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

pyTEMlib/low_loss_widget.py

@@ -0,0 +1,176 @@
+from typing import Any
+
+import numpy as np
+import os
+import ipywidgets
+import matplotlib.pylab as plt
+import matplotlib
+from IPython.display import display
+
+import sidpy
+# from pyTEMlib.microscope import microscope
+from pyTEMlib import file_tools
+from pyTEMlib import eels_tools
+
+
+def get_low_loss_sidebar() -> Any:
+    side_bar = ipywidgets.GridspecLayout(9, 3, width='auto', grid_gap="0px")
+
+    side_bar[0, :2] = ipywidgets.Dropdown(
+            options=[('None', 0)],
+            value=0,
+            description='Main Dataset:',
+            disabled=False)
+    
+    row = 1
+    
+    side_bar[row, :3] = ipywidgets.Button(description='Resolution Function',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='fit width:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
+    row +=1
+    side_bar[row, 0] = ipywidgets.widgets.Label(value="thickness", layout=ipywidgets.Layout(width='100px'))
+    side_bar[row, 1] = ipywidgets.widgets.Label(value="", layout=ipywidgets.Layout(width='100px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="* iMFP", layout=ipywidgets.Layout(width='100px'))
+    row +=1
+    side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Res.Fct.',
+                                               disabled=False,
+                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
+                                               tooltip='Plots resolution function on right',
+                                               layout=ipywidgets.Layout(width='100px'))
+    
+    side_bar[row, 2] = ipywidgets.ToggleButton(description='Probability',
+                                               disabled=False,
+                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
+                                               tooltip='Changes y-axis to probability if flux is given',
+                                               layout=ipywidgets.Layout(width='100px'))
+    
+    
+    row += 1
+    side_bar[row, :3] = ipywidgets.Button(description='Drude',
+                                          layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                                          style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Start Fit:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5, description='End Fit:', disabled=False, color='black',
+                                             layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='50px'))
+    row +=1
+    side_bar[row, 0] = ipywidgets.ToggleButton(description='Plot Drude',
+                                               disabled=False,
+                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
+                                               tooltip='Plots resolution function on right',
+                                               layout=ipywidgets.Layout(width='100px'))
+    
+    side_bar[row, 2] = ipywidgets.ToggleButton(description='Plot Diel.Fct.',
+                                               disabled=False,
+                                               button_style='',  # 'success', 'info', 'warning', 'danger' or ''
+                                               tooltip='Changes y-axis to probability if flux is given',
+                                               layout=ipywidgets.Layout(width='100px'))
+    
+    
+    return side_bar
+
+class LowLoss(object):
+    def __init__(self, sidebar=None, parent=None):
+        self.parent = parent
+        self.dataset = parent.dataset
+        self.low_loss_tab = sidebar
+        self.set_ll_action()
+        self.update_ll_sidebar()
+
+    def update_ll_sidebar(self):
+        spectrum_list = ['None']
+        for index, key in enumerate(self.parent.datasets.keys()):
+            if isinstance(self.parent.datasets[key], sidpy.Dataset):
+                if 'SPECTR' in self.parent.datasets[key].data_type.name:
+                    energy_offset = self.parent.datasets[key].get_spectral_dims(return_axis=True)[0][0]
+                    if energy_offset < 0:
+                        spectrum_list.append(f'{key}: {self.parent.datasets[key].title}') 
+        
+        self.low_loss_tab[0, 0].options = spectrum_list
+
+    def get_resolution_function(self, value):
+        self.low_loss_tab[4, 0].value = False
+        zero_loss_fit_width=self.low_loss_tab[2, 0].value
+        self.parent.datasets['resolution_functions'] = eels_tools.get_resolution_functions(self.parent.dataset,
+                                                                                    startFitEnergy=-zero_loss_fit_width, 
+                                                                                    endFitEnergy=zero_loss_fit_width)
+        if 'low_loss' not in self.dataset.metadata:
+            self.dataset.metadata['zero_loss'] = {}
+        self.dataset.metadata['zero_loss'].update(self.parent.datasets['resolution_functions'].metadata['zero_loss'])
+        self.low_loss_tab[4, 0].value = True
+        self.low_loss_tab[3, 1].value = f"{np.log(self.parent.dataset.sum()/self.parent.datasets['resolution_functions'].sum())}"
+
+    
+
+    def set_ll_action(self):
+        self.low_loss_tab[0, 0].observe(self.update_ll_dataset)
+        #self.low_loss_tab[1, 0].on_click(self.fix_energy_scale)
+        #self.low_loss_tab[2, 0].observe(self.set_energy_scale, names='value')
+        #self.low_loss_tab[3, 0].observe(self.set_energy_scale, names='value')
+        self.low_loss_tab[1, 0].on_click(self.get_resolution_function)
+        self.low_loss_tab[4, 2].observe(self.parent.info.set_y_scale, names='value')
+        self.low_loss_tab[4, 0].observe(self._update, names='value')
+        
+    def _update(self, ev=0):
+        self.parent._update(ev)
+        
+        if self.low_loss_tab[4, 0].value:
+            if 'resolution_functions' in self.parent.datasets:
+                resolution_function = self.get_additional_spectrum('resolution_functions')
+                self.parent.axis.plot(self.parent.energy_scale, resolution_function, label='resolution_function')
+                self.parent.axis.plot(self.parent.energy_scale, 
+                                      self.parent.spectrum -resolution_function, label='difference')
+
+                self.parent.axis.legend()
+
+    def get_additional_spectrum(self, key):
+        if key not in self.parent.datasets.keys():
+            return
+        
+        if self.parent.datasets[key].data_type == sidpy.DataType.SPECTRUM:
+            self.spectrum = self.parent.datasets[key].copy()
+        else:
+            image_dims = self.parent.datasets[key].get_dimensions_by_type(sidpy.DimensionType.SPATIAL)
+            selection = []
+            for dim, axis in self.parent.datasets[key]._axes.items():
+                # print(dim, axis.dimension_type)
+                if axis.dimension_type == sidpy.DimensionType.SPATIAL:
+                    if dim == image_dims[0]:
+                        selection.append(slice(self.x, self.x + self.bin_x))
+                    else:
+                        selection.append(slice(self.y, self.y + self.bin_y))
+
+                elif axis.dimension_type == sidpy.DimensionType.SPECTRAL:
+                    selection.append(slice(None))
+                elif axis.dimension_type == sidpy.DimensionType.CHANNEL:
+                    selection.append(slice(None))
+                else:
+                    selection.append(slice(0, 1))
+            
+            self.spectrum = self.parent.datasets[key][tuple(selection)].mean(axis=tuple(image_dims))
+            
+        self.spectrum *= self.parent.y_scale
+        
+        return self.spectrum.squeeze()
+    
+    def update_ll_dataset(self, value=0):
+        self.ll_key = self.low_loss_tab[0, 0].value.split(':')[0]
+        self.parent.set_dataset(self.ll_key)
+        self.dataset = self.parent.dataset
+
+    
+    def set_binning(self, value):
+        if 'SPECTRAL' in self.dataset.data_type.name:
+            bin_x = self.info_tab[15, 0].value
+            bin_y = self.info_tab[16, 0].value
+            self.dataset.view.set_bin([bin_x, bin_y])
+            self.datasets[self.key].metadata['experiment']['SI_bin_x'] = bin_x
+            self.datasets[self.key].metadata['experiment']['SI_bin_y'] = bin_y

pyTEMlib/microscope.py

@@ -1,78 +1,61 @@
-# -*- coding: cp1252 -*-
-#################################################################
-# Read microscope CSV file
-# Original by EELSLab Author: Francisco Javier de la Pe�a
-# Made more flexible for load microscopes with csv.DictReader
-# for pyTEMLib by Gerd
-# copyright 2012, Gerd Duscher
-################################################################
-
-import csv
-import os.path
-
-from pyTEMlib.config_dir import config_path
-from pyTEMlib.defaults_parser import defaults
-
-microscopes_file = os.path.join(config_path, 'microscopes.csv')
-
-
-class Microscope(object):
-    microscopes = {}
-    name = None
-    E0 = None
-    alpha = None
-    beta = None
-    pppc = None
-    correlation_factor = None
-
-    def __init__(self):
-        self.load_microscopes()
-        
-        defaults.microscope = defaults.microscope.replace('.', ' ')
-        self.set_microscope(defaults.microscope)
-    
-    def load_microscopes(self):
-        f = open(microscopes_file, 'r')
-
-        labels = f.readline().strip().split(',')
-#        print labels
-        csv_read = csv.DictReader(f, labels, delimiter=",")
-        
-        for line in csv_read:
-            tem = line['Microscope']
-            self.microscopes[tem] = line
-            for i in self.microscopes[tem]:
-                if i != 'Microscope':
-                    self.microscopes[tem][i] = float(self.microscopes[tem][i])
-            
-        f.close()
-        
-    def get_available_microscope_names(self):
-        tem = []
-        for scope in self.microscopes.keys():
-            tem.append(scope)
-        return tem
-    
-    def set_microscope(self, microscope_name):
-        
-        for key in self.microscopes[microscope_name]:
-            exec('self.%s = self.microscopes[\'%s\'][\'%s\']' % (key, microscope_name, key))
-        self.name = microscope_name
-    
-    def __repr__(self):
-        info = '''
-        Microscope parameters:
-        -----------------------------
-        
-        Microscope: %s
-        Convergence angle: %1.2f mrad
-        Collection angle: %1.2f mrad
-        Beam energy: %1.2E eV
-        pppc: %1.2f
-        Correlation factor: %1.2f
-        ''' % (self.name, self.alpha, self.beta, self.E0,
-               self.pppc, self.correlation_factor)
-        return info
-
-
-microscope = Microscope()
+""" default microscope parameters from config file
+
+Read microscope CSV file
+
+for pyTEMLib by Gerd
+
+copyright 2012, Gerd Duscher
+updated 2021
+"""
+# -*- coding: utf-8 -*-
+
+import csv
+import os.path
+
+from pyTEMlib.config_dir import config_path
+microscopes_file = os.path.join(config_path, 'microscopes.csv')
+
+
+
+class Microscope(object):
+    """Class to read configuration file and provide microscope information"""
+    microscopes = {}
+    name = None
+    E0 = None
+    alpha = None
+    beta = None
+    pppc = None
+    correlation_factor = None
+
+    def __init__(self):
+        self.load_microscopes()
+        default_tem = self.microscopes[list(self.microscopes.keys())[0]]
+        self.set_microscope(default_tem['Microscope'])
+
+    def load_microscopes(self):
+        f = open(microscopes_file, 'r')
+
+        labels = f.readline().strip().split(',')
+        # print labels
+        csv_read = csv.DictReader(f, labels, delimiter=",")
+
+        for line in csv_read:
+            tem = line['Microscope']
+            self.microscopes[tem] = line
+            for i in self.microscopes[tem]:
+                if i != 'Microscope':
+                    self.microscopes[tem][i] = float(self.microscopes[tem][i])
+        f.close()
+
+    def get_available_microscope_names(self):
+        tem = []
+        for scope in self.microscopes.keys():
+            tem.append(scope)
+        return tem
+
+    def set_microscope(self, microscope_name):
+        if microscope_name in self.microscopes:
+            self.name = microscope_name
+
+
+microscope = Microscope()