| 1 | import copy |
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| 2 | |
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| 3 | from PyQt5 import QtCore |
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| 4 | from PyQt5 import QtGui |
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| 5 | from PyQt5 import QtWidgets |
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| 6 | |
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| 7 | import numpy |
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| 8 | |
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| 9 | from sas.qtgui.Plotting.PlotterData import Data1D |
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| 10 | from sas.qtgui.Plotting.PlotterData import Data2D |
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| 11 | |
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| 12 | model_header_captions = ['Parameter', 'Value', 'Min', 'Max', 'Units'] |
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| 13 | |
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| 14 | model_header_tooltips = ['Select parameter for fitting', |
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| 15 | 'Enter parameter value', |
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| 16 | 'Enter minimum value for parameter', |
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| 17 | 'Enter maximum value for parameter', |
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| 18 | 'Unit of the parameter'] |
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| 19 | |
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| 20 | poly_header_captions = ['Parameter', 'PD[ratio]', 'Min', 'Max', 'Npts', 'Nsigs', |
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| 21 | 'Function', 'Filename'] |
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| 22 | |
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| 23 | poly_header_tooltips = ['Select parameter for fitting', |
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| 24 | 'Enter polydispersity ratio (STD/mean). ' |
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| 25 | 'STD: standard deviation from the mean value', |
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| 26 | 'Enter minimum value for parameter', |
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| 27 | 'Enter maximum value for parameter', |
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| 28 | 'Enter number of points for parameter', |
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| 29 | 'Enter number of sigmas parameter', |
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| 30 | 'Select distribution function', |
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| 31 | 'Select filename with user-definable distribution'] |
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| 32 | |
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| 33 | error_tooltip = 'Error value for fitted parameter' |
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| 34 | header_error_caption = 'Error' |
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| 35 | |
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| 36 | def replaceShellName(param_name, value): |
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| 37 | """ |
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| 38 | Updates parameter name from <param_name>[n_shell] to <param_name>value |
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| 39 | """ |
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| 40 | assert '[' in param_name |
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| 41 | return param_name[:param_name.index('[')]+str(value) |
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| 42 | |
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| 43 | def getIterParams(model): |
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| 44 | """ |
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| 45 | Returns a list of all multi-shell parameters in 'model' |
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| 46 | """ |
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| 47 | return list([par for par in model.iq_parameters if "[" in par.name]) |
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| 48 | |
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| 49 | def getMultiplicity(model): |
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| 50 | """ |
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| 51 | Finds out if 'model' has multishell parameters. |
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| 52 | If so, returns the name of the counter parameter and the number of shells |
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| 53 | """ |
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| 54 | iter_params = getIterParams(model) |
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| 55 | param_name = "" |
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| 56 | param_length = 0 |
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| 57 | if iter_params: |
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| 58 | param_length = iter_params[0].length |
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| 59 | param_name = iter_params[0].length_control |
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| 60 | if param_name is None and '[' in iter_params[0].name: |
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| 61 | param_name = iter_params[0].name[:iter_params[0].name.index('[')] |
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| 62 | return (param_name, param_length) |
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| 63 | |
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| 64 | def addParametersToModel(parameters, kernel_module, is2D): |
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| 65 | """ |
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| 66 | Update local ModelModel with sasmodel parameters |
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| 67 | """ |
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| 68 | multishell_parameters = getIterParams(parameters) |
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| 69 | multishell_param_name, _ = getMultiplicity(parameters) |
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| 70 | |
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| 71 | if is2D: |
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| 72 | params = [p for p in parameters.kernel_parameters if p.type != 'magnetic'] |
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| 73 | else: |
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| 74 | params = parameters.iq_parameters |
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| 75 | item = [] |
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| 76 | for param in params: |
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| 77 | # don't include shell parameters |
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| 78 | if param.name == multishell_param_name: |
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| 79 | continue |
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| 80 | # Modify parameter name from <param>[n] to <param>1 |
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| 81 | item_name = param.name |
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| 82 | if param in multishell_parameters: |
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| 83 | continue |
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| 84 | # item_name = replaceShellName(param.name, 1) |
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| 85 | |
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| 86 | item1 = QtGui.QStandardItem(item_name) |
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| 87 | item1.setCheckable(True) |
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| 88 | item1.setEditable(False) |
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| 89 | # item_err = QtGui.QStandardItem() |
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| 90 | # check for polydisp params |
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| 91 | if param.polydisperse: |
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| 92 | poly_item = QtGui.QStandardItem("Polydispersity") |
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| 93 | poly_item.setEditable(False) |
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| 94 | item1_1 = QtGui.QStandardItem("Distribution") |
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| 95 | item1_1.setEditable(False) |
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| 96 | # Find param in volume_params |
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| 97 | for p in parameters.form_volume_parameters: |
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| 98 | if p.name != param.name: |
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| 99 | continue |
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| 100 | width = kernel_module.getParam(p.name+'.width') |
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| 101 | type = kernel_module.getParam(p.name+'.type') |
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| 102 | |
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| 103 | item1_2 = QtGui.QStandardItem(str(width)) |
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| 104 | item1_2.setEditable(False) |
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| 105 | item1_3 = QtGui.QStandardItem() |
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| 106 | item1_3.setEditable(False) |
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| 107 | item1_4 = QtGui.QStandardItem() |
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| 108 | item1_4.setEditable(False) |
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| 109 | item1_5 = QtGui.QStandardItem(type) |
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| 110 | item1_5.setEditable(False) |
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| 111 | poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) |
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| 112 | break |
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| 113 | # Add the polydisp item as a child |
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| 114 | item1.appendRow([poly_item]) |
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| 115 | # Param values |
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| 116 | item2 = QtGui.QStandardItem(str(param.default)) |
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| 117 | # TODO: the error column. |
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| 118 | # Either add a proxy model or a custom view delegate |
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| 119 | #item_err = QtGui.QStandardItem() |
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| 120 | item3 = QtGui.QStandardItem(str(param.limits[0])) |
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| 121 | item4 = QtGui.QStandardItem(str(param.limits[1])) |
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| 122 | item5 = QtGui.QStandardItem(param.units) |
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| 123 | item5.setEditable(False) |
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| 124 | item.append([item1, item2, item3, item4, item5]) |
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| 125 | return item |
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| 126 | |
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| 127 | def addSimpleParametersToModel(parameters, is2D): |
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| 128 | """ |
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| 129 | Update local ModelModel with sasmodel parameters |
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| 130 | """ |
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| 131 | if is2D: |
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| 132 | params = [p for p in parameters.kernel_parameters if p.type != 'magnetic'] |
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| 133 | else: |
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| 134 | params = parameters.iq_parameters |
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| 135 | item = [] |
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| 136 | for param in params: |
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| 137 | # Create the top level, checkable item |
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| 138 | item_name = param.name |
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| 139 | item1 = QtGui.QStandardItem(item_name) |
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| 140 | item1.setCheckable(True) |
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| 141 | item1.setEditable(False) |
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| 142 | # Param values |
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| 143 | # TODO: add delegate for validation of cells |
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| 144 | item2 = QtGui.QStandardItem(str(param.default)) |
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| 145 | item4 = QtGui.QStandardItem(str(param.limits[0])) |
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| 146 | item5 = QtGui.QStandardItem(str(param.limits[1])) |
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| 147 | item6 = QtGui.QStandardItem(param.units) |
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| 148 | item6.setEditable(False) |
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| 149 | item.append([item1, item2, item4, item5, item6]) |
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| 150 | return item |
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| 151 | |
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| 152 | def addCheckedListToModel(model, param_list): |
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| 153 | """ |
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| 154 | Add a QItem to model. Makes the QItem checkable |
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| 155 | """ |
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| 156 | assert isinstance(model, QtGui.QStandardItemModel) |
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| 157 | item_list = [QtGui.QStandardItem(item) for item in param_list] |
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| 158 | item_list[0].setCheckable(True) |
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| 159 | model.appendRow(item_list) |
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| 160 | |
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| 161 | def addHeadersToModel(model): |
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| 162 | """ |
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| 163 | Adds predefined headers to the model |
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| 164 | """ |
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| 165 | for i, item in enumerate(model_header_captions): |
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| 166 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 167 | |
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| 168 | model.header_tooltips = copy.copy(model_header_tooltips) |
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| 169 | |
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| 170 | def addErrorHeadersToModel(model): |
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| 171 | """ |
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| 172 | Adds predefined headers to the model |
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| 173 | """ |
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| 174 | model_header_error_captions = copy.copy(model_header_captions) |
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| 175 | model_header_error_captions.insert(2, header_error_caption) |
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| 176 | for i, item in enumerate(model_header_error_captions): |
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| 177 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 178 | |
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| 179 | model_header_error_tooltips = copy.copy(model_header_tooltips) |
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| 180 | model_header_error_tooltips.insert(2, error_tooltip) |
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| 181 | model.header_tooltips = copy.copy(model_header_error_tooltips) |
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| 182 | |
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| 183 | def addPolyHeadersToModel(model): |
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| 184 | """ |
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| 185 | Adds predefined headers to the model |
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| 186 | """ |
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| 187 | for i, item in enumerate(poly_header_captions): |
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| 188 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 189 | |
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| 190 | model.header_tooltips = copy.copy(poly_header_tooltips) |
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| 191 | |
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| 192 | |
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| 193 | def addErrorPolyHeadersToModel(model): |
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| 194 | """ |
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| 195 | Adds predefined headers to the model |
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| 196 | """ |
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| 197 | poly_header_error_captions = copy.copy(poly_header_captions) |
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| 198 | poly_header_error_captions.insert(2, header_error_caption) |
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| 199 | for i, item in enumerate(poly_header_error_captions): |
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| 200 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 201 | |
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| 202 | poly_header_error_tooltips = copy.copy(poly_header_tooltips) |
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| 203 | poly_header_error_tooltips.insert(2, error_tooltip) |
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| 204 | model.header_tooltips = copy.copy(poly_header_error_tooltips) |
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| 205 | |
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| 206 | def addShellsToModel(parameters, model, index): |
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| 207 | """ |
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| 208 | Find out multishell parameters and update the model with the requested number of them |
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| 209 | """ |
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| 210 | multishell_parameters = getIterParams(parameters) |
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| 211 | |
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| 212 | for i in range(index): |
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| 213 | for par in multishell_parameters: |
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| 214 | # Create the name: <param>[<i>], e.g. "sld1" for parameter "sld[n]" |
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| 215 | param_name = replaceShellName(par.name, i+1) |
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| 216 | item1 = QtGui.QStandardItem(param_name) |
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| 217 | item1.setCheckable(True) |
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| 218 | # check for polydisp params |
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| 219 | if par.polydisperse: |
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| 220 | poly_item = QtGui.QStandardItem("Polydispersity") |
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| 221 | item1_1 = QtGui.QStandardItem("Distribution") |
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| 222 | # Find param in volume_params |
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| 223 | for p in parameters.form_volume_parameters: |
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| 224 | if p.name != par.name: |
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| 225 | continue |
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| 226 | item1_2 = QtGui.QStandardItem(str(p.default)) |
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| 227 | item1_3 = QtGui.QStandardItem(str(p.limits[0])) |
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| 228 | item1_4 = QtGui.QStandardItem(str(p.limits[1])) |
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| 229 | item1_5 = QtGui.QStandardItem(p.units) |
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| 230 | poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) |
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| 231 | break |
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| 232 | item1.appendRow([poly_item]) |
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| 233 | |
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| 234 | item2 = QtGui.QStandardItem(str(par.default)) |
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| 235 | item3 = QtGui.QStandardItem(str(par.limits[0])) |
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| 236 | item4 = QtGui.QStandardItem(str(par.limits[1])) |
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| 237 | item5 = QtGui.QStandardItem(par.units) |
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| 238 | model.appendRow([item1, item2, item3, item4, item5]) |
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| 239 | |
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| 240 | def calculateChi2(reference_data, current_data): |
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| 241 | """ |
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| 242 | Calculate Chi2 value between two sets of data |
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| 243 | """ |
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| 244 | |
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| 245 | # WEIGHING INPUT |
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| 246 | #from sas.sasgui.perspectives.fitting.utils import get_weight |
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| 247 | #flag = self.get_weight_flag() |
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| 248 | #weight = get_weight(data=self.data, is2d=self._is_2D(), flag=flag) |
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| 249 | chisqr = None |
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| 250 | if reference_data is None: |
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| 251 | return chisqr |
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| 252 | |
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| 253 | # temporary default values for index and weight |
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| 254 | index = None |
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| 255 | weight = None |
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| 256 | |
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| 257 | # Get data: data I, theory I, and data dI in order |
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| 258 | if isinstance(reference_data, Data2D): |
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| 259 | if index is None: |
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| 260 | index = numpy.ones(len(current_data.data), dtype=bool) |
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| 261 | if weight is not None: |
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| 262 | current_data.err_data = weight |
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| 263 | # get rid of zero error points |
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| 264 | index = index & (current_data.err_data != 0) |
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| 265 | index = index & (numpy.isfinite(current_data.data)) |
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| 266 | fn = current_data.data[index] |
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| 267 | gn = reference_data.data[index] |
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| 268 | en = current_data.err_data[index] |
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| 269 | else: |
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| 270 | # 1 d theory from model_thread is only in the range of index |
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| 271 | if index is None: |
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| 272 | index = numpy.ones(len(current_data.y), dtype=bool) |
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| 273 | if weight is not None: |
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| 274 | current_data.dy = weight |
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| 275 | if current_data.dy is None or current_data.dy == []: |
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| 276 | dy = numpy.ones(len(current_data.y)) |
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| 277 | else: |
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| 278 | ## Set consistently w/AbstractFitengine: |
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| 279 | # But this should be corrected later. |
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| 280 | dy = copy.deepcopy(current_data.dy) |
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| 281 | dy[dy == 0] = 1 |
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| 282 | fn = current_data.y[index] |
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| 283 | gn = reference_data.y |
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| 284 | en = dy[index] |
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| 285 | # Calculate the residual |
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| 286 | try: |
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| 287 | res = (fn - gn) / en |
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| 288 | except ValueError: |
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| 289 | #print "Chi2 calculations: Unmatched lengths %s, %s, %s" % (len(fn), len(gn), len(en)) |
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| 290 | return None |
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| 291 | |
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| 292 | residuals = res[numpy.isfinite(res)] |
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| 293 | chisqr = numpy.average(residuals * residuals) |
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| 294 | |
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| 295 | return chisqr |
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| 296 | |
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| 297 | def residualsData1D(reference_data, current_data): |
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| 298 | """ |
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| 299 | Calculate the residuals for difference of two Data1D sets |
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| 300 | """ |
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| 301 | # temporary default values for index and weight |
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| 302 | index = None |
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| 303 | weight = None |
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| 304 | |
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| 305 | # 1d theory from model_thread is only in the range of index |
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| 306 | if current_data.dy is None or current_data.dy == []: |
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| 307 | dy = numpy.ones(len(current_data.y)) |
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| 308 | else: |
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| 309 | dy = weight if weight is not None else numpy.ones(len(current_data.y)) |
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| 310 | dy[dy == 0] = 1 |
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| 311 | fn = current_data.y[index][0] |
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| 312 | gn = reference_data.y |
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| 313 | en = dy[index][0] |
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| 314 | # build residuals |
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| 315 | residuals = Data1D() |
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| 316 | if len(fn) == len(gn): |
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| 317 | y = (fn - gn)/en |
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| 318 | residuals.y = -y |
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| 319 | else: |
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| 320 | # TODO: fix case where applying new data from file on top of existing model data |
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| 321 | try: |
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| 322 | y = (fn - gn[index][0]) / en |
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| 323 | residuals.y = y |
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| 324 | except ValueError: |
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| 325 | # value errors may show up every once in a while for malformed columns, |
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| 326 | # just reuse what's there already |
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| 327 | pass |
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| 328 | |
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| 329 | residuals.x = current_data.x[index][0] |
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| 330 | residuals.dy = numpy.ones(len(residuals.y)) |
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| 331 | residuals.dx = None |
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| 332 | residuals.dxl = None |
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| 333 | residuals.dxw = None |
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| 334 | residuals.ytransform = 'y' |
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| 335 | # For latter scale changes |
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| 336 | residuals.xaxis('\\rm{Q} ', 'A^{-1}') |
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| 337 | residuals.yaxis('\\rm{Residuals} ', 'normalized') |
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| 338 | |
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| 339 | return residuals |
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| 340 | |
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| 341 | def residualsData2D(reference_data, current_data): |
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| 342 | """ |
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| 343 | Calculate the residuals for difference of two Data2D sets |
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| 344 | """ |
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| 345 | # temporary default values for index and weight |
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| 346 | # index = None |
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| 347 | weight = None |
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| 348 | |
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| 349 | # build residuals |
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| 350 | residuals = Data2D() |
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| 351 | # Not for trunk the line below, instead use the line above |
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| 352 | current_data.clone_without_data(len(current_data.data), residuals) |
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| 353 | residuals.data = None |
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| 354 | fn = current_data.data |
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| 355 | gn = reference_data.data |
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| 356 | en = current_data.err_data if weight is None else weight |
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| 357 | residuals.data = (fn - gn) / en |
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| 358 | residuals.qx_data = current_data.qx_data |
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| 359 | residuals.qy_data = current_data.qy_data |
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| 360 | residuals.q_data = current_data.q_data |
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| 361 | residuals.err_data = numpy.ones(len(residuals.data)) |
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| 362 | residuals.xmin = min(residuals.qx_data) |
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| 363 | residuals.xmax = max(residuals.qx_data) |
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| 364 | residuals.ymin = min(residuals.qy_data) |
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| 365 | residuals.ymax = max(residuals.qy_data) |
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| 366 | residuals.q_data = current_data.q_data |
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| 367 | residuals.mask = current_data.mask |
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| 368 | residuals.scale = 'linear' |
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| 369 | # check the lengths |
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| 370 | if len(residuals.data) != len(residuals.q_data): |
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| 371 | return None |
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| 372 | return residuals |
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| 373 | |
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| 374 | def plotResiduals(reference_data, current_data): |
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| 375 | """ |
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| 376 | Create Data1D/Data2D with residuals, ready for plotting |
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| 377 | """ |
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| 378 | data_copy = copy.deepcopy(current_data) |
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| 379 | # Get data: data I, theory I, and data dI in order |
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| 380 | method_name = current_data.__class__.__name__ |
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| 381 | residuals_dict = {"Data1D": residualsData1D, |
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| 382 | "Data2D": residualsData2D} |
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| 383 | |
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| 384 | residuals = residuals_dict[method_name](reference_data, data_copy) |
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| 385 | |
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| 386 | theory_name = str(current_data.name.split()[0]) |
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| 387 | residuals.name = "Residuals for " + str(theory_name) + "[" + \ |
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| 388 | str(reference_data.filename) + "]" |
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| 389 | residuals.title = residuals.name |
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| 390 | residuals.ytransform = 'y' |
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| 391 | |
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| 392 | # when 2 data have the same id override the 1 st plotted |
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| 393 | # include the last part if keeping charts for separate models is required |
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| 394 | residuals.id = "res" + str(reference_data.id) # + str(theory_name) |
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| 395 | # group_id specify on which panel to plot this data |
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| 396 | group_id = reference_data.group_id |
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| 397 | residuals.group_id = "res" + str(group_id) |
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| 398 | |
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| 399 | # Symbol |
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| 400 | residuals.symbol = 0 |
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| 401 | residuals.hide_error = False |
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| 402 | |
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| 403 | return residuals |
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| 404 | |
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| 405 | def binary_encode(i, digits): |
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| 406 | return [i >> d & 1 for d in range(digits)] |
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| 407 | |
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| 408 | def getWeight(data, is2d, flag=None): |
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| 409 | """ |
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| 410 | Received flag and compute error on data. |
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| 411 | :param flag: flag to transform error of data. |
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| 412 | """ |
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| 413 | weight = None |
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| 414 | if is2d: |
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| 415 | dy_data = data.err_data |
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| 416 | data = data.data |
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| 417 | else: |
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| 418 | dy_data = data.dy |
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| 419 | data = data.y |
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| 420 | |
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| 421 | if flag == 0: |
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| 422 | weight = numpy.ones_like(data) |
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| 423 | elif flag == 1: |
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| 424 | weight = dy_data |
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| 425 | elif flag == 2: |
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| 426 | weight = numpy.sqrt(numpy.abs(data)) |
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| 427 | elif flag == 3: |
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| 428 | weight = numpy.abs(data) |
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| 429 | return weight |
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| 430 | |
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| 431 | def updateKernelWithResults(kernel, results): |
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| 432 | """ |
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| 433 | Takes model kernel and applies results dict to its parameters, |
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| 434 | returning the modified (deep) copy of the kernel. |
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| 435 | """ |
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| 436 | assert(isinstance(results, dict)) |
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| 437 | local_kernel = copy.deepcopy(kernel) |
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| 438 | |
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| 439 | for parameter in results.keys(): |
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| 440 | # Update the parameter value - note: this supports +/-inf as well |
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| 441 | local_kernel.setParam(parameter, results[parameter][0]) |
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| 442 | |
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| 443 | return local_kernel |
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| 444 | |
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| 445 | |
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| 446 | def getStandardParam(model=None): |
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| 447 | """ |
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| 448 | Returns a list with standard parameters for the current model |
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| 449 | """ |
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| 450 | param = [] |
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| 451 | num_rows = model.rowCount() |
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| 452 | if num_rows < 1: |
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| 453 | return None |
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| 454 | |
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| 455 | for row in range(num_rows): |
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| 456 | param_name = model.item(row, 0).text() |
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| 457 | checkbox_state = model.item(row,0).checkState() == QtCore.Qt.Checked |
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| 458 | value= model.item(row, 1).text() |
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| 459 | column_shift = 0 |
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| 460 | if model.columnCount() == 5: # no error column |
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| 461 | error_state = False |
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| 462 | error_value = 0.0 |
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| 463 | else: |
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| 464 | error_state = True |
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| 465 | error_value = model.item(row, 2).text() |
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| 466 | column_shift = 1 |
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| 467 | min_state = True |
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| 468 | max_state = True |
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| 469 | min_value = model.item(row, 2+column_shift).text() |
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| 470 | max_value = model.item(row, 3+column_shift).text() |
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| 471 | unit = "" |
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| 472 | if model.item(row, 4+column_shift) is not None: |
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| 473 | unit = model.item(row, 4+column_shift).text() |
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| 474 | |
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| 475 | param.append([checkbox_state, param_name, value, "", |
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| 476 | [error_state, error_value], |
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| 477 | [min_state, min_value], |
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| 478 | [max_state, max_value], unit]) |
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| 479 | |
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| 480 | return param |
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| 481 | |
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| 482 | def getOrientationParam(kernel_module=None): |
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| 483 | """ |
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| 484 | Get the dictionary with orientation parameters |
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| 485 | """ |
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| 486 | param = [] |
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| 487 | if kernel_module is None: |
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| 488 | return None |
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| 489 | for param_name in list(kernel_module.params.keys()): |
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| 490 | name = param_name |
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| 491 | value = kernel_module.params[param_name] |
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| 492 | min_state = True |
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| 493 | max_state = True |
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| 494 | error_state = False |
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| 495 | error_value = 0.0 |
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| 496 | checkbox_state = True #?? |
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| 497 | details = kernel_module.details[param_name] #[unit, mix, max] |
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| 498 | param.append([checkbox_state, name, value, "", |
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| 499 | [error_state, error_value], |
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| 500 | [min_state, details[1]], |
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| 501 | [max_state, details[2]], details[0]]) |
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| 502 | |
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| 503 | return param |
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