pyTEMlib 0.2025.4.2__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

build/lib/pyTEMlib/__init__.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+"""
+PyTEMlib
+--------
+A Python package for analyzing and processing transmission electron microscopy (TEM) data.
+This package provides tools for data quantification through a model-based approach, 
+including functionalities for imaging, spectra analysis, and data visualization.
+
+The package is part of the pycrosccopy ecosystem and the dataformat is based on sidpy, 
+the fileformat is based on pyNSDI.
+Created on Sat Jan 19 10:07:35 2019
+Update on Sun Jul 20 2025
+
+@author: gduscher
+"""
+from .version import  __version__
+
+from . import file_tools
+from . import  image_tools
+from .image import image_atoms as atom_tools
+from . import graph_tools
+from . import probe_tools
+from . import eels_tools
+from . import eds_tools
+from . import crystal_tools
+from . import kinematic_scattering
+from . import dynamic_scattering
+from .config_dir import config_path
+
+__all__ = ['__version__', 'file_tools', 'image_tools', 'atom_tools',
+           'graph_tools', 'probe_tools', 'eels_tools', 'eds_tools',
+           'crystal_tools', 'kinematic_scattering', 'dynamic_scattering', 'config_path']
+__author__ = 'Gerd Duscher'

build/lib/pyTEMlib/animation.py

@@ -0,0 +1,640 @@
+"""Figures and Animations for TEM in jupyter notebooks
+part of MSE 672 course at UTK
+
+Author: Gerd Duscher
+revision: 01/11/2021
+03/17/2021 added Aberration Animation
+ """
+
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib import patches
+
+from ipywidgets import widgets
+from IPython.display import display
+
+import pyTEMlib.kinematic_scattering as ks
+
+
+def geometric_ray_diagram(focal_length=1., magnification=False):
+    """ Sketch of geometric ray diagram od one lens
+
+    Parameters
+    ----------
+    focal_length: float
+        focal length of lens
+    magnification: boolean
+        draw magnification on the side
+
+    Returns
+    -------
+    matplotlib figure
+    """
+
+    f = focal_length
+
+    u = 1.5
+    v = 1 / (1 / f - 1 / u)
+    m = v / u
+    if magnification:
+        line_strong = .5
+    else:
+        line_strong = 2
+
+    x = 0.4
+
+    fig, ax = plt.subplots()
+
+    # add an ellipse
+    ellipse = patches.Ellipse((0.0, 0.0), 3.4, 0.3, alpha=0.3, color='blue')
+    ax.add_patch(ellipse)
+    ax.plot([1.5, -1.5], [0, 0], '--', color='black')
+    ax.plot([0, 0], [u, -v], '--', color='black')
+    single_prop = {"arrowstyle": '->', "shrinkA": 0, "shrinkB": 0}
+    double_prop = {"arrowstyle": "<->", "shrinkA": 0, "shrinkB": 0}
+
+    if magnification:
+        ax.annotate("", xy=(-x, u), xytext=(x, u), arrowprops=single_prop)
+        ax.annotate("", xy=(x * m, -v), xytext=(-x * m, -v), arrowprops=single_prop)
+
+    else:
+        ax.annotate("", xy=(-x, u), xytext=(0, u), arrowprops=single_prop)
+        ax.annotate("", xy=(x * m, -v), xytext=(0, -v), arrowprops=single_prop)
+
+    ax.text(x + 0.1, u, 'object plane', va='center')
+    ax.plot([1, -1], [-f, -f], '--', color='black')
+    ax.text(1.1, -f, 'back focal\n plane', va='center')
+    ax.text(x * m + 0.1, -v, 'image plane', va='center')
+
+    ax.annotate("", xy=(-.9, 0), xytext=(-.9, -f), arrowprops=double_prop)
+    ax.text(-1, -f / 2, 'f')
+    if magnification:
+        ax.annotate("", xy=(-1.8, 0), xytext=(-1.8, -v), arrowprops=double_prop)
+        ax.text(-1.7, -v / 2, 'v')
+        ax.annotate("", xy=(-1.8, 0), xytext=(-1.8, u), arrowprops=double_prop)
+        ax.text(-1.7, u / 2, 'u')
+
+    ax.plot([-x, x * m], [u, -v], color='black', linewidth=line_strong)
+    ax.plot([-x, -x], [u, 0], color='black', linewidth=line_strong)
+    ax.plot([-x, x * m], [0, -v], color='black', linewidth=line_strong)
+
+    ax.plot([-x, -2 * x], [u, 0], color='black', linewidth=0.5)
+    ax.plot([-2 * x, x * m], [0, -v], color='black', linewidth=0.5)
+    if magnification:
+        ax.plot([x, -x * m], [u, -v], color='black', linewidth=0.5)
+        ax.plot([x, x], [u, 0], color='black', linewidth=0.5)
+        ax.plot([x, -x * m], [0, -v], color='black', linewidth=0.5)
+
+        ax.plot([x, 2 * x], [u, 0], color='black', linewidth=0.5)
+        ax.plot([2 * x, -x * m], [0, -v], color='black', linewidth=0.5)
+    else:
+        ax.plot([-x, x * m], [u, 0], color='black', linewidth=0.5)
+        ax.plot([x * m, x * m], [0, -v], color='black', linewidth=0.5)
+
+    ax.set_xlim(-2, 3)
+    ax.set_ylim(-3.5, 2)
+    ax.set_aspect('equal')
+
+
+# ----------------------------------------------------------------
+# Modified from Michael Fairchild :simply draws a thin-lens at the provided location parameters:
+#     - z:    location along the optical axis (in mm)
+#     - f:    focal length (in mm, can be negative if div. lens)
+#     - diam: lens diameter in mm
+#     - lens_labels:  label to identify the lens on the drawing
+# ----------------------------------------------------------------
+def add_lens(z, f, diam, lens_labels):
+    """add lens to propagate beam plot"""
+    ww, tw, rad = diam / 10.0, diam / 3.0, diam / 2.0
+    plt.plot([z, z], [-rad, rad], 'k', linewidth=2)
+    plt.plot([z, z + tw], [-rad, -rad + np.sign(f) * ww], 'k', linewidth=2)
+    plt.plot([z, z - tw], [-rad, -rad + np.sign(f) * ww], 'k', linewidth=2)
+    plt.plot([z, z + tw], [rad, rad - np.sign(f) * ww], 'k', linewidth=2)
+    plt.plot([z, z - tw], [rad, rad - np.sign(f) * ww], 'k', linewidth=2)
+    plt.plot([z + f, z + f], [-ww, ww], 'k', linewidth=2)
+    plt.plot([z - f, z - f], [-ww, ww], 'k', linewidth=2)
+    plt.text(z, rad + 5.0, lens_labels, fontsize=12)
+    plt.text(z, rad + 2.0, 'f=' + str(int(f)), fontsize=10)
+
+
+def add_aperture(z, diam, radius, lens_labels):
+    """add aperture to propagate beam plot"""
+
+    # ww, tw, rad = diam / 10.0, diam / 3.0, diam / 2.0
+    rad = diam / 2
+    radius = radius / 2
+    plt.plot([z, z], [-rad, -radius], 'k', linewidth=2)
+    plt.plot([z, z], [rad, radius], 'k', linewidth=2)
+    plt.text(z, -rad - 2.0, lens_labels, fontsize=12)
+
+
+def propagate_beam(source_position, numerical_aperture, number_of_rays, 
+                   lens_positions, focal_lengths,
+                   lens_labels='', color='b'):
+    """geometrical propagation of light rays from given source
+
+    Parameters
+    ----------
+    source_position:  list
+        location of the source (z0, x0) along and off axis (in mm)
+    numerical_aperture:  float
+        numerical aperture of the beam (in degrees)
+    number_of_rays:  int
+        number of rays to trace
+    lens_positions:  numpy array
+        array with the location of the lenses
+    focal_lengths:  numpy array
+        array with the focal length of lenses
+    lens_labels: list of string
+        label for the nature of lenses
+    color: str
+        color of the rays on plot
+    """
+
+    plt.figure()
+    z_max = 1600.
+
+    # aperture (maximum angle) in radians
+    apa = numerical_aperture * np.pi / 180.0
+
+    for i in range(np.size(lens_positions)):
+        add_lens(lens_positions[i], focal_lengths[i], 25, lens_labels[i])
+
+    add_aperture(840, 25, 7, 'CA')
+
+    # position of source is z0,x0
+    z0 = source_position[0]
+    if np.size(source_position) == 2:
+        x0 = source_position[1]
+    else:
+        x0 = 0.0
+
+    # list of lens positions
+    zl1, ff1 = lens_positions[(z0 < lens_positions)], focal_lengths[(z0 < lens_positions)]
+    nl = np.size(zl1)  # number of lenses
+
+    zz, xx, tani = np.zeros(nl + 2), np.zeros(nl + 2), np.zeros(nl + 2)
+    tan0 = np.tan(apa / 2.0) - np.tan(apa) * np.arange(number_of_rays) / (number_of_rays - 1)
+
+    for i in range(number_of_rays):
+        tani[0] = tan0[i]  # initial incidence angle
+        zz[0], xx[0] = z0, x0
+        for j in range(nl):
+            zz[j + 1] = zl1[j]
+            xx[j + 1] = xx[j] + (zz[j + 1] - zz[j]) * tani[j]
+            tani[j + 1] = tani[j] - xx[j + 1] / ff1[j]
+
+        zz[nl + 1] = z_max
+        xx[nl + 1] = xx[nl] + (zz[nl + 1] - zz[nl]) * tani[nl]
+        plt.plot(zz, xx, color)
+        plt.axis([-20, z_max, -20, 20])
+
+
+def deficient_holz_line(exact_bragg=False, shift=False, laue_zone=1, color='black'):
+    """
+    Ewald sphere construction to explain Laue Circle and deficient HOLZ lines
+
+    Parameters:
+    exact_bragg: boolean
+        whether to tilt into exact Bragg condition or along zone axis
+    shift: boolean
+        whether to shift exact Bragg-condition onto zone axis origin
+    laue_zone: int
+        first or second Laue zone only
+    color: string
+        color of wave vectors and Ewald sphere
+    """
+
+    k_0 = [0, 1 / ks.get_wavelength(600)]
+
+    d = 5.  # lattice parameter in nm
+
+    if laue_zone == 0:
+        s_g = 1 / d + 0.06
+    else:
+        s_g = .1
+
+    g = np.linspace(-5, 6, 12) * 1 / d
+    g_d = np.array([5. / d + laue_zone * 1 / d / 2, laue_zone * 1 / d])
+    g_sg = g_d.copy()
+    g_sg[1] = g_d[1] + s_g  # point on Ewald sphere
+
+    # reciprocal lattice
+    plt.scatter(g[:-1], [0] * 11, color='red')
+    plt.scatter(g - 1 / d / 2, [1 / d] * 12, color='blue')
+
+    shift_x = shift_y = 0.
+    d_theta = d_theta1 = d_theta2 = 0
+
+    if exact_bragg:
+
+        d_theta1 = np.arctan((1 / d * laue_zone + s_g) / g_d[0])
+        d_theta2 = np.arctan((1 / d * laue_zone) / g_d[0])
+        d_theta = -(d_theta1 - d_theta2)
+        s_g = 0
+        s = np.sin(d_theta)
+        c = np.cos(d_theta)
+        k_0 = [-s * k_0[1], c * k_0[1]]
+        if shift:
+            shift_x = -k_0[0]
+            shift_y = np.linalg.norm(k_0) - k_0[1]
+        d_theta = np.degrees(d_theta)
+
+    k_0[0] += shift_x
+    k_0[1] += shift_y
+
+    # Ewald Sphere
+    ewald_sphere = patches.Circle((k_0[0], k_0[1]), radius=np.linalg.norm(k_0), 
+                                  clip_on=False, zorder=10, linewidth=1,
+                                  edgecolor=color, fill=False)
+    plt.gca().add_artist(ewald_sphere)
+
+    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, 1 / d / 2, head_width=0.03, 
+                    head_length=0.04, fc='k', ec='k', length_includes_head=True)
+    plt.gca().arrow(g[-1] + .1 / d / 4, 1 / d / 2, 0, -1 / d / 2, head_width=0.03, 
+                    head_length=0.04, fc='k', ec='k', length_includes_head=True)
+    plt.gca().annotate("$|g_{HOLZ}|$", xytext=(g[-1] + .1 / d / 3, 1 / d / 3), 
+                       xy=(g[-1] + 1 / d / 3, 1 / d / 3))
+    plt.scatter(k_0[0], k_0[1])
+    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + shift_x, -k_0[1] + shift_y, head_width=0.03, 
+                    head_length=0.04, fc=color, ec=color, length_includes_head=True)
+    plt.gca().annotate("K$_0$", xytext=(k_0[0] / 2, k_0[1] / 3), xy=(k_0[0] / 2, k_0[1] / 2))
+
+    # K_d Bragg of HOLZ reflection
+    plt.gca().arrow(k_0[0], k_0[1], -k_0[0] + g_d[0] + shift_x, -k_0[1] + g_d[1] + s_g + shift_y, 
+                    head_width=0.03, head_length=0.04, fc=color, ec=color, 
+                    length_includes_head=True)
+    plt.gca().annotate("K$_d$", xytext=(k_0[0] + (g_d[0] - k_0[0]) / 2, k_0[1] / 2), 
+                       xy=(6.5 / d / 2, k_0[1] / 2))
+
+    # s_g excitation Error of HOLZ reflection
+    if s_g > 0:
+        plt.gca().arrow(g_d[0], g_d[1], 0, s_g, head_width=0.03, head_length=0.04, fc='k',
+                        ec='k', length_includes_head=True)
+        plt.gca().annotate("s$_g$", xytext=(g_d[0] * 1.01, g_d[1] + s_g / 3), 
+                           xy=(g_d[0] * 1.01, g_d[1] + s_g / 3))
+
+    # Bragg angle
+    g_sg = g_d
+    g_sg[1] = g_d[1] + s_g
+    plt.plot([0 + shift_x, g_sg[0] + shift_x], [0 + shift_y, g_d[1] + shift_y], color=color, linewidth=1, alpha=0.5,
+             linestyle='--')
+    plt.plot([k_0[0], g_sg[0] / 2 + shift_x], [k_0[1], g_sg[1] / 2 + shift_y], color=color, linewidth=1, alpha=0.5,
+             linestyle='--')
+    # d_theta = np.degrees(np.arctan(k_0[0]/k_0[1]))
+    bragg_angle = patches.Arc((k_0[0], k_0[1]), width=k_0[1], height=k_0[1], theta1=-90 + d_theta,
+                              theta2=-90 + d_theta + np.degrees(np.arcsin(np.linalg.norm(g_sg / 2) / k_0[1])), fc=color,
+                              ec=color)
+
+    plt.gca().annotate(r"$\theta $", xytext=(k_0[0] / 1.3, k_0[1] / 1.5), xy=(k_0[0] / 2 + g_d[0] / 4, k_0[1] / 2))
+    plt.gca().add_patch(bragg_angle)
+
+    # deviation/tilt angle
+    if np.abs(d_theta) > 0:
+        if shift:
+            deviation_angle = patches.Arc((k_0[0], k_0[1]), width=k_0[1] * 1.5, height=k_0[1] * 1.5,
+                                          theta1=-90 + d_theta,
+                                          theta2=-90,
+                                          fc=color, ec=color, linewidth=3)
+            plt.gca().annotate(r"$d \theta $", xytext=(k_0[0] - .13, k_0[1] / 3.7),
+                               xy=(k_0[0] + g_d[0] / 4, k_0[1] / 2))
+            plt.gca().arrow(shift_x, -.2, 0, .2, head_width=0.05, head_length=0.06, fc=color, ec='black',
+                            length_includes_head=True, linewidth=3)
+            plt.gca().annotate("deficient line", xytext=(shift_x * 2, -.2), xy=(shift_x, 0))
+        else:
+            deviation_angle = patches.Arc((0, 0), width=k_0[1], height=k_0[1],
+                                          theta1=np.degrees(d_theta2),
+                                          theta2=np.degrees(d_theta1),
+                                          fc=color, ec=color, linewidth=3)
+            plt.gca().annotate(r"$d \theta $", xytext=(g_d[0] * .8, 1 / d / 3), xy=(g_d[0], 1 / d))
+
+        plt.gca().add_patch(deviation_angle)
+    plt.gca().set_aspect('equal')
+    plt.gca().set_ylim(-.5, 2.2)
+    plt.gca().set_xlim(-1.1, 1.6)
+
+
+def deficient_kikuchi_line(s_g=0., color_b='black'):
+    """Draw the deficient Kikuchi line in the plot."""
+    k_len = 1 / ks.get_wavelength(20)
+    d = 2  # lattice parameter in nm
+
+    g = np.linspace(-2, 2, 5) * 1 / d
+    g_d = np.array([1 / d, 0])
+
+    # reciprocal lattice
+    plt.scatter(g, [0] * 5, color='blue')
+
+    alpha = -np.arctan(s_g / g_d[0])
+    theta = -np.arcsin(g_d[0] / 2 / k_len)
+
+    k_0 = np.array([-np.sin(theta - alpha) * k_len, np.cos(theta - alpha) * k_len])
+    k_d = np.array([-np.sin(-theta - alpha) * k_len, np.cos(-theta - alpha) * k_len])
+    k_i = np.array([-np.sin(theta - alpha) * 1., np.cos(theta - alpha) * 1.])
+    k_i_t = np.array([-np.sin(-alpha), np.cos(-alpha)])
+
+    kk_e = np.array([-np.sin(-theta) * k_len, np.cos(-theta) * k_len])
+    kk_d = np.array([-np.sin(theta) * k_len, np.cos(theta) * k_len])
+
+    # Ewald Sphere
+    ewald_sphere = patches.Circle((k_0[0], k_0[1]), radius=np.linalg.norm(k_0), clip_on=False, zorder=10, linewidth=1,
+                                  edgecolor=color_b, fill=False)
+    plt.gca().add_artist(ewald_sphere)
+
+    # K_0
+    plt.plot([k_0[0], k_0[0]], [k_0[1], k_0[1] + .4], color='gray', linestyle='-', alpha=0.3)
+
+    plt.gca().arrow(k_0[0] + k_i[0], k_0[1] + k_i[1], -k_i[0], -k_i[1], head_width=0.01, head_length=0.015, fc=color_b,
+                    ec=color_b, length_includes_head=True)
+    plt.plot([k_0[0] + k_i_t[0], k_0[0] - k_i_t[0]], [k_0[1] + k_i_t[1], k_0[1] - k_i_t[1]], color='black',
+             linestyle='--', alpha=0.5)
+    plt.scatter(k_0[0], k_0[1], color='black')
+    plt.gca().arrow(k_0[0], k_0[1], -k_0[0], -k_0[1], head_width=0.01, head_length=0.015, fc=color_b,
+                    ec=color_b, length_includes_head=True)
+    plt.gca().annotate("K$_0$", xytext=(-k_0[0] / 2, 0), xy=(k_0[0] / 2, 0))
+
+    plt.gca().arrow(k_0[0], k_0[1], -k_d[0], -k_d[1], head_width=0.01, head_length=0.015, fc=color_b,
+                    ec=color_b, length_includes_head=True)
+    # K_e excess line
+    plt.gca().arrow(k_0[0], k_0[1], -kk_e[0], -kk_e[1], head_width=0.01, head_length=0.015, fc='red',
+                    ec='red', length_includes_head=True)
+    plt.gca().annotate("excess", xytext=(k_0[0] - kk_e[0], -1), xy=(-kk_e[0] + k_0[0], 0))
+    plt.plot([k_0[0] - kk_e[0], k_0[0] - kk_e[0]], [-.1, .1], color='red')
+
+    # k_d deficient line
+    plt.gca().arrow(k_0[0], k_0[1], -kk_d[0], -kk_d[1], head_width=0.01, head_length=0.015, fc='blue',
+                    ec='blue', length_includes_head=True)
+    plt.plot([k_0[0] - kk_d[0], k_0[0] - kk_d[0]], [-.1, .1], color='blue')
+    plt.gca().annotate("deficient", xytext=(k_0[0] - kk_d[0], -1), xy=(k_0[0] - kk_d[0], 0))
+
+    # s_g excitation Error of HOLZ reflection
+    plt.gca().arrow(g_d[0], g_d[1], 0, s_g, head_width=0.01, head_length=0.015, fc='k',
+                    ec='k', length_includes_head=True)
+    plt.gca().annotate("s$_g$", xytext=(g_d[0] * 1.01, g_d[1] + s_g / 3), xy=(g_d[0] * 1.01, g_d[1] + s_g / 3))
+
+    theta = np.degrees(theta)
+    alpha = np.degrees(alpha)
+
+    bragg_angle = patches.Arc((k_0[0], k_0[1]), width=.55, height=.55,
+                              theta1=90 + theta - alpha, theta2=90 - alpha, fc='black', ec='black')
+    if alpha > 0:
+        deviation_angle = patches.Arc((k_0[0], k_0[1]), width=.6, height=.6,
+                                      theta1=90 - alpha, theta2=90, fc='black', ec='red')
+    else:
+        deviation_angle = patches.Arc((k_0[0], k_0[1]), width=.6, height=.6,
+                                      theta1=90, theta2=90 - alpha, fc='black', ec='red')
+
+    plt.gca().annotate(r"$\theta$", xytext=(k_0[0] + k_i_t[0] / 20, k_0[1] + .2), xy=(k_0[0] + k_i_t[0], k_0[1] + .2))
+    plt.gca().annotate(r"$\alpha$", xytext=(k_0[0] + k_i_t[0] / 10, k_0[1] + .3), xy=(k_0[0] + k_i_t[0], k_0[1] + .3),
+                       color='red')
+    plt.gca().add_patch(bragg_angle)
+    plt.gca().add_patch(deviation_angle)
+
+    plt.gca().set_aspect('equal')
+    plt.gca().set_xlabel(r'angle (1/$\AA$)')
+    plt.gca().set_ylim(-.1, k_0[1] * 2.2)
+    plt.gca().set_xlim(-.2, 1.03)
+
+
+class InteractiveAberration():
+    """
+    ### Interactive explanation of aberrations
+
+    """
+
+    def __init__(self, horizontal=True):
+
+        box_layout = widgets.Layout(display='flex',
+                                    flex_flow='row',
+                                    align_items='stretch',
+                                    width='100%')
+
+        self.words = ['ideal rays', 'aberrated rays', 'aberrated wavefront', 'aberration function']
+
+        self.buttons = [widgets.ToggleButton(value=False, description=word, disabled=False) for word in self.words]
+        box = widgets.Box(children=self.buttons, layout=box_layout)
+        display(box)
+
+        # Button(description='edge_quantification')
+        for button in self.buttons:
+            button.observe(self.on_button_clicked, 'value')  # on_click(self.on_button_clicked)
+
+        self.figure = plt.figure()
+        self.ax = plt.gca()
+        self.horizontal = horizontal
+        self.ax.set_aspect('equal')
+        self.analysis = []
+        self.update()
+        # self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
+
+    def on_button_clicked(self, b):
+        """Handle button click events to update the analysis options"""
+        # print(b['owner'].description)
+        selection = b['owner'].description
+        if selection in self.analysis:
+            self.analysis.remove(selection)
+        else:
+            self.analysis.append(selection)
+        self.update()
+
+    def update(self):
+        """Update the plot based on the selected analysis options"""
+        ax = self.ax
+        ax.clear()
+        selection = self.analysis
+        ax.plot([0, 15], [0, 0], color='black')
+        ax.plot([9, 9], [-.3, .3], color='black')
+        lens = patches.Ellipse((2, 0),
+                               width=.4,
+                               height=7,
+                               facecolor='gray')
+        ax.add_patch(lens)
+        ax.set_ylim(-6.5, 6.5)
+        ax.set_aspect('equal')
+
+        if self.words[0] in selection:
+            color = 'gray'
+            ax.plot([0, 2], [1, 1], color=color)
+            ax.plot([0, 2], [-1, -1], color=color)
+            ax.plot([2, 9], [1, 0], color=color)
+            ax.plot([2, 9], [-1, 0], color=color)
+
+            gauss = patches.Ellipse((9, 0),
+                                    width=12,
+                                    height=12,
+                                    fill=False)
+            ax.add_patch(gauss)
+
+        if self.words[1] in selection:
+            color = 'blue'
+            ax.plot([0, 2], [2, 2], color=color)
+            ax.plot([0, 2], [-2, -2], color=color)
+            ax.plot([2, 7], [2, 0], color=color)
+            ax.plot([2, 7], [-2, 0], color=color)
+            gauss2 = patches.Ellipse((7, 0),
+                                     width=8,
+                                     height=8,
+                                     fill=False,
+                                     color=color, linestyle='--')
+            plt.gca().add_patch(gauss2)
+
+        if self.words[2] in selection:
+            color = 'red'
+            ax.plot([0, 2], [2, 2], color=color)
+            ax.plot([0, 2], [-2, -2], color=color)
+            ax.plot([2, 7], [2, 0], color=color)
+            ax.plot([2, 7], [-2, 0], color=color)
+            ax.plot([0, 2], [1, 1], color=color)
+            ax.plot([0, 2], [-1, -1], color=color)
+            ax.plot([2, 9], [1, 0], color=color)
+            ax.plot([2, 9], [-1, 0], color=color)
+            gauss3 = patches.Ellipse((9, 0),
+                                     width=12,
+                                     height=9.7,
+                                     fill=False,
+                                     color=color)
+            plt.gca().add_patch(gauss3)
+
+        if self.words[3] in selection:
+            color = 'green'
+            x = np.arange(100) / 100 - 6
+            x2 = np.arange(100) / 100 * 1.5 - 6
+            b = 4.8
+            a = 6
+            y = np.sqrt(a ** 2 - x ** 2)
+            y2 = b / a * np.sqrt(a ** 2 - x2 ** 2)
+
+            x = np.append(x[::-1], x[1:])
+            y = np.append(y[::-1], -y[1:])
+            x2 = np.append(x2[::-1], x2[1:])
+            y2 = np.append(y2[::-1], -y2[1:])
+
+            dif = y2 - y
+
+            x = np.append(x[::-1], x2)
+            y = np.append(y[::-1], y2)
+            aberration = patches.Polygon(np.array([x + 9, y]).T,
+                                         fill=True,
+                                         color=color, alpha=.5)
+
+            aberration2 = patches.Polygon(np.array(
+                [np.append(np.abs(dif), [0, 0]) * 2 + 2.5, np.append(np.linspace(-3.3, 3.3, len(dif)), [3.3, -3.3])]).T,
+                                          fill=True,
+                                          color=color, alpha=.9)
+
+            plt.gca().add_patch(aberration)
+            plt.gca().add_patch(aberration2)
+
+
+class InteractiveRonchigramMagnification():
+    """    
+    ### Interactive explanation of magnification 
+
+    """
+
+    def __init__(self, horizontal=True):
+
+        box_layout = widgets.Layout(display='flex',
+                                    flex_flow='row',
+                                    align_items='stretch',
+                                    width='100%')
+
+        self.words = ['ideal rays', 'radial circle rays', 'axial circle rays', 'over-focused rays']
+
+        self.buttons = [widgets.ToggleButton(value=False, description=word, disabled=False) for word in self.words]
+        box = widgets.Box(children=self.buttons, layout=box_layout)
+        display(box)
+
+        # Button(description='edge_quantification')
+        for button in self.buttons:
+            button.observe(self.on_button_clicked, 'value')  # on_click(self.on_button_clicked)
+
+        self.figure = plt.figure()
+        self.ax = plt.gca()
+        self.horizontal = horizontal
+        self.ax.set_aspect('equal')
+        self.analysis = []
+        self.update()
+        # self.cid = self.figure.canvas.mpl_connect('button_press_event', self.onclick)
+
+    def on_button_clicked(self, b):
+        """Handle button click events"""
+        # print(b['owner'].description)
+        selection = b['owner'].description
+        if selection in self.analysis:
+            self.analysis.remove(selection)
+        else:
+            self.analysis.append(selection)
+        self.update()
+
+    def update(self):
+        """Update the plot based on the selected analysis options"""
+        ax = self.ax
+        ax.clear()
+        selection = self.analysis
+        ax.plot([0, 24], [0, 0], color='black')
+        ax.plot([14, 14], [-.3, .3], color='black')
+        ax.text(14, 1, s='f')
+        lens = patches.Ellipse((4, 0),
+                               width=.8,
+                               height=14,
+                               facecolor='gray')
+        ax.add_patch(lens)
+        ax.text(4, 8, s='lens')
+        sample = patches.Rectangle((10, -2),
+                                   width=.2,
+                                   height=4,
+                                   facecolor='gray')
+
+        ax.add_patch(sample)
+        ax.text(9, 3, s='sample')
+        ax.set_ylim(-10, 10)
+        ax.set_aspect('equal')
+
+        if self.words[0] in selection:
+            color = 'gray'
+            ax.plot([0, 4], [1, 1], color=color)
+            ax.plot([0, 4], [-1, -1], color=color)
+            ax.plot([4, 24], [1, -1], color=color)
+            ax.plot([4, 24], [-1, 1], color=color)
+
+            circle1 = patches.Ellipse((24, 0), width=.2, height=2, fill=False, color=color)
+            ax.add_patch(circle1)
+
+        if self.words[1] in selection:
+            color = 'red'
+            ax.plot([0, 4], [3, 3], color=color)
+            ax.plot([0, 4], [-3, -3], color=color)
+            ax.plot([4, 24], [3, -4], color=color)
+            ax.plot([4, 24], [-3, 4], color=color)
+            ax.plot([0, 4], [2.5, 2.5], color=color)
+            ax.plot([0, 4], [-2.50, -2.5], color=color)
+            ax.plot([4, 24], [2.5, -2.8], color=color)
+            ax.plot([4, 24], [-2.5, 2.8], color=color)
+
+            circle2 = patches.Ellipse((24, 0), width=.9, height=8, fill=False, color=color)
+            ax.add_patch(circle2)
+            circle3 = patches.Ellipse((24, 0), width=.6, height=5.6, fill=False, color=color)
+            ax.add_patch(circle3)
+            circle3 = patches.Ellipse((24, 0), width=.7, height=7.3, fill=False, color=color, linewidth=5, alpha=.5)
+            ax.add_patch(circle3)
+
+        if self.words[2] in selection:
+            color = 'orange'
+            ax.plot([0, 4], [4, 4], color=color)
+            ax.plot([0, 4], [-4, -4], color=color)
+            ax.plot([4, 24], [4, -9.25], color=color)
+            ax.plot([4, 24], [-4, 9.25], color=color)
+
+            circle4 = patches.Ellipse((24, 0), width=2, height=18.5, fill=False, color=color)
+            plt.gca().add_patch(circle4)
+
+        if self.words[3] in selection:
+            color = 'green'
+            ax.plot([0, 4], [5, 5], color=color, linestyle='--')
+            ax.plot([0, 4], [-5, -5], color=color, linestyle='--')
+            ax.plot([4, 24], [5, -13], color=color, linestyle='--')
+            ax.plot([4, 24], [-5, 13], color=color, linestyle='--')
+
+            circle6 = patches.Ellipse((24, 0), width=4, height=26, fill=False, color=color, linestyle='--')
+            plt.gca().add_patch(circle6)