Source code for sas.qtgui.Perspectives.Fitting.FittingUtilities

import copy

from PyQt5 import QtCore
from PyQt5 import QtGui

import numpy

from sas.qtgui.Plotting.PlotterData import Data1D
from sas.qtgui.Plotting.PlotterData import Data2D

from sas.qtgui.Perspectives.Fitting.AssociatedComboBox import AssociatedComboBox

model_header_captions = ['Parameter', 'Value', 'Min', 'Max', 'Units']

model_header_tooltips = ['Select parameter for fitting',
                         'Enter parameter value',
                         'Enter minimum value for parameter',
                         'Enter maximum value for parameter',
                         'Unit of the parameter']

poly_header_captions = ['Parameter', 'PD[ratio]', 'Min', 'Max', 'Npts', 'Nsigs',
                        'Function', 'Filename']

poly_header_tooltips = ['Select parameter for fitting',
                        'Enter polydispersity ratio (Std deviation/mean).\n'+
                        'For angles this can be either std deviation or half width (for uniform distributions) in degrees',
                        'Enter minimum value for parameter',
                        'Enter maximum value for parameter',
                        'Enter number of points for parameter',
                        'Enter number of sigmas parameter',
                        'Select distribution function',
                        'Select filename with user-definable distribution']

error_tooltip = 'Error value for fitted parameter'
header_error_caption = 'Error'

[docs]def replaceShellName(param_name, value): """ Updates parameter name from <param_name>[n_shell] to <param_name>value """ assert '[' in param_name return param_name[:param_name.index('[')]+str(value)
[docs]def getIterParams(model): """ Returns a list of all multi-shell parameters in 'model' """ return list([par for par in model.iq_parameters if "[" in par.name])
[docs]def getMultiplicity(model): """ Finds out if 'model' has multishell parameters. If so, returns the name of the counter parameter and the number of shells """ iter_params = getIterParams(model) param_name = "" param_length = 0 if iter_params: param_length = iter_params[0].length param_name = iter_params[0].length_control if param_name is None and '[' in iter_params[0].name: param_name = iter_params[0].name[:iter_params[0].name.index('[')] return (param_name, param_length)
[docs]def createFixedChoiceComboBox(param, item_row): """ Determines whether param is a fixed-choice parameter, modifies items in item_row appropriately and returns a combo box containing the fixed choices. Returns None if param is not fixed-choice. item_row is a list of QStandardItem objects for insertion into the parameter table. """ # Determine whether this is a fixed-choice parameter. There are lots of conditionals, simply because the # implementation is not yet concrete; there are several possible indicators that the parameter is fixed-choice. # TODO: (when the sasmodels implementation is concrete, clean this up) choices = None if isinstance(param.choices, (list, tuple)) and len(param.choices) > 0: # The choices property is concrete in sasmodels, probably will use this choices = param.choices elif isinstance(param.units, (list, tuple)): choices = [str(x) for x in param.units] cbox = None if choices is not None: # Use combo box for input, if it is fixed-choice cbox = AssociatedComboBox(item_row[1], idx_as_value=True) cbox.addItems(choices) if param.default is not None and param.default <= len(choices): # set the param default value in the combobox cbox.setCurrentIndex(param.default) item_row[2].setEditable(False) item_row[3].setEditable(False) return cbox
[docs]def addParametersToModel(parameters, kernel_module, is2D, model=None, view=None): """ Update local ModelModel with sasmodel parameters. Actually appends to model, if model and view params are not None. Always returns list of lists of QStandardItems. """ multishell_parameters = getIterParams(parameters) multishell_param_name, _ = getMultiplicity(parameters) if is2D: params = [p for p in parameters.kernel_parameters if p.type != 'magnetic'] else: params = parameters.iq_parameters rows = [] for param in params: # don't include shell parameters if param.name == multishell_param_name: continue # Modify parameter name from <param>[n] to <param>1 item_name = param.name if param in multishell_parameters: continue item1 = QtGui.QStandardItem(item_name) item1.setCheckable(True) item1.setEditable(False) # check for polydisp params if param.polydisperse: poly_item = QtGui.QStandardItem("Polydispersity") poly_item.setEditable(False) poly_item.setSelectable(False) item1_1 = QtGui.QStandardItem("Distribution") item1_1.setEditable(False) item1_1.setSelectable(False) # Find param in volume_params poly_pars = copy.deepcopy(parameters.form_volume_parameters) if is2D: poly_pars += parameters.orientation_parameters for p in poly_pars: if p.name != param.name: continue width = kernel_module.getParam(p.name+'.width') ptype = kernel_module.getParam(p.name+'.type') item1_2 = QtGui.QStandardItem(str(width)) item1_2.setEditable(False) item1_2.setSelectable(False) item1_3 = QtGui.QStandardItem() item1_3.setEditable(False) item1_3.setSelectable(False) item1_4 = QtGui.QStandardItem() item1_4.setEditable(False) item1_4.setSelectable(False) item1_5 = QtGui.QStandardItem(ptype) item1_5.setEditable(False) item1_5.setSelectable(False) poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) break # Add the polydisp item as a child item1.appendRow([poly_item]) # Param values item2 = QtGui.QStandardItem(str(param.default)) item3 = QtGui.QStandardItem(str(param.limits[0])) item4 = QtGui.QStandardItem(str(param.limits[1])) item5 = QtGui.QStandardItem(str(param.units)) item5.setEditable(False) # Check if fixed-choice (returns combobox, if so, also makes some items uneditable) row = [item1, item2, item3, item4, item5] cbox = createFixedChoiceComboBox(param, row) # Append to the model and use the combobox, if required if None not in (model, view): model.appendRow(row) if cbox: view.setIndexWidget(item2.index(), cbox) rows.append(row) return rows
[docs]def addSimpleParametersToModel(parameters, is2D, parameters_original=None, model=None, view=None, row_num=None): """ Update local ModelModel with sasmodel parameters (non-dispersed, non-magnetic) Actually appends to model, if model and view params are not None. Always returns list of lists of QStandardItems. parameters_original: list of parameters before any tagging on their IDs, e.g. for product model (so that those are the display names; see below) """ if is2D: params = [p for p in parameters.kernel_parameters if p.type != 'magnetic'] else: params = parameters.iq_parameters if parameters_original: # 'parameters_original' contains the parameters as they are to be DISPLAYED, while 'parameters' # contains the parameters as they were renamed; this is for handling name collisions in product model. # The 'real name' of the parameter will be stored in the item's user data. if is2D: params_orig = [p for p in parameters_original.kernel_parameters if p.type != 'magnetic'] else: params_orig = parameters_original.iq_parameters else: # no difference in names anyway params_orig = params rows = [] for param, param_orig in zip(params, params_orig): # Create the top level, checkable item item_name = param_orig.name item1 = QtGui.QStandardItem(item_name) item1.setData(param.name, QtCore.Qt.UserRole) item1.setCheckable(False) item1.setEditable(False) # Param values # TODO: add delegate for validation of cells item2 = QtGui.QStandardItem(str(param.default)) item3 = QtGui.QStandardItem(str(param.limits[0])) item4 = QtGui.QStandardItem(str(param.limits[1])) item5 = QtGui.QStandardItem(str(param.units)) item5.setEditable(False) # Check if fixed-choice (returns combobox, if so, also makes some items uneditable) row = [item1, item2, item3, item4, item5] cbox = createFixedChoiceComboBox(param, row) # Append to the model and use the combobox, if required if None not in (model, view): if row_num is None: model.appendRow(row) else: model.insertRow(row_num, row) row_num += 1 if cbox: item1.setCheckable(False) item3.setText("") item4.setText("") item3.setEditable(False) item4.setEditable(False) view.setIndexWidget(item2.index(), cbox) else: item1.setCheckable(True) rows.append(row) return rows
[docs]def markParameterDisabled(model, row): """Given the QModel row number, format to show it is not available for fitting""" # If an error column is present, there are a total of 6 columns. items = [model.item(row, c) for c in range(6)] model.blockSignals(True) for item in items: if item is None: continue item.setEditable(False) item.setCheckable(False) item = items[0] font = QtGui.QFont() font.setItalic(True) item.setFont(font) item.setForeground(QtGui.QBrush(QtGui.QColor(100, 100, 100))) item.setToolTip("This parameter cannot be fitted.") model.blockSignals(False)
[docs]def addCheckedListToModel(model, param_list): """ Add a QItem to model. Makes the QItem checkable """ assert isinstance(model, QtGui.QStandardItemModel) item_list = [QtGui.QStandardItem(item) for item in param_list] item_list[0].setCheckable(True) model.appendRow(item_list)
[docs]def addHeadingRowToModel(model, name): """adds a non-interactive top-level row to the model""" header_row = [QtGui.QStandardItem() for i in range(5)] header_row[0].setText(name) font = header_row[0].font() font.setBold(True) header_row[0].setFont(font) for item in header_row: item.setEditable(False) item.setCheckable(False) item.setSelectable(False) model.appendRow(header_row)
[docs]def addHeadersToModel(model): """ Adds predefined headers to the model """ for i, item in enumerate(model_header_captions): model.setHeaderData(i, QtCore.Qt.Horizontal, item) model.header_tooltips = copy.copy(model_header_tooltips)
[docs]def addErrorHeadersToModel(model): """ Adds predefined headers to the model """ model_header_error_captions = copy.copy(model_header_captions) model_header_error_captions.insert(2, header_error_caption) for i, item in enumerate(model_header_error_captions): model.setHeaderData(i, QtCore.Qt.Horizontal, item) model_header_error_tooltips = copy.copy(model_header_tooltips) model_header_error_tooltips.insert(2, error_tooltip) model.header_tooltips = copy.copy(model_header_error_tooltips)
[docs]def addPolyHeadersToModel(model): """ Adds predefined headers to the model """ for i, item in enumerate(poly_header_captions): model.setHeaderData(i, QtCore.Qt.Horizontal, item) model.header_tooltips = copy.copy(poly_header_tooltips)
[docs]def addErrorPolyHeadersToModel(model): """ Adds predefined headers to the model """ poly_header_error_captions = copy.copy(poly_header_captions) poly_header_error_captions.insert(2, header_error_caption) for i, item in enumerate(poly_header_error_captions): model.setHeaderData(i, QtCore.Qt.Horizontal, item) poly_header_error_tooltips = copy.copy(poly_header_tooltips) poly_header_error_tooltips.insert(2, error_tooltip) model.header_tooltips = copy.copy(poly_header_error_tooltips)
[docs]def addShellsToModel(parameters, model, index, row_num=None, view=None): """ Find out multishell parameters and update the model with the requested number of them. Inserts them after the row at row_num, if not None; otherwise, appends to end. If view param is not None, supports fixed-choice params. Returns a list of lists of QStandardItem objects. """ multishell_parameters = getIterParams(parameters) rows = [] for i in range(index): for par in multishell_parameters: # Create the name: <param>[<i>], e.g. "sld1" for parameter "sld[n]" param_name = replaceShellName(par.name, i+1) item1 = QtGui.QStandardItem(param_name) item1.setCheckable(True) # check for polydisp params if par.polydisperse: poly_item = QtGui.QStandardItem("Polydispersity") item1_1 = QtGui.QStandardItem("Distribution") # Find param in volume_params for p in parameters.form_volume_parameters: if p.name != par.name: continue item1_2 = QtGui.QStandardItem(str(p.default)) item1_3 = QtGui.QStandardItem(str(p.limits[0])) item1_4 = QtGui.QStandardItem(str(p.limits[1])) item1_5 = QtGui.QStandardItem(str(p.units)) poly_item.appendRow([item1_1, item1_2, item1_3, item1_4, item1_5]) break item1.appendRow([poly_item]) item2 = QtGui.QStandardItem(str(par.default)) item3 = QtGui.QStandardItem(str(par.limits[0])) item4 = QtGui.QStandardItem(str(par.limits[1])) item5 = QtGui.QStandardItem(str(par.units)) item5.setEditable(False) # Check if fixed-choice (returns combobox, if so, also makes some items uneditable) row = [item1, item2, item3, item4, item5] cbox = createFixedChoiceComboBox(par, row) # Apply combobox if required if None not in (view, cbox): # set the min/max cell to be empty item3.setText("") item4.setText("") # Always add to the model if row_num is None: model.appendRow(row) else: model.insertRow(row_num, row) row_num += 1 if cbox is not None: view.setIndexWidget(item2.index(), cbox) rows.append(row) return rows
[docs]def calculateChi2(reference_data, current_data, weight): """ Calculate Chi2 value between two sets of data """ if reference_data is None or current_data is None: return None chisqr = None if reference_data is None: return chisqr # temporary default values for index and weight index = None # Get data: data I, theory I, and data dI in order if isinstance(reference_data, Data2D): if index is None: index = numpy.ones(len(current_data.data), dtype=bool) if weight is not None: current_data.err_data = weight # get rid of zero error points index = index & (current_data.err_data != 0) index = index & (numpy.isfinite(current_data.data)) fn = current_data.data[index] gn = reference_data.data[index] en = current_data.err_data[index] else: if index is None: index = numpy.ones(len(current_data.y), dtype=bool) if current_data.dy is None or current_data.dy == []: dy = numpy.ones(len(current_data.y)) else: dy = weight dy[dy == 0] = 1 fn = current_data.y[index] gn = reference_data.y en = dy[index] x_current = current_data.x x_reference = reference_data.x if len(fn) > len(gn): fn = fn[0:len(gn)] en = en[0:len(gn)] else: try: y = numpy.zeros(len(current_data.y)) begin = 0 for i, x_value in enumerate(x_reference): if x_value in x_current: begin = i break end = len(x_reference) endl = 0 for i, x_value in enumerate(list(x_reference)[::-1]): if x_value in x_current: endl = i break en = en[begin:end-endl] y = (fn - gn[begin:end-endl])/en except ValueError: # value errors may show up every once in a while for malformed columns, # just reuse what's there already pass # Calculate the residual try: res = (fn - gn) / en except ValueError: #print "Chi2 calculations: Unmatched lengths %s, %s, %s" % (len(fn), len(gn), len(en)) return None residuals = res[numpy.isfinite(res)] chisqr = numpy.average(residuals * residuals) return chisqr
[docs]def residualsData1D(reference_data, current_data, weights): """ Calculate the residuals for difference of two Data1D sets """ # temporary default values for index and weight index = None weight = None # 1d theory from model_thread is only in the range of index if current_data.dy is None or current_data.dy == []: dy = numpy.ones(len(current_data.y)) else: #dy = weight if weight is not None else numpy.ones(len(current_data.y)) if numpy.all(current_data.dy): dy = current_data.dy else: dy = weights dy[dy == 0] = 1 fn = current_data.y[index][0] gn = reference_data.y en = dy[index][0] # x values x_current = current_data.x x_reference = reference_data.x # build residuals residuals = Data1D() if len(fn) == len(gn): y = (fn - gn)/en residuals.y = -y elif len(fn) > len(gn): residuals.y = -(fn - gn[1:len(fn)])/en else: try: y = numpy.zeros(len(current_data.y)) begin = 0 for i, x_value in enumerate(x_reference): if x_value in x_current: begin = i break end = len(x_reference) endl = 0 for i, x_value in enumerate(list(x_reference)[::-1]): if x_value in x_current: endl = i break en = en[begin:end-endl] y = (fn - gn[begin:end-endl])/en residuals.y = -y except ValueError: # value errors may show up every once in a while for malformed columns, # just reuse what's there already pass residuals.x = current_data.x[index][0] residuals.dy = numpy.ones(len(residuals.y)) residuals.dx = None residuals.dxl = None residuals.dxw = None residuals.ytransform = 'y' # For latter scale changes residuals.xaxis('\\rm{Q} ', 'A^{-1}') residuals.yaxis('\\rm{Residuals} ', 'normalized') return residuals
[docs]def residualsData2D(reference_data, current_data, weight): """ Calculate the residuals for difference of two Data2D sets """ # build residuals residuals = Data2D() # Not for trunk the line below, instead use the line above current_data.clone_without_data(len(current_data.data), residuals) residuals.data = None fn = current_data.data gn = reference_data.data if weight is None: en = current_data.err_data else: en = weight residuals.data = (fn - gn) / en residuals.qx_data = current_data.qx_data residuals.qy_data = current_data.qy_data residuals.q_data = current_data.q_data residuals.err_data = numpy.ones(len(residuals.data)) residuals.xmin = min(residuals.qx_data) residuals.xmax = max(residuals.qx_data) residuals.ymin = min(residuals.qy_data) residuals.ymax = max(residuals.qy_data) residuals.q_data = current_data.q_data residuals.mask = current_data.mask residuals.scale = 'linear' # check the lengths if len(residuals.data) != len(residuals.q_data): return None return residuals
[docs]def plotResiduals(reference_data, current_data, weights): """ Create Data1D/Data2D with residuals, ready for plotting """ data_copy = copy.deepcopy(current_data) # Get data: data I, theory I, and data dI in order method_name = current_data.__class__.__name__ residuals_dict = {"Data1D": residualsData1D, "Data2D": residualsData2D} try: residuals = residuals_dict[method_name](reference_data, data_copy, weights) except ValueError: return None theory_name = str(current_data.name.split()[0]) res_name = reference_data.filename if reference_data.filename else reference_data.name residuals.name = "Residuals for " + str(theory_name) + "[" + res_name + "]" residuals.title = residuals.name residuals.ytransform = 'y' # when 2 data have the same id override the 1 st plotted # include the last part if keeping charts for separate models is required residuals.id = "res" + str(reference_data.id) # + str(theory_name) # group_id specify on which panel to plot this data group_id = reference_data.group_id residuals.group_id = "res" + str(group_id) # Symbol residuals.symbol = 0 residuals.hide_error = False return residuals
[docs]def plotPolydispersities(model): plots = [] if model is None: return plots # test for model being a sasmodels.sasview_model.SasviewModel? for name in model.dispersion.keys(): xarr, yarr = model.get_weights(name) if len(xarr) <= 1: # param name not found or no polydisp. continue # create Data1D as in residualsData1D() and fill x/y members # similar to FittingLogic._create1DPlot() but different data/axes data1d = Data1D(x=xarr, y=yarr) xunit = model.details[name][0] data1d.xaxis(r'\rm{{{}}}'.format(name.replace('_', '\_')), xunit) data1d.yaxis(r'\rm{probability}', 'normalized') data1d.scale = 'linear' data1d.symbol = 'Line' data1d.name = "{} polydispersity".format(name) data1d.id = data1d.name # placeholder, has to be completed later data1d.plot_role = Data1D.ROLE_RESIDUAL plots.append(data1d) return plots
[docs]def binary_encode(i, digits): return [i >> d & 1 for d in range(digits)]
[docs]def getWeight(data, is2d, flag=None): """ Received flag and compute error on data. :param flag: flag to transform error of data. """ weight = None if data is None: return [] if is2d: if not hasattr(data, 'err_data'): return [] dy_data = data.err_data data = data.data else: if not hasattr(data, 'dy'): return [] dy_data = data.dy data = data.y if flag == 0: weight = numpy.ones_like(data) elif flag == 1: weight = dy_data elif flag == 2: weight = numpy.sqrt(numpy.abs(data)) elif flag == 3: weight = numpy.abs(data) return weight
[docs]def updateKernelWithResults(kernel, results): """ Takes model kernel and applies results dict to its parameters, returning the modified (deep) copy of the kernel. """ assert isinstance(results, dict) local_kernel = copy.deepcopy(kernel) for parameter in results.keys(): # Update the parameter value - note: this supports +/-inf as well local_kernel.setParam(parameter, results[parameter][0]) return local_kernel
[docs]def getStandardParam(model=None): """ Returns a list with standard parameters for the current model """ param = [] num_rows = model.rowCount() if num_rows < 1: return param for row in range(num_rows): param_name = model.item(row, 0).text() checkbox_state = model.item(row, 0).checkState() == QtCore.Qt.Checked value = model.item(row, 1).text() column_shift = 0 if model.columnCount() == 5: # no error column error_state = False error_value = 0.0 else: error_state = True error_value = model.item(row, 2).text() column_shift = 1 min_state = True max_state = True min_value = model.item(row, 2+column_shift).text() max_value = model.item(row, 3+column_shift).text() unit = "" if model.item(row, 4+column_shift) is not None: u = model.item(row, 4+column_shift).text() # This isn't a unit if it is a number (polyd./magn.) unit = "" if isNumber(u) else u param.append([checkbox_state, param_name, value, "", [error_state, error_value], [min_state, min_value], [max_state, max_value], unit]) return param
[docs]def isNumber(s): """ Checks if string 's' is an int/float """ if s.isdigit(): # check int return True else: try: # check float _ = float(s) except ValueError: return False return True
[docs]def getOrientationParam(kernel_module=None): """ Get the dictionary with orientation parameters """ param = [] if kernel_module is None: return None for param_name in list(kernel_module.params.keys()): name = param_name value = kernel_module.params[param_name] min_state = True max_state = True error_state = False error_value = 0.0 checkbox_state = True #?? details = kernel_module.details[param_name] #[unit, mix, max] param.append([checkbox_state, name, value, "", [error_state, error_value], [min_state, details[1]], [max_state, details[2]], details[0]]) return param
[docs]def formatParameters(parameters, Check=True): """ Prepare the parameter string in the standard SasView layout """ assert parameters is not None assert isinstance(parameters, list) output_string = "sasview_parameter_values:" for parameter in parameters: # recast tuples into strings parameter = [str(p) for p in parameter] output_string += ",".join([p for p in parameter if p is not None]) output_string += ":" if Check == False: new_string = output_string.replace(':', '\n') return new_string else: return output_string
[docs]def formatParametersExcel(parameters): """ Prepare the parameter string in the Excel format (tab delimited) """ assert parameters is not None assert isinstance(parameters, list) crlf = chr(13) + chr(10) tab = chr(9) output_string = "" # names names = "" values = "" check = "" for parameter in parameters: names += parameter[0]+tab # Add the error column if fitted if parameter[1] == "True" and parameter[3] is not None: names += parameter[0]+"_err"+tab values += parameter[2]+tab check += parameter[1]+tab if parameter[1] == "True" and parameter[3] is not None: values += parameter[3]+tab # add .npts and .nsigmas when necessary if parameter[0][-6:] == ".width": names += parameter[0].replace('.width', '.nsigmas') + tab names += parameter[0].replace('.width', '.npts') + tab values += parameter[5] + tab + parameter[4] + tab output_string = names + crlf + values + crlf + check return output_string
[docs]def formatParametersLatex(parameters): """ Prepare the parameter string in latex """ assert parameters is not None assert isinstance(parameters, list) output_string = r'\begin{table}' output_string += r'\begin{tabular}[h]' crlf = chr(13) + chr(10) output_string += '{|' output_string += 'l|l|'*len(parameters) output_string += r'}\hline' output_string += crlf for index, parameter in enumerate(parameters): name = parameter[0] # Parameter name output_string += name.replace('_', r'\_') # Escape underscores # Add the error column if fitted if parameter[1] == "True" and parameter[3] is not None: output_string += ' & ' output_string += parameter[0]+r'\_err' if index < len(parameters) - 1: output_string += ' & ' # add .npts and .nsigmas when necessary if parameter[0][-6:] == ".width": output_string += parameter[0].replace('.width', '.nsigmas') + ' & ' output_string += parameter[0].replace('.width', '.npts') if index < len(parameters) - 1: output_string += ' & ' output_string += r'\\ \hline' output_string += crlf # Construct row of values and errors for index, parameter in enumerate(parameters): output_string += parameter[2] if parameter[1] == "True" and parameter[3] is not None: output_string += ' & ' output_string += parameter[3] if index < len(parameters) - 1: output_string += ' & ' # add .npts and .nsigmas when necessary if parameter[0][-6:] == ".width": output_string += parameter[5] + ' & ' output_string += parameter[4] if index < len(parameters) - 1: output_string += ' & ' output_string += r'\\ \hline' output_string += crlf output_string += r'\end{tabular}' output_string += r'\end{table}' return output_string
[docs]def isParamPolydisperse(param_name, kernel_params, is2D=False): """ Simple lookup for polydispersity for the given param name """ parameters = kernel_params.form_volume_parameters if is2D: parameters += kernel_params.orientation_parameters has_poly = False for param in parameters: if param.name==param_name and param.polydisperse: has_poly = True break return has_poly