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
from sas.sascalc.fit.expression import check_constraints
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 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.name if reference_data.name else reference_data.filename
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 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
[docs]def checkConstraints(symtab, constraints):
# type: (Dict[str, float], Sequence[Tuple[str, str]]) -> str
"""
Compile and evaluate the constraints in the context of the initial values
and return the list of errors.
Errors are returned as an html string where errors are tagged with <b>
markups:
Unknown symbol: tags unknown symbols in *constraints*
Syntax error: tags the beginning of a syntax error in *constraints*
Cyclic dependency: tags comma separated parameters that have
cyclic dependency
The errors are wrapped in a <div class = "error"> and a style header is
added
"""
# Note: dict(constraints) will choose the latest definition if
# there are duplicates.
errors = "<br>".join(check_constraints(symtab, dict(constraints),
html=True))
# wrap everything in <div class = "error">
if errors:
errors = "<div class = \"error\">" + errors + "</div>"
header = "<style type=\"text/css\"> div.error b { "\
"font-weight: normal; color:red;}</style>"
return header + errors
else:
return []