[3964f92] | 1 | """ |
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| 2 | Convert models to and from sasview. |
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| 3 | """ |
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[1b49bf8] | 4 | from __future__ import print_function, division |
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[256dfe1] | 5 | |
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[c5ac2b2] | 6 | import math |
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[3964f92] | 7 | import warnings |
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[32e3c9b] | 8 | |
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[32398dc] | 9 | import numpy as np |
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| 10 | |
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[32e3c9b] | 11 | from .conversion_table import CONVERSION_TABLE |
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[aea515c] | 12 | from .core import load_model_info |
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[3964f92] | 13 | |
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| 14 | # List of models which SasView versions don't contain the explicit 'scale' argument. |
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| 15 | # When converting such a model, please update this list. |
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[310ddcb] | 16 | MODELS_WITHOUT_SCALE = [ |
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[3964f92] | 17 | 'teubner_strey', |
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| 18 | 'broad_peak', |
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| 19 | 'two_lorentzian', |
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[34d6cab] | 20 | "two_power_law", |
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[3964f92] | 21 | 'gauss_lorentz_gel', |
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| 22 | 'be_polyelectrolyte', |
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| 23 | 'correlation_length', |
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[74f7238] | 24 | 'fractal_core_shell', |
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[17bbadd] | 25 | 'binary_hard_sphere', |
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[bad8b12] | 26 | 'raspberry' |
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[3964f92] | 27 | ] |
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| 28 | |
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| 29 | # List of models which SasView versions don't contain the explicit 'background' argument. |
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| 30 | # When converting such a model, please update this list. |
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[310ddcb] | 31 | MODELS_WITHOUT_BACKGROUND = [ |
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[3964f92] | 32 | 'guinier', |
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| 33 | ] |
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| 34 | |
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[256dfe1] | 35 | MODELS_WITHOUT_VOLFRACTION = [ |
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| 36 | 'fractal', |
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| 37 | 'vesicle', |
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| 38 | 'multilayer_vesicle', |
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| 39 | ] |
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| 40 | |
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[f1765a2] | 41 | MAGNETIC_SASVIEW_MODELS = [ |
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| 42 | 'core_shell', |
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| 43 | 'core_multi_shell', |
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| 44 | 'cylinder', |
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| 45 | 'parallelepiped', |
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| 46 | 'sphere', |
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| 47 | ] |
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| 48 | |
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[256dfe1] | 49 | |
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[f247314] | 50 | # Convert new style names for polydispersity info to old style names |
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[3964f92] | 51 | PD_DOT = [ |
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| 52 | ("_pd", ".width"), |
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| 53 | ("_pd_n", ".npts"), |
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| 54 | ("_pd_nsigma", ".nsigmas"), |
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| 55 | ("_pd_type", ".type"), |
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[e1ea6b5] | 56 | (".lower", ".lower"), |
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| 57 | (".upper", ".upper"), |
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| 58 | (".fittable", ".fittable"), |
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| 59 | (".std", ".std"), |
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| 60 | (".units", ".units"), |
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| 61 | ("", "") |
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[3964f92] | 62 | ] |
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[f247314] | 63 | |
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[aea515c] | 64 | def _rescale(par, scale): |
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| 65 | return [pk*scale for pk in par] if isinstance(par, list) else par*scale |
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[3964f92] | 66 | |
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[e65c3ba] | 67 | def _is_sld(model_info, par): |
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[3964f92] | 68 | """ |
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[aea515c] | 69 | Return True if parameter is a magnetic magnitude or SLD parameter. |
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[3964f92] | 70 | """ |
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[e65c3ba] | 71 | if par.startswith('M0:'): |
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[32e3c9b] | 72 | return True |
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[e65c3ba] | 73 | if '_pd' in par or '.' in par: |
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[32e3c9b] | 74 | return False |
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[aea515c] | 75 | for p in model_info.parameters.call_parameters: |
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[e65c3ba] | 76 | if p.id == par: |
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[32e3c9b] | 77 | return p.type == 'sld' |
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| 78 | # check through kernel parameters in case it is a named as a vector |
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[aea515c] | 79 | for p in model_info.parameters.kernel_parameters: |
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[e65c3ba] | 80 | if p.id == par: |
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[32e3c9b] | 81 | return p.type == 'sld' |
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[d2fb4af] | 82 | return False |
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[32e3c9b] | 83 | |
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[aea515c] | 84 | def _rescale_sld(model_info, pars, scale): |
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[3964f92] | 85 | """ |
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[aea515c] | 86 | rescale all sld parameters in the new model definition by *scale* so the |
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[3964f92] | 87 | numbers are nicer. Relies on the fact that all sld parameters in the |
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[aea515c] | 88 | new model definition end with sld. For backward conversion use |
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| 89 | *scale=1e-6*. For forward conversion use *scale=1e6*. |
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[3964f92] | 90 | """ |
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[e65c3ba] | 91 | return dict((par, (_rescale(v, scale) if _is_sld(model_info, par) else v)) |
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| 92 | for par, v in pars.items()) |
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[3964f92] | 93 | |
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[aea515c] | 94 | |
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[e65c3ba] | 95 | def _get_translation_table(model_info, version=(3, 1, 2)): |
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[07c8d46] | 96 | conv_param = CONVERSION_TABLE.get(version, {}).get(model_info.id, [None, {}]) |
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| 97 | translation = conv_param[1].copy() |
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[aea515c] | 98 | for p in model_info.parameters.kernel_parameters: |
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| 99 | if p.length > 1: |
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| 100 | newid = p.id |
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| 101 | oldid = translation.get(p.id, p.id) |
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| 102 | translation.pop(newid, None) |
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| 103 | for k in range(1, p.length+1): |
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| 104 | if newid+str(k) not in translation: |
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| 105 | translation[newid+str(k)] = oldid+str(k) |
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| 106 | # Remove control parameter from the result |
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| 107 | if model_info.control: |
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| 108 | translation[model_info.control] = "CONTROL" |
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| 109 | return translation |
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| 110 | |
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| 111 | # ========= FORWARD CONVERSION sasview 3.x => sasmodels =========== |
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| 112 | def _dot_pd_to_underscore_pd(par): |
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| 113 | if par.endswith(".width"): |
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| 114 | return par[:-6]+"_pd" |
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| 115 | elif par.endswith(".type"): |
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| 116 | return par[:-5]+"_pd_type" |
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| 117 | elif par.endswith(".nsigmas"): |
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| 118 | return par[:-8]+"_pd_nsigma" |
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| 119 | elif par.endswith(".npts"): |
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| 120 | return par[:-5]+"_pd_n" |
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| 121 | else: |
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| 122 | return par |
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| 123 | |
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| 124 | def _pd_to_underscores(pars): |
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| 125 | return dict((_dot_pd_to_underscore_pd(k), v) for k, v in pars.items()) |
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| 126 | |
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| 127 | def _convert_pars(pars, mapping): |
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[3964f92] | 128 | """ |
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[aea515c] | 129 | Rename the parameters and any associated polydispersity attributes. |
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| 130 | """ |
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| 131 | newpars = pars.copy() |
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| 132 | for new, old in mapping.items(): |
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[e65c3ba] | 133 | if old == new: |
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| 134 | continue |
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| 135 | if old is None: |
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| 136 | continue |
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| 137 | for _, dot in PD_DOT: |
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[aea515c] | 138 | source = old+dot |
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| 139 | if source in newpars: |
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| 140 | if new is not None: |
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| 141 | target = new+dot |
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| 142 | else: |
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| 143 | target = None |
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| 144 | if source != target: |
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| 145 | if target: |
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| 146 | newpars[target] = pars[old+dot] |
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| 147 | del newpars[source] |
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| 148 | return newpars |
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[3964f92] | 149 | |
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[32398dc] | 150 | def _conversion_target(model_name, version=(3, 1, 2)): |
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[3964f92] | 151 | """ |
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[aea515c] | 152 | Find the sasmodel name which translates into the sasview name. |
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| 153 | |
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| 154 | Note: *CoreShellEllipsoidModel* translates into *core_shell_ellipsoid:1*. |
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| 155 | This is necessary since there is only one variant in sasmodels for the |
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| 156 | two variants in sasview. |
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| 157 | """ |
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[119fa13] | 158 | for sasmodels_name, sasview_dict in \ |
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[a297255] | 159 | CONVERSION_TABLE.get(version, {}).items(): |
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[119fa13] | 160 | if sasview_dict[0] == model_name: |
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[aea515c] | 161 | return sasmodels_name |
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| 162 | return None |
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| 163 | |
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[e65c3ba] | 164 | def _hand_convert(name, oldpars, version=(3, 1, 2)): |
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| 165 | if version == (3, 1, 2): |
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[54fb5d8] | 166 | oldpars = _hand_convert_3_1_2_to_4_1(name, oldpars) |
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[610ef23] | 167 | if version < (4, 2, 0): |
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| 168 | oldpars = _rename_magnetic_pars(oldpars) |
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[54fb5d8] | 169 | return oldpars |
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| 170 | |
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[610ef23] | 171 | def _rename_magnetic_pars(pars): |
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| 172 | """ |
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| 173 | Change from M0:par to par_M0, etc. |
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| 174 | """ |
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| 175 | keys = list(pars.items()) |
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| 176 | for k in keys: |
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| 177 | if k.startswith('M0:'): |
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| 178 | pars[k[3:]+'_M0'] = pars.pop(k) |
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| 179 | elif k.startswith('mtheta:'): |
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| 180 | pars[k[7:]+'_mtheta'] = pars.pop(k) |
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| 181 | elif k.startswith('mphi:'): |
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| 182 | pars[k[5:]+'_mphi'] = pars.pop(k) |
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| 183 | elif k.startswith('up:'): |
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| 184 | pars['up_'+k[3:]] = pars.pop(k) |
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| 185 | return pars |
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| 186 | |
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[54fb5d8] | 187 | def _hand_convert_3_1_2_to_4_1(name, oldpars): |
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| 188 | if name == 'core_shell_parallelepiped': |
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[aea515c] | 189 | # Make sure pd on rim parameters defaults to zero |
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| 190 | # ... probably not necessary. |
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| 191 | oldpars['rimA.width'] = 0.0 |
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| 192 | oldpars['rimB.width'] = 0.0 |
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| 193 | oldpars['rimC.width'] = 0.0 |
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[54fb5d8] | 194 | elif name == 'core_shell_ellipsoid:1': |
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[037aa3d] | 195 | # Reverse translation (from new to old), from core_shell_ellipsoid.c |
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| 196 | # equat_shell = equat_core + thick_shell |
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| 197 | # polar_core = equat_core * x_core |
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| 198 | # polar_shell = equat_core * x_core + thick_shell*x_polar_shell |
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| 199 | # Forward translation (from old to new), inverting reverse translation: |
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| 200 | # thick_shell = equat_shell - equat_core |
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| 201 | # x_core = polar_core / equat_core |
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| 202 | # x_polar_shell = (polar_shell - polar_core)/(equat_shell - equat_core) |
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| 203 | # Auto translation (old <=> new) happens after hand_convert |
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| 204 | # equat_shell <=> thick_shell |
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| 205 | # polar_core <=> x_core |
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| 206 | # polar_shell <=> x_polar_shell |
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| 207 | # So... |
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| 208 | equat_core, equat_shell = oldpars['equat_core'], oldpars['equat_shell'] |
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| 209 | polar_core, polar_shell = oldpars['polar_core'], oldpars['polar_shell'] |
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| 210 | oldpars['equat_shell'] = equat_shell - equat_core |
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| 211 | oldpars['polar_core'] = polar_core / equat_core |
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| 212 | oldpars['polar_shell'] = (polar_shell-polar_core)/(equat_shell-equat_core) |
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[54fb5d8] | 213 | elif name == 'hollow_cylinder': |
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[aea515c] | 214 | # now uses radius and thickness |
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| 215 | thickness = oldpars['radius'] - oldpars['core_radius'] |
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| 216 | oldpars['radius'] = thickness |
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[f8f5a37] | 217 | if 'radius.width' in oldpars: |
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| 218 | pd = oldpars['radius.width']*oldpars['radius']/thickness |
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| 219 | oldpars['radius.width'] = pd |
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[54fb5d8] | 220 | elif name == 'multilayer_vesicle': |
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[077666e] | 221 | if 'scale' in oldpars: |
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| 222 | oldpars['volfraction'] = oldpars['scale'] |
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| 223 | oldpars['scale'] = 1.0 |
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| 224 | if 'scale.lower' in oldpars: |
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| 225 | oldpars['volfraction.lower'] = oldpars['scale.lower'] |
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| 226 | if 'scale.upper' in oldpars: |
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| 227 | oldpars['volfraction.upper'] = oldpars['scale.upper'] |
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| 228 | if 'scale.fittable' in oldpars: |
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| 229 | oldpars['volfraction.fittable'] = oldpars['scale.fittable'] |
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| 230 | if 'scale.std' in oldpars: |
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| 231 | oldpars['volfraction.std'] = oldpars['scale.std'] |
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| 232 | if 'scale.units' in oldpars: |
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| 233 | oldpars['volfraction.units'] = oldpars['scale.units'] |
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[54fb5d8] | 234 | elif name == 'pearl_necklace': |
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[aea515c] | 235 | pass |
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| 236 | #_remove_pd(oldpars, 'num_pearls', name) |
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| 237 | #_remove_pd(oldpars, 'thick_string', name) |
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[54fb5d8] | 238 | elif name == 'polymer_micelle': |
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[aea515c] | 239 | if 'ndensity' in oldpars: |
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| 240 | oldpars['ndensity'] /= 1e15 |
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[8d06779] | 241 | if 'ndensity.lower' in oldpars: |
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[88fafac] | 242 | oldpars['ndensity.lower'] /= 1e15 |
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[8d06779] | 243 | if 'ndensity.upper' in oldpars: |
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[88fafac] | 244 | oldpars['ndensity.upper'] /= 1e15 |
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[54fb5d8] | 245 | elif name == 'rpa': |
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[aea515c] | 246 | # convert scattering lengths from femtometers to centimeters |
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| 247 | for p in "L1", "L2", "L3", "L4": |
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[88fafac] | 248 | if p in oldpars: |
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| 249 | oldpars[p] /= 1e-13 |
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[8d06779] | 250 | if p + ".lower" in oldpars: |
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[88fafac] | 251 | oldpars[p + ".lower"] /= 1e-13 |
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[8d06779] | 252 | if p + ".upper" in oldpars: |
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[88fafac] | 253 | oldpars[p + ".upper"] /= 1e-13 |
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[54fb5d8] | 254 | elif name == 'spherical_sld': |
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[16fd9e5] | 255 | j = 0 |
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| 256 | while "func_inter" + str(j) in oldpars: |
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| 257 | name = "func_inter" + str(j) |
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| 258 | new_name = "shape" + str(j + 1) |
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| 259 | if oldpars[name] == 'Erf(|nu|*z)': |
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| 260 | oldpars[new_name] = int(0) |
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| 261 | elif oldpars[name] == 'RPower(z^|nu|)': |
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| 262 | oldpars[new_name] = int(1) |
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| 263 | elif oldpars[name] == 'LPower(z^|nu|)': |
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| 264 | oldpars[new_name] = int(2) |
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| 265 | elif oldpars[name] == 'RExp(-|nu|*z)': |
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| 266 | oldpars[new_name] = int(3) |
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| 267 | elif oldpars[name] == 'LExp(-|nu|*z)': |
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| 268 | oldpars[new_name] = int(4) |
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| 269 | else: |
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| 270 | oldpars[new_name] = int(0) |
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| 271 | oldpars.pop(name) |
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| 272 | oldpars['n_shells'] = str(j + 1) |
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| 273 | j += 1 |
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[54fb5d8] | 274 | elif name == 'teubner_strey': |
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[aea515c] | 275 | # basically undoing the entire Teubner-Strey calculations here. |
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| 276 | # drho = (sld_a - sld_b) |
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| 277 | # k = 2.0*math.pi*xi/d |
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| 278 | # a2 = (1.0 + k**2)**2 |
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| 279 | # c1 = 2.0 * xi**2 * (1.0 - k**2) |
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| 280 | # c2 = xi**4 |
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| 281 | # prefactor = 8.0*math.pi*phi*(1.0-phi)*drho**2*c2/xi |
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| 282 | # scale = 1e-4*prefactor |
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| 283 | # oldpars['scale'] = a2/scale |
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| 284 | # oldpars['c1'] = c1/scale |
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| 285 | # oldpars['c2'] = c2/scale |
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| 286 | |
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| 287 | # need xi, d, sld_a, sld_b, phi=volfraction_a |
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| 288 | # assume contrast is 1.0e-6, scale=1, background=0 |
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| 289 | sld_a, sld_b = 1.0, 0. |
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| 290 | drho = sld_a - sld_b |
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| 291 | |
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| 292 | # find xi |
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| 293 | p_scale = oldpars['scale'] |
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| 294 | p_c1 = oldpars['c1'] |
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[2d81cfe] | 295 | p_c2 = oldpars['c2'] |
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[f8f5a37] | 296 | i_1 = 0.5*p_c1/p_c2 |
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| 297 | i_2 = math.sqrt(math.fabs(p_scale/p_c2)) |
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| 298 | i_3 = 2/(i_1 + i_2) |
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| 299 | xi = math.sqrt(math.fabs(i_3)) |
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[aea515c] | 300 | |
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| 301 | # find d from xi |
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[f8f5a37] | 302 | k = math.sqrt(math.fabs(1 - 0.5*p_c1/p_c2*xi**2)) |
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[aea515c] | 303 | d = 2*math.pi*xi/k |
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| 304 | |
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[999c87f] | 305 | # solve quadratic phi (1-phi) = xi/(1e-4 8 pi drho^2 c2) |
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[aea515c] | 306 | # favour volume fraction in [0, 0.5] |
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[999c87f] | 307 | c = xi / (1e-4 * 8.0 * math.pi * drho**2 * p_c2) |
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[aea515c] | 308 | phi = 0.5 - math.sqrt(0.25 - c) |
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| 309 | |
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| 310 | # scale sld_a by 1e-6 because the translator will scale it back |
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| 311 | oldpars.update(volfraction_a=phi, xi=xi, d=d, sld_a=sld_a*1e-6, |
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| 312 | sld_b=sld_b, scale=1.0) |
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| 313 | oldpars.pop('c1') |
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| 314 | oldpars.pop('c2') |
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| 315 | |
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| 316 | return oldpars |
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| 317 | |
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[e65c3ba] | 318 | def convert_model(name, pars, use_underscore=False, model_version=(3, 1, 2)): |
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[aea515c] | 319 | """ |
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| 320 | Convert model from old style parameter names to new style. |
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| 321 | """ |
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[4b4eee1] | 322 | newpars = pars |
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[0795293] | 323 | keys = sorted(CONVERSION_TABLE.keys()) |
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| 324 | for i, version in enumerate(keys): |
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[a297255] | 325 | # Don't allow indices outside list |
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| 326 | next_i = i + 1 |
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| 327 | if next_i == len(keys): |
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| 328 | next_i = i |
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[0795293] | 329 | # If the save state is from a later version, skip the check |
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[a297255] | 330 | if model_version <= keys[next_i]: |
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| 331 | newname = _conversion_target(name, version) |
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| 332 | else: |
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| 333 | newname = None |
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[0795293] | 334 | # If no conversion is found, move on |
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[4b4eee1] | 335 | if newname is None: |
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| 336 | newname = name |
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| 337 | continue |
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| 338 | if ':' in newname: # core_shell_ellipsoid:1 |
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| 339 | model_info = load_model_info(newname[:-2]) |
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[298621b] | 340 | # Know the table exists and isn't multiplicity so grab it directly |
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[4b4eee1] | 341 | # Can't use _get_translation_table since that will return the 'bare' |
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| 342 | # version. |
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[a297255] | 343 | translation = CONVERSION_TABLE.get(version, {})[newname][1] |
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[4b4eee1] | 344 | else: |
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| 345 | model_info = load_model_info(newname) |
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| 346 | translation = _get_translation_table(model_info, version) |
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| 347 | newpars = _hand_convert(newname, newpars, version) |
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| 348 | newpars = _convert_pars(newpars, translation) |
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[86e8e66] | 349 | # TODO: Still not convinced this is the best check |
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[e65c3ba] | 350 | if not model_info.structure_factor and version == (3, 1, 2): |
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[4b4eee1] | 351 | newpars = _rescale_sld(model_info, newpars, 1e6) |
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| 352 | newpars.setdefault('scale', 1.0) |
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| 353 | newpars.setdefault('background', 0.0) |
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| 354 | if use_underscore: |
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| 355 | newpars = _pd_to_underscores(newpars) |
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| 356 | name = newname |
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[aea515c] | 357 | return newname, newpars |
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| 358 | |
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| 359 | # ========= BACKWARD CONVERSION sasmodels => sasview 3.x =========== |
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[3964f92] | 360 | |
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| 361 | def _revert_pars(pars, mapping): |
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| 362 | """ |
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| 363 | Rename the parameters and any associated polydispersity attributes. |
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| 364 | """ |
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| 365 | newpars = pars.copy() |
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| 366 | |
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| 367 | for new, old in mapping.items(): |
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[40a87fa] | 368 | for underscore, dot in PD_DOT: |
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| 369 | if old and old+underscore == new+dot: |
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[3964f92] | 370 | continue |
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[40a87fa] | 371 | if new+underscore in newpars: |
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[3964f92] | 372 | if old is not None: |
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[40a87fa] | 373 | newpars[old+dot] = pars[new+underscore] |
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| 374 | del newpars[new+underscore] |
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[3964f92] | 375 | for k in list(newpars.keys()): |
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[40a87fa] | 376 | for underscore, dot in PD_DOT[1:]: # skip "" => "" |
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| 377 | if k.endswith(underscore): |
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| 378 | newpars[k[:-len(underscore)]+dot] = newpars[k] |
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[3964f92] | 379 | del newpars[k] |
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| 380 | return newpars |
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| 381 | |
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[f247314] | 382 | def revert_name(model_info): |
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[40a87fa] | 383 | oldname, _ = CONVERSION_TABLE.get(model_info.id, [None, {}]) |
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[f247314] | 384 | return oldname |
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| 385 | |
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[aea515c] | 386 | def _remove_pd(pars, key, name): |
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| 387 | """ |
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| 388 | Remove polydispersity from the parameter list. |
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| 389 | |
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| 390 | Note: operates in place |
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| 391 | """ |
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| 392 | # Bumps style parameter names |
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| 393 | width = pars.pop(key+".width", 0.0) |
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| 394 | n_points = pars.pop(key+".npts", 0) |
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| 395 | if width != 0.0 and n_points != 0: |
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| 396 | warnings.warn("parameter %s not polydisperse in sasview %s"%(key, name)) |
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| 397 | pars.pop(key+".nsigmas", None) |
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| 398 | pars.pop(key+".type", None) |
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| 399 | return pars |
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[256dfe1] | 400 | |
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| 401 | def _trim_vectors(model_info, pars, oldpars): |
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| 402 | _, translation = CONVERSION_TABLE.get(model_info.id, [None, {}]) |
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| 403 | for p in model_info.parameters.kernel_parameters: |
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| 404 | if p.length_control is not None: |
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| 405 | n = int(pars[p.length_control]) |
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| 406 | oldname = translation.get(p.id, p.id) |
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| 407 | for k in range(n+1, p.length+1): |
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| 408 | for _, old in PD_DOT: |
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| 409 | oldpars.pop(oldname+str(k)+old, None) |
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[f247314] | 410 | return oldpars |
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| 411 | |
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[17bbadd] | 412 | def revert_pars(model_info, pars): |
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[3964f92] | 413 | """ |
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| 414 | Convert model from new style parameter names to old style. |
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| 415 | """ |
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[6d6508e] | 416 | if model_info.composition is not None: |
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| 417 | composition_type, parts = model_info.composition |
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[f247314] | 418 | if composition_type == 'product': |
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[e85aa2e] | 419 | translation = _get_translation_table(parts[0]) |
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| 420 | # structure factor models include scale:scale_factor mapping |
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[6dc78e4] | 421 | translation.update(_get_translation_table(parts[1])) |
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[f247314] | 422 | else: |
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| 423 | raise NotImplementedError("cannot convert to sasview sum") |
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| 424 | else: |
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[256dfe1] | 425 | translation = _get_translation_table(model_info) |
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[aea515c] | 426 | oldpars = _revert_pars(_rescale_sld(model_info, pars, 1e-6), translation) |
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[6dc78e4] | 427 | oldpars = _trim_vectors(model_info, pars, oldpars) |
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[f247314] | 428 | |
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[bd49c79] | 429 | # Make sure the control parameter is an integer |
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| 430 | if "CONTROL" in oldpars: |
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| 431 | oldpars["CONTROL"] = int(oldpars["CONTROL"]) |
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[3964f92] | 432 | |
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| 433 | # Note: update compare.constrain_pars to match |
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[6d6508e] | 434 | name = model_info.id |
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| 435 | if name in MODELS_WITHOUT_SCALE or model_info.structure_factor: |
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[3964f92] | 436 | if oldpars.pop('scale', 1.0) != 1.0: |
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| 437 | warnings.warn("parameter scale not used in sasview %s"%name) |
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[6d6508e] | 438 | if name in MODELS_WITHOUT_BACKGROUND or model_info.structure_factor: |
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[3964f92] | 439 | if oldpars.pop('background', 0.0) != 0.0: |
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| 440 | warnings.warn("parameter background not used in sasview %s"%name) |
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[17bbadd] | 441 | |
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[f1765a2] | 442 | # Remove magnetic parameters from non-magnetic sasview models |
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| 443 | if name not in MAGNETIC_SASVIEW_MODELS: |
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[40a87fa] | 444 | oldpars = dict((k, v) for k, v in oldpars.items() if ':' not in k) |
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[228cbd3] | 445 | |
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[17bbadd] | 446 | # If it is a product model P*S, then check the individual forms for special |
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| 447 | # cases. Note: despite the structure factor alone not having scale or |
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| 448 | # background, the product model does, so this is below the test for |
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| 449 | # models without scale or background. |
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| 450 | namelist = name.split('*') if '*' in name else [name] |
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| 451 | for name in namelist: |
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[256dfe1] | 452 | if name in MODELS_WITHOUT_VOLFRACTION: |
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| 453 | del oldpars['volfraction'] |
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[f1765a2] | 454 | elif name == 'core_multi_shell': |
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| 455 | # kill extra shells |
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| 456 | for k in range(5, 11): |
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| 457 | oldpars.pop('sld_shell'+str(k), 0) |
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| 458 | oldpars.pop('thick_shell'+str(k), 0) |
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| 459 | oldpars.pop('mtheta:sld'+str(k), 0) |
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| 460 | oldpars.pop('mphi:sld'+str(k), 0) |
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| 461 | oldpars.pop('M0:sld'+str(k), 0) |
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| 462 | _remove_pd(oldpars, 'sld_shell'+str(k), 'sld') |
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| 463 | _remove_pd(oldpars, 'thick_shell'+str(k), 'thickness') |
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| 464 | elif name == 'core_shell_parallelepiped': |
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| 465 | _remove_pd(oldpars, 'rimA', name) |
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[1b49bf8] | 466 | _remove_pd(oldpars, 'rimB', name) |
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| 467 | _remove_pd(oldpars, 'rimC', name) |
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| 468 | elif name == 'hollow_cylinder': |
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| 469 | # now uses radius and thickness |
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[aea515c] | 470 | thickness = oldpars['core_radius'] |
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| 471 | oldpars['radius'] += thickness |
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| 472 | oldpars['radius.width'] *= thickness/oldpars['radius'] |
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| 473 | #elif name in ['mono_gauss_coil', 'poly_gauss_coil']: |
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| 474 | # del oldpars['i_zero'] |
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[f1765a2] | 475 | elif name == 'onion': |
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| 476 | oldpars.pop('n_shells', None) |
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[1b49bf8] | 477 | elif name == 'pearl_necklace': |
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| 478 | _remove_pd(oldpars, 'num_pearls', name) |
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| 479 | _remove_pd(oldpars, 'thick_string', name) |
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| 480 | elif name == 'polymer_micelle': |
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| 481 | if 'ndensity' in oldpars: |
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| 482 | oldpars['ndensity'] *= 1e15 |
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[17bbadd] | 483 | elif name == 'rpa': |
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| 484 | # convert scattering lengths from femtometers to centimeters |
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[8bd7b77] | 485 | for p in "L1", "L2", "L3", "L4": |
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[17bbadd] | 486 | if p in oldpars: oldpars[p] *= 1e-13 |
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[51ec7e8] | 487 | if pars['case_num'] < 2: |
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| 488 | for k in ("a", "b"): |
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| 489 | for p in ("L", "N", "Phi", "b", "v"): |
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| 490 | oldpars.pop(p+k, None) |
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| 491 | for k in "Kab,Kac,Kad,Kbc,Kbd".split(','): |
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| 492 | oldpars.pop(k, None) |
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| 493 | elif pars['case_num'] < 5: |
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| 494 | for k in ("a",): |
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| 495 | for p in ("L", "N", "Phi", "b", "v"): |
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| 496 | oldpars.pop(p+k, None) |
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| 497 | for k in "Kab,Kac,Kad".split(','): |
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| 498 | oldpars.pop(k, None) |
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[1b49bf8] | 499 | elif name == 'spherical_sld': |
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| 500 | oldpars["CONTROL"] -= 1 |
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| 501 | # remove polydispersity from shells |
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| 502 | for k in range(1, 11): |
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| 503 | _remove_pd(oldpars, 'thick_flat'+str(k), 'thickness') |
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| 504 | _remove_pd(oldpars, 'thick_inter'+str(k), 'interface') |
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| 505 | # remove extra shells |
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| 506 | for k in range(int(pars['n_shells']), 11): |
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| 507 | oldpars.pop('sld_flat'+str(k), 0) |
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| 508 | oldpars.pop('thick_flat'+str(k), 0) |
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| 509 | oldpars.pop('thick_inter'+str(k), 0) |
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| 510 | oldpars.pop('func_inter'+str(k), 0) |
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| 511 | oldpars.pop('nu_inter'+str(k), 0) |
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| 512 | elif name == 'stacked_disks': |
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| 513 | _remove_pd(oldpars, 'n_stacking', name) |
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| 514 | elif name == 'teubner_strey': |
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| 515 | # basically redoing the entire Teubner-Strey calculations here. |
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| 516 | volfraction = oldpars.pop('volfraction_a') |
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| 517 | xi = oldpars.pop('xi') |
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| 518 | d = oldpars.pop('d') |
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| 519 | sld_a = oldpars.pop('sld_a') |
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| 520 | sld_b = oldpars.pop('sld_b') |
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| 521 | drho = 1e6*(sld_a - sld_b) # conversion autoscaled these |
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| 522 | k = 2.0*math.pi*xi/d |
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| 523 | a2 = (1.0 + k**2)**2 |
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| 524 | c1 = 2.0 * xi**2 * (1.0 - k**2) |
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| 525 | c2 = xi**4 |
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| 526 | prefactor = 8.0*math.pi*volfraction*(1.0-volfraction)*drho**2*c2/xi |
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| 527 | scale = 1e-4*prefactor |
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| 528 | oldpars['scale'] = a2/scale |
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| 529 | oldpars['c1'] = c1/scale |
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| 530 | oldpars['c2'] = c2/scale |
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[17bbadd] | 531 | |
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[54bcd4a] | 532 | #print("convert from",list(sorted(pars))) |
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| 533 | #print("convert to",list(sorted(oldpars.items()))) |
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[17bbadd] | 534 | return oldpars |
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| 535 | |
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| 536 | def constrain_new_to_old(model_info, pars): |
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[3964f92] | 537 | """ |
---|
| 538 | Restrict parameter values to those that will match sasview. |
---|
| 539 | """ |
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[6d6508e] | 540 | name = model_info.id |
---|
[3964f92] | 541 | # Note: update convert.revert_model to match |
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[6d6508e] | 542 | if name in MODELS_WITHOUT_SCALE or model_info.structure_factor: |
---|
[3964f92] | 543 | pars['scale'] = 1 |
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[6d6508e] | 544 | if name in MODELS_WITHOUT_BACKGROUND or model_info.structure_factor: |
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[0a4628d] | 545 | pars['background'] = 0 |
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[667a6f2] | 546 | # sasview multiplies background by structure factor |
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| 547 | if '*' in name: |
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| 548 | pars['background'] = 0 |
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[9a66e65] | 549 | |
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[f1765a2] | 550 | # Shut off magnetism when comparing non-magnetic sasview models |
---|
| 551 | if name not in MAGNETIC_SASVIEW_MODELS: |
---|
| 552 | suppress_magnetism = False |
---|
| 553 | for key in pars.keys(): |
---|
| 554 | if key.startswith("M0:"): |
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[2c74c11] | 555 | suppress_magnetism = suppress_magnetism or (pars[key] != 0) |
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[f1765a2] | 556 | pars[key] = 0 |
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| 557 | if suppress_magnetism: |
---|
| 558 | warnings.warn("suppressing magnetism for comparison with sasview") |
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| 559 | |
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| 560 | # Shut off theta polydispersity since algorithm has changed |
---|
| 561 | if 'theta_pd_n' in pars: |
---|
| 562 | if pars['theta_pd_n'] != 0: |
---|
| 563 | warnings.warn("suppressing theta polydispersity for comparison with sasview") |
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| 564 | pars['theta_pd_n'] = 0 |
---|
| 565 | |
---|
[17bbadd] | 566 | # If it is a product model P*S, then check the individual forms for special |
---|
| 567 | # cases. Note: despite the structure factor alone not having scale or |
---|
| 568 | # background, the product model does, so this is below the test for |
---|
| 569 | # models without scale or background. |
---|
| 570 | namelist = name.split('*') if '*' in name else [name] |
---|
| 571 | for name in namelist: |
---|
[256dfe1] | 572 | if name in MODELS_WITHOUT_VOLFRACTION: |
---|
| 573 | pars['volfraction'] = 1 |
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[1b49bf8] | 574 | if name == 'core_multi_shell': |
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| 575 | pars['n'] = min(math.ceil(pars['n']), 4) |
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| 576 | elif name == 'gel_fit': |
---|
| 577 | pars['scale'] = 1 |
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[17bbadd] | 578 | elif name == 'line': |
---|
| 579 | pars['scale'] = 1 |
---|
| 580 | pars['background'] = 0 |
---|
[228cbd3] | 581 | elif name == 'mono_gauss_coil': |
---|
[aea515c] | 582 | pars['scale'] = 1 |
---|
[d119f34] | 583 | elif name == 'onion': |
---|
| 584 | pars['n_shells'] = math.ceil(pars['n_shells']) |
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[1b49bf8] | 585 | elif name == 'pearl_necklace': |
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| 586 | pars['string_thickness_pd_n'] = 0 |
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| 587 | pars['number_of_pearls_pd_n'] = 0 |
---|
| 588 | elif name == 'poly_gauss_coil': |
---|
[aea515c] | 589 | pars['scale'] = 1 |
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[1b49bf8] | 590 | elif name == 'rpa': |
---|
| 591 | pars['case_num'] = int(pars['case_num']) |
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[a0494e9] | 592 | elif name == 'spherical_sld': |
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[0dd4199] | 593 | pars['n_shells'] = math.ceil(pars['n_shells']) |
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[54bcd4a] | 594 | pars['n_steps'] = math.ceil(pars['n_steps']) |
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[51241113] | 595 | for k in range(1, 11): |
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[54bcd4a] | 596 | pars['shape%d'%k] = math.trunc(pars['shape%d'%k]+0.5) |
---|
[51241113] | 597 | for k in range(2, 11): |
---|
[54bcd4a] | 598 | pars['thickness%d_pd_n'%k] = 0 |
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| 599 | pars['interface%d_pd_n'%k] = 0 |
---|
[1b49bf8] | 600 | elif name == 'teubner_strey': |
---|
| 601 | pars['scale'] = 1 |
---|
[aea515c] | 602 | if pars['volfraction_a'] > 0.5: |
---|
| 603 | pars['volfraction_a'] = 1.0 - pars['volfraction_a'] |
---|
| 604 | elif name == 'unified_power_Rg': |
---|
| 605 | pars['level'] = int(pars['level']) |
---|
| 606 | |
---|
| 607 | def _check_one(name, seed=None): |
---|
| 608 | """ |
---|
| 609 | Generate a random set of parameters for *name*, and check that they can |
---|
| 610 | be converted back to SasView 3.x and forward again to sasmodels. Raises |
---|
| 611 | an error if the parameters are changed. |
---|
| 612 | """ |
---|
| 613 | from . import compare |
---|
| 614 | |
---|
| 615 | model_info = load_model_info(name) |
---|
| 616 | |
---|
| 617 | old_name = revert_name(model_info) |
---|
| 618 | if old_name is None: |
---|
| 619 | return |
---|
| 620 | |
---|
| 621 | pars = compare.get_pars(model_info, use_demo=False) |
---|
[32398dc] | 622 | if seed is not None: |
---|
| 623 | np.random.seed(seed) |
---|
| 624 | pars = compare.randomize_pars(model_info, pars) |
---|
[aea515c] | 625 | if name == "teubner_strey": |
---|
| 626 | # T-S model is underconstrained, so fix the assumptions. |
---|
| 627 | pars['sld_a'], pars['sld_b'] = 1.0, 0.0 |
---|
| 628 | compare.constrain_pars(model_info, pars) |
---|
| 629 | constrain_new_to_old(model_info, pars) |
---|
| 630 | old_pars = revert_pars(model_info, pars) |
---|
| 631 | new_name, new_pars = convert_model(old_name, old_pars, use_underscore=True) |
---|
| 632 | if 1: |
---|
| 633 | print("==== %s in ====="%name) |
---|
| 634 | print(str(compare.parlist(model_info, pars, True))) |
---|
| 635 | print("==== %s ====="%old_name) |
---|
| 636 | for k, v in sorted(old_pars.items()): |
---|
| 637 | print(k, v) |
---|
| 638 | print("==== %s out ====="%new_name) |
---|
| 639 | print(str(compare.parlist(model_info, new_pars, True))) |
---|
[e65c3ba] | 640 | assert name == new_name, "%r != %r"%(name, new_name) |
---|
[aea515c] | 641 | for k, v in new_pars.items(): |
---|
| 642 | assert k in pars, "%s: %r appeared from conversion"%(name, k) |
---|
| 643 | if isinstance(v, float): |
---|
[e65c3ba] | 644 | assert abs(v-pars[k]) <= abs(1e-12*v), \ |
---|
| 645 | "%s: %r %s != %s"%(name, k, v, pars[k]) |
---|
[aea515c] | 646 | else: |
---|
| 647 | assert v == pars[k], "%s: %r %s != %s"%(name, k, v, pars[k]) |
---|
| 648 | for k, v in pars.items(): |
---|
| 649 | assert k in pars, "%s: %r not converted"%(name, k) |
---|
[256dfe1] | 650 | |
---|
[aea515c] | 651 | def test_backward_forward(): |
---|
| 652 | from .core import list_models |
---|
[a69d8cd] | 653 | L = lambda name: _check_one(name, seed=1) |
---|
[aea515c] | 654 | for name in list_models('all'): |
---|
[a69d8cd] | 655 | yield L, name |
---|