pyTEMlib 0.2024.2.1__py2.py3-none-any.whl → 0.2024.6.0__py2.py3-none-any.whl

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Files changed (15) hide show
  1. pyTEMlib/core_loss_widget.py +658 -0
  2. pyTEMlib/eels_dialog.py +13 -12
  3. pyTEMlib/eels_dialog_utilities.py +2 -3
  4. pyTEMlib/eels_tools.py +56 -71
  5. pyTEMlib/file_tools.py +12 -5
  6. pyTEMlib/image_tools.py +168 -36
  7. pyTEMlib/info_widget.py +301 -365
  8. pyTEMlib/low_loss_widget.py +176 -0
  9. pyTEMlib/version.py +2 -2
  10. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/METADATA +4 -4
  11. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/RECORD +15 -13
  12. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/WHEEL +1 -1
  13. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/LICENSE +0 -0
  14. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/entry_points.txt +0 -0
  15. {pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/top_level.txt +0 -0
pyTEMlib/low_loss_widget.py ADDED
@@ -0,0 +1,176 @@
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+ from typing import Any
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+
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+ import numpy as np
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+ import os
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+ import ipywidgets
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+ import matplotlib.pylab as plt
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+ import matplotlib
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+ from IPython.display import display
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+
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+ import sidpy
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+ # from pyTEMlib.microscope import microscope
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+ from pyTEMlib import file_tools
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+ from pyTEMlib import eels_tools
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+
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+
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+ def get_low_loss_sidebar() -> Any:
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+ side_bar = ipywidgets.GridspecLayout(9, 3, width='auto', grid_gap="0px")
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+
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+ side_bar[0, :2] = ipywidgets.Dropdown(
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+ options=[('None', 0)],
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+ value=0,
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+ description='Main Dataset:',
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+ disabled=False)
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+
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+ row = 1
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+
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+ side_bar[row, :3] = ipywidgets.Button(description='Resolution Function',
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+ layout=ipywidgets.Layout(width='auto', grid_area='header'),
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+ style=ipywidgets.ButtonStyle(button_color='lightblue'))
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+ row += 1
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+ side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='fit width:', disabled=False, color='black',
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+ layout=ipywidgets.Layout(width='200px'))
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+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
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+ row +=1
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+ side_bar[row, 0] = ipywidgets.widgets.Label(value="thickness", layout=ipywidgets.Layout(width='100px'))
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+ side_bar[row, 1] = ipywidgets.widgets.Label(value="", layout=ipywidgets.Layout(width='100px'))
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+ side_bar[row, 2] = ipywidgets.widgets.Label(value="* iMFP", layout=ipywidgets.Layout(width='100px'))
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+ row +=1
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+ side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Res.Fct.',
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+ disabled=False,
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+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
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+ tooltip='Plots resolution function on right',
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+ layout=ipywidgets.Layout(width='100px'))
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+
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+ side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
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+ disabled=False,
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+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
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+ tooltip='Changes y-axis to probability if flux is given',
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+ layout=ipywidgets.Layout(width='100px'))
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+
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+
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+ row += 1
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+ side_bar[row, :3] = ipywidgets.Button(description='Drude',
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+ layout=ipywidgets.Layout(width='auto', grid_area='header'),
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+ style=ipywidgets.ButtonStyle(button_color='lightblue'))
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+ row += 1
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+ side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Start Fit:', disabled=False, color='black',
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+ layout=ipywidgets.Layout(width='200px'))
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+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
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+ row += 1
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+ side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='End Fit:', disabled=False, color='black',
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+ layout=ipywidgets.Layout(width='200px'))
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+ side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
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+ row +=1
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+ side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Drude',
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+ disabled=False,
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+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
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+ tooltip='Plots resolution function on right',
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+ layout=ipywidgets.Layout(width='100px'))
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+
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+ side_bar[row, 2] = ipywidgets.ToggleButton(description='Plot Diel.Fct.',
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+ disabled=False,
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+ button_style='', # 'success', 'info', 'warning', 'danger' or ''
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+ tooltip='Changes y-axis to probability if flux is given',
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+ layout=ipywidgets.Layout(width='100px'))
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+
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+
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+ return side_bar
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+
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+ class LowLoss(object):
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+ def __init__(self, sidebar=None, parent=None):
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+ self.parent = parent
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+ self.dataset = parent.dataset
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+ self.low_loss_tab = sidebar
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+ self.set_ll_action()
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+ self.update_ll_sidebar()
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+
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+ def update_ll_sidebar(self):
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+ spectrum_list = ['None']
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+ for index, key in enumerate(self.parent.datasets.keys()):
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+ if isinstance(self.parent.datasets[key], sidpy.Dataset):
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+ if 'SPECTR' in self.parent.datasets[key].data_type.name:
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+ energy_offset = self.parent.datasets[key].get_spectral_dims(return_axis=True)[0][0]
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+ if energy_offset < 0:
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+ spectrum_list.append(f'{key}: {self.parent.datasets[key].title}')
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+
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+ self.low_loss_tab[0, 0].options = spectrum_list
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+
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+ def get_resolution_function(self, value):
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+ self.low_loss_tab[4, 0].value = False
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+ zero_loss_fit_width=self.low_loss_tab[2, 0].value
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+ self.parent.datasets['resolution_functions'] = eels_tools.get_resolution_functions(self.parent.dataset,
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+ startFitEnergy=-zero_loss_fit_width,
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+ endFitEnergy=zero_loss_fit_width)
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+ if 'low_loss' not in self.dataset.metadata:
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+ self.dataset.metadata['zero_loss'] = {}
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+ self.dataset.metadata['zero_loss'].update(self.parent.datasets['resolution_functions'].metadata['zero_loss'])
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+ self.low_loss_tab[4, 0].value = True
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+ self.low_loss_tab[3, 1].value = f"{np.log(self.parent.dataset.sum()/self.parent.datasets['resolution_functions'].sum())}"
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+
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+
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+
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+ def set_ll_action(self):
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+ self.low_loss_tab[0, 0].observe(self.update_ll_dataset)
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+ #self.low_loss_tab[1, 0].on_click(self.fix_energy_scale)
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+ #self.low_loss_tab[2, 0].observe(self.set_energy_scale, names='value')
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+ #self.low_loss_tab[3, 0].observe(self.set_energy_scale, names='value')
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+ self.low_loss_tab[1, 0].on_click(self.get_resolution_function)
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+ self.low_loss_tab[4, 2].observe(self.parent.info.set_y_scale, names='value')
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+ self.low_loss_tab[4, 0].observe(self._update, names='value')
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+
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+ def _update(self, ev=0):
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+ self.parent._update(ev)
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+
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+ if self.low_loss_tab[4, 0].value:
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+ if 'resolution_functions' in self.parent.datasets:
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+ resolution_function = self.get_additional_spectrum('resolution_functions')
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+ self.parent.axis.plot(self.parent.energy_scale, resolution_function, label='resolution_function')
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+ self.parent.axis.plot(self.parent.energy_scale,
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+ self.parent.spectrum -resolution_function, label='difference')
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+
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+ self.parent.axis.legend()
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+
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+ def get_additional_spectrum(self, key):
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+ if key not in self.parent.datasets.keys():
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+ return
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+
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+ if self.parent.datasets[key].data_type == sidpy.DataType.SPECTRUM:
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+ self.spectrum = self.parent.datasets[key].copy()
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+ else:
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+ image_dims = self.parent.datasets[key].get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
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+ selection = []
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+ for dim, axis in self.parent.datasets[key]._axes.items():
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+ # print(dim, axis.dimension_type)
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+ if axis.dimension_type == sidpy.DimensionType.SPATIAL:
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+ if dim == image_dims[0]:
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+ selection.append(slice(self.x, self.x + self.bin_x))
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+ else:
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+ selection.append(slice(self.y, self.y + self.bin_y))
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+
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+ elif axis.dimension_type == sidpy.DimensionType.SPECTRAL:
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+ selection.append(slice(None))
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+ elif axis.dimension_type == sidpy.DimensionType.CHANNEL:
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+ selection.append(slice(None))
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+ else:
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+ selection.append(slice(0, 1))
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+
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+ self.spectrum = self.parent.datasets[key][tuple(selection)].mean(axis=tuple(image_dims))
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+
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+ self.spectrum *= self.parent.y_scale
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+
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+ return self.spectrum.squeeze()
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+
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+ def update_ll_dataset(self, value=0):
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+ self.ll_key = self.low_loss_tab[0, 0].value.split(':')[0]
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+ self.parent.set_dataset(self.ll_key)
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+ self.dataset = self.parent.dataset
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+
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+
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+ def set_binning(self, value):
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+ if 'SPECTRAL' in self.dataset.data_type.name:
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+ bin_x = self.info_tab[15, 0].value
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+ bin_y = self.info_tab[16, 0].value
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+ self.dataset.view.set_bin([bin_x, bin_y])
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+ self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
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+ self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y
pyTEMlib/version.py CHANGED
@@ -1,6 +1,6 @@
1
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  """
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  version
3
3
  """
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- _version = '0.2024.02.1'
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+ _version = '0.2024.06.0'
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  __version__ = _version
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- _time = '2024-02-18 19:58:26'
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+ _time = '2024-06-10 19:58:26'
{pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
2
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  Name: pyTEMlib
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- Version: 0.2024.2.1
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+ Version: 0.2024.6.0
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  Summary: pyTEM: TEM Data Quantification library through a model-based approach
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  Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
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  Author: Gerd Duscher
@@ -38,9 +38,9 @@ Requires-Dist: ipympl
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  Requires-Dist: spglib
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  Requires-Dist: scikit-image
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  Requires-Dist: scikit-learn
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- Requires-Dist: pyNSID >=0.0.7
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- Requires-Dist: sidpy >=0.12.1
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- Requires-Dist: SciFiReaders >=0.0.8
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+ Requires-Dist: pyNSID>=0.0.7
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+ Requires-Dist: sidpy>=0.12.1
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+ Requires-Dist: SciFiReaders>=0.0.8
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44
 
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  pyTEMlib
46
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  ========
{pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/RECORD RENAMED
@@ -2,34 +2,36 @@ pyTEMlib/__init__.py,sha256=nEN93amIEoZxO7rJgN71ABeCoXrnmaywBbE97l5lPio,178
2
2
  pyTEMlib/animation.py,sha256=oPxbTuy8LfdH2mOOgm9Q40ArFAJmXM_58UV97ptcNAY,25187
3
3
  pyTEMlib/atom_tools.py,sha256=ViO4ZZZoCZ_Cp2KijiqKKOiQhGOWnye45T0rsiPhf4I,7314
4
4
  pyTEMlib/config_dir.py,sha256=4evlo9P2Yht-AnqaLI-WweLjDQcislbAP3I7P7EZsPU,2085
5
+ pyTEMlib/core_loss_widget.py,sha256=BPGGNcYkdiX3pIfe600ERVAJjUHw5C2BA7idroP1pgU,29746
5
6
  pyTEMlib/crystal_tools.py,sha256=g4OXyvd5NLw7vaXhjDP3P6VZpVV6eiyuPn8MdgR2amI,61652
6
7
  pyTEMlib/diffraction_plot.py,sha256=pM5d3bdBGa8LlPZ5lw8sLT94mlYTXELxPLv-jUP2FWY,27959
7
8
  pyTEMlib/dynamic_scattering.py,sha256=O9MxnxfndWJ2VhQRjksKNQ4yY7y-gN_hitRQ4Qox4ns,9472
8
9
  pyTEMlib/eds_tools.py,sha256=34YYoix9rhq0aYnZrHVi0A8gQeu9XZ9fGGT0VxPQo8Y,24882
9
- pyTEMlib/eels_dialog.py,sha256=x5AOe2SjL4R8aR6X92HOWdC9mL0M-jKtSiNfR-SHQr8,32327
10
- pyTEMlib/eels_dialog_utilities.py,sha256=srkRvRDUWIzN38EWNGRWimsJLK4YXSnGEfL6Dd1V3IY,51778
11
- pyTEMlib/eels_tools.py,sha256=pzsiMY-1ZXth5ZIrPaRNOs6R3gMAyZr8TVYf-Lxnn5Y,77781
12
- pyTEMlib/file_tools.py,sha256=RqYPMAkz7pNorvTUhazXk7aQltjOvQPqo_PhA9Iz-Bw,46371
10
+ pyTEMlib/eels_dialog.py,sha256=oWLivCQ96Fq0tj52wbfs-5qKccUSWk2k1iP2TVneXZA,32379
11
+ pyTEMlib/eels_dialog_utilities.py,sha256=73W9jFbPx-eeLEiSaBptTgGLr40bIYYfSyzLnZbhfvo,51761
12
+ pyTEMlib/eels_tools.py,sha256=O22WENQ04fCfVvI4ktJdx6GfE8ZSNb-E6dAu4ZbfHqw,76041
13
+ pyTEMlib/file_tools.py,sha256=UScJenVk73MZUW-laoKymnO27eCUC0vlRxxlQ4Kq2Hg,46923
13
14
  pyTEMlib/file_tools_qt.py,sha256=tLZACS4JyGH_AOzNR_SGAhjA01y4VJB261opPhGMlm8,7223
14
15
  pyTEMlib/graph_tools.py,sha256=iu0Y2hIPU6CkQHQEh-dI1vKnUHnSNXx4-CXs2M-1Sr8,44097
15
16
  pyTEMlib/graph_viz.py,sha256=m5PwSn6l2r0bsaLWBDSHc9IGR3_PneG2BrZgnEdi07I,13644
16
17
  pyTEMlib/image_dialog.py,sha256=F-ZgKq7UnMtPPd1b9eqb7t8MXDfWN-8hVKwB2Il0x28,6235
17
18
  pyTEMlib/image_dlg.py,sha256=n5gradDiYOFGEQ3k_Wlk9RUYYzl4bl_hKLzNVcYteNE,5694
18
- pyTEMlib/image_tools.py,sha256=IoRBmKsL6o4V9xGAKoSUV0hOJhr0QXIPCbEiAPWLOq0,43231
19
- pyTEMlib/info_widget.py,sha256=G8MArXYI_xdvRY3cD7-3UxUjczEUWPjlrGJOj2BKU2Y,49903
19
+ pyTEMlib/image_tools.py,sha256=PU13i2KgKVoAf_NyCRdCGTfb6c42UZqprmgJ9zthMCw,48970
20
+ pyTEMlib/info_widget.py,sha256=wd1F6UDcLMsWEg1DHHVPa1P7_MRGv8iLOUjRsYkZOQY,46453
20
21
  pyTEMlib/interactive_image.py,sha256=5PwypcA1OjLAD-fi8bmWWFHuOjdIPVY9Dh59V24WuDA,34
21
22
  pyTEMlib/kinematic_scattering.py,sha256=CUdJnclkok7d8qm_jDUF92MVHrmaTeMkKdvxxB6AqvA,43309
23
+ pyTEMlib/low_loss_widget.py,sha256=nSU6-pu7gP8ch61w2wpImNNIuo_3bBN1HAB3UVlEJoQ,9043
22
24
  pyTEMlib/microscope.py,sha256=iigUF1UImHEfmL2wqEBBj3aNRgEYouDbIln8VCo4_KM,1545
23
25
  pyTEMlib/peak_dialog.py,sha256=-HhgmoscfJMme9N495hDzfniYwuhn7iBzsDwZOOhTd4,48260
24
26
  pyTEMlib/peak_dlg.py,sha256=qcjcnhwpGa4jBCeXzwQz9sCyX-tHsLLQ67ToqfKOiQY,11550
25
27
  pyTEMlib/probe_tools.py,sha256=8tPQuANClLsGAKnZo6Vo4gNIGKfyDR6WUMO3dXcm_4k,27177
26
28
  pyTEMlib/sidpy_tools.py,sha256=0oIx-qMtEmcZmLazQKW19dd-KoxyY3B15aIeMcyHA8E,4878
27
29
  pyTEMlib/simulation_tools.py,sha256=RmegD5TpQMU68uASvzZWVplAqs7bM5KkF6bWDWLjyc0,2799
28
- pyTEMlib/version.py,sha256=MZcxHaXQNxHcqfqpaIveaRQuHCBQUOgbj06fYbRsGHk,94
30
+ pyTEMlib/version.py,sha256=eTxYL1VM1SZB6XwKQ7HgZ3bzXDIpG0PDiLYHW8AqAyw,94
29
31
  pyTEMlib/xrpa_x_sections.py,sha256=peb2pozcH0T-3zlWITx-5rdyeoP2YhOfBpwsWD1-4T4,1813751
30
- pyTEMlib-0.2024.2.1.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
31
- pyTEMlib-0.2024.2.1.dist-info/METADATA,sha256=x-LlDmscwdMmOeVPFlS0sNkjHKs5c9ElaCEbNRMk2zg,3306
32
- pyTEMlib-0.2024.2.1.dist-info/WHEEL,sha256=-G_t0oGuE7UD0DrSpVZnq1hHMBV9DD2XkS5v7XpmTnk,110
33
- pyTEMlib-0.2024.2.1.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
34
- pyTEMlib-0.2024.2.1.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
35
- pyTEMlib-0.2024.2.1.dist-info/RECORD,,
32
+ pyTEMlib-0.2024.6.0.dist-info/LICENSE,sha256=7HdBF6SXIBd38bHOKkQd4DYR1KV-OYm9mwB16fM-984,1062
33
+ pyTEMlib-0.2024.6.0.dist-info/METADATA,sha256=5wU66BPQnYNIQK_7KmkB3N_dDgzahaDzk9L41GaB6CM,3303
34
+ pyTEMlib-0.2024.6.0.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
35
+ pyTEMlib-0.2024.6.0.dist-info/entry_points.txt,sha256=qiIFPP3ffSz-gxj-TowzbA0Setq5Lo0RJTVtSrqD1IY,44
36
+ pyTEMlib-0.2024.6.0.dist-info/top_level.txt,sha256=rPLVH0UJxrPSPgSoKScTjL1K_X69JFzsYYnDnYTYIlU,9
37
+ pyTEMlib-0.2024.6.0.dist-info/RECORD,,
{pyTEMlib-0.2024.2.1.dist-info → pyTEMlib-0.2024.6.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.42.0)
2
+ Generator: bdist_wheel (0.44.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any