def setUp(self):
self.data = load_data()
# Note: to generate target values from the GUI:
# * load the data from test/corfunc/test/98929.txt
# * set qrange to (0, 0.013), (0.15, 0.24)
# * select fourier transform type
# * click Calculate Bg
# * click Extrapolate
# * click Compute Parameters
# * copy the Guinier and Porod values to the extrapolate function
# * for each graph, grab the data from DataInfo and store it in _out.txt
self.calculator = CorfuncCalculator(data=self.data, lowerq=0.013,
upperq=(0.15, 0.24))
self.calculator.background = 0.3
self.extrapolation = None
self.transformation = None
self.results = [np.loadtxt(find(filename+"_out.txt")).T[2]
for filename in ("gamma1", "gamma3", "idf")]
def __init__(self, parent, data=None, manager=None, *args, **kwds):
kwds["size"] = (PANEL_WIDTH, PANEL_HEIGHT)
kwds["style"] = wx.FULL_REPAINT_ON_RESIZE
ScrolledPanel.__init__(self, parent=parent, *args, **kwds)
PanelBase.__init__(self, parent)
self.SetupScrolling()
self.SetWindowVariant(variant=FONT_VARIANT)
self._manager = manager
# The data with no correction for background values
self._data = data # The data to be analysed (corrected fr background)
self._extrapolated_data = None # The extrapolated data set
# Callable object of class CorfuncCalculator._Interpolator representing
# the extrapolated and interpolated data
self._extrapolated_fn = None
self._transformed_data = None # Fourier trans. of the extrapolated data
self._calculator = CorfuncCalculator()
self._data_name_box = None # Text box to show name of file
self._background_input = None
self._qmin_input = None
self._qmax1_input = None
self._qmax2_input = None
self._extrapolate_btn = None
self._transform_btn = None
self._extract_btn = None
self.qmin = 0
self.qmax = (0, 0)
self.background = 0
self.extracted_params = None
self.transform_type = 'fourier'
self._extrapolation_outputs = {}
# Dictionary for saving refs to text boxes used to display output data
self._output_boxes = None
self.state = None
self._do_layout()
self._disable_inputs()
self.set_state()
self._qmin_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax1_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax2_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmin_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax1_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax2_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._background_input.Bind(wx.EVT_TEXT, self._on_enter_input)
def __init__(self, parent, data=None, manager=None, *args, **kwds):
kwds["size"] = (PANEL_WIDTH, PANEL_HEIGHT)
kwds["style"] = wx.FULL_REPAINT_ON_RESIZE
ScrolledPanel.__init__(self, parent=parent, *args, **kwds)
PanelBase.__init__(self, parent)
self.SetupScrolling()
self.SetWindowVariant(variant=FONT_VARIANT)
self._manager = manager
# The data with no correction for background values
self._data = data # The data to be analysed (corrected fr background)
self._extrapolated_data = None # The extrapolated data set
# Callable object of class CorfuncCalculator._Interpolator representing
# the extrapolated and interpolated data
self._extrapolated_fn = None
self._transformed_data = None # Fourier trans. of the extrapolated data
self._calculator = CorfuncCalculator()
self._data_name_box = None # Text box to show name of file
self._background_input = None
self._qmin_input = None
self._qmax1_input = None
self._qmax2_input = None
self._extrapolate_btn = None
self._transform_btn = None
self._extract_btn = None
self.qmin = 0
self.qmax = (0, 0)
self.background = 0
self.extracted_params = None
self.transform_type = 'fourier'
self._extrapolation_outputs = {}
# Dictionary for saving refs to text boxes used to display output data
self._output_boxes = None
self.state = None
self._do_layout()
self._disable_inputs()
self.set_state()
self._qmin_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax1_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax2_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmin_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax1_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax2_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._background_input.Bind(wx.EVT_TEXT, self._on_enter_input)
class CorfuncPanel(ScrolledPanel, PanelBase):
window_name = "Correlation Function"
window_caption = "Correlation Function"
CENTER_PANE = True
def __init__(self, parent, data=None, manager=None, *args, **kwds):
kwds["size"] = (PANEL_WIDTH, PANEL_HEIGHT)
kwds["style"] = wx.FULL_REPAINT_ON_RESIZE
ScrolledPanel.__init__(self, parent=parent, *args, **kwds)
PanelBase.__init__(self, parent)
self.SetupScrolling()
self.SetWindowVariant(variant=FONT_VARIANT)
self._manager = manager
# The data with no correction for background values
self._data = data # The data to be analysed (corrected fr background)
self._extrapolated_data = None # The extrapolated data set
self._transformed_data = None # Fourier trans. of the extrapolated data
self._calculator = CorfuncCalculator()
self._data_name_box = None # Text box to show name of file
self._background_input = None
self._qmin_input = None
self._qmax1_input = None
self._qmax2_input = None
self._extrapolate_btn = None
self._transform_btn = None
self._extract_btn = None
self.qmin = 0
self.qmax = (0, 0)
self.background = 0
self.extracted_params = None
self.transform_type = 'fourier'
self._extrapolation_outputs = {}
# Dictionary for saving refs to text boxes used to display output data
self._output_boxes = None
self.state = None
self._do_layout()
self._disable_inputs()
self.set_state()
self._qmin_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax1_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax2_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmin_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax1_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax2_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._background_input.Bind(wx.EVT_TEXT, self._on_enter_input)
def set_state(self, state=None, data=None):
"""
Set the state of the panel. If no state is provided, the panel will
be set to the default state.
:param state: A CorfuncState object
:param data: A Data1D object
"""
if state is None:
self.state = CorfuncState()
else:
self.state = state
if data is not None:
self.state.data = data
self.set_data(data, set_qrange=False)
if self.state.qmin is not None:
self.set_qmin(self.state.qmin)
if self.state.qmax is not None and self.state.qmax != (None, None):
self.set_qmax(tuple(self.state.qmax))
if self.state.background is not None:
self.set_background(self.state.background)
if self.state.is_extrapolated:
self.compute_extrapolation()
else:
return
if self.state.is_transformed:
self.transform_type = self.state.transform_type
self.compute_transform()
else:
return
if self.state.outputs is not None and self.state.outputs != {}:
self.set_extracted_params(self.state.outputs, reset=True)
def get_state(self):
"""
Return the state of the panel
"""
state = CorfuncState()
state.set_saved_state('qmin_tcl', self.qmin)
state.set_saved_state('qmax1_tcl', self.qmax[0])
state.set_saved_state('qmax2_tcl', self.qmax[1])
state.set_saved_state('background_tcl', self.background)
state.outputs = self.extracted_params
if self._data is not None:
state.file = self._data.title
state.data = self._data
if self._extrapolated_data is not None:
state.is_extrapolated = True
if self._transformed_data is not None:
state.is_transformed = True
state.transform_type = self.transform_type
self.state = state
return self.state
def onSetFocus(self, evt):
if evt is not None:
evt.Skip()
self._validate_inputs()
def set_data(self, data=None, set_qrange=True):
"""
Update the GUI to reflect new data that has been loaded in
:param data: The data that has been loaded
"""
if data is None:
self._disable_inputs()
# Reset outputs
self.set_extracted_params(reset=True)
self.set_extrapolation_params()
self._data = None
return
self._enable_inputs()
self._transform_btn.Disable()
self._extract_btn.Disable()
self._data_name_box.SetValue(str(data.title))
self._data = data
self._calculator.set_data(data)
# Reset the outputs
self.set_extracted_params(None, reset=True)
if self._manager is not None:
self._manager.clear_data()
self._manager.show_data(self._data, IQ_DATA_LABEL, reset=True)
if set_qrange:
lower = data.x[-1] * 0.05
upper1 = data.x[-1] - lower * 5
upper2 = data.x[-1]
self.set_qmin(lower)
self.set_qmax((upper1, upper2))
self._compute_background()
def get_data(self):
return self._data
def radio_changed(self, event=None):
"""
Called when the "Transform type" radio button are changed
"""
if event is not None:
self.transform_type = event.GetEventObject().GetName()
def compute_extrapolation(self, event=None):
"""
Compute and plot the extrapolated data.
Called when Extrapolate button is pressed.
"""
if not self._validate_inputs:
msg = "Invalid Q range entered."
wx.PostEvent(self.parent.parent, StatusEvent(status=msg))
return
warning_msg = ""
if self.background < 0:
warning_msg += "Negative background value entered."
if any((self._data.y - self.background) < 0):
if warning_msg != "":
warning_msg += "\n"
warning_msg += "Background value results in negative Intensity values."
if warning_msg != "":
self._background_input.SetBackgroundColour('yellow')
wx.PostEvent(self._manager.parent,
StatusEvent(status=warning_msg, info='warning'))
else:
self._background_input.SetBackgroundColour(wx.WHITE)
self._background_input.Refresh()
self._calculator.set_data(self._data)
self._calculator.lowerq = self.qmin
self._calculator.upperq = self.qmax
self._calculator.background = self.background
try:
params, self._extrapolated_data = self._calculator.compute_extrapolation(
)
except Exception as e:
msg = "Error extrapolating data:\n"
msg += str(e)
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="error"))
self._transform_btn.Disable()
return
self._manager.show_data(self._extrapolated_data,
IQ_EXTRAPOLATED_DATA_LABEL)
# Update state of the GUI
self._transform_btn.Enable()
self._extract_btn.Disable()
self.set_extracted_params(reset=True)
self.set_extrapolation_params(params)
def compute_transform(self, event=None):
"""
Compute and plot the transformed data.
Called when Transform button is pressed.
"""
if not self._calculator.transform_isrunning():
self._calculator.compute_transform(
self._extrapolated_data,
self.transform_type,
background=self.background,
completefn=self.transform_complete,
updatefn=self.transform_update)
self._transform_btn.SetLabel("Stop Transform")
else:
self._calculator.stop_transform()
self.transform_update("Transform cancelled.")
self._transform_btn.SetLabel("Transform")
def transform_update(self, msg=""):
"""
Called from FourierThread to update on status of calculation
"""
wx.PostEvent(self._manager.parent, StatusEvent(status=msg))
def transform_complete(self, transform=None):
"""
Called from FourierThread when calculation has completed
"""
self._transform_btn.SetLabel("Transform")
if transform is None:
msg = "Error calculating Transform."
if self.transform_type == 'hilbert':
msg = "Not yet implemented"
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
self._extract_btn.Disable()
return
self._transformed_data = transform
import numpy as np
plot_x = transform.x[np.where(transform.x <= 200)]
plot_y = transform.y[np.where(transform.x <= 200)]
self._manager.show_data(Data1D(plot_x, plot_y), TRANSFORM_LABEL1)
# Only enable extract params button if a fourier trans. has been done
if self.transform_type == 'fourier':
self._extract_btn.Enable()
else:
self._extract_btn.Disable()
def extract_parameters(self, event=None):
"""
Called when "Extract Parameters" is clicked
"""
try:
params = self._calculator.extract_parameters(
self._transformed_data)
except:
params = None
if params is None:
msg = "Error extracting parameters."
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
return
self.set_extracted_params(params)
def on_help(self, event=None):
"""
Show the corfunc documentation
"""
tree_location = "user/sasgui/perspectives/corfunc/corfunc_help.html"
doc_viewer = DocumentationWindow(self, -1, tree_location, "",
"Correlation Function Help")
def get_save_flag(self):
if self._data is not None:
return True
return False
def on_set_focus(self, event=None):
if self._manager.parent is not None:
wx.PostEvent(self._manager.parent, PanelOnFocusEvent(panel=self))
def on_save(self, event=None):
"""
Save corfunc state into a file
"""
# Ask the user the location of the file to write to.
path = None
default_save_location = os.getcwd()
if self._manager.parent is not None:
default_save_location = self._manager.parent.get_save_location()
dlg = wx.FileDialog(self, "Choose a file",
default_save_location, \
self.window_caption, "*.crf", wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
default_save_location = os.path.dirname(path)
if self._manager.parent is not None:
self._manager.parent._default_save_location = default_save_location
else:
return None
dlg.Destroy()
# MAC always needs the extension for saving
extens = ".crf"
# Make sure the ext included in the file name
f_name = os.path.splitext(path)[0] + extens
self._manager.state_reader.write(f_name, self._data, self.get_state())
def save_project(self, doc=None):
"""
Return an XML node containing the state of the panel
:param doc: Am xml node to attach the project state to (optional)
"""
data = self._data
state = self.get_state()
if data is not None:
new_doc, sasentry = self._manager.state_reader._to_xml_doc(data)
new_doc = state.toXML(doc=new_doc, entry_node=sasentry)
if new_doc is not None:
if doc is not None and hasattr(doc, "firstChild"):
child = new_doc.getElementsByTagName("SASentry")
for item in child:
doc.firstChild.appendChild(item)
else:
doc = new_doc
return doc
def set_qmin(self, qmin):
self.qmin = qmin
self._qmin_input.SetValue(str(qmin))
def set_qmax(self, qmax):
self.qmax = qmax
self._qmax1_input.SetValue(str(qmax[0]))
self._qmax2_input.SetValue(str(qmax[1]))
def set_background(self, bg):
self.background = bg
self._background_input.SetValue(str(bg))
self._calculator.background = bg
def set_extrapolation_params(self, params=None):
"""
Displays the value of the parameters calculated in the extrapolation
"""
if params is None:
# Reset outputs
for output in self._extrapolation_outputs.values():
output.SetValue('-')
return
for key, value in params.iteritems():
output = self._extrapolation_outputs[key]
rounded = self._round_sig_figs(value, 6)
output.SetValue(rounded)
def set_extracted_params(self, params=None, reset=False):
"""
Displays the values of the parameters extracted from the Fourier
transform
"""
self.extracted_params = params
error = False
if params is None:
if not reset: error = True
for output in self._output_boxes.values():
output.SetValue('-')
else:
if len(params) < len(OUTPUT_STRINGS):
# Not all parameters were calculated
error = True
for key, value in params.iteritems():
rounded = self._round_sig_figs(value, 6)
self._output_boxes[key].SetValue(rounded)
if error:
msg = 'Not all parameters were able to be calculated'
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info='error'))
def plot_qrange(self, active=None, leftdown=False):
if active is None:
active = self._qmin_input
wx.PostEvent(
self._manager.parent,
PlotQrangeEvent(
ctrl=[self._qmin_input, self._qmax1_input, self._qmax2_input],
active=active,
id=IQ_DATA_LABEL,
is_corfunc=True,
group_id=GROUP_ID_IQ_DATA,
leftdown=leftdown))
def _compute_background(self, event=None):
"""
Compute the background level based on the position of the upper q bars
"""
if event is not None:
event.Skip()
self._on_enter_input()
try:
bg = self._calculator.compute_background(self.qmax)
self.set_background(bg)
except Exception as e:
msg = "Error computing background level:\n"
msg += str(e)
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="error"))
def _on_enter_input(self, event=None):
"""
Read values from input boxes and save to memory.
"""
if event is not None: event.Skip()
if not self._validate_inputs():
return
self.qmin = float(self._qmin_input.GetValue())
new_qmax1 = float(self._qmax1_input.GetValue())
new_qmax2 = float(self._qmax2_input.GetValue())
self.qmax = (new_qmax1, new_qmax2)
self.background = float(self._background_input.GetValue())
self._calculator.background = self.background
if event is not None:
active_ctrl = event.GetEventObject()
if active_ctrl == self._background_input:
self._manager.show_data(self._data,
IQ_DATA_LABEL,
reset=False,
active_ctrl=active_ctrl)
def _on_click_qrange(self, event=None):
if event is None:
return
event.Skip()
if not self._validate_inputs(): return
self.plot_qrange(active=event.GetEventObject(),
leftdown=event.LeftDown())
def _validate_inputs(self):
"""
Check that the values for qmin and qmax in the input boxes are valid
"""
if self._data is None:
return False
qmin_valid = check_float(self._qmin_input)
qmax1_valid = check_float(self._qmax1_input)
qmax2_valid = check_float(self._qmax2_input)
qmax_valid = qmax1_valid and qmax2_valid
background_valid = check_float(self._background_input)
msg = ""
if (qmin_valid and qmax_valid and background_valid):
qmin = float(self._qmin_input.GetValue())
qmax1 = float(self._qmax1_input.GetValue())
qmax2 = float(self._qmax2_input.GetValue())
background = float(self._background_input.GetValue())
if not qmin > self._data.x.min():
msg = "qmin must be greater than the lowest q value"
qmin_valid = False
elif qmax2 < qmax1:
msg = "qmax1 must be less than qmax2"
qmax_valid = False
elif qmin > qmax1:
msg = "qmin must be less than qmax"
qmin_valid = False
elif background > self._data.y.max():
msg = "background must be less than highest I"
background_valid = False
if not qmin_valid:
self._qmin_input.SetBackgroundColour('pink')
if not qmax_valid:
self._qmax1_input.SetBackgroundColour('pink')
self._qmax2_input.SetBackgroundColour('pink')
if not background_valid:
self._background_input.SetBackgroundColour('pink')
if msg != "":
wx.PostEvent(self._manager.parent, StatusEvent(status=msg))
if (qmin_valid and qmax_valid and background_valid):
self._qmin_input.SetBackgroundColour(wx.WHITE)
self._qmax1_input.SetBackgroundColour(wx.WHITE)
self._qmax2_input.SetBackgroundColour(wx.WHITE)
self._background_input.SetBackgroundColour(wx.WHITE)
self._qmin_input.Refresh()
self._qmax1_input.Refresh()
self._qmax2_input.Refresh()
self._background_input.Refresh()
return (qmin_valid and qmax_valid and background_valid)
def _do_layout(self):
"""
Draw the window content
"""
vbox = wx.GridBagSizer(0, 0)
# I(q) data box
databox = wx.StaticBox(self, -1, "I(Q) Data Source")
databox_sizer = wx.StaticBoxSizer(databox, wx.VERTICAL)
file_sizer = wx.GridBagSizer(5, 5)
y = 0
file_name_label = wx.StaticText(self, -1, "Name:")
file_sizer.Add(file_name_label, (0, 0), (1, 1),
wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
self._data_name_box = OutputTextCtrl(self, -1, size=(300, 20))
file_sizer.Add(self._data_name_box, (0, 1), (1, 1),
wx.CENTER | wx.ADJUST_MINSIZE, 15)
file_sizer.AddSpacer((1, 25), pos=(0, 2))
databox_sizer.Add(file_sizer, wx.TOP, 15)
vbox.Add(databox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE | wx.TOP,
15)
y += 1
# Parameters
qbox = wx.StaticBox(self, -1, "Input Parameters")
qbox_sizer = wx.StaticBoxSizer(qbox, wx.VERTICAL)
qbox_sizer.SetMinSize((_STATICBOX_WIDTH, 75))
q_sizer = wx.GridBagSizer(5, 5)
# Explanation
explanation_txt = (
"Corfunc will use all values in the lower range for"
" Guinier back extrapolation, and all values in the upper range "
"for Porod forward extrapolation.")
explanation_label = wx.StaticText(self,
-1,
explanation_txt,
size=(_STATICBOX_WIDTH, 60))
q_sizer.Add(explanation_label, (0, 0), (1, 4), wx.LEFT | wx.EXPAND, 5)
qrange_label = wx.StaticText(self, -1, "Q Range:", size=(50, 20))
q_sizer.Add(qrange_label, (1, 0), (1, 1), wx.LEFT | wx.EXPAND, 5)
# Lower Q Range
qmin_label = wx.StaticText(self, -1, "Lower:", size=(50, 20))
qmin_dash_label = wx.StaticText(self,
-1,
"-",
size=(10, 20),
style=wx.ALIGN_CENTER_HORIZONTAL)
qmin_lower = OutputTextCtrl(self, -1, size=(75, 20), value="0.0")
self._qmin_input = ModelTextCtrl(
self,
-1,
size=(75, 20),
style=wx.TE_PROCESS_ENTER,
name='qmin_input',
text_enter_callback=self._on_enter_input)
self._qmin_input.SetToolTipString(("Values with q < qmin will be used "
"for Guinier back extrapolation"))
q_sizer.Add(qmin_label, (2, 0), (1, 1), wx.LEFT | wx.EXPAND, 5)
q_sizer.Add(qmin_lower, (2, 1), (1, 1), wx.LEFT, 5)
q_sizer.Add(qmin_dash_label, (2, 2), (1, 1), wx.CENTER | wx.EXPAND, 5)
q_sizer.Add(self._qmin_input, (2, 3), (1, 1), wx.LEFT, 5)
# Upper Q range
qmax_tooltip = ("Values with qmax1 < q < qmax2 will be used for Porod"
" forward extrapolation")
qmax_label = wx.StaticText(self, -1, "Upper:", size=(50, 20))
qmax_dash_label = wx.StaticText(self,
-1,
"-",
size=(10, 20),
style=wx.ALIGN_CENTER_HORIZONTAL)
self._qmax1_input = ModelTextCtrl(
self,
-1,
size=(75, 20),
style=wx.TE_PROCESS_ENTER,
name="qmax1_input",
text_enter_callback=self._on_enter_input)
self._qmax1_input.SetToolTipString(qmax_tooltip)
self._qmax2_input = ModelTextCtrl(
self,
-1,
size=(75, 20),
style=wx.TE_PROCESS_ENTER,
name="qmax2_input",
text_enter_callback=self._on_enter_input)
self._qmax2_input.SetToolTipString(qmax_tooltip)
q_sizer.Add(qmax_label, (3, 0), (1, 1), wx.LEFT | wx.EXPAND, 5)
q_sizer.Add(self._qmax1_input, (3, 1), (1, 1), wx.LEFT, 5)
q_sizer.Add(qmax_dash_label, (3, 2), (1, 1), wx.CENTER | wx.EXPAND, 5)
q_sizer.Add(self._qmax2_input, (3, 3), (1, 1), wx.LEFT, 5)
qbox_sizer.Add(q_sizer, wx.TOP, 0)
vbox.Add(qbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
extrapolation_box = wx.StaticBox(self, -1, "Extrapolation Parameters")
extrapolation_sizer = wx.StaticBoxSizer(extrapolation_box, wx.VERTICAL)
params_sizer = wx.GridBagSizer(5, 5)
guinier_label = wx.StaticText(self, -1, "Guinier:")
params_sizer.Add(guinier_label, (0, 0), (1, 1),
wx.ALL | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
a_label = wx.StaticText(self, -1, "A: ")
params_sizer.Add(a_label, (1, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
a_output = OutputTextCtrl(self,
wx.NewId(),
value="-",
style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(a_output, (1, 1), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['A'] = a_output
b_label = wx.StaticText(self, -1, "B: ")
params_sizer.Add(b_label, (2, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
b_output = OutputTextCtrl(self,
wx.NewId(),
value="-",
style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(b_output, (2, 1), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['B'] = b_output
porod_label = wx.StaticText(self, -1, "Porod: ")
params_sizer.Add(porod_label, (0, 2), (1, 1),
wx.ALL | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
k_label = wx.StaticText(self, -1, "K: ")
params_sizer.Add(k_label, (1, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
k_output = OutputTextCtrl(self,
wx.NewId(),
value="-",
style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(k_output, (1, 3), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['K'] = k_output
sigma_label = wx.StaticText(self, -1, u'\u03C3: ')
params_sizer.Add(sigma_label, (2, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
sigma_output = OutputTextCtrl(self,
wx.NewId(),
value="-",
style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(sigma_output, (2, 3), (1, 1), wx.RIGHT | wx.EXPAND,
15)
self._extrapolation_outputs['sigma'] = sigma_output
bg_label = wx.StaticText(self, -1, "Bg: ")
params_sizer.Add(bg_label, (3, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
self._background_input = ModelTextCtrl(
self,
-1,
value="0.0",
style=wx.TE_PROCESS_ENTER | wx.TE_CENTRE,
name='background_input',
text_enter_callback=self._on_enter_input)
self._background_input.SetToolTipString(
("A background value to "
"subtract from all intensity values"))
params_sizer.Add(self._background_input, (3, 3), (1, 1),
wx.RIGHT | wx.EXPAND, 15)
background_button = wx.Button(self,
wx.NewId(),
"Calculate Bg",
size=(75, -1))
background_button.Bind(wx.EVT_BUTTON, self._compute_background)
params_sizer.Add(background_button, (4, 3), (1, 1),
wx.EXPAND | wx.RIGHT, 15)
extrapolation_sizer.Add(params_sizer)
vbox.Add(extrapolation_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Transform type
transform_box = wx.StaticBox(self, -1, "Transform Type")
transform_sizer = wx.StaticBoxSizer(transform_box, wx.VERTICAL)
radio_sizer = wx.GridBagSizer(5, 5)
fourier_btn = wx.RadioButton(self,
-1,
"Fourier",
name='fourier',
style=wx.RB_GROUP)
hilbert_btn = wx.RadioButton(self, -1, "Hilbert", name='hilbert')
fourier_btn.Bind(wx.EVT_RADIOBUTTON, self.radio_changed)
hilbert_btn.Bind(wx.EVT_RADIOBUTTON, self.radio_changed)
radio_sizer.Add(fourier_btn, (0, 0), (1, 1), wx.LEFT | wx.EXPAND)
radio_sizer.Add(hilbert_btn, (0, 1), (1, 1), wx.RIGHT | wx.EXPAND)
transform_sizer.Add(radio_sizer, wx.TOP, 0)
vbox.Add(transform_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Output data
outputbox = wx.StaticBox(self, -1, "Output Parameters")
outputbox_sizer = wx.StaticBoxSizer(outputbox, wx.VERTICAL)
output_sizer = wx.GridBagSizer(5, 5)
self._output_boxes = dict()
i = 0
for key, value in OUTPUT_STRINGS.iteritems():
# Create a label and a text box for each poperty
label = wx.StaticText(self, -1, value)
output_box = OutputTextCtrl(self,
wx.NewId(),
value="-",
style=wx.ALIGN_CENTER_HORIZONTAL)
# Save the ID of each of the text boxes for accessing after the
# output data has been calculated
self._output_boxes[key] = output_box
output_sizer.Add(label, (i, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
output_sizer.Add(output_box, (i, 2), (1, 1), wx.RIGHT | wx.EXPAND,
15)
i += 1
outputbox_sizer.Add(output_sizer, wx.TOP, 0)
vbox.Add(outputbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Controls
controlbox = wx.StaticBox(self, -1, "Controls")
controlbox_sizer = wx.StaticBoxSizer(controlbox, wx.VERTICAL)
controls_sizer = wx.BoxSizer(wx.VERTICAL)
self._extrapolate_btn = wx.Button(self, wx.NewId(), "Extrapolate")
self._transform_btn = wx.Button(self, wx.NewId(), "Transform")
self._extract_btn = wx.Button(self, wx.NewId(), "Compute Parameters")
help_btn = wx.Button(self, -1, "HELP")
self._transform_btn.Disable()
self._extract_btn.Disable()
self._extrapolate_btn.Bind(wx.EVT_BUTTON, self.compute_extrapolation)
self._transform_btn.Bind(wx.EVT_BUTTON, self.compute_transform)
self._extract_btn.Bind(wx.EVT_BUTTON, self.extract_parameters)
help_btn.Bind(wx.EVT_BUTTON, self.on_help)
controls_sizer.Add(self._extrapolate_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(self._transform_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(self._extract_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(help_btn, wx.CENTER | wx.EXPAND)
controlbox_sizer.Add(controls_sizer, wx.TOP | wx.EXPAND, 0)
vbox.Add(controlbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
self.SetSizer(vbox)
def _disable_inputs(self):
"""
Disable all input fields
"""
self._qmin_input.Disable()
self._qmax1_input.Disable()
self._qmax2_input.Disable()
self._background_input.Disable()
self._extrapolate_btn.Disable()
def _enable_inputs(self):
"""
Enable all input fields
"""
self._qmin_input.Enable()
self._qmax1_input.Enable()
self._qmax2_input.Enable()
self._background_input.Enable()
self._extrapolate_btn.Enable()
def _round_sig_figs(self, x, sigfigs):
"""
Round a number to a given number of significant figures.
:param x: The value to round
:param sigfigs: How many significant figures to round to
:return rounded_str: x rounded to the given number of significant
figures, as a string
"""
rounded_str = ""
try:
# Index of first significant digit
significant_digit = -int(np.floor(np.log10(np.abs(x))))
if np.abs(significant_digit > 4):
# Use scientific notation if x > 1e5 or x < 1e4
rounded_str = "{1:.{0}E}".format(sigfigs - 1, x)
else:
# Format as a standard decimal
# Number of digits required for correct number of sig figs
digits = significant_digit + (sigfigs - 1)
rounded = np.round(x, decimals=digits)
rounded_str = "{1:.{0}f}".format(
sigfigs - 1 + significant_digit, rounded)
except:
# Method for finding significant_digit fails if x is 0 (since log10(0)=inf)
if x == 0.0:
rounded_str = "0.0"
else:
rounded_str = "-"
return rounded_str
class TestCalculator(unittest.TestCase):
def setUp(self):
self.data = load_data()
# Note: to generate target values from the GUI:
# * load the data from test/corfunc/test/98929.txt
# * set qrange to (0, 0.013), (0.15, 0.24)
# * select fourier transform type
# * click Calculate Bg
# * click Extrapolate
# * click Compute Parameters
# * copy the Guinier and Porod values to the extrapolate function
# * for each graph, grab the data from DataInfo and store it in _out.txt
self.calculator = CorfuncCalculator(data=self.data, lowerq=0.013,
upperq=(0.15, 0.24))
self.calculator.background = 0.3
self.extrapolation = None
self.transformation = None
self.results = [np.loadtxt(find(filename+"_out.txt")).T[2]
for filename in ("gamma1", "gamma3", "idf")]
def extrapolate(self):
params, extrapolation, s2 = self.calculator.compute_extrapolation()
# Check the extrapolation parameters
self.assertAlmostEqual(params['A'], 4.18970, places=5)
self.assertAlmostEqual(params['B'], -25469.9, places=1)
self.assertAlmostEqual(params['K'], 4.44660e-5, places=10)
#self.assertAlmostEqual(params['sigma'], 1.70181e-10, places=15)
# Ensure the extraplation tends to the background value
self.assertAlmostEqual(extrapolation.y[-1], self.calculator.background)
# Test extrapolation for q values between 0.02 and 0.24
mask = np.logical_and(self.data.x > 0.02, self.data.x < 0.24)
qs = self.data.x[mask]
iqs = self.data.y[mask]
for q, iq in zip(qs, iqs):
# Find the q value in the extraplation nearest to the value in
# the data
q_extrap = min(extrapolation.x, key=lambda x:abs(x-q))
# Find the index of this value in the extrapolation
index = list(extrapolation.x).index(q_extrap)
# Find it's corresponding intensity value
iq_extrap = extrapolation.y[index]
# Check the extrapolation agrees to the data at this point to 1 d.p
self.assertAlmostEqual(iq_extrap, iq, 1)
self.extrapolation = extrapolation
def transform(self):
self.calculator.compute_transform(self.extrapolation, 'fourier',
completefn=self.transform_callback)
# Transform is performed asynchronously; give it time to run
while True:
time.sleep(0.001)
if (not self.calculator.transform_isrunning() and
self.transformation is not None):
break
transform1, transform3, idf = self.transformation
self.assertIsNotNone(transform1)
self.assertAlmostEqual(transform1.y[0], 1)
self.assertAlmostEqual(transform1.y[-1], 0, 5)
def transform_callback(self, transforms):
self.transformation = transforms
def extract_params(self):
params = self.calculator.extract_parameters(self.transformation[0])
self.assertIsNotNone(params)
self.assertEqual(len(params), 6)
self.assertLess(abs(params['max']-75), 2.5) # L_p ~= 75
def check_transforms(self):
gamma1, gamma3, idf = self.transformation
gamma1_out, gamma3_out, idf_out = self.results
def compare(a, b):
return max(abs((a-b)/b))
#print("gamma1 diff", compare(gamma1.y[gamma1.x<=200.], gamma1_out))
#print("gamma3 diff", compare(gamma3.y[gamma3.x<=200.], gamma3_out))
#print("idf diff", compare(idf.y[idf.x<=200.], idf_out))
#self.assertLess(compare(gamma1.y[gamma1.x<=200.], gamma1_out), 1e-10)
#self.assertLess(compare(gamma3.y[gamma3.x<=200.], gamma3_out), 1e-10)
#self.assertLess(compare(idf.y[idf.x<=200.], idf_out), 1e-10)
# Ensure tests are ran in correct order;
# Each test depends on the one before it
def test_calculator(self):
steps = [self.extrapolate, self.transform, self.extract_params, self.check_transforms]
for test in steps:
try:
test()
except Exception as e:
raise
self.fail("{} failed ({}: {})".format(test, type(e), e))
def setUp(self):
self.data = load_data()
self.calculator = CorfuncCalculator(data=self.data,
lowerq=0.013,
upperq=(0.15, 0.24))
self.extrapolation = None
class TestCalculator(unittest.TestCase):
def setUp(self):
self.data = load_data()
self.calculator = CorfuncCalculator(data=self.data,
lowerq=0.013,
upperq=(0.15, 0.24))
self.extrapolation = None
def extrapolate(self):
params, extrapolation = self.calculator.compute_extrapolation()
# Check the extrapolation parameters
self.assertAlmostEqual(params['A'], 4.19, places=2)
self.assertAlmostEqual(params['B'], -25470, places=0)
self.assertAlmostEqual(params['K'], 4.5e-5, places=2)
self.assertAlmostEqual(params['sigma'], 2.2e-10, places=2)
# Ensure the extraplation tends to the background value
self.assertAlmostEqual(extrapolation.y[-1], self.calculator.background)
# Test extrapolation for q values between 0.02 and 0.24
mask = np.logical_and(self.data.x > 0.02, self.data.x < 0.24)
qs = self.data.x[mask]
iqs = self.data.y[mask]
for q, iq in zip(qs, iqs):
# Find the q value in the extraplation nearest to the value in
# the data
q_extrap = min(extrapolation.x, key=lambda x: abs(x - q))
# Find the index of this value in the extrapolation
index = list(extrapolation.x).index(q_extrap)
# Find it's corresponding intensity value
iq_extrap = extrapolation.y[index]
# Check the extrapolation agrees to the data at this point to 1 d.p
self.assertAlmostEqual(iq_extrap, iq, 1)
self.extrapolation = extrapolation
def transform(self):
self.calculator.compute_transform(self.extrapolation,
'fourier',
completefn=self.transform_callback)
# Transform is performed asynchronously; give it time to run
while True:
time.sleep(0.001)
if not self.calculator.transform_isrunning():
break
def transform_callback(self, transform):
self.assertIsNotNone(transform)
self.assertAlmostEqual(transform.y[0], 1)
self.assertAlmostEqual(transform.y[-1], 0, 5)
self.transformation = transform
def extract_params(self):
params = self.calculator.extract_parameters(self.transformation)
self.assertIsNotNone(params)
self.assertEqual(len(params), 6)
self.assertLess(abs(params['max'] - 75), 2.5) # L_p ~= 75
# Ensure tests are ran in correct order;
# Each test depends on the one before it
def test_calculator(self):
steps = [self.extrapolate, self.transform, self.extract_params]
for test in steps:
try:
test()
except Exception as e:
self.fail("{} failed ({}: {})".format(test, type(e), e))
class CorfuncPanel(ScrolledPanel,PanelBase):
window_name = "Correlation Function"
window_caption = "Correlation Function"
CENTER_PANE = True
def __init__(self, parent, data=None, manager=None, *args, **kwds):
kwds["size"] = (PANEL_WIDTH, PANEL_HEIGHT)
kwds["style"] = wx.FULL_REPAINT_ON_RESIZE
ScrolledPanel.__init__(self, parent=parent, *args, **kwds)
PanelBase.__init__(self, parent)
self.SetupScrolling()
self.SetWindowVariant(variant=FONT_VARIANT)
self._manager = manager
# The data with no correction for background values
self._data = data # The data to be analysed (corrected fr background)
self._extrapolated_data = None # The extrapolated data set
self._transformed_data = None # Fourier trans. of the extrapolated data
self._calculator = CorfuncCalculator()
self._data_name_box = None # Text box to show name of file
self._background_input = None
self._qmin_input = None
self._qmax1_input = None
self._qmax2_input = None
self._extrapolate_btn = None
self._transform_btn = None
self._extract_btn = None
self.qmin = 0
self.qmax = (0, 0)
self.background = 0
self.extracted_params = None
self.transform_type = 'fourier'
self._extrapolation_outputs = {}
# Dictionary for saving refs to text boxes used to display output data
self._output_boxes = None
self.state = None
self._do_layout()
self._disable_inputs()
self.set_state()
self._qmin_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax1_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmax2_input.Bind(wx.EVT_TEXT, self._on_enter_input)
self._qmin_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax1_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._qmax2_input.Bind(wx.EVT_MOUSE_EVENTS, self._on_click_qrange)
self._background_input.Bind(wx.EVT_TEXT, self._on_enter_input)
def set_state(self, state=None, data=None):
"""
Set the state of the panel. If no state is provided, the panel will
be set to the default state.
:param state: A CorfuncState object
:param data: A Data1D object
"""
if state is None:
self.state = CorfuncState()
else:
self.state = state
if data is not None:
self.state.data = data
self.set_data(data, set_qrange=False)
if self.state.qmin is not None:
self.set_qmin(self.state.qmin)
if self.state.qmax is not None and self.state.qmax != (None, None):
self.set_qmax(tuple(self.state.qmax))
if self.state.background is not None:
self.set_background(self.state.background)
if self.state.is_extrapolated:
self.compute_extrapolation()
else:
return
if self.state.is_transformed:
self.transform_type = self.state.transform_type
self.compute_transform()
else:
return
if self.state.outputs is not None and self.state.outputs != {}:
self.set_extracted_params(self.state.outputs, reset=True)
def get_state(self):
"""
Return the state of the panel
"""
state = CorfuncState()
state.set_saved_state('qmin_tcl', self.qmin)
state.set_saved_state('qmax1_tcl', self.qmax[0])
state.set_saved_state('qmax2_tcl', self.qmax[1])
state.set_saved_state('background_tcl', self.background)
state.outputs = self.extracted_params
if self._data is not None:
state.file = self._data.title
state.data = self._data
if self._extrapolated_data is not None:
state.is_extrapolated = True
if self._transformed_data is not None:
state.is_transformed = True
state.transform_type = self.transform_type
self.state = state
return self.state
def onSetFocus(self, evt):
if evt is not None:
evt.Skip()
self._validate_inputs()
def set_data(self, data=None, set_qrange=True):
"""
Update the GUI to reflect new data that has been loaded in
:param data: The data that has been loaded
"""
if data is None:
self._disable_inputs()
# Reset outputs
self.set_extracted_params(reset=True)
self.set_extrapolation_params()
self._data = None
return
self._enable_inputs()
self._transform_btn.Disable()
self._extract_btn.Disable()
self._data_name_box.SetValue(str(data.title))
self._data = data
self._calculator.set_data(data)
# Reset the outputs
self.set_extracted_params(None, reset=True)
if self._manager is not None:
self._manager.clear_data()
self._manager.show_data(self._data, IQ_DATA_LABEL, reset=True)
if set_qrange:
lower = data.x[-1]*0.05
upper1 = data.x[-1] - lower*5
upper2 = data.x[-1]
self.set_qmin(lower)
self.set_qmax((upper1, upper2))
self._compute_background()
def get_data(self):
return self._data
def radio_changed(self, event=None):
"""
Called when the "Transform type" radio button are changed
"""
if event is not None:
self.transform_type = event.GetEventObject().GetName()
def compute_extrapolation(self, event=None):
"""
Compute and plot the extrapolated data.
Called when Extrapolate button is pressed.
"""
if not self._validate_inputs:
msg = "Invalid Q range entered."
wx.PostEvent(self.parent.parent, StatusEvent(status=msg))
return
warning_msg = ""
if self.background < 0:
warning_msg += "Negative background value entered."
if any((self._data.y - self.background) < 0):
if warning_msg != "":
warning_msg += "\n"
warning_msg += "Background value results in negative Intensity values."
if warning_msg != "":
self._background_input.SetBackgroundColour('yellow')
wx.PostEvent(self._manager.parent, StatusEvent(status=warning_msg, info='warning'))
else:
self._background_input.SetBackgroundColour(wx.WHITE)
self._background_input.Refresh()
self._calculator.set_data(self._data)
self._calculator.lowerq = self.qmin
self._calculator.upperq = self.qmax
self._calculator.background = self.background
try:
params, self._extrapolated_data = self._calculator.compute_extrapolation()
except Exception as e:
msg = "Error extrapolating data:\n"
msg += str(e)
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="error"))
self._transform_btn.Disable()
return
self._manager.show_data(self._extrapolated_data, IQ_EXTRAPOLATED_DATA_LABEL)
# Update state of the GUI
self._transform_btn.Enable()
self._extract_btn.Disable()
self.set_extracted_params(reset=True)
self.set_extrapolation_params(params)
def compute_transform(self, event=None):
"""
Compute and plot the transformed data.
Called when Transform button is pressed.
"""
if not self._calculator.transform_isrunning():
self._calculator.compute_transform(self._extrapolated_data,
self.transform_type, background=self.background,
completefn=self.transform_complete,
updatefn=self.transform_update)
self._transform_btn.SetLabel("Stop Transform")
else:
self._calculator.stop_transform()
self.transform_update("Transform cancelled.")
self._transform_btn.SetLabel("Transform")
def transform_update(self, msg=""):
"""
Called from FourierThread to update on status of calculation
"""
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg))
def transform_complete(self, transform=None):
"""
Called from FourierThread when calculation has completed
"""
self._transform_btn.SetLabel("Transform")
if transform is None:
msg = "Error calculating Transform."
if self.transform_type == 'hilbert':
msg = "Not yet implemented"
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
self._extract_btn.Disable()
return
self._transformed_data = transform
import numpy as np
plot_x = transform.x[np.where(transform.x <= 200)]
plot_y = transform.y[np.where(transform.x <= 200)]
self._manager.show_data(Data1D(plot_x, plot_y), TRANSFORM_LABEL1)
# Only enable extract params button if a fourier trans. has been done
if self.transform_type == 'fourier':
self._extract_btn.Enable()
else:
self._extract_btn.Disable()
def extract_parameters(self, event=None):
"""
Called when "Extract Parameters" is clicked
"""
try:
params = self._calculator.extract_parameters(self._transformed_data)
except:
params = None
if params is None:
msg = "Error extracting parameters."
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
return
self.set_extracted_params(params)
def on_help(self, event=None):
"""
Show the corfunc documentation
"""
tree_location = "user/sasgui/perspectives/corfunc/corfunc_help.html"
doc_viewer = DocumentationWindow(self, -1, tree_location, "",
"Correlation Function Help")
def get_save_flag(self):
if self._data is not None:
return True
return False
def on_set_focus(self, event=None):
if self._manager.parent is not None:
wx.PostEvent(self._manager.parent, PanelOnFocusEvent(panel=self))
def on_save(self, event=None):
"""
Save corfunc state into a file
"""
# Ask the user the location of the file to write to.
path = None
default_save_location = os.getcwd()
if self._manager.parent is not None:
default_save_location = self._manager.parent.get_save_location()
dlg = wx.FileDialog(self, "Choose a file",
default_save_location, \
self.window_caption, "*.crf", wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
default_save_location = os.path.dirname(path)
if self._manager.parent is not None:
self._manager.parent._default_save_location = default_save_location
else:
return None
dlg.Destroy()
# MAC always needs the extension for saving
extens = ".crf"
# Make sure the ext included in the file name
f_name = os.path.splitext(path)[0] + extens
self._manager.state_reader.write(f_name, self._data, self.get_state())
def save_project(self, doc=None):
"""
Return an XML node containing the state of the panel
:param doc: Am xml node to attach the project state to (optional)
"""
data = self._data
state = self.get_state()
if data is not None:
new_doc, sasentry = self._manager.state_reader._to_xml_doc(data)
new_doc = state.toXML(doc=new_doc, entry_node=sasentry)
if new_doc is not None:
if doc is not None and hasattr(doc, "firstChild"):
child = new_doc.getElementsByTagName("SASentry")
for item in child:
doc.firstChild.appendChild(item)
else:
doc = new_doc
return doc
def set_qmin(self, qmin):
self.qmin = qmin
self._qmin_input.SetValue(str(qmin))
def set_qmax(self, qmax):
self.qmax = qmax
self._qmax1_input.SetValue(str(qmax[0]))
self._qmax2_input.SetValue(str(qmax[1]))
def set_background(self, bg):
self.background = bg
self._background_input.SetValue(str(bg))
self._calculator.background = bg
def set_extrapolation_params(self, params=None):
"""
Displays the value of the parameters calculated in the extrapolation
"""
if params is None:
# Reset outputs
for output in self._extrapolation_outputs.values():
output.SetValue('-')
return
for key, value in params.iteritems():
output = self._extrapolation_outputs[key]
rounded = self._round_sig_figs(value, 6)
output.SetValue(rounded)
def set_extracted_params(self, params=None, reset=False):
"""
Displays the values of the parameters extracted from the Fourier
transform
"""
self.extracted_params = params
error = False
if params is None:
if not reset: error = True
for output in self._output_boxes.values():
output.SetValue('-')
else:
if len(params) < len(OUTPUT_STRINGS):
# Not all parameters were calculated
error = True
for key, value in params.iteritems():
rounded = self._round_sig_figs(value, 6)
self._output_boxes[key].SetValue(rounded)
if error:
msg = 'Not all parameters were able to be calculated'
wx.PostEvent(self._manager.parent, StatusEvent(
status=msg, info='error'))
def plot_qrange(self, active=None, leftdown=False):
if active is None:
active = self._qmin_input
wx.PostEvent(self._manager.parent, PlotQrangeEvent(
ctrl=[self._qmin_input, self._qmax1_input, self._qmax2_input],
active=active, id=IQ_DATA_LABEL, is_corfunc=True,
group_id=GROUP_ID_IQ_DATA, leftdown=leftdown))
def _compute_background(self, event=None):
"""
Compute the background level based on the position of the upper q bars
"""
if event is not None:
event.Skip()
self._on_enter_input()
try:
bg = self._calculator.compute_background(self.qmax)
self.set_background(bg)
except Exception as e:
msg = "Error computing background level:\n"
msg += str(e)
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="error"))
def _on_enter_input(self, event=None):
"""
Read values from input boxes and save to memory.
"""
if event is not None: event.Skip()
if not self._validate_inputs():
return
self.qmin = float(self._qmin_input.GetValue())
new_qmax1 = float(self._qmax1_input.GetValue())
new_qmax2 = float(self._qmax2_input.GetValue())
self.qmax = (new_qmax1, new_qmax2)
self.background = float(self._background_input.GetValue())
self._calculator.background = self.background
if event is not None:
active_ctrl = event.GetEventObject()
if active_ctrl == self._background_input:
self._manager.show_data(self._data, IQ_DATA_LABEL,
reset=False, active_ctrl=active_ctrl)
def _on_click_qrange(self, event=None):
if event is None:
return
event.Skip()
if not self._validate_inputs(): return
self.plot_qrange(active=event.GetEventObject(),
leftdown=event.LeftDown())
def _validate_inputs(self):
"""
Check that the values for qmin and qmax in the input boxes are valid
"""
if self._data is None:
return False
qmin_valid = check_float(self._qmin_input)
qmax1_valid = check_float(self._qmax1_input)
qmax2_valid = check_float(self._qmax2_input)
qmax_valid = qmax1_valid and qmax2_valid
background_valid = check_float(self._background_input)
msg = ""
if (qmin_valid and qmax_valid and background_valid):
qmin = float(self._qmin_input.GetValue())
qmax1 = float(self._qmax1_input.GetValue())
qmax2 = float(self._qmax2_input.GetValue())
background = float(self._background_input.GetValue())
if not qmin > self._data.x.min():
msg = "qmin must be greater than the lowest q value"
qmin_valid = False
elif qmax2 < qmax1:
msg = "qmax1 must be less than qmax2"
qmax_valid = False
elif qmin > qmax1:
msg = "qmin must be less than qmax"
qmin_valid = False
elif background > self._data.y.max():
msg = "background must be less than highest I"
background_valid = False
if not qmin_valid:
self._qmin_input.SetBackgroundColour('pink')
if not qmax_valid:
self._qmax1_input.SetBackgroundColour('pink')
self._qmax2_input.SetBackgroundColour('pink')
if not background_valid:
self._background_input.SetBackgroundColour('pink')
if msg != "":
wx.PostEvent(self._manager.parent, StatusEvent(status=msg))
if (qmin_valid and qmax_valid and background_valid):
self._qmin_input.SetBackgroundColour(wx.WHITE)
self._qmax1_input.SetBackgroundColour(wx.WHITE)
self._qmax2_input.SetBackgroundColour(wx.WHITE)
self._background_input.SetBackgroundColour(wx.WHITE)
self._qmin_input.Refresh()
self._qmax1_input.Refresh()
self._qmax2_input.Refresh()
self._background_input.Refresh()
return (qmin_valid and qmax_valid and background_valid)
def _do_layout(self):
"""
Draw the window content
"""
vbox = wx.GridBagSizer(0,0)
# I(q) data box
databox = wx.StaticBox(self, -1, "I(Q) Data Source")
databox_sizer = wx.StaticBoxSizer(databox, wx.VERTICAL)
file_sizer = wx.GridBagSizer(5, 5)
y = 0
file_name_label = wx.StaticText(self, -1, "Name:")
file_sizer.Add(file_name_label, (0, 0), (1, 1),
wx.LEFT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
self._data_name_box = OutputTextCtrl(self, -1,
size=(300,20))
file_sizer.Add(self._data_name_box, (0, 1), (1, 1),
wx.CENTER | wx.ADJUST_MINSIZE, 15)
file_sizer.AddSpacer((1, 25), pos=(0,2))
databox_sizer.Add(file_sizer, wx.TOP, 15)
vbox.Add(databox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE | wx.TOP, 15)
y += 1
# Parameters
qbox = wx.StaticBox(self, -1, "Input Parameters")
qbox_sizer = wx.StaticBoxSizer(qbox, wx.VERTICAL)
qbox_sizer.SetMinSize((_STATICBOX_WIDTH, 75))
q_sizer = wx.GridBagSizer(5, 5)
# Explanation
explanation_txt = ("Corfunc will use all values in the lower range for"
" Guinier back extrapolation, and all values in the upper range "
"for Porod forward extrapolation.")
explanation_label = wx.StaticText(self, -1, explanation_txt,
size=(_STATICBOX_WIDTH, 60))
q_sizer.Add(explanation_label, (0,0), (1,4), wx.LEFT | wx.EXPAND, 5)
qrange_label = wx.StaticText(self, -1, "Q Range:", size=(50,20))
q_sizer.Add(qrange_label, (1,0), (1,1), wx.LEFT | wx.EXPAND, 5)
# Lower Q Range
qmin_label = wx.StaticText(self, -1, "Lower:", size=(50,20))
qmin_dash_label = wx.StaticText(self, -1, "-", size=(10,20),
style=wx.ALIGN_CENTER_HORIZONTAL)
qmin_lower = OutputTextCtrl(self, -1, size=(75, 20), value="0.0")
self._qmin_input = ModelTextCtrl(self, -1, size=(75, 20),
style=wx.TE_PROCESS_ENTER, name='qmin_input',
text_enter_callback=self._on_enter_input)
self._qmin_input.SetToolTipString(("Values with q < qmin will be used "
"for Guinier back extrapolation"))
q_sizer.Add(qmin_label, (2, 0), (1, 1), wx.LEFT | wx.EXPAND, 5)
q_sizer.Add(qmin_lower, (2, 1), (1, 1), wx.LEFT, 5)
q_sizer.Add(qmin_dash_label, (2, 2), (1, 1), wx.CENTER | wx.EXPAND, 5)
q_sizer.Add(self._qmin_input, (2, 3), (1, 1), wx.LEFT, 5)
# Upper Q range
qmax_tooltip = ("Values with qmax1 < q < qmax2 will be used for Porod"
" forward extrapolation")
qmax_label = wx.StaticText(self, -1, "Upper:", size=(50,20))
qmax_dash_label = wx.StaticText(self, -1, "-", size=(10,20),
style=wx.ALIGN_CENTER_HORIZONTAL)
self._qmax1_input = ModelTextCtrl(self, -1, size=(75, 20),
style=wx.TE_PROCESS_ENTER, name="qmax1_input",
text_enter_callback=self._on_enter_input)
self._qmax1_input.SetToolTipString(qmax_tooltip)
self._qmax2_input = ModelTextCtrl(self, -1, size=(75, 20),
style=wx.TE_PROCESS_ENTER, name="qmax2_input",
text_enter_callback=self._on_enter_input)
self._qmax2_input.SetToolTipString(qmax_tooltip)
q_sizer.Add(qmax_label, (3, 0), (1, 1), wx.LEFT | wx.EXPAND, 5)
q_sizer.Add(self._qmax1_input, (3, 1), (1, 1), wx.LEFT, 5)
q_sizer.Add(qmax_dash_label, (3, 2), (1, 1), wx.CENTER | wx.EXPAND, 5)
q_sizer.Add(self._qmax2_input, (3,3), (1, 1), wx.LEFT, 5)
qbox_sizer.Add(q_sizer, wx.TOP, 0)
vbox.Add(qbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
extrapolation_box = wx.StaticBox(self, -1, "Extrapolation Parameters")
extrapolation_sizer = wx.StaticBoxSizer(extrapolation_box, wx.VERTICAL)
params_sizer = wx.GridBagSizer(5, 5)
guinier_label = wx.StaticText(self, -1, "Guinier:")
params_sizer.Add(guinier_label, (0, 0), (1,1),
wx.ALL | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
a_label = wx.StaticText(self, -1, "A: ")
params_sizer.Add(a_label, (1, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
a_output = OutputTextCtrl(self, wx.NewId(),
value="-", style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(a_output, (1, 1), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['A'] = a_output
b_label = wx.StaticText(self, -1, "B: ")
params_sizer.Add(b_label, (2, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
b_output = OutputTextCtrl(self, wx.NewId(),
value="-", style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(b_output, (2, 1), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['B'] = b_output
porod_label = wx.StaticText(self, -1, "Porod: ")
params_sizer.Add(porod_label, (0, 2), (1, 1),
wx.ALL | wx.EXPAND | wx.ADJUST_MINSIZE, 5)
k_label = wx.StaticText(self, -1, "K: ")
params_sizer.Add(k_label, (1, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
k_output = OutputTextCtrl(self, wx.NewId(),
value="-", style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(k_output, (1, 3), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['K'] = k_output
sigma_label = wx.StaticText(self, -1, u'\u03C3: ')
params_sizer.Add(sigma_label, (2, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
sigma_output = OutputTextCtrl(self, wx.NewId(),
value="-", style=wx.ALIGN_CENTER_HORIZONTAL)
params_sizer.Add(sigma_output, (2, 3), (1, 1), wx.RIGHT | wx.EXPAND, 15)
self._extrapolation_outputs['sigma'] = sigma_output
bg_label = wx.StaticText(self, -1, "Bg: ")
params_sizer.Add(bg_label, (3, 2), (1, 1), wx.LEFT | wx.EXPAND, 15)
self._background_input = ModelTextCtrl(self, -1, value="0.0",
style=wx.TE_PROCESS_ENTER | wx.TE_CENTRE, name='background_input',
text_enter_callback=self._on_enter_input)
self._background_input.SetToolTipString(("A background value to "
"subtract from all intensity values"))
params_sizer.Add(self._background_input, (3, 3), (1, 1), wx.RIGHT | wx.EXPAND, 15)
background_button = wx.Button(self, wx.NewId(), "Calculate Bg",
size=(75, -1))
background_button.Bind(wx.EVT_BUTTON, self._compute_background)
params_sizer.Add(background_button, (4,3), (1, 1), wx.EXPAND | wx.RIGHT, 15)
extrapolation_sizer.Add(params_sizer)
vbox.Add(extrapolation_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Transform type
transform_box = wx.StaticBox(self, -1, "Transform Type")
transform_sizer = wx.StaticBoxSizer(transform_box, wx.VERTICAL)
radio_sizer = wx.GridBagSizer(5,5)
fourier_btn = wx.RadioButton(self, -1, "Fourier", name='fourier',
style=wx.RB_GROUP)
hilbert_btn = wx.RadioButton(self, -1, "Hilbert", name='hilbert')
fourier_btn.Bind(wx.EVT_RADIOBUTTON, self.radio_changed)
hilbert_btn.Bind(wx.EVT_RADIOBUTTON, self.radio_changed)
radio_sizer.Add(fourier_btn, (0,0), (1,1), wx.LEFT | wx.EXPAND)
radio_sizer.Add(hilbert_btn, (0,1), (1,1), wx.RIGHT | wx.EXPAND)
transform_sizer.Add(radio_sizer, wx.TOP, 0)
vbox.Add(transform_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Output data
outputbox = wx.StaticBox(self, -1, "Output Parameters")
outputbox_sizer = wx.StaticBoxSizer(outputbox, wx.VERTICAL)
output_sizer = wx.GridBagSizer(5, 5)
self._output_boxes = dict()
i = 0
for key, value in OUTPUT_STRINGS.iteritems():
# Create a label and a text box for each poperty
label = wx.StaticText(self, -1, value)
output_box = OutputTextCtrl(self, wx.NewId(),
value="-", style=wx.ALIGN_CENTER_HORIZONTAL)
# Save the ID of each of the text boxes for accessing after the
# output data has been calculated
self._output_boxes[key] = output_box
output_sizer.Add(label, (i, 0), (1, 1), wx.LEFT | wx.EXPAND, 15)
output_sizer.Add(output_box, (i, 2), (1, 1),
wx.RIGHT | wx.EXPAND, 15)
i += 1
outputbox_sizer.Add(output_sizer, wx.TOP, 0)
vbox.Add(outputbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
y += 1
# Controls
controlbox = wx.StaticBox(self, -1, "Controls")
controlbox_sizer = wx.StaticBoxSizer(controlbox, wx.VERTICAL)
controls_sizer = wx.BoxSizer(wx.VERTICAL)
self._extrapolate_btn = wx.Button(self, wx.NewId(), "Extrapolate")
self._transform_btn = wx.Button(self, wx.NewId(), "Transform")
self._extract_btn = wx.Button(self, wx.NewId(), "Compute Parameters")
help_btn = wx.Button(self, -1, "HELP")
self._transform_btn.Disable()
self._extract_btn.Disable()
self._extrapolate_btn.Bind(wx.EVT_BUTTON, self.compute_extrapolation)
self._transform_btn.Bind(wx.EVT_BUTTON, self.compute_transform)
self._extract_btn.Bind(wx.EVT_BUTTON, self.extract_parameters)
help_btn.Bind(wx.EVT_BUTTON, self.on_help)
controls_sizer.Add(self._extrapolate_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(self._transform_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(self._extract_btn, wx.CENTER | wx.EXPAND)
controls_sizer.Add(help_btn, wx.CENTER | wx.EXPAND)
controlbox_sizer.Add(controls_sizer, wx.TOP | wx.EXPAND, 0)
vbox.Add(controlbox_sizer, (y, 0), (1, 1),
wx.LEFT | wx.RIGHT | wx.EXPAND | wx.ADJUST_MINSIZE, 15)
self.SetSizer(vbox)
def _disable_inputs(self):
"""
Disable all input fields
"""
self._qmin_input.Disable()
self._qmax1_input.Disable()
self._qmax2_input.Disable()
self._background_input.Disable()
self._extrapolate_btn.Disable()
def _enable_inputs(self):
"""
Enable all input fields
"""
self._qmin_input.Enable()
self._qmax1_input.Enable()
self._qmax2_input.Enable()
self._background_input.Enable()
self._extrapolate_btn.Enable()
def _round_sig_figs(self, x, sigfigs):
"""
Round a number to a given number of significant figures.
:param x: The value to round
:param sigfigs: How many significant figures to round to
:return rounded_str: x rounded to the given number of significant
figures, as a string
"""
rounded_str = ""
try:
# Index of first significant digit
significant_digit = -int(np.floor(np.log10(np.abs(x))))
if np.abs(significant_digit > 4):
# Use scientific notation if x > 1e5 or x < 1e4
rounded_str = "{1:.{0}E}".format(sigfigs-1, x)
else:
# Format as a standard decimal
# Number of digits required for correct number of sig figs
digits = significant_digit + (sigfigs - 1)
rounded = np.round(x, decimals=digits)
rounded_str = "{1:.{0}f}".format(sigfigs -1 + significant_digit,
rounded)
except:
# Method for finding significant_digit fails if x is 0 (since log10(0)=inf)
if x == 0.0:
rounded_str = "0.0"
else:
rounded_str = "-"
return rounded_str
def setUp(self):
self.data = load_data()
self.calculator = CorfuncCalculator(data=self.data, lowerq=0.013,
upperq=(0.15, 0.24))
self.extrapolation = None
class TestCalculator(unittest.TestCase):
def setUp(self):
self.data = load_data()
self.calculator = CorfuncCalculator(data=self.data, lowerq=0.013,
upperq=(0.15, 0.24))
self.extrapolation = None
def extrapolate(self):
params, extrapolation = self.calculator.compute_extrapolation()
# Check the extrapolation parameters
self.assertAlmostEqual(params['A'], 4.19, places=2)
self.assertAlmostEqual(params['B'], -25470, places=0)
self.assertAlmostEqual(params['K'], 4.5e-5, places=2)
self.assertAlmostEqual(params['sigma'], 2.2e-10, places=2)
# Ensure the extraplation tends to the background value
self.assertAlmostEqual(extrapolation.y[-1], self.calculator.background)
# Test extrapolation for q values between 0.02 and 0.24
mask = np.logical_and(self.data.x > 0.02, self.data.x < 0.24)
qs = self.data.x[mask]
iqs = self.data.y[mask]
for q, iq in zip(qs, iqs):
# Find the q value in the extraplation nearest to the value in
# the data
q_extrap = min(extrapolation.x, key=lambda x:abs(x-q))
# Find the index of this value in the extrapolation
index = list(extrapolation.x).index(q_extrap)
# Find it's corresponding intensity value
iq_extrap = extrapolation.y[index]
# Check the extrapolation agrees to the data at this point to 1 d.p
self.assertAlmostEqual(iq_extrap, iq, 1)
self.extrapolation = extrapolation
def transform(self):
self.calculator.compute_transform(self.extrapolation, 'fourier',
completefn=self.transform_callback)
# Transform is performed asynchronously; give it time to run
while True:
time.sleep(0.001)
if not self.calculator.transform_isrunning():
break
def transform_callback(self, transform):
self.assertIsNotNone(transform)
self.assertAlmostEqual(transform.y[0], 1)
self.assertAlmostEqual(transform.y[-1], 0, 5)
self.transformation = transform
def extract_params(self):
params = self.calculator.extract_parameters(self.transformation)
self.assertIsNotNone(params)
self.assertEqual(len(params), 6)
self.assertLess(abs(params['max']-75), 2.5) # L_p ~= 75
# Ensure tests are ran in correct order;
# Each test depends on the one before it
def test_calculator(self):
steps = [self.extrapolate, self.transform, self.extract_params]
for test in steps:
try:
test()
except Exception as e:
self.fail("{} failed ({}: {})".format(test, type(e), e))