def plot_1d(self): self.parent.ui.graphicsView_fitResult.reset_viewer() # get the sample log/meta data name o_gui = GuiUtilities(parent=self.parent) x_axis_name = str(self.parent.ui.comboBox_xaxisNames.currentText()) y_axis_name = str(self.parent.ui.comboBox_yaxisNames.currentText()) x_axis_peak_index = o_gui.get_plot1d_axis_peak_label_index(is_xaxis=True) y_axis_peak_index = o_gui.get_plot1d_axis_peak_label_index(is_xaxis=False) o_data_retriever = DataRetriever(parent=self.parent) is_plot_with_error = False axis_x_data, axis_x_error = o_data_retriever.get_data(name=x_axis_name, peak_index=x_axis_peak_index) axis_y_data, axis_y_error = o_data_retriever.get_data(name=y_axis_name, peak_index=y_axis_peak_index) if ((x_axis_name in LIST_AXIS_TO_PLOT['fit'].keys()) or (y_axis_name in LIST_AXIS_TO_PLOT['fit'].keys())): is_plot_with_error = True # is_plot_with_error = False # REMOVE that line once the error bars are correctAT if is_plot_with_error: self.parent.ui.graphicsView_fitResult.plot_scatter_with_errors(vec_x=axis_x_data, vec_y=axis_y_data, vec_x_error=axis_x_error, vec_y_error=axis_y_error, x_label=x_axis_name, y_label=y_axis_name) else: self.parent.ui.graphicsView_fitResult.plot_scatter(axis_x_data, axis_y_data, x_axis_name, y_axis_name)
def update_fit_peak_ranges_table(self, **kwargs): self.parent.ui.peak_range_table.blockSignals(True) def __get_kwargs_value(key='', data_type='boolean'): if data_type == 'boolean': _default = False elif data_type == 'array': _default = [] return kwargs[key] if key in kwargs.keys() else _default # click = __get_kwargs_value('click', data_type='boolean') # move = __get_kwargs_value('move', data_type='boolean') # release = __get_kwargs_value('release', data_type='boolean') list_fit_peak_ranges = __get_kwargs_value('list_fit_peak_ranges', data_type='array') # list_fit_peak_ranges_matplotlib_id = __get_kwargs_value('list_fit_peak_ranges_matplotlib_id', # data_type='array') list_fit_peak_labels = __get_kwargs_value('list_fit_peak_labels', data_type='array') list_fit_peak_d0 = __get_kwargs_value('list_fit_peak_d0', data_type='array') o_gui = GuiUtilities(parent=self.parent) o_gui.reset_peak_range_table() o_gui.fill_peak_range_table(list_fit_peak_ranges=list_fit_peak_ranges, list_fit_peak_labels=list_fit_peak_labels, list_fit_peak_d0=list_fit_peak_d0) self.parent.ui.peak_range_table.blockSignals(False) o_gui.check_if_fitting_widgets_can_be_enabled()
def list_subruns_2dplot(self): raw_input = str(self.parent.ui.lineEdit_subruns_2dplot.text()) o_gui = GuiUtilities(parent=self.parent) try: parse_input = parse_integers(raw_input) o_gui.make_visible_listsubruns_warning(False) except RuntimeError: o_gui.make_visible_listsubruns_warning(True) return parse_input
def fit_multi_peaks(self): QApplication.setOverrideCursor(Qt.WaitCursor) _peak_range_list = [ tuple(_range) for _range in self.parent._ui_graphicsView_fitSetup.list_peak_ranges ] _peak_center_list = [ np.mean([left, right]) for (left, right) in _peak_range_list ] _peak_tag_list = [ "peak{}".format(_index) for _index, _ in enumerate(_peak_center_list) ] _peak_function_name = str( self.parent.ui.comboBox_peakType.currentText()) _peak_xmin_list = [left for (left, _) in _peak_range_list] _peak_xmax_list = [right for (_, right) in _peak_range_list] # Fit peak hd_ws = self.parent.hidra_workspace _wavelength = hd_ws.get_wavelength(True, True) fit_engine = PeakFitEngineFactory.getInstance(hd_ws, _peak_function_name, 'Linear', wavelength=_wavelength) fit_result = fit_engine.fit_multiple_peaks(_peak_tag_list, _peak_xmin_list, _peak_xmax_list) self.parent.fit_result = fit_result self.parent.populate_fit_result_table(fit_result=fit_result) # self.parent.update_list_of_2d_plots_axis() o_gui = GuiUtilities(parent=self.parent) o_gui.set_1D_2D_axis_comboboxes(with_clear=True, fill_raw=True, fill_fit=True) o_gui.initialize_combobox() o_gui.enabled_export_csv_widgets(enabled=True) o_gui.enabled_2dplot_widgets(enabled=True) o_plot = Plot(parent=self.parent) o_plot.plot_2d() QApplication.restoreOverrideCursor()
def peak_range_table_right_click(self, position=-1): nbr_row = self.parent.ui.peak_range_table.rowCount() if nbr_row == 0: return menu = QMenu(self.parent) _remove_row = menu.addAction("Remove") action = menu.exec_(QCursor.pos()) if action == _remove_row: self.remove_peak_range_table_row() o_gui = GuiUtilities(parent=self.parent) o_gui.check_if_fitting_widgets_can_be_enabled()
def load_and_plot(self, hidra_file_name): try: o_load = Load(parent=self.parent) o_load.load(project_file=hidra_file_name) except RuntimeError as run_err: pop_message(self, 'Failed to load {}'.format(hidra_file_name), str(run_err), 'error') except KeyError as key_err: pop_message(self, 'Failed to load {}'.format(hidra_file_name), str(key_err), 'error') self.parent.current_root_statusbar_message = "Working with: {} " \ "\t\t\t\t Project Name: {}" \ "".format(hidra_file_name, self.parent._project_name) self.parent.ui.statusbar.showMessage( self.parent.current_root_statusbar_message) try: o_plot = Plot(parent=self.parent) o_plot.plot_diff_data(plot_model=False) o_plot.reset_fitting_plot() except RuntimeError as run_err: pop_message(self, 'Failed to plot {}'.format(hidra_file_name), str(run_err), 'error') try: o_fit = Fit(parent=self.parent) o_fit.initialize_fitting_table() # enabled all fitting widgets and main plot o_gui = GuiUtilities(parent=self.parent) o_gui.check_if_fitting_widgets_can_be_enabled() o_gui.enabled_sub_runs_interation_widgets(True) # o_gui.enabled_fitting_widgets(True) o_gui.enabled_data_fit_plot(True) o_gui.enabled_peak_ranges_widgets(True) o_gui.enabled_1dplot_widgets(True) except RuntimeError as run_err: pop_message( self, 'Failed to initialize widgets for {}'.format(hidra_file_name), str(run_err), 'error')
def load(self, project_file=None): if project_file is None: return try: self.__set_up_project_name(project_file=project_file) ws = self.parent._core.load_hidra_project( project_file, project_name=self.parent._project_name, load_detector_counts=False, load_diffraction=True) # Record data key and next self.parent._curr_file_name = project_file self.parent.hidra_workspace = ws self.parent.create_plot_color_range() except (RuntimeError, TypeError) as run_err: pop_message(self, 'Unable to load {}'.format(project_file), detailed_message=str(run_err), message_type='error') # # Edit information on the UI for user to visualize # self.parent.ui.label_loadedFileInfo.setText('Loaded {}; Project name: {}' # .format(project_file, self.parent._project_name)) # Get and set the range of sub runs o_utility = Utilities(parent=self.parent) sub_run_list = o_utility.get_subruns_limit() o_gui = GuiUtilities(parent=self.parent) o_gui.initialize_fitting_slider(max=len(sub_run_list)) o_gui.set_1D_2D_axis_comboboxes(with_clear=True, fill_raw=True) o_gui.enabled_1dplot_widgets(enabled=True) o_gui.initialize_combobox()
def fit_peaks(self, all_sub_runs=False): """ Fit peaks either all peaks or selected peaks The workflow includes 1. parse sub runs, peak and background type 2. fit peaks 3. show the fitting result in table 4. plot the peak in first sub runs that is fit :param all_sub_runs: Flag to fit peaks of all sub runs without checking :return: """ # Get the sub runs to fit or all the peaks # if not all_sub_runs: # # Parse sub runs specified in lineEdit_scanNumbers # o_utilities = Utilities(parent=self.parent) # sub_run_list = o_utilities.parse_sub_runs() # else: sub_run_list = None # Get peak function and background function peak_function = str(self.parent.ui.comboBox_peakType.currentText()) bkgd_function = str( self.parent.ui.comboBox_backgroundType.currentText()) # Get peak fitting range from the range of figure fit_range = self.parent._ui_graphicsView_fitSetup.get_x_limit() print('[INFO] Peak fit range: {0}'.format(fit_range)) # Fit Peaks: It is better to fit all the peaks at the same time after testing guessed_peak_center = 0.5 * (fit_range[0] + fit_range[1]) peak_info_dict = { 'Peak 1': { 'Center': guessed_peak_center, 'Range': fit_range } } self.parent._core.fit_peaks(project_name=self.parent._project_name, sub_run_list=sub_run_list, peak_type=peak_function, background_type=bkgd_function, peaks_fitting_setup=peak_info_dict) # Process fitted peaks # TEST - #84 - This shall be reviewed! try: # FIXME - effective_parameter=True will fail! # FIXME - other than return_format=dict will fail! # FIXME - need to give a real value to default_tag # FIXME - this only works if fitting 1 peak a time default_tag = peak_info_dict.keys()[0] function_params, fit_values = self.parent._core.get_peak_fitting_result( self.parent._project_name, default_tag, return_format=dict, effective_parameter=False, fitting_function=peak_function) except AttributeError as err: pop_message(self, 'Zoom in/out to only show peak to fit!', str(err), "error") return # TODO - #84+ - Need to implement the option as effective_parameter=True print('[DB...BAT...FITWINDOW....FIT] returned = {}, {}'.format( function_params, fit_values)) self.parent._sample_log_names_mutex = True for param_name in function_params: self.parent._function_param_name_set.add(param_name) # # log index and center of mass # size_x = len(self.parent._sample_log_names) + len(self.parent._function_param_name_set) + 2 # # # center of mass # size_y = len(self.parent._sample_log_names) + len(self.parent._function_param_name_set) + 1 # release the mutex: because re-plot is required anyway self.parent._sample_log_names_mutex = False # Show fitting result in Table # TODO - could add an option to show native or effective peak parameters try: self.show_fit_result_table(peak_function, function_params, fit_values, is_effective=False) except IndexError: return # plot the model and difference if sub_run_list is None: o_plot = Plot(parent=self.parent) o_plot.plot_diff_and_fitted_data(1, True) o_gui = GuiUtilities(parent=self.parent) o_gui.set_1D_2D_axis_comboboxes(fill_fit=True) o_gui.enabled_export_csv_widgets(True)
def plot_2d(self): o_gui = GuiUtilities(parent=self.parent) x_axis_name = str( self.parent.ui.comboBox_xaxisNames_2dplot.currentText()) y_axis_name = str( self.parent.ui.comboBox_yaxisNames_2dplot.currentText()) z_axis_name = str( self.parent.ui.comboBox_zaxisNames_2dplot.currentText()) x_axis_peak_index = o_gui.get_plot2d_axis_peak_label_index(axis='x') y_axis_peak_index = o_gui.get_plot2d_axis_peak_label_index(axis='y') z_axis_peak_index = o_gui.get_plot2d_axis_peak_label_index(axis='z') o_data_retriever = DataRetriever(parent=self.parent) axis_x_data, axis_x_error = o_data_retriever.get_data( name=x_axis_name, peak_index=x_axis_peak_index) axis_y_data, axis_y_error = o_data_retriever.get_data( name=y_axis_name, peak_index=y_axis_peak_index) axis_z_data, axis_z_error = o_data_retriever.get_data( name=z_axis_name, peak_index=z_axis_peak_index) if not self.parent.ui.radioButton_3dscatter.isChecked(): array_dict = self.format_3D_axis_data(axis_x=axis_x_data, axis_y=axis_y_data, axis_z=axis_z_data) x_axis = array_dict['x_axis'] y_axis = array_dict['y_axis'] z_axis = array_dict['z_axis'] if len(x_axis) < 2: return self.parent.ui.graphicsView_plot2D.ax.clear() if self.parent.ui.graphicsView_plot2D.colorbar: self.parent.ui.graphicsView_plot2D.colorbar.remove() self.parent.ui.graphicsView_plot2D.colorbar = None if self.parent.ui.radioButton_contour.isChecked(): self.parent.ui.graphicsView_plot2D.ax = self.parent.ui.graphicsView_plot2D.figure.gca( ) my_plot = self.parent.ui.graphicsView_plot2D.ax.contourf( x_axis, y_axis, z_axis) self.parent.ui.graphicsView_plot2D.colorbar = \ self.parent.ui.graphicsView_plot2D.figure.colorbar(my_plot) self.parent.ui.graphicsView_plot2D._myCanvas.draw() self.parent.ui.graphicsView_plot2D.ax.set_xlabel(x_axis_name) self.parent.ui.graphicsView_plot2D.ax.set_ylabel(y_axis_name) elif self.parent.ui.radioButton_3dline.isChecked(): x, y = np.meshgrid(x_axis, y_axis) self.parent.ui.graphicsView_plot2D.ax = self.parent.ui.graphicsView_plot2D.figure.gca( projection='3d') my_plot = self.parent.ui.graphicsView_plot2D.ax.plot_surface( x, y, z_axis, cmap=cm.coolwarm, linewidth=0, antialiased=False) self.parent.ui.graphicsView_plot2D.colorbar = self.parent.ui.graphicsView_plot2D.figure.colorbar( my_plot) self.parent.ui.graphicsView_plot2D.ax.set_xlabel(x_axis_name) self.parent.ui.graphicsView_plot2D.ax.set_ylabel(y_axis_name) self.parent.ui.graphicsView_plot2D.ax.set_zlabel(z_axis_name) # maybe look at projections on the wall (matplotlib.org/gallery/mplot3d/contour3d_3.html) self.parent.ui.graphicsView_plot2D.ax.contour( x, y, z_axis, zdir='z', offset=np.nanmin(z_axis), cmap=cm.coolwarm) self.parent.ui.graphicsView_plot2D.ax.contour(x, y, z_axis, zdir='y', offset=np.nanmax(y), cmap=cm.coolwarm) self.parent.ui.graphicsView_plot2D.ax.contour(x, y, z_axis, zdir='x', offset=np.nanmax(x), cmap=cm.coolwarm) self.parent.ui.graphicsView_plot2D._myCanvas.draw() else: self.parent.ui.graphicsView_plot2D.ax = self.parent.ui.graphicsView_plot2D.figure.gca( projection='3d') self.parent.ui.graphicsView_plot2D.ax.scatter( axis_x_data, axis_y_data, axis_z_data) self.parent.ui.graphicsView_plot2D._myCanvas.draw() self.parent.ui.graphicsView_plot2D.ax.set_xlabel(x_axis_name) self.parent.ui.graphicsView_plot2D.ax.set_ylabel(y_axis_name) self.parent.ui.graphicsView_plot2D.ax.set_zlabel(z_axis_name)
def setup_ui(self): """define the layout, widgets and signals""" # promote self.ui.graphicsView_fitResult = qt_util.promote_widget(self, self.ui.graphicsView_fitResult_frame, GeneralDiffDataView) self.ui.graphicsView_fitResult.setEnabled(False) self.ui.graphicsView_fitResult.set_subplots(1, 1) self.ui.graphicsView_plot2D = qt_util.promote_widget(self, self.ui.graphicsView_2dPlot_frame, MplGraphicsViewContourPlot) self.ui.tableView_fitSummary = qt_util.promote_widget(self, self.ui.tableView_fitSummary_frame, FitResultTable) self._promote_peak_fit_setup() self._init_widgets() # set up handling self.ui.pushButton_browseHDF.clicked.connect(self.browse_hdf) self.ui.lineEdit_listSubRuns.returnPressed.connect(self.plot_diff_data) self.ui.pushButton_FitPeaks.clicked.connect(self.fit_peaks) self.ui.horizontalScrollBar_SubRuns.valueChanged.connect(self.plot_scan) self.ui.radioButton_individualSubRuns.clicked.connect(self.individual_sub_runs) self.ui.radioButton_listSubRuns.clicked.connect(self.list_sub_runs) self.ui.actionQuit.triggered.connect(self.do_quit) self.ui.actionSave.triggered.connect(self.save) self.ui.actionSaveAs.triggered.connect(self.save_as) self.ui.actionAdvanced_Peak_Fit_Settings.triggered.connect(self.do_launch_adv_fit) self.ui.pushButton_exportCSV.clicked.connect(self.export_csv) self.ui.actionQuick_Fit_Result_Check.triggered.connect(self.do_make_movie) self.ui.lineEdit_subruns_2dplot.returnPressed.connect(self.list_subruns_2dplot_returned) self.ui.lineEdit_subruns_2dplot.textChanged.connect(self.list_subruns_2dplot_changed) self.ui.pushButton_save_peak_range.clicked.connect(self.clicked_save_peak_range) self.ui.pushButton_load_peak_range.clicked.connect(self.clicked_load_peak_range) self.ui.tableView_fitSummary.itemSelectionChanged.connect(self.fit_result_table_selection_changed) self.ui.radioButton_fit_value.clicked.connect(self.fit_table_radio_buttons) self.ui.radioButton_fit_error.clicked.connect(self.fit_table_radio_buttons) self.ui.spinBox_peak_index.valueChanged.connect(self.fit_table_radio_buttons) self.ui.comboBox_xaxisNames.currentIndexChanged.connect(self.axis_1d_changed) self.ui.comboBox_yaxisNames.currentIndexChanged.connect(self.axis_1d_changed) self.ui.plot1d_xaxis_peak_label_comboBox.currentIndexChanged.connect(self.axis_1d_changed) self.ui.plot1d_yaxis_peak_label_comboBox.currentIndexChanged.connect(self.axis_1d_changed) self.ui.comboBox_xaxisNames_2dplot.currentIndexChanged.connect(self.axis_2d_changed) self.ui.comboBox_yaxisNames_2dplot.currentIndexChanged.connect(self.axis_2d_changed) self.ui.comboBox_zaxisNames_2dplot.currentIndexChanged.connect(self.axis_2d_changed) self.ui.plot2d_xaxis_peak_label_comboBox.currentIndexChanged.connect(self.axis_2d_changed) self.ui.plot2d_yaxis_peak_label_comboBox.currentIndexChanged.connect(self.axis_2d_changed) self.ui.plot2d_zaxis_peak_label_comboBox.currentIndexChanged.connect(self.axis_2d_changed) self.ui.radioButton_contour.clicked.connect(self.axis_2d_changed) self.ui.radioButton_3dline.clicked.connect(self.axis_2d_changed) self.ui.radioButton_3dscatter.clicked.connect(self.axis_2d_changed) self.ui.peak_range_table.cellChanged.connect(self.peak_range_table_changed) # tracker for sample log names and peak parameter names self._sample_log_name_set = set() self._function_param_name_set = set() # mutexes self._sample_log_names_mutex = False # TODO - 20181124 - New GUI parameters (After FitPeaks) # checkBox_showFitError # checkBox_showFitValue # others # TODO - 20181124 - Make this table's column flexible! self.ui.tableView_fitSummary.setup(peak_param_names=list()) o_gui = GuiUtilities(parent=self) o_gui.enabled_fitting_widgets(False) o_gui.enabled_1dplot_widgets(False) o_gui.check_axis1d_status() o_gui.enabled_2dplot_widgets(False) o_gui.check_axis2d_status() o_gui.make_visible_listsubruns_warning(False) o_gui.enabled_export_csv_widgets(False) o_gui.enabled_peak_ranges_widgets(False) o_gui.enabled_save_peak_range_widget(False) o_gui.enabled_sub_runs_interation_widgets(False) # for debugging only self.ui.radioButton_contour.setEnabled(False) self.ui.radioButton_3dline.setEnabled(False)
def update_save_peak_range_widget(self): o_gui = GuiUtilities(parent=self) o_gui.update_save_peak_range_widget_status()
def axis_2d_changed(self): o_gui = GuiUtilities(parent=self) o_gui.check_axis2d_status() o_plot = Plot(parent=self) o_plot.plot_2d()
def check_subRunsDisplayMode(self): o_gui = GuiUtilities(parent=self) o_gui.check_subRuns_display_mode()
def browse_load_plot_hdf(self): if self.parent._core is None: raise RuntimeError('Not set up yet!') # o_utility = Utilities(parent=self.parent) # hydra_file_name = o_utility.get_default_hdf() hidra_file_name = None if hidra_file_name is None: # No default Hidra file: browse the file file_filter = 'HDF (*.hdf);H5 (*.h5)' hidra_file_name = browse_file(self.parent, 'HIDRA Project File', os.getcwd(), file_filter, file_list=False, save_file=False) if hidra_file_name is None: return # user clicked cancel self.parent.current_hidra_file_name = hidra_file_name try: o_load = Load(parent=self.parent) o_load.load(project_file=hidra_file_name) except RuntimeError as run_err: pop_message(self, 'Failed to load {}'.format(hidra_file_name), str(run_err), 'error') except KeyError as key_err: pop_message(self, 'Failed to load {}'.format(hidra_file_name), str(key_err), 'error') self.parent.current_root_statusbar_message = "Working with: {} " \ "\t\t\t\t Project Name: {}" \ "".format(hidra_file_name, self.parent._project_name) self.parent.ui.statusbar.showMessage( self.parent.current_root_statusbar_message) try: o_plot = Plot(parent=self.parent) o_plot.plot_diff_data(plot_model=False) o_plot.reset_fitting_plot() except RuntimeError as run_err: pop_message(self, 'Failed to plot {}'.format(hidra_file_name), str(run_err), 'error') try: o_fit = Fit(parent=self.parent) o_fit.initialize_fitting_table() # enabled all fitting widgets and main plot o_gui = GuiUtilities(parent=self.parent) o_gui.check_if_fitting_widgets_can_be_enabled() o_gui.enabled_sub_runs_interation_widgets(True) # o_gui.enabled_fitting_widgets(True) o_gui.enabled_data_fit_plot(True) o_gui.enabled_peak_ranges_widgets(True) o_gui.enabled_1dplot_widgets(True) except RuntimeError as run_err: pop_message( self, 'Failed to initialize widgets for {}'.format(hidra_file_name), str(run_err), 'error')