pyTEMlib 0.2023.8.0__py2.py3-none-any.whl → 0.2024.2.0__py2.py3-none-any.whl
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- pyTEMlib/config_dir.py +0 -1
- pyTEMlib/crystal_tools.py +22 -26
- pyTEMlib/eds_tools.py +499 -46
- pyTEMlib/eels_dialog.py +284 -899
- pyTEMlib/eels_dialog_utilities.py +218 -341
- pyTEMlib/eels_tools.py +1526 -1583
- pyTEMlib/file_tools.py +52 -48
- pyTEMlib/graph_tools.py +3 -4
- pyTEMlib/image_tools.py +171 -41
- pyTEMlib/info_widget.py +618 -276
- pyTEMlib/kinematic_scattering.py +77 -512
- pyTEMlib/peak_dialog.py +162 -288
- pyTEMlib/version.py +2 -2
- pyTEMlib/xrpa_x_sections.py +173 -97
- {pyTEMlib-0.2023.8.0.dist-info → pyTEMlib-0.2024.2.0.dist-info}/LICENSE +1 -1
- {pyTEMlib-0.2023.8.0.dist-info → pyTEMlib-0.2024.2.0.dist-info}/METADATA +2 -2
- pyTEMlib-0.2024.2.0.dist-info/RECORD +35 -0
- {pyTEMlib-0.2023.8.0.dist-info → pyTEMlib-0.2024.2.0.dist-info}/WHEEL +1 -1
- pyTEMlib/eels_dlg.py +0 -252
- pyTEMlib/info_dialog.py +0 -665
- pyTEMlib/info_dlg.py +0 -239
- pyTEMlib/interactive_eels.py +0 -35
- pyTEMlib/viz.py +0 -481
- pyTEMlib-0.2023.8.0.dist-info/RECORD +0 -40
- {pyTEMlib-0.2023.8.0.dist-info → pyTEMlib-0.2024.2.0.dist-info}/entry_points.txt +0 -0
- {pyTEMlib-0.2023.8.0.dist-info → pyTEMlib-0.2024.2.0.dist-info}/top_level.txt +0 -0
pyTEMlib/info_widget.py
CHANGED
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@@ -1,22 +1,20 @@
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import sidpy
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from typing import Any
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import
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import
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from pyTEMlib.microscope import microscope
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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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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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def get_info_sidebar() -> Any:
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side_bar = ipywidgets.GridspecLayout(18, 3, width='auto', grid_gap="0px")
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side_bar[0, :2] = ipywidgets.Dropdown(
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options=[('None', 0)],
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@@ -26,116 +24,243 @@ def get_info_sidebar():
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row = 1
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side_bar[row, :3] = ipywidgets.Button(description='Energy Scale',
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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='Offset:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Offset:', 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='20px'))
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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', 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='20px'))
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row += 1
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side_bar[row, :3] = ipywidgets.Button(description='Microscope',
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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='Conv.Angle:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Conv.Angle:', 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="mrad", layout=ipywidgets.Layout(width='100px'))
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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Coll.Angle:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Coll.Angle:', 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="mrad", layout=ipywidgets.Layout(width='100px'))
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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Acc Voltage:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Acc Voltage:', 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="keV", layout=ipywidgets.Layout(width='100px'))
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row += 1
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side_bar[row, :3] = ipywidgets.Button(description='Calibration',
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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, :3] = ipywidgets.Button(description='Quantification',
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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.Dropdown(
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options=[('None', 0)],
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value=0,
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description='Reference:',
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disabled=False)
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side_bar[row,2] = ipywidgets.ToggleButton(
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row
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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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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Exp_Time:', 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="s", 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='Flux:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Flux:', 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="Mcounts", layout=ipywidgets.Layout(width='50px'))
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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', 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="e⁻/counts", layout=ipywidgets.Layout(width='100px'))
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row += 1
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', 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="pA", layout=ipywidgets.Layout(width='100px'))
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row += 1
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side_bar[row, 0] = ipywidgets.Button(description='Get Shift', disabled=True,
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layout=ipywidgets.Layout(width='auto'),
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style=ipywidgets.ButtonStyle(button_color='lightblue'))
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side_bar[row, 1] = ipywidgets.Button(description='Shift Spec', disabled=True,
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layout=ipywidgets.Layout(width='auto'),
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style=ipywidgets.ButtonStyle(button_color='lightblue'))
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side_bar[row, 2] = ipywidgets.Button(description='Res.Fct.', disabled=True,
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layout=ipywidgets.Layout(width='auto'),
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style=ipywidgets.ButtonStyle(button_color='lightblue'))
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row += 1
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side_bar[row, :3] = ipywidgets.Button(description='Spectrum Image',
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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.IntText(value=1, description='bin X:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
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layout=ipywidgets.Layout(width='200px'))
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row += 1
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side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
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side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
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layout=ipywidgets.Layout(width='200px'))
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for i in range(
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for i in range(15, 18):
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side_bar[i, 0].layout.display = "none"
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return side_bar
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def get_file_widget_ui():
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side_bar = ipywidgets.GridspecLayout(6, 3, height='500px', width='auto', grid_gap="0px")
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row = 0
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side_bar[row, :3] = ipywidgets.Dropdown(options=['None'], value='None', description='directory:', disabled=False,
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button_style='', layout=ipywidgets.Layout(width='auto', grid_area='header'))
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row += 1
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side_bar[row, :3] = ipywidgets.Select(options=['.'], value='.', description='Select file:', disabled=False,
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rows=10, layout=ipywidgets.Layout(width='auto'))
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row += 1
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side_bar[row, 0] = ipywidgets.Button(description='Select Main',
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layout=ipywidgets.Layout(width='100px'),
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style=ipywidgets.ButtonStyle(button_color='lightblue'))
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side_bar[row, 1] = ipywidgets.Button(description='Add',
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layout=ipywidgets.Layout(width='50px'),
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style=ipywidgets.ButtonStyle(button_color='lightblue'))
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side_bar[row, 2] = ipywidgets.Dropdown(options=['None'], value='None', description='loaded:', disabled=False,
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button_style='')
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row += 1
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side_bar[row, :3] = ipywidgets.Select(options=['None'], value='None', description='Spectral:',
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disabled=False, rows=3, layout=ipywidgets.Layout(width='auto'))
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row += 1
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side_bar[row, :3] = ipywidgets.Select(options=['Sum'], value='Sum', description='Images:',
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disabled=False, rows=3, layout=ipywidgets.Layout(width='auto'))
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row += 1
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side_bar[row, :3] = ipywidgets.Select(options=['None'], value='None', description='Survey:',
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disabled=False, rows=2, layout=ipywidgets.Layout(width='auto'))
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for i in range(3, 6):
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side_bar[i, 0].layout.display = "none"
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return side_bar
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class EELSWidget(object):
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def __init__(self, datasets, sidebar, tab_title=None):
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self.datasets = datasets
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self.dataset = None
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self.save_path = False
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self.dir_dictionary = {}
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self.dir_list = ['.', '..']
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self.display_list = ['.', '..']
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self.dataset_list = ['None']
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self.image_list = ['Sum']
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self.dir_name = file_tools.get_last_path()
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self.save_path = True
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if not os.path.isdir(self.dir_name):
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self.dir_name = '.'
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self.get_directory(self.dir_name)
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self.dir_list = ['.']
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self.extensions = '*'
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self.file_name = ''
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self.datasets = {}
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self.dataset = None
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self.bin_x = 0
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self.bin_y = 0
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self.start_channel = -1
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self.end_channel = -2
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self.file_bar = get_file_widget_ui()
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if isinstance(sidebar, dict):
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tab = ipywidgets.Tab()
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children = [self.file_bar]
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titles = ['File']
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for sidebar_key, sidebar_gui in sidebar.items():
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children.append(sidebar_gui)
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titles.append(sidebar_key)
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tab.children = children
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tab.titles = titles
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elif not isinstance(sidebar, list):
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tab = ipywidgets.Tab()
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tab.children = [
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tab.titles = ['
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tab.children = [self.file_bar, sidebar]
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tab.titles = ['File', 'Info']
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else:
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tab = sidebar
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self.sidebar = sidebar
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with plt.ioff():
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self.figure = plt.figure()
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self.figure.canvas.toolbar_position = 'right'
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self.figure.canvas.toolbar_visible = True
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self.start_cursor = ipywidgets.FloatText(value=0, description='Start:', disabled=False, color='black',
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self.
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self.start_cursor = ipywidgets.FloatText(value=0, description='Start:', disabled=False, color='black',
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layout=ipywidgets.Layout(width='200px'))
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self.end_cursor = ipywidgets.FloatText(value=0, description='End:', disabled=False, color='black',
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layout=ipywidgets.Layout(width='200px'))
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self.panel = ipywidgets.VBox([ipywidgets.HBox([ipywidgets.Label('', layout=ipywidgets.Layout(width='100px')),
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ipywidgets.Label('Cursor:'),
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self.start_cursor, ipywidgets.Label('eV'),
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self.end_cursor, ipywidgets.Label('eV')]),
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self.figure.canvas])
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self.axis.set_ylabel(self.datasets[self.key].data_descriptor)
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self.axis.ticklabel_format(style='sci', scilimits=(-2, 4))
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# if scale:
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# self.axis.set_ylim(np.array(y_limit)*self.change_y_scale)
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self.axis.set_ylabel('scattering probability (ppm/eV)')
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props=dict(facecolor='blue', alpha=0.2))
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def _update(self, ev=None):
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if hasattr(self, 'axes'):
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xlim = np.array(self.axes[1].get_xlim())
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ylim = np.array(self.axes[1].get_ylim())
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self.axes[1].clear()
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self.axis = self.axes[-1]
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else:
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xlim = np.array(self.axis.get_xlim())
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ylim = np.array(self.axis.get_ylim())
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self.axis.clear()
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self.get_spectrum()
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if len(self.energy_scale)!=self.spectrum.shape[0]:
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if len(self.energy_scale) != self.spectrum.shape[0]:
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self.spectrum = self.spectrum.T
|
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self.
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self.axis.plot(self.energy_scale, self.spectrum.compute(), label='experiment')
|
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314
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self.
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self.axis.set_title(f'spectrum {self.x}, {self.y}')
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self.figure.tight_layout()
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self.selector = matplotlib.widgets.SpanSelector(self.axis, self.line_select_callback,
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self.
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self.
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self.
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self.
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318
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+
direction="horizontal",
|
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+
interactive=True,
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+
props=dict(facecolor='blue', alpha=0.2))
|
|
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+
|
|
322
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+
self.axis.set_xlim(xlim)
|
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323
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+
self.axis.set_ylim(ylim*self.change_y_scale)
|
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324
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+
self.axis.set_xlabel(self.xlabel)
|
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325
|
+
self.axis.set_ylabel(self.ylabel)
|
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326
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self.change_y_scale = 1.0
|
|
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327
|
self.figure.canvas.draw_idle()
|
|
197
328
|
|
|
@@ -208,7 +339,7 @@ class EELSWidget(object):
|
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208
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if x <= self.rectangle[1] and y <= self.rectangle[3]:
|
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|
self.x = int(x / (self.rect.get_width() / self.bin_x))
|
|
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|
self.y = int(y / (self.rect.get_height() / self.bin_y))
|
|
211
|
-
image_dims = self.dataset.
|
|
342
|
+
image_dims = self.dataset.get_image_dims()
|
|
212
343
|
|
|
213
344
|
if self.x + self.bin_x > self.dataset.shape[image_dims[0]]:
|
|
214
345
|
self.x = self.dataset.shape[image_dims[0]] - self.bin_x
|
|
@@ -234,7 +365,7 @@ class EELSWidget(object):
|
|
|
234
365
|
self.axis.set_ylim(bottom=bottom, top=top)
|
|
235
366
|
|
|
236
367
|
def get_spectrum(self):
|
|
237
|
-
if self.dataset.data_type ==
|
|
368
|
+
if self.dataset.data_type.name == 'SPECTRUM':
|
|
238
369
|
self.spectrum = self.dataset.copy()
|
|
239
370
|
else:
|
|
240
371
|
image_dims = self.dataset.get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
|
|
@@ -245,7 +376,6 @@ class EELSWidget(object):
|
|
|
245
376
|
selection = []
|
|
246
377
|
self.axis.clear()
|
|
247
378
|
for dim, axis in self.dataset._axes.items():
|
|
248
|
-
# print(dim, axis.dimension_type)
|
|
249
379
|
if axis.dimension_type == sidpy.DimensionType.SPATIAL:
|
|
250
380
|
if dim == image_dims[0]:
|
|
251
381
|
selection.append(slice(self.x, self.x + self.bin_x))
|
|
@@ -260,7 +390,7 @@ class EELSWidget(object):
|
|
|
260
390
|
selection.append(slice(0, 1))
|
|
261
391
|
|
|
262
392
|
self.spectrum = self.dataset[tuple(selection)].mean(axis=tuple(image_dims))
|
|
263
|
-
|
|
393
|
+
|
|
264
394
|
self.spectrum *= self.y_scale
|
|
265
395
|
|
|
266
396
|
return self.spectrum.squeeze()
|
|
@@ -269,24 +399,13 @@ class EELSWidget(object):
|
|
|
269
399
|
self.axes = self.figure.subplots(ncols=2)
|
|
270
400
|
self.axis = self.axes[-1]
|
|
271
401
|
|
|
272
|
-
|
|
273
|
-
if len(spec_dim) != 1:
|
|
274
|
-
raise ValueError('Only one spectral dimension')
|
|
275
|
-
|
|
276
|
-
channel_dim = self.dataset.get_dimensions_by_type(sidpy.DimensionType.CHANNEL)
|
|
277
|
-
channel_dim =[]
|
|
278
|
-
if len(channel_dim) > 1:
|
|
279
|
-
raise ValueError('Maximal one channel dimension')
|
|
280
|
-
|
|
281
|
-
if len(channel_dim) > 0:
|
|
282
|
-
self.image = self.dataset.mean(axis=(spec_dim[0] ,channel_dim[0]))
|
|
283
|
-
else:
|
|
284
|
-
self.image = self.dataset.mean(axis=(spec_dim[0]))
|
|
285
|
-
|
|
402
|
+
self.set_image()
|
|
286
403
|
self.rect = matplotlib.patches.Rectangle((0, 0), self.bin_x, self.bin_y, linewidth=1, edgecolor='r',
|
|
287
|
-
|
|
288
|
-
|
|
289
|
-
|
|
404
|
+
facecolor='red', alpha=0.2)
|
|
405
|
+
image_dims = self.dataset.get_image_dims()
|
|
406
|
+
|
|
407
|
+
size_x = self.dataset.shape[image_dims[0]]
|
|
408
|
+
size_y = self.dataset.shape[image_dims[1]]
|
|
290
409
|
self.extent = [0, size_x, size_y, 0]
|
|
291
410
|
self.rectangle = [0, size_x, 0, size_y]
|
|
292
411
|
self.axes[0].imshow(self.image.T, extent=self.extent)
|
|
@@ -294,33 +413,42 @@ class EELSWidget(object):
|
|
|
294
413
|
self.axes[0].add_patch(self.rect)
|
|
295
414
|
self.cid = self.axes[0].figure.canvas.mpl_connect('button_press_event', self._onclick)
|
|
296
415
|
|
|
297
|
-
|
|
298
416
|
def line_select_callback(self, x_min, x_max):
|
|
299
417
|
self.start_cursor.value = np.round(x_min, 3)
|
|
300
418
|
self.end_cursor.value = np.round(x_max, 3)
|
|
301
|
-
self.start_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.start_cursor.value)
|
|
302
|
-
self.end_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.end_cursor.value)
|
|
303
419
|
|
|
304
|
-
|
|
420
|
+
energy_scale = self.dataset.get_spectral_dims(return_axis=True)[0]
|
|
421
|
+
self.start_channel = np.searchsorted(energy_scale, self.start_cursor.value)
|
|
422
|
+
self.end_channel = np.searchsorted(energy_scale, self.end_cursor.value)
|
|
305
423
|
|
|
424
|
+
def set_dataset(self, key=None):
|
|
306
425
|
if len(self.datasets) == 0:
|
|
307
426
|
data_set = sidpy.Dataset.from_array([0, 1], name='generic')
|
|
308
|
-
data_set.set_dimension(0, sidpy.Dimension([0,1], 'energy_loss', units='channel', quantity='generic',
|
|
427
|
+
data_set.set_dimension(0, sidpy.Dimension([0, 1], 'energy_loss', units='channel', quantity='generic',
|
|
309
428
|
dimension_type='spectral'))
|
|
310
429
|
data_set.data_type = 'spectrum'
|
|
311
|
-
data_set.metadata= {'experiment':{'convergence_angle': 0,
|
|
312
|
-
|
|
313
|
-
|
|
314
|
-
|
|
315
|
-
self.datasets={'Channel_000': data_set}
|
|
316
|
-
|
|
430
|
+
data_set.metadata = {'experiment': {'convergence_angle': 0,
|
|
431
|
+
'collection_angle': 0,
|
|
432
|
+
'acceleration_voltage': 0,
|
|
433
|
+
'exposure_time': 0}}
|
|
434
|
+
self.datasets = {'Channel_000': data_set}
|
|
435
|
+
key = 'Channel_000'
|
|
436
|
+
dataset_key = key
|
|
317
437
|
|
|
318
|
-
|
|
319
|
-
|
|
320
|
-
|
|
438
|
+
self.dataset_list = []
|
|
439
|
+
dataset_keys = []
|
|
440
|
+
for key in self.datasets.keys():
|
|
441
|
+
if isinstance(self.datasets[key], sidpy.Dataset):
|
|
442
|
+
if 'SPECTR' in self.datasets[key].data_type.name:
|
|
443
|
+
self.dataset_list.append(f'{key}: {self.datasets[key].title}')
|
|
444
|
+
dataset_keys.append(key)
|
|
445
|
+
if dataset_key not in dataset_keys:
|
|
446
|
+
dataset_key = dataset_keys[0]
|
|
447
|
+
self.key = dataset_key
|
|
448
|
+
|
|
321
449
|
self.dataset = self.datasets[self.key]
|
|
450
|
+
self.energy_scale = self.dataset.get_spectral_dims(return_axis=True)[0]
|
|
322
451
|
|
|
323
|
-
self._udpate_sidbar()
|
|
324
452
|
self.y_scale = 1.0
|
|
325
453
|
self.change_y_scale = 1.0
|
|
326
454
|
self.x = 0
|
|
@@ -330,124 +458,332 @@ class EELSWidget(object):
|
|
|
330
458
|
self.count = 0
|
|
331
459
|
|
|
332
460
|
self.plot()
|
|
461
|
+
self.update_sidebar()
|
|
333
462
|
|
|
334
|
-
def
|
|
335
|
-
pass
|
|
463
|
+
def update_sidebar(self):
|
|
464
|
+
pass
|
|
465
|
+
|
|
466
|
+
def select_main(self, value=0):
|
|
467
|
+
self.datasets = {}
|
|
468
|
+
# self.loaded_datasets.options = self.dataset_list
|
|
336
469
|
|
|
337
|
-
|
|
338
|
-
|
|
339
|
-
|
|
340
|
-
self.
|
|
341
|
-
self.
|
|
342
|
-
self.
|
|
470
|
+
self.datasets = file_tools.open_file(self.file_name)
|
|
471
|
+
file_tools.save_path(self.file_name)
|
|
472
|
+
self.dataset_list = []
|
|
473
|
+
self.image_list = ['Sum']
|
|
474
|
+
self.survey_list = ['None']
|
|
475
|
+
for key in self.datasets.keys():
|
|
476
|
+
if isinstance(self.datasets[key], sidpy.Dataset):
|
|
477
|
+
if 'SPECTR' in self.datasets[key].data_type.name:
|
|
478
|
+
self.dataset_list.append(f'{key}: {self.datasets[key].title}')
|
|
479
|
+
if 'IMAGE' == self.datasets[key].data_type.name:
|
|
480
|
+
if 'survey' in self.datasets[key].title.lower():
|
|
481
|
+
self.survey_list.append(f'{key}: {self.datasets[key].title}')
|
|
482
|
+
else:
|
|
483
|
+
self.image_list.append(f'{key}: {self.datasets[key].title}')
|
|
484
|
+
|
|
485
|
+
# self.survey_list.extend(self.image_list)
|
|
486
|
+
self.set_dataset()
|
|
487
|
+
self.key = self.dataset_list[0].split(':')[0]
|
|
488
|
+
self.dataset = self.datasets[self.key]
|
|
489
|
+
|
|
490
|
+
self.selected_dataset = self.dataset
|
|
491
|
+
if len(self.image_list) > 0:
|
|
492
|
+
self.file_bar[4, 0].options = self.image_list
|
|
493
|
+
self.file_bar[5, 0].options = self.survey_list
|
|
494
|
+
self.file_bar[4, 0].layout.display = "flex"
|
|
495
|
+
self.file_bar[4, 0].value = self.image_list[0]
|
|
496
|
+
self.file_bar[5, 0].layout.display = "flex"
|
|
497
|
+
self.file_bar[5, 0].value = self.survey_list[0]
|
|
498
|
+
|
|
499
|
+
self.file_bar[3, 0].options = self.dataset_list
|
|
500
|
+
self.loaded_datasets.options = self.dataset_list
|
|
501
|
+
self.loaded_datasets.value = self.dataset_list[0]
|
|
502
|
+
|
|
503
|
+
def add_dataset(self, value=0):
|
|
504
|
+
key = file_tools.add_dataset_from_file(self.datasets, self.file_name, 'Channel')
|
|
505
|
+
self.dataset_list.append(f'{key}: {self.datasets[key].title}')
|
|
506
|
+
self.loaded_datasets.options = self.dataset_list
|
|
507
|
+
self.loaded_datasets.value = self.dataset_list[-1]
|
|
508
|
+
|
|
509
|
+
def get_directory(self, directory='.'):
|
|
510
|
+
self.dir_name = directory
|
|
511
|
+
self.dir_dictionary = {}
|
|
512
|
+
self.dir_list = []
|
|
513
|
+
self.dir_list = ['.', '..'] + os.listdir(directory)
|
|
514
|
+
|
|
515
|
+
def set_dir(self, value=0):
|
|
516
|
+
self.dir_name = self.path_choice.value
|
|
517
|
+
self.select_files.index = 0
|
|
518
|
+
self.set_file_options()
|
|
519
|
+
|
|
520
|
+
def select_dataset(self, value=0):
|
|
521
|
+
key = self.loaded_datasets.value.split(':')[0]
|
|
522
|
+
if key != 'None':
|
|
523
|
+
self.selected_dataset = self.datasets[key]
|
|
524
|
+
self.selected_key = key
|
|
525
|
+
self.key = key
|
|
526
|
+
self.datasets['_relationship'] = {'main_dataset': self.key}
|
|
343
527
|
|
|
344
|
-
|
|
345
|
-
|
|
346
|
-
|
|
347
|
-
|
|
348
|
-
|
|
349
|
-
|
|
350
|
-
|
|
351
|
-
|
|
352
|
-
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
528
|
+
self.set_dataset()
|
|
529
|
+
|
|
530
|
+
def set_file_options(self):
|
|
531
|
+
self.dir_name = os.path.abspath(os.path.join(self.dir_name, self.dir_list[self.select_files.index]))
|
|
532
|
+
dir_list = os.listdir(self.dir_name)
|
|
533
|
+
file_dict = file_tools.update_directory_list(self.dir_name)
|
|
534
|
+
|
|
535
|
+
sort = np.argsort(file_dict['directory_list'])
|
|
536
|
+
self.dir_list = ['.', '..']
|
|
537
|
+
self.display_list = ['.', '..']
|
|
538
|
+
for j in sort:
|
|
539
|
+
self.display_list.append(f" * {file_dict['directory_list'][j]}")
|
|
540
|
+
self.dir_list.append(file_dict['directory_list'][j])
|
|
541
|
+
|
|
542
|
+
sort = np.argsort(file_dict['display_file_list'])
|
|
543
|
+
|
|
544
|
+
for i, j in enumerate(sort):
|
|
545
|
+
if '--' in dir_list[j]:
|
|
546
|
+
self.display_list.append(f" {i:3} {file_dict['display_file_list'][j]}")
|
|
547
|
+
else:
|
|
548
|
+
self.display_list.append(f" {i:3} {file_dict['display_file_list'][j]}")
|
|
549
|
+
self.dir_list.append(file_dict['file_list'][j])
|
|
550
|
+
|
|
551
|
+
self.dir_label = os.path.split(self.dir_name)[-1] + ':'
|
|
552
|
+
self.select_files.options = self.display_list
|
|
553
|
+
|
|
554
|
+
path = self.dir_name
|
|
555
|
+
old_path = ' '
|
|
556
|
+
path_list = []
|
|
557
|
+
while path != old_path:
|
|
558
|
+
path_list.append(path)
|
|
559
|
+
old_path = path
|
|
560
|
+
path = os.path.split(path)[0]
|
|
561
|
+
self.path_choice.options = path_list
|
|
562
|
+
self.path_choice.value = path_list[0]
|
|
563
|
+
|
|
564
|
+
def get_file_name(self, b):
|
|
565
|
+
|
|
566
|
+
if os.path.isdir(os.path.join(self.dir_name, self.dir_list[self.select_files.index])):
|
|
567
|
+
self.set_file_options()
|
|
568
|
+
|
|
569
|
+
elif os.path.isfile(os.path.join(self.dir_name, self.dir_list[self.select_files.index])):
|
|
570
|
+
self.file_name = os.path.join(self.dir_name, self.dir_list[self.select_files.index])
|
|
571
|
+
|
|
356
572
|
|
|
357
573
|
class InfoWidget(EELSWidget):
|
|
358
|
-
def __init__(self, datasets):
|
|
574
|
+
def __init__(self, datasets=None):
|
|
359
575
|
|
|
360
|
-
sidebar = get_info_sidebar()
|
|
576
|
+
sidebar = {'Info': get_info_sidebar(),
|
|
577
|
+
'LowLoss': get_low_loss_sidebar()}
|
|
361
578
|
super().__init__(datasets, sidebar)
|
|
579
|
+
self.info_tab = sidebar['Info']
|
|
580
|
+
super().set_dataset()
|
|
581
|
+
|
|
362
582
|
self.set_action()
|
|
363
583
|
|
|
364
|
-
def
|
|
365
|
-
self.datasets[self.key].
|
|
366
|
-
|
|
584
|
+
def set_energy_scale(self, value):
|
|
585
|
+
self.energy_scale = self.datasets[self.key].get_spectral_dims(return_axis=True)[0]
|
|
586
|
+
dispersion = self.datasets[self.key].get_dimension_slope(self.energy_scale)
|
|
587
|
+
self.energy_scale *= (self.info_tab[3, 0].value / dispersion)
|
|
588
|
+
self.energy_scale += (self.info_tab[2, 0].value - self.energy_scale[0])
|
|
589
|
+
self.plot()
|
|
590
|
+
|
|
591
|
+
def set_y_scale(self, value):
|
|
592
|
+
self.count += 1
|
|
593
|
+
self.change_y_scale = 1.0 / self.y_scale
|
|
594
|
+
if self.datasets[self.key].metadata['experiment']['flux_ppm'] > 1e-12:
|
|
595
|
+
|
|
596
|
+
if self.info_tab[9, 2].value:
|
|
597
|
+
dispersion = self.datasets[self.key].get_dimension_slope(self.energy_scale)
|
|
598
|
+
self.y_scale = 1 / self.datasets[self.key].metadata['experiment']['flux_ppm'] * dispersion
|
|
599
|
+
self.ylabel = 'scattering probability (ppm)'
|
|
600
|
+
else:
|
|
601
|
+
self.y_scale = 1.0
|
|
602
|
+
self.ylabel = 'intensity (counts)'
|
|
603
|
+
self.change_y_scale *= self.y_scale
|
|
604
|
+
self._update()
|
|
605
|
+
|
|
606
|
+
def set_flux(self, value):
|
|
607
|
+
self.datasets[self.key].metadata['experiment']['exposure_time'] = self.info_tab[10, 0].value
|
|
608
|
+
if self.info_tab[9, 0].value == 'None':
|
|
367
609
|
self.datasets[self.key].metadata['experiment']['flux_ppm'] = 0.
|
|
368
610
|
else:
|
|
369
|
-
key =
|
|
370
|
-
self.datasets[
|
|
611
|
+
key = self.info_tab[9, 0].value.split(':')[0]
|
|
612
|
+
self.datasets['_relationship']['low_loss'] = key
|
|
613
|
+
spectrum_dimensions = self.dataset.get_spectral_dims()
|
|
614
|
+
|
|
615
|
+
number_of_pixels = 1
|
|
616
|
+
for index, dimension in enumerate(self.dataset.shape):
|
|
617
|
+
if index not in spectrum_dimensions:
|
|
618
|
+
number_of_pixels *= dimension
|
|
619
|
+
if self.datasets[key].metadata['experiment']['exposure_time'] == 0.0:
|
|
620
|
+
if self.datasets[key].metadata['experiment']['single_exposure_time'] == 0.0:
|
|
621
|
+
return
|
|
622
|
+
else:
|
|
623
|
+
self.datasets[key].metadata['experiment']['exposure_time'] = (self.datasets[key].metadata['experiment']['single_exposure_time'] *
|
|
624
|
+
self.datasets[key].metadata['experiment']['number_of_frames'])
|
|
625
|
+
|
|
626
|
+
self.datasets[self.key].metadata['experiment']['flux_ppm'] = ((np.array(self.datasets[key])*1e-6).sum() /
|
|
627
|
+
self.datasets[key].metadata['experiment']['exposure_time'] /
|
|
628
|
+
number_of_pixels)
|
|
371
629
|
self.datasets[self.key].metadata['experiment']['flux_ppm'] *= self.datasets[self.key].metadata['experiment']['exposure_time']
|
|
372
|
-
|
|
373
|
-
|
|
630
|
+
if 'SPECT' in self.datasets[key].data_type.name:
|
|
631
|
+
self.info_tab[14, 0].disabled = False
|
|
632
|
+
self.info_tab[11, 0].value = np.round(self.datasets[self.key].metadata['experiment']['flux_ppm'], 2)
|
|
633
|
+
|
|
374
634
|
def set_microscope_parameter(self, value):
|
|
375
|
-
self.datasets[self.key].metadata['experiment']['convergence_angle'] = self.
|
|
376
|
-
self.datasets[self.key].metadata['experiment']['collection_angle'] = self.
|
|
377
|
-
self.datasets[self.key].metadata['experiment']['acceleration_voltage'] = self.
|
|
635
|
+
self.datasets[self.key].metadata['experiment']['convergence_angle'] = self.info_tab[5, 0].value
|
|
636
|
+
self.datasets[self.key].metadata['experiment']['collection_angle'] = self.info_tab[6, 0].value
|
|
637
|
+
self.datasets[self.key].metadata['experiment']['acceleration_voltage'] = self.info_tab[7, 0].value*1000
|
|
378
638
|
|
|
379
639
|
def cursor2energy_scale(self, value):
|
|
640
|
+
self.energy_scale = self.datasets[self.key].get_spectral_dims(return_axis=True)[0]
|
|
380
641
|
dispersion = (self.end_cursor.value - self.start_cursor.value) / (self.end_channel - self.start_channel)
|
|
381
|
-
|
|
382
|
-
self.
|
|
642
|
+
|
|
643
|
+
self.energy_scale *= (self.info_tab[3, 0].value/dispersion)
|
|
644
|
+
self.info_tab[3, 0].value = dispersion
|
|
383
645
|
offset = self.start_cursor.value - self.start_channel * dispersion
|
|
384
|
-
self.
|
|
385
|
-
self.
|
|
646
|
+
self.energy_scale += (self.info_tab[2, 0].value-self.energy_scale[0])
|
|
647
|
+
self.info_tab[2, 0].value = offset
|
|
386
648
|
self.plot()
|
|
387
649
|
|
|
388
650
|
def set_binning(self, value):
|
|
389
651
|
if 'SPECTRAL' in self.dataset.data_type.name:
|
|
390
|
-
|
|
391
|
-
|
|
392
|
-
self.
|
|
393
|
-
self.
|
|
394
|
-
self.
|
|
395
|
-
|
|
396
|
-
|
|
652
|
+
image_dims = self.dataset.get_image_dims()
|
|
653
|
+
|
|
654
|
+
self.bin_x = int(self.info_tab[16, 0].value)
|
|
655
|
+
self.bin_y = int(self.info_tab[17, 0].value)
|
|
656
|
+
if self.bin_x < 1:
|
|
657
|
+
self.bin_x = 1
|
|
658
|
+
self.info_tab[16, 0].value = self.bin_x
|
|
659
|
+
if self.bin_y < 1:
|
|
660
|
+
self.bin_y = 1
|
|
661
|
+
self.info_tab[17, 0].value = self.bin_y
|
|
662
|
+
if self.bin_x > self.dataset.shape[image_dims[0]]:
|
|
663
|
+
self.bin_x = self.dataset.shape[image_dims[0]]
|
|
664
|
+
self.info_tab[16, 0].value = self.bin_x
|
|
665
|
+
if self.bin_y > self.dataset.shape[image_dims[1]]:
|
|
666
|
+
self.bin_y = self.dataset.shape[image_dims[1]]
|
|
667
|
+
self.info_tab[17, 0].value = self.bin_y
|
|
668
|
+
|
|
669
|
+
self.datasets[self.key].metadata['experiment']['SI_bin_x'] = self.bin_x
|
|
670
|
+
self.datasets[self.key].metadata['experiment']['SI_bin_y'] = self.bin_y
|
|
671
|
+
self.plot()
|
|
672
|
+
|
|
673
|
+
def update_sidebar(self):
|
|
397
674
|
spectrum_list = []
|
|
398
|
-
reference_list =[
|
|
399
|
-
for
|
|
400
|
-
if
|
|
401
|
-
if '
|
|
402
|
-
|
|
403
|
-
|
|
675
|
+
reference_list = ['None']
|
|
676
|
+
for key in self.datasets.keys():
|
|
677
|
+
if isinstance(self.datasets[key], sidpy.Dataset):
|
|
678
|
+
if 'Reference' not in key:
|
|
679
|
+
if 'SPECTR' in self.datasets[key].data_type.name:
|
|
680
|
+
spectrum_list.append(f'{key}: {self.datasets[key].title}')
|
|
681
|
+
reference_list.append(f'{key}: {self.datasets[key].title}')
|
|
404
682
|
|
|
405
|
-
self.
|
|
406
|
-
self.
|
|
407
|
-
|
|
683
|
+
self.info_tab[0, 0].options = spectrum_list
|
|
684
|
+
self.info_tab[9, 0].options = reference_list
|
|
685
|
+
|
|
408
686
|
if 'SPECTRUM' in self.dataset.data_type.name:
|
|
409
|
-
|
|
410
|
-
self.
|
|
687
|
+
for i in range(15, 18):
|
|
688
|
+
self.info_tab[i, 0].layout.display = "none"
|
|
411
689
|
else:
|
|
412
|
-
for i in range(
|
|
413
|
-
self.
|
|
414
|
-
#self.
|
|
415
|
-
self.
|
|
416
|
-
self.
|
|
417
|
-
self.
|
|
418
|
-
self.
|
|
419
|
-
self.
|
|
420
|
-
self.
|
|
690
|
+
for i in range(15, 18):
|
|
691
|
+
self.info_tab[i, 0].layout.display = "flex"
|
|
692
|
+
# self.info_tab[0,0].value = dataset_index #f'{self.key}: {self.datasets[self.key].title}'
|
|
693
|
+
self.info_tab[2, 0].value = np.round(self.datasets[self.key].energy_loss[0], 3)
|
|
694
|
+
self.info_tab[3, 0].value = np.round(self.datasets[self.key].energy_loss[1] - self.datasets[self.key].energy_loss[0], 4)
|
|
695
|
+
self.info_tab[5, 0].value = np.round(self.datasets[self.key].metadata['experiment']['convergence_angle'], 1)
|
|
696
|
+
self.info_tab[6, 0].value = np.round(self.datasets[self.key].metadata['experiment']['collection_angle'], 1)
|
|
697
|
+
self.info_tab[7, 0].value = np.round(self.datasets[self.key].metadata['experiment']['acceleration_voltage']/1000, 1)
|
|
698
|
+
self.info_tab[10, 0].value = np.round(self.datasets[self.key].metadata['experiment']['exposure_time'], 4)
|
|
421
699
|
if 'flux_ppm' not in self.datasets[self.key].metadata['experiment']:
|
|
422
700
|
self.datasets[self.key].metadata['experiment']['flux_ppm'] = 0
|
|
423
|
-
self.
|
|
701
|
+
self.info_tab[11, 0].value = self.datasets[self.key].metadata['experiment']['flux_ppm']
|
|
424
702
|
if 'count_conversion' not in self.datasets[self.key].metadata['experiment']:
|
|
425
703
|
self.datasets[self.key].metadata['experiment']['count_conversion'] = 1
|
|
426
|
-
self.
|
|
704
|
+
self.info_tab[12, 0].value = self.datasets[self.key].metadata['experiment']['count_conversion']
|
|
427
705
|
if 'beam_current' not in self.datasets[self.key].metadata['experiment']:
|
|
428
706
|
self.datasets[self.key].metadata['experiment']['beam_current'] = 0
|
|
429
|
-
self.
|
|
707
|
+
self.info_tab[13, 0].value = self.datasets[self.key].metadata['experiment']['beam_current']
|
|
430
708
|
|
|
431
|
-
def update_dataset(self):
|
|
432
|
-
|
|
433
|
-
self.set_dataset(
|
|
709
|
+
def update_dataset(self, value=0):
|
|
710
|
+
key = self.info_tab[0, 0].value.split(':')[0]
|
|
711
|
+
self.set_dataset(key)
|
|
712
|
+
|
|
713
|
+
def shift_low_loss(self, value=0):
|
|
714
|
+
if 'low_loss' in self.datasets['_relationship']:
|
|
715
|
+
low_loss = self.datasets[self.datasets['_relationship']['low_loss']]
|
|
716
|
+
self.datasets[self.datasets['_relationship']['low_loss']] = eels_tools.align_zero_loss(low_loss)
|
|
717
|
+
print('1')
|
|
718
|
+
print('2')
|
|
719
|
+
if 'low_loss' in self.datasets['_relationship']:
|
|
720
|
+
if 'zero_loss' in self.datasets[self.datasets['_relationship']['low_loss']].metadata:
|
|
721
|
+
if 'shifted' in self.datasets[self.datasets['_relationship']['low_loss']].metadata['zero_loss'].keys():
|
|
722
|
+
self.info_tab[14, 1].disabled = False
|
|
723
|
+
print('shifted')
|
|
724
|
+
|
|
725
|
+
def shift_spectrum(self, value=0):
|
|
726
|
+
shifts = self.dataset.shape
|
|
727
|
+
if 'low_loss' in self.datasets['_relationship']:
|
|
728
|
+
if 'zero_loss' in self.datasets[self.datasets['_relationship']['low_loss']].metadata:
|
|
729
|
+
if 'shifted' in self.datasets[self.datasets['_relationship']['low_loss']].metadata['zero_loss'].keys():
|
|
730
|
+
shifts = self.datasets[self.datasets['_relationship']['low_loss']].metadata['zero_loss']['shifted']
|
|
731
|
+
shifts_new = shifts.copy()
|
|
732
|
+
if 'zero_loss' in self.dataset.metadata:
|
|
733
|
+
if 'shifted' in self.dataset.metadata['zero_loss'].keys():
|
|
734
|
+
shifts_new = shifts-self.dataset.metadata['zero_loss']['shifted']
|
|
735
|
+
else:
|
|
736
|
+
self.dataset.metadata['zero_loss'] = {}
|
|
737
|
+
print(shifts_new)
|
|
738
|
+
|
|
739
|
+
self.dataset = eels_tools.shift_energy(self.dataset, shifts_new)
|
|
740
|
+
self.dataset.metadata['zero_loss']['shifted'] = shifts
|
|
741
|
+
self.plot()
|
|
742
|
+
|
|
743
|
+
def get_resolution_function(self, value=0):
|
|
744
|
+
if 'low_loss' in self.datasets['_relationship']:
|
|
745
|
+
if 'zero_loss' in self.datasets[self.datasets['_relationship']['low_loss']].metadata:
|
|
746
|
+
if 'shifted' in self.datasets[self.datasets['_relationship']['low_loss']].metadata['zero_loss']:
|
|
747
|
+
low_loss = self.datasets[self.datasets['_relationship']['low_loss']]
|
|
748
|
+
zero_channel = np.searchsorted(low_loss.energy_loss, 0)
|
|
749
|
+
channels = np.argwhere(np.array(low_loss) > low_loss.max()/100).flatten()
|
|
750
|
+
energy = self.dataset.get_spectral_dims(return_axis=True)[0].values
|
|
751
|
+
self.datasets['resolution_function'] = eels_tools.get_resolution_functions(low_loss,
|
|
752
|
+
energy[channels[0]],
|
|
753
|
+
energy[channels[-1]])
|
|
754
|
+
self.datasets['resolution_function'].title = 'resolution_function'
|
|
755
|
+
self.axis.plot(self.datasets['resolution_function'].energy_loss,
|
|
756
|
+
self.datasets['resolution_function'],
|
|
757
|
+
label='resolution_function')
|
|
758
|
+
self.axis.legend()
|
|
759
|
+
|
|
760
|
+
resolution_key = self.dataset_list.append(f'resolution_function: resolution_function')
|
|
761
|
+
if resolution_key not in self.dataset_list:
|
|
762
|
+
self.dataset_list.append(resolution_key)
|
|
763
|
+
self.loaded_datasets.options = self.dataset_list
|
|
764
|
+
self.info_tab[0, 0].options = self.dataset_list
|
|
434
765
|
|
|
435
766
|
def set_action(self):
|
|
436
|
-
self.
|
|
437
|
-
self.
|
|
438
|
-
self.
|
|
439
|
-
self.
|
|
440
|
-
self.
|
|
441
|
-
self.
|
|
442
|
-
self.
|
|
443
|
-
self.
|
|
444
|
-
self.
|
|
445
|
-
self.
|
|
446
|
-
self.
|
|
447
|
-
self.
|
|
767
|
+
self.info_tab[0, 0].observe(self.update_dataset, names='value')
|
|
768
|
+
self.info_tab[1, 0].on_click(self.cursor2energy_scale)
|
|
769
|
+
self.info_tab[2, 0].observe(self.set_energy_scale, names='value')
|
|
770
|
+
self.info_tab[3, 0].observe(self.set_energy_scale, names='value')
|
|
771
|
+
self.info_tab[5, 0].observe(self.set_microscope_parameter)
|
|
772
|
+
self.info_tab[6, 0].observe(self.set_microscope_parameter)
|
|
773
|
+
self.info_tab[7, 0].observe(self.set_microscope_parameter)
|
|
774
|
+
self.info_tab[9, 0].observe(self.set_flux, names='value')
|
|
775
|
+
self.info_tab[9, 2].observe(self.set_y_scale, names='value')
|
|
776
|
+
self.info_tab[10, 0].observe(self.set_flux)
|
|
777
|
+
self.info_tab[14, 0].on_click(self.shift_low_loss)
|
|
778
|
+
self.info_tab[14, 1].on_click(self.shift_spectrum)
|
|
779
|
+
self.info_tab[14, 2].on_click(self.get_resolution_function)
|
|
448
780
|
|
|
781
|
+
self.info_tab[16, 0].observe(self.set_binning)
|
|
782
|
+
self.info_tab[17, 0].observe(self.set_binning)
|
|
783
|
+
|
|
784
|
+
|
|
449
785
|
def get_low_loss_sidebar():
|
|
450
|
-
side_bar = ipywidgets.GridspecLayout(17, 3,width='auto', grid_gap="0px")
|
|
786
|
+
side_bar = ipywidgets.GridspecLayout(17, 3, width='auto', grid_gap="0px")
|
|
451
787
|
|
|
452
788
|
side_bar[0, :2] = ipywidgets.Dropdown(
|
|
453
789
|
options=[('None', 0)],
|
|
@@ -457,128 +793,136 @@ def get_low_loss_sidebar():
|
|
|
457
793
|
|
|
458
794
|
row = 1
|
|
459
795
|
side_bar[row, :3] = ipywidgets.Button(description='Fix Energy Scale',
|
|
460
|
-
|
|
461
|
-
|
|
796
|
+
layout=ipywidgets.Layout(width='auto', grid_area='header'),
|
|
797
|
+
style=ipywidgets.ButtonStyle(button_color='lightblue'))
|
|
462
798
|
row += 1
|
|
463
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Offset:', disabled=False, color='black',
|
|
799
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Offset:', disabled=False, color='black',
|
|
800
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
464
801
|
side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
|
|
465
802
|
row += 1
|
|
466
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', disabled=False, color='black',
|
|
803
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Dispersion:', disabled=False, color='black',
|
|
804
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
467
805
|
side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
|
|
468
806
|
|
|
469
807
|
row += 1
|
|
470
808
|
side_bar[row, :3] = ipywidgets.Button(description='Resolution_function',
|
|
471
|
-
|
|
472
|
-
|
|
809
|
+
layout=ipywidgets.Layout(width='auto', grid_area='header'),
|
|
810
|
+
style=ipywidgets.ButtonStyle(button_color='lightblue'))
|
|
473
811
|
row += 1
|
|
474
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=0.3, description='Fit Window:', disabled=False, color='black',
|
|
812
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=0.3, description='Fit Window:', disabled=False, color='black',
|
|
813
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
475
814
|
side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
|
|
476
815
|
row += 1
|
|
477
|
-
side_bar[row
|
|
478
|
-
|
|
479
|
-
|
|
480
|
-
|
|
481
|
-
|
|
482
|
-
|
|
483
|
-
|
|
484
|
-
|
|
485
|
-
|
|
486
|
-
|
|
487
|
-
tooltip='Changes y-axis to probability if flux is given',
|
|
488
|
-
layout=ipywidgets.Layout(width='100px'))
|
|
816
|
+
side_bar[row, :2] = ipywidgets.ToggleButton(description='Show Resolution Function',
|
|
817
|
+
disabled=False,
|
|
818
|
+
button_style='', # 'success', 'info', 'warning', 'danger' or ''
|
|
819
|
+
tooltip='Changes y-axis to probability if flux is given',
|
|
820
|
+
layout=ipywidgets.Layout(width='100px'))
|
|
821
|
+
side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
|
|
822
|
+
disabled=False,
|
|
823
|
+
button_style='', # 'success', 'info', 'warning', 'danger' or ''
|
|
824
|
+
tooltip='Changes y-axis to probability if flux is given',
|
|
825
|
+
layout=ipywidgets.Layout(width='100px'))
|
|
489
826
|
row += 2
|
|
490
827
|
|
|
491
828
|
side_bar[row, :3] = ipywidgets.Button(description='Drude Fit',
|
|
492
|
-
|
|
493
|
-
|
|
494
|
-
row+=1
|
|
495
|
-
side_bar[row, :2] = ipywidgets.Dropdown(
|
|
496
|
-
|
|
497
|
-
|
|
498
|
-
|
|
499
|
-
|
|
500
|
-
|
|
501
|
-
|
|
502
|
-
|
|
503
|
-
|
|
504
|
-
|
|
505
|
-
|
|
506
|
-
|
|
507
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Exp_Time:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
|
|
829
|
+
layout=ipywidgets.Layout(width='auto', grid_area='header'),
|
|
830
|
+
style=ipywidgets.ButtonStyle(button_color='lightblue'))
|
|
831
|
+
row += 1
|
|
832
|
+
side_bar[row, :2] = ipywidgets.Dropdown(options=[('None', 0)],
|
|
833
|
+
value=0,
|
|
834
|
+
description='Low_Loss:',
|
|
835
|
+
disabled=False)
|
|
836
|
+
side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
|
|
837
|
+
disabled=False,
|
|
838
|
+
button_style='',
|
|
839
|
+
tooltip='Changes y-axis to probability if flux is given',
|
|
840
|
+
layout=ipywidgets.Layout(width='100px'))
|
|
841
|
+
row += 1
|
|
842
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Exp_Time:', disabled=False, color='black',
|
|
843
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
508
844
|
side_bar[row, 2] = ipywidgets.widgets.Label(value="s", layout=ipywidgets.Layout(width='100px'))
|
|
509
845
|
row += 1
|
|
510
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Flux:', disabled=False, color='black',
|
|
846
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='Flux:', disabled=False, color='black',
|
|
847
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
511
848
|
side_bar[row, 2] = ipywidgets.widgets.Label(value="Mcounts", layout=ipywidgets.Layout(width='100px'))
|
|
512
849
|
row += 1
|
|
513
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', disabled=False, color='black',
|
|
850
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Conversion:', disabled=False, color='black',
|
|
851
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
514
852
|
side_bar[row, 2] = ipywidgets.widgets.Label(value=r"e$^-$/counts", layout=ipywidgets.Layout(width='100px'))
|
|
515
853
|
row += 1
|
|
516
|
-
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', disabled=False, color='black',
|
|
517
|
-
|
|
854
|
+
side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Current:', disabled=False, color='black',
|
|
855
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
856
|
+
side_bar[row, 2] = ipywidgets.widgets.Label(value="pA", layout=ipywidgets.Layout(width='100px'))
|
|
518
857
|
|
|
519
858
|
row += 1
|
|
520
859
|
|
|
521
860
|
side_bar[row, :3] = ipywidgets.Button(description='Spectrum Image',
|
|
522
|
-
|
|
523
|
-
|
|
861
|
+
layout=ipywidgets.Layout(width='auto', grid_area='header'),
|
|
862
|
+
style=ipywidgets.ButtonStyle(button_color='lightblue'))
|
|
524
863
|
|
|
525
864
|
row += 1
|
|
526
|
-
side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
|
|
865
|
+
side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
|
|
866
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
527
867
|
row += 1
|
|
528
|
-
side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
|
|
868
|
+
side_bar[row, :2] = ipywidgets.IntText(value=1, description='bin X:', disabled=False, color='black',
|
|
869
|
+
layout=ipywidgets.Layout(width='200px'))
|
|
529
870
|
|
|
530
|
-
for i in range(
|
|
871
|
+
for i in range(15, 18):
|
|
531
872
|
pass
|
|
532
873
|
# side_bar[i, 0].layout.display = "none"
|
|
533
874
|
return side_bar
|
|
534
875
|
|
|
876
|
+
|
|
535
877
|
class LowLossWidget(EELSWidget):
|
|
536
878
|
def __init__(self, datasets):
|
|
537
879
|
sidebar = get_low_loss_sidebar()
|
|
538
880
|
super().__init__(datasets, sidebar)
|
|
539
|
-
self.
|
|
540
|
-
self.
|
|
881
|
+
self.info_tab[3, 0].value = self.energy_scale[0]
|
|
882
|
+
self.info_tab[4, 0].value = self.energy_scale[1] - self.energy_scale[0]
|
|
541
883
|
|
|
542
884
|
self.set_action()
|
|
543
885
|
|
|
544
|
-
def
|
|
886
|
+
def update_sidebar(self):
|
|
545
887
|
spectrum_list = []
|
|
546
|
-
reference_list =[('None', -1)]
|
|
888
|
+
reference_list = [('None', -1)]
|
|
547
889
|
for index, key in enumerate(self.datasets.keys()):
|
|
548
|
-
if
|
|
549
|
-
if '
|
|
550
|
-
|
|
551
|
-
|
|
890
|
+
if isinstance(self.datasets[key], sidpy.Dataset):
|
|
891
|
+
if 'Reference' not in key:
|
|
892
|
+
if 'SPECTR' in self.datasets[key].data_type.name:
|
|
893
|
+
spectrum_list.append((f'{key}: {self.datasets[key].title}', index))
|
|
894
|
+
reference_list.append((f'{key}: {self.datasets[key].title}', index))
|
|
552
895
|
|
|
553
|
-
self.
|
|
554
|
-
self.
|
|
896
|
+
self.info_tab[0, 0].options = spectrum_list
|
|
897
|
+
self.info_tab[9, 0].options = reference_list
|
|
555
898
|
|
|
556
899
|
if 'SPECTRUM' in self.dataset.data_type.name:
|
|
557
|
-
|
|
558
|
-
self.
|
|
900
|
+
for i in range(14, 17):
|
|
901
|
+
self.info_tab[i, 0].layout.display = "none"
|
|
559
902
|
else:
|
|
560
903
|
for i in range(14, 17):
|
|
561
|
-
self.
|
|
904
|
+
self.info_tab[i, 0].layout.display = "flex"
|
|
562
905
|
|
|
563
906
|
def get_resolution_function(self, value):
|
|
564
|
-
self.datasets['resolution_functions'] = eels_tools.get_resolution_functions(self.dataset,
|
|
907
|
+
self.datasets['resolution_functions'] = eels_tools.get_resolution_functions(self.dataset,
|
|
908
|
+
zero_loss_fit_width=self.info_tab[5, 0].value)
|
|
565
909
|
if 'low_loss' not in self.dataset.metadata:
|
|
566
910
|
self.dataset.metadata['low_loss'] = {}
|
|
567
911
|
self.dataset.metadata['low_loss'].update(self.datasets['resolution_functions'].metadata['low_loss'])
|
|
568
|
-
self.
|
|
912
|
+
self.info_tab[6, 0].value = True
|
|
569
913
|
|
|
570
914
|
def update_dataset(self):
|
|
571
|
-
dataset_index = self.
|
|
915
|
+
dataset_index = self.info_tab[0, 0].value
|
|
572
916
|
self.set_dataset(dataset_index)
|
|
573
917
|
|
|
574
918
|
def set_action(self):
|
|
575
|
-
self.
|
|
576
|
-
self.
|
|
577
|
-
self.
|
|
578
|
-
self.
|
|
579
|
-
self.
|
|
580
|
-
self.
|
|
581
|
-
self.
|
|
919
|
+
self.info_tab[0, 0].observe(self.update_dataset)
|
|
920
|
+
self.info_tab[1, 0].on_click(self.fix_energy_scale)
|
|
921
|
+
self.info_tab[2, 0].observe(self.set_energy_scale, names='value')
|
|
922
|
+
self.info_tab[3, 0].observe(self.set_energy_scale, names='value')
|
|
923
|
+
self.info_tab[4, 0].on_click(self.get_resolution_function)
|
|
924
|
+
self.info_tab[6, 2].observe(self.set_y_scale, names='value')
|
|
925
|
+
self.info_tab[6, 0].observe(self._update, names='value')
|
|
582
926
|
|
|
583
927
|
def fix_energy_scale(self, value=0):
|
|
584
928
|
self.dataset = eels_tools.shift_on_same_scale(self.dataset)
|
|
@@ -586,11 +930,10 @@ class LowLossWidget(EELSWidget):
|
|
|
586
930
|
if 'resolution_functions' in self.datasets:
|
|
587
931
|
self.datasets['resolution_functions'] = eels_tools.shift_on_same_scale(self.datasets['resolution_functions'])
|
|
588
932
|
self._update()
|
|
589
|
-
|
|
590
933
|
|
|
591
934
|
def set_y_scale(self, value):
|
|
592
935
|
self.change_y_scale = 1.0/self.y_scale
|
|
593
|
-
if self.
|
|
936
|
+
if self.info_tab[6, 2].value:
|
|
594
937
|
dispersion = self.dataset.energy_loss[1] - self.dataset.energy_loss[0]
|
|
595
938
|
if self.dataset.data_type.name == 'SPECTRUM':
|
|
596
939
|
sum = self.dataset.sum()
|
|
@@ -600,16 +943,16 @@ class LowLossWidget(EELSWidget):
|
|
|
600
943
|
|
|
601
944
|
self.y_scale = 1/sum * dispersion * 1e6
|
|
602
945
|
# self.datasets[self.key].metadata['experiment']['flux_ppm'] * dispersion
|
|
603
|
-
self.ylabel='scattering probability (ppm)'
|
|
946
|
+
self.ylabel = 'scattering probability (ppm)'
|
|
604
947
|
else:
|
|
605
948
|
self.y_scale = 1.0
|
|
606
|
-
self.ylabel='intensity (counts)'
|
|
949
|
+
self.ylabel = 'intensity (counts)'
|
|
607
950
|
self.change_y_scale *= self.y_scale
|
|
608
951
|
self._update()
|
|
609
952
|
|
|
610
953
|
def _update(self, ev=0):
|
|
611
954
|
super()._update(ev)
|
|
612
|
-
if self.
|
|
955
|
+
if self.info_tab[6, 0].value:
|
|
613
956
|
if 'resolution_functions' in self.datasets:
|
|
614
957
|
resolution_function = self.get_additional_spectrum('resolution_functions')
|
|
615
958
|
self.axis.plot(self.energy_scale, resolution_function, label='resolution_function')
|
|
@@ -647,9 +990,8 @@ class LowLossWidget(EELSWidget):
|
|
|
647
990
|
|
|
648
991
|
def set_binning(self, value):
|
|
649
992
|
if 'SPECTRAL' in self.dataset.data_type.name:
|
|
650
|
-
bin_x = self.
|
|
651
|
-
bin_y = self.
|
|
993
|
+
bin_x = self.info_tab[15, 0].value
|
|
994
|
+
bin_y = self.info_tab[16, 0].value
|
|
652
995
|
self.dataset.view.set_bin([bin_x, bin_y])
|
|
653
996
|
self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
|
|
654
997
|
self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y
|
|
655
|
-
|