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

pyTEMlib/core_loss_widget.py

@@ -1,721 +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
-
-
-def get_core_loss_sidebar():
-    side_bar = ipywidgets.GridspecLayout(15, 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.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, 1:3] = 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 CoreLoss(object):
-    def __init__(self, sidebar=None, parent=None):
-        self.parent = parent
-        self.dataset = parent.dataset
-        self.core_loss_tab = sidebar
-
-        self.model = []
-        self.edges = {}
-        self.count = 0
-        self.cl_key = 'None'
-
-        self.periodic_table = eels_dialog_utilities.PeriodicTableWidget(
-            self.parent.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.update_cl_sidebar()
-        self.set_cl_action()
-
-    def update_cl_key(self, value=0):
-        self.cl_key = self.core_loss_tab[0, 0].value.split(':')[0]
-        self.parent.coreloss_key = self.cl_key
-        if 'None' in self.cl_key:
-            return
-        self.parent.set_dataset(self.cl_key)
-
-        self.dataset = self.parent.datasets[self.cl_key]
-    
-
-    def update_cl_sidebar(self):
-        spectrum_list = ['None']
-        cl_index = 0
-        self.cl_key = self.parent.coreloss_key
-        for index, key in enumerate(self.parent.datasets.keys()):
-            if isinstance(self.parent.datasets[key], sidpy.Dataset):
-                if 'SPECTR' in self.parent.datasets[key].data_type.name:
-                    spectrum_list.append(
-                        f'{key}: {self.parent.datasets[key].title}')
-                if key == self.cl_key:
-                    cl_index = index+1
-        self.core_loss_tab[0, 0].options = spectrum_list
-        self.core_loss_tab[0, 0].value = spectrum_list[cl_index]
-        if '_relationship' in self.parent.datasets.keys():
-            self.update_cl_dataset()
-            self.set_fit_start()
-            self.parent.plot()
-        
-    def update_cl_dataset(self, value=0):
-        self.cl_key = self.core_loss_tab[0, 0].value.split(':')[0]
-        self.parent.coreloss_key = self.cl_key
-        if '_relationship' in self.parent.datasets.keys():
-            self.parent.datasets['_relationship']['core_loss'] = self.cl_key
-        
-        if 'None' in self.cl_key:
-            return
-        self.parent.set_dataset(self.cl_key)
-        self.dataset = self.parent.dataset
-
-    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.cl_key].energy_loss, self.start_cursor.value)
-        self.end_channel = np.searchsorted(
-            self.datasets[self.cl_key].energy_loss, self.end_cursor.value)
-
-    def plot(self, scale=True):
-        self.parent.dataset.metadata['edges'] = self.edges
-        self.parent.plot(scale=scale)
-        y_scale = self.parent.y_scale
-        spectrum = self.parent.spectrum
-        if len(self.model) > 1:
-            self.model = self.edges['model']['spectrum'].copy()
-            # self.parent.axis.plot(self.parent.energy_scale, (self.edges['model']['spectrum'])*y_scale, label='difference')
-            self.parent.axis.plot(self.parent.energy_scale,
-                                  self.model*y_scale, label='model')
-            self.parent.axis.plot(self.parent.energy_scale,
-                                  spectrum-self.model*y_scale, label='difference')
-            self.parent.axis.legend()
-            pass
-        if self.core_loss_tab[13, 2].value:
-            self.show_edges()
-        if self.core_loss_tab[1, 0].value:
-            self.plot_regions()
-        self.parent.figure.canvas.draw_idle()
-
-    def plot_regions(self):
-        axis = self.parent.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.parent.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 update_element(self, z=0, index=-1):
-        # We check whether this element is already in the
-        if z == 0:
-            z = self.core_loss_tab[6, 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.parent.energy_scale[edge_start] < x_section[key]['onset'] < self.parent.energy_scale[-edge_start]:
-                    if key in ['K1', 'L3', 'M5']:
-                        major_edge = key
-                    elif key in self.core_loss_tab[7, 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.core_loss_tab[5, 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.parent.energy_scale[1]-self.parent.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.parent.energy_scale[-3]:
-            edge['end_exclude'] = self.parent.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():
-                    if 'element' in self.edges[key]:
-                        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.core_loss_tab[6, 0].value)
-        # self.sort_elements()
-        self.update()
-
-    def set_fit_start(self, value=0):
-        if 'edges' not in self.dataset.metadata:
-            self.edges = self.dataset.metadata['edges'] = {}
-        if 'fit_area' not in self.edges:
-            self.edges['fit_area'] = {'fit_start': self.parent.energy_scale[10],
-                                      'fit_end': self.parent.energy_scale[-10]}
-            self.core_loss_tab[3, 0].value = str(
-                self.edges['fit_area']['fit_end'])
-            self.core_loss_tab[2, 0].value = str(
-                self.edges['fit_area']['fit_start'])
-        if self.core_loss_tab[2, 0].value < self.parent.energy_scale[0]:
-            self.core_loss_tab[2, 0].value = self.parent.energy_scale[10]
-        self.edges['fit_area']['fit_start'] = float(
-            self.core_loss_tab[2, 0].value)
-        self.parent.plot()
-
-    def set_fit_end(self, value=0):
-        if 'edges' not in self.dataset.metadata:
-            self.edges = self.dataset.metadata['edges'] = {}
-        if 'fit_area' not in self.edges:
-            self.edges['fit_area'] = {'fit_start': self.parent.energy_scale[10],
-                                      'fit_end': self.parent.energy_scale[-10]}
-            self.core_loss_tab[3, 0].value = str(
-                self.edges['fit_area']['fit_end'])
-            self.core_loss_tab[2, 0].value = str(
-                self.edges['fit_area']['fit_start'])
-        if self.core_loss_tab[3, 0].value > self.parent.energy_scale[-1]:
-            self.core_loss_tab[3, 0].value = self.parent.energy_scale[-10]
-        self.edges['fit_area']['fit_end'] = self.core_loss_tab[3, 0].value
-        self.parent.plot()
-
-    def set_fit_area(self, value=1):
-        if 'fit_area' not in self.edges:
-            self.edges['fit_area'] = {'fit_start': self.parent.energy_scale[10],
-                                      'fit_end': self.parent.energy_scale[-10]}
-
-        fit_end = str(self.edges['fit_area']['fit_end'])
-        fit_start = str(self.edges['fit_area']['fit_start'])
-
-        if fit_end > fit_start:
-            fit_start = self.parent.energy_scale[10]
-            fit_end = self.parent.energy_scale[-10]
-        self.core_loss_tab[2, 0].value = fit_start
-        self.core_loss_tab[3, 0].value = fit_end
-        self.edges['fit_area']['fit_start'] = self.core_loss_tab[2, 0].value
-        self.edges['fit_area']['fit_end'] = self.core_loss_tab[3, 0].value
-
-        self.parent.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.periodic_table.periodic_table
-        self.parent.app_layout.center = self.periodic_table_panel
-
-    def set_figure_pane(self, value=0):
-        self.parent.app_layout.center = self.parent.panel
-
-    def update(self, index=0):
-        self.dataset = self.parent.dataset
-        index = self.core_loss_tab[5, 0].value  # which edge
-        if index < 0:
-            options = list(self.core_loss_tab[5, 0].options)
-            options.insert(-1, (f'Edge {len(self.core_loss_tab[5, 0].options)}', len(
-                self.sidebar[4, 0].options)-1))
-            self.core_loss_tab[5, 0].options = options
-            self.core_loss_tab[5, 0].value = len(
-                self.core_loss_tab[5, 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.core_loss_tab[6, 0].value = edge['z']
-        self.core_loss_tab[6, 2].value = edge['element']
-        self.core_loss_tab[7, 0].value = edge['symmetry']
-        self.core_loss_tab[8, 0].value = edge['onset']
-        self.core_loss_tab[9, 0].value = edge['start_exclude']
-        self.core_loss_tab[10, 0].value = edge['end_exclude']
-        self.core_loss_tab[13, 0].value = self.parent.info_tab[9, 2].value
-        if self.parent.y_scale == 1.0:
-            self.core_loss_tab[11, 0].value = edge['areal_density']
-            self.core_loss_tab[11, 2].value = 'a.u.'
-        else:
-            dispersion = self.parent.energy_scale.slope
-            self.core_loss_tab[11, 0].value = np.round(
-                edge['areal_density']/self.dataset.metadata['experiment']['flux_ppm']*1e-6, 2)
-            self.core_loss_tab[11, 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:
-                self.parent.status_message('Aborted Quantification: need a convergence_angle in experiment of metadata dictionary')
-                return
-    
-            alpha = exp['convergence_angle']
-            beta = exp['collection_angle']
-            beam_kv = exp['acceleration_voltage']
-            if beam_kv < 20:
-                self.parent.status_message('Aborted Quantification: no acceleration voltage')
-                return
-        else:
-            raise ValueError(
-                'need a experiment parameter in metadata dictionary')
-
-        self.parent.status_message('Fitting cross-sections ')
-        eff_beta = eels.effective_collection_angle(
-            self.parent.energy_scale, alpha, beta, beam_kv)
-        self.dataset.metadata['experiment']['eff_beta'] = eff_beta
-        self.low_loss = None
-        if self.core_loss_tab[13, 1].value:
-            if 'low_loss' in self.parent.datasets['_relationship'].keys():
-                ll_key = self.parent.datasets['_relationship']['low_loss']
-                self.low_loss = np.array(self.parent.datasets[ll_key] / \
-                                    self.parent.datasets[ll_key].sum())
-                    
-
-        edges = eels.make_cross_sections(self.edges, np.array(
-            self.parent.energy_scale), beam_kv, eff_beta, self.low_loss)
-        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
-            spectrum = self.parent.get_spectrum()
-        else:
-            spectrum = self.dataset
-        self.edges = eels.fit_edges2(spectrum, self.parent.energy_scale, edges)
-        self.model = self.edges['model']['spectrum'].copy()
-        print('set_model',  self.edges['model']['spectrum'][0], self.model[0])
-
-        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.update()
-        self.plot()
-        self.parent.status_message('Fitting cross-sections -- success')
-
-    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.parent.lowloss_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.parent
-        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.core_loss_tab[5, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['onset'] = self.core_loss_tab[8, 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.core_loss_tab[5, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['start_exclude'] = self.core_loss_tab[9, 0].value
-        self.plot()
-
-    def modify_end_exclude(self, value=-1):
-        edge_index = self.core_loss_tab[5, 0].value
-        edge = self.edges[str(edge_index)]
-        edge['end_exclude'] = self.core_loss_tab[10, 0].value
-        self.plot()
-
-    def modify_areal_density(self, value=-1):
-        edge_index = self.core_loss_tab[5, 0].value
-        edge = self.edges[str(edge_index)]
-
-        edge['areal_density'] = self.core_loss_tab[11, 0].value
-        if self.parent.y_scale != 1.0:
-            dispersion = self.parent.energy_scale.slope
-            edge['areal_density'] = self.core_loss_tab[11, 0].value * \
-                self.dataset.metadata['experiment']['flux_ppm']/1e-6
-        if 'model' in self.edges:
-            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.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_y_scale(self, value):
-        self.parent.info_tab[9, 2].value = self.core_loss_tab[13, 0].value
-        self.update()
-        
-    def set_convolution(self, value=0):
-        self.do_fit()
-    
-    
-    def set_cl_action(self):
-
-        self.core_loss_tab[0, 0].observe(self.update_cl_dataset, names='value')
-        self.core_loss_tab[2, 0].observe(self.set_fit_start, names='value')
-        self.core_loss_tab[3, 0].observe(self.set_fit_end, names='value')
-
-        self.core_loss_tab[4, 0].on_click(self.find_elements)
-        self.core_loss_tab[5, 0].observe(self.update, names='value')
-        self.core_loss_tab[6, 0].observe(self.set_element, names='value')
-
-        self.core_loss_tab[8, 0].observe(self.modify_onset, names='value')
-        self.core_loss_tab[9, 0].observe(
-            self.modify_start_exclude, names='value')
-        self.core_loss_tab[10, 0].observe(
-            self.modify_end_exclude, names='value')
-        self.core_loss_tab[11, 0].observe(
-            self.modify_areal_density, names='value')
-
-        self.core_loss_tab[12, 0].on_click(self.do_fit)
-        self.core_loss_tab[13, 2].observe(self.plot, names='value')
-        self.core_loss_tab[1, 0].observe(self.plot, names='value')
-        self.core_loss_tab[13, 0].observe(self.set_y_scale, names='value')
-        self.core_loss_tab[13, 1].observe(self.set_convolution, names='value')
-        self.core_loss_tab[14, 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)