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))