore |
---|
| 653 | info.Iq = getattr(kernel_module, 'Iq', None) # type: ignore |
---|
| 654 | info.Iqxy = getattr(kernel_module, 'Iqxy', None) # type: ignore |
---|
| 655 | info.profile = getattr(kernel_module, 'profile', None) # type: ignore |
---|
| 656 | info.sesans = getattr(kernel_module, 'sesans', None) # type: ignore |
---|
[04045f4] | 657 | info.control = getattr(kernel_module, 'control', None) |
---|
| 658 | info.hidden = getattr(kernel_module, 'hidden', None) # type: ignore |
---|
[6d6508e] | 659 | |
---|
| 660 | # Precalculate the monodisperse parameter details |
---|
| 661 | info.mono_details = mono_details(info) |
---|
| 662 | return info |
---|
| 663 | |
---|
| 664 | class ModelInfo(object): |
---|
| 665 | """ |
---|
| 666 | Interpret the model definition file, categorizing the parameters. |
---|
| 667 | |
---|
| 668 | The module can be loaded with a normal python import statement if you |
---|
| 669 | know which module you need, or with __import__('sasmodels.model.'+name) |
---|
| 670 | if the name is in a string. |
---|
| 671 | |
---|
[7edce22] | 672 | The structure should be mostly static, other than the delayed definition |
---|
| 673 | of *Iq* and *Iqxy* if they need to be defined. |
---|
[6d6508e] | 674 | """ |
---|
[a5b8477] | 675 | #: Full path to the file defining the kernel, if any. |
---|
| 676 | filename = None # type: Optiona[str] |
---|
| 677 | #: Id of the kernel used to load it from the filesystem. |
---|
[a86f6c0] | 678 | id = None # type: str |
---|
[a5b8477] | 679 | #: Display name of the model, which defaults to the model id but with |
---|
| 680 | #: capitalization of the parts so for example core_shell defaults to |
---|
| 681 | #: "Core Shell". |
---|
[a86f6c0] | 682 | name = None # type: str |
---|
[a5b8477] | 683 | #: Short description of the model. |
---|
[a86f6c0] | 684 | title = None # type: str |
---|
[a5b8477] | 685 | #: Long description of the model. |
---|
[a86f6c0] | 686 | description = None # type: str |
---|
[a5b8477] | 687 | #: Model parameter table. Parameters are defined using a list of parameter |
---|
| 688 | #: definitions, each of which is contains parameter name, units, |
---|
| 689 | #: default value, limits, type and description. See :class:`Parameter` |
---|
| 690 | #: for details on the individual parameters. The parameters are gathered |
---|
| 691 | #: into a :class:`ParameterTable`, which provides various views into the |
---|
| 692 | #: parameter list. |
---|
[a86f6c0] | 693 | parameters = None # type: ParameterTable |
---|
[a5b8477] | 694 | #: Demo parameters as a *parameter:value* map used as the default values |
---|
| 695 | #: for :mod:`compare`. Any parameters not set in *demo* will use the |
---|
| 696 | #: defaults from the parameter table. That means no polydispersity, and |
---|
| 697 | #: in the case of multiplicity models, a minimal model with no interesting |
---|
| 698 | #: scattering. |
---|
[a86f6c0] | 699 | demo = None # type: Dict[str, float] |
---|
[a5b8477] | 700 | #: Composition is None if this is an independent model, or it is a |
---|
| 701 | #: tuple with comoposition type ('product' or 'misture') and a list of |
---|
| 702 | #: :class:`ModelInfo` blocks for the composed objects. This allows us |
---|
| 703 | #: to rebuild a complete mixture or product model from the info block. |
---|
| 704 | #: *composition* is not given in the model definition file, but instead |
---|
| 705 | #: arises when the model is constructed using names such as |
---|
| 706 | #: *sphere*hardsphere* or *cylinder+sphere*. |
---|
[a86f6c0] | 707 | composition = None # type: Optional[Tuple[str, List[ModelInfo]]] |
---|
[a5b8477] | 708 | #: Name of the control parameter for a variant model such as :ref:`rpa`. |
---|
| 709 | #: The *control* parameter should appear in the parameter table, with |
---|
| 710 | #: limits defined as *[CASES]*, for case names such as |
---|
| 711 | #: *CASES = ["diblock copolymer", "triblock copolymer", ...]*. |
---|
| 712 | #: This should give *limits=[[case1, case2, ...]]*, but the |
---|
| 713 | #: model loader translates this to *limits=[0, len(CASES)-1]*, and adds |
---|
| 714 | #: *choices=CASES* to the :class:`Parameter` definition. Note that |
---|
| 715 | #: models can use a list of cases as a parameter without it being a |
---|
| 716 | #: control parameter. Either way, the parameter is sent to the model |
---|
| 717 | #: evaluator as *float(choice_num)*, where choices are numbered from 0. |
---|
| 718 | #: See also :attr:`hidden`. |
---|
[04045f4] | 719 | control = None # type: str |
---|
[a5b8477] | 720 | #: Different variants require different parameters. In order to show |
---|
| 721 | #: just the parameters needed for the variant selected by :attr:`control`, |
---|
| 722 | #: you should provide a function *hidden(control) -> set(['a', 'b', ...])* |
---|
| 723 | #: indicating which parameters need to be hidden. For multiplicity |
---|
| 724 | #: models, you need to use the complete name of the parameter, including |
---|
| 725 | #: its number. So for example, if variant "a" uses only *sld1* and *sld2*, |
---|
| 726 | #: then *sld3*, *sld4* and *sld5* of multiplicity parameter *sld[5]* |
---|
| 727 | #: should be in the hidden set. |
---|
| 728 | hidden = None # type: Optional[Callable[[int], Set[str]]] |
---|
| 729 | #: Doc string from the top of the model file. This should be formatted |
---|
| 730 | #: using ReStructuredText format, with latex markup in ".. math" |
---|
| 731 | #: environments, or in dollar signs. This will be automatically |
---|
| 732 | #: extracted to a .rst file by :func:`generate.make_docs`, then |
---|
| 733 | #: converted to HTML or PDF by Sphinx. |
---|
[a86f6c0] | 734 | docs = None # type: str |
---|
[a5b8477] | 735 | #: Location of the model description in the documentation. This takes the |
---|
| 736 | #: form of "section" or "section:subsection". So for example, |
---|
| 737 | #: :ref:`porod` uses *category="shape-independent"* so it is in the |
---|
| 738 | #: :ref:`Shape-independent` section whereas |
---|
| 739 | #: :ref:`capped_cylinder` uses: *category="shape:cylinder"*, which puts |
---|
| 740 | #: it in the :ref:`shape-cylinder` section. |
---|
[a86f6c0] | 741 | category = None # type: Optional[str] |
---|
[a5b8477] | 742 | #: True if the model can be computed accurately with single precision. |
---|
| 743 | #: This is True by default, but models such as :ref:`bcc_paracrystal` set |
---|
| 744 | #: it to False because they require double precision calculations. |
---|
[a86f6c0] | 745 | single = None # type: bool |
---|
[a5b8477] | 746 | #: True if the model is a structure factor used to model the interaction |
---|
| 747 | #: between form factor models. This will default to False if it is not |
---|
| 748 | #: provided in the file. |
---|
[a86f6c0] | 749 | structure_factor = None # type: bool |
---|
[a5b8477] | 750 | #: List of C source files used to define the model. The source files |
---|
| 751 | #: should define the *Iq* function, and possibly *Iqxy*, though a default |
---|
| 752 | #: *Iqxy = Iq(sqrt(qx**2+qy**2)* will be created if no *Iqxy* is provided. |
---|
| 753 | #: Files containing the most basic functions must appear first in the list, |
---|
| 754 | #: followed by the files that use those functions. Form factors are |
---|
| 755 | #: indicated by providing a :attr:`ER` function. |
---|
[a86f6c0] | 756 | source = None # type: List[str] |
---|
[a5b8477] | 757 | #: The set of tests that must pass. The format of the tests is described |
---|
| 758 | #: in :mod:`model_test`. |
---|
[a86f6c0] | 759 | tests = None # type: List[TestCondition] |
---|
[a5b8477] | 760 | #: Returns the effective radius of the model given its volume parameters. |
---|
| 761 | #: The presence of *ER* indicates that the model is a form factor model |
---|
| 762 | #: that may be used together with a structure factor to form an implicit |
---|
| 763 | #: multiplication model. |
---|
| 764 | #: |
---|
| 765 | #: The parameters to the *ER* function must be marked with type *volume*. |
---|
| 766 | #: in the parameter table. They will appear in the same order as they |
---|
| 767 | #: do in the table. The values passed to *ER* will be vectors, with one |
---|
| 768 | #: value for each polydispersity condition. For example, if the model |
---|
| 769 | #: is polydisperse over both length and radius, then both length and |
---|
| 770 | #: radius will have the same number of values in the vector, with one |
---|
| 771 | #: value for each *length X radius*. If only *radius* is polydisperse, |
---|
| 772 | #: then the value for *length* will be repeated once for each value of |
---|
| 773 | #: *radius*. The *ER* function should return one effective radius for |
---|
| 774 | #: each parameter set. Multiplicity parameters will be received as |
---|
| 775 | #: arrays, with one row per polydispersity condition. |
---|
[c1a888b] | 776 | ER = None # type: Optional[Callable[[np.ndarray], np.ndarray]] |
---|
[a5b8477] | 777 | #: Returns the occupied volume and the total volume for each parameter set. |
---|
| 778 | #: See :attr:`ER` for details on the parameters. |
---|
[c1a888b] | 779 | VR = None # type: Optional[Callable[[np.ndarray], Tuple[np.ndarray, np.ndarray]]] |
---|
[a5b8477] | 780 | #: Returns the form volume for python-based models. Form volume is needed |
---|
| 781 | #: for volume normalization in the polydispersity integral. If no |
---|
| 782 | #: parameters are *volume* parameters, then form volume is not needed. |
---|
| 783 | #: For C-based models, (with :attr:`sources` defined, or with :attr:`Iq` |
---|
| 784 | #: defined using a string containing C code), form_volume must also be |
---|
| 785 | #: C code, either defined as a string, or in the sources. |
---|
[f619de7] | 786 | form_volume = None # type: Union[None, str, Callable[[np.ndarray], float]] |
---|
[a5b8477] | 787 | #: Returns *I(q, a, b, ...)* for parameters *a*, *b*, etc. defined |
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| 788 | #: by the parameter table. *Iq* can be defined as a python function, or |
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| 789 | #: as a C function. If it is defined in C, then set *Iq* to the body of |
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| 790 | #: the C function, including the return statement. This function takes |
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| 791 | #: values for *q* and each of the parameters as separate *double* values |
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| 792 | #: (which may be converted to float or long double by sasmodels). All |
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| 793 | #: source code files listed in :attr:`sources` will be loaded before the |
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| 794 | #: *Iq* function is defined. If *Iq* is not present, then sources should |
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| 795 | #: define *static double Iq(double q, double a, double b, ...)* which |
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| 796 | #: will return *I(q, a, b, ...)*. Multiplicity parameters are sent as |
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| 797 | #: pointers to doubles. Constants in floating point expressions should |
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| 798 | #: include the decimal point. See :mod:`generate` for more details. |
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[f619de7] | 799 | Iq = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
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[a5b8477] | 800 | #: Returns *I(qx, qy, a, b, ...)*. The interface follows :attr:`Iq`. |
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[f619de7] | 801 | Iqxy = None # type: Union[None, str, Callable[[np.ndarray], np.ndarray]] |
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[a5b8477] | 802 | #: Returns a model profile curve *x, y*. If *profile* is defined, this |
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| 803 | #: curve will appear in response to the *Show* button in SasView. Use |
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| 804 | #: :attr:`profile_axes` to set the axis labels. Note that *y* values |
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| 805 | #: will be scaled by 1e6 before plotting. |
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[c1a888b] | 806 | profile = None # type: Optional[Callable[[np.ndarray], None]] |
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[a5b8477] | 807 | #: Axis labels for the :attr:`profile` plot. The default is *['x', 'y']*. |
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| 808 | #: Only the *x* component is used for now. |
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| 809 | profile_axes = None # type: Tuple[str, str] |
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| 810 | #: Returns *sesans(z, a, b, ...)* for models which can directly compute |
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| 811 | #: the SESANS correlation function. Note: not currently implemented. |
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[c1a888b] | 812 | sesans = None # type: Optional[Callable[[np.ndarray], np.ndarray]] |
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[a5b8477] | 813 | #: :class:details.CallDetails data for mono-disperse function evaluation. |
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| 814 | #: This field is created automatically by the model loader, and should |
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| 815 | #: not be defined as part of the model definition file. |
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[a86f6c0] | 816 | mono_details = None # type: CallDetails |
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[6d6508e] | 817 | |
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| 818 | def __init__(self): |
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[a86f6c0] | 819 | # type: () -> None |
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[6d6508e] | 820 | pass |
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| 821 | |
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[04045f4] | 822 | def get_hidden_parameters(self, control): |
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[a5b8477] | 823 | """ |
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| 824 | Returns the set of hidden parameters for the model. *control* is the |
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| 825 | value of the control parameter. Note that multiplicity models have |
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| 826 | an implicit control parameter, which is the parameter that controls |
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| 827 | the multiplicity. |
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| 828 | """ |
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[04045f4] | 829 | if self.hidden is not None: |
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| 830 | hidden = self.hidden(control) |
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| 831 | else: |
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| 832 | controls = [p for p in self.parameters.kernel_parameters] |
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| 833 | if len(controls) != 1: |
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| 834 | raise ValueError("more than one control parameter") |
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| 835 | hidden = set(p.id+str(k) |
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| 836 | for p in self.parameters.kernel_parameters |
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| 837 | for k in range(control+1, p.length+1) |
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| 838 | if p.length > 1) |
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| 839 | return hidden |
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