TEMUL Toolkit
latest
Contents
Installation
Getting started
Analysis Workflows
Finding Polarisation Vectors
Plotting Polarisation and Movement Vectors
Plot Lattice Structure Maps
Calculation of Atom Plane Curvature
Analysis of PTO Domain Wall Junction
Masked FFT and iFFT
Line Intensity Profile Comparisons
Interactive Image Filtering
API documentation
TEMUL Toolkit
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Index
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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P
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R
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S
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T
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V
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W
A
angle_label() (in module temul.topotem.polarisation)
assign_z_height() (in module temul.model_creation)
assign_z_height_to_sublattice() (in module temul.model_creation)
atom_deviation_from_straight_line_fit() (in module temul.topotem.polarisation)
atom_to_atom_distance_grouped_mean() (in module temul.topotem.polarisation)
atomic_radii_in_pixels() (in module temul.element_tools)
auto_generate_sublattice_element_list() (in module temul.model_creation)
B
batch_convert_emd_to_image() (in module temul.io)
C
calculate_atom_plane_curvature() (in module temul.topotem.lattice_structure_tools)
calibrate_intensity_distance_with_sublattice_roi() (in module temul.signal_processing)
change_sublattice_atoms_via_intensity() (in module temul.model_creation)
change_sublattice_pseudo_inplace() (in module temul.model_creation)
choose_mask_coordinates() (in module temul.topotem.fft_mapping)
choose_points_on_image() (in module temul.topotem.fft_mapping)
color_palettes() (in module temul.signal_plotting)
combine_atom_deviations_from_zone_axes() (in module temul.topotem.polarisation)
combine_element_lists() (in module temul.element_tools)
compare_count_atoms_in_sublattice_list() (in module temul.model_creation)
compare_images_line_profile_one_image() (in module temul.signal_plotting)
compare_images_line_profile_two_images() (in module temul.signal_plotting)
compare_two_image_and_create_filtered_image() (in module temul.signal_processing)
convert_numpy_z_coords_to_z_height_string() (in module temul.model_creation)
convert_vesta_xyz_to_prismatic_xyz() (in module temul.io)
correct_background_elements() (in module temul.model_creation)
correct_off_tilt_vectors() (in module temul.topotem.polarisation)
corrected_vectors_via_average() (in module temul.topotem.polarisation)
corrected_vectors_via_center_of_mass() (in module temul.topotem.polarisation)
count_all_individual_elements() (in module temul.model_creation)
count_atoms_in_sublattice_list() (in module temul.model_creation)
count_element_in_pandas_df() (in module temul.model_creation)
create_dataframe_for_cif() (in module temul.model_creation)
create_dataframe_for_xyz() (in module temul.io)
create_rgb_array() (in module temul.signal_plotting)
crop_image_hs() (in module temul.signal_processing)
D
delete_atom_planes_from_sublattice() (in module temul.topotem.polarisation)
distance_vector() (in module temul.signal_processing)
dm3_stack_to_tiff_stack() (in module temul.io)
double_gaussian_fft_filter() (in module temul.signal_processing)
double_gaussian_fft_filter_optimised() (in module temul.signal_processing)
E
expand_palette() (in module temul.signal_plotting)
F
find_middle_and_edge_intensities() (in module temul.model_creation)
find_middle_and_edge_intensities_for_background() (in module temul.model_creation)
find_polarisation_vectors() (in module temul.topotem.polarisation)
find_polarization_vectors() (in module temul.topotem.polarisation)
fit_1D_gaussian_to_data() (in module temul.signal_processing)
full_atom_plane_deviation_from_straight_line_fit() (in module temul.topotem.polarisation)
G
get_and_return_element() (in module temul.element_tools)
get_angles_from_uv() (in module temul.topotem.polarisation)
get_average_polarisation_in_regions() (in module temul.topotem.polarisation)
get_average_polarisation_in_regions_square() (in module temul.topotem.polarisation)
get_average_polarization_in_regions() (in module temul.topotem.polarisation)
get_average_polarization_in_regions_square() (in module temul.topotem.polarisation)
get_cell_image() (in module temul.signal_processing)
get_cropping_area() (in module temul.signal_plotting)
get_distorted_cubic_signal_adjustable() (in module temul.dummy_data)
get_distorted_cubic_sublattice_adjustable() (in module temul.dummy_data)
get_divide_into() (in module temul.topotem.polarisation)
get_fitting_tools_for_plotting_gaussians() (in module temul.signal_processing)
get_individual_elements_from_element_list() (in module temul.element_tools)
get_masked_ifft() (in module temul.topotem.fft_mapping)
get_max_number_atoms_z() (in module temul.model_creation)
get_most_common_sublattice_element() (in module temul.model_creation)
get_pixel_count_from_image_slice() (in module temul.intensity_tools)
get_polar_2d_colorwheel_color_list() (in module temul.signal_plotting)
get_polarisation_dummy_dataset() (in module temul.dummy_data)
get_polarisation_dummy_dataset_bora() (in module temul.dummy_data)
get_polarised_single_sublattice() (in module temul.dummy_data)
get_polarised_single_sublattice_rotated() (in module temul.dummy_data)
get_positions_from_sublattices() (in module temul.model_creation)
get_scaled_middle_limit_intensity_list() (in module temul.signal_processing)
get_simple_cubic_signal() (in module temul.dummy_data)
get_simple_cubic_sublattice() (in module temul.dummy_data)
get_simple_cubic_sublattice_positions_on_vac() (in module temul.dummy_data)
get_strain_map() (in module temul.topotem.polarisation)
get_sublattice_intensity() (in module temul.intensity_tools)
get_vector_magnitudes() (in module temul.topotem.polarisation)
get_xydata_from_list_of_intensities() (in module temul.signal_processing)
get_xyuv_from_line_fit() (in module temul.topotem.polarisation)
H
hex_to_rgb() (in module temul.signal_plotting)
I
image_difference_intensity() (in module temul.model_creation)
image_difference_position() (in module temul.model_creation)
image_difference_position_new_sub() (in module temul.model_creation)
L
load_and_compare_images() (in module temul.signal_processing)
load_data_and_sampling() (in module temul.io)
load_example_Au_nanoparticle() (in module temul.example_data)
load_example_Cu_nanoparticle_sim() (in module temul.example_data)
load_prismatic_mrc_with_hyperspy() (in module temul.io)
load_Se_implanted_MoS2_data() (in module temul.example_data)
load_Se_implanted_MoS2_simulation() (in module temul.example_data)
M
make_gaussian() (in module temul.signal_processing)
make_gaussian_pos_neg() (in module temul.signal_processing)
make_polarised_sublattice_bora_return() (in module temul.dummy_data)
mean_and_std_nearest_neighbour_distances() (in module temul.signal_processing)
measure_image_errors() (in module temul.signal_processing)
module
temul.dummy_data
temul.element_tools
temul.example_data
temul.intensity_tools
temul.io
temul.model_creation
temul.signal_plotting
temul.signal_processing
temul.topotem.fft_mapping
temul.topotem.lattice_structure_tools
temul.topotem.polarisation
mse() (in module temul.signal_processing)
P
path_to_example_data_MoS2_hex_prismatic() (in module temul.example_data)
path_to_example_data_MoS2_vesta_xyz() (in module temul.example_data)
plot_atom_deviation_from_all_zone_axes() (in module temul.topotem.polarisation)
plot_atom_energies() (in module temul.signal_plotting)
plot_gaussian_fit() (in module temul.signal_processing)
plot_gaussian_fitting_for_multiple_fits() (in module temul.signal_processing)
plot_polarisation_vectors() (in module temul.topotem.polarisation)
plot_polarization_vectors() (in module temul.topotem.polarisation)
polarisation_colorwheel_test_dataset() (in module temul.dummy_data)
print_sublattice_elements() (in module temul.model_creation)
R
ratio_of_lattice_spacings() (in module temul.topotem.polarisation)
remove_average_background() (in module temul.intensity_tools)
remove_image_intensity_in_data_slice() (in module temul.signal_processing)
remove_local_background() (in module temul.intensity_tools)
return_fitting_of_1D_gaussian() (in module temul.signal_processing)
return_xyz_coordinates() (in module temul.model_creation)
return_z_coordinates() (in module temul.model_creation)
rgb_to_dec() (in module temul.signal_plotting)
rotation_of_atom_planes() (in module temul.topotem.polarisation)
S
save_individual_images_from_image_stack() (in module temul.io)
scaled() (temul.signal_plotting.Sublattice_Hover_Intensity method)
scaling_z_contrast() (in module temul.model_creation)
setup_annotation() (temul.signal_plotting.Sublattice_Hover_Intensity method)
sine_wave_function_strain_gradient() (in module temul.topotem.lattice_structure_tools)
sine_wave_sublattice() (in module temul.dummy_data)
snap() (temul.signal_plotting.Sublattice_Hover_Intensity method)
sort_sublattice_intensities() (in module temul.model_creation)
split_and_sort_element() (in module temul.element_tools)
Sublattice_Hover_Intensity (class in temul.signal_plotting)
T
temul.dummy_data
module
temul.element_tools
module
temul.example_data
module
temul.intensity_tools
module
temul.io
module
temul.model_creation
module
temul.signal_plotting
module
temul.signal_processing
module
temul.topotem.fft_mapping
module
temul.topotem.lattice_structure_tools
module
temul.topotem.polarisation
module
toggle_atom_refine_position_automatically() (in module temul.signal_processing)
V
visualise_dg_filter() (in module temul.signal_processing)
W
write_cif_from_dataframe() (in module temul.io)
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