pyTEMlib 0.2025.4.2__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/low_loss_widget.py

@@ -1,479 +0,0 @@
-from typing import Any
-
-import numpy as np
-import os
-import ipywidgets
-import matplotlib.pylab as plt
-import matplotlib
-from IPython.display import display
-
-import sidpy
-# from pyTEMlib.microscope import microscope
-from pyTEMlib import file_tools
-from pyTEMlib import eels_tools
-
-
-def get_low_loss_sidebar() -> Any:
-    side_bar = ipywidgets.GridspecLayout(17, 3, width='auto', grid_gap="0px")
-
-    side_bar[0, :2] = ipywidgets.Dropdown(
-            options=[('None', 0)],
-            value=0,
-            description='Low-Loss:',
-            disabled=False)
-    
-    row = 1
-    
-    side_bar[row, :3] = ipywidgets.Button(description='Resolution Function',
-                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='fit width:', 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, 0] = ipywidgets.ToggleButton(description='Plot Res.Fct.',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Plots resolution function on right',
-                                               layout=ipywidgets.Layout(width='100px'))
-    
-    side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Changes y-axis to probability if flux is given',
-                                               layout=ipywidgets.Layout(width='100px'))
-    
-    
-    row += 1
-    side_bar[row, :3] = ipywidgets.Button(description='Drude',
-                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=5, description='Start Fit:', 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=25, description='End Fit:', disabled=False, color='black',
-                                             layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=5, description='Energy:', 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=25, description='Width:', disabled=False, color='black',
-                                             layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=25, description='Amplitude:', disabled=False, color='black',
-                                             layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
-    row +=1
-    side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Drude',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Plots resolution function on right',
-                                               layout=ipywidgets.Layout(width='100px'))
-    
-    side_bar[row, 2] = ipywidgets.ToggleButton(description='Plot Diel.Fct.',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Changes y-axis to probability if flux is given',
-                                               layout=ipywidgets.Layout(width='100px'))
-    side_bar[row, 1] = ipywidgets.ToggleButton(description='Do All',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Changes y-axis to probability if flux is given',
-                                               layout=ipywidgets.Layout(width='100px'))
-    row += 1
-    side_bar[row, :3] = ipywidgets.Button(description='Multiple Scattering',
-                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
-                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
-    row += 1
-    side_bar[row, :2] = ipywidgets.FloatText(value=5, description='Start Fit:', 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=-1, description='End Fit:', disabled=False, color='black',
-                                             layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
-    row +=1
-    side_bar[row, :2] = ipywidgets.FloatText(value=25, description='thickness:', disabled=False, color='black',
-                                             layout=ipywidgets.Layout(width='200px'))
-    side_bar[row, 2] = ipywidgets.widgets.Label(value="* iMFP", layout=ipywidgets.Layout(width='50px'))
-    
-    row +=1
-    side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot LowLoss',
-                                               disabled=False,
-                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
-                                               tooltip='Plots resolution function on right',
-                                               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 LowLoss(object):
-    def __init__(self, sidebar=None, parent=None):
-        self.parent = parent
-        self.dataset = parent.dataset
-        self.low_loss_tab = sidebar
-        self.set_ll_action()
-        self.ll_key = ''
-        self.update_ll_sidebar()
-
-    def update_ll_sidebar(self):
-        spectrum_list = ['None']
-        ll_index = 0
-        self.ll_key = self.parent.lowloss_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:
-                    energy_offset = self.parent.datasets[key].get_spectral_dims(return_axis=True)[0][0]
-                    if energy_offset < 0:
-                        spectrum_list.append(f'{key}: {self.parent.datasets[key].title}')
-                if key == self.ll_key:
-                    ll_index = index-1
-
-        if ll_index >len(spectrum_list) - 1:
-            ll_index = len(spectrum_list) - 1
-
-        self.low_loss_tab[0, 0].options = spectrum_list
-        self.low_loss_tab[0, 0].value = spectrum_list[ll_index]
-        
-        self.update_ll_dataset()
-        
-    def update_ll_dataset(self, value=0):
-        self.ll_key = self.low_loss_tab[0, 0].value.split(':')[0]
-        self.parent.lowloss_key = self.ll_key
-        if 'None' in self.ll_key:
-            return
-        self.parent.set_dataset(self.ll_key)
-        self.dataset = self.parent.dataset
-        if self.low_loss_tab[13, 0].value < 0:
-            energy_scale = self.dataset.get_spectral_dims(return_axis=True)[0]
-            self.low_loss_tab[13, 0].value = np.round(self.dataset.get_spectral_dims(return_axis=True)[0][-2], 3)
-
-        
-    def get_resolution_function(self, value=0):
-        
-        zero_loss_fit_width=self.low_loss_tab[2, 0].value
-        spectrum = self.parent.spectrum
-        if 'zero_loss' not in self.parent.datasets.keys():
-            self.parent.datasets['zero_loss'] = self.parent.dataset.copy()*0
-        # if 'zero_loss' not in self.parent.datasets['zero_loss'].metadata.keys():
-        self.parent.datasets['zero_loss'].metadata['zero_loss']={}
-        self.parent.datasets['zero_loss'].metadata['zero_loss']['parameter'] = np.zeros([self.dataset.shape[0], self.dataset.shape[1], 6])
-          
-           
-        res  = eels_tools.get_resolution_functions(spectrum, startFitEnergy=-zero_loss_fit_width, endFitEnergy=zero_loss_fit_width)
-        if len(self.parent.datasets['zero_loss'].shape) > 2:
-            self.parent.datasets['zero_loss'][self.parent.x, self.parent.y] = np.array(res)
-            self.parent.datasets['zero_loss'].metadata['zero_loss'][self.parent.x, self.parent.y] = res.metadata['zero_loss']['fit_parameter']
-        else:
-            self.parent.datasets['zero_loss'] = res
-            self.parent.datasets['zero_loss'].metadata['zero_loss'].update(res.metadata['zero_loss'])
-
-        self.parent.datasets['_relationship']['resolution_function'] = 'zero_loss'
-        
-        self.parent.dataset.metadata['zero_loss'].update(self.parent.datasets['zero_loss'].metadata['zero_loss'])
-        
-        if self.low_loss_tab[3, 0].value: 
-            self.parent._update()
-        else:
-            self.low_loss_tab[3, 0].value = True
-        self.low_loss_tab[14, 1].value = np.round(np.log(self.parent.spectrum.sum()/res.sum()), 4)
-        self.parent.status_message('Fitted zero-loss peak')
-        
-    def get_drude(self, value=0):
-        self.low_loss_tab[8, 0].value = False
-        fit_start = self.low_loss_tab[5, 0].value
-        fit_end = self.low_loss_tab[6, 0].value
-        if 'plasmon' not in self.parent.datasets.keys():
-            self.parent.datasets['plasmon'] = self.parent.dataset.copy()*0
-        if 'plasmon' not in self.parent.datasets['plasmon'].metadata.keys():
-            self.parent.datasets['plasmon'].metadata['plasmon'] = {}
-        if 'fit_parameter' not in self.parent.datasets['plasmon'].metadata['plasmon'].keys():
-            if len(self.dataset.shape) > 2:
-                self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'] = np.zeros([self.dataset.shape[0], self.dataset.shape[1], 4])
-                self.parent.datasets['plasmon'].metadata['plasmon']['IMFP'] = np.zeros([self.dataset.shape[0], self.dataset.shape[1]])
-            
-        if 'low_loss_model' not in self.parent.datasets.keys():
-            self.parent.datasets['low_loss_model'] = self.parent.dataset.copy()*0
-        self.parent.status_message(str(self.parent.x))
-        plasmon = eels_tools.fit_plasmon(self.parent.spectrum, fit_start, fit_end)
-        
-        p = plasmon.metadata['plasmon']['parameter']
-        p = list(np.abs(p))
-        p.append(self.low_loss_tab[14, 0].value)
-
-        
-        anglog, _, _ = eels_tools.angle_correction(self.parent.spectrum)
-        
-        low_loss = eels_tools.multiple_scattering(self.parent.energy_scale, p) * anglog
-            
-
-        if len(self.parent.datasets['plasmon'].shape) > 2:
-            self.parent.datasets['plasmon'][self.parent.x, self.parent.y] = np.array(plasmon)
-            self.parent.datasets['low_loss_model'][self.parent.x, self.parent.y] = np.array(low_loss)
-            self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'][self.parent.x, self.parent.y] = p
-        
-            if 'zero_loss' in self.parent.datasets:
-                res = self.parent.datasets['zero_loss'][self.parent.x, self.parent.y]
-           
-        else:
-            self.parent.datasets['plasmon'] = plasmon
-            self.parent.datasets['low_loss_model'] = low_loss
-            if 'zero_loss' in self.parent.datasets:
-                res = self.parent.datasets['zero_loss']
-        self.parent.datasets['_relationship']['plasmon'] = 'plasmon'
-        self.parent.datasets['_relationship']['low_loss_model'] = 'low_loss_model'
-        
-        #self.dataset.metadata['plasmon'].update(self.parent.datasets['plasmon'].metadata['zero_loss'])
-        if self.low_loss_tab[10, 0].value:
-            self.parent._update() 
-            self._update()
-        else:
-            self.low_loss_tab[10, 0].value = True
-        
-        self.low_loss_tab[7, 0].value = np.round(np.abs(p[0]),3)
-        self.low_loss_tab[8, 0].value = np.round(p[1],3)
-        self.low_loss_tab[9, 0].value = np.round(p[2],1)
-
-        _, dsdo, _ = eels_tools.angle_correction(self.parent.spectrum)
-
-        if 'zero_loss' in self.parent.datasets:
-            I0 = res.sum() + p[2] 
-        else:
-            I0 = self.parent.spectrum.sum()
-        # I0 = self.parent.spectrum.sum()
-        # print(I0)
-        # T = m_0 v**2 !!!  a_0 = 0.05292 nm p[2] = S(E)/elf
-        t_nm  = p[2]/I0*dsdo  #Egerton equ 4.26% probability per eV
-        relative_thickness = self.low_loss_tab[14, 0].value
-        imfp, _ = eels_tools.inelatic_mean_free_path(p[0], self.parent.spectrum)
-        t_nm = float(relative_thickness * imfp)
-        # print(t_nm, relative_thickness, imfp)
-        self.parent.status_message(f'Fitted plasmon peak: thickness :{t_nm:.1f} nm and IMFP: {t_nm/relative_thickness:.1f} nm in free electron approximation')
-
-        if self.dataset.ndim>1:
-            # self.parent.datasets['plasmon'].metadata['plasmon'][self.parent.x, self.parent.y]['thickness'] = t_nm
-            # self.parent.datasets['plasmon'].metadata['plasmon'][self.parent.x, self.parent.y]['relative_thickness'] = relative_thickness
-            self.parent.datasets['plasmon'].metadata['plasmon']['IMFP'][self.parent.x, self.parent.y] = t_nm/relative_thickness
-
-        else:
-            self.parent.datasets['plasmon'].metadata['plasmon']['thickness'] = t_nm
-            self.parent.datasets['plasmon'].metadata['plasmon']['relative_thickness'] = relative_thickness
-            self.parent.datasets['plasmon'].metadata['plasmon']['IMFP'] = t_nm/relative_thickness
-
-
-    def multiple_scattering(self, value=0):
-        if self.dataset.ndim >1:
-            anglog, dsdo, _ = eels_tools.angle_correction(self.parent.spectrum)
-            par = np.array(self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'])
-            for x in range(self.parent.dataset.shape[0]):
-                for y in range(self.parent.dataset.shape[1]):
-                    self.parent.datasets['low_loss_model'][x, y] = eels_tools.multiple_scattering(self.parent.energy_scale, par[x, y]) * anglog
-        
-
-    def do_all(self, value=0):
-        if len(self.parent.dataset.shape) < 3:
-            return
-            
-        zero_loss_fit_width=self.low_loss_tab[2, 0].value
-        fit_start = self.low_loss_tab[5, 0].value
-        fit_end = self.low_loss_tab[6, 0].value
-        
-        
-        if 'low_loss_model' not in self.parent.datasets.keys():
-            self.parent.datasets['low_loss_model'] = self.parent.dataset.copy()*0
-            self.parent.datasets['low_loss_model'].title = self.parent.dataset.title + ' low_loss_model'
-        
-        self.low_loss_tab[15,1].max = self.parent.dataset.shape[0]*self.parent.dataset.shape[1]
-        
-        self.parent.datasets['zero_loss']  = eels_tools.get_resolution_functions(self.dataset, startFitEnergy=-zero_loss_fit_width, endFitEnergy=zero_loss_fit_width)
-        self.parent.datasets['zero_loss'].title = self.parent.dataset.title + ' zero_loss'
-        self.parent.status_message('Fitted zero-loss peak')
-
-        self.parent.datasets['plasmon'] = eels_tools.fit_plasmon(self.dataset, fit_start, fit_end)
-        self.parent.datasets['plasmon'].title = self.parent.dataset.title + ' plasmon'
-        
-        self.parent.status_message('Fitted zero-loss + plasmon peak')
-
-        
-        """
-        anglog, _, _ = eels_tools.angle_correction(self.parent.spectrum)
-        i = 0
-        for x in range(self.parent.dataset.shape[0]):   
-            for y in range(self.parent.dataset.shape[1]):
-                self.low_loss_tab[15,1].value = i
-                i+= 1
-
-                spectrum = self.parent.dataset[x, y]
-                
-                plasmon = eels_tools.fit_plasmon(spectrum, fit_start, fit_end)
-                p =np.abs(plasmon.metadata['plasmon']['parameter'])
-                p = list(np.abs(p))
-                
-                p.append(np.log(spectrum.sum()/self.parent.datasets['zero_loss'][x,y].sum()))
-                if p[-1] is np.nan:
-                    p[-1] = 0
-                low_loss = eels_tools.multiple_scattering(self.parent.energy_scale, p) * anglog
-                self.parent.datasets['plasmon'][x, y] = np.array(plasmon.compute())
-                self.parent.datasets['low_loss_model'][x, y] = np.array(low_loss)
-                drude_p[x, y, :] = np.array(p)
-
-       
-
-        self.parent.datasets['plasmon'].metadata['plasmon'].update({'parameter': drude_p})
-        self.parent.datasets['low_loss_model'].metadata['low_loss'] = ({'parameter': drude_p})
-        """
-
-        imfp = np.log(self.parent.dataset.sum(axis=2)/self.parent.datasets['zero_loss'].sum(axis=2)) 
-        self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'] = np.append(self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'], imfp[..., np.newaxis], axis=2)
-        E_p = self.parent.datasets['plasmon'].metadata['plasmon']['fit_parameter'][:,:,0]    
-        self.parent.datasets['plasmon'].metadata['plasmon']['IMFP'], _ = eels_tools.inelatic_mean_free_path(E_p, self.parent.spectrum)
-        self.parent.datasets['_relationship']['zero_loss'] = 'zero_loss'
-        self.parent.datasets['_relationship']['plasmon'] = 'plasmon'
-        self.multiple_scattering()        
-        self.parent.datasets['_relationship']['low_loss_model'] = 'low_loss_model'
-        
-        self.low_loss_tab[10, 1].value = False
-            
-    def get_multiple_scattering(self, value=0):
-        self.low_loss_tab[15, 0].value = False
-        fit_start = self.low_loss_tab[12, 0].value
-        fit_end = self.low_loss_tab[13, 0].value
-        
-        p = [self.low_loss_tab[7, 0].value, self.low_loss_tab[8, 0].value, self.low_loss_tab[9, 0].value, self.low_loss_tab[14, 0].value]
-        low_loss = eels_tools.fit_multiple_scattering(self.parent.spectrum, fit_start, fit_end, pin=p)
-        
-
-        self.parent.datasets['multiple_scattering'] = low_loss
-        self.parent.datasets['_relationship']['multiple_scattering'] = 'multiple_scattering'
-        self.low_loss_tab[10, 0].value = False
-        self.low_loss_tab[15, 0].value = True
-        p = low_loss.metadata['multiple_scattering']['parameter']
-        self.low_loss_tab[14, 0].value = np.round(p[3],3)
-        
-        self.parent.status_message('Fitted multiple scattering')
-        
-
-        return low_loss
-
-    def set_ll_action(self):
-        self.low_loss_tab[0, 0].observe(self.update_ll_dataset)
-        #self.low_loss_tab[1, 0].on_click(self.fix_energy_scale)
-        #self.low_loss_tab[2, 0].observe(self.set_energy_scale, names='value')
-        #self.low_loss_tab[3, 0].observe(self.set_energy_scale, names='value')
-        self.low_loss_tab[1, 0].on_click(self.get_resolution_function)
-        self.low_loss_tab[3, 2].observe(self.parent.info.set_y_scale, names='value')
-        self.low_loss_tab[3, 0].observe(self._update, names='value')
-        self.low_loss_tab[4, 0].on_click(self.get_drude)
-        self.low_loss_tab[10, 0].observe(self._update, names='value')
-        self.low_loss_tab[10, 1].observe(self.do_all, names='value')
-        self.low_loss_tab[10, 2].observe(self._update, names='value')
-        self.low_loss_tab[11, 0].on_click(self.get_multiple_scattering)
-        self.low_loss_tab[15, 0].observe(self._update, names='value')
-        
-    
-    def _update(self, ev=0):
-        low_loss = None
-        plasmon = None
-        resolution_function = None
-        if 'zero_loss' in self.parent.added_spectra.keys():
-            del self.parent.added_spectra['zero_loss']
-        if 'plasmon' in self.parent.added_spectra.keys():
-            del self.parent.added_spectra['plasmon']
-        if 'low_loss_model' in self.parent.added_spectra.keys():
-            del self.parent.added_spectra['low_loss_model']
-        
-        if self .low_loss_tab[3, 0].value:
-            if 'zero_loss' in self.parent.datasets.keys():
-                resolution_function = np.array(self.parent.get_additional_spectrum('zero_loss'))
-                self.parent.added_spectra.update({'zero_loss': 'resolution'})
-        if self.low_loss_tab[10, 0].value:
-            if 'plasmon' in self.parent.datasets.keys():
-                plasmon = self.parent.get_additional_spectrum('plasmon')
-                if len(self.dataset.shape) > 1:
-                    p = np.round(plasmon.metadata['plasmon']['fit_parameter'][self.parent.x, self.parent.y], 3)
-                    imfp = np.array(plasmon.metadata['plasmon']['IMFP'][self.parent.x, self.parent.y])
-                else:
-                    p = np.round(plasmon.metadata['plasmon']['fit_parameter'], 3)
-                    imfp = plasmon.metadata['plasmon']['IMFP']
-                
-                self.parent.added_spectra.update({'plasmon': 'plasmon'})
-                self.low_loss_tab[7, 1].value =p[0]
-                self.low_loss_tab[8, 1].value = p[1]
-                self.low_loss_tab[8, 1].value = p[2]
-                
-                self.low_loss_tab[14, 1].value =p[-1]
-                t_nm = float(p[-1] * imfp)
-                # print(t_nm, p[-1], imfp)
-                self.parent.status_message(f'Fitted plasmon peak: thickness :{t_nm:.1f} nm and IMFP: {imfp:.1f} nm in free electron approximation')
-
-        if self.low_loss_tab[15, 0].value:
-            low_loss = np.array(self.parent.get_additional_spectrum('low_loss_model'))
-            self.parent.added_spectra.update({'low_loss': 'low_loss'})
-        
-        if self.low_loss_tab[3, 0].value + self.low_loss_tab[10, 0].value + self.low_loss_tab[15, 0].value > 0:
-            self.parent.datasets['_difference'] = np.array(self.parent.spectrum)
-            if resolution_function is not None:
-                self.parent.datasets['_difference'] -= resolution_function
-            if low_loss is not None:
-                self.parent.datasets['_difference'] -= low_loss
-            else:
-                if plasmon is not None:
-                    self.parent.datasets['_difference'] -= np.array(plasmon)
-            self.parent.added_spectra.update({'_difference': 'difference'})
-        else:
-            if '_difference' in self.parent.datasets.keys():
-                del self.parent.datasets['_difference']
-        self.parent._update()
-
-    def get_additional_spectrum(self, key):
-        if key not in self.parent.datasets.keys():
-            return
-        
-        if self.parent.datasets[key].data_type == sidpy.DataType.SPECTRUM:
-            spectrum = self.parent.datasets[key].copy()
-        else:
-            image_dims = self.parent.datasets[key].get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
-            selection = []
-            x = self.parent.x
-            y = self.parent.y
-            bin_x = self.parent.bin_x
-            bin_y = self.parent.bin_y
-            for dim, axis in self.parent.datasets[key]._axes.items():
-                # print(dim, axis.dimension_type)
-                if axis.dimension_type == sidpy.DimensionType.SPATIAL:
-                    if dim == image_dims[0]:
-                        selection.append(slice(x, x + bin_x))
-                    else:
-                        selection.append(slice(y, y + bin_y))
-
-                elif axis.dimension_type == sidpy.DimensionType.SPECTRAL:
-                    selection.append(slice(None))
-                elif axis.dimension_type == sidpy.DimensionType.CHANNEL:
-                    selection.append(slice(None))
-                else:
-                    selection.append(slice(0, 1))
-            
-            spectrum = self.parent.datasets[key][tuple(selection)].mean(axis=tuple(image_dims))
-            
-        spectrum *= self.parent.y_scale
-        
-        return spectrum.squeeze()
-    
-    
-
-    
-    def set_binning(self, value):
-        if 'SPECTRAL' in self.dataset.data_type.name:
-            bin_x = self.info_tab[15, 0].value
-            bin_y = self.info_tab[16, 0].value
-            self.dataset.view.set_bin([bin_x, bin_y])
-            self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
-            self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y