pyTEMlib 0.2020.11.1__py3-none-any.whl → 0.2024.8.4__py3-none-any.whl

pyTEMlib/info_widget.py

@@ -0,0 +1,933 @@
+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
+from pyTEMlib.core_loss_widget import get_core_loss_sidebar, CoreLoss
+from pyTEMlib.low_loss_widget import get_low_loss_sidebar, LowLoss
+
+def get_image_sidebar() -> Any:
+    side_bar = ipywidgets.GridspecLayout(14, 3, width='auto', grid_gap="0px")
+
+    side_bar[0, :2] = ipywidgets.Dropdown(
+            options=[('None', 0)],
+            value=0,
+            description='Main Dataset:',
+            disabled=False)
+    row = 1
+    side_bar[row, :3] = ipywidgets.Button(description='Image Scale',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='x dim:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="nm", layout=ipywidgets.Layout(width='20px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='y dim:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="nm", layout=ipywidgets.Layout(width='20px'))
+    row += 1
+
+    side_bar[row, :3] = ipywidgets.Button(description='Microscope',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Conv.Angle:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Coll.Angle:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Acc Voltage:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="keV", layout=ipywidgets.Layout(width='100px'))
+    
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Calibration',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Pixel_Time:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="μs", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Screen Curr:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="pA", layout=ipywidgets.Layout(width='50px'))
+    row += 1
+
+    side_bar[row, 0] = ipywidgets.Button(description='FFT', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 1] = ipywidgets.Button(description='LR-Decon', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 2] = ipywidgets.Button(description='Find atoms', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Image Stack',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, 0] = ipywidgets.Button(description='Rig Reg.', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 1] = ipywidgets.Button(description='Demon', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 2] = ipywidgets.Button(description='Sum', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+   
+    side_bar[-2, 0].layout.display = "none"
+    for i in range(3):
+        side_bar[-1, i].layout.display = "none"
+    return side_bar
+    
+
+def get_info_sidebar() -> Any:
+    side_bar = ipywidgets.GridspecLayout(18, 3, width='auto', grid_gap="0px")
+
+    side_bar[0, :2] = ipywidgets.Dropdown(
+            options=[('None', 0)],
+            value=0,
+            description='Main Dataset:',
+            disabled=False)
+    
+    row = 1
+    side_bar[row, :3] = ipywidgets.Button(description='Energy Scale',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Offset:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Microscope',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Conv.Angle:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Coll.Angle:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="mrad", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Acc Voltage:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="keV", layout=ipywidgets.Layout(width='100px'))
+    
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Calibration',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.Dropdown(
+            options=[('None', 0)],
+            value=0,
+            description='Reference:',
+            disabled=False)
+    side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
+                                               disabled=False,
+                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
+                                               tooltip='Changes y-axis to probability if flux is given',
+                                               layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Exp_Time:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="s", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Flux:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="Mcounts", layout=ipywidgets.Layout(width='50px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="e⁻/counts", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="pA", layout=ipywidgets.Layout(width='100px'))
+    
+    row += 1
+    side_bar[row, 0] = ipywidgets.Button(description='Get Shift', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 1] = ipywidgets.Button(description='Shift Spec', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 2] = ipywidgets.Button(description='Res.Fct.', disabled=True,
+                                         layout=ipywidgets.Layout(width='auto'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Spectrum Image',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    
+    row += 1
+    side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
+                                           layout=ipywidgets.Layout(width='200px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
+                                           layout=ipywidgets.Layout(width='200px'))
+    
+    for i in range(15, 18):
+        side_bar[i, 0].layout.display = "none"
+    return side_bar
+
+
+
+def get_file_widget_ui():
+    side_bar = ipywidgets.GridspecLayout(7, 3, height='500px', width='auto', grid_gap="0px")
+    row = 0
+    side_bar[row, :3] = ipywidgets.Dropdown(options=['None'], value='None', description='directory:', disabled=False,
+                                            button_style='', layout=ipywidgets.Layout(width='auto', grid_area='header'))
+    row += 1
+    side_bar[row, :3] = ipywidgets.Select(options=['.'], value='.', description='Select file:', disabled=False,
+                                          rows=10, layout=ipywidgets.Layout(width='auto'))
+    row += 1
+    side_bar[row, 0] = ipywidgets.Button(description='Select Main',
+                                         layout=ipywidgets.Layout(width='100px'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 1] = ipywidgets.Button(description='Add',
+                                         layout=ipywidgets.Layout(width='50px'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    side_bar[row, 2] = ipywidgets.Dropdown(options=['None'], value='None', description='loaded:', disabled=False,
+                                           button_style='')
+
+    row += 1
+    side_bar[row, :3] = ipywidgets.Select(options=['None'], value='None', description='Spectral:',
+                                          disabled=False, rows=3, layout=ipywidgets.Layout(width='auto'))
+    row += 1
+    side_bar[row, :3] = ipywidgets.Select(options=['Sum'], value='Sum', description='Images:',
+                                          disabled=False, rows=3, layout=ipywidgets.Layout(width='auto'))
+    row += 1
+    side_bar[row, :3] = ipywidgets.Select(options=['None'], value='None', description='Survey:',
+                                          disabled=False, rows=2, layout=ipywidgets.Layout(width='auto'))
+    for i in range(3, 6):
+        side_bar[i, 0].layout.display = "none"
+
+    row += 1
+    side_bar[row, 0] = ipywidgets.Button(description='Save',
+                                         layout=ipywidgets.Layout(width='100px'),
+                                         style=ipywidgets.ButtonStyle(button_color='lightblue'))
+
+    return side_bar  
+
+
+class EELSBaseWidget(object):
+
+    def __init__(self, datasets, sidebar, tab_title=None):
+        
+        self.datasets = datasets
+        self.dataset = None
+        self.save_path = False
+        self.dir_dictionary = {}
+        self.dir_list = ['.', '..']
+        self.display_list = ['.', '..']
+        self.dataset_list = ['None']
+        self.image_list = ['Sum']
+        self.dir_name = file_tools.get_last_path()
+
+        self.save_path = True
+
+        if not os.path.isdir(self.dir_name):
+            self.dir_name = '.'
+
+        self.get_directory(self.dir_name)
+        self.dir_list = ['.']
+        self.extensions = '*'
+        self.file_name = ''
+        self.datasets = {}
+        self.dataset = None
+        self.sd0 = 0
+        self.sds = 0
+
+        self.bin_x = 0
+        self.bin_y = 0
+
+        self.start_channel = -1
+        self.end_channel = -2
+
+        self.file_bar = get_file_widget_ui()
+        if isinstance(sidebar, dict):
+            tab = ipywidgets.Tab()
+            children = [self.file_bar]
+            titles = ['File']
+            for sidebar_key, sidebar_gui in sidebar.items():
+                children.append(sidebar_gui)
+                titles.append(sidebar_key)
+            tab.children = children
+            tab.titles = titles
+        elif not isinstance(sidebar, list):
+            tab = ipywidgets.Tab()
+            tab.children = [self.file_bar, sidebar]
+            tab.titles = ['File', 'Info']
+        else:
+            tab = sidebar
+        self.tab = tab
+        with plt.ioff():
+            self.figure = plt.figure()
+        
+        self.figure.canvas.toolbar_position = 'right'
+        self.figure.canvas.toolbar_visible = True
+
+        self.start_cursor = ipywidgets.FloatText(value=0, description='Start:', disabled=False, color='black',
+                                                 layout=ipywidgets.Layout(width='200px'))
+        self.end_cursor = ipywidgets.FloatText(value=0, description='End:', disabled=False, color='black',
+                                               layout=ipywidgets.Layout(width='200px'))
+        self.panel = ipywidgets.VBox([ipywidgets.HBox([ipywidgets.Label('', layout=ipywidgets.Layout(width='100px')),
+                                                       ipywidgets.Label('Cursor:'),
+                                                       self.start_cursor, ipywidgets.Label('eV'),
+                                                       self.end_cursor, ipywidgets.Label('eV')]),
+                                      self.figure.canvas])
+        
+        self.app_layout = ipywidgets.AppLayout(
+            left_sidebar=tab,
+            center=self.panel,
+            footer=None,  # message_bar,
+            pane_heights=[0, 10, 0],
+            pane_widths=[4, 10, 0],
+        )
+        # self.set_dataset()
+        self.change_y_scale = 1.0
+        self.x = 0
+        self.y = 0
+        self.bin_x = 1
+        self.bin_y = 1
+        self.count = 0
+        display(self.app_layout)
+
+        self.select_files = self.file_bar[1, 0]
+        self.path_choice = self.file_bar[0, 0]
+        self.set_file_options()
+        select_button = self.file_bar[2, 0]
+        add_button = self.file_bar[2, 1]
+        self.loaded_datasets = self.file_bar[2, 2]
+        self.select_files.observe(self.get_file_name, names='value')
+        self.path_choice.observe(self.set_dir, names='value')
+
+        select_button.on_click(self.select_main)
+        add_button.on_click(self.add_dataset)
+        self.loaded_datasets.observe(self.select_dataset, names='value')
+        self.file_bar[4, 0].observe(self.plot, names='value')
+
+    def set_image(self, key=None):
+        if self.file_bar[4, 0].value == 'Sum':
+            spec_dim = self.dataset.get_dimensions_by_type(sidpy.DimensionType.SPECTRAL)
+            if len(spec_dim) != 1:
+                raise ValueError('Only one spectral dimension')
+
+            channel_dim = self.dataset.get_dimensions_by_type(sidpy.DimensionType.CHANNEL)
+
+            if len(channel_dim) > 1:
+                raise ValueError('Maximal one channel dimension')
+
+            if len(channel_dim) > 0:
+                self.image = self.dataset.mean(axis=(spec_dim[0], channel_dim[0]))
+            else:
+                self.image = self.dataset.mean(axis=(spec_dim[0]))
+        else:
+            image_key = self.file_bar[4, 0].value.split(':')[0]
+            self.image = self.datasets[image_key]
+
+    def plot(self, scale=True):
+        self.figure.clear()
+        spec_dims = self.dataset.get_spectral_dims(return_axis=True)
+        if len(spec_dims)>0:
+            self.energy_scale = spec_dims[0]
+            if self.dataset.data_type.name == 'SPECTRUM':
+                self.axis = self.figure.subplots(ncols=1)
+            else:
+                self.plot_spectrum_image() 
+                self.axis = self.axes[-1]
+            self.spectrum = self.get_spectrum()
+            self.plot_spectrum()
+    
+        else:
+            self.axis = self.figure.subplots(ncols=1)
+            self.plot_image()
+        
+    def plot_image(self): 
+        # image_dims = self.dataset.get_image_dims()
+        image_dims = []
+        for dim, axis in self.dataset._axes.items():
+            if axis.dimension_type in [sidpy.DimensionType.SPATIAL, sidpy.DimensionType.RECIPROCAL]:
+                image_dims.append(dim)
+        self.img = self.axis.imshow(self.dataset, extent=self.dataset.get_extent(image_dims))
+        self.axis.set_xlabel(self.dataset.labels[image_dims[0]])
+        self.axis.set_ylabel(self.dataset.labels[image_dims[1]])
+        
+        cbar = self.figure.colorbar(self.img)
+        cbar.set_label(self.dataset.data_descriptor)
+
+        self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
+        self.figure.tight_layout()
+        self.figure.canvas.draw_idle()
+
+
+    def plot_spectrum(self):    
+        self.axis.plot(self.energy_scale, self.spectrum, label='spectrum')
+        x_limit = self.axis.get_xlim()
+        y_limit = np.array(self.axis.get_ylim())
+        self.xlabel = self.datasets[self.key].labels[0]
+        self.ylabel = self.datasets[self.key].data_descriptor
+        self.axis.set_xlabel(self.datasets[self.key].labels[0])
+        self.axis.set_ylabel(self.datasets[self.key].data_descriptor)
+        self.axis.ticklabel_format(style='sci', scilimits=(-2, 4))
+        
+        # if scale:
+        #    self.axis.set_ylim(np.array(y_limit)*self.change_y_scale)
+        self.change_y_scale = 1.0
+        if self.y_scale != 1.:
+            self.axis.set_ylabel('scattering probability (ppm/eV)')
+        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
+                                                        direction="horizontal",
+                                                        interactive=True,
+                                                        props=dict(facecolor='blue', alpha=0.2))
+        self.axis.legend()
+        if self.dataset.data_type.name == 'SPECTRUM':
+            self.axis.set_title(self.dataset.title)
+        else:
+            self.axis.set_title(f'spectrum {self.x}, {self.y}')
+        self.figure.canvas.draw_idle()
+
+    def _update(self, ev=None):
+        if hasattr(self, 'axes'):
+            xlim = np.array(self.axes[1].get_xlim())
+            ylim = np.array(self.axes[1].get_ylim())
+            self.axes[1].clear()
+            self.axis = self.axes[-1]
+        else:
+            xlim = np.array(self.axis.get_xlim())
+            ylim = np.array(self.axis.get_ylim())
+            self.axis.clear()
+        self.get_spectrum()
+        if len(self.energy_scale) != self.spectrum.shape[0]:
+            self.spectrum = self.spectrum.T
+        self.axis.plot(self.energy_scale, self.spectrum.compute(), label='experiment')
+
+        self.axis.set_title(f'spectrum {self.x}, {self.y}')
+        self.figure.tight_layout()
+        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
+                                                        direction="horizontal",
+                                                        interactive=True,
+                                                        props=dict(facecolor='blue', alpha=0.2))
+
+        self.axis.set_xlim(xlim)
+        self.axis.set_ylim(ylim*self.change_y_scale)
+        self.axis.set_xlabel(self.xlabel)
+        self.axis.set_ylabel(self.ylabel)
+        self.change_y_scale = 1.0
+        self.figure.canvas.draw_idle()
+
+    def _onclick(self, event):
+        self.event = event
+        if event.inaxes in [self.axes[0]]:
+            x = int(event.xdata)
+            y = int(event.ydata)
+
+            x = int(x - self.rectangle[0])
+            y = int(y - self.rectangle[2])
+
+            if x >= 0 and y >= 0:
+                if x <= self.rectangle[1] and y <= self.rectangle[3]:
+                    self.x = int(x / (self.rect.get_width() / self.bin_x))
+                    self.y = int(y / (self.rect.get_height() / self.bin_y))
+                    image_dims = self.dataset.get_image_dims()
+            
+                    if self.x + self.bin_x > self.dataset.shape[image_dims[0]]:
+                        self.x = self.dataset.shape[image_dims[0]] - self.bin_x
+                    if self.y + self.bin_y > self.dataset.shape[image_dims[1]]:
+                        self.y = self.dataset.shape[image_dims[1]] - self.bin_y
+            
+                    self.rect.set_xy([self.x * self.rect.get_width() / self.bin_x + self.rectangle[0],
+                                      self.y * self.rect.get_height() / self.bin_y + self.rectangle[2]])
+                # self.get_spectrum()
+                self._update()
+        else:
+            if event.dblclick:
+                bottom = float(self.spectrum.min())
+                if bottom < 0:
+                    bottom *= 1.02
+                else:
+                    bottom *= 0.98
+                top = float(self.spectrum.max())
+                if top > 0:
+                    top *= 1.02
+                else:
+                    top *= 0.98
+                self.axis.set_ylim(bottom=bottom, top=top)
+
+    def get_spectrum(self):
+        if self.dataset.data_type.name == 'SPECTRUM':
+            self.spectrum = self.dataset.copy()
+        else:
+            image_dims = self.dataset.get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
+            if self.x > self.dataset.shape[image_dims[0]] - self.bin_x:
+                self.x = self.dataset.shape[image_dims[0]] - self.bin_x
+            if self.y > self.dataset.shape[image_dims[1]] - self.bin_y:
+                self.y = self.dataset.shape[image_dims[1]] - self.bin_y
+            selection = []
+            self.axis.clear()
+            for dim, axis in self.dataset._axes.items():
+                if axis.dimension_type == sidpy.DimensionType.SPATIAL:
+                    if dim == image_dims[0]:
+                        selection.append(slice(self.x, self.x + self.bin_x))
+                    else:
+                        selection.append(slice(self.y, self.y + self.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))
+            
+            self.spectrum = self.dataset[tuple(selection)].mean(axis=tuple(image_dims))
+
+        self.spectrum *= self.y_scale
+        
+        return self.spectrum.squeeze()
+
+    def plot_spectrum_image(self): 
+        self.axes = self.figure.subplots(ncols=2)
+        self.axis = self.axes[-1]
+
+        self.set_image()
+        self.rect = matplotlib.patches.Rectangle((0, 0), self.bin_x, self.bin_y, linewidth=1, edgecolor='r',
+                                                 facecolor='red', alpha=0.2)
+        image_dims = self.dataset.get_image_dims()
+
+        size_x = self.dataset.shape[image_dims[0]]
+        size_y = self.dataset.shape[image_dims[1]]
+        self.extent = [0, size_x, size_y, 0]
+        self.rectangle = [0, size_x, 0, size_y]
+        self.axes[0].imshow(self.image.T, extent=self.extent)
+        self.axes[0].set_aspect('equal')
+        self.axes[0].add_patch(self.rect)
+        self.cid = self.axes[0].figure.canvas.mpl_connect('button_press_event', self._onclick)
+
+    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)
+
+        energy_scale = self.dataset.get_spectral_dims(return_axis=True)[0]
+        self.start_channel = np.searchsorted(energy_scale, self.start_cursor.value)
+        self.end_channel = np.searchsorted(energy_scale, self.end_cursor.value)
+
+    def set_dataset(self, key=None):
+         
+        if len(self.datasets) == 0:
+            data_set = sidpy.Dataset.from_array([0, 1], name='generic')
+            data_set.set_dimension(0, sidpy.Dimension([0, 1], 'energy_loss',  units='channel', quantity='generic',
+                                                      dimension_type='spectral'))
+            data_set.data_type = 'spectrum'
+            data_set.metadata = {'experiment': {'convergence_angle': 0,
+                                                'collection_angle': 0,
+                                                'acceleration_voltage': 0,
+                                                'exposure_time': 0}}
+            self.datasets = {'Nothing': data_set}
+            key = 'Nothing'
+        
+        dataset_key = key
+        
+        self.dataset_list = []
+        dataset_keys = []
+        for key in self.datasets.keys():
+            if isinstance(self.datasets[key], sidpy.Dataset):
+                self.dataset_list.append(f'{key}: {self.datasets[key].title}')
+                dataset_keys.append(key)
+        if dataset_key not in dataset_keys:
+            dataset_key = dataset_keys[0]
+        self.key = dataset_key
+
+        self.dataset = self.datasets[self.key]
+        
+        spectral_dims = self.dataset.get_spectral_dims(return_axis=True)
+        if len(spectral_dims) >0:
+            self.energy_scale = spectral_dims[0]
+        self.y_scale = 1.0
+        self.change_y_scale = 1.0
+        self.x = 0
+        self.y = 0
+        self.bin_x = 1
+        self.bin_y = 1
+        self.count = 0
+
+        self.update_sidebars()
+        #self.update_sidebar()
+        self.plot()
+        
+    def update_sidebars(self):
+        pass
+
+    def select_main(self, value=0):
+        self.sds +=1
+        self.datasets = {}
+        # self.loaded_datasets.options = self.dataset_list
+        
+        self.datasets = file_tools.open_file(self.file_name)
+        file_tools.save_path(self.file_name)
+        self.dataset_list = []
+        self.image_list = ['Sum']
+        self.survey_list = ['None']
+        self.spectral_list = ['None']
+        for key in self.datasets.keys():
+            if isinstance(self.datasets[key], sidpy.Dataset):
+                self.dataset_list.append(f'{key}: {self.datasets[key].title}')
+                if 'SPECTR' in self.datasets[key].data_type.name:
+                    self.spectral_list.append(f'{key}: {self.datasets[key].title}')
+                if 'IMAGE' == self.datasets[key].data_type.name:
+                    if 'survey' in self.datasets[key].title.lower():
+                        self.survey_list.append(f'{key}: {self.datasets[key].title}')
+                    else:
+                        self.image_list.append(f'{key}: {self.datasets[key].title}')
+
+        
+        self.key = self.dataset_list[0].split(':')[0]
+        self.dataset = self.datasets[self.key]
+
+        self.selected_dataset = self.dataset
+        if len(self.image_list) > 0:
+            self.file_bar[4, 0].options = self.image_list
+            self.file_bar[5, 0].options = self.survey_list
+            self.file_bar[4, 0].layout.display = "flex"
+            self.file_bar[4, 0].value = self.image_list[0]
+            self.file_bar[5, 0].layout.display = "flex"
+            self.file_bar[5, 0].value = self.survey_list[0]
+
+        self.file_bar[3, 0].options = self.dataset_list
+        self.loaded_datasets.options = self.dataset_list
+        self.loaded_datasets.value = self.dataset_list[0]
+
+    def add_dataset(self, value=0):
+        key = file_tools.add_dataset_from_file(self.datasets, self.file_name, 'Channel')
+        self.dataset_list.append(f'{key}: {self.datasets[key].title}')
+        self.loaded_datasets.options = self.dataset_list
+        self.loaded_datasets.value = self.dataset_list[-1]
+
+    def get_directory(self, directory='.'):
+        self.dir_name = directory
+        self.dir_dictionary = {}
+        self.dir_list = []
+        self.dir_list = ['.', '..'] + os.listdir(directory)
+
+    def set_dir(self, value=0):
+        self.dir_name = self.path_choice.value
+        self.select_files.index = 0
+        self.set_file_options()
+
+    def select_dataset(self, value=0):
+        key = self.loaded_datasets.value.split(':')[0]
+        if key != 'None':
+            self.selected_dataset = self.datasets[key]
+            self.selected_key = key
+            self.key = key
+        self.datasets['_relationship'] = {'main_dataset': self.key}
+        
+        self.set_dataset()
+
+    def set_file_options(self):
+        self.dir_name = os.path.abspath(os.path.join(self.dir_name, self.dir_list[self.select_files.index]))
+        dir_list = os.listdir(self.dir_name)
+        file_dict = file_tools.update_directory_list(self.dir_name)
+
+        sort = np.argsort(file_dict['directory_list'])
+        self.dir_list = ['.', '..']
+        self.display_list = ['.', '..']
+        for j in sort:
+            self.display_list.append(f" * {file_dict['directory_list'][j]}")
+            self.dir_list.append(file_dict['directory_list'][j])
+
+        sort = np.argsort(file_dict['display_file_list'])
+
+        for i, j in enumerate(sort):
+            if '--' in dir_list[j]:
+                self.display_list.append(f" {i:3} {file_dict['display_file_list'][j]}")
+            else:
+                self.display_list.append(f" {i:3}   {file_dict['display_file_list'][j]}")
+            self.dir_list.append(file_dict['file_list'][j])
+
+        self.dir_label = os.path.split(self.dir_name)[-1] + ':'
+        self.select_files.options = self.display_list
+        
+        path = self.dir_name
+        old_path = ' '
+        path_list = []
+        while path != old_path:
+            path_list.append(path)
+            old_path = path
+            path = os.path.split(path)[0]
+        self.path_choice.options = path_list
+        self.path_choice.value = path_list[0]
+
+    def get_file_name(self, b):
+
+        if os.path.isdir(os.path.join(self.dir_name, self.dir_list[self.select_files.index])):
+            self.set_file_options()
+
+        elif os.path.isfile(os.path.join(self.dir_name, self.dir_list[self.select_files.index])):
+            self.file_name = os.path.join(self.dir_name, self.dir_list[self.select_files.index])
+
+class EELSWidget(EELSBaseWidget):
+    def __init__(self, datasets=None):
+        
+        sidebar = {'Spec.': get_info_sidebar(),
+                   'LowLoss': get_low_loss_sidebar(),
+                   'CoreLoss': get_core_loss_sidebar()}
+        super().__init__(datasets, sidebar)
+        self.info_tab = sidebar['Spec.']
+        self.core_loss_tab = sidebar['CoreLoss']
+        self.low_loss_tab = sidebar['LowLoss']
+        super().set_dataset()
+        self.info = Info(self.info_tab, self)
+        self.low_loss = LowLoss(self.low_loss_tab, self)
+        self.core_loss = CoreLoss(self.core_loss_tab, self)
+        
+        self.set_action()
+    
+    def set_action(self):
+        self.tab.observe(self.tab_activated)
+
+    def tab_activated(self, val=0):
+        if isinstance(val.new, int):
+            self.tabval = val.new
+            self.update_sidebars()
+            if val.new == 1:
+                self.info.update_dataset()
+            elif val.new == 2:
+                self.low_loss.update_ll_dataset()
+            elif val.new == 3:
+                self.core_loss.update_cl_sidebar()
+
+    def update_sidebars(self):
+        if hasattr(self, 'info'):
+            self.info.update_sidebar()
+        #if hasattr(self, 'low_loss'):
+        #    self.low_loss.update_ll_sidebar()
+        #if hasattr(self, 'core_loss'):
+        #    self.core_loss.update_cl_sidebar()
+
+class Info(object):
+    def __init__(self, sidebar=None, parent=None):
+        self.parent = parent
+        self.info_tab = sidebar
+        self.key = self.parent.key
+        self.update_sidebar()        
+        self.set_action()
+        self.count =0
+
+    def set_energy_scale(self, value):
+        self.ens = 1
+        self.energy_scale = self.parent.datasets[self.key].get_spectral_dims(return_axis=True)[0]
+        dispersion = self.parent.datasets[self.key].get_dimension_slope(self.energy_scale)
+        self.ens = dispersion
+        self.energy_scale *= (self.info_tab[3, 0].value / dispersion)
+        self.energy_scale += (self.info_tab[2, 0].value - self.energy_scale[0])
+        self.parent.plot()
+
+    def set_y_scale(self, value):
+        self.count += 1
+        self.parent.change_y_scale = 1.0 / self.parent.y_scale
+        if self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] > 1e-12:
+            if self.info_tab[9, 2].value:
+                dispersion = self.parent.datasets[self.key].get_dimension_slope(self.energy_scale)
+                self.parent.y_scale = 1 / self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] * dispersion
+                self.parent.ylabel = 'scattering probability (ppm)'
+            else:
+                self.parent.y_scale = 1.0
+                self.parent.ylabel = 'intensity (counts)'
+            self.parent.change_y_scale *= self.parent.y_scale
+            self.parent._update()
+
+    def set_flux(self, value):
+        # self.parent.datasets[self.key].metadata['experiment']['exposure_time'] = self.info_tab[10, 0].value
+        if self.info_tab[9, 0].value == 'None':
+            self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] = 0.
+        else:
+            ll_key = self.info_tab[9, 0].value.split(':')[0]
+            self.parent.datasets['_relationship']['low_loss'] = ll_key
+            spectrum_dimensions = self.parent.dataset.get_spectral_dims()
+
+            number_of_pixels = 1
+            for index, dimension in enumerate(self.parent.dataset.shape):
+                if index not in spectrum_dimensions:
+                    number_of_pixels *= dimension
+            if self.parent.datasets[ll_key].metadata['experiment']['exposure_time'] == 0.0:
+                if self.parent.datasets[ll_key].metadata['experiment']['single_exposure_time'] == 0.0:
+                    return
+                else:
+                    self.parent.datasets[ll_key].metadata['experiment']['exposure_time'] = (self.parent.datasets[ll_key].metadata['experiment']['single_exposure_time'] *
+                                                                                     self.parent.datasets[ll_key].metadata['experiment']['number_of_frames'])
+
+            self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] = ((np.array(self.parent.datasets[ll_key])*1e-6).sum() /
+                                                                          self.parent.datasets[ll_key].metadata['experiment']['exposure_time'] /
+                                                                          number_of_pixels)
+            self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] *= self.parent.datasets[self.key].metadata['experiment']['exposure_time']
+            if 'SPECT' in self.parent.datasets[ll_key].data_type.name:
+                self.info_tab[14, 0].disabled = False
+        self.info_tab[11, 0].value = np.round(self.parent.datasets[self.key].metadata['experiment']['flux_ppm'], 2)
+
+    def set_microscope_parameter(self, value):
+        self.parent.datasets[self.key].metadata['experiment']['convergence_angle'] = self.info_tab[5, 0].value
+        self.parent.datasets[self.key].metadata['experiment']['collection_angle'] = self.info_tab[6, 0].value
+        self.parent.datasets[self.key].metadata['experiment']['acceleration_voltage'] = self.info_tab[7, 0].value*1000
+    
+    def cursor2energy_scale(self, value):
+        self.energy_scale = self.parent.datasets[self.key].get_spectral_dims(return_axis=True)[0]
+        dispersion = (self.parent.end_cursor.value - self.parent.start_cursor.value) / (self.parent.end_channel - self.parent.start_channel)
+
+        self.energy_scale *= (self.info_tab[3, 0].value/dispersion)
+        
+        offset = self.parent.start_cursor.value - self.parent.start_channel * dispersion
+        self.parent.energy_scale += (self.info_tab[2, 0].value-self.parent.energy_scale[0])
+        self.info_tab[2, 0].value = np.round(offset,4)
+        self.info_tab[3, 0].value = np.round(dispersion,4)
+        self.parent.plot()
+
+    def set_binning(self, value):
+        if 'SPECTRAL' in self.parent.dataset.data_type.name:
+            image_dims = self.parent.dataset.get_image_dims()
+
+            self.bin_x = int(self.info_tab[16, 0].value)
+            self.bin_y = int(self.info_tab[17, 0].value)
+            if self.bin_x < 1:
+                self.bin_x = 1
+                self.info_tab[16, 0].value = self.bin_x
+            if self.bin_y < 1:
+                self.bin_y = 1
+                self.info_tab[17, 0].value = self.bin_y
+            if self.bin_x > self.parent.dataset.shape[image_dims[0]]:
+                self.bin_x = self.parent.dataset.shape[image_dims[0]]
+                self.info_tab[16, 0].value = self.bin_x
+            if self.bin_y > self.parent.dataset.shape[image_dims[1]]:
+                self.bin_y = self.parent.dataset.shape[image_dims[1]]
+                self.info_tab[17, 0].value = self.bin_y
+
+            self.parent.datasets[self.key].metadata['experiment']['SI_bin_x'] = self.bin_x
+            self.parent.datasets[self.key].metadata['experiment']['SI_bin_y'] = self.bin_y
+            self.plot()
+
+    
+
+    def update_sidebar(self):
+        spectrum_list = ['None']
+        reference_list = ['None']
+        data_list = []
+        self.key = self.parent.key
+        spectrum_data = False
+        for key in self.parent.datasets.keys():
+            if isinstance(self.parent.datasets[key], sidpy.Dataset):
+                if key[0] != '_' :
+                    data_list.append(f'{key}: {self.parent.datasets[key].title}')
+                    if 'SPECTR' in self.parent.datasets[key].data_type.name:
+                        spectrum_data = True
+                        spectrum_list.append(f'{key}: {self.parent.datasets[key].title}')
+                reference_list.append(f'{key}: {self.parent.datasets[key].title}')
+        self.info_tab[0, 0].options = spectrum_list
+        self.info_tab[9, 0].options = reference_list
+
+        if 'SPECTRUM' in self.parent.dataset.data_type.name:
+            for i in range(15, 18):
+                self.info_tab[i, 0].layout.display = "none"
+        else:
+            for i in range(15, 18):
+                self.info_tab[i, 0].layout.display = "flex"
+        
+        if spectrum_data:
+            offset = self.parent.datasets[self.key].energy_loss[0]
+            dispersion = self.parent.datasets[self.key].energy_loss[1] - offset
+            
+            # self.info_tab[0,0].value = dataset_index #f'{self.key}: {self.parent.datasets[self.key].title}'
+            self.info_tab[2, 0].value = np.round(offset, 3)
+            self.info_tab[3, 0].value = np.round(dispersion, 4)
+            self.info_tab[5, 0].value = np.round(self.parent.datasets[self.key].metadata['experiment']['convergence_angle'], 1)
+            self.info_tab[6, 0].value = np.round(self.parent.datasets[self.key].metadata['experiment']['collection_angle'], 1)
+            self.info_tab[7, 0].value = np.round(self.parent.datasets[self.key].metadata['experiment']['acceleration_voltage']/1000, 1)
+            self.info_tab[10, 0].value = np.round(self.parent.datasets[self.key].metadata['experiment']['exposure_time'], 4)
+            if 'flux_ppm' not in self.parent.datasets[self.key].metadata['experiment']:
+                self.parent.datasets[self.key].metadata['experiment']['flux_ppm'] = 0
+            self.info_tab[11, 0].value = self.parent.datasets[self.key].metadata['experiment']['flux_ppm']
+            if 'count_conversion' not in self.parent.datasets[self.key].metadata['experiment']:
+                self.parent.datasets[self.key].metadata['experiment']['count_conversion'] = 1
+            self.info_tab[12, 0].value = self.parent.datasets[self.key].metadata['experiment']['count_conversion']
+            if 'beam_current' not in self.parent.datasets[self.key].metadata['experiment']:
+                self.parent.datasets[self.key].metadata['experiment']['beam_current'] = 0
+            self.info_tab[13, 0].value = self.parent.datasets[self.key].metadata['experiment']['beam_current']
+            ll_key = 'None'
+            if '_relationship' in self.parent.datasets:
+                if 'low_loss' in self.parent.datasets['_relationship']:
+                    ll_key = self.parent.datasets['_relationship']['low_loss']  
+                    ll_key = f'{ll_key}: {self.parent.datasets[ll_key].title}'
+            self.info_tab[9, 0].value = ll_key
+
+    def update_dataset(self, value=0):
+        key = self.info_tab[0, 0].value.split(':')[0]
+        self.parent.set_dataset(key)
+
+    def shift_low_loss(self,  value=0):
+        if 'low_loss' in self.parent.datasets['_relationship']:
+            low_loss = self.parent.datasets[self.parent.datasets['_relationship']['low_loss']]
+            self.parent.datasets[self.parent.datasets['_relationship']['low_loss']] = eels_tools.align_zero_loss(low_loss)
+           
+        if 'low_loss' in self.parent.datasets['_relationship']:
+            if 'zero_loss' in self.parent.datasets[self.parent.datasets['_relationship']['low_loss']].metadata:
+                if 'shifted' in self.parent.datasets[self.parent.datasets['_relationship']['low_loss']].metadata['zero_loss'].keys():
+                    self.info_tab[14, 1].disabled = False
+                    
+
+    def shift_spectrum(self,  value=0):
+        shifts = self.parent.dataset.shape
+        if 'low_loss' in self.parent.datasets['_relationship']:
+            if 'zero_loss' in self.parent.datasets[self.parent.datasets['_relationship']['low_loss']].metadata:
+                if 'shifted' in self.parent.datasets[self.parent.datasets['_relationship']['low_loss']].metadata['zero_loss'].keys():
+                    shifts = self.parent.datasets[self.parent.datasets['_relationship']['low_loss']].metadata['zero_loss']['shifted']
+                    shifts_new = shifts.copy()
+                    if 'zero_loss' in self.parent.dataset.metadata:
+                        if 'shifted' in self.parent.dataset.metadata['zero_loss'].keys():
+                            shifts_new = shifts-self.parent.dataset.metadata['zero_loss']['shifted']
+                    else:
+                        self.parent.dataset.metadata['zero_loss'] = {}
+                    
+
+                    self.parent.dataset = eels_tools.shift_energy(self.parent.dataset, shifts_new)
+                    self.parent.dataset.metadata['zero_loss']['shifted'] = shifts
+                    self.parent.plot()
+
+
+    def set_action(self):
+        self.info_tab[0, 0].observe(self.update_dataset, names='value')
+        self.info_tab[1, 0].on_click(self.cursor2energy_scale)
+        self.info_tab[2, 0].observe(self.set_energy_scale, names='value')
+        self.info_tab[3, 0].observe(self.set_energy_scale, names='value')
+        self.info_tab[5, 0].observe(self.set_microscope_parameter)
+        self.info_tab[6, 0].observe(self.set_microscope_parameter)
+        self.info_tab[7, 0].observe(self.set_microscope_parameter)
+        self.info_tab[9, 0].observe(self.set_flux, names='value')
+        self.info_tab[9, 2].observe(self.set_y_scale, names='value')
+        self.info_tab[10, 0].observe(self.set_flux)
+        self.info_tab[14, 0].on_click(self.shift_low_loss)
+        self.info_tab[14, 1].on_click(self.shift_spectrum)
+        
+        self.info_tab[16, 0].observe(self.set_binning)
+        self.info_tab[17, 0].observe(self.set_binning)