pyTEMlib 0.2020.11.0__py3-none-any.whl → 0.2024.8.4__py3-none-any.whl

pyTEMlib/{interactive_eels.py → eels_dialog_utilities.py}

@@ -1,1524 +1,1199 @@
-
-import numpy as np
-
-from PyQt5 import QtWidgets, QtCore, QtGui
-import sidpy
-import matplotlib.patches as patches
-from matplotlib.widgets import RectangleSelector, SpanSelector
-
-import h5py  # TODO: needs to go
-import matplotlib.pyplot as plt
-
-from IPython.display import display
-import ipywidgets as widgets
-
-from pyTEMlib import eels_tools as eels
-from pyTEMlib import eels_dialog
-from pyTEMlib import info_dialog
-from pyTEMlib import peak_dialog
-
-major_edges = ['K1', 'L3', 'M5', 'N5']
-all_edges = ['K1', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5', 'N1', 'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2',
-             'O3', 'O4', 'O5', 'O6', 'O7', 'P1', 'P2', 'P3']
-first_close_edges = ['K1', 'L3', 'M5', 'M3', 'N5', 'N3']
-
-CompositionDialog = eels_dialog.EELSDialog
-InfoDialog = info_dialog.InfoDialog
-PeakFitDialog = peak_dialog.PeakFitDialog
-
-
-class PeriodicTableDialog(QtWidgets.QDialog):
-    """
-    Modal dialog to get a selection of elements.
-
-    Elements that are not having a valid cross sections are disabled.
-
-    optional input is:
-    initial_elements: list of str
-        the elements that are already selected
-    energy_scale: list or numpy array
-        energy-scale of spectrum/spectra to determine likely edges
-
-
-    Returns:
-    list of strings: elements.
-    Usage:
-    >> PT_dialog =  periodic_table_dialog(None, ['Mn', 'O'])
-    >> if PT_dialog.exec_() == periodic_table_dialog.Accepted:
-    >>     selected_elements = PT_dialog.get_output()
-    >> print(selected_elements)
-    """
-
-    signal_selected = QtCore.pyqtSignal(list)
-
-    def __init__(self, initial_elements=None, energy_scale=None, parent=None):
-        super(PeriodicTableDialog, self).__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-
-        if initial_elements is None:
-            initial_elements = [' ']
-        if energy_scale is None:
-            energy_scale = [100., 150., 200.]
-        self.parent = parent
-        self._output = []
-        self.elements_selected = initial_elements
-        self.energy_scale = np.array(energy_scale)
-
-        self.setWindowTitle("Periodic Table")
-        likely_edges = get_likely_edges(self.energy_scale)
-        self.likely_edges = likely_edges
-
-        # GD:font = wx.Font(10, wx.MODERN, wx.NORMAL, wx.BOLD)
-        self.buttons1 = []
-        self.button = []
-        self.pt_info = get_periodic_table_info()
-        self.init_ui()
-
-        for button in self.button:
-            if button.text() in initial_elements:
-                button.toggle()
-            pass
-
-    def on_close(self):
-        self.get_output()
-        self.signal_selected[list].emit(self._output)
-        self.accept()
-
-    def get_output(self):
-        self._output = []
-        for btn in self.button:
-            if btn.isChecked():
-                self._output.append(btn.text())
-
-    def exec_(self):
-        super(PeriodicTableDialog, self).exec_()
-        return self._output
-
-    def init_ui(self):
-
-        v_sizer = QtWidgets.QVBoxLayout()
-        g_sizer = QtWidgets.QGridLayout()
-
-        main_group = QtWidgets.QWidget()
-
-        color1 = "background-color: lightblue;\n"
-        color1l = "background-color: dodgerblue;\n"
-        color2 = "background-color: coral;\n"
-
-        for symbol, parameter in self.pt_info.items():
-            self.button.append(QtWidgets.QPushButton(symbol))
-            if parameter['PT_row'] > 7:
-                self.button[-1].setStyleSheet(color2)
-            elif '*' in symbol:
-                self.button[-1].setStyleSheet(color2)
-            else:
-                if symbol in self.likely_edges:
-                    self.button[-1].setStyleSheet(color1l)
-                else:
-                    self.button[-1].setStyleSheet(color1)
-            if parameter['Z'] == 0:
-                self.button[-1].setEnabled(False)
-            self.button[-1].setFixedWidth(50)
-            self.button[-1].setCheckable(True)
-            g_sizer.addWidget(self.button[-1], parameter['PT_row'], parameter['PT_col'])
-        main_group.setLayout(g_sizer)
-
-        v_sizer.addWidget(main_group)
-        self.setLayout(v_sizer)
-
-        ok_button = QtWidgets.QPushButton('OK')
-        ok_button.clicked.connect(self.on_close)
-
-        v_sizer.addWidget(ok_button)
-        self.setLayout(v_sizer)
-
-
-class EnergySelector(QtWidgets.QDialog):
-    signal_selected = QtCore.pyqtSignal(bool)
-
-    def __init__(self, dset=None):
-        super(EnergySelector, self).__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-
-        if not isinstance(dset, sidpy.Dataset):
-            return
-        if dset is None:
-            return
-        if dset.view is None:
-            return
-        self.dataset = dset
-
-        if hasattr(dset.view, 'axis'):
-            self.axis = dset.view.axis
-            self.setWindowTitle('p')
-        elif hasattr(dset.view, 'axes'):
-            self.axis = dset.view.axes[1]
-        else:
-            return
-
-        self.spec_dim = -1
-        for dim, axis in self.dataset._axes.items():
-            if axis.dimension_type == sidpy.DimensionTypes.SPECTRAL:
-                self.spec_dim = dim
-        if self.spec_dim < 0:
-            raise TypeError('We need at least one SPECTRAL dimension')
-
-        self.energy_scale = self.dataset._axes[self.spec_dim].values
-        self.dispersion = self.energy_scale[1] - self.energy_scale[0]
-        self.offset = self.energy_scale[0]
-        self.spectrum = np.zeros(2)
-
-        self.change = 0
-
-        self.x_min = self.energy_scale[int(len(self.energy_scale)/4)]
-        self.x_max = self.energy_scale[int(len(self.energy_scale) / 4*3)]
-        self.setWindowTitle("Select Energy")
-
-        valid_float = QtGui.QDoubleValidator()
-
-        layout = QtWidgets.QGridLayout()
-        layout.setVerticalSpacing(2)
-        self.label1 = QtWidgets.QLabel('Start:')
-        self.edit1 = QtWidgets.QLineEdit('0')
-        self.edit1.setValidator(valid_float)
-        self.unit1 = QtWidgets.QLabel('eV')
-
-        self.label2 = QtWidgets.QLabel('End:')
-        self.edit2 = QtWidgets.QLineEdit('0')
-        self.edit2.setValidator(valid_float)
-        self.unit2 = QtWidgets.QLabel('eV')
-
-        self.label3 = QtWidgets.QLabel('Dispersion:')
-        self.edit3 = QtWidgets.QLineEdit('0')
-        self.edit3.setValidator(valid_float)
-        self.unit3 = QtWidgets.QLabel('eV')
-
-        self.edit1.editingFinished.connect(self.on_enter)
-        self.edit2.editingFinished.connect(self.on_enter)
-        self.edit3.editingFinished.connect(self.on_enter)
-
-        layout.addWidget(self.label1, 0, 0)
-        layout.addWidget(self.edit1, 0, 1)
-        layout.addWidget(self.unit1, 0, 2)
-
-        layout.addWidget(self.label2, 1, 0)
-        layout.addWidget(self.edit2, 1, 1)
-        layout.addWidget(self.unit2, 1, 2)
-
-        layout.addWidget(self.label3, 2, 0)
-        layout.addWidget(self.edit3, 2, 1)
-        layout.addWidget(self.unit3, 2, 2)
-
-        self.ok_button = QtWidgets.QPushButton('OK')
-        self.ok_button.clicked.connect(self.on_close)
-        self.cancel_button = QtWidgets.QPushButton('Cancel')
-        self.cancel_button.clicked.connect(self.on_close)
-
-        layout.addWidget(self.ok_button, 3, 0)
-        layout.addWidget(self.cancel_button, 3, 2)
-
-        self.setLayout(layout)
-        self.edit1.setFocus()
-        self.plot()
-
-        self.selector = RangeSelector(self.axis, self.line_select_callback)
-        self.edit1.setText(f'{self.x_min:.4f}')
-        self.edit2.setText(f'{self.x_max:.4f}')
-        self.edit3.setText(f'{self.dispersion:.4f}')
-        self.update()
-
-    def line_select_callback(self, eclick, erelease):
-        y_min, y_max = self.axis.get_ylim()
-        self.x_min = self.selector.extents[0]
-        self.x_max = self.selector.extents[1]
-        self.selector.extents = (self.x_min, self.x_max, y_min, y_max)
-
-        self.edit1.setText(f'{self.x_min:.3f}')
-        self.edit2.setText(f'{self.x_max:.3f}')
-
-    def on_enter(self):
-        sender = self.sender()
-
-        if sender == self.edit1:
-            value = float(str(sender.displayText()).strip())
-            if value == self.x_min:
-                return
-            self.change = value - self.x_min
-            self.x_min += self.change
-            self.x_max += self.change
-            self.offset += self.change
-
-            self.edit1.setText(f"{self.x_min:.2f}")
-            self.edit2.setText(f"{self.x_max:.2f}")
-
-            self.energy_scale = np.arange(len(self.energy_scale)) * self.dispersion + self.offset
-
-            self.update()
-            # self.axis.draw()
-            self.setWindowTitle(f'shift, {self.change}, {self.x_min}')
-
-        elif sender == self.edit2:
-            value = float(str(sender.displayText()).strip())
-            if value == self.x_max:
-                return
-            start_channel = np.searchsorted(self.energy_scale, self.x_min)
-            end_channel = np.searchsorted(self.energy_scale, self.x_max)
-
-            self.x_max = value
-
-            if end_channel - start_channel != 0:
-                self.dispersion = (self.x_max - self.x_min) / (end_channel - start_channel)
-            self.offset = self.x_min - start_channel * self.dispersion
-            self.edit2.setText(f"{self.x_max:.2f}")
-            self.edit3.setText(f"{self.dispersion:.2f}")
-            self.energy_scale = np.arange(len(self.energy_scale)) * self.dispersion + self.offset
-
-            self.update()
-            # self.axis.draw()
-            self.setWindowTitle(f'range, {self.change}, {self.dispersion}')
-
-        elif sender == self.edit3:
-            value = float(str(sender.displayText()).strip())
-            if self.dispersion == value:
-                return
-
-            start_channel = np.searchsorted(self.energy_scale, self.x_min)
-            end_channel = np.searchsorted(self.energy_scale, self.x_max)
-            self.dispersion = value
-            self.energy_scale = np.arange(len(self.energy_scale)) * self.dispersion + self.offset
-            self.x_min = self.energy_scale[start_channel]
-            self.x_max = self.energy_scale[end_channel]
-            self.update()
-            # self.axis.draw()
-            self.edit3.setText(f"{self.dispersion:.3f}")
-            self.change = 0
-
-    def on_close(self):
-        sender = self.sender()
-        if sender == self.ok_button:
-            pass
-            self.dataset.set_dimension(self.spec_dim, sidpy.Dimension(self.energy_scale, name='energy_scale',
-                                                                      units='eV', quantity='energy loss',
-                                                                      dimension_type='spectral'))
-        else:
-            pass
-        self.selector.set_active(False)
-        self.signal_selected[bool].emit(True)
-        self.accept()
-
-    def plot(self):
-        if self.dataset.data_type == sidpy.DataTypes.SPECTRAL_IMAGE:
-            self.spectrum = self.dataset.view.get_spectrum()
-        else:
-            self.spectrum = np.array(self.dataset)
-        x_limit = self.axis.get_xlim()
-        y_limit = self.axis.get_ylim()
-
-        self.axis.clear()
-        self.cplot = self.axis.plot(self.energy_scale, self.spectrum, label='spectrum')
-        self.axis.set_xlim(x_limit)
-        self.axis.set_ylim(y_limit)
-
-        self.axis.figure.canvas.draw()
-
-    def update(self):
-        x_limit = self.axis.get_xlim()
-        y_limit = self.axis.get_ylim()
-        self.selector.extents = (self.x_min, self.x_max, y_limit[0], y_limit[1])
-
-        x_limit = np.array(x_limit) + self.change
-
-        self.cplot[0].set_data(self.energy_scale, self.spectrum)
-        self.axis.set_xlim(x_limit)
-        self.axis.set_ylim(y_limit)
-        self.axis.figure.canvas.draw()
-
-
-class RegionSelector(object):
-    """
-        Selects fitting region and the regions that are excluded for each edge.
-
-        Select a region with a spanSelector and then type 'a' for all of the fitting region or a number for the edge
-        you want to define the region excluded from the fit (solid state effects).
-
-        see Chapter4 'CH4-Working_with_X-Sections,ipynb' notebook
-
-    """
-
-    def __init__(self, ax):
-        self.ax = ax
-        self.regions = {}
-        self.rect = None
-        self.xmin = 0
-        self.width = 0
-
-        self.span = SpanSelector(ax, self.onselect1, 'horizontal', useblit=True,
-                                 rectprops=dict(alpha=0.5, facecolor='red'), span_stays=True)
-        self.cid = ax.figure.canvas.mpl_connect('key_press_event', self.click)
-        self.draw = ax.figure.canvas.mpl_connect('draw_event', self.onresize)
-
-    def onselect1(self, xmin, xmax):
-        self.xmin = xmin
-        self.width = xmax - xmin
-
-    def onresize(self, event):
-        self.update()
-
-    def delete_region(self, key):
-        if key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-            del (self.regions[key])
-
-    def update(self):
-
-        y_min, y_max = self.ax.get_ylim()
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-
-            xmin = self.regions[key]['xmin']
-            width = self.regions[key]['width']
-            height = y_max - y_min
-            alpha = self.regions[key]['alpha']
-            color = self.regions[key]['color']
-            self.regions[key]['Rect'] = patches.Rectangle((xmin, y_min), width, height,
-                                                          edgecolor=color, alpha=alpha, facecolor=color)
-            self.ax.add_patch(self.regions[key]['Rect'])
-
-            self.regions[key]['Text'] = self.ax.text(xmin, y_max, self.regions[key]['text'], verticalalignment='top')
-
-    def click(self, event):
-        if str(event.key) in ['1', '2', '3', '4', '5', '6']:
-            key = str(event.key)
-            text = 'exclude \nedge ' + key
-            alpha = 0.5
-            color = 'red'
-        elif str(event.key) in ['a', 'A', 'B', 'b', 'f', 'F']:
-            key = '0'
-            color = 'blue'
-            alpha = 0.2
-            text = 'fit region'
-        else:
-            return
-
-        if key not in self.regions:
-            self.regions[key] = {}
-
-        self.regions[key]['xmin'] = self.xmin
-        self.regions[key]['width'] = self.width
-        self.regions[key]['color'] = color
-        self.regions[key]['alpha'] = alpha
-        self.regions[key]['text'] = text
-
-        self.update()
-
-    def set_regions(self, region, start_x, width):
-        key = ''
-        if 'fit' in str(region):
-            key = '0'
-        if region in ['0', '1', '2', '3', '4', '5', '6']:
-            key = region
-        if region in [0, 1, 2, 3, 4, 5, 6]:
-            key = str(region)
-
-        if key not in self.regions:
-            self.regions[key] = {}
-            if key in ['1', '2', '3', '4', '5', '6']:
-                self.regions[key]['text'] = 'exclude \nedge ' + key
-                self.regions[key]['alpha'] = 0.5
-                self.regions[key]['color'] = 'red'
-            elif key == '0':
-                self.regions[key]['text'] = 'fit region'
-                self.regions[key]['alpha'] = 0.2
-                self.regions[key]['color'] = 'blue'
-
-        self.regions[key]['xmin'] = start_x
-        self.regions[key]['width'] = width
-
-        self.update()
-
-    def get_regions(self):
-        tags = {}
-        for key in self.regions:
-            if key == '0':
-                area = 'fit_area'
-            else:
-                area = key
-            tags[area] = {}
-            tags[area]['start_x'] = self.regions[key]['xmin']
-            tags[area]['width_x'] = self.regions[key]['width']
-
-        return tags
-
-    def disconnect(self):
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-        del self.span
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-        # self.ax.figure.canvas.mpl_disconnect(self.draw)
-        pass
-
-
-class RangeSelector(RectangleSelector):
-    def __init__(self, ax, onselect):
-        drawtype = 'box'
-        spancoords = 'data'
-        rectprops = dict(facecolor="blue", edgecolor="black", alpha=0.2, fill=True)
-
-        super().__init__(ax, onselect, drawtype=drawtype,
-                         minspanx=0, minspany=0, useblit=False,
-                         lineprops=None, rectprops=rectprops, spancoords=spancoords,
-                         button=None, maxdist=10, marker_props=None,
-                         interactive=True, state_modifier_keys=None)
-
-        self.artists = [self.to_draw, self._center_handle.artist,
-                        self._edge_handles.artist]
-
-    def draw_shape(self, extents):
-        x0, x1, y0, y1 = extents
-        xmin, xmax = sorted([x0, x1])
-        # ymin, ymax = sorted([y0, y1])
-        xlim = sorted(self.ax.get_xlim())
-        ylim = sorted(self.ax.get_ylim())
-
-        xmin = max(xlim[0], xmin)
-        ymin = ylim[0]
-        xmax = min(xmax, xlim[1])
-        ymax = ylim[1]
-
-        self.to_draw.set_x(xmin)
-        self.to_draw.set_y(ymin)
-        self.to_draw.set_width(xmax - xmin)
-        self.to_draw.set_height(ymax - ymin)
-
-
-def get_likely_edges(energy_scale):
-    x_sections = eels.get_x_sections()
-    # print(energy_scale)
-    energy_origin = energy_scale[0]
-    energy_window = energy_scale[-1] - energy_origin
-    selected_edges_unsorted = {}
-    likely_edges = []
-    selected_elements = []
-    for element in range(1, 83):
-        # print(element)
-        element_z = str(eels.get_z(element))
-
-        for key in x_sections[element_z]:
-            if key in all_edges:
-                onset = x_sections[element_z][key]['onset']
-                if onset > energy_origin:
-                    if onset - energy_origin < energy_window:
-                        if element not in selected_edges_unsorted:
-                            selected_edges_unsorted[element] = {}
-                        # print(element, x_sections[element]['name'], key, x_sections[element][key]['onset'])
-                        # text = f"\n {x_sections[element_z]['name']:2s}-{key}: " \
-                        #       f"{x_sections[element_z][key]['onset']:8.1f} eV "
-                        # print(text)
-
-                        selected_edges_unsorted[element][key] = {}
-                        selected_edges_unsorted[element][key]['onset'] = x_sections[element_z][key]['onset']
-
-                        if key in major_edges:
-                            selected_edges_unsorted[element][key]['intensity'] = 'major'
-                            selected_elements.append(x_sections[element_z]['name'])
-                        else:
-                            selected_edges_unsorted[element][key]['intensity'] = 'minor'
-
-        if element in selected_edges_unsorted:
-            for key in selected_edges_unsorted[element]:
-                if selected_edges_unsorted[element][key]['intensity'] == 'major':
-                    likely_edges.append(x_sections[str(element)]['name'])  # = {'Z':element, 'symmetry': key}
-
-    return likely_edges
-
-
-def get_periodic_table_info():
-    pt_info = \
-        {'H': {'PT_row': 0, 'PT_col': 0, 'Z': 0},
-         'He': {'PT_row': 0, 'PT_col': 17, 'Z': 2}, 'Li': {'PT_row': 1, 'PT_col': 0, 'Z': 3},
-         'Be': {'PT_row': 1, 'PT_col': 1, 'Z': 4}, 'B': {'PT_row': 1, 'PT_col': 12, 'Z': 5},
-         'C': {'PT_row': 1, 'PT_col': 13, 'Z': 6}, 'N': {'PT_row': 1, 'PT_col': 14, 'Z': 7},
-         'O': {'PT_row': 1, 'PT_col': 15, 'Z': 8}, 'F': {'PT_row': 1, 'PT_col': 16, 'Z': 9},
-         'Ne': {'PT_row': 1, 'PT_col': 17, 'Z': 10}, 'Na': {'PT_row': 2, 'PT_col': 0, 'Z': 11},
-         'Mg': {'PT_row': 2, 'PT_col': 1, 'Z': 12}, 'Al': {'PT_row': 2, 'PT_col': 12, 'Z': 13},
-         'Si': {'PT_row': 2, 'PT_col': 13, 'Z': 14}, 'P': {'PT_row': 2, 'PT_col': 14, 'Z': 15},
-         'S': {'PT_row': 2, 'PT_col': 15, 'Z': 16}, 'Cl': {'PT_row': 2, 'PT_col': 16, 'Z': 17},
-         'Ar': {'PT_row': 2, 'PT_col': 17, 'Z': 18}, 'K': {'PT_row': 3, 'PT_col': 0, 'Z': 19},
-         'Ca': {'PT_row': 3, 'PT_col': 1, 'Z': 20}, 'Sc': {'PT_row': 3, 'PT_col': 2, 'Z': 21},
-         'Ti': {'PT_row': 3, 'PT_col': 3, 'Z': 22}, 'V ': {'PT_row': 3, 'PT_col': 4, 'Z': 23},
-         'Cr': {'PT_row': 3, 'PT_col': 5, 'Z': 24}, 'Mn': {'PT_row': 3, 'PT_col': 6, 'Z': 25},
-         'Fe': {'PT_row': 3, 'PT_col': 7, 'Z': 26}, 'Co': {'PT_row': 3, 'PT_col': 8, 'Z': 27},
-         'Ni': {'PT_row': 3, 'PT_col': 9, 'Z': 28}, 'Cu': {'PT_row': 3, 'PT_col': 10, 'Z': 29},
-         'Zn': {'PT_row': 3, 'PT_col': 11, 'Z': 30}, 'Ga': {'PT_row': 3, 'PT_col': 12, 'Z': 31},
-         'Ge': {'PT_row': 3, 'PT_col': 13, 'Z': 32}, 'As': {'PT_row': 3, 'PT_col': 14, 'Z': 33},
-         'Se': {'PT_row': 3, 'PT_col': 15, 'Z': 34}, 'Br': {'PT_row': 3, 'PT_col': 16, 'Z': 35},
-         'Kr': {'PT_row': 3, 'PT_col': 17, 'Z': 36}, 'Rb': {'PT_row': 4, 'PT_col': 0, 'Z': 37},
-         'Sr': {'PT_row': 4, 'PT_col': 1, 'Z': 38}, 'Y': {'PT_row': 4, 'PT_col': 2, 'Z': 39},
-         'Zr': {'PT_row': 4, 'PT_col': 3, 'Z': 40}, 'Nb': {'PT_row': 4, 'PT_col': 4, 'Z': 41},
-         'Mo': {'PT_row': 4, 'PT_col': 5, 'Z': 42}, 'Tc': {'PT_row': 4, 'PT_col': 6, 'Z': 43},
-         'Ru': {'PT_row': 4, 'PT_col': 7, 'Z': 44}, 'Rh': {'PT_row': 4, 'PT_col': 8, 'Z': 45},
-         'Pd': {'PT_row': 4, 'PT_col': 9, 'Z': 46}, 'Ag': {'PT_row': 4, 'PT_col': 10, 'Z': 47},
-         'Cd': {'PT_row': 4, 'PT_col': 11, 'Z': 48}, 'In': {'PT_row': 4, 'PT_col': 12, 'Z': 49},
-         'Sn': {'PT_row': 4, 'PT_col': 13, 'Z': 50}, 'Sb': {'PT_row': 4, 'PT_col': 14, 'Z': 51},
-         'Te': {'PT_row': 4, 'PT_col': 15, 'Z': 52}, 'I': {'PT_row': 4, 'PT_col': 16, 'Z': 53},
-         'Xe': {'PT_row': 4, 'PT_col': 17, 'Z': 54}, 'Cs': {'PT_row': 5, 'PT_col': 0, 'Z': 55},
-         'Ba': {'PT_row': 5, 'PT_col': 1, 'Z': 56}, 'Hf': {'PT_row': 5, 'PT_col': 3, 'Z': 72},
-         'Ta': {'PT_row': 5, 'PT_col': 4, 'Z': 73}, 'W': {'PT_row': 5, 'PT_col': 5, 'Z': 74},
-         'Re': {'PT_row': 5, 'PT_col': 6, 'Z': 75}, 'Os': {'PT_row': 5, 'PT_col': 7, 'Z': 76},
-         'Ir': {'PT_row': 5, 'PT_col': 8, 'Z': 77}, 'Pt': {'PT_row': 5, 'PT_col': 9, 'Z': 78},
-         'Au': {'PT_row': 5, 'PT_col': 10, 'Z': 79}, 'Hg': {'PT_row': 5, 'PT_col': 11, 'Z': 80},
-         'Pb': {'PT_row': 5, 'PT_col': 13, 'Z': 82}, 'Bi': {'PT_row': 5, 'PT_col': 14, 'Z': 0},
-         'Po': {'PT_row': 5, 'PT_col': 15, 'Z': 0}, 'At': {'PT_row': 5, 'PT_col': 16, 'Z': 0},
-         'Rn': {'PT_row': 5, 'PT_col': 17, 'Z': 0}, 'Fr': {'PT_row': 6, 'PT_col': 0, 'Z': 0},
-         'Ra': {'PT_row': 6, 'PT_col': 1, 'Z': 0}, 'Rf': {'PT_row': 6, 'PT_col': 3, 'Z': 0},
-         'Db': {'PT_row': 6, 'PT_col': 4, 'Z': 0}, 'Sg': {'PT_row': 6, 'PT_col': 5, 'Z': 0},
-         'Bh': {'PT_row': 6, 'PT_col': 6, 'Z': 0}, 'Hs': {'PT_row': 6, 'PT_col': 7, 'Z': 0},
-         'Mt': {'PT_row': 6, 'PT_col': 8, 'Z': 0}, 'Ds': {'PT_row': 6, 'PT_col': 9, 'Z': 0},
-         'Rg': {'PT_row': 6, 'PT_col': 10, 'Z': 0}, 'La': {'PT_row': 8, 'PT_col': 3, 'Z': 57},
-         'Ce': {'PT_row': 8, 'PT_col': 4, 'Z': 58}, 'Pr': {'PT_row': 8, 'PT_col': 5, 'Z': 59},
-         'Nd': {'PT_row': 8, 'PT_col': 6, 'Z': 60}, 'Pm': {'PT_row': 8, 'PT_col': 7, 'Z': 61},
-         'Sm': {'PT_row': 8, 'PT_col': 8, 'Z': 62}, 'Eu': {'PT_row': 8, 'PT_col': 9, 'Z': 63},
-         'Gd': {'PT_row': 8, 'PT_col': 10, 'Z': 64}, 'Tb': {'PT_row': 8, 'PT_col': 11, 'Z': 65},
-         'Dy': {'PT_row': 8, 'PT_col': 12, 'Z': 66}, 'Ho': {'PT_row': 8, 'PT_col': 13, 'Z': 67},
-         'Er': {'PT_row': 8, 'PT_col': 14, 'Z': 68}, 'Tm': {'PT_row': 8, 'PT_col': 15, 'Z': 69},
-         'Yb': {'PT_row': 8, 'PT_col': 16, 'Z': 70}, 'Lu': {'PT_row': 8, 'PT_col': 17, 'Z': 71},
-         'Ac': {'PT_row': 9, 'PT_col': 3, 'Z': 0}, 'Th': {'PT_row': 9, 'PT_col': 4, 'Z': 0},
-         'Pa': {'PT_row': 9, 'PT_col': 5, 'Z': 0}, 'U': {'PT_row': 9, 'PT_col': 6, 'Z': 0},
-         'Np': {'PT_row': 9, 'PT_col': 7, 'Z': 0}, 'Pu': {'PT_row': 9, 'PT_col': 8, 'Z': 0},
-         'Am': {'PT_row': 9, 'PT_col': 9, 'Z': 0}, 'Cm': {'PT_row': 9, 'PT_col': 10, 'Z': 0},
-         'Bk': {'PT_row': 9, 'PT_col': 11, 'Z': 0}, 'Cf': {'PT_row': 9, 'PT_col': 12, 'Z': 0},
-         'Es': {'PT_row': 9, 'PT_col': 13, 'Z': 0}, 'Fm': {'PT_row': 9, 'PT_col': 14, 'Z': 0},
-         'Md': {'PT_row': 9, 'PT_col': 15, 'Z': 0}, 'No': {'PT_row': 9, 'PT_col': 16, 'Z': 0},
-         'Lr': {'PT_row': 9, 'PT_col': 17, 'Z': 0},
-         '*': {'PT_row': 5, 'PT_col': 2, 'PT_col2': 8, 'PT_row2': 2, 'Z': 0},
-         '**': {'PT_row': 6, 'PT_col': 2, 'PT_col2': 9, 'PT_row2': 2, 'Z': 0}}
-
-    return pt_info
-
-
-class InteractiveSpectrumImage(object):
-    """
-    ### Interactive spectrum imaging plot
-
-    Input tags: dictionary with a minimum of the following keys:
-        ['image']: displayed image
-        ['data']:  data cube
-        [if ]'intensity_scale_ppm']: intensity scale
-        ['ylabel']: intensity label
-        ['spectra'] dictionary which contains dictionaries for each spectrum style ['1-2']:
-            ['spectrum'] = tags['cube'][y,x,:]
-            ['spectra'][f'{x}-{y}']['energy_scale'] = tags['energy_scale']
-            ['intensity_scale'] = 1/tags['cube'][y,x,:].sum()*1e6
-
-    Please note the possibility to load any image for the selection of the spectrum
-    Also there is the possibility to display the survey image.
-
-    For analysis we have the following options:
-        'fix_energy': set zero-loss peak maximum to zero !! Low loss spectra only!!
-        'fit_zero_loss': fit zero-loss peak with model function !! Low loss spectra only!!
-        'fit_low_loss': fit low-loss spectrum with model peaks !! Low loss spectra only!!
-
-
-        'fit_composition': fit core-loss spectrum with background and cross sections!! Core loss spectra only!!
-        'fit_ELNES': fit core-loss edge with model peaks  !! Core loss spectra only!!
-    """
-
-    def __init__(self, data_source, horizontal=True):
-
-        box_layout = widgets.Layout(display='flex',
-                                    flex_flow='row',
-                                    align_items='stretch',
-                                    width='100%')
-
-        words = ['fix_energy', 'fit_zero_loss', 'fit_low_loss', 'fit_composition', 'fit_ELNES']
-
-        self.buttons = [widgets.ToggleButton(value=False, description=word, disabled=False) for word in words]
-        box = widgets.Box(children=self.buttons, layout=box_layout)
-        display(box)
-
-        # MAKE Dictionary
-
-        if isinstance(data_source, dict):
-            self.tags = data_source
-        elif isinstance(data_source, h5py.Group):
-            self.tags = self.set_tags(data_source)
-        else:
-            print('Data source must be a dictionary or channel')
-            return
-
-        # Button(description='edge_quantification')
-        for button in self.buttons:
-            button.observe(self.on_button_clicked, 'value')  # on_click(self.on_button_clicked)
-
-        self.figure = plt.figure()
-        self.horizontal = horizontal
-        self.x = 0
-        self.y = 0
-
-        self.extent = [0, self.tags['cube'].shape[1], self.tags['cube'].shape[0], 0]
-        self.rectangle = [0, self.tags['cube'].shape[1], 0, self.tags['cube'].shape[0]]
-        self.scaleX = 1.0
-        self.scaleY = 1.0
-        self.analysis = []
-        self.plot_legend = False
-        if 'ylabel' not in self.tags:
-            self.tags['ylabel'] = 'intensity [a.u.]'
-        self.SI = False
-
-        if horizontal:
-            self.ax1 = plt.subplot(1, 2, 1)
-            self.ax2 = plt.subplot(1, 2, 2)
-        else:
-            self.ax1 = plt.subplot(2, 1, 1)
-            self.ax2 = plt.subplot(2, 1, 2)
-
-        self.cube = self.tags['cube']
-        self.image = self.tags['cube'].sum(axis=2)
-
-        self.ax1.imshow(self.image, extent=self.extent)
-        if horizontal:
-            self.ax1.set_xlabel('distance [pixels]')
-        else:
-            self.ax1.set_ylabel('distance [pixels]')
-        self.ax1.set_aspect('equal')
-
-        self.rect = patches.Rectangle((0, 0), 1, 1, linewidth=1, edgecolor='r', facecolor='red', alpha=0.2)
-        self.ax1.add_patch(self.rect)
-        self.intensity_scale = self.tags['spectra'][f'{self.x}-{self.y}']['intensity_scale']
-        self.spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
-        self.energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
-
-        self.ax2.plot(self.energy_scale, self.spectrum)
-        self.ax2.set_title(f' spectrum {self.x},{self.y} ')
-        self.ax2.set_xlabel('energy loss [eV]')
-        self.ax2.set_ylabel(self.tags['ylabel'])
-        self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
-
-        plt.tight_layout()
-
-    def on_button_clicked(self, b):
-        # print(b['owner'].description)
-        selection = b['owner'].description
-        if b['new']:
-            if selection == 'fit_composition':
-                if 'region_tags' in self.tags and 'edges_present' in self.tags \
-                        and 'acceleration_voltage' in self.tags \
-                        and 'collection_angle' in self.tags:
-                    pass
-                else:
-                    self.buttons[3].value = False
-                    return
-            elif selection in ['fix_energy', 'fit_zero_loss']:
-                if self.energy_scale[0] > 0:
-                    button_index = ['fix_energy', 'fit_zero_loss'].index(selection)
-                    self.buttons[button_index].value = False
-                    return
-            self.analysis.append(selection)
-            self.update()
-        else:
-
-            if selection in self.analysis:
-                self.analysis.remove(selection)
-
-    def do_all(self, selection=None, verbose=True):
-        x = self.x
-        y = self.y
-        if selection is None:
-            selection = self.analysis
-        for self.x in range(self.cube.shape[1]):
-            if verbose:
-                print(f' row: {self.x}')
-            for self.y in range(self.cube.shape[0]):
-
-                if 'fit_zero_loss' in selection:
-                    title = self.fit_zero_loss(plot_this=False)
-
-                elif 'fix_energy' in selection:
-                    self.ax2.set_title('bn')
-                    title = self.fix_energy()
-
-                elif 'fit_composition' in selection:
-                    title = self.fit_quantification(plot_this=False)
-
-        self.x = x
-        self.y = y
-
-    def onclick(self, event):
-        x = int(event.xdata)
-        y = int(event.ydata)
-
-        # print(x,y)
-        if self.rectangle[0] <= x < self.rectangle[0] + self.rectangle[1]:
-            if self.rectangle[2] <= y < self.rectangle[2] + self.rectangle[3]:
-                self.x = int((x - self.rectangle[0]) / self.rectangle[1] * self.cube.shape[1])
-                self.y = int((y - self.rectangle[2]) / self.rectangle[3] * self.cube.shape[0])
-            else:
-                return
-        else:
-            return
-
-        if event.inaxes in [self.ax1]:
-            x = (self.x * self.rectangle[1] / self.cube.shape[1] + self.rectangle[0])
-            y = (self.y * self.rectangle[3] / self.cube.shape[0] + self.rectangle[2])
-
-            self.rect.set_xy([x, y])
-            self.update()
-
-    def update(self):
-        xlim = self.ax2.get_xlim()
-        ylim = self.ax2.get_ylim()
-        self.ax2.clear()
-        self.intensity_scale = self.tags['spectra'][f'{self.x}-{self.y}']['intensity_scale']
-        self.spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
-        self.energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
-
-        if 'fit_zero_loss' in self.analysis:
-            title = self.fit_zero_loss()
-            self.ax2.set_title(title)
-        elif 'fix_energy' in self.analysis:
-            self.ax2.set_title('bn')
-            title = self.fix_energy()
-            self.ax2.set_title(title)
-
-        elif 'fit_composition' in self.analysis:
-            title = self.fit_quantification()
-            self.ax2.set_title(title)
-
-        else:
-            self.ax2.set_title(f' spectrum {self.x},{self.y} ')
-        self.ax2.plot(self.energy_scale, self.spectrum, color='#1f77b4', label='experiment')
-
-        if self.plot_legend:
-            self.ax2.legend(shadow=True)
-        self.ax2.set_xlim(xlim)
-        self.ax2.set_ylim(ylim)
-        self.ax2.set_xlabel('energy loss [eV]')
-        self.ax2.set_ylabel(self.tags['ylabel'])
-        self.ax2.set_xlim(xlim)
-
-        # self.ax2.draw()
-
-    def set_tags(self, channel):
-        # TODO: change to sidpy dataset tags = ft.h5_get_dictionary(channel)
-        tags = {}
-        if tags['data_type'] == 'spectrum_image':
-            tags['image'] = tags['data']
-            tags['data'] = tags['cube'][0, 0, :]
-            if 'intentsity_scale_ppm' not in channel:
-                channel['intentsity_scale_ppm'] = 1
-
-            tags['ylabel'] = 'intensity [a.u.]'
-            tags['spectra'] = {}
-            for x in range(tags['spatial_size_y']):
-                for y in range(tags['spatial_size_x']):
-                    tags['spectra'][f'{x}-{y}'] = {}
-                    tags['spectra'][f'{x}-{y}']['spectrum'] = tags['cube'][y, x, :]
-                    tags['spectra'][f'{x}-{y}']['energy_scale'] = tags['energy_scale']
-                    tags['spectra'][f'{x}-{y}']['intensity_scale'] = 1 / tags['cube'][y, x, :].sum() * 1e6
-            tags['ylabel'] = 'inel. scat. int.  [ppm]'
-
-        return tags
-
-    def fix_energy(self):
-
-        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
-        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
-        fwhm, delta_e = eels.fix_energy_scale(spectrum, energy_scale)
-        self.tags['spectra'][f'{self.x}-{self.y}']['delta_e'] = delta_e
-        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm'] = fwhm
-        self.energy_scale = energy_scale - delta_e
-        title = f'spectrum {self.x},{self.y} fwhm: {fwhm:.2f}, dE: {delta_e:.3f}'
-        return title
-
-    def fit_zero_loss(self, plot_this=True):
-
-        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
-        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
-        if 'zero_loss_fit_width' not in self.tags:
-            self.tags['zero_loss_fit_width'] = .5
-        if self.tags['zero_loss_fit_width'] / (energy_scale[1] - energy_scale[0]) < 6:
-            self.tags['zero_loss_fit_width'] = (energy_scale[1] - energy_scale[0]) * 6
-        fwhm, delta_e = eels.fix_energy_scale(spectrum, energy_scale)
-        energy_scale = energy_scale - delta_e
-        z_oss, p_zl = eels.resolution_function(energy_scale, spectrum, self.tags['zero_loss_fit_width'])
-        fwhm2, delta_e2 = eels.fix_energy_scale(z_oss, energy_scale)
-
-        self.tags['spectra'][f'{self.x}-{self.y}']['resolution_function'] = z_oss
-        self.tags['spectra'][f'{self.x}-{self.y}']['p_zl'] = p_zl
-        self.tags['spectra'][f'{self.x}-{self.y}']['delta_e'] = delta_e
-        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm_resolution'] = fwhm2
-        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm'] = fwhm
-
-        if plot_this:
-            self.ax2.plot(energy_scale, z_oss, label='resolution function', color='black')
-            self.ax2.plot(energy_scale, self.spectrum - z_oss, label='difference', color='orange')
-            self.ax2.axhline(linewidth=0.5, color='black')
-        self.energy_scale = energy_scale
-        title = f'spectrum {self.x},{self.y} fwhm: {fwhm:.2f}'  # ', dE: {delta_e2:.5e}'
-        return title
-
-    def fit_quantification(self, plot_this=True):
-        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
-        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
-        edges = eels.make_edges(self.tags['edges_present'], energy_scale, self.tags['acceleration_voltage'],
-                                self.tags['collection_angle'])
-        edges = eels.fit_edges(spectrum, self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale'],
-                               self.tags['region_tags'], edges)
-        self.tags['spectra'][f'{self.x}-{self.y}']['edges'] = edges.copy()
-        if plot_this:
-            self.ax2.plot(energy_scale, edges['model']['spectrum'], label='model')
-            self.ax2.plot(energy_scale, self.spectrum - edges['model']['spectrum'], label='difference')
-            self.ax2.axhline(linewidth=0.5, color='black')
-        else:
-            self.tags['spectra'][f'{self.x}-{self.y}']['do_all'] = 'done'
-        title = f'spectrum {self.x},{self.y} '
-
-        for key in edges:
-            if key.isdigit():
-                title = title + f"{edges[key]['element']}:  {edges[key]['areal_density']:.2e};  "
-
-        return title
-
-    def set_legend(self, set_legend):
-        self.plot_legend = set_legend
-
-    def get_xy(self):
-        return [self.x, self.y]
-
-    def get_current_spectrum(self):
-        return self.cube[self.y, self.x, :]
-
-    def set_Zcontrast_image(self, z_channel=None):
-        if z_channel is not None:
-            self.tags['Zcontrast_channel'] = z_channel
-        if 'Zcontrast_channel' not in self.tags:
-            print('add Z contrast channel group to dictionary first!')
-            return
-        # get dictionary from current channel in pyUSID file
-        z_tags = {}   # TODO change to sidpy datasetft.h5_get_dictionary(z_channel)
-        extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
-                  self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
-        self.ax1.imshow(z_tags['data'], extent=extent, cmap='gray')
-
-    def overlay_Zcontrast_image(self, z_channel=None):
-
-        if self.SI:
-            if z_channel is not None:
-                self.tags['Zcontrast_channel'] = z_channel
-            if 'Zcontrast_channel' not in self.tags:
-                print('add survey channel group to dictionary first!')
-                return
-
-            z_tags = {}  # TODO: change to sidpy ft.h5_get_dictionary(self.tags['Zcontrast_channel'])
-
-            xlim = self.ax1.get_xlim()
-            ylim = self.ax1.get_ylim()
-            extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
-                      self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
-            self.ax1.imshow(z_tags['data'], extent=extent, cmap='viridis', alpha=0.5)
-            self.ax1.set_ylim(ylim)
-            self.ax1.set_xlim(xlim)
-
-    def overlay_data(self, data=None):
-
-        if self.SI:
-            if data is None:
-                data = self.cube.sum(axis=2)
-
-            xlim = self.ax1.get_xlim()
-            ylim = self.ax1.get_ylim()
-            extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
-                      self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
-            self.ax1.imshow(data, extent=extent, alpha=0.7, cmap='viridis')
-            self.ax1.set_ylim(ylim)
-            self.ax1.set_xlim(xlim)
-
-    def set_survey_image(self, si_channel=None):
-
-        # get dictionary from current channel in pyUSID file
-        if si_channel is not None:
-            self.tags['survey_channel'] = si_channel
-        if 'survey_channel' not in self.tags:
-            print('add survey channel group to dictionary first!')
-            return
-        si_channel = self.tags['survey_channel']
-        si_tags = {}  # TODO: change to sidpy  ft.h5_get_dictionary(si_channel)
-        tags2 = dict(si_channel.attrs)
-
-        self.ax1.set_aspect('equal')
-        self.scaleX = si_channel['spatial_scale_x'][()]
-        self.scaleY = si_channel['spatial_scale_y'][()]
-
-        self.ax1.imshow(si_tags['data'], extent=si_tags['extent'], cmap='gray')
-        if self.horizontal:
-            self.ax1.set_xlabel('distance [nm]')
-        else:
-            self.ax1.set_ylabel('distance [nm]')
-
-        annotation_done = []
-        for key in tags2:
-            if 'annotations' in key:
-                annotation_number = key[12]
-                if annotation_number not in annotation_done:
-                    annotation_done.append(annotation_number)
-
-                    if tags2['annotations_' + annotation_number + '_type'] == 'text':
-                        x = tags2['annotations_' + annotation_number + '_x']
-                        y = tags2['annotations_' + annotation_number + '_y']
-                        text = tags2['annotations_' + annotation_number + '_text']
-                        self.ax1.text(x, y, text, color='r')
-
-                    elif tags2['annotations_' + annotation_number + '_type'] == 'circle':
-                        radius = 20 * self.scaleX  # tags['annotations'][key]['radius']
-                        xy = tags2['annotations_' + annotation_number + '_position']
-                        circle = patches.Circle(xy, radius, color='r', fill=False)
-                        self.ax1.add_artist(circle)
-
-                    elif tags2['annotations_' + annotation_number + '_type'] == 'spectrum image':
-                        width = tags2['annotations_' + annotation_number + '_width']
-                        height = tags2['annotations_' + annotation_number + '_height']
-                        position = tags2['annotations_' + annotation_number + '_position']
-                        rectangle = patches.Rectangle(position, width, height, color='r', fill=False)
-                        self.rectangle = [position[0], width, position[1], height]
-                        self.ax1.add_artist(rectangle)
-                        self.ax1.text(position[0], position[1], 'Spectrum Image', color='r')
-                        self.rect.set_width(width / self.cube.shape[1])
-                        self.rect.set_height(height / self.cube.shape[0])
-        self.SI = True
-
-
-class ElementalEdges(object):
-    """
-        The necessary initialization parameter are:
-        ax: matplotlib axis
-
-
-        There is an optional parameter maximum_chemical_shift which allows to change
-        the energy range in which the edges are searched.
-
-        available functions:
-        - update(): updates the drawing of ionization edges
-        - set_edge(Z) : changes atomic number and updates everything accordingly
-        - disconnect: makes everything invisible and stops drawing
-        - reconnect: undo of disconnect
-
-        usage:
-        >> fig, ax = plt.subplots()
-        >> ax.plot(energy_scale, spectrum)
-        >> Z= 42
-        >> cursor = ElementalEdges(ax, Z)
-
-
-        see Chapter4 'CH4-Working_with_X-Sections' notebook
-    """
-
-    def __init__(self, ax, z):
-        self.ax = ax
-        self.labels = None
-        self.lines = None
-        self.Z = eels.get_z(z)
-        self.color = 'black'
-        self.x_sections = eels.get_x_sections()
-        self.cid = ax.figure.canvas.mpl_connect('draw_event', self.onresize)
-        # self.update() is not necessary because of a drawing event is issued
-
-    def set_edge(self, z):
-        self.Z = eels.get_z(z)
-        if self.cid is None:
-            self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.onresize)
-        self.update()
-
-    def onresize(self, event):
-        self.update()
-
-    def update(self):
-        if self.labels is not None:
-            for label in self.labels:
-                label.remove()
-        if self.lines is not None:
-            for line in self.lines:
-                line.remove()
-        self.labels = []
-        self.lines = []
-        x_min, x_max = self.ax.get_xlim()
-        y_min, y_max = self.ax.get_ylim()
-
-        element = str(self.Z)
-        x_sections = self.x_sections
-        for key in all_edges:
-            if key in x_sections[element] and 'onset' in x_sections[element][key]:
-                x = x_sections[element][key]['onset']
-                if x_min < x < x_max:
-                    if key in first_close_edges:
-                        label2 = self.ax.text(x, y_max, f"{x_sections[element]['name']}-{key}",
-                                              verticalalignment='top', rotation=0, color=self.color)
-                    else:
-                        label2 = self.ax.text(x, y_max, f"\n{x_sections[element]['name']}-{key}",
-                                              verticalalignment='top', color=self.color)
-                    line2 = self.ax.axvline(x, ymin=0, ymax=1, color=self.color)
-
-                    self.labels.append(label2)
-                    self.lines.append(line2)
-
-    def reconnect(self):
-        self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.onresize)
-        self.update()
-
-    def disconnect(self):
-        if self.labels is not None:
-            for label in self.labels:
-                label.remove()
-        if self.lines is not None:
-            for line in self.lines:
-                line.remove()
-        self.labels = None
-        self.lines = None
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-
-
-class RegionSelector(object):
-    """
-        Selects fitting region and the regions that are excluded for each edge.
-
-        Select a region with a spanSelector and then type 'a' for all of the fitting region or a number for the 
-        edge you want to define the region excluded from the fit (solid state effects).
-
-        see Chapter4 'CH4-Working_with_X-Sections,ipynb' notebook
-
-    """
-
-    def __init__(self, ax):
-        self.ax = ax
-        self.regions = {}
-        self.rect = None
-        self.xmin = 0
-        self.xwidth = 0
-
-        self.span = SpanSelector(ax, self.onselect1, 'horizontal', useblit=True,
-                                 rectprops=dict(alpha=0.5, facecolor='red'), span_stays=True)
-        self.cid = ax.figure.canvas.mpl_connect('key_press_event', self.click)
-        self.draw = ax.figure.canvas.mpl_connect('draw_event', self.onresize)
-
-    def onselect1(self, xmin, xmax):
-        self.xmin = xmin
-        self.width = xmax - xmin
-
-    def onresize(self, event):
-        self.update()
-
-    def delete_region(self, key):
-        if key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-            del (self.regions[key])
-
-    def update(self):
-
-        y_min, y_max = self.ax.get_ylim()
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-
-            xmin = self.regions[key]['xmin']
-            width = self.regions[key]['width']
-            height = y_max - y_min
-            alpha = self.regions[key]['alpha']
-            color = self.regions[key]['color']
-            self.regions[key]['Rect'] = patches.Rectangle((xmin, y_min), width, height,
-                                                          edgecolor=color, alpha=alpha, facecolor=color)
-            self.ax.add_patch(self.regions[key]['Rect'])
-
-            self.regions[key]['Text'] = self.ax.text(xmin, y_max, self.regions[key]['text'], verticalalignment='top')
-
-    def click(self, event):
-        if str(event.key) in ['1', '2', '3', '4', '5', '6']:
-            key = str(event.key)
-            text = 'exclude \nedge ' + key
-            alpha = 0.5
-            color = 'red'
-        elif str(event.key) in ['a', 'A', 'b', 'B', 'f', 'F']:
-            key = '0'
-            color = 'blue'
-            alpha = 0.2
-            text = 'fit region'
-        else:
-            return
-
-        if key not in self.regions:
-            self.regions[key] = {}
-
-        self.regions[key]['xmin'] = self.xmin
-        self.regions[key]['width'] = self.width
-        self.regions[key]['color'] = color
-        self.regions[key]['alpha'] = alpha
-        self.regions[key]['text'] = text
-
-        self.update()
-
-    def set_regions(self, region, start_x, width):
-        if 'fit' in str(region):
-            key = '0'
-        if region in ['0', '1', '2', '3', '4', '5', '6']:
-            key = region
-        if region in [0, 1, 2, 3, 4, 5, 6]:
-            key = str(region)
-
-        if key not in self.regions:
-            self.regions[key] = {}
-            if key in ['1', '2', '3', '4', '5', '6']:
-                self.regions[key]['text'] = 'exclude \nedge ' + key
-                self.regions[key]['alpha'] = 0.5
-                self.regions[key]['color'] = 'red'
-            elif key == '0':
-                self.regions[key]['text'] = 'fit region'
-                self.regions[key]['alpha'] = 0.2
-                self.regions[key]['color'] = 'blue'
-
-        self.regions[key]['xmin'] = start_x
-        self.regions[key]['width'] = width
-
-        self.update()
-
-    def get_regions(self):
-        tags = {}
-        for key in self.regions:
-            if key == '0':
-                area = 'fit_area'
-            else:
-                area = key
-            tags[area] = {}
-            tags[area]['start_x'] = self.regions[key]['xmin']
-            tags[area]['width_x'] = self.regions[key]['width']
-
-        return tags
-
-    def disconnect(self):
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-        del self.span
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-        # self.ax.figure.canvas.mpl_disconnect(self.draw)
-        pass
-
-
-class EdgesatCursor(object):
-    """
-        Adds a Cursor to a plot, which plots all major (possible) ionization edges at
-        the cursor location if left (right) mosue button is clicked.
-
-        The necessary initializtion parameter are:
-        ax: matplotlib axis
-        x: energy_scale of spectrum
-        y: intensities of spectrum
-
-        There is an optional parameter maximum_chemical_shift which allows to change
-        the energy range in which the edges are searched.
-
-        usage:
-        fig, ax = plt.subplots()
-        ax.plot(energy_scale, spectrum)
-        cursor = EdgesatCursor(ax, energy_scale, spectrum)
-
-        see Chapter4 'CH4-Working_with_X-Sections' notebook
-
-    """
-
-    def __init__(self, ax, x, y, maximal_chemical_shift=5):
-        self.ax = ax
-        self.ly = ax.axvline(x[0], color='k', alpha=0.2)  # the vert line
-        self.marker, = ax.plot(x[0], y[0], marker="o", color="crimson", zorder=3)
-        self.x = x
-        self.y = y
-        self.txt = ax.text(0.7, 0.9, '', verticalalignment='bottom')
-        self.select = 0
-        self.label = None
-        self.line = None
-        self.cid = ax.figure.canvas.mpl_connect('button_press_event', self.click)
-        self.mouse_cid = ax.figure.canvas.mpl_connect('motion_notify_event', self.mouse_move)
-        self.maximal_chemical_shift = maximal_chemical_shift
-
-    def click(self, event):
-
-        # print('click', event)
-        if not event.inaxes: 
-            return
-        x, y = event.xdata, event.ydata
-
-        indx = np.searchsorted(self.x, [x])[0]
-        x = self.x[indx]
-        y = self.y[indx]
-        self.select = x
-
-        y_min, y_max = self.ax.get_ylim()
-
-        if self.label is not None:
-            self.label.remove()
-            self.line.remove()
-        if event.button == 1:
-            self.label = self.ax.text(x, y_max, eels.find_major_edges(event.xdata, self.maximal_chemical_shift),
-                                      verticalalignment='top')
-            self.line, = self.ax.plot([x, x], [y_min, y_max], color='black')
-        if event.button == 3:
-            self.line, = self.ax.plot([x, x], [y_min, y_max], color='black')
-            self.label = self.ax.text(x, y_max, eels.find_all_edges(event.xdata, self.maximal_chemical_shift),
-                                      verticalalignment='top')
-        self.ax.set_ylim(y_min, y_max)
-
-    def mouse_move(self, event):
-
-        if not event.inaxes: 
-            return
-
-        x, y = event.xdata, event.ydata
-        indx = np.searchsorted(self.x, [x])[0]
-        x = self.x[indx]
-        y = self.y[indx]
-        self.select = x
-        self.ly.set_xdata(x)
-        self.marker.set_data([x], [y])
-        self.txt.set_text(f'\n x={x:1.2f}, y={y:1.2g}\n')
-
-        # self.ax.text(x, y*2,find_major_edges(x))
-        self.txt.set_position((x, y))
-        self.ax.figure.canvas.draw_idle()
-
-    def del_edges(self):
-        if self.label is not None:
-            self.label.remove()
-            self.line.remove()
-            self.label = None
-
-    def disconnect(self):
-        self.ly.remove()
-        self.marker.remove()
-        self.txt.remove()
-
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-        self.ax.figure.canvas.mpl_disconnect(self.mouse_cid)
-
-
-class ElementalEdges(object):
-    """
-        The necessary initialization parameter are:
-        ax: matplotlib axis
-
-
-        There is an optional parameter maximum_chemical_shift which allows to change
-        the energy range in which the edges are searched.
-
-        available functions:
-        - update(): updates the drawing of ionization edges
-        - set_edge(z) : changes atomic number and updates everything accordingly
-        - disconnect: makes everything invisible and stops drawing
-        - reconnect: undo of disconnect
-
-        usage:
-        >>  fig, ax = plt.subplots()
-        >>  ax.plot(energy_scale, spectrum)
-        >>  z= 42
-        >>  cursor = ElementalEdges(ax, z)
-
-
-        see Chapter4 'CH4-Working_with_X-Sections' notebook
-    """
-
-    def __init__(self, ax, z):
-        self.ax = ax
-        self.labels = None
-        self.lines = None
-        self.z = eels.get_z(z)
-        self.color = 'black'
-        self.x_sections = eels.get_x_sections()
-        self.cid = ax.figure.canvas.mpl_connect('draw_event', self.on_resize)
-        # self.update() is not necessary because of a drawing event is issued
-
-    def set_edge(self, z):
-        self.z = eels.get_z(z)
-        if self.cid is None:
-            self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.on_resize)
-        self.update()
-
-    def on_resize(self, event):
-        self.update()
-
-    def update(self):
-        if self.labels is not None:
-            for label in self.labels:
-                label.remove()
-        if self.lines is not None:
-            for line in self.lines:
-                line.remove()
-        self.labels = []
-        self.lines = []
-        x_min, x_max = self.ax.get_xlim()
-        y_min, y_max = self.ax.get_ylim()
-
-        element = str(self.z)
-        x_sections = self.x_sections
-        for key in all_edges:
-            if key in x_sections[element]:
-                if 'onset' in x_sections[element][key]:
-                    x = x_sections[element][key]['onset']
-                    if x_min < x < x_max:
-                        if key in first_close_edges:
-                            label2 = self.ax.text(x, y_max, f"{x_sections[element]['name']}-{key}",
-                                                  verticalalignment='top', rotation=0, color=self.color)
-                        else:
-                            label2 = self.ax.text(x, y_max, f"\n{x_sections[element]['name']}-{key}",
-                                                  verticalalignment='top', color=self.color)
-                        line2 = self.ax.axvline(x, ymin=0, ymax=1, color=self.color)
-
-                        self.labels.append(label2)
-                        self.lines.append(line2)
-
-    def reconnect(self):
-        self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.on_resize)
-        self.update()
-
-    def disconnect(self):
-        if self.labels is not None:
-            for label in self.labels:
-                label.remove()
-        if self.lines is not None:
-            for line in self.lines:
-                line.remove()
-        self.labels = None
-        self.lines = None
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-
-
-class RegionSelector(object):
-    """
-        Selects fitting region and the regions that are excluded for each edge.
-
-        Select a region with a spanSelector and then type 'a' for all of the fitting region or a number for the edge
-        you want to define the region excluded from the fit (solid state effects).
-
-        see Chapter4 'CH4-Working_with_X-Sections,ipynb' notebook
-
-    """
-
-    def __init__(self, ax):
-        self.ax = ax
-        self.regions = {}
-        self.rect = None
-        self.xmin = 0
-        self.width = 0
-
-        self.span = SpanSelector(ax, self.onselect1, 'horizontal', useblit=True,
-                                 rectprops=dict(alpha=0.5, facecolor='red'), span_stays=True)
-        self.cid = ax.figure.canvas.mpl_connect('key_press_event', self.click)
-        self.draw = ax.figure.canvas.mpl_connect('draw_event', self.on_resize)
-
-    def onselect1(self, xmin, xmax):
-        self.xmin = xmin
-        self.width = xmax - xmin
-
-    def on_resize(self, event):
-        self.update()
-
-    def delete_region(self, key):
-        if key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-            del (self.regions[key])
-
-    def update(self):
-
-        y_min, y_max = self.ax.get_ylim()
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-
-            xmin = self.regions[key]['xmin']
-            width = self.regions[key]['width']
-            height = y_max - y_min
-            alpha = self.regions[key]['alpha']
-            color = self.regions[key]['color']
-            self.regions[key]['Rect'] = patches.Rectangle((xmin, y_min), width, height,
-                                                          edgecolor=color, alpha=alpha, facecolor=color)
-            self.ax.add_patch(self.regions[key]['Rect'])
-
-            self.regions[key]['Text'] = self.ax.text(xmin, y_max, self.regions[key]['text'], verticalalignment='top')
-
-    def click(self, event):
-        if str(event.key) in ['1', '2', '3', '4', '5', '6']:
-            key = str(event.key)
-            text = 'exclude \nedge ' + key
-            alpha = 0.5
-            color = 'red'
-        elif str(event.key) in ['a', 'A', 'B', 'b', 'f', 'F']:
-            key = '0'
-            color = 'blue'
-            alpha = 0.2
-            text = 'fit region'
-        else:
-            return
-
-        if key not in self.regions:
-            self.regions[key] = {}
-
-        self.regions[key]['xmin'] = self.xmin
-        self.regions[key]['width'] = self.width
-        self.regions[key]['color'] = color
-        self.regions[key]['alpha'] = alpha
-        self.regions[key]['text'] = text
-
-        self.update()
-
-    def set_regions(self, region, start_x, width):
-        if 'fit' in str(region):
-            key = '0'
-        if region in ['0', '1', '2', '3', '4', '5', '6']:
-            key = region
-        if region in [0, 1, 2, 3, 4, 5, 6]:
-            key = str(region)
-
-        if key not in self.regions:
-            self.regions[key] = {}
-            if key in ['1', '2', '3', '4', '5', '6']:
-                self.regions[key]['text'] = 'exclude \nedge ' + key
-                self.regions[key]['alpha'] = 0.5
-                self.regions[key]['color'] = 'red'
-            elif key == '0':
-                self.regions[key]['text'] = 'fit region'
-                self.regions[key]['alpha'] = 0.2
-                self.regions[key]['color'] = 'blue'
-
-        self.regions[key]['xmin'] = start_x
-        self.regions[key]['width'] = width
-
-        self.update()
-
-    def get_regions(self):
-        tags = {}
-        for key in self.regions:
-            if key == '0':
-                area = 'fit_area'
-            else:
-                area = key
-            tags[area] = {}
-            tags[area]['start_x'] = self.regions[key]['xmin']
-            tags[area]['width_x'] = self.regions[key]['width']
-
-        return tags
-
-    def disconnect(self):
-        for key in self.regions:
-            if 'Rect' in self.regions[key]:
-                self.regions[key]['Rect'].remove()
-                self.regions[key]['Text'].remove()
-        del self.span
-        self.ax.figure.canvas.mpl_disconnect(self.cid)
-        # self.ax.figure.canvas.mpl_disconnect(self.draw)
-        pass
+""" Interactive routines for EELS analysis
+
+this file provides additional dialogs for EELS quantification
+
+Author: Gerd Duscher
+"""
+
+import numpy as np
+
+import sidpy
+import matplotlib
+import matplotlib.pyplot as plt
+
+import matplotlib.patches as patches
+from matplotlib.widgets import RectangleSelector, SpanSelector
+
+import h5py  # TODO: needs to go
+
+from IPython.display import display
+import ipywidgets
+
+from pyTEMlib import eels_tools as eels
+from pyTEMlib import file_tools as ft
+
+major_edges = ['K1', 'L3', 'M5', 'N5']
+all_edges = ['K1', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5', 'N1', 'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2',
+             'O3', 'O4', 'O5', 'O6', 'O7', 'P1', 'P2', 'P3']
+first_close_edges = ['K1', 'L3', 'M5', 'M3', 'N5', 'N3']
+
+
+
+class RegionSelector(object):
+    """Selects fitting region and the regions that are excluded for each edge.
+
+        Select a region with a spanSelector and then type 'a' for all the fitting region or a number for the edge
+        you want to define the region excluded from the fit (solid state effects).
+
+        see Chapter4 'CH4-Working_with_X-Sections,ipynb' notebook
+
+    """
+
+    def __init__(self, ax):
+        self.ax = ax
+        self.regions = {}
+        self.rect = None
+        self.xmin = 0
+        self.width = 0
+
+        self.span = SpanSelector(ax, self.on_select1, 
+                                 direction="horizontal",
+                                 interactive=True,
+                                 props=dict(facecolor='blue', alpha=0.2))
+        self.cid = ax.figure.canvas.mpl_connect('key_press_event', self.click)
+        self.draw = ax.figure.canvas.mpl_connect('draw_event', self.onresize)
+
+    def on_select1(self, xmin, xmax):
+        self.xmin = xmin
+        self.width = xmax - xmin
+
+    def onresize(self, event):
+        self.update()
+
+    def delete_region(self, key):
+        if key in self.regions:
+            if 'Rect' in self.regions[key]:
+                self.regions[key]['Rect'].remove()
+                self.regions[key]['Text'].remove()
+            del (self.regions[key])
+
+    def update(self):
+
+        y_min, y_max = self.ax.get_ylim()
+        for key in self.regions:
+            if 'Rect' in self.regions[key]:
+                self.regions[key]['Rect'].remove()
+                self.regions[key]['Text'].remove()
+
+            xmin = self.regions[key]['xmin']
+            width = self.regions[key]['width']
+            height = y_max - y_min
+            alpha = self.regions[key]['alpha']
+            color = self.regions[key]['color']
+            self.regions[key]['Rect'] = patches.Rectangle((xmin, y_min), width, height,
+                                                          edgecolor=color, alpha=alpha, facecolor=color)
+            self.ax.add_patch(self.regions[key]['Rect'])
+
+            self.regions[key]['Text'] = self.ax.text(xmin, y_max, self.regions[key]['text'], verticalalignment='top')
+
+    def click(self, event):
+        if str(event.key) in ['1', '2', '3', '4', '5', '6']:
+            key = str(event.key)
+            text = 'exclude \nedge ' + key
+            alpha = 0.5
+            color = 'red'
+        elif str(event.key) in ['a', 'A', 'B', 'b', 'f', 'F']:
+            key = '0'
+            color = 'blue'
+            alpha = 0.2
+            text = 'fit region'
+        else:
+            return
+
+        if key not in self.regions:
+            self.regions[key] = {}
+
+        self.regions[key]['xmin'] = self.xmin
+        self.regions[key]['width'] = self.width
+        self.regions[key]['color'] = color
+        self.regions[key]['alpha'] = alpha
+        self.regions[key]['text'] = text
+
+        self.update()
+
+    def set_regions(self, region, start_x, width):
+        key = ''
+        if 'fit' in str(region):
+            key = '0'
+        if region in ['0', '1', '2', '3', '4', '5', '6']:
+            key = region
+        if region in [0, 1, 2, 3, 4, 5, 6]:
+            key = str(region)
+
+        if key not in self.regions:
+            self.regions[key] = {}
+            if key in ['1', '2', '3', '4', '5', '6']:
+                self.regions[key]['text'] = 'exclude \nedge ' + key
+                self.regions[key]['alpha'] = 0.5
+                self.regions[key]['color'] = 'red'
+            elif key == '0':
+                self.regions[key]['text'] = 'fit region'
+                self.regions[key]['alpha'] = 0.2
+                self.regions[key]['color'] = 'blue'
+
+        self.regions[key]['xmin'] = start_x
+        self.regions[key]['width'] = width
+
+        self.update()
+
+    def get_regions(self):
+        tags = {}
+        for key in self.regions:
+            if key == '0':
+                area = 'fit_area'
+            else:
+                area = key
+            tags[area] = {}
+            tags[area]['start_x'] = self.regions[key]['xmin']
+            tags[area]['width_x'] = self.regions[key]['width']
+
+        return tags
+
+    def disconnect(self):
+        for key in self.regions:
+            if 'Rect' in self.regions[key]:
+                self.regions[key]['Rect'].remove()
+                self.regions[key]['Text'].remove()
+        del self.span
+        self.ax.figure.canvas.mpl_disconnect(self.cid)
+        # self.ax.figure.canvas.mpl_disconnect(self.draw)
+        pass
+
+
+class RangeSelector(RectangleSelector):
+    """Select ranges of edge fitting interactively"""
+    def __init__(self, ax, on_select):
+        drawtype = 'box'
+        spancoords = 'data'
+        rectprops = dict(facecolor="blue", edgecolor="black", alpha=0.2, fill=True)
+
+        super().__init__(ax, on_select, drawtype=drawtype,
+                         minspanx=0, minspany=0, useblit=False,
+                         lineprops=None, rectprops=rectprops, spancoords=spancoords,
+                         button=None, maxdist=10, marker_props=None,
+                         interactive=True, state_modifier_keys=None)
+
+        self.artists = [self.to_draw, self._center_handle.artist,
+                        self._edge_handles.artist]
+
+    def draw_shape(self, extents):
+        x0, x1, y0, y1 = extents
+        xmin, xmax = sorted([x0, x1])
+        # ymin, ymax = sorted([y0, y1])
+        xlim = sorted(self.ax.get_xlim())
+        ylim = sorted(self.ax.get_ylim())
+
+        xmin = max(xlim[0], xmin)
+        ymin = ylim[0]
+        xmax = min(xmax, xlim[1])
+        ymax = ylim[1]
+
+        self.to_draw.set_x(xmin)
+        self.to_draw.set_y(ymin)
+        self.to_draw.set_width(xmax - xmin)
+        self.to_draw.set_height(ymax - ymin)
+
+
+def get_likely_edges(energy_scale):
+    """get likely ionization edges within energy_scale"""
+    x_sections = eels.get_x_sections()
+    # print(energy_scale)
+    energy_origin = energy_scale[0]
+    energy_window = energy_scale[-1] - energy_origin
+    selected_edges_unsorted = {}
+    likely_edges = []
+    selected_elements = []
+    for element in range(1, 83):
+        # print(element)
+        element_z = str(eels.get_z(element))
+
+        for key in x_sections[element_z]:
+            if key in all_edges:
+                onset = x_sections[element_z][key]['onset']
+                if onset > energy_origin:
+                    if onset - energy_origin < energy_window:
+                        if element not in selected_edges_unsorted:
+                            selected_edges_unsorted[element] = {}
+                        # print(element, x_sections[element]['name'], key, x_sections[element][key]['onset'])
+                        # text = f"\n {x_sections[element_z]['name']:2s}-{key}: " \
+                        #       f"{x_sections[element_z][key]['onset']:8.1f} eV "
+                        # print(text)
+
+                        selected_edges_unsorted[element][key] = {}
+                        selected_edges_unsorted[element][key]['onset'] = x_sections[element_z][key]['onset']
+
+                        if key in major_edges:
+                            selected_edges_unsorted[element][key]['intensity'] = 'major'
+                            selected_elements.append(x_sections[element_z]['name'])
+                        else:
+                            selected_edges_unsorted[element][key]['intensity'] = 'minor'
+
+        if element in selected_edges_unsorted:
+            for key in selected_edges_unsorted[element]:
+                if selected_edges_unsorted[element][key]['intensity'] == 'major':
+                    likely_edges.append(x_sections[str(element)]['name'])  # = {'z':element, 'symmetry': key}
+
+    return likely_edges
+
+        
+class SpectrumPlot(sidpy.viz.dataset_viz.CurveVisualizer):
+    def __init__(self, dset, spectrum_number=0, figure=None, **kwargs):
+        with plt.ioff():
+            self.figure = plt.figure()
+        self.figure.canvas.toolbar_position = 'right'
+        self.figure.canvas.toolbar_visible = True
+
+        super().__init__(dset, spectrum_number=spectrum_number, figure=self.figure, **kwargs)
+        try:
+            self.dataset = self.dset
+        except:
+            pass
+        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.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
+                                         direction="horizontal",
+                                         interactive=True,
+                                         props=dict(facecolor='blue', alpha=0.2))
+        
+    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.dataset.energy_loss, self.start_cursor.value)
+        self.end_channel = np.searchsorted(self.dataset.energy_loss, self.end_cursor.value)
+    
+    def plot(self, scale=True, additional_spectra=None):
+        self.dataset = self.dset
+        self.energy_scale = self.dataset.energy_loss.values
+        x_limit = self.axis.get_xlim()
+        y_limit = np.array(self.axis.get_ylim())
+        
+        self.axis.clear()
+
+        self.axis.plot(self.energy_scale, self.dataset*self.y_scale, label='spectrum')
+                
+        if additional_spectra is not None:
+            if isinstance(additional_spectra, dict):
+                for key, spectrum in additional_spectra.items():
+                    self.axis.plot(self.energy_scale, spectrum*self.y_scale, label=key)
+
+        self.axis.set_xlabel(self.dataset.labels[0])
+        self.axis.set_ylabel(self.dataset.data_descriptor)
+        self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
+        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()
+        self.figure.canvas.draw_idle()
+        
+
+class SIPlot(sidpy.viz.dataset_viz.SpectralImageVisualizerBase):
+    def __init__(self, dset, figure=None, horizontal=True, **kwargs):
+        if figure is None:
+            with plt.ioff():
+                self.figure = plt.figure()
+        else:
+            self.figure = figure
+        self.figure.canvas.toolbar_position = 'right'
+        self.figure.canvas.toolbar_visible = True
+        self.dset = dset
+        super().__init__(self.dset, figure=self.figure, horizontal=horizontal, **kwargs)
+        
+        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.axis = self.axes[-1]
+        self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
+                                         direction="horizontal",
+                                         interactive=True,
+                                         props=dict(facecolor='blue', alpha=0.2))
+       
+    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.dataset.energy_loss, self.start_cursor.value)
+        self.end_channel = np.searchsorted(self.dataset.energy_loss, self.end_cursor.value)
+    
+    def plot(self, scale=True, additional_spectra=None):
+        
+        xlim = self.axes[1].get_xlim()
+        ylim = self.axes[1].get_ylim()
+        self.axes[1].clear()
+        self.get_spectrum()
+        if len(self.energy_scale)!=self.spectrum.shape[0]:
+            self.spectrum = self.spectrum.T
+        self.axes[1].plot(self.energy_scale, self.spectrum.compute(), label='experiment')
+        if additional_spectra is not None:
+            if isinstance(additional_spectra, dict):
+                for key, spectrum in additional_spectra.items():
+                    self.axes[1].plot(self.energy_scale, spectrum, label=key)
+
+        if self.set_title:
+            self.axes[1].set_title('spectrum {}, {}'.format(self.x, self.y))
+        self.fig.tight_layout()
+        self.selector = matplotlib.widgets.SpanSelector(self.axes[1], self.line_select_callback,
+                                         direction="horizontal",
+                                         interactive=True,
+                                         props=dict(facecolor='blue', alpha=0.2))
+        
+        self.axes[1].set_xlim(xlim)
+        self.axes[1].set_ylim(ylim)
+        self.axes[1].set_xlabel(self.xlabel)
+        self.axes[1].set_ylabel(self.ylabel)
+
+        self.fig.canvas.draw_idle()
+
+
+def get_periodic_table_widget(energy_scale=None):
+
+    if energy_scale is None:
+        energy_scale = [100., 150., 200.]
+    
+    likely_edges = get_likely_edges(energy_scale)
+    
+    pt_info =  get_periodic_table_info()
+    table = ipywidgets.GridspecLayout(10, 18,width= '60%', grid_gap="0px")
+    for symbol, parameter in pt_info.items():
+        #print(parameter['PT_row'], parameter['PT_col'])
+        if parameter['PT_row'] > 7:
+            color = 'warning'
+        elif '*' in symbol:
+            color = 'warning'
+        else:
+            if symbol in likely_edges:
+                color = 'primary'
+            else:
+                color = 'info'
+        table[parameter['PT_row'], parameter['PT_col']] = ipywidgets.ToggleButton(description=symbol, 
+                                                                                  value=False, 
+                                                                                  button_style=color,
+                                                                                  layout=ipywidgets.Layout(width='auto'),
+                                                                                  style={"button_width": "30px"})
+    return table
+
+
+class PeriodicTableWidget(object):
+    """ ipywidget to get a selection of elements.
+
+    Elements that are not having a valid cross-sections are disabled.
+
+    Parameters
+    ----------
+    initial_elements: list of str
+        the elements that are already selected
+    energy_scale: list or numpy array
+        energy-scale of spectrum/spectra to determine likely edges
+
+    Returns
+    -------
+    list of strings: elements.
+        use get_output() function
+    """
+
+    def __init__(self, initial_elements=None, energy_scale=None):
+
+        if initial_elements is None:
+            initial_elements = [' ']
+        self.elements_selected = initial_elements
+        if energy_scale is None:
+            energy_scale = [100., 150., 200.]
+        self._output = []
+        self.energy_scale = np.array(energy_scale)
+        self.pt_info =  get_periodic_table_info()
+    
+        self.periodic_table = get_periodic_table_widget(energy_scale) 
+        self.update()
+
+    def get_output(self):
+        self.elements_selected = []
+        for symbol, parameter in self.pt_info.items():
+            if self.periodic_table[parameter['PT_row'], parameter['PT_col']].value == True:  # [parameter['PT_row'], parameter['PT_col']]
+                self.elements_selected.append(self.periodic_table[parameter['PT_row'], parameter['PT_col']].description)
+        return self.elements_selected
+    
+    def update(self):
+        for symbol, parameter in self.pt_info.items():
+            if str(self.periodic_table[parameter['PT_row'], parameter['PT_col']].description) in list(self.elements_selected):
+                self.periodic_table[parameter['PT_row'], parameter['PT_col']].value = True
+
+
+
+
+def get_periodic_table_info():
+    """Info for periodic table dialog"""
+    pt_info = \
+        {'H': {'PT_row': 0, 'PT_col': 0, 'Z': 0},
+         'He': {'PT_row': 0, 'PT_col': 17, 'Z': 2}, 'Li': {'PT_row': 1, 'PT_col': 0, 'Z': 3},
+         'Be': {'PT_row': 1, 'PT_col': 1, 'Z': 4}, 'B': {'PT_row': 1, 'PT_col': 12, 'Z': 5},
+         'C': {'PT_row': 1, 'PT_col': 13, 'Z': 6}, 'N': {'PT_row': 1, 'PT_col': 14, 'Z': 7},
+         'O': {'PT_row': 1, 'PT_col': 15, 'Z': 8}, 'F': {'PT_row': 1, 'PT_col': 16, 'Z': 9},
+         'Ne': {'PT_row': 1, 'PT_col': 17, 'Z': 10}, 'Na': {'PT_row': 2, 'PT_col': 0, 'Z': 11},
+         'Mg': {'PT_row': 2, 'PT_col': 1, 'Z': 12}, 'Al': {'PT_row': 2, 'PT_col': 12, 'Z': 13},
+         'Si': {'PT_row': 2, 'PT_col': 13, 'Z': 14}, 'P': {'PT_row': 2, 'PT_col': 14, 'Z': 15},
+         'S': {'PT_row': 2, 'PT_col': 15, 'Z': 16}, 'Cl': {'PT_row': 2, 'PT_col': 16, 'Z': 17},
+         'Ar': {'PT_row': 2, 'PT_col': 17, 'Z': 18}, 'K': {'PT_row': 3, 'PT_col': 0, 'Z': 19},
+         'Ca': {'PT_row': 3, 'PT_col': 1, 'Z': 20}, 'Sc': {'PT_row': 3, 'PT_col': 2, 'Z': 21},
+         'Ti': {'PT_row': 3, 'PT_col': 3, 'Z': 22}, 'V ': {'PT_row': 3, 'PT_col': 4, 'Z': 23},
+         'Cr': {'PT_row': 3, 'PT_col': 5, 'Z': 24}, 'Mn': {'PT_row': 3, 'PT_col': 6, 'Z': 25},
+         'Fe': {'PT_row': 3, 'PT_col': 7, 'Z': 26}, 'Co': {'PT_row': 3, 'PT_col': 8, 'Z': 27},
+         'Ni': {'PT_row': 3, 'PT_col': 9, 'Z': 28}, 'Cu': {'PT_row': 3, 'PT_col': 10, 'Z': 29},
+         'Zn': {'PT_row': 3, 'PT_col': 11, 'Z': 30}, 'Ga': {'PT_row': 3, 'PT_col': 12, 'Z': 31},
+         'Ge': {'PT_row': 3, 'PT_col': 13, 'Z': 32}, 'As': {'PT_row': 3, 'PT_col': 14, 'Z': 33},
+         'Se': {'PT_row': 3, 'PT_col': 15, 'Z': 34}, 'Br': {'PT_row': 3, 'PT_col': 16, 'Z': 35},
+         'Kr': {'PT_row': 3, 'PT_col': 17, 'Z': 36}, 'Rb': {'PT_row': 4, 'PT_col': 0, 'Z': 37},
+         'Sr': {'PT_row': 4, 'PT_col': 1, 'Z': 38}, 'Y': {'PT_row': 4, 'PT_col': 2, 'Z': 39},
+         'Zr': {'PT_row': 4, 'PT_col': 3, 'Z': 40}, 'Nb': {'PT_row': 4, 'PT_col': 4, 'Z': 41},
+         'Mo': {'PT_row': 4, 'PT_col': 5, 'Z': 42}, 'Tc': {'PT_row': 4, 'PT_col': 6, 'Z': 43},
+         'Ru': {'PT_row': 4, 'PT_col': 7, 'Z': 44}, 'Rh': {'PT_row': 4, 'PT_col': 8, 'Z': 45},
+         'Pd': {'PT_row': 4, 'PT_col': 9, 'Z': 46}, 'Ag': {'PT_row': 4, 'PT_col': 10, 'Z': 47},
+         'Cd': {'PT_row': 4, 'PT_col': 11, 'Z': 48}, 'In': {'PT_row': 4, 'PT_col': 12, 'Z': 49},
+         'Sn': {'PT_row': 4, 'PT_col': 13, 'Z': 50}, 'Sb': {'PT_row': 4, 'PT_col': 14, 'Z': 51},
+         'Te': {'PT_row': 4, 'PT_col': 15, 'Z': 52}, 'I': {'PT_row': 4, 'PT_col': 16, 'Z': 53},
+         'Xe': {'PT_row': 4, 'PT_col': 17, 'Z': 54}, 'Cs': {'PT_row': 5, 'PT_col': 0, 'Z': 55},
+         'Ba': {'PT_row': 5, 'PT_col': 1, 'Z': 56}, 'Hf': {'PT_row': 5, 'PT_col': 3, 'Z': 72},
+         'Ta': {'PT_row': 5, 'PT_col': 4, 'Z': 73}, 'W': {'PT_row': 5, 'PT_col': 5, 'Z': 74},
+         'Re': {'PT_row': 5, 'PT_col': 6, 'Z': 75}, 'Os': {'PT_row': 5, 'PT_col': 7, 'Z': 76},
+         'Ir': {'PT_row': 5, 'PT_col': 8, 'Z': 77}, 'Pt': {'PT_row': 5, 'PT_col': 9, 'Z': 78},
+         'Au': {'PT_row': 5, 'PT_col': 10, 'Z': 79}, 'Hg': {'PT_row': 5, 'PT_col': 11, 'Z': 80},
+         'Pb': {'PT_row': 5, 'PT_col': 13, 'Z': 82}, 'Bi': {'PT_row': 5, 'PT_col': 14, 'Z': 0},
+         'Po': {'PT_row': 5, 'PT_col': 15, 'Z': 0}, 'At': {'PT_row': 5, 'PT_col': 16, 'Z': 0},
+         'Rn': {'PT_row': 5, 'PT_col': 17, 'Z': 0}, 'Fr': {'PT_row': 6, 'PT_col': 0, 'Z': 0},
+         'Ra': {'PT_row': 6, 'PT_col': 1, 'Z': 0}, 'Rf': {'PT_row': 6, 'PT_col': 3, 'Z': 0},
+         'Db': {'PT_row': 6, 'PT_col': 4, 'Z': 0}, 'Sg': {'PT_row': 6, 'PT_col': 5, 'Z': 0},
+         'Bh': {'PT_row': 6, 'PT_col': 6, 'Z': 0}, 'Hs': {'PT_row': 6, 'PT_col': 7, 'Z': 0},
+         'Mt': {'PT_row': 6, 'PT_col': 8, 'Z': 0}, 'Ds': {'PT_row': 6, 'PT_col': 9, 'Z': 0},
+         'Rg': {'PT_row': 6, 'PT_col': 10, 'Z': 0}, 'La': {'PT_row': 8, 'PT_col': 3, 'Z': 57},
+         'Ce': {'PT_row': 8, 'PT_col': 4, 'Z': 58}, 'Pr': {'PT_row': 8, 'PT_col': 5, 'Z': 59},
+         'Nd': {'PT_row': 8, 'PT_col': 6, 'Z': 60}, 'Pm': {'PT_row': 8, 'PT_col': 7, 'Z': 61},
+         'Sm': {'PT_row': 8, 'PT_col': 8, 'Z': 62}, 'Eu': {'PT_row': 8, 'PT_col': 9, 'Z': 63},
+         'Gd': {'PT_row': 8, 'PT_col': 10, 'Z': 64}, 'Tb': {'PT_row': 8, 'PT_col': 11, 'Z': 65},
+         'Dy': {'PT_row': 8, 'PT_col': 12, 'Z': 66}, 'Ho': {'PT_row': 8, 'PT_col': 13, 'Z': 67},
+         'Er': {'PT_row': 8, 'PT_col': 14, 'Z': 68}, 'Tm': {'PT_row': 8, 'PT_col': 15, 'Z': 69},
+         'Yb': {'PT_row': 8, 'PT_col': 16, 'Z': 70}, 'Lu': {'PT_row': 8, 'PT_col': 17, 'Z': 71},
+         'Ac': {'PT_row': 9, 'PT_col': 3, 'Z': 0}, 'Th': {'PT_row': 9, 'PT_col': 4, 'Z': 0},
+         'Pa': {'PT_row': 9, 'PT_col': 5, 'Z': 0}, 'U': {'PT_row': 9, 'PT_col': 6, 'Z': 0},
+         'Np': {'PT_row': 9, 'PT_col': 7, 'Z': 0}, 'Pu': {'PT_row': 9, 'PT_col': 8, 'Z': 0},
+         'Am': {'PT_row': 9, 'PT_col': 9, 'Z': 0}, 'Cm': {'PT_row': 9, 'PT_col': 10, 'Z': 0},
+         'Bk': {'PT_row': 9, 'PT_col': 11, 'Z': 0}, 'Cf': {'PT_row': 9, 'PT_col': 12, 'Z': 0},
+         'Es': {'PT_row': 9, 'PT_col': 13, 'Z': 0}, 'Fm': {'PT_row': 9, 'PT_col': 14, 'Z': 0},
+         'Md': {'PT_row': 9, 'PT_col': 15, 'Z': 0}, 'No': {'PT_row': 9, 'PT_col': 16, 'Z': 0},
+         'Lr': {'PT_row': 9, 'PT_col': 17, 'Z': 0},
+         '*': {'PT_row': 5, 'PT_col': 2, 'PT_col2': 8, 'PT_row2': 2, 'Z': 0},
+         '**': {'PT_row': 6, 'PT_col': 2, 'PT_col2': 9, 'PT_row2': 2, 'Z': 0}}
+
+    return pt_info
+
+
+class InteractiveSpectrumImage(object):
+    """Interactive spectrum imaging plot
+
+    Attributes:
+    -----------
+    dictionary with a minimum of the following keys:
+        ['image']: displayed image
+        ['data']:  data cube
+        ['intensity_scale_ppm']: intensity scale
+        ['ylabel']: intensity label
+        ['spectra'] dictionary which contains dictionaries for each spectrum style ['1-2']:
+            ['spectrum'] = tags['cube'][y,x,:]
+            ['spectra'][f'{x}-{y}']['energy_scale'] = tags['energy_scale']
+            ['intensity_scale'] = 1/tags['cube'][y,x,:].sum()*1e6
+
+    Please note the possibility to load any image for the selection of the spectrum
+    Also there is the possibility to display the survey image.
+
+    For analysis, we have the following options:
+        'fix_energy': set zero-loss peak maximum to zero !! Low loss spectra only!!
+        'fit_zero_loss': fit zero-loss peak with model function !! Low loss spectra only!!
+        'fit_low_loss': fit low-loss spectrum with model peaks !! Low loss spectra only!!
+
+
+        'fit_composition': fit core-loss spectrum with background and cross-sections!! Core loss spectra only!!
+        'fit_ELNES': fit core-loss edge with model peaks  !! Core loss spectra only!!
+    """
+
+    def __init__(self, data_source, horizontal=True):
+
+        box_layout = ipywidgets.Layout(display='flex',
+                                    flex_flow='row',
+                                    align_items='stretch',
+                                    width='100%')
+
+        words = ['fix_energy', 'fit_zero_loss', 'fit_low_loss', 'fit_composition', 'fit_ELNES']
+
+        self.buttons = [ipywidgets.ToggleButton(value=False, description=word, disabled=False) for word in words]
+        box = ipywidgets.Box(children=self.buttons, layout=box_layout)
+        display(box)
+
+        # MAKE Dictionary
+
+        if isinstance(data_source, dict):
+            self.tags = data_source
+        elif isinstance(data_source, h5py.Group):
+            self.tags = self.set_tags(data_source)
+        else:
+            print('Data source must be a dictionary or channel')
+            return
+
+        # Button(description='edge_quantification')
+        for button in self.buttons:
+            button.observe(self.on_button_clicked, 'value')  # on_click(self.on_button_clicked)
+
+        self.figure = plt.figure()
+        self.horizontal = horizontal
+        self.x = 0
+        self.y = 0
+
+        self.extent = [0, self.tags['cube'].shape[1], self.tags['cube'].shape[0], 0]
+        self.rectangle = [0, self.tags['cube'].shape[1], 0, self.tags['cube'].shape[0]]
+        self.scaleX = 1.0
+        self.scaleY = 1.0
+        self.analysis = []
+        self.plot_legend = False
+        if 'ylabel' not in self.tags:
+            self.tags['ylabel'] = 'intensity [a.u.]'
+        self.SI = False
+
+        if horizontal:
+            self.ax1 = plt.subplot(1, 2, 1)
+            self.ax2 = plt.subplot(1, 2, 2)
+        else:
+            self.ax1 = plt.subplot(2, 1, 1)
+            self.ax2 = plt.subplot(2, 1, 2)
+
+        self.cube = self.tags['cube']
+        self.image = self.tags['cube'].sum(axis=2)
+
+        self.ax1.imshow(self.image, extent=self.extent)
+        if horizontal:
+            self.ax1.set_xlabel('distance [pixels]')
+        else:
+            self.ax1.set_ylabel('distance [pixels]')
+        self.ax1.set_aspect('equal')
+
+        self.rect = patches.Rectangle((0, 0), 1, 1, linewidth=1, edgecolor='r', facecolor='red', alpha=0.2)
+        self.ax1.add_patch(self.rect)
+        self.intensity_scale = self.tags['spectra'][f'{self.x}-{self.y}']['intensity_scale']
+        self.spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
+        self.energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
+
+        self.ax2.plot(self.energy_scale, self.spectrum)
+        self.ax2.set_title(f' spectrum {self.x},{self.y} ')
+        self.ax2.set_xlabel('energy loss [eV]')
+        self.ax2.set_ylabel(self.tags['ylabel'])
+        self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
+
+        plt.tight_layout()
+
+    def on_button_clicked(self, b):
+        # print(b['owner'].description)
+        selection = b['owner'].description
+        if b['new']:
+            if selection == 'fit_composition':
+                if 'region_tags' in self.tags and 'edges_present' in self.tags \
+                        and 'acceleration_voltage' in self.tags \
+                        and 'collection_angle' in self.tags:
+                    pass
+                else:
+                    self.buttons[3].value = False
+                    return
+            elif selection in ['fix_energy', 'fit_zero_loss']:
+                if self.energy_scale[0] > 0:
+                    button_index = ['fix_energy', 'fit_zero_loss'].index(selection)
+                    self.buttons[button_index].value = False
+                    return
+            self.analysis.append(selection)
+            self.update()
+        else:
+
+            if selection in self.analysis:
+                self.analysis.remove(selection)
+
+    def do_all(self, selection=None, verbose=True):
+        x = self.x
+        y = self.y
+        if selection is None:
+            selection = self.analysis
+        for self.x in range(self.cube.shape[1]):
+            if verbose:
+                print(f' row: {self.x}')
+            for self.y in range(self.cube.shape[0]):
+
+                if 'fit_zero_loss' in selection:
+                    title = self.fit_zero_loss(plot_this=False)
+
+                elif 'fix_energy' in selection:
+                    self.ax2.set_title('bn')
+                    title = self.fix_energy()
+
+                elif 'fit_composition' in selection:
+                    title = self.fit_quantification(plot_this=False)
+
+        self.x = x
+        self.y = y
+
+    def onclick(self, event):
+        x = int(event.xdata)
+        y = int(event.ydata)
+
+        # print(x,y)
+        if self.rectangle[0] <= x < self.rectangle[0] + self.rectangle[1]:
+            if self.rectangle[2] <= y < self.rectangle[2] + self.rectangle[3]:
+                self.x = int((x - self.rectangle[0]) / self.rectangle[1] * self.cube.shape[1])
+                self.y = int((y - self.rectangle[2]) / self.rectangle[3] * self.cube.shape[0])
+            else:
+                return
+        else:
+            return
+
+        if event.inaxes in [self.ax1]:
+            x = (self.x * self.rectangle[1] / self.cube.shape[1] + self.rectangle[0])
+            y = (self.y * self.rectangle[3] / self.cube.shape[0] + self.rectangle[2])
+
+            self.rect.set_xy([x, y])
+            self.update()
+
+    def update(self):
+        xlim = self.ax2.get_xlim()
+        ylim = self.ax2.get_ylim()
+        self.ax2.clear()
+        self.intensity_scale = self.tags['spectra'][f'{self.x}-{self.y}']['intensity_scale']
+        self.spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
+        self.energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
+
+        if 'fit_zero_loss' in self.analysis:
+            title = self.fit_zero_loss()
+            self.ax2.set_title(title)
+        elif 'fix_energy' in self.analysis:
+            self.ax2.set_title('bn')
+            title = self.fix_energy()
+            self.ax2.set_title(title)
+
+        elif 'fit_composition' in self.analysis:
+            title = self.fit_quantification()
+            self.ax2.set_title(title)
+
+        else:
+            self.ax2.set_title(f' spectrum {self.x},{self.y} ')
+        self.ax2.plot(self.energy_scale, self.spectrum, color='#1f77b4', label='experiment')
+
+        if self.plot_legend:
+            self.ax2.legend(shadow=True)
+        self.ax2.set_xlim(xlim)
+        self.ax2.set_ylim(ylim)
+        self.ax2.set_xlabel('energy loss [eV]')
+        self.ax2.set_ylabel(self.tags['ylabel'])
+        self.ax2.set_xlim(xlim)
+
+        # self.ax2.draw()
+
+    def set_tags(self, channel):
+        # TODO: change to sidpy dataset tags = ft.h5_get_dictionary(channel)
+        tags = {}
+        if tags['data_type'] == 'spectrum_image':
+            tags['image'] = tags['data']
+            tags['data'] = tags['cube'][0, 0, :]
+            if 'intensity_scale_ppm' not in channel:
+                channel['intensity_scale_ppm'] = 1
+
+            tags['ylabel'] = 'intensity [a.u.]'
+            tags['spectra'] = {}
+            for x in range(tags['spatial_size_y']):
+                for y in range(tags['spatial_size_x']):
+                    tags['spectra'][f'{x}-{y}'] = {}
+                    tags['spectra'][f'{x}-{y}']['spectrum'] = tags['cube'][y, x, :]
+                    tags['spectra'][f'{x}-{y}']['energy_scale'] = tags['energy_scale']
+                    tags['spectra'][f'{x}-{y}']['intensity_scale'] = 1 / tags['cube'][y, x, :].sum() * 1e6
+            tags['ylabel'] = 'inel. scat. int.  [ppm]'
+
+        return tags
+
+    def fix_energy(self):
+
+        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
+        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
+        fwhm, delta_e = eels.fix_energy_scale(spectrum, energy_scale)
+        self.tags['spectra'][f'{self.x}-{self.y}']['delta_e'] = delta_e
+        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm'] = fwhm
+        self.energy_scale = energy_scale - delta_e
+        title = f'spectrum {self.x},{self.y} fwhm: {fwhm:.2f}, dE: {delta_e:.3f}'
+        return title
+
+    def fit_zero_loss(self, plot_this=True):
+
+        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
+        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
+        if 'zero_loss_fit_width' not in self.tags:
+            self.tags['zero_loss_fit_width'] = .5
+        if self.tags['zero_loss_fit_width'] / (energy_scale[1] - energy_scale[0]) < 6:
+            self.tags['zero_loss_fit_width'] = (energy_scale[1] - energy_scale[0]) * 6
+        fwhm, delta_e = eels.fix_energy_scale(spectrum, energy_scale)
+        energy_scale = energy_scale - delta_e
+        z_oss, p_zl = eels.resolution_function(energy_scale, spectrum, self.tags['zero_loss_fit_width'])
+        fwhm2, delta_e2 = eels.fix_energy_scale(z_oss, energy_scale)
+
+        self.tags['spectra'][f'{self.x}-{self.y}']['resolution_function'] = z_oss
+        self.tags['spectra'][f'{self.x}-{self.y}']['p_zl'] = p_zl
+        self.tags['spectra'][f'{self.x}-{self.y}']['delta_e'] = delta_e
+        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm_resolution'] = fwhm2
+        self.tags['spectra'][f'{self.x}-{self.y}']['fwhm'] = fwhm
+
+        if plot_this:
+            self.ax2.plot(energy_scale, z_oss, label='resolution function', color='black')
+            self.ax2.plot(energy_scale, self.spectrum - z_oss, label='difference', color='orange')
+            self.ax2.axhline(linewidth=0.5, color='black')
+        self.energy_scale = energy_scale
+        title = f'spectrum {self.x},{self.y} fwhm: {fwhm:.2f}'  # ', dE: {delta_e2:.5e}'
+        return title
+
+    def fit_quantification(self, plot_this=True):
+        energy_scale = self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale']
+        spectrum = self.tags['spectra'][f'{self.x}-{self.y}']['spectrum'] * self.intensity_scale
+        edges = eels.make_edges(self.tags['edges_present'], energy_scale, self.tags['acceleration_voltage'],
+                                self.tags['collection_angle'])
+        edges = eels.fit_edges(spectrum, self.tags['spectra'][f'{self.x}-{self.y}']['energy_scale'],
+                               self.tags['region_tags'], edges)
+        self.tags['spectra'][f'{self.x}-{self.y}']['edges'] = edges.copy()
+        if plot_this:
+            self.ax2.plot(energy_scale, edges['model']['spectrum'], label='model')
+            self.ax2.plot(energy_scale, self.spectrum - edges['model']['spectrum'], label='difference')
+            self.ax2.axhline(linewidth=0.5, color='black')
+        else:
+            self.tags['spectra'][f'{self.x}-{self.y}']['do_all'] = 'done'
+        title = f'spectrum {self.x},{self.y} '
+
+        for key in edges:
+            if key.isdigit():
+                title = title + f"{edges[key]['element']}:  {edges[key]['areal_density']:.2e};  "
+
+        return title
+
+    def set_legend(self, set_legend):
+        self.plot_legend = set_legend
+
+    def get_xy(self):
+        return [self.x, self.y]
+
+    def get_current_spectrum(self):
+        return self.cube[self.y, self.x, :]
+
+    def set_z_contrast_image(self, z_channel=None):
+        if z_channel is not None:
+            self.tags['Z_contrast_channel'] = z_channel
+        if 'Z_contrast_channel' not in self.tags:
+            print('add Z contrast channel group to dictionary first!')
+            return
+
+        z_tags = {}   # TODO change to sidpy dataset ft.h5_get_dictionary(z_channel)
+        extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
+                  self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
+        self.ax1.imshow(z_tags['data'], extent=extent, cmap='gray')
+
+    def overlay_z_contrast_image(self, z_channel=None):
+
+        if self.SI:
+            if z_channel is not None:
+                self.tags['Z_contrast_channel'] = z_channel
+            if 'Z_contrast_channel' not in self.tags:
+                print('add survey channel group to dictionary first!')
+                return
+
+            z_tags = {}  # TODO: change to sidpy ft.h5_get_dictionary(self.tags['Z_contrast_channel'])
+
+            xlim = self.ax1.get_xlim()
+            ylim = self.ax1.get_ylim()
+            extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
+                      self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
+            self.ax1.imshow(z_tags['data'], extent=extent, cmap='viridis', alpha=0.5)
+            self.ax1.set_ylim(ylim)
+            self.ax1.set_xlim(xlim)
+
+    def overlay_data(self, data=None):
+
+        if self.SI:
+            if data is None:
+                data = self.cube.sum(axis=2)
+
+            xlim = self.ax1.get_xlim()
+            ylim = self.ax1.get_ylim()
+            extent = [self.rectangle[0], self.rectangle[0] + self.rectangle[1],
+                      self.rectangle[2] + self.rectangle[3], self.rectangle[2]]
+            self.ax1.imshow(data, extent=extent, alpha=0.7, cmap='viridis')
+            self.ax1.set_ylim(ylim)
+            self.ax1.set_xlim(xlim)
+
+    def set_survey_image(self, si_channel=None):
+
+        if si_channel is not None:
+            self.tags['survey_channel'] = si_channel
+        if 'survey_channel' not in self.tags:
+            print('add survey channel group to dictionary first!')
+            return
+        si_channel = self.tags['survey_channel']
+        si_tags = {}  # TODO: change to sidpy  ft.h5_get_dictionary(si_channel)
+        tags2 = dict(si_channel.attrs)
+
+        self.ax1.set_aspect('equal')
+        self.scaleX = si_channel['spatial_scale_x'][()]
+        self.scaleY = si_channel['spatial_scale_y'][()]
+
+        self.ax1.imshow(si_tags['data'], extent=si_tags['extent'], cmap='gray')
+        if self.horizontal:
+            self.ax1.set_xlabel('distance [nm]')
+        else:
+            self.ax1.set_ylabel('distance [nm]')
+
+        annotation_done = []
+        for key in tags2:
+            if 'annotations' in key:
+                annotation_number = key[12]
+                if annotation_number not in annotation_done:
+                    annotation_done.append(annotation_number)
+
+                    if tags2['annotations_' + annotation_number + '_type'] == 'text':
+                        x = tags2['annotations_' + annotation_number + '_x']
+                        y = tags2['annotations_' + annotation_number + '_y']
+                        text = tags2['annotations_' + annotation_number + '_text']
+                        self.ax1.text(x, y, text, color='r')
+
+                    elif tags2['annotations_' + annotation_number + '_type'] == 'circle':
+                        radius = 20 * self.scaleX  # tags['annotations'][key]['radius']
+                        xy = tags2['annotations_' + annotation_number + '_position']
+                        circle = patches.Circle(xy, radius, color='r', fill=False)
+                        self.ax1.add_artist(circle)
+
+                    elif tags2['annotations_' + annotation_number + '_type'] == 'spectrum image':
+                        width = tags2['annotations_' + annotation_number + '_width']
+                        height = tags2['annotations_' + annotation_number + '_height']
+                        position = tags2['annotations_' + annotation_number + '_position']
+                        rectangle = patches.Rectangle(position, width, height, color='r', fill=False)
+                        self.rectangle = [position[0], width, position[1], height]
+                        self.ax1.add_artist(rectangle)
+                        self.ax1.text(position[0], position[1], 'Spectrum Image', color='r')
+                        self.rect.set_width(width / self.cube.shape[1])
+                        self.rect.set_height(height / self.cube.shape[0])
+        self.SI = True
+
+
+class ElementalEdges(object):
+    """ Adds ionization edges of element z to plot with axis ax
+
+        There is an optional parameter maximum_chemical_shift which allows to change
+        the energy range in which the edges are searched.
+
+        available functions:
+        - update(): updates the drawing of ionization edges
+        - set_edge(Z) : changes atomic number and updates everything accordingly
+        - disconnect: makes everything invisible and stops drawing
+        - reconnect: undo of disconnect
+
+        usage:
+        >> fig, ax = plt.subplots()
+        >> ax.plot(energy_scale, spectrum)
+        >> Z= 42
+        >> cursor = ElementalEdges(ax, Z)
+
+
+        see Chapter4 'CH4-Working_with_X-Sections' notebook
+    """
+
+    def __init__(self, ax, z):
+        self.ax = ax
+        self.labels = None
+        self.lines = None
+        self.Z = eels.get_z(z)
+        self.color = 'black'
+        self.x_sections = eels.get_x_sections()
+        self.cid = ax.figure.canvas.mpl_connect('draw_event', self.onresize)
+        # self.update() is not necessary because of a drawing event is issued
+
+    def set_edge(self, z):
+        self.Z = eels.get_z(z)
+        if self.cid is None:
+            self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.onresize)
+        self.update()
+
+    def onresize(self, event):
+        self.update()
+
+    def update(self):
+        if self.labels is not None:
+            for label in self.labels:
+                label.remove()
+        if self.lines is not None:
+            for line in self.lines:
+                line.remove()
+        self.labels = []
+        self.lines = []
+        x_min, x_max = self.ax.get_xlim()
+        y_min, y_max = self.ax.get_ylim()
+
+        element = str(self.Z)
+        x_sections = self.x_sections
+        for key in all_edges:
+            if key in x_sections[element] and 'onset' in x_sections[element][key]:
+                x = x_sections[element][key]['onset']
+                if x_min < x < x_max:
+                    if key in first_close_edges:
+                        label2 = self.ax.text(x, y_max, f"{x_sections[element]['name']}-{key}",
+                                              verticalalignment='top', rotation=0, color=self.color)
+                    else:
+                        label2 = self.ax.text(x, y_max, f"\n{x_sections[element]['name']}-{key}",
+                                              verticalalignment='top', color=self.color)
+                    line2 = self.ax.axvline(x, ymin=0, ymax=1, color=self.color)
+
+                    self.labels.append(label2)
+                    self.lines.append(line2)
+
+    def reconnect(self):
+        self.cid = self.ax.figure.canvas.mpl_connect('draw_event', self.onresize)
+        self.update()
+
+    def disconnect(self):
+        if self.labels is not None:
+            for label in self.labels:
+                label.remove()
+        if self.lines is not None:
+            for line in self.lines:
+                line.remove()
+        self.labels = None
+        self.lines = None
+        self.ax.figure.canvas.mpl_disconnect(self.cid)
+
+
+class EdgesAtCursor(object):
+    """
+        Adds a Cursor to a plot, which plots all major (possible) ionization edges at
+        the cursor location if left (right) mouse button is clicked.
+
+        Attributes
+        ----------
+        ax: matplotlib axis
+        x: numpy array
+            energy_scale of spectrum
+        y: numpy array
+            intensities of spectrum
+        maximal_chemical_shift: float
+            optional parameter maximum_chemical_shift which allows to change the energy range in which the edges
+            are searched.
+
+        Example
+        -------
+        fig, ax = plt.subplots()
+        ax.plot(energy_scale, spectrum)
+        cursor = EdgesAtCursor(ax, energy_scale, spectrum)
+
+        see Chapter4 'CH4-Working_with_X-Sections' notebook
+
+    """
+
+    def __init__(self, ax, x, y, maximal_chemical_shift=5):
+        self.ax = ax
+        self.ly = ax.axvline(x[0], color='k', alpha=0.2)  # the vert line
+        self.marker, = ax.plot(x[0], y[0], marker="o", color="crimson", zorder=3)
+        self.x = x
+        self.y = y
+        self.txt = ax.text(0.7, 0.9, '', verticalalignment='bottom')
+        self.select = 0
+        self.label = None
+        self.line = None
+        self.cid = ax.figure.canvas.mpl_connect('button_press_event', self.click)
+        self.mouse_cid = ax.figure.canvas.mpl_connect('motion_notify_event', self.mouse_move)
+        self.maximal_chemical_shift = maximal_chemical_shift
+
+    def click(self, event):
+
+        # print('click', event)
+        if not event.inaxes:
+            return
+        x, y = event.xdata, event.ydata
+
+        index = np.searchsorted(self.x, [x])[0]
+        x = self.x[index]
+        y = self.y[index]
+        self.select = x
+
+        y_min, y_max = self.ax.get_ylim()
+
+        if self.label is not None:
+            self.label.remove()
+            self.line.remove()
+        if event.button == 1:
+            self.label = self.ax.text(x, y_max, eels.find_all_edges(event.xdata, self.maximal_chemical_shift, major_edges_only=True),
+                                      verticalalignment='top')
+            self.line, = self.ax.plot([x, x], [y_min, y_max], color='black')
+        if event.button == 3:
+            self.line, = self.ax.plot([x, x], [y_min, y_max], color='black')
+            self.label = self.ax.text(x, y_max, eels.find_all_edges(event.xdata, self.maximal_chemical_shift), verticalalignment='top')
+        self.ax.set_ylim(y_min, y_max)
+
+    def mouse_move(self, event):
+        if not event.inaxes:
+            return
+
+        x, y = event.xdata, event.ydata
+        index = np.searchsorted(self.x, [x])[0]
+        x = self.x[index]
+        y = self.y[index]
+        self.select = x
+        self.ly.set_xdata(x)
+        self.marker.set_data([x], [y])
+        self.txt.set_text(f'\n x={x:1.2f}, y={y:1.2g}\n')
+
+        # self.ax.text(x, y*2,find_major_edges(x))
+        self.txt.set_position((x, y))
+        self.ax.figure.canvas.draw_idle()
+
+    def del_edges(self):
+        if self.label is not None:
+            self.label.remove()
+            self.line.remove()
+            self.label = None
+
+    def disconnect(self):
+        self.ly.remove()
+        self.marker.remove()
+        self.txt.remove()
+
+        self.ax.figure.canvas.mpl_disconnect(self.cid)
+        self.ax.figure.canvas.mpl_disconnect(self.mouse_cid)
+
+
+def make_box_layout():
+    return ipywidgets.Layout(border='solid 1px black', margin='0px 10px 10px 0px', padding='5px 5px 5px 5px')
+    
+
+class plot_EELS(ipywidgets.HBox):
+    def __init__(self, dataset):
+        super().__init__()
+        output = ipywidgets.Output()
+        self.dataset = dataset
+        self.spec_dim = 0
+        initial_color = '#FF00DD'
+ 
+        with output:
+            self.fig, self.axis = plt.subplots(constrained_layout=True, figsize=(5, 3.5))
+        
+        self.axis.set_title(dataset.title.split('/')[-1])
+        self.line, = self.axis.plot(dataset.dim_0.values, dataset, lw=2, label='spectrum')
+        legend = self.axis.legend(fancybox=True, shadow=True)
+
+        lines = [self.line]
+        self.line_dictionary = {}  # Will map legend lines to original lines.
+        for legend_line, original_line in zip(legend.get_lines(), lines):
+            legend_line.set_picker(True)  # Enable picking on the legend line.
+            self.line_dictionary[legend_line] = original_line
+        self.ax = self.axis
+        self.fig.canvas.toolbar_position = 'bottom'
+        self.fig.canvas.mpl_connect('pick_event', self.on_legend_pick)
+        
+        # define widgets
+        int_slider = ipywidgets.IntSlider(
+            value=1, 
+            min=0, 
+            max=10, 
+            step=1, 
+            description='freq'
+        )
+        self.offset = ipywidgets.Text(
+            value='0', 
+            width=5,
+            description='offset', 
+            continuous_update=False
+        )
+        self.dispersion = ipywidgets.Text(
+            value='0', 
+            width=5,
+            description='dispersion', 
+            continuous_update=False
+        )
+
+        self.exposure = ipywidgets.Text(
+            value='0', 
+            width=5,
+            description='exposure', 
+            continuous_update=False
+        )
+        
+        button_energy_scale = ipywidgets.Button(description='Cursor')
+        button_elements_at_cursor = ipywidgets.Button(description='Elements Cursor')
+        button_main_elements = ipywidgets.Button(description='Main Elements')
+        
+        controls = ipywidgets.VBox([
+            ipywidgets.HBox([self.offset, ipywidgets.Label('eV')]),
+            ipywidgets.HBox([self.dispersion, ipywidgets.Label('eV/channel')]),
+            ipywidgets.HBox([self.exposure, ipywidgets.Label('s')]),
+            button_energy_scale,
+            ipywidgets.HBox([button_elements_at_cursor, button_main_elements])
+        ])
+            
+        controls.layout = make_box_layout()
+         
+        out_box = ipywidgets.Box([output])
+        output.layout = make_box_layout()
+ 
+        # observe stuff
+        int_slider.observe(self.update, 'value')
+        
+        self.offset.value = f'{self.dataset.dim_0.values[0]}'
+        self.offset.observe(self.set_dimension, 'value')
+        self.offset.value = f'{self.dataset.dim_0.values[0]}'
+        
+        self.dispersion.observe(self.set_dimension, 'value')
+        self.dispersion.value = f'{self.dataset.dim_0.values[1] - self.dataset.dim_0.values[0]}'
+        self.dispersion.value = '0'
+        self.exposure.observe(self.update_exposure, 'value')
+        self.exposure.value = '0'
+ 
+        # add to children
+        self.children = [controls, output]
+        
+    def update(self):
+        """Draw line in plot"""
+        self.line.set_ydata(self.dataset)
+        self.line.set_xdata(self.dataset.dim_0.values)
+        # self.axis.plot(self.dataset.energy_loss, self.dataset)
+        self.fig.canvas.draw()
+        
+    def line_color(self, change):
+        self.line.set_color(change.new)
+        
+    def update_exposure(self):
+        pass
+  
+    def update_ylabel(self, change):
+        self.ax.set_ylabel(change.new)
+    
+    def set_dimension(self, change):
+        self.spec_dim = ft.get_dimensions_by_type('SPECTRAL', self.dataset)
+        self.spec_dim = self.spec_dim[0]
+        old_energy_scale = self.spec_dim[1]
+        energy_scale = np.arange(len(self.dataset.dim_0.values))*float(self.dispersion.value)+float(self.offset.value)
+        self.dataset.set_dimension(self.spec_dim[0], sidpy.Dimension(energy_scale,
+                                                                     name=old_energy_scale.name,
+                                                                     dimension_type='SPECTRAL',
+                                                                     units='eV',
+                                                                     quantity='energy loss'))
+        self.update()
+
+    def on_legend_pick(self, event):
+        legend_line = event.artist
+        original_line = self.line_dictionary[legend_line]
+        visible = not original_line.get_visible()
+        original_line.set_visible(visible)
+        legend_line.set_alpha(1.0 if visible else 0.2)
+        self.fig.canvas.draw()