def mfit(data, xmin, xmax, ymin, ymax, dy):
fs = [Function('Linear', linear), Function('Gaussian', gaussian)]
x = np.linspace(xmin, xmax, 200)
ylo, yhi = ymin, ymin+dy
while yhi < ymax:
slab = data[ylo:yhi,xmin:xmax]
diff = slab.nxsignal.shape[0]
cut = slab.sum([0])
cut.plot()
fit = Fit(cut, fs, use_errors=True)
y = np.array(fit.y)
for f in fs:
f.guess_parameters(fit.x, y)
y = y - f.function_values(fit.x)
fit.fit_data()
NXdata(fit.get_model(x), x).oplot('-')
if raw_input('Keep? [y,N] ') == 'y':
data[ylo:yhi,xmin:xmax] = slab - fit.get_model(f=fs[1]) / diff
ylo = yhi
yhi = ylo + dy
return data
def get_model(self, f=None):
self.read_parameters()
fit = Fit(self.data, self.functions)
if self.plot_checkbox.isChecked():
x = fit.x
else:
x = np.linspace(float(self.plot_minbox.text()),
float(self.plot_maxbox.text()), 1001)
return NXdata(NXfield(fit.get_model(x, f), name='model'),
NXfield(x, name=fit.data.nxaxes[0].nxname),
title='Fit Results')
def get_model(self, f=None):
self.read_parameters()
fit = Fit(self.data, self.functions)
if self.plot_checkbox.isChecked():
x = fit.x
else:
x = np.linspace(float(self.plot_minbox.text()),
float(self.plot_maxbox.text()), 1001)
return NXdata(NXfield(fit.get_model(x,f), name='model'),
NXfield(x, name=fit.data.nxaxes[0].nxname),
title = 'Fit Results')
def guess_parameters(self):
fit = Fit(self.data, self.functions)
y = np.array(fit.y)
for f in self.functions:
guess = f.module.guess(fit.x, y)
map(lambda p, g: p.__setattr__('value', g), f.parameters, guess)
y = y - f.module.values(fit.x, guess)
def mfit(data, xmin, xmax, ymin, ymax, dy):
fs = [Function('Linear', linear), Function('Gaussian', gaussian)]
x = np.linspace(xmin, xmax, 200)
ylo, yhi = ymin, ymin + dy
while yhi < ymax:
slab = data[ylo:yhi, xmin:xmax]
diff = slab.nxsignal.shape[0]
cut = slab.sum([0])
cut.plot()
fit = Fit(cut, fs, use_errors=True)
y = np.array(fit.y)
for f in fs:
f.guess_parameters(fit.x, y)
y = y - f.function_values(fit.x)
fit.fit_data()
NXdata(fit.get_model(x), x).oplot('-')
if raw_input('Keep? [y,N] ') == 'y':
data[ylo:yhi, xmin:xmax] = slab - fit.get_model(f=fs[1]) / diff
ylo = yhi
yhi = ylo + dy
return data
def fit_data(self):
self.read_parameters()
if self.fit_checkbox.isChecked():
use_errors = True
else:
use_errors = False
from nexpy.gui.mainwindow import report_error
try:
self.fit = Fit(self.data, self.functions, use_errors)
self.fit.fit_data()
except Exception as error:
report_error("Fitting Data", error)
if self.fit.result.success:
self.fit_label.setText('Fit Successful Chi^2 = %s' %
self.fit.result.redchi)
else:
self.fit_label.setText('Fit Failed Chi^2 = %s' %
self.fit.result.redchi)
self.write_parameters()
if not self.fitted:
self.action_layout.addWidget(self.report_button)
self.action_layout.addWidget(self.restore_button)
self.save_button.setText('Save Fit')
self.fitted = True
def fit_data(self):
self.read_parameters()
if self.fit_checkbox.isChecked():
use_errors = True
else:
use_errors = False
self.fit = Fit(self.data, self.functions, use_errors)
self.fit.fit_data()
if self.fit.result.success:
self.fit_label.setText('Fit Successful Chi^2 = %s' % self.fit.result.redchi)
else:
self.fit_label.setText('Fit Failed Chi^2 = %s' % self.fit.result.redchi)
self.write_parameters()
if not self.fitted:
self.action_layout.addWidget(self.report_button)
self.action_layout.addWidget(self.restore_button)
self.save_button.setText('Save Fit')
self.fitted = True
def fit_data(self):
self.read_parameters()
if self.fit_checkbox.isChecked():
use_errors = True
else:
use_errors = False
from nexpy.gui.mainwindow import report_error
try:
self.fit = Fit(self.data, self.functions, use_errors)
self.fit.fit_data()
except Exception as error:
report_error("Fitting Data", error)
if self.fit.result.success:
self.fit_label.setText('Fit Successful Chi^2 = %s' % self.fit.result.redchi)
else:
self.fit_label.setText('Fit Failed Chi^2 = %s' % self.fit.result.redchi)
self.write_parameters()
if not self.fitted:
self.action_layout.addWidget(self.report_button)
self.action_layout.addWidget(self.restore_button)
self.save_button.setText('Save Fit')
self.fitted = True
class FitDialog(BaseDialog):
"""Dialog to fit one-dimensional NeXus data"""
def __init__(self, entry, parent=None):
super(FitDialog, self).__init__(parent)
self.setMinimumWidth(850)
self.data = self.initialize_data(entry.data)
from nexpy.gui.consoleapp import _tree
self.tree = _tree
from nexpy.gui.plotview import plotview
self.plotview = plotview
self.functions = []
self.parameters = []
self.first_time = True
self.fitted = False
self.fit = None
self.initialize_functions()
function_layout = QtGui.QHBoxLayout()
self.functioncombo = QtGui.QComboBox()
for name in sorted(self.function_module.keys()):
self.functioncombo.addItem(name)
self.functioncombo.setSizeAdjustPolicy(
QtGui.QComboBox.AdjustToContents)
self.functioncombo.setMinimumWidth(100)
add_button = QtGui.QPushButton("Add Function")
add_button.clicked.connect(self.add_function)
function_layout.addWidget(self.functioncombo)
function_layout.addWidget(add_button)
function_layout.addStretch()
self.header_font = QtGui.QFont()
self.header_font.setBold(True)
self.parameter_layout = self.initialize_parameter_grid()
self.remove_layout = QtGui.QHBoxLayout()
remove_button = QtGui.QPushButton("Remove Function")
remove_button.clicked.connect(self.remove_function)
self.removecombo = QtGui.QComboBox()
self.removecombo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.removecombo.setMinimumWidth(100)
self.remove_layout.addWidget(remove_button)
self.remove_layout.addWidget(self.removecombo)
self.remove_layout.addStretch()
self.plot_layout = QtGui.QHBoxLayout()
plot_data_button = QtGui.QPushButton('Plot Data')
plot_data_button.clicked.connect(self.plot_data)
plot_function_button = QtGui.QPushButton('Plot Function')
plot_function_button.clicked.connect(self.plot_model)
self.plotcombo = QtGui.QComboBox()
self.plotcombo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.plotcombo.setMinimumWidth(100)
plot_label = QtGui.QLabel('X-axis:')
self.plot_minbox = QtGui.QLineEdit(str(self.plotview.xtab.axis.min))
self.plot_minbox.setAlignment(QtCore.Qt.AlignRight)
plot_tolabel = QtGui.QLabel(' to ')
self.plot_maxbox = QtGui.QLineEdit(str(self.plotview.xtab.axis.max))
self.plot_maxbox.setAlignment(QtCore.Qt.AlignRight)
self.plot_checkbox = QtGui.QCheckBox('Use Data Points')
self.plot_layout.addWidget(plot_data_button)
self.plot_layout.addWidget(plot_function_button)
self.plot_layout.addWidget(self.plotcombo)
self.plot_layout.addWidget(plot_label)
self.plot_layout.addWidget(self.plot_minbox)
self.plot_layout.addWidget(plot_tolabel)
self.plot_layout.addWidget(self.plot_maxbox)
self.plot_layout.addWidget(self.plot_checkbox)
self.plot_layout.addStretch()
self.action_layout = QtGui.QHBoxLayout()
fit_button = QtGui.QPushButton("Fit")
fit_button.clicked.connect(self.fit_data)
self.fit_label = QtGui.QLabel()
if self.data.nxerrors:
self.fit_checkbox = QtGui.QCheckBox('Use Errors')
self.fit_checkbox.setCheckState(QtCore.Qt.Checked)
else:
self.fit_checkbox = QtGui.QCheckBox('Use Poisson Errors')
self.fit_checkbox.setCheckState(QtCore.Qt.Unchecked)
self.fit_checkbox.stateChanged.connect(self.define_errors)
self.report_button = QtGui.QPushButton("Show Fit Report")
self.report_button.clicked.connect(self.report_fit)
self.save_button = QtGui.QPushButton("Save Parameters")
self.save_button.clicked.connect(self.save_fit)
self.restore_button = QtGui.QPushButton("Restore Parameters")
self.restore_button.clicked.connect(self.restore_parameters)
self.action_layout.addWidget(fit_button)
self.action_layout.addWidget(self.fit_label)
self.action_layout.addStretch()
self.action_layout.addWidget(self.fit_checkbox)
self.action_layout.addWidget(self.save_button)
self.layout = QtGui.QVBoxLayout()
self.layout.addLayout(function_layout)
self.layout.addWidget(self.close_buttons())
self.setLayout(self.layout)
self.setWindowTitle("Fit NeXus Data")
self.load_entry(entry)
def initialize_data(self, data):
if isinstance(data, NXdata):
if len(data.nxsignal.shape) > 1:
raise NeXusError(
"Fitting only possible on one-dimensional arrays")
fit_data = NXdata(data.nxsignal, data.nxaxes, title=data.nxtitle)
if data.nxerrors:
fit_data.errors = data.nxerrors
return fit_data
else:
raise NeXusError("Must be an NXdata group")
def initialize_functions(self):
filenames = set()
private_path = os.path.join(os.path.expanduser('~'), '.nexpy',
'functions')
if os.path.isdir(private_path):
sys.path.append(private_path)
for file_ in os.listdir(private_path):
name, ext = os.path.splitext(file_)
if name != '__init__' and ext.startswith('.py'):
filenames.add(name)
functions_path = pkg_resources.resource_filename(
'nexpy.api.frills', 'functions')
sys.path.append(functions_path)
for file_ in os.listdir(functions_path):
name, ext = os.path.splitext(file_)
if name != '__init__' and ext.startswith('.py'):
filenames.add(name)
self.function_module = {}
for name in sorted(filenames):
fp, pathname, description = imp.find_module(name)
try:
function_module = imp.load_module(name, fp, pathname,
description)
finally:
if fp:
fp.close()
if hasattr(function_module, 'function_name'):
self.function_module[
function_module.function_name] = function_module
def initialize_parameter_grid(self):
grid_layout = QtGui.QVBoxLayout()
scroll_area = QtGui.QScrollArea()
scroll_area.setWidgetResizable(True)
scroll_widget = QtGui.QWidget()
self.parameter_grid = QtGui.QGridLayout()
self.parameter_grid.setSpacing(10)
headers = [
'Function', 'Np', 'Name', 'Value', '', 'Min', 'Max', 'Fixed'
]
width = [100, 50, 100, 100, 100, 100, 100, 50, 100]
column = 0
for header in headers:
label = QtGui.QLabel()
label.setFont(self.header_font)
label.setAlignment(QtCore.Qt.AlignHCenter)
label.setText(header)
self.parameter_grid.addWidget(label, 0, column)
self.parameter_grid.setColumnMinimumWidth(column, width[column])
column += 1
scroll_widget.setLayout(self.parameter_grid)
scroll_area.setWidget(scroll_widget)
scroll_area.setMinimumHeight(200)
grid_layout.addWidget(scroll_area)
return grid_layout
def compressed_name(self, name):
return re.sub(r'([a-zA-Z]*) # (\d*)', r'\1\2', name)
def expanded_name(self, name):
return re.sub(r'([a-zA-Z]*)(\d*)', r'\1 # \2', name)
def parse_function_name(self, name):
match = re.match(r'([a-zA-Z]*)(\d*)', name)
return match.group(1), match.group(2)
def load_entry(self, entry):
if 'fit' in entry.entries:
for group in entry.entries:
name, n = self.parse_function_name(group)
if name in self.function_module:
module = self.function_module[name]
parameters = []
for p in module.parameters:
if p in entry[group].parameters.entries:
parameter = Parameter(p)
parameter.value = entry[group].parameters[p].nxdata
parameter.min = float(
entry[group].parameters[p].attrs['min'].nxdata)
parameter.max = float(
entry[group].parameters[p].attrs['max'].nxdata)
parameters.append(parameter)
f = Function(group, module, parameters, n)
self.functions.append(f)
self.functions = sorted(self.functions)
for f in self.functions:
self.add_function_rows(f)
self.write_parameters()
def add_function(self):
module = self.function_module[self.functioncombo.currentText()]
function_index = len(self.functions) + 1
name = '%s%s' % (module.function_name, str(function_index))
parameters = [Parameter(p) for p in module.parameters]
f = Function(name, module, parameters, function_index)
self.functions.append(f)
self.index_parameters()
self.guess_parameters()
self.add_function_rows(f)
self.write_parameters()
def index_parameters(self):
np = 0
for f in sorted(self.functions):
for p in f.parameters:
np += 1
p.parameter_index = np
def add_function_rows(self, f):
self.add_parameter_rows(f)
if self.first_time:
self.layout.insertLayout(1, self.parameter_layout)
self.layout.insertLayout(2, self.remove_layout)
self.layout.insertLayout(3, self.plot_layout)
self.layout.insertLayout(4, self.action_layout)
self.plotcombo.addItem('All')
self.plotcombo.insertSeparator(1)
self.removecombo.addItem(self.expanded_name(f.name))
self.plotcombo.addItem(self.expanded_name(f.name))
self.first_time = False
def remove_function(self):
expanded_name = self.removecombo.currentText()
name = self.compressed_name(expanded_name)
f = filter(lambda x: x.name == name, self.functions)[0]
for row in f.rows:
for column in range(8):
item = self.parameter_grid.itemAtPosition(row, column)
if item is not None:
widget = item.widget()
if widget is not None:
widget.setVisible(False)
self.parameter_grid.removeWidget(widget)
widget.deleteLater()
self.functions.remove(f)
self.plotcombo.removeItem(self.plotcombo.findText(expanded_name))
self.removecombo.removeItem(self.removecombo.findText(expanded_name))
del f
nf = 0
np = 0
for f in sorted(self.functions):
nf += 1
name = '%s%s' % (f.module.function_name, str(nf))
self.rename_function(f.name, name)
f.name = name
f.label_box.setText(self.expanded_name(f.name))
for p in f.parameters:
np += 1
p.parameter_index = np
p.parameter_box.setText(str(p.parameter_index))
def rename_function(self, old_name, new_name):
old_name, new_name = self.expanded_name(old_name), self.expanded_name(
new_name)
plot_index = self.plotcombo.findText(old_name)
self.plotcombo.setItemText(plot_index, new_name)
remove_index = self.removecombo.findText(old_name)
self.removecombo.setItemText(remove_index, new_name)
def add_parameter_rows(self, f):
row = self.parameter_grid.rowCount()
name = self.expanded_name(f.name)
f.rows = []
f.label_box = QtGui.QLabel(name)
self.parameter_grid.addWidget(f.label_box, row, 0)
for p in f.parameters:
p.parameter_index = row
p.parameter_box = QtGui.QLabel(str(p.parameter_index))
p.value_box = QtGui.QLineEdit()
p.value_box.setAlignment(QtCore.Qt.AlignRight)
p.error_box = QtGui.QLabel()
p.min_box = QtGui.QLineEdit('-inf')
p.min_box.setAlignment(QtCore.Qt.AlignRight)
p.max_box = QtGui.QLineEdit('inf')
p.max_box.setAlignment(QtCore.Qt.AlignRight)
p.fixed_box = QtGui.QCheckBox()
# p.bound_box = QtGui.QLineEdit()
self.parameter_grid.addWidget(p.parameter_box,
row,
1,
alignment=QtCore.Qt.AlignHCenter)
self.parameter_grid.addWidget(QtGui.QLabel(p.name), row, 2)
self.parameter_grid.addWidget(p.value_box, row, 3)
self.parameter_grid.addWidget(p.error_box, row, 4)
self.parameter_grid.addWidget(p.min_box, row, 5)
self.parameter_grid.addWidget(p.max_box, row, 6)
self.parameter_grid.addWidget(p.fixed_box,
row,
7,
alignment=QtCore.Qt.AlignHCenter)
# self.parameter_grid.addWidget(p.bound_box, row, 8)
f.rows.append(row)
row += 1
self.parameter_grid.setRowStretch(self.parameter_grid.rowCount(), 10)
def read_parameters(self):
def make_float(value):
try:
return float(value)
except Exception:
return None
for f in self.functions:
for p in f.parameters:
p.value = make_float(p.value_box.text())
p.min = make_float(p.min_box.text())
p.max = make_float(p.max_box.text())
p.vary = not p.fixed_box.checkState()
def write_parameters(self):
for f in self.functions:
for p in f.parameters:
if p.parameter_index:
p.parameter_box.setText(str(p.parameter_index))
if p.value:
p.value_box.setText('%.6g' % p.value)
if p.vary and p.stderr:
p.error_box.setText('+/- %.6g' % p.stderr)
else:
p.error_box.setText(' ')
if p.min:
p.min_box.setText('%.6g' % p.min)
if p.max:
p.max_box.setText('%.6g' % p.max)
def guess_parameters(self):
fit = Fit(self.data, self.functions)
y = np.array(fit.y)
for f in self.functions:
guess = f.module.guess(fit.x, y)
map(lambda p, g: p.__setattr__('value', g), f.parameters, guess)
y = y - f.module.values(fit.x, guess)
def get_model(self, f=None):
self.read_parameters()
fit = Fit(self.data, self.functions)
if self.plot_checkbox.isChecked():
x = fit.x
else:
x = np.linspace(float(self.plot_minbox.text()),
float(self.plot_maxbox.text()), 1001)
return NXdata(NXfield(fit.get_model(x, f), name='model'),
NXfield(x, name=fit.data.nxaxes[0].nxname),
title='Fit Results')
def plot_data(self):
self.data.plot()
def plot_model(self):
plot_function = self.plotcombo.currentText()
if plot_function == 'All':
self.get_model().oplot('-')
else:
name = self.compressed_name(plot_function)
f = filter(lambda x: x.name == name, self.functions)[0]
self.get_model(f).oplot('--')
def define_errors(self):
if self.fit_checkbox.isChecked():
self.data.errors = np.sqrt(self.data.nxsignal)
def fit_data(self):
self.read_parameters()
if self.fit_checkbox.isChecked():
use_errors = True
else:
use_errors = False
from nexpy.gui.mainwindow import report_error
try:
self.fit = Fit(self.data, self.functions, use_errors)
self.fit.fit_data()
except Exception as error:
report_error("Fitting Data", error)
if self.fit.result.success:
self.fit_label.setText('Fit Successful Chi^2 = %s' %
self.fit.result.redchi)
else:
self.fit_label.setText('Fit Failed Chi^2 = %s' %
self.fit.result.redchi)
self.write_parameters()
if not self.fitted:
self.action_layout.addWidget(self.report_button)
self.action_layout.addWidget(self.restore_button)
self.save_button.setText('Save Fit')
self.fitted = True
def report_fit(self):
message_box = QtGui.QMessageBox()
message_box.setText("Fit Results")
if self.fit.result.success:
summary = 'Fit Successful'
else:
summary = 'Fit Failed'
if self.fit.result.errorbars:
errors = 'Uncertainties estimated'
else:
errors = 'Uncertainties not estimated'
text = '%s\n' % summary +\
'%s\n' % self.fit.result.message +\
'%s\n' % self.fit.result.lmdif_message +\
'scipy.optimize.leastsq error value = %s\n' % self.fit.result.ier +\
'Chi^2 = %s\n' % self.fit.result.chisqr +\
'Reduced Chi^2 = %s\n' % self.fit.result.redchi +\
'%s\n' % errors +\
'No. of Function Evaluations = %s\n' % self.fit.result.nfev +\
'No. of Variables = %s\n' % self.fit.result.nvarys +\
'No. of Data Points = %s\n' % self.fit.result.ndata +\
'No. of Degrees of Freedom = %s\n' % self.fit.result.nfree +\
'%s' % self.fit.fit_report()
message_box.setInformativeText(text)
message_box.setStandardButtons(QtGui.QMessageBox.Ok)
spacer = QtGui.QSpacerItem(500, 0, QtGui.QSizePolicy.Minimum,
QtGui.QSizePolicy.Expanding)
layout = message_box.layout()
layout.addItem(spacer, layout.rowCount(), 0, 1, layout.columnCount())
message_box.exec_()
def save_fit(self):
"""Saves fit results to an NXentry"""
self.read_parameters()
entry = NXentry()
entry['data'] = self.data
for f in self.functions:
entry[f.name] = self.get_model(f)
parameters = NXparameters()
for p in f.parameters:
parameters[p.name] = NXfield(p.value,
error=p.stderr,
initial_value=p.init_value,
min=str(p.min),
max=str(p.max))
entry[f.name].insert(parameters)
if self.fit is not None:
entry['title'] = 'Fit Results'
entry['fit'] = self.get_model()
fit = NXparameters()
fit.nfev = self.fit.result.nfev
fit.ier = self.fit.result.ier
fit.chisq = self.fit.result.chisqr
fit.redchi = self.fit.result.redchi
fit.message = self.fit.result.message
fit.lmdif_message = self.fit.result.lmdif_message
entry['statistics'] = fit
else:
entry['title'] = 'Fit Model'
entry['model'] = self.get_model()
if 'w0' not in self.tree.keys():
self.tree.add(NXroot(name='w0'))
ind = []
for key in self.tree['w0'].keys():
try:
if key.startswith('f'):
ind.append(int(key[1:]))
except ValueError:
pass
if not ind:
ind = [0]
name = 'f' + str(sorted(ind)[-1] + 1)
self.tree['w0'][name] = entry
def restore_parameters(self):
for f in self.functions:
for p in f.parameters:
p.value = p.init_value
p.stderr = None
self.fit_label.setText(' ')
self.write_parameters()
def accept(self):
super(FitDialog, self).accept()
def reject(self):
super(FitDialog, self).reject()
def closeEvent(self, event):
event.accept()
class FitDialog(QtGui.QDialog):
"""Dialog to fit one-dimensional NeXus data"""
def __init__(self, entry, parent=None):
QtGui.QDialog.__init__(self, parent)
self.data = entry.data
from nexpy.gui.consoleapp import _tree
self.tree = _tree
self.functions = []
self.parameters = []
self.first_time = True
self.fitted = False
self.initialize_functions()
function_layout = QtGui.QHBoxLayout()
self.functioncombo = QtGui.QComboBox()
for name in sorted(self.function_module.keys()):
self.functioncombo.addItem(name)
self.functioncombo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.functioncombo.setMinimumWidth(100)
add_button = QtGui.QPushButton("Add Function")
add_button.clicked.connect(self.add_function)
function_layout.addWidget(self.functioncombo)
function_layout.addWidget(add_button)
function_layout.addStretch()
self.header_font = QtGui.QFont()
self.header_font.setBold(True)
self.parameter_grid = self.initialize_parameter_grid()
self.remove_layout = QtGui.QHBoxLayout()
remove_button = QtGui.QPushButton("Remove Function")
remove_button.clicked.connect(self.remove_function)
self.removecombo = QtGui.QComboBox()
self.removecombo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.removecombo.setMinimumWidth(100)
self.remove_layout.addWidget(remove_button)
self.remove_layout.addWidget(self.removecombo)
self.remove_layout.addStretch()
from nexpy.gui.consoleapp import _shell
self.plot_layout = QtGui.QHBoxLayout()
plot_data_button = QtGui.QPushButton('Plot Data')
plot_data_button.clicked.connect(self.plot_data)
plot_function_button = QtGui.QPushButton('Plot Function')
plot_function_button.clicked.connect(self.plot_model)
self.plotcombo = QtGui.QComboBox()
self.plotcombo.setSizeAdjustPolicy(QtGui.QComboBox.AdjustToContents)
self.plotcombo.setMinimumWidth(100)
plot_label = QtGui.QLabel('X-axis:')
self.plot_minbox = QtGui.QLineEdit(str(_shell['plotview'].xtab.axis.min))
self.plot_minbox.setAlignment(QtCore.Qt.AlignRight)
plot_tolabel = QtGui.QLabel(' to ')
self.plot_maxbox = QtGui.QLineEdit(str(_shell['plotview'].xtab.axis.max))
self.plot_maxbox.setAlignment(QtCore.Qt.AlignRight)
self.plot_checkbox = QtGui.QCheckBox('Use Data Points')
self.plot_layout.addWidget(plot_data_button)
self.plot_layout.addWidget(plot_function_button)
self.plot_layout.addWidget(self.plotcombo)
self.plot_layout.addWidget(plot_label)
self.plot_layout.addWidget(self.plot_minbox)
self.plot_layout.addWidget(plot_tolabel)
self.plot_layout.addWidget(self.plot_maxbox)
self.plot_layout.addWidget(self.plot_checkbox)
self.plot_layout.addStretch()
self.action_layout = QtGui.QHBoxLayout()
fit_button = QtGui.QPushButton("Fit")
fit_button.clicked.connect(self.fit_data)
self.fit_label = QtGui.QLabel()
self.fit_checkbox = QtGui.QCheckBox('Use Errors')
if self.data.nxerrors:
self.fit_checkbox.setCheckState(QtCore.Qt.Checked)
else:
self.fit_checkbox.setCheckState(QtCore.Qt.Unchecked)
self.fit_checkbox.setVisible(False)
self.report_button = QtGui.QPushButton("Show Fit Report")
self.report_button.clicked.connect(self.report_fit)
self.save_button = QtGui.QPushButton("Save Parameters")
self.save_button.clicked.connect(self.save_fit)
self.restore_button = QtGui.QPushButton("Restore Parameters")
self.restore_button.clicked.connect(self.restore_parameters)
self.action_layout.addWidget(fit_button)
self.action_layout.addWidget(self.fit_checkbox)
self.action_layout.addWidget(self.fit_label)
self.action_layout.addStretch()
self.action_layout.addWidget(self.save_button)
button_box = QtGui.QDialogButtonBox(self)
button_box.setOrientation(QtCore.Qt.Horizontal)
button_box.setStandardButtons(QtGui.QDialogButtonBox.Cancel|
QtGui.QDialogButtonBox.Ok)
button_box.accepted.connect(self.accept)
button_box.rejected.connect(self.reject)
self.layout = QtGui.QVBoxLayout()
self.layout.addLayout(function_layout)
self.layout.addWidget(button_box)
self.setLayout(self.layout)
self.setWindowTitle("Fit NeXus Data")
self.load_entry(entry)
def initialize_functions(self):
filenames = set()
private_path = os.path.join(os.path.expanduser('~'), '.nexpy', 'functions')
if os.path.isdir(private_path):
sys.path.append(private_path)
for file in os.listdir(private_path):
name, ext = os.path.splitext(file)
if name <> '__init__' and ext.startswith('.py'):
filenames.add(name)
base_path = os.path.abspath(os.path.dirname(__file__))
functions_path = os.path.join(os.path.abspath(os.path.dirname(base_path)),
'api', 'frills', 'functions')
sys.path.append(functions_path)
for file in os.listdir(functions_path):
name, ext = os.path.splitext(file)
if name <> '__init__' and ext.startswith('.py'):
filenames.add(name)
self.function_module = {}
for name in sorted(filenames):
fp, pathname, description = imp.find_module(name)
try:
function_module = imp.load_module(name, fp, pathname, description)
finally:
if fp:
fp.close()
if hasattr(function_module, 'function_name'):
self.function_module[function_module.function_name] = function_module
def initialize_parameter_grid(self):
grid = QtGui.QGridLayout()
grid.setSpacing(10)
headers = ['Function', 'Np', 'Name', 'Value', '', 'Min', 'Max', 'Fixed', 'Bound']
width = [100, 50, 100, 100, 100, 100, 100, 50, 100]
column = 0
for header in headers:
label = QtGui.QLabel()
label.setFont(self.header_font)
label.setAlignment(QtCore.Qt.AlignHCenter)
label.setText(header)
grid.addWidget(label, 0, column)
grid.setColumnMinimumWidth(column, width[column])
column += 1
return grid
def compressed_name(self, name):
return re.sub(r'([a-zA-Z]*) # (\d*)',r'\1\2', name)
def expanded_name(self, name):
return re.sub(r'([a-zA-Z]*)(\d*)',r'\1 # \2', name)
def parse_function_name(self, name):
match = re.match(r'([a-zA-Z]*)(\d*)',name)
return match.group(1), match.group(2)
def load_entry(self, entry):
if 'fit' in entry.entries:
for group in entry.entries:
name, n = self.parse_function_name(group)
if name in self.function_module:
module = self.function_module[name]
parameters = []
for p in module.parameters:
if p in entry[group].parameters.entries:
parameter = Parameter(p)
parameter.value = entry[group].parameters[p].nxdata
parameter.min = float(entry[group].parameters[p].attrs['min'].nxdata)
parameter.max = float(entry[group].parameters[p].attrs['max'].nxdata)
parameters.append(parameter)
f = Function(group, module, parameters, n)
self.functions.append(f)
self.functions = sorted(self.functions)
for f in self.functions:
self.add_function_rows(f)
self.write_parameters()
def add_function(self):
module = self.function_module[self.functioncombo.currentText()]
function_index = len(self.functions) + 1
name = '%s%s' %(module.function_name,str(function_index))
parameters = [Parameter(p) for p in module.parameters]
f = Function(name, module, parameters, function_index)
self.functions.append(f)
self.index_parameters()
self.guess_parameters()
self.add_function_rows(f)
self.write_parameters()
def index_parameters(self):
np = 0
for f in sorted(self.functions):
for p in f.parameters:
np += 1
p.parameter_index = np
def add_function_rows(self, f):
self.add_parameter_rows(f)
if self.first_time:
self.layout.insertLayout(1, self.parameter_grid)
self.layout.insertLayout(2, self.remove_layout)
self.layout.insertLayout(3, self.plot_layout)
self.layout.insertLayout(4, self.action_layout)
self.plotcombo.addItem('All')
self.plotcombo.insertSeparator(1)
self.removecombo.addItem(self.expanded_name(f.name))
self.plotcombo.addItem(self.expanded_name(f.name))
self.first_time = False
def remove_function(self):
expanded_name = self.removecombo.currentText()
name = self.compressed_name(expanded_name)
f=filter(lambda x: x.name==name, self.functions)[0]
for row in f.rows:
for column in range(9):
item = self.parameter_grid.itemAtPosition(row, column)
if item is not None:
widget = item.widget()
if widget is not None:
widget.setVisible(False)
self.parameter_grid.removeWidget(widget)
widget.deleteLater()
self.functions.remove(f)
self.plotcombo.removeItem(self.plotcombo.findText(expanded_name))
self.removecombo.removeItem(self.removecombo.findText(expanded_name))
del(f)
nf = 0
np = 0
for f in sorted(self.functions):
nf += 1
name = '%s%s' %(f.module.function_name,str(nf))
self.rename_function(f.name, name)
f.name = name
f.label_box.setText(self.expanded_name(f.name))
for p in f.parameters:
np += 1
p.parameter_index = np
p.parameter_box.setText(str(p.parameter_index))
def rename_function(self, old_name, new_name):
old_name, new_name = self.expanded_name(old_name), self.expanded_name(new_name)
plot_index = self.plotcombo.findText(old_name)
self.plotcombo.setItemText(plot_index, new_name)
remove_index = self.removecombo.findText(old_name)
self.removecombo.setItemText(remove_index, new_name)
def add_parameter_rows(self, f):
row = self.parameter_grid.rowCount()
name = self.expanded_name(f.name)
f.rows = []
f.label_box = QtGui.QLabel(name)
self.parameter_grid.addWidget(f.label_box, row, 0)
for p in f.parameters:
p.parameter_index = row
p.parameter_box = QtGui.QLabel(str(p.parameter_index))
p.value_box = QtGui.QLineEdit()
p.value_box.setAlignment(QtCore.Qt.AlignRight)
p.error_box = QtGui.QLabel()
p.min_box = QtGui.QLineEdit('-inf')
p.min_box.setAlignment(QtCore.Qt.AlignRight)
p.max_box = QtGui.QLineEdit('inf')
p.max_box.setAlignment(QtCore.Qt.AlignRight)
p.fixed_box = QtGui.QCheckBox()
p.bound_box = QtGui.QLineEdit()
self.parameter_grid.addWidget(p.parameter_box, row, 1,
alignment = QtCore.Qt.AlignHCenter)
self.parameter_grid.addWidget(QtGui.QLabel(p.name), row, 2)
self.parameter_grid.addWidget(p.value_box, row, 3)
self.parameter_grid.addWidget(p.error_box, row, 4)
self.parameter_grid.addWidget(p.min_box, row, 5)
self.parameter_grid.addWidget(p.max_box, row, 6)
self.parameter_grid.addWidget(p.fixed_box, row, 7,
alignment = QtCore.Qt.AlignHCenter)
self.parameter_grid.addWidget(p.bound_box, row, 8)
f.rows.append(row)
row += 1
def read_parameters(self):
def make_float(value):
try:
return float(value)
except:
return None
for f in self.functions:
for p in f.parameters:
p.value = make_float(p.value_box.text())
p.min = make_float(p.min_box.text())
p.max = make_float(p.max_box.text())
p.vary = not p.fixed_box.checkState()
def write_parameters(self):
for f in self.functions:
for p in f.parameters:
if p.parameter_index:
p.parameter_box.setText(str(p.parameter_index))
if p.value:
p.value_box.setText('%.6g' % p.value)
if p.vary and p.stderr:
p.error_box.setText('+/- %.6g' % p.stderr)
else:
p.error_box.setText(' ')
if p.min:
p.min_box.setText('%.6g' % p.min)
if p.max:
p.max_box.setText('%.6g' % p.max)
def guess_parameters(self):
fit = Fit(self.data, self.functions)
y = np.array(fit.y)
for f in self.functions:
guess = f.module.guess(fit.x, y)
map(lambda p,g: p.__setattr__('value', g), f.parameters, guess)
y = y - f.module.values(fit.x, guess)
def get_model(self, f=None):
self.read_parameters()
fit = Fit(self.data, self.functions)
if self.plot_checkbox.isChecked():
x = fit.x
else:
x = np.linspace(float(self.plot_minbox.text()),
float(self.plot_maxbox.text()), 1001)
return NXdata(NXfield(fit.get_model(x,f), name='model'),
NXfield(x, name=fit.data.nxaxes[0].nxname),
title = 'Fit Results')
def plot_data(self):
self.data.plot()
def plot_model(self):
plot_function = self.plotcombo.currentText()
if plot_function == 'All':
self.get_model().oplot('-')
else:
name = self.compressed_name(plot_function)
f=filter(lambda x: x.name==name, self.functions)[0]
self.get_model(f).oplot('--')
def fit_data(self):
self.read_parameters()
if self.fit_checkbox.isChecked():
use_errors = True
else:
use_errors = False
self.fit = Fit(self.data, self.functions, use_errors)
self.fit.fit_data()
if self.fit.result.success:
self.fit_label.setText('Fit Successful Chi^2 = %s' % self.fit.result.redchi)
else:
self.fit_label.setText('Fit Failed Chi^2 = %s' % self.fit.result.redchi)
self.write_parameters()
if not self.fitted:
self.action_layout.addWidget(self.report_button)
self.action_layout.addWidget(self.restore_button)
self.save_button.setText('Save Fit')
self.fitted = True
def report_fit(self):
message_box = QtGui.QMessageBox()
message_box.setText("Fit Results")
if self.fit.result.success:
summary = 'Fit Successful'
else:
summary = 'Fit Failed'
if self.fit.result.errorbars:
errors = 'Uncertainties estimated'
else:
errors = 'Uncertainties not estimated'
text = '%s\n' % summary +\
'%s\n' % self.fit.result.message +\
'%s\n' % self.fit.result.lmdif_message +\
'scipy.optimize.leastsq error value = %s\n' % self.fit.result.ier +\
'Chi^2 = %s\n' % self.fit.result.chisqr +\
'Reduced Chi^2 = %s\n' % self.fit.result.redchi +\
'%s\n' % errors +\
'No. of Function Evaluations = %s\n' % self.fit.result.nfev +\
'No. of Variables = %s\n' % self.fit.result.nvarys +\
'No. of Data Points = %s\n' % self.fit.result.ndata +\
'No. of Degrees of Freedom = %s\n' % self.fit.result.nfree +\
'%s' % self.fit.fit_report()
message_box.setInformativeText(text)
message_box.setStandardButtons(QtGui.QMessageBox.Ok)
spacer = QtGui.QSpacerItem(500, 0,
QtGui.QSizePolicy.Minimum,
QtGui.QSizePolicy.Expanding)
layout = message_box.layout()
layout.addItem(spacer, layout.rowCount(), 0, 1, layout.columnCount())
message_box.exec_()
def save_fit(self):
self.read_parameters()
if 'w0' not in self.tree.keys():
scratch_space = self.tree.add(NXroot(name='w0'))
ind = []
for key in self.tree['w0'].keys():
try:
if key.startswith('f'):
ind.append(int(key[1:]))
except ValueError:
pass
if ind == []: ind = [0]
name = 'f'+str(sorted(ind)[-1]+1)
self.tree['w0'][name] = NXentry()
self.tree['w0'][name].title = 'Fit Results'
self.tree['w0'][name]['data'] = self.data
self.tree['w0'][name]['fit'] = self.get_model()
for f in self.functions:
self.tree['w0'][name][f.name] = self.get_model(f)
parameters = NXparameters()
for p in f.parameters:
parameters[p.name] = NXfield(p.value, error=p.stderr,
initial_value=p.init_value,
min=str(p.min), max=str(p.max))
self.tree['w0'][name][f.name].insert(parameters)
fit = NXparameters()
fit.nfev = self.fit.result.nfev
fit.ier = self.fit.result.ier
fit.chisq = self.fit.result.chisqr
fit.redchi = self.fit.result.redchi
fit.message = self.fit.result.message
fit.lmdif_message = self.fit.result.lmdif_message
self.tree['w0'][name]['statistics'] = fit
def restore_parameters(self):
for f in self.functions:
for p in f.parameters:
p.value = p.init_value
p.stderr = None
self.fit_label.setText(' ')
self.write_parameters()
def accept(self):
QtGui.QDialog.accept(self)
def reject(self):
QtGui.QDialog.reject(self)