pyTEMlib 0.2023.8.0__py2.py3-none-any.whl → 0.2024.2.0__py2.py3-none-any.whl

pyTEMlib/info_dialog.py

@@ -1,665 +0,0 @@
-"""
-Input Dialog for EELS Analysis
-
-Author: Gerd Duscher
-
-"""
-import numpy as np
-import sidpy
-
-Qt_available = True
-try:
-    from PyQt5 import QtCore,  QtWidgets
-except:
-    Qt_available = False
-    # print('Qt dialogs are not available')
-
-
-import pyTEMlib.eels_dialog_utilities as ieels
-from pyTEMlib.microscope import microscope
-import ipywidgets
-import matplotlib.pylab as plt
-import matplotlib
-from IPython.display import display
-from pyTEMlib import file_tools as ft
-_version = 000
-
-
-if Qt_available:
-    from pyTEMlib import info_dlg
-    class InfoDialog(QtWidgets.QDialog):
-        """
-        Input Dialog for EELS Analysis
-
-        Opens a PyQt5 GUi Dialog that allows to set the experimental parameter necessary for a Quantification.
-
-
-        The dialog operates on a sidpy dataset
-        """
-
-        def __init__(self, datasets=None, key=None):
-            super().__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-            # Create an instance of the GUI
-            self.ui = info_dlg.UiDialog(self)
-            self.set_action()
-            self.datasets = datasets
-
-            self.spec_dim = []
-            self.energy_scale = np.array([])
-            self.experiment = {}
-            self.energy_dlg = None
-            self.axis = None
-            
-            self.y_scale = 1.0
-            self.change_y_scale = 1.0
-            self.show()
-
-            if self.datasets is None:
-                # make a dummy dataset for testing
-                key = 'Channel_000'
-                self.datasets={key: ft.make_dummy_dataset(sidpy.DataType.SPECTRUM)}
-            if key is None:
-                key = list(self.datasets.keys())[0]
-            self.dataset = self.datasets[key]
-            self.key = key
-            if not isinstance(self.dataset, sidpy.Dataset):
-                raise TypeError('dataset has to be a sidpy dataset')
-
-            self.set_dataset(self.dataset)
-
-            view = self.dataset.plot()
-            if hasattr(self.dataset.view, 'axes'):
-                self.axis = self.dataset.view.axes[-1]
-            elif hasattr(self.dataset.view, 'axis'):
-                self.axis = self.dataset.view.axis
-            self.figure = self.axis.figure
-            self.plot()
-            self.update()
-
-        def set_dataset(self, dataset):
-            self.dataset = dataset
-            if not hasattr(self.dataset, '_axes'):
-                self.dataset._axes = self.dataset.axes
-            if not hasattr(self.dataset, 'meta_data'):
-                self.dataset.meta_data = {}
-
-            spec_dim = dataset.get_dimensions_by_type(sidpy.DimensionType.SPECTRAL)
-            if len(spec_dim) != 1:
-                raise TypeError('We need exactly one SPECTRAL dimension')
-            self.spec_dim = self.dataset._axes[spec_dim[0]]
-            self.energy_scale = self.spec_dim.values.copy()
-
-            minimum_info = {'offset': self.energy_scale[0],
-                            'dispersion': self.energy_scale[1] - self.energy_scale[0],
-                            'exposure_time': 0.0,
-                            'convergence_angle': 0.0, 'collection_angle': 0.0,
-                            'acceleration_voltage': 100.0, 'binning': 1, 'conversion': 1.0,
-                            'flux_ppm': -1.0, 'flux_unit': 'counts', 'current': 1.0, 'SI_bin_x': 1, 'SI_bin_y': 1}
-            if 'experiment' not in self.dataset.metadata:
-                self.dataset.metadata['experiment'] = minimum_info
-            self.experiment = self.dataset.metadata['experiment']
-
-            for key, item in minimum_info.items():
-                if key not in self.experiment:
-                    self.experiment[key] = item
-            self.set_flux_list()
-
-        def set_dimension(self):
-            spec_dim = self.dataset.get_dimensions_by_type(sidpy.DimensionType.SPECTRAL)
-            self.spec_dim = self.dataset._axes[spec_dim[0]]
-            old_energy_scale = self.spec_dim
-            self.dataset.set_dimension(spec_dim[0], sidpy.Dimension(np.array(self.energy_scale),
-                                                                    name=old_energy_scale.name,
-                                                                    dimension_type=sidpy.DimensionType.SPECTRAL,
-                                                                    units='eV',
-                                                                    quantity='energy loss'))
-
-        def update(self):
-
-            self.ui.offsetEdit.setText(f"{self.experiment['offset']:.3f}")
-            self.ui.dispersionEdit.setText(f"{self.experiment['dispersion']:.3f}")
-            self.ui.timeEdit.setText(f"{self.experiment['exposure_time']:.6f}")
-
-            self.ui.convEdit.setText(f"{self.experiment['convergence_angle']:.2f}")
-            self.ui.collEdit.setText(f"{self.experiment['collection_angle']:.2f}")
-            self.ui.E0Edit.setText(f"{self.experiment['acceleration_voltage']/1000.:.2f}")
-
-            self.ui.binningEdit.setText(f"{self.experiment['binning']}")
-            self.ui.conversionEdit.setText(f"{self.experiment['conversion']:.2f}")
-            self.ui.fluxEdit.setText(f"{self.experiment['flux_ppm']:.2f}")
-            self.ui.fluxUnit.setText(f"{self.experiment['flux_unit']}")
-            self.ui.VOAEdit.setText(f"{self.experiment['current']:.2f}")
-            self.ui.statusBar.showMessage('Message in statusbar.')
-
-        def on_enter(self):
-            sender = self.sender()
-
-            if sender == self.ui.offsetEdit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['offset'] = value
-                sender.setText(f"{value:.2f}")
-                self.energy_scale = self.energy_scale - self.energy_scale[0] + value
-                self.set_dimension()
-                self.plot()
-            elif sender == self.ui.dispersionEdit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['dispersion'] = value
-                self.energy_scale = np.arange(len(self.energy_scale)) * value + self.energy_scale[0]
-                self.set_dimension()
-                self.plot()
-                sender.setText(f"{value:.3f}")
-            elif sender == self.ui.timeEdit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['exposure_time'] = value
-                sender.setText(f"{value:.2f}")
-            elif sender == self.ui.convEdit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['convergence_angle'] = value
-                sender.setText(f"{value:.2f}")
-            elif sender == self.ui.collEdit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['collection_angle'] = value
-                sender.setText(f"{value:.2f}")
-            elif sender == self.ui.E0Edit:
-                value = float(str(sender.displayText()).strip())
-                self.experiment['acceleration_voltage'] = value*1000.0
-                sender.setText(f"{value:.2f}")
-            elif sender == self.ui.fluxEdit:
-                value = float(str(sender.displayText()).strip())
-                if value == 0:
-                    self.set_flux()
-                else:
-                    self.experiment['flux_ppm'] = value
-                    sender.setText(f"{value:.2f}")
-            elif sender == self.ui.binXEdit or sender == self.ui.binYEdit:
-                if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-                    bin_x = int(self.ui.binXEdit.displayText())
-                    bin_y = int(self.ui.binYEdit.displayText())
-                    self.experiment['SI_bin_x'] = bin_x
-                    self.experiment['SI_bin_y'] = bin_y
-                    self.dataset.view.set_bin([bin_x, bin_y])
-                    self.ui.binXEdit.setText(str(self.dataset.view.bin_x))
-                    self.ui.binYEdit.setText(str(self.dataset.view.bin_y))
-            else:
-                print('not supported yet')
-
-        def plot(self):
-            if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-                spectrum = self.dataset.view.get_spectrum()
-                self.axis = self.dataset.view.axes[1]
-            else:
-                spectrum = np.array(self.dataset)
-                self.axis = self.dataset.view.axis
-
-            spectrum *= self.y_scale
-
-            x_limit = self.axis.get_xlim()
-            y_limit = np.array(self.axis.get_ylim())
-            self.axis.clear()
-            
-
-            self.axis.plot(self.energy_scale, spectrum, label='spectrum')
-            self.axis.set_xlim(x_limit)
-            if self.change_y_scale !=1.0:
-                y_limit *= self.change_y_scale
-                self.change_y_scale = 1.0
-            self.axis.set_ylim(y_limit)
-            
-            if self.y_scale != 1.:
-                self.axis.set_ylabel('scattering intensity (ppm)')
-                
-            self.axis.set_xlabel('energy_loss (eV)')
-
-            self.figure.canvas.draw_idle()
-
-        def on_list_enter(self):
-            sender = self.sender()
-            if sender == self.ui.TEMList:
-                microscope.set_microscope(self.ui.TEMList.currentText())
-                self.experiment['microscope'] = microscope.name
-                self.experiment['convergence_angle'] = microscope.alpha
-                self.experiment['collection_angle'] = microscope.beta
-                self.experiment['acceleration_voltage'] = microscope.E0
-                self.update()
-
-        def set_energy_scale(self):
-            self.energy_dlg = ieels.EnergySelector(self.dataset)
-
-            self.energy_dlg.signal_selected[bool].connect(self.set_energy)
-            self.energy_dlg.show()
-
-        def set_energy(self, k):
-            spec_dim = self.dataset.get_dimensions_by_type(sidpy.DimensionType.SPECTRAL)
-            self.spec_dim = self.dataset._axes[spec_dim[0]]
-
-            self.energy_scale = self.spec_dim.values
-            self.experiment['offset'] = self.energy_scale[0]
-            self.experiment['dispersion'] = self.energy_scale[1] - self.energy_scale[0]
-            self.update()
-
-        def set_flux(self, key):
-            self.ui.statusBar.showMessage('on_set_flux')
-            new_flux = 1.0
-            title = key
-            metadata = {}
-            if key in self.datasets.keys():
-                flux_dataset = self.datasets[key]
-                if isinstance(flux_dataset, sidpy.Dataset):
-                    exposure_time = -1.0
-                    flux_dataset = self.datasets[key]
-                    if flux_dataset.data_type.name == 'IMAGE' or 'SPECTRUM' in flux_dataset.data_type.name:
-                        if 'exposure_time' in flux_dataset.metadata['experiment']:
-                            if 'number_of_frames' in flux_dataset.metadata['experiment']:
-                                exposure_time = flux_dataset.metadata['experiment']['single_exposure_time'] * flux_dataset.metadata['experiment']['number_of_frames'] 
-                            else:
-                                exposure_time = flux_dataset.metadata['experiment']['exposure_time']
-                        else:
-                            exposure_time = -1.0
-                            flux_dataset.metadata['experiment']['exposure_time'] = -1
-                            print('Did not find exposure time assume 1s')
-                        if exposure_time > 0:
-                            new_flux  = np.sum(np.array(flux_dataset*1e-6))/exposure_time*self.dataset.metadata['experiment']['exposure_time']
-                            title = flux_dataset.title
-                            metadata = flux_dataset.metadata
-                            self.experiment['flux_ppm'] = new_flux
-                            self.experiment['flux_units'] = 'Mcounts '
-                            self.experiment['flux_source'] = title
-                            self.experiment['flux_metadata'] = metadata
-    
-                            self.update()
-
-        def on_check(self):
-            sender = self.sender()
-        
-            if sender.objectName() == 'probability':
-                dispersion = self.energy_scale[1]-self.energy_scale[0]
-                if sender.isChecked():
-                    self.y_scale = 1/self.experiment['flux_ppm']*dispersion
-                    self.change_y_scale = 1/self.experiment['flux_ppm']*dispersion
-                else:
-                    self.y_scale = 1.
-                    self.change_y_scale = self.experiment['flux_ppm']/dispersion
-                self.plot()
-
-        def set_flux_list(self):
-            length_list = self.ui.select_flux.count()+1
-            for i in range(2, length_list):
-                self.ui.select_flux.removeItem(i)
-            for key in self.datasets.keys():
-                if isinstance(self.datasets[key], sidpy.Dataset):
-                    if self.datasets[key].title != self.dataset.title:
-                        self.ui.select_flux.addItem(key+': '+self.datasets[key].title)
-
-        def on_list_enter(self):
-            self.ui.statusBar.showMessage('on_list')
-            sender = self.sender()
-            if sender.objectName() == 'select_flux_list':
-                self.ui.statusBar.showMessage('list')
-                index = self.ui.select_flux.currentIndex()
-                self.ui.statusBar.showMessage('list'+str(index))
-                if index == 1:
-                    ft.add_dataset_from_file(self.datasets, key_name='Reference')
-                    self.set_flux_list()
-                else:
-                    key = str(self.ui.select_flux.currentText()).split(':')[0]
-                    self.set_flux(key)
-                    
-                self.update()
-
-        def set_action(self):
-            self.ui.statusBar.showMessage('action')
-            self.ui.offsetEdit.editingFinished.connect(self.on_enter)
-            self.ui.dispersionEdit.editingFinished.connect(self.on_enter)
-            self.ui.timeEdit.editingFinished.connect(self.on_enter)
-
-            self.ui.TEMList.activated[str].connect(self.on_list_enter)
-
-            self.ui.convEdit.editingFinished.connect(self.on_enter)
-            self.ui.collEdit.editingFinished.connect(self.on_enter)
-            self.ui.E0Edit.editingFinished.connect(self.on_enter)
-            self.ui.binningEdit.editingFinished.connect(self.on_enter)
-            self.ui.conversionEdit.editingFinished.connect(self.on_enter)
-            self.ui.fluxEdit.editingFinished.connect(self.on_enter)
-            self.ui.VOAEdit.editingFinished.connect(self.on_enter)
-            self.ui.energy_button.clicked.connect(self.set_energy_scale)
-            self.ui.select_flux.activated[str].connect(self.on_list_enter)
-
-            self.ui.check_probability.clicked.connect(self.on_check)
-            
-            self.ui.binXEdit.editingFinished.connect(self.on_enter)
-            self.ui.binYEdit.editingFinished.connect(self.on_enter)
-
-
-def get_sidebar():
-    side_bar = ipywidgets.GridspecLayout(17, 3,width='auto', grid_gap="0px")
-
-    side_bar[0, :2] = ipywidgets.Dropdown(
-            options=[('None', 0)],
-            value=0,
-            description='Main Dataset:',
-            disabled=False)
-    
-    row = 1
-    side_bar[row, :3] = ipywidgets.Button(description='Energy Scale',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Offset:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
-    
-    row += 1
-    side_bar[row, :3] = ipywidgets.Button(description='Microscope',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Conv.Angle:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Coll.Angle:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Acc Voltage:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="keV", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-
-    side_bar[row, :3] = ipywidgets.Button(description='Quantification',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row+=1
-    side_bar[row, :2] = ipywidgets.Dropdown(
-            options=[('None', 0)],
-            value=0,
-            description='Reference:',
-            disabled=False)
-    side_bar[row,2] = ipywidgets.ToggleButton(
-            description='Probability',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Changes y-axis to probability if flux is given',
-                     layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Exp_Time:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="s", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Flux:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="Mcounts", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value=r"e$^-$/counts", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="pA", layout=ipywidgets.Layout(width='100px') )
-    
-    row += 1
-
-    side_bar[row, :3] = ipywidgets.Button(description='Spectrum Image',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    
-    row += 1
-    side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    
-    for i in range(14, 17):
-        side_bar[i, 0].layout.display = "none"
-    return side_bar
-
-
-class SpectrumPlot(sidpy.viz.dataset_viz.CurveVisualizer):
-    def __init__(self, dset, spectrum_number=0, figure=None, **kwargs):
-        with plt.ioff():
-            self.figure = plt.figure()
-        self.figure.canvas.toolbar_position = 'right'
-        self.figure.canvas.toolbar_visible = True
-
-        super().__init__(dset, spectrum_number=spectrum_number, figure=self.figure, **kwargs)
-        
-        self.start_cursor = ipywidgets.FloatText(value=0, description='Start:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-        self.end_cursor = ipywidgets.FloatText(value=0, description='End:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-        self.panel = ipywidgets.VBox([ipywidgets.HBox([ipywidgets.Label('',layout=ipywidgets.Layout(width='100px')), ipywidgets.Label('Cursor:'),
-                                                       self.start_cursor,ipywidgets.Label('eV'), 
-                                                       self.end_cursor, ipywidgets.Label('eV')]),
-                                      self.figure.canvas])
-        
-        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
-                                         direction="horizontal",
-                                         interactive=True,
-                                         props=dict(facecolor='blue', alpha=0.2))
-        #self.axis.legend()
-        display(self.panel)
-
-    def line_select_callback(self, x_min, x_max):
-        self.start_cursor.value = np.round(x_min, 3)
-        self.end_cursor.value = np.round(x_max, 3)
-        self.start_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.start_cursor.value)
-        self.end_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.end_cursor.value)
-
-    
-class SIPlot(sidpy.viz.dataset_viz.SpectralImageVisualizer):
-    def __init__(self, dset, figure=None, horizontal=True, **kwargs):
-        if figure is None:
-            with plt.ioff():
-                self.figure = plt.figure()
-        else:
-            self.figure = figure
-        self.figure.canvas.toolbar_position = 'right'
-        self.figure.canvas.toolbar_visible = True
-
-        super().__init__(dset, figure= self.figure, horizontal=horizontal, **kwargs)
-        
-        self.start_cursor = ipywidgets.FloatText(value=0, description='Start:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-        self.end_cursor = ipywidgets.FloatText(value=0, description='End:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-        self.panel = ipywidgets.VBox([ipywidgets.HBox([ipywidgets.Label('',layout=ipywidgets.Layout(width='100px')), ipywidgets.Label('Cursor:'),
-                                                       self.start_cursor,ipywidgets.Label('eV'), 
-                                                       self.end_cursor, ipywidgets.Label('eV')]),
-                                      self.figure.canvas])
-        self.axis = self.axes[-1]
-        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
-                                         direction="horizontal",
-                                         interactive=True,
-                                         props=dict(facecolor='blue', alpha=0.2))
-       
-    def line_select_callback(self, x_min, x_max):
-        self.start_cursor.value = np.round(x_min, 3)
-        self.end_cursor.value = np.round(x_max, 3)
-        self.start_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.start_cursor.value)
-        self.end_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.end_cursor.value)
-
-    def _update(self, ev=None):
-
-        xlim = self.axes[1].get_xlim()
-        ylim = self.axes[1].get_ylim()
-        self.axes[1].clear()
-        self.get_spectrum()
-        if len(self.energy_scale)!=self.spectrum.shape[0]:
-            self.spectrum = self.spectrum.T
-        self.axes[1].plot(self.energy_scale, self.spectrum.compute(), label='experiment')
-
-        if self.set_title:
-            self.axes[1].set_title('spectrum {}, {}'.format(self.x, self.y))
-        self.fig.tight_layout()
-        self.selector = matplotlib.widgets.SpanSelector(self.axes[1], self.line_select_callback,
-                                         direction="horizontal",
-                                         interactive=True,
-                                         props=dict(facecolor='blue', alpha=0.2))
-        
-        self.axes[1].set_xlim(xlim)
-        self.axes[1].set_ylim(ylim)
-        self.axes[1].set_xlabel(self.xlabel)
-        self.axes[1].set_ylabel(self.ylabel)
-
-        self.fig.canvas.draw_idle()
-
-class InfoWidget(object):
-    def __init__(self, datasets=None):
-        self.datasets = datasets
-        self.dataset = None
-
-        self.sidebar = get_sidebar()
-        
-        self.set_dataset()
-        self.set_action()
-        
-                                      
-        self.app_layout = ipywidgets.AppLayout(
-            left_sidebar=self.sidebar,
-            center=self.view.panel,
-            footer=None,#message_bar,
-            pane_heights=[0, 10, 0],
-            pane_widths=[4, 10, 0],
-        )
-        
-        display(self.app_layout)
-        
-            
-    def get_spectrum(self):
-        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-            spectrum = self.dataset.view.get_spectrum()
-            self.axis = self.dataset.view.axes[1]
-        else:
-            spectrum = np.array(self.dataset)
-            self.axis = self.dataset.view.axis
-
-        spectrum *= self.y_scale
-        return spectrum
-
-    def plot(self, scale=True):
-        spectrum = self.get_spectrum()
-        self.energy_scale = self.dataset.energy_loss.values
-        x_limit = self.axis.get_xlim()
-        y_limit = np.array(self.axis.get_ylim())
-        """
-        self.axis.clear()
-
-        self.axis.plot(self.energy_scale, spectrum, label='spectrum')
-                
-        
-        self.axis.set_xlabel(self.datasets[self.key].labels[0])
-        self.axis.set_ylabel(self.datasets[self.key].data_descriptor)
-        self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
-        if scale:
-            self.axis.set_ylim(np.array(y_limit)*self.change_y_scale)
-        self.change_y_scale = 1.0
-        if self.y_scale != 1.:
-                self.axis.set_ylabel('scattering probability (ppm/eV)')
-        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
-                                         direction="horizontal",
-                                         interactive=True,
-                                         props=dict(facecolor='blue', alpha=0.2))
-        self.axis.legend()
-        self.figure.canvas.draw_idle()
-        """
-
-    def set_dataset(self, index=0):
-       
-        spectrum_list = []
-        reference_list =[('None', -1)]
-        dataset_index = self.sidebar[0, 0].value
-        for index, key in enumerate(self.datasets.keys()):
-            if 'Reference' not in key:
-                if 'SPECTR' in self.datasets[key].data_type.name:
-                    spectrum_list.append((f'{key}: {self.datasets[key].title}', index)) 
-            reference_list.append((f'{key}: {self.datasets[key].title}', index))
-       
-        self.sidebar[0,0].options = spectrum_list
-        self.sidebar[9,0].options = reference_list
-        self.key = list(self.datasets)[dataset_index]
-        self.dataset = self.datasets[self.key]
-        if 'SPECTRUM' in self.dataset.data_type.name:
-           for i in range(14, 17):
-                self.sidebar[i, 0].layout.display = "none"
-        else:
-            for i in range(14, 17):
-                self.sidebar[i, 0].layout.display = "flex"
-        #self.sidebar[0,0].value = dataset_index #f'{self.key}: {self.datasets[self.key].title}'
-        self.sidebar[2,0].value = np.round(self.datasets[self.key].energy_loss[0], 3)  
-        self.sidebar[3,0].value = np.round(self.datasets[self.key].energy_loss[1] - self.datasets[self.key].energy_loss[0], 4)  
-        self.sidebar[5,0].value = np.round(self.datasets[self.key].metadata['experiment']['convergence_angle'], 1)  
-        self.sidebar[6,0].value = np.round(self.datasets[self.key].metadata['experiment']['collection_angle'], 1)
-        self.sidebar[7,0].value = np.round(self.datasets[self.key].metadata['experiment']['acceleration_voltage']/1000, 1)
-        self.sidebar[10,0].value = np.round(self.datasets[self.key].metadata['experiment']['exposure_time'], 4)
-        if 'flux_ppm' not in self.datasets[self.key].metadata['experiment']:
-            self.datasets[self.key].metadata['experiment']['flux_ppm'] = 0
-        self.sidebar[11,0].value = self.datasets[self.key].metadata['experiment']['flux_ppm']
-        if 'count_conversion' not in self.datasets[self.key].metadata['experiment']:
-            self.datasets[self.key].metadata['experiment']['count_conversion'] = 1
-        self.sidebar[12,0].value = self.datasets[self.key].metadata['experiment']['count_conversion']
-        if 'beam_current' not in self.datasets[self.key].metadata['experiment']:
-            self.datasets[self.key].metadata['experiment']['beam_current'] = 0
-        self.sidebar[13,0].value = self.datasets[self.key].metadata['experiment']['beam_current']
-        
-        self.view = SIPlot(self.dataset)
-        
-        self.y_scale = 1.0
-        self.change_y_scale = 1.0
-        
-        
-    def cursor2energy_scale(self, value):
-       
-        dispersion = (self.end_cursor.value - self.start_cursor.value) / (self.end_channel - self.start_channel)
-        self.datasets[self.key].energy_loss *= (self.sidebar[3, 0].value/dispersion)
-        self.sidebar[3, 0].value = dispersion
-        offset = self.start_cursor.value - self.start_channel * dispersion
-        self.datasets[self.key].energy_loss += (self.sidebar[2, 0].value-self.datasets[self.key].energy_loss[0])
-        self.sidebar[2, 0].value = offset
-        self.plot()
-        
-    def set_energy_scale(self, value):
-        dispersion = self.datasets[self.key].energy_loss[1] - self.datasets[self.key].energy_loss[0]
-        self.datasets[self.key].energy_loss *= (self.sidebar[3, 0].value/dispersion)
-        self.datasets[self.key].energy_loss += (self.sidebar[2, 0].value-self.datasets[self.key].energy_loss[0])
-        self.plot()
-        
-    def set_y_scale(self, value):  
-        self.change_y_scale = 1/self.y_scale
-        if self.sidebar[9,2].value:
-            dispersion = self.datasets[self.key].energy_loss[1] - self.datasets[self.key].energy_loss[0]
-            self.y_scale = 1/self.datasets[self.key].metadata['experiment']['flux_ppm'] * dispersion
-        else:
-            self.y_scale = 1.0
-            
-        self.change_y_scale *= self.y_scale
-        self.plot()
-        
-    
-    def set_flux(self, value):  
-        self.datasets[self.key].metadata['experiment']['exposure_time'] = self.sidebar[10,0].value
-        if self.sidebar[9,0].value < 0:
-            self.datasets[self.key].metadata['experiment']['flux_ppm'] = 0.
-        else:
-            key = list(self.datasets.keys())[self.sidebar[9,0].value]
-            self.datasets[self.key].metadata['experiment']['flux_ppm'] = (np.array(self.datasets[key])*1e-6).sum() / self.datasets[key].metadata['experiment']['exposure_time']
-            self.datasets[self.key].metadata['experiment']['flux_ppm'] *= self.datasets[self.key].metadata['experiment']['exposure_time']
-        self.sidebar[11,0].value = np.round(self.datasets[self.key].metadata['experiment']['flux_ppm'], 2)
-        
-    def set_microscope_parameter(self, value):
-        self.datasets[self.key].metadata['experiment']['convergence_angle'] = self.sidebar[5,0].value
-        self.datasets[self.key].metadata['experiment']['collection_angle'] = self.sidebar[6,0].value
-        self.datasets[self.key].metadata['experiment']['acceleration_voltage'] = self.sidebar[7,0].value*1000
-    
-    def set_binning(self, value):
-        if 'SPECTRAL' in self.dataset.data_type.name:
-            bin_x = self.sidebar[15,0].value
-            bin_y = self.sidebar[16,0].value
-            self.dataset.view.set_bin([bin_x, bin_y])
-            self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
-            self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y
-
-    def set_action(self):
-        self.sidebar[0,0].observe(self.set_dataset)
-        self.sidebar[1,0].on_click(self.cursor2energy_scale)
-        self.sidebar[2,0].observe(self.set_energy_scale, names='value')
-        self.sidebar[3,0].observe(self.set_energy_scale, names='value')
-        self.sidebar[5,0].observe(self.set_microscope_parameter)
-        self.sidebar[6,0].observe(self.set_microscope_parameter)
-        self.sidebar[7,0].observe(self.set_microscope_parameter)
-        self.sidebar[9,0].observe(self.set_flux)
-        self.sidebar[9,2].observe(self.set_y_scale)
-        self.sidebar[10,0].observe(self.set_flux)
-        self.sidebar[15,0].observe(self.set_binning)
-        self.sidebar[16,0].observe(self.set_binning)
-