Documentation

model.py

class temgymbasic.model.Model(components, beam_z=1, num_rays=256, beam_type='point', beam_semi_angle=0.7853981633974483, beam_tilt_x=0, beam_tilt_y=0, beam_width=0.2, detector_size=0.5, detector_pixels=128)

Generates a model electron microscope. This class generates performs the matrix multiplication and function updates to calculate their positions throughout the column.

__init__(components, beam_z=1, num_rays=256, beam_type='point', beam_semi_angle=0.7853981633974483, beam_tilt_x=0, beam_tilt_y=0, beam_width=0.2, detector_size=0.5, detector_pixels=128)

Parameters

• components (list) – List of components to electron microscope component to input into the model

• beam_z (int, optional) – Sets the initial height of the beam, by default 1

• num_rays (int, optional) – Sets the number of rays generated at the beam_z position. A large number of rays will in general slow down the programme quite a lot. , by default 256

• beam_type (str, optional) –

  Choose the type of beam:

  -‘point’ beam creates a set of rays that start from a single point and

  spread out like a cone.

  -‘paralell’ beam creates a set of rays that start from the same position, but each have the same angle. - ‘axial’ creates a beam which is only visible on the x and y axis. - ‘x_axial’ creates a beam which is only visible on the x-axis. This is only used for matplotlib diagrams, by default ‘point’

• beam_semi_angle (float, optional) – Set the semi angle of the beam in radians., by default np.pi/4

• beam_tilt_x (int, optional) – Set the tilt of the beam in the x direction, by default 0

• beam_tilt_y (int, optional) – Set the tilt of the beam in the y direction, by default 0

• beam_width (float, optional) – Set the width of the beam - only matters if “paralell” beam type is selected

• detector_size (float, optional) – Set the size of the detector, by default 0.5

• detector_pixels (int, optional) – Set the number of pixels in the detector. A large number of pixels will probably considerably hinder performance, by default 128

create_gui()

Create the GUI

generate_rays()

Generate electron rays

propagate(z)

Propagation matrix

Parameters

z (float) – Distance to propagate rays

Returns

Propagation matrix

Return type

ndarray

set_model_labels()

Set labels of the model inside the GUI

set_z_positions()

Create the z position list of all components in the model

step()

Master function that updates the matrices and perfroms ray propagation

Returns

r – Returns the array of ray positions

Return type

ndarray

update_component_matrix()

Update the matrix of each component

update_gui()

Update the GUI

update_rays_stepwise()

Perform the neccessary matrix multiplications and function multiplications to propagate the beam through the column

components.py

class temgymbasic.components.Aperture(z, name='Aperture', aperture_radius_inner=0.005, aperture_radius_outer=0.25, label_radius=0.3, num_points=50, x=0, y=0)

Creates an aperture component and handles calls to GUI creation, updates to GUI and stores the component parameters. Important to note that the transfer matrix of the aperture only propagates rays. The logic of blocking rays is handled inside the “model” function.

__init__(z, name='Aperture', aperture_radius_inner=0.005, aperture_radius_outer=0.25, label_radius=0.3, num_points=50, x=0, y=0)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘Aperture’

• aperture_radius_inner (float, optional) – Inner radius of the aperture, by default 0.005

• aperture_radius_outer (float, optional) – Outer radius of the aperture, by default 0.25

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

• x (int, optional) – X position of the centre of the aperture, by default 0

• y (int, optional) – Y position of the centre of the aperture, by default 0

aperture_matrix()

Aperture transfer matrix - simply a unit matrix of ones because we only need to propagate rays that pass through the centre of the aperture.

Returns

unit matrix

Return type

ndarray

create_gui()

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

update_mesh()

class temgymbasic.components.AstigmaticLens(z, name='', fx=- 0.5, fy=- 0.5, label_radius=0.3, radius=0.25, num_points=50)

Creates an Astigmatic lens component and handles calls to GUI creation, updates to GUI and stores the component matrix.

__init__(z, name='', fx=- 0.5, fy=- 0.5, label_radius=0.3, radius=0.25, num_points=50)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• fx (float, optional,) – Focal length of this lens in x, by default -0.5

• fx – Focal length of this lens in y, by default -0.5

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

create_gui()

lens_matrix(fx, fy)

Astigmatic lens ray transfer matrix

Parameters

• fx (float) – focal length in x

• fy (float) – focal length in y

Returns

Output Ray Transfer Matrix

Return type

ndarray

set_flabel()

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

class temgymbasic.components.Biprism(z, name='', deflection=0.5, theta=0, label_radius=0.3, radius=0.25, width=0.01, num_points=50)

Creates a biprism component and handles calls to GUI creation, updates to GUI and stores the component parameters. Important to note that the transfer matrix of the biprism is only cosmetic: It still need to be multiplied by the sign of the position of the ray to perform like a biprism.

__init__(z, name='', deflection=0.5, theta=0, label_radius=0.3, radius=0.25, width=0.01, num_points=50)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• deflection (float, optional) – Biprism deflection kick in slope units to the incoming ray angle, by default 0.5

• theta (int, optional) – Angle of the biprism - Two options - 0 or 1. 0 for 0 degree rotation, 1 for 90 degree rotation, by default 0

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• width (float, optional) – Width of the biprism model, by default 0.01

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

biprism_matrix(deflection)

Biprims deflection matrix - only used to store values.

Parameters

deflection (float) – update deflection kick to rays in slope coordinates

Returns

Output transfer matrix

Return type

ndarray

create_gui()

set_gl_geom()

set_gl_label()

set_gui_label()

set_matrix()

update_geometry()

update_gui()

class temgymbasic.components.Deflector(z, name='', defx=0.5, defy=0.5, label_radius=0.3, radius=0.25, num_points=50)

Creates a single deflector component and handles calls to GUI creation, updates to GUI and stores the component matrix. See Double Deflector component for a more useful version

__init__(z, name='', defx=0.5, defy=0.5, label_radius=0.3, radius=0.25, num_points=50)

_summary_

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• defx (float, optional) – deflection kick in slope units to the incoming ray x angle, by default 0.5

• defy (float, optional) – deflection kick in slope units to the incoming ray y angle, by default 0.5

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

create_gui()

deflector_matrix(def_x, def_y)

Single deflector ray transfer matrix

Parameters

• def_x (float) – deflection in x in slope units

• def_y (_type_) – deflection in y in slope units

Returns

Output ray transfer matrix

Return type

ndarray

set_deflabel()

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

class temgymbasic.components.DoubleDeflector(z_up, z_low, name='', updefx=0.0, updefy=0.0, lowdefx=0.0, lowdefy=0.0, label_radius=0.3, radius=0.25, num_points=50)

Creates a double deflector component and handles calls to GUI creation, updates to GUI and stores the component matrix. Primarily used in the Beam Tilt/Shift alignment.

__init__(z_up, z_low, name='', updefx=0.0, updefy=0.0, lowdefx=0.0, lowdefy=0.0, label_radius=0.3, radius=0.25, num_points=50)

Parameters

• z_up (float) – Position of the upper deflection component in optic axis

• z_low (float) – Position of the lower deflection component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• updefx (float, optional) – deflection kick of upper deflector in slope units to the incoming ray x angle, by default 0.0

• updefy (float, optional) – deflection kick of upper deflector in slope units to the incoming ray y angle, by default 0.0

• lowdefx (float, optional) – deflection kick of lower deflector in slope units to the incoming ray x angle, by default 0.0

• lowdefy (float, optional) – deflection kick of lower deflector in slope units to the incoming ray y angle, by default 0.0

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

create_gui()

deflector_matrix(def_x, def_y)

Single deflector ray transfer matrix

Parameters

• def_x (float) – deflection in x in slope units

• def_y (_type_) – deflection in y in slope units

Returns

Output ray transfer matrix

Return type

ndarray

set_deflabel()

set_gl_geom()

set_gl_label()

set_matrices()

update_gui()

class temgymbasic.components.Lens(z, name='', f=0.5, label_radius=0.3, radius=0.25, num_points=50)

Creates a lens component and handles calls to GUI creation, updates to GUI and stores the component matrix.

__init__(z, name='', f=0.5, label_radius=0.3, radius=0.25, num_points=50)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• f (float, optional,) – Focal length of this lens, by default 0.5

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

create_gui()

lens_matrix(f)

Lens ray transfer matrix

Parameters

f (float) – Focal length of lens

Returns

Output Ray Transfer Matrix

Return type

ndarray

set_flabel()

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

class temgymbasic.components.Quadrupole(z, name='', fx=- 0.5, fy=- 0.5, label_radius=0.3, radius=0.25, num_points=50)

Creates a quadrupole component and handles calls to GUI creation, updates to GUI and stores the component matrix. Almost exactly the same as astigmatic lens component

__init__(z, name='', fx=- 0.5, fy=- 0.5, label_radius=0.3, radius=0.25, num_points=50)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• fx (float, optional,) – Focal length of this quadrupole in x, by default -0.5

• fx – Focal length of this quadrupole in y, by default -0.5

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

create_gui()

lens_matrix(fx, fy)

Astigmatic lens ray transfer matrix

Parameters

• fx (float) – focal length in x

• fy (float) – focal length in y

Returns

Output Ray Transfer Matrix

Return type

ndarray

set_flabel()

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

class temgymbasic.components.Sample(z, name='', label_radius=0.3, width=0.25, num_points=50, x=0.0, y=0.0)

Creates a sample component which serves only as a visualisation on the 3D model.

__init__(z, name='', label_radius=0.3, width=0.25, num_points=50, x=0.0, y=0.0)

Parameters

• z (float) – Position of component in optic axis

• name (str, optional) – Name of this component which will be displayed by GUI, by default ‘’

• label_radius (float, optional) – Location to place the label in the 3D GUI, by default 0.3

• radius (float, optional) – Radius of the 3D model of this component, by default 0.25

• num_points (int, optional) – Number of points to use to make the 3D model, by default 50

• x (float, optional) – X position of sample model, by default 0

• y (int, optional) – Y position of sample model, by default 0

create_gui()

sample_matrix()

Sample transfer matrix - simply a unit matrix of ones because we don’t interact with the sample yet.

Returns

unit matrix

Return type

ndarray

set_gl_geom()

set_gl_label()

set_matrix()

update_gui()

update_mesh()

run.py

class temgymbasic.run.LinearTEMCtrl(model, view)

Control code which links the model and 3D viewer

__init__(model, view)

Parameters

• model (class) – Microscope model

• view (class) – UI Viewer

connectSignals()

Connect the updates to the model to the GUI

set_camera_params(btn)

Parameters

btn (PyQt5 Button) –

’’

timerstart(btn, component)

Start a timer

Parameters

• btn (PyQt5 Button) –

  ’’

• component (class) – Check which component GUI has clicked the button, so we know what timer to start

update()

Update the model

class temgymbasic.run.LinearTEMUi(model)

Create the UI Window

Parameters

QMainWindow (class) – Pyqt5’s Main window Class

__init__(model)

Init important parameters

Parameters

model (class) – Microscope model

create3DDisplay()

Create the 3D Display

createDetectorDisplay()

Create the detector display

createGUI()

Create the gui display

temgymbasic.run.run_pyqt(model)

Main code to run a pyqt model

Parameters

model (class) – Microscope Model

temgymbasic.run.show_matplotlib(model, name='model.svg', component_lw=4, edge_lw=1, label_fontsize=20)

Code to show a matplotlib model

Parameters

• model (class) – Microscope Model

• name (str, optional) – Name of file, by default ‘model.svg’

• component_lw (int, optional) – Linewidth of component outline, by default 4

• edge_lw (int, optional) – Linewidth of highlight to edges, by default 1

• label_fontsize (int, optional) – Fontsize of labels, by default 20

Returns

• fig (class) – Matplotlib figure object

• ax (class) – Matplotlib axis object of the figure

shapes.py

temgymbasic.shapes.aperture(r_i, r_o, n_i, n_o, x, y, z)

3D vertices model of an aperture

Parameters

• r_i (float) – Radius of inner aperture model

• r_o (float) – Radius of outer aperture model

• n_i (int) – Number of points used to represent inner aperture model

• n_o (int) – Number of points used to represent outer aperture model

• x (float) – X position of aperture

• y (float) – Y position of aperture

• z (float) – Z position of aperture

Returns

verts3D – 3D array of vertices that represent the aperture model

Return type

ndarray

temgymbasic.shapes.biprism(r, z, theta)

Wire model geometry for biprism

Parameters

• r (float) – Radius of wire

• z (float) – Z position of wire

• theta (float) – Angle of wire - Two options, 0 or np.pi/2

Returns

points – Points array of wire geometry

Return type

ndarray

temgymbasic.shapes.deflector(r, phi, z, n_arc)

Wire model geometry of deflector

Parameters

• r (float) – Radius of deflector geometry

• phi (float) – Angular width of deflector mode

• z (float) – Z position of deflector geometry

• n_arc (int) – Number of arcs to use to make up the model

Returns

• points_arc_1 (ndarray) – Points of a circle to represent the lens geometry

• points_arc_2 (ndarray) – Points of a circle to represent the lens geometry

temgymbasic.shapes.lens(r, z, n_arc)

Wire model geometry of lens

Parameters

• r (float) – Radius of lens geometry

• z (float) – Z position of lens geometry

• n_arc (int) – Number of arcs to use to make up the model

Returns

points_circle – Points of a circle to represent the lens geometry

Return type

ndarray

temgymbasic.shapes.quadrupole(r, phi, z, n_arc)

Wire model geometry of deflector

Parameters

• r (float) – Radius of quadrupole geometry

• phi (float) – Angular width of quadrupole mode

• z (float) – Z position of quadrupole geometry

• n_arc (int) – Number of arcs to use to make up the model

Returns

• points_arc_1 (ndarray) – Points of first semi circle that represent the quadrupole geometry

• points_arc_2 (ndarray) – Points of second semi circle that represent the quadrupole geometry

• points_arc_3 (ndarray) – Points of third semi circle that represent the quadrupole geometry

• points_arc_4 (ndarray) – Points of fourth semi circle that represent the quadrupole geometry

temgymbasic.shapes.square(w, x, y, z)

Generates vertices for a square 3D model. Used to represent the detector

Parameters

• w (float) – Width of the square wire model

• x (float) – X position of the square wire model

• y (float) – Wire position of the square wire model

• z (float) – Wire position of the square wire model

Returns

verts3D – vertices to draw a 3D model

Return type

ndarray

functions.py

temgymbasic.functions.axial_point_beam(r, beam_semi_angle)

Generates a cross shaped initial beam on the x and y axis that spreads out with semi angle ‘beam_semi_angle’

Parameters

• r (ndarray) – Ray position and slope matrix

• beam_semi_angle (float) – Beam semi angle in radians

Returns

r – Updated ray position & slope matrix which create a circular beam

Return type

ndarray

temgymbasic.functions.circular_beam(r, outer_radius)

Generates a circular paralell initial beam

Parameters

• r (ndarray) – Ray position and slope matrix

• outer_radius (float) – Outer radius of the circular beam

Returns

• r (ndarray) – Updated ray position & slope matrix which create a circular beam

• num_points_kth_ring (ndarray) – Array of the number of points on each ring of our circular beam

temgymbasic.functions.get_image_from_rays(rays_x, rays_y, detector_size, detector_pixels)

From an image of rays that hit the detector at the base of the TEM

Parameters

• rays_x (ndarray) – X position of rays that hit the detector

• rays_y (ndarray) – X position of rays that hit the detector

• detector_size (float) – Real size of the detector in the model. Single value that describes it’s edge length. Note that the detector is always square

• detector_pixels (int) – Resolution of the detector.

Returns

• detector_image (ndarray) – Image of where rays have hit the detector

• image_pixel_coords (ndarray) – Coordinates of where reach ray has hit the detector

temgymbasic.functions.point_beam(r, beam_semi_angle)

Generates a point initial beam that spreads out with semi angle ‘beam_semi_angle’

Parameters

• r (ndarray) – Ray position and slope matrix

• beam_semi_angle (float) – Beam semi angle in radians

Returns

• r (ndarray) – Updated ray position & slope matrix which create a circular beam

• num_points_kth_ring (ndarray) – Array of the number of points on each ring of our circular beam

temgymbasic.functions.x_axial_point_beam(r, beam_semi_angle)

Generates a cross shaped initial beam on the x axis that spreads out with semi angle ‘beam_semi_angle’

Parameters

• r (ndarray) – Ray position and slope matrix

• beam_semi_angle (float) – Beam semi angle in radians

Returns

r – Updated ray position & slope matrix which create a circular beam

Return type

ndarray

gui.py

class temgymbasic.gui.ApertureGui(name, min_radius, max_radius, inner_radius, x, y)

GUI for the aperture component

__init__(name, min_radius, max_radius, inner_radius, x, y)

Parameters

• name (str) – Name of component

• min_radius (float) – Minimum radius of the aperture

• max_radius (float) – Max radius of the aperture

• inner_radius (float) – Initial inner radius of the aperture

• x (float) – X position of component

• y (float) – y position of component

class temgymbasic.gui.AstigmaticLensGui(name, gui_label, fx, fy)

Gui for the Astigmatic Lens component

__init__(name, gui_label, fx, fy)

Parameters

• name (str) – Name of component

• gui_label (str) – Label of focal length slider in GUI

• fx (float) – Focal length in x axis

• fy (float) – Focal length in y axis

class temgymbasic.gui.BiprismGui(name, deflection, theta)

GUI for the biprism component

__init__(name, deflection, theta)

Parameters

• name (str) – Name of component

• deflection (float) – Deflection angle in Slope units

• theta (int) – Angle of biprism. Determines if the biprism creates deflects in the x or y direction. Two options: 0 or 1. 0 for 0 degrees, 1 for 90 degree rotation.

class temgymbasic.gui.DeflectorGui(name, defx, defy)

GUI for the deflector component

__init__(name, defx, defy)

Parameters

• name (str) – Name of component

• defx (float) – Initial X deflection of deflector

• defy (float) – Initial Y deflection of deflector

class temgymbasic.gui.DoubleDeflectorGui(name, updefx, updefy, lowdefx, lowdefy)

GUI for the double deflector component

__init__(name, updefx, updefy, lowdefx, lowdefy)

Parameters

• name (str) – Name of component

• updefx (float) – Initial X deflection of upper deflector

• updefy (float) – Initial Y deflection of upper deflector

• lowdefx (float) – Initial X deflection of lower deflector

• lowdefy (float) – Initial Y deflection of lower deflector

class temgymbasic.gui.ModelGui(num_rays, beam_type, beam_semi_angle, beam_tilt_x, beam_tilt_y)

Overall GUI of the model

__init__(num_rays, beam_type, beam_semi_angle, beam_tilt_x, beam_tilt_y)

Parameters

• num_rays (int) – Number of rays in the model

• beam_type (str) – Type of initial beam: Axial, paralell of point.

• beam_semi_angle (float) – Semi angle of the beam

• beam_tilt_x (float) – Initial x tilt of the beam in radians

• beam_tilt_y (float) – Initial y tilt of the beam in radians

uncheck(btn)

Determines which button is checked, and unchecks others

Parameters

btn (Pyqt5 Button) –

class temgymbasic.gui.SampleGui(name, x, y)

Gui to allow a user to move the sample in the 3D model

__init__(name, x, y)

Parameters

• name (str) – Name of the component

• x (float) – X position of component

• y (float) – Y position of component