| 1 | from copy import deepcopy |
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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 | params = parameters.iqxy_parameters if is2D else parameters.iq_parameters |
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| 71 | item = [] |
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| 72 | for param in params: |
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| 73 | # don't include shell parameters |
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| 74 | if param.name == multishell_param_name: |
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| 75 | continue |
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| 76 | # Modify parameter name from <param>[n] to <param>1 |
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| 77 | item_name = param.name |
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| 78 | if param in multishell_parameters: |
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| 79 | continue |
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| 80 | # item_name = replaceShellName(param.name, 1) |
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| 81 | |
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| 82 | item1 = QtGui.QStandardItem(item_name) |
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| 83 | item1.setCheckable(True) |
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| 84 | item1.setEditable(False) |
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| 85 | # item_err = QtGui.QStandardItem() |
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| 86 | # check for polydisp params |
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| 87 | if param.polydisperse: |
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| 88 | poly_item = QtGui.QStandardItem("Polydispersity") |
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| 89 | poly_item.setEditable(False) |
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| 90 | item1_1 = QtGui.QStandardItem("Distribution") |
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| 91 | item1_1.setEditable(False) |
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| 92 | # Find param in volume_params |
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| 93 | for p in parameters.form_volume_parameters: |
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| 94 | if p.name != param.name: |
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| 95 | continue |
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| 96 | width = kernel_module.getParam(p.name+'.width') |
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| 97 | type = kernel_module.getParam(p.name+'.type') |
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| 98 | |
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| 99 | item1_2 = QtGui.QStandardItem(str(width)) |
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| 100 | item1_2.setEditable(False) |
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| 101 | item1_3 = QtGui.QStandardItem() |
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| 102 | item1_3.setEditable(False) |
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| 103 | item1_4 = QtGui.QStandardItem() |
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| 104 | item1_4.setEditable(False) |
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| 105 | item1_5 = QtGui.QStandardItem(type) |
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| 106 | item1_5.setEditable(False) |
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| 107 | poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) |
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| 108 | break |
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| 109 | # Add the polydisp item as a child |
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| 110 | item1.appendRow([poly_item]) |
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| 111 | # Param values |
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| 112 | item2 = QtGui.QStandardItem(str(param.default)) |
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| 113 | # TODO: the error column. |
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| 114 | # Either add a proxy model or a custom view delegate |
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| 115 | #item_err = QtGui.QStandardItem() |
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| 116 | item3 = QtGui.QStandardItem(str(param.limits[0])) |
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| 117 | item4 = QtGui.QStandardItem(str(param.limits[1])) |
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| 118 | item5 = QtGui.QStandardItem(param.units) |
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| 119 | item5.setEditable(False) |
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| 120 | item.append([item1, item2, item3, item4, item5]) |
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| 121 | return item |
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| 122 | |
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| 123 | def addSimpleParametersToModel(parameters, is2D): |
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| 124 | """ |
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| 125 | Update local ModelModel with sasmodel parameters |
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| 126 | """ |
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| 127 | params = parameters.iqxy_parameters if is2D else parameters.iq_parameters |
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| 128 | item = [] |
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| 129 | for param in params: |
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| 130 | # Create the top level, checkable item |
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| 131 | item_name = param.name |
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| 132 | item1 = QtGui.QStandardItem(item_name) |
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| 133 | item1.setCheckable(True) |
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| 134 | item1.setEditable(False) |
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| 135 | # Param values |
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| 136 | # TODO: add delegate for validation of cells |
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| 137 | item2 = QtGui.QStandardItem(str(param.default)) |
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| 138 | item4 = QtGui.QStandardItem(str(param.limits[0])) |
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| 139 | item5 = QtGui.QStandardItem(str(param.limits[1])) |
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| 140 | item6 = QtGui.QStandardItem(param.units) |
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| 141 | item6.setEditable(False) |
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| 142 | item.append([item1, item2, item4, item5, item6]) |
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| 143 | return item |
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| 144 | |
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| 145 | def addCheckedListToModel(model, param_list): |
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| 146 | """ |
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| 147 | Add a QItem to model. Makes the QItem checkable |
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| 148 | """ |
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| 149 | assert isinstance(model, QtGui.QStandardItemModel) |
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| 150 | item_list = [QtGui.QStandardItem(item) for item in param_list] |
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| 151 | item_list[0].setCheckable(True) |
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| 152 | model.appendRow(item_list) |
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| 153 | |
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| 154 | def addHeadersToModel(model): |
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| 155 | """ |
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| 156 | Adds predefined headers to the model |
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| 157 | """ |
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| 158 | for i, item in enumerate(model_header_captions): |
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| 159 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 160 | |
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| 161 | model.header_tooltips = model_header_tooltips |
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| 162 | |
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| 163 | def addErrorHeadersToModel(model): |
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| 164 | """ |
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| 165 | Adds predefined headers to the model |
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| 166 | """ |
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| 167 | model_header_error_captions = model_header_captions |
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| 168 | model_header_error_captions.insert(2, header_error_caption) |
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| 169 | for i, item in enumerate(model_header_error_captions): |
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| 170 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 171 | |
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| 172 | model_header_error_tooltips = model_header_tooltips |
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| 173 | model_header_error_tooltips.insert(2, error_tooltip) |
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| 174 | model.header_tooltips = model_header_error_tooltips |
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| 175 | |
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| 176 | def addPolyHeadersToModel(model): |
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| 177 | """ |
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| 178 | Adds predefined headers to the model |
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| 179 | """ |
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| 180 | for i, item in enumerate(poly_header_captions): |
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| 181 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 182 | |
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| 183 | model.header_tooltips = poly_header_tooltips |
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| 184 | |
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| 185 | |
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| 186 | def addErrorPolyHeadersToModel(model): |
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| 187 | """ |
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| 188 | Adds predefined headers to the model |
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| 189 | """ |
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| 190 | poly_header_error_captions = poly_header_captions |
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| 191 | poly_header_error_captions.insert(2, header_error_caption) |
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| 192 | for i, item in enumerate(poly_header_error_captions): |
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| 193 | model.setHeaderData(i, QtCore.Qt.Horizontal, item) |
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| 194 | |
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| 195 | poly_header_error_tooltips = poly_header_tooltips |
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| 196 | poly_header_error_tooltips.insert(2, error_tooltip) |
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| 197 | model.header_tooltips = poly_header_error_tooltips |
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| 198 | |
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| 199 | def addShellsToModel(parameters, model, index): |
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| 200 | """ |
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| 201 | Find out multishell parameters and update the model with the requested number of them |
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| 202 | """ |
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| 203 | multishell_parameters = getIterParams(parameters) |
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| 204 | |
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| 205 | for i in range(index): |
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| 206 | for par in multishell_parameters: |
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| 207 | # Create the name: <param>[<i>], e.g. "sld1" for parameter "sld[n]" |
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| 208 | param_name = replaceShellName(par.name, i+1) |
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| 209 | item1 = QtGui.QStandardItem(param_name) |
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| 210 | item1.setCheckable(True) |
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| 211 | # check for polydisp params |
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| 212 | if par.polydisperse: |
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| 213 | poly_item = QtGui.QStandardItem("Polydispersity") |
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| 214 | item1_1 = QtGui.QStandardItem("Distribution") |
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| 215 | # Find param in volume_params |
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| 216 | for p in parameters.form_volume_parameters: |
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| 217 | if p.name != par.name: |
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| 218 | continue |
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| 219 | item1_2 = QtGui.QStandardItem(str(p.default)) |
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| 220 | item1_3 = QtGui.QStandardItem(str(p.limits[0])) |
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| 221 | item1_4 = QtGui.QStandardItem(str(p.limits[1])) |
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| 222 | item1_5 = QtGui.QStandardItem(p.units) |
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| 223 | poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) |
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| 224 | break |
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| 225 | item1.appendRow([poly_item]) |
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| 226 | |
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| 227 | item2 = QtGui.QStandardItem(str(par.default)) |
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| 228 | item3 = QtGui.QStandardItem(str(par.limits[0])) |
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| 229 | item4 = QtGui.QStandardItem(str(par.limits[1])) |
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| 230 | item5 = QtGui.QStandardItem(par.units) |
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| 231 | model.appendRow([item1, item2, item3, item4, item5]) |
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| 232 | |
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| 233 | def calculateChi2(reference_data, current_data): |
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| 234 | """ |
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| 235 | Calculate Chi2 value between two sets of data |
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| 236 | """ |
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| 237 | |
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| 238 | # WEIGHING INPUT |
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| 239 | #from sas.sasgui.perspectives.fitting.utils import get_weight |
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| 240 | #flag = self.get_weight_flag() |
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| 241 | #weight = get_weight(data=self.data, is2d=self._is_2D(), flag=flag) |
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| 242 | chisqr = None |
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| 243 | if reference_data is None: |
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| 244 | return chisqr |
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| 245 | |
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| 246 | # temporary default values for index and weight |
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| 247 | index = None |
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| 248 | weight = None |
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| 249 | |
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| 250 | # Get data: data I, theory I, and data dI in order |
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| 251 | if isinstance(reference_data, Data2D): |
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| 252 | if index is None: |
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| 253 | index = numpy.ones(len(current_data.data), dtype=bool) |
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| 254 | if weight is not None: |
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| 255 | current_data.err_data = weight |
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| 256 | # get rid of zero error points |
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| 257 | index = index & (current_data.err_data != 0) |
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| 258 | index = index & (numpy.isfinite(current_data.data)) |
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| 259 | fn = current_data.data[index] |
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| 260 | gn = reference_data.data[index] |
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| 261 | en = current_data.err_data[index] |
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| 262 | else: |
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| 263 | # 1 d theory from model_thread is only in the range of index |
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| 264 | if index is None: |
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| 265 | index = numpy.ones(len(current_data.y), dtype=bool) |
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| 266 | if weight is not None: |
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| 267 | current_data.dy = weight |
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| 268 | if current_data.dy is None or current_data.dy == []: |
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| 269 | dy = numpy.ones(len(current_data.y)) |
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| 270 | else: |
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| 271 | ## Set consistently w/AbstractFitengine: |
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| 272 | # But this should be corrected later. |
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| 273 | dy = deepcopy(current_data.dy) |
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| 274 | dy[dy == 0] = 1 |
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| 275 | fn = current_data.y[index] |
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| 276 | gn = reference_data.y |
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| 277 | en = dy[index] |
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| 278 | # Calculate the residual |
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| 279 | try: |
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| 280 | res = (fn - gn) / en |
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| 281 | except ValueError: |
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| 282 | #print "Chi2 calculations: Unmatched lengths %s, %s, %s" % (len(fn), len(gn), len(en)) |
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| 283 | return None |
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| 284 | |
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| 285 | residuals = res[numpy.isfinite(res)] |
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| 286 | chisqr = numpy.average(residuals * residuals) |
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| 287 | |
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| 288 | return chisqr |
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| 289 | |
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| 290 | def residualsData1D(reference_data, current_data): |
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| 291 | """ |
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| 292 | Calculate the residuals for difference of two Data1D sets |
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| 293 | """ |
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| 294 | # temporary default values for index and weight |
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| 295 | index = None |
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| 296 | weight = None |
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| 297 | |
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| 298 | # 1d theory from model_thread is only in the range of index |
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| 299 | if current_data.dy is None or current_data.dy == []: |
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| 300 | dy = numpy.ones(len(current_data.y)) |
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| 301 | else: |
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| 302 | dy = weight if weight is not None else numpy.ones(len(current_data.y)) |
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| 303 | dy[dy == 0] = 1 |
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| 304 | fn = current_data.y[index][0] |
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| 305 | gn = reference_data.y |
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| 306 | en = dy[index][0] |
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| 307 | # build residuals |
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| 308 | residuals = Data1D() |
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| 309 | if len(fn) == len(gn): |
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| 310 | y = (fn - gn)/en |
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| 311 | residuals.y = -y |
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| 312 | else: |
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| 313 | # TODO: fix case where applying new data from file on top of existing model data |
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| 314 | try: |
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| 315 | y = (fn - gn[index][0]) / en |
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| 316 | residuals.y = y |
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| 317 | except ValueError: |
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| 318 | # value errors may show up every once in a while for malformed columns, |
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| 319 | # just reuse what's there already |
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| 320 | pass |
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| 321 | |
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| 322 | residuals.x = current_data.x[index][0] |
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| 323 | residuals.dy = numpy.ones(len(residuals.y)) |
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| 324 | residuals.dx = None |
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| 325 | residuals.dxl = None |
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| 326 | residuals.dxw = None |
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| 327 | residuals.ytransform = 'y' |
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| 328 | # For latter scale changes |
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| 329 | residuals.xaxis('\\rm{Q} ', 'A^{-1}') |
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| 330 | residuals.yaxis('\\rm{Residuals} ', 'normalized') |
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| 331 | |
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| 332 | return residuals |
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| 333 | |
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| 334 | def residualsData2D(reference_data, current_data): |
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| 335 | """ |
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| 336 | Calculate the residuals for difference of two Data2D sets |
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| 337 | """ |
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| 338 | # temporary default values for index and weight |
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| 339 | # index = None |
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| 340 | weight = None |
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| 341 | |
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| 342 | # build residuals |
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| 343 | residuals = Data2D() |
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| 344 | # Not for trunk the line below, instead use the line above |
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| 345 | current_data.clone_without_data(len(current_data.data), residuals) |
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| 346 | residuals.data = None |
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| 347 | fn = current_data.data |
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| 348 | gn = reference_data.data |
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| 349 | en = current_data.err_data if weight is None else weight |
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| 350 | residuals.data = (fn - gn) / en |
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| 351 | residuals.qx_data = current_data.qx_data |
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| 352 | residuals.qy_data = current_data.qy_data |
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| 353 | residuals.q_data = current_data.q_data |
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| 354 | residuals.err_data = numpy.ones(len(residuals.data)) |
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| 355 | residuals.xmin = min(residuals.qx_data) |
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| 356 | residuals.xmax = max(residuals.qx_data) |
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| 357 | residuals.ymin = min(residuals.qy_data) |
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| 358 | residuals.ymax = max(residuals.qy_data) |
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| 359 | residuals.q_data = current_data.q_data |
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| 360 | residuals.mask = current_data.mask |
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| 361 | residuals.scale = 'linear' |
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| 362 | # check the lengths |
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| 363 | if len(residuals.data) != len(residuals.q_data): |
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| 364 | return None |
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| 365 | return residuals |
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| 366 | |
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| 367 | def plotResiduals(reference_data, current_data): |
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| 368 | """ |
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| 369 | Create Data1D/Data2D with residuals, ready for plotting |
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| 370 | """ |
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| 371 | data_copy = deepcopy(current_data) |
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| 372 | # Get data: data I, theory I, and data dI in order |
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| 373 | method_name = current_data.__class__.__name__ |
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| 374 | residuals_dict = {"Data1D": residualsData1D, |
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| 375 | "Data2D": residualsData2D} |
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| 376 | |
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| 377 | residuals = residuals_dict[method_name](reference_data, data_copy) |
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| 378 | |
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| 379 | theory_name = str(current_data.name.split()[0]) |
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| 380 | residuals.name = "Residuals for " + str(theory_name) + "[" + \ |
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| 381 | str(reference_data.filename) + "]" |
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| 382 | residuals.title = residuals.name |
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| 383 | residuals.ytransform = 'y' |
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| 384 | |
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| 385 | # when 2 data have the same id override the 1 st plotted |
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| 386 | # include the last part if keeping charts for separate models is required |
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| 387 | residuals.id = "res" + str(reference_data.id) # + str(theory_name) |
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| 388 | # group_id specify on which panel to plot this data |
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| 389 | group_id = reference_data.group_id |
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| 390 | residuals.group_id = "res" + str(group_id) |
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| 391 | |
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| 392 | # Symbol |
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| 393 | residuals.symbol = 0 |
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| 394 | residuals.hide_error = False |
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| 395 | |
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| 396 | return residuals |
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| 397 | |
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| 398 | def binary_encode(i, digits): |
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| 399 | return [i >> d & 1 for d in range(digits)] |
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| 400 | |
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| 401 | def getWeight(data, is2d, flag=None): |
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| 402 | """ |
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| 403 | Received flag and compute error on data. |
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| 404 | :param flag: flag to transform error of data. |
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| 405 | """ |
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| 406 | weight = None |
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| 407 | if is2d: |
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| 408 | dy_data = data.err_data |
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| 409 | data = data.data |
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| 410 | else: |
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| 411 | dy_data = data.dy |
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| 412 | data = data.y |
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| 413 | |
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| 414 | if flag == 0: |
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| 415 | weight = numpy.ones_like(data) |
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| 416 | elif flag == 1: |
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| 417 | weight = dy_data |
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| 418 | elif flag == 2: |
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| 419 | weight = numpy.sqrt(numpy.abs(data)) |
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| 420 | elif flag == 3: |
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| 421 | weight = numpy.abs(data) |
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| 422 | return weight |
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