pyTEMlib 0.2024.2.2__tar.gz → 0.2024.6.0__tar.gz

{pyTEMlib-0.2024.2.2/pyTEMlib.egg-info → pyTEMlib-0.2024.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyTEMlib
-Version: 0.2024.2.2
+Version: 0.2024.6.0
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
 Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
 Author: Gerd Duscher

pyTEMlib-0.2024.6.0/pyTEMlib/core_loss_widget.py

@@ -0,0 +1,658 @@
+"""
+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] = 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 = ''
+        
+        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.set_dataset(self.cl_key)
+    
+        self.dataset = self.parent.dataset
+        print(self.cl_key, self.core_loss_tab[0, 0].value)
+
+    def update_cl_dataset(self, value=0):
+        if self.cl_key not in self.core_loss_tab[0, 0].options:
+            self.cl_key = self.core_loss_tab[0, 0].value.split(':')[0]
+        self.parent.set_dataset(self.cl_key)
+    
+        self.dataset = self.parent.dataset
+
+    def update_cl_sidebar(self):
+        self.count+=1
+        spectrum_list = ['None '+str(self.count)]
+        cl_index = 0
+        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
+        self.cl_key = spectrum_list[cl_index]
+        self.core_loss_tab[0, 0].options = spectrum_list
+        self.core_loss_tab[0, 0].value = spectrum_list[cl_index]
+
+        
+        
+    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.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.parent.app_layout.center = self.periodic_table_panel # self.periodic_table.periodic_table
+
+    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[1]-self.parent.energy_scale[0]
+            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:
+                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.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:
+            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.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()
+
+    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.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[1]-self.parent.energy_scale[0]
+            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_cl_action(self):
+
+        self.core_loss_tab[0, 0].observe(self.update_cl_key, 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[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)