pyTEMlib 0.2025.4.1__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/eels_dialog.py

@@ -1,754 +0,0 @@
-"""
-Author: Gerd Duscher
-"""
-
-
-import numpy as np
-import warnings
-
-import ipywidgets
-import IPython.display
-# from IPython.display import display
-import matplotlib
-import matplotlib.pylab as plt
-import matplotlib.patches as patches
-
-from pyTEMlib import file_tools as ft
-from pyTEMlib import eels_tools as eels
-from pyTEMlib import eels_dialog_utilities
-
-import sidpy
-
-
-class CurveVisualizer(object):
-    """Plots a sidpy.Dataset with spectral dimension-type
-
-    """
-    def __init__(self, dset, spectrum_number=None, axis=None, leg=None, **kwargs):
-        if not isinstance(dset, sidpy.Dataset):
-            raise TypeError('dset should be a sidpy.Dataset object')
-        if axis is None:
-            self.fig = plt.figure()
-            self.axis = self.fig.add_subplot(1, 1, 1)
-        else:
-            self.axis = axis
-            self.fig = axis.figure
-
-        self.dset = dset
-        self.selection = []
-        [self.spec_dim, self.energy_scale] = ft.get_dimensions_by_type('spectral', self.dset)[0]
-
-        self.lined = dict()
-        self.plot(**kwargs)
-
-    def plot(self, **kwargs):
-        if self.dset.data_type.name == 'IMAGE_STACK':
-            line1, = self.axis.plot(self.energy_scale.values, self.dset[0, 0], label='spectrum', **kwargs)
-        else:
-            line1, = self.axis.plot(self.energy_scale.values, self.dset, label='spectrum', **kwargs)
-        lines = [line1]
-        if 'add2plot' in self.dset.metadata:
-            data = self.dset.metadata['add2plot']
-            for key, line in data.items():
-                line_add, = self.axis.plot(self.energy_scale.values,  line['data'], label=line['legend'])
-                lines.append(line_add)
-
-            legend = self.axis.legend(loc='upper right', fancybox=True, shadow=True)
-            legend.get_frame().set_alpha(0.4)
-
-            for legline, origline in zip(legend.get_lines(), lines):
-                legline.set_picker(True)
-                legline.set_pickradius(5)  # 5 pts tolerance
-                self.lined[legline] = origline
-            self.fig.canvas.mpl_connect('pick_event', self.onpick)
-
-        self.axis.axhline(0, color='gray', alpha=0.6)
-        self.axis.set_xlabel(self.dset.labels[0])
-        self.axis.set_ylabel(self.dset.data_descriptor)
-        self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
-        self.fig.canvas.draw_idle()
-
-    def update(self, **kwargs):
-        x_limit = self.axis.get_xlim()
-        y_limit = self.axis.get_ylim()
-        self.axis.clear()
-        self.plot(**kwargs)
-        self.axis.set_xlim(x_limit)
-        self.axis.set_ylim(y_limit)
-
-    def onpick(self, event):
-        # on the pick event, find the orig line corresponding to the
-        # legend proxy line, and toggle the visibility
-        legline = event.artist
-        origline = self.lined[legline]
-        vis = not origline.get_visible()
-        origline.set_visible(vis)
-        # Change the alpha on the line in the legend, so we can see what lines
-        # have been toggled
-        if vis:
-            legline.set_alpha(1.0)
-        else:
-            legline.set_alpha(0.2)
-        self.fig.canvas.draw()
-
-def get_core_loss_sidebar():
-    side_bar = ipywidgets.GridspecLayout(14, 3,width='auto', grid_gap="0px")
-
-    
-    row = 0
-    side_bar[row, :3] = ipywidgets.ToggleButton(description='Fit Area',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     tooltip='Shows fit regions and regions excluded from fit', 
-                     button_style='info') #ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Fit Start:', 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='Fit End:', 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='Elements',
-                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.Dropdown(
-            options=[('Edge 1', 0), ('Edge 2', 1), ('Edge 3', 2), ('Edge 4', 3),('Add Edge', -1)],
-            value=0,
-            description='Edges:',
-            disabled=False,
-            layout=ipywidgets.Layout(width='200px'))
-    """side_bar[row,2] = ipywidgets.ToggleButton(
-            description='Regions',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Shows fit regions and regions excluded from fit', 
-            layout=ipywidgets.Layout(width='100px')
-        )
-    """
-    row += 1
-    side_bar[row, :2] = ipywidgets.IntText(value=7.5,description='Z:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.Dropdown(
-            options=['K1','L3', 'M5', 'M3', 'M1', 'N7', 'N5', 'N3', 'N1'],
-            value='K1',
-            description='Symmetry:',
-            disabled=False,
-            layout=ipywidgets.Layout(width='200px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Onset:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Excl.Start:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Excl.End:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Mutliplier:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="a.u.", 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,0] = ipywidgets.ToggleButton(
-            description='Probabiity',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Changes y-axis to probability of flux is given', 
-            layout=ipywidgets.Layout(width='100px')
-        )
-    side_bar[row,1] = ipywidgets.ToggleButton(
-            description='Conv.LL',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Changes y-axis to probability of flux is given', 
-            layout=ipywidgets.Layout(width='100px')
-        )
-    side_bar[row,2] = ipywidgets.ToggleButton(
-            description='Show Edges',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Changes y-axis to probability of flux is given', 
-            layout=ipywidgets.Layout(width='100px')
-        )
-    
-    row += 1
-    side_bar[row,0] = ipywidgets.ToggleButton(
-            description='Do All',
-            disabled=False,
-            button_style='', # 'success', 'info', 'warning', 'danger' or ''
-            tooltip='Fits all spectra of spectrum image', 
-            layout=ipywidgets.Layout(width='100px')
-            )
-
-    side_bar[row,1] = ipywidgets.IntProgress(value=0, min=0, max=10, description=' ', bar_style='', # 'success', 'info', 'warning', 'danger' or ''
-                                             style={'bar_color': 'maroon'}, orientation='horizontal')
-    return side_bar
-
-
-
-class CompositionWidget(object):
-    def __init__(self, datasets=None):
-        
-        if not isinstance(datasets, dict):
-            raise TypeError('dataset or first item has to be a sidpy dataset')
-        self.datasets = datasets
-
-        
-        self.model = []
-        self.sidebar = get_core_loss_sidebar()
-        
-        self.set_dataset()
-        
-        self.periodic_table = eels_dialog_utilities.PeriodicTableWidget(self.energy_scale)
-        self.elements_cancel_button = ipywidgets.Button(description='Cancel')
-        self.elements_select_button = ipywidgets.Button(description='Select')
-        self.elements_auto_button = ipywidgets.Button(description='Auto ID')
-       
-        self.periodic_table_panel = ipywidgets.VBox([self.periodic_table.periodic_table,
-                                                     ipywidgets.HBox([self.elements_cancel_button, self.elements_auto_button, self.elements_select_button])])
-        
-                                      
-        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],
-        )
-        self.set_action()
-        IPython.display.display(self.app_layout)
-
-        
-    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 plot(self, scale=True):
-        self.view.change_y_scale = self.change_y_scale
-        self.view.y_scale = self.y_scale
-        self.energy_scale = self.dataset.energy_loss.values
-        
-        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-            spectrum = self.view.get_spectrum()
-        else:
-            spectrum = self.dataset
-        if len(self.model) > 1:
-            additional_spectra = {'model': self.model,
-                                  'difference': spectrum-self.model}   
-        else:
-            additional_spectra = None
-        self.view.plot(scale=True, additional_spectra=additional_spectra )
-        self.change_y_scale = 1.
-    
-        if self.sidebar[12, 2].value:
-            self.show_edges()
-        if self.sidebar[0, 0].value:
-            self.plot_regions()
-        self.view.figure.canvas.draw_idle()
-        
-        
-    def plot_regions(self):
-        axis = self.view.figure.gca()
-        y_min, y_max = axis.get_ylim()
-        height = y_max - y_min
-
-        rect = []
-        if 'fit_area' in self.edges:
-            color = 'blue'
-            alpha = 0.2
-            x_min = self.edges['fit_area']['fit_start']
-            width = self.edges['fit_area']['fit_end'] - x_min
-            rect.append(patches.Rectangle((x_min, y_min), width, height,
-                                          edgecolor=color, alpha=alpha, facecolor=color))
-            axis.add_patch(rect[0])
-            axis.text(x_min, y_max, 'fit region', verticalalignment='top')
-        color = 'red'
-        alpha = 0.5
-        
-        for key in self.edges:
-            if key.isdigit():
-                x_min = self.edges[key]['start_exclude']
-                width = self.edges[key]['end_exclude']-x_min
-                rect.append(patches.Rectangle((x_min, y_min), width, height,
-                                              edgecolor=color, alpha=alpha, facecolor=color))
-                axis.add_patch(rect[-1])
-                axis.text(x_min, y_max, f"exclude\n edge {int(key)+1}", verticalalignment='top')
-
-    def show_edges(self):
-        axis = self.view.figure.gca()
-        x_min, x_max = axis.get_xlim()
-        y_min, y_max = axis.get_ylim()
-        
-        for key, edge in self.edges.items():
-            i = 0
-            if key.isdigit():
-                element = edge['element']
-                for sym in edge['all_edges']:
-                    x = edge['all_edges'][sym]['onset'] + edge['chemical_shift']
-                    if x_min < x < x_max:
-                        axis.text(x, y_max, '\n' * i + f"{element}-{sym}",
-                                       verticalalignment='top', color='black')
-                        axis.axvline(x, ymin=0, ymax=1, color='gray')
-                        i += 1
-
-        
-    
-        
-    def set_dataset(self, set_key=None):
-        spectrum_list = []
-        self.spectrum_keys_list = []
-        reference_list =[('None', -1)]
-        
-        for index, key in enumerate(self.datasets.keys()):
-            if '_rel' not in key:
-                if 'Reference' not in key :
-                    if 'SPECTR' in self.datasets[key].data_type.name:
-                        spectrum_list.append((f'{key}: {self.datasets[key].title}', index)) 
-                        self.spectrum_keys_list.append(key)
-                        if key == self.parent.coreloss_key:
-                            self.key = key
-                            self.coreloss_key = self.key
-                            dataset_index = len(spectrum_list)-1
-
-                reference_list.append((f'{key}: {self.datasets[key].title}', index))  
-        self.sidebar[0, 0].options = spectrum_list
-        self.sidebar[0, 0].value = dataset_index
-
-        if self.coreloss_key is None:
-            return
-        self.dataset = self.datasets[self.coreloss_key]
-        
-        self.spec_dim = self.dataset.get_spectral_dims(return_axis=True)[0]
-
-        self.energy_scale = self.spec_dim.values
-        self.dd = (self.energy_scale[0], self.energy_scale[1])
-
-        self.dataset.metadata['experiment']['offset'] = self.energy_scale[0]
-        self.dataset.metadata['experiment']['dispersion'] = self.spec_dim.slope
-        if 'edges' not in self.dataset.metadata or self.dataset.metadata['edges'] == {}:
-            self.dataset.metadata['edges'] = {'0': {}, 'model': {}, 'use_low_loss': False}
-       
-        self.edges = self.dataset.metadata['edges']
-        if '0' not in self.edges:
-            self.edges['0'] = {}
-        
-        if 'fit_area' not in self.edges:
-            self.edges['fit_area'] = {}
-        if 'fit_start' not in self.edges['fit_area']:
-            self.sidebar[1,0].value = np.round(self.energy_scale[50], 3)
-            self.edges['fit_area']['fit_start'] = self.sidebar[1,0].value 
-        else:
-            self.sidebar[1,0].value = np.round(self.edges['fit_area']['fit_start'],3)
-        if 'fit_end' not in self.edges['fit_area']:
-            self.sidebar[2,0].value = np.round(self.energy_scale[-2], 3)
-            self.edges['fit_area']['fit_end'] = self.sidebar[2,0].value 
-        else:
-            self.sidebar[2,0].value = np.round(self.edges['fit_area']['fit_end'],3)
-        
-        if self.dataset.data_type.name == 'SPECTRAL_IMAGE':
-            if 'SI_bin_x' not in self.dataset.metadata['experiment']:
-                self.dataset.metadata['experiment']['SI_bin_x'] = 1
-                self.dataset.metadata['experiment']['SI_bin_y'] = 1
-
-            bin_x = self.dataset.metadata['experiment']['SI_bin_x']
-            bin_y = self.dataset.metadata['experiment']['SI_bin_y']
-            # self.dataset.view.set_bin([bin_x, bin_y])
-        if self.dataset.data_type.name =='SPECTRAL_IMAGE':
-            self.view = eels_dialog_utilities.SIPlot(self.dataset)
-        else:
-            self.view = eels_dialog_utilities.SpectrumPlot(self.dataset)    
-        self.y_scale = 1.0
-        self.change_y_scale = 1.0
-        
-        self.update()
-        
-    def update_element(self, z=0, index=-1):
-        # We check whether this element is already in the
-        if z == 0:
-            z = self.sidebar[5,0].value
-    
-        zz = eels.get_z(z)
-        for key, edge in self.edges.items():
-            if key.isdigit():
-                if 'z' in edge:
-                    if zz == edge['z']:
-                        return False
-
-        major_edge = ''
-        minor_edge = ''
-        all_edges = {}
-        x_section = eels.get_x_sections(zz)
-        edge_start = 10  # int(15./ft.get_slope(self.energy_scale)+0.5)
-        for key in x_section:
-            if len(key) == 2 and key[0] in ['K', 'L', 'M', 'N', 'O'] and key[1].isdigit():
-                if self.energy_scale[edge_start] < x_section[key]['onset'] < self.energy_scale[-edge_start]:
-                    if key in ['K1', 'L3', 'M5']:
-                        major_edge = key
-                    elif key in self.sidebar[6,0].options:
-                        if minor_edge == '':
-                            minor_edge = key
-                        if int(key[-1]) % 2 > 0:
-                            if int(minor_edge[-1]) % 2 == 0 or key[-1] > minor_edge[-1]:
-                                minor_edge = key
-
-                    all_edges[key] = {'onset': x_section[key]['onset']}
-
-        if major_edge != '':
-            key = major_edge
-        elif minor_edge != '':
-            key = minor_edge
-        else:
-            print(f'Could not find no edge of {zz} in spectrum')
-            return False
-        if index == -1:
-            index = self.sidebar[4, 0].value
-        # self.ui.dialog.setWindowTitle(f'{index}, {zz}')
-
-        if str(index) not in self.edges:
-            self.edges[str(index)] = {}
-
-        start_exclude = x_section[key]['onset'] - x_section[key]['excl before']
-        end_exclude = x_section[key]['onset'] + x_section[key]['excl after']
-
-        self.edges[str(index)] = {'z': zz, 'symmetry': key, 'element': eels.elements[zz],
-                                  'onset': x_section[key]['onset'], 'end_exclude': end_exclude,
-                                  'start_exclude': start_exclude}
-        self.edges[str(index)]['all_edges'] = all_edges
-        self.edges[str(index)]['chemical_shift'] = 0.0
-        self.edges[str(index)]['areal_density'] = 0.0
-        self.edges[str(index)]['original_onset'] = self.edges[str(index)]['onset']
-        return True
-    
-    def sort_elements(self):
-        onsets = []
-        for index, edge in self.edges.items():
-            if index.isdigit():
-                onsets.append(float(edge['onset']))
-
-        arg_sorted = np.argsort(onsets)
-        edges = self.edges.copy()
-        for index, i_sorted in enumerate(arg_sorted):
-            self.edges[str(index)] = edges[str(i_sorted)].copy()
-
-        index = 0
-        edge = self.edges['0']
-        dispersion = self.energy_scale[1]-self.energy_scale[0]
-
-        while str(index + 1) in self.edges:
-            next_edge = self.edges[str(index + 1)]
-            if edge['end_exclude'] > next_edge['start_exclude'] - 5 * dispersion:
-                edge['end_exclude'] = next_edge['start_exclude'] - 5 * dispersion
-            edge = next_edge
-            index += 1
-
-        if edge['end_exclude'] > self.energy_scale[-3]:
-            edge['end_exclude'] = self.energy_scale[-3]
-
-    def set_elements(self, value=0):
-        selected_elements = self.periodic_table.get_output()
-        edges = self.edges.copy()
-        to_delete = []
-        old_elements = []
-        if len(selected_elements) > 0:
-            for key in self.edges:
-                if key.isdigit():
-                    to_delete.append(key)
-                    old_elements.append(self.edges[key]['element'])
-
-        for key in to_delete:
-            edges[key] = self.edges[key]
-            del self.edges[key]
-    
-        for index, elem in enumerate(selected_elements):
-            if elem  in old_elements:
-                self.edges[str(index)] = edges[str(old_elements.index(elem))]   
-            else:
-                self.update_element(elem, index=index)
-        self.sort_elements()
-        self.update()
-        self.set_figure_pane()
-
-    def set_element(self, elem):
-        self.update_element(self.sidebar[5, 0].value)
-        # self.sort_elements()
-        self.update()
-       
-    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_fit_area(self, value):
-        if self.sidebar[1,0].value > self.sidebar[2,0].value:
-            self.sidebar[1,0].value = self.sidebar[2,0].value -1
-        if self.sidebar[1,0].value < self.energy_scale[0]:
-            self.sidebar[1,0].value = self.energy_scale[0]
-        if self.sidebar[2,0].value > self.energy_scale[-1]:
-            self.sidebar[2,0].value = self.energy_scale[-1]
-        self.edges['fit_area']['fit_start'] = self.sidebar[1,0].value 
-        self.edges['fit_area']['fit_end'] = self.sidebar[2,0].value 
-        
-        self.plot()
-        
-    def set_y_scale(self, value):  
-        self.change_y_scale = 1/self.y_scale
-        self.y_scale = 1.0
-        if self.dataset.metadata['experiment']['flux_ppm'] > 0:
-            if self.sidebar[12, 0].value:
-                dispersion = self.energy_scale[1] - self.energy_scale[0]
-                self.y_scale = 1/self.dataset.metadata['experiment']['flux_ppm'] * dispersion
-            
-        self.change_y_scale *= self.y_scale
-        self.update()
-        self.plot()
-
-    def auto_id(self, value=0):
-        found_edges = eels.auto_id_edges(self.dataset)
-        if len(found_edges) > 0:
-            self.periodic_table.elements_selected = found_edges
-            self.periodic_table.update()
-        
-    def find_elements(self, value=0):
-        
-        if '0' not in self.edges:
-            self.edges['0'] = {}
-        # found_edges = eels.auto_id_edges(self.dataset)
-        found_edges = {}
-
-        selected_elements = []
-        elements = self.edges.copy()
-
-        for key in self.edges:
-            if key.isdigit():
-                if 'element' in self.edges[key]:
-                    selected_elements.append(self.edges[key]['element'])
-        self.periodic_table.elements_selected = selected_elements
-        self.periodic_table.update()
-        self.app_layout.center = self.periodic_table_panel # self.periodic_table.periodic_table
-
-    def set_figure_pane(self, value=0):
-        
-        self.app_layout.center = self.view.panel
-    
-    def update(self, index=0):
-        
-        index = self.sidebar[4,0].value  # which edge
-        if index < 0:
-            options  = list(self.sidebar[4,0].options)
-            options.insert(-1, (f'Edge {len(self.sidebar[4,0].options)}', len(self.sidebar[4,0].options)-1))
-            self.sidebar[4,0].options= options
-            self.sidebar[4,0].value = len(self.sidebar[4,0].options)-2
-        if str(index) not in self.edges:
-            self.edges[str(index)] = {'z': 0,  'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
-                                     'areal_density': 0, 'chemical_shift':0}
-        if 'z' not in self.edges[str(index)]:
-             self.edges[str(index)] = {'z': 0,  'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
-                                      'areal_density': 0, 'chemical_shift':0}
-        edge = self.edges[str(index)]
-            
-        self.sidebar[5,0].value = edge['z']
-        self.sidebar[5,2].value = edge['element']
-        self.sidebar[6,0].value = edge['symmetry']
-        self.sidebar[7,0].value = edge['onset']
-        self.sidebar[8,0].value = edge['start_exclude']
-        self.sidebar[9,0].value = edge['end_exclude']
-        if self.y_scale == 1.0:
-            self.sidebar[10, 0].value = edge['areal_density']
-            self.sidebar[10, 2].value =  'a.u.'
-        else:
-            dispersion = self.energy_scale[1]-self.energy_scale[0]
-            self.sidebar[10, 0].value = np.round(edge['areal_density']/self.dataset.metadata['experiment']['flux_ppm']*1e-6, 2)
-            self.sidebar[10, 2].value = 'atoms/nm²'
-        
-    
-    def do_fit(self, value=0):
-        if 'experiment' in self.dataset.metadata:
-            exp = self.dataset.metadata['experiment']
-            if 'convergence_angle' not in exp:
-                raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
-            alpha = exp['convergence_angle']
-            beta = exp['collection_angle']
-            beam_kv = exp['acceleration_voltage']
-
-        else:
-            raise ValueError('need a experiment parameter in metadata dictionary')
-        
-        eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
-
-        self.low_loss = None
-        if self.sidebar[12, 1].value:
-            for key in self.datasets.keys():
-                if key != self.key:
-                    if isinstance(self.datasets[key], sidpy.Dataset):
-                        if self.datasets[key].data_type.name == 'SPECTRUM':
-                            if self.datasets[key].energy_loss[0] < 0:
-                                self.low_loss = self.datasets[key]/self.datasets[key].sum()
-
-        edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta, self.low_loss)
-
-        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-            spectrum = self.view.get_spectrum()
-        else:
-            spectrum = self.dataset
-        self.edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
-        areal_density = []
-        elements = []
-        for key in edges:
-            if key.isdigit():  # only edges have numbers in that dictionary
-                elements.append(edges[key]['element'])
-                areal_density.append(edges[key]['areal_density'])
-        areal_density = np.array(areal_density)
-        out_string = '\nRelative composition: \n'
-        for i, element in enumerate(elements):
-            out_string += f'{element}: {areal_density[i] / areal_density.sum() * 100:.1f}%  '
-
-        self.model = self.edges['model']['spectrum']
-        self.update()
-        self.plot()
-
-    def do_all_button_click(self, value=0):
-            if self.sidebar[13,0].value==False:
-                return
-            
-            if self.dataset.data_type.name != 'SPECTRAL_IMAGE':
-                self.do_fit()
-                return
-
-            if 'experiment' in self.dataset.metadata:
-                exp = self.dataset.metadata['experiment']
-                if 'convergence_angle' not in exp:
-                    raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
-                alpha = exp['convergence_angle']
-                beta = exp['collection_angle']
-                beam_kv = exp['acceleration_voltage']
-            else:
-                raise ValueError('need a experiment parameter in metadata dictionary')
-
-            eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
-            eff_beta = beta
-            self.low_loss = None
-            if self.sidebar[12, 1].value:
-                for key in self.datasets.keys():
-                    if key != self.key:
-                        if isinstance(self.datasets[key], sidpy.Dataset):
-                            if 'SPECTR' in self.datasets[key].data_type.name:
-                                if self.datasets[key].energy_loss[0] < 0:
-                                    self.low_loss = self.datasets[key]/self.datasets[key].sum()
-
-            edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta, self.low_loss)
-    
-            view = self.view
-            bin_x = view.bin_x
-            bin_y = view.bin_y
-
-            start_x = view.x
-            start_y = view.y
-
-            number_of_edges = 0
-            for key in self.edges:
-                if key.isdigit():
-                    number_of_edges += 1
-
-            results = np.zeros([int(self.dataset.shape[0]/bin_x), int(self.dataset.shape[1]/bin_y), number_of_edges])
-            total_spec = int(self.dataset.shape[0]/bin_x)*int(self.dataset.shape[1]/bin_y)
-            self.sidebar[13,1].max = total_spec
-            #self.ui.progress.setMaximum(total_spec)
-            #self.ui.progress.setValue(0)
-            ind = 0
-            for x in range(int(self.dataset.shape[0]/bin_x)):
-                for y in range(int(self.dataset.shape[1]/bin_y)):
-                    ind += 1
-                    self.sidebar[13,1].value = ind
-                    view.x = x*bin_x
-                    view.y = y*bin_y
-                    spectrum = view.get_spectrum()
-                    with warnings.catch_warnings():
-                        warnings.simplefilter("ignore")
-                        edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
-                    for key, edge in edges.items():
-                        if key.isdigit():
-                            # element.append(edge['element'])
-                            results[x, y, int(key)] = edge['areal_density']
-            edges['spectrum_image_quantification'] = results
-            self.sidebar[13,1].value = total_spec
-            view.x = start_x
-            view.y = start_y
-            self.sidebar[13,0].value = False
-            
-    
-    def modify_onset(self, value=-1):
-        edge_index = self.sidebar[4, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['onset'] = self.sidebar[7,0].value
-        if 'original_onset' not in edge:
-            edge['original_onset'] = edge['onset']
-        edge['chemical_shift'] = edge['onset'] -  edge['original_onset']
-        self.update()
-        
-            
-    def modify_start_exclude(self, value=-1):
-        edge_index = self.sidebar[4, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['start_exclude'] = self.sidebar[8,0].value
-        self.plot()
-        
-    def modify_end_exclude(self, value=-1):
-        edge_index = self.sidebar[4, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['end_exclude'] = self.sidebar[9,0].value
-        self.plot()
-    
-    def modify_areal_density(self, value=-1):
-        edge_index = self.sidebar[4, 0].value
-        edge = self.edges[str(edge_index)]
-        
-        edge['areal_density'] = self.sidebar[10, 0].value
-        if self.y_scale != 1.0:
-            dispersion = self.energy_scale[1]-self.energy_scale[0]
-            edge['areal_density'] = self.sidebar[10, 0].value *self.dataset.metadata['experiment']['flux_ppm']/1e-6
-
-        self.model = self.edges['model']['background']
-        for key in self.edges:
-            if key.isdigit():
-                if 'data' in self.edges[key]:
-
-                    self.model = self.model + self.edges[key]['areal_density'] * self.edges[key]['data']
-        self.plot()
-
-    def set_action(self):
-        self.sidebar[1, 0].observe(self.set_fit_area, names='value')
-        self.sidebar[2, 0].observe(self.set_fit_area, names='value')
-        
-        self.sidebar[3, 0].on_click(self.find_elements)
-        self.sidebar[4, 0].observe(self.update, names='value')
-        self.sidebar[5, 0].observe(self.set_element, names='value')
-
-        self.sidebar[7, 0].observe(self.modify_onset, names='value')
-        self.sidebar[8, 0].observe(self.modify_start_exclude, names='value')
-        self.sidebar[9, 0].observe(self.modify_end_exclude, names='value')
-        self.sidebar[10, 0].observe(self.modify_areal_density, names='value')
-        
-        self.sidebar[11, 0].on_click(self.do_fit)
-        self.sidebar[12, 2].observe(self.plot, names='value')
-        self.sidebar[0, 0].observe(self.set_dataset, names='value')
-        self.sidebar[12,0].observe(self.set_y_scale, names='value')
-        self.sidebar[13,0].observe(self.do_all_button_click, names='value')
-
-        self.elements_cancel_button.on_click(self.set_figure_pane)
-        self.elements_auto_button.on_click(self.auto_id)
-        self.elements_select_button.on_click(self.set_elements)