Index

A

add_keyboard() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_endpoint_details() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_image_series() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_img_overlays() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_line_features() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_save_as_json() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_shifts() (microscopy_data_analysis.visualisation.image_plotting method) addfunc_text_input() (microscopy_data_analysis.visualisation.image_plotting method) align() (in module microscopy_data_analysis.image_aligning) align_com_precise() (in module microscopy_data_analysis.image_aligning) align_image_fast1() (in module microscopy_data_analysis.image_aligning)

align_image_fast2() (in module microscopy_data_analysis.image_aligning) align_images() (in module microscopy_data_analysis.image_aligning) align_pair() (in module microscopy_data_analysis.image_aligning) align_pair_special() (in module microscopy_data_analysis.image_aligning) all_connected_points() (microscopy_data_analysis.line_analysis.line_analysis_object method) assure_multiple() (in module microscopy_data_analysis.general_util) asym_pseudo_voigt() (in module microscopy_data_analysis.peak_fitting) asym_pseudo_voigt_center() (in module microscopy_data_analysis.peak_fitting) asym_pseudo_voigt_normalized_asym() (in module microscopy_data_analysis.peak_fitting) asym_pseudo_voigt_parameter_bounds() (in module microscopy_data_analysis.peak_fitting) asym_pseudo_voigt_peakheight() (in module microscopy_data_analysis.peak_fitting) asym_pseudo_voigt_table() (in module microscopy_data_analysis.peak_fitting)

B

bin_centering() (in module microscopy_data_analysis.general_util)

C

calculate_FWHM() (in module microscopy_data_analysis.peak_fitting) ccw() (in module microscopy_data_analysis.general_util) center_of_mass() (in module microscopy_data_analysis.peak_fitting) change_source_imgs() (microscopy_data_analysis.stacks.image_stack method) changed (microscopy_data_analysis.visualisation.line_object attribute) check_intersection_type() (microscopy_data_analysis.line_analysis.line_analysis_object method) check_line_vars() (microscopy_data_analysis.line_analysis.line_analysis_object method) check_misclassification() (microscopy_data_analysis.line_analysis.line_analysis_object method) check_pairs() (microscopy_data_analysis.stacks.image_stack method) circle_perimeter_points() (in module microscopy_data_analysis.general_util) click() (in module microscopy_data_analysis.image_aligning)

clip() (microscopy_data_analysis.stacks.image_stack method) close_translation_by_phase_correlation() (in module microscopy_data_analysis.image_aligning) compute_M() (in module microscopy_data_analysis.line_analysis) connection_groups() (microscopy_data_analysis.stacks.image_stack method) convert_dm4_to_png() (in module microscopy_data_analysis.data_formats_io) convert_to_uint16() (microscopy_data_analysis.stacks.image_stack method) create_bins() (in module microscopy_data_analysis.general_util) create_h5cube_duplicate_for_modifying() (microscopy_data_analysis.stacks.image_stack method) create_rois() (in module microscopy_data_analysis.peak_fitting) crop_from_points() (microscopy_data_analysis.stacks.image_stack method) custom_colormap() (in module microscopy_data_analysis.general_util)

D

determine_thresh() (in module microscopy_data_analysis.general_util) draw_dashed_line() (in module microscopy_data_analysis.general_util)

dust_from_flat_field() (microscopy_data_analysis.stacks.image_stack method) dust_removal() (microscopy_data_analysis.stacks.image_stack method) dust_removal_all() (microscopy_data_analysis.stacks.image_stack method)

E

eliminate_side_maxima_checkmaps() (microscopy_data_analysis.line_analysis.line_analysis_object method)

eliminate_side_maxima_image() (microscopy_data_analysis.line_analysis.line_analysis_object method)

F

fft_circ_mask() (in module microscopy_data_analysis.general_util) find_next_cut() (in module microscopy_data_analysis.general_util)

flat_field_correction() (microscopy_data_analysis.stacks.image_stack method) flat_field_generation() (microscopy_data_analysis.stacks.image_stack method) folder_file() (in module microscopy_data_analysis.general_util)

G

gaussian() (in module microscopy_data_analysis.peak_fitting) gaussian_A() (in module microscopy_data_analysis.peak_fitting) gaussian_parameter_bounds() (in module microscopy_data_analysis.peak_fitting) gaussian_peakheight() (in module microscopy_data_analysis.peak_fitting) get_all_files() (in module microscopy_data_analysis.general_util) get_angular_dist() (in module microscopy_data_analysis.general_util) get_connected_points() (in module microscopy_data_analysis.line_analysis) get_connections() (microscopy_data_analysis.line_analysis.line_analysis_object method) get_dm4_with_metadata() (in module microscopy_data_analysis.data_formats_io) get_emd_with_metadata() (in module microscopy_data_analysis.data_formats_io)

get_files_of_format() (in module microscopy_data_analysis.general_util) get_img() (microscopy_data_analysis.stacks.image_stack method) get_indices_sparse() (in module microscopy_data_analysis.line_analysis) get_methods() (microscopy_data_analysis.line_analysis.line_analysis_object method) get_n_peaks_1d() (in module microscopy_data_analysis.peak_fitting) get_next_line_index() (microscopy_data_analysis.visualisation.image_plotting static method) get_number_of_connections() (microscopy_data_analysis.line_analysis.line_analysis_object method) get_outer_polygon_limits() (microscopy_data_analysis.stacks.image_stack method) get_SEMtif_with_metadata() (in module microscopy_data_analysis.data_formats_io) get_shift() (microscopy_data_analysis.visualisation.image_plotting static method)

H

h5_to_pyramidal_tiff() (in module microscopy_data_analysis.data_formats_io)

h5_to_tiff() (in module microscopy_data_analysis.data_formats_io)

I

image_plotting (class in microscopy_data_analysis.visualisation) image_stack (class in microscopy_data_analysis.stacks) img_add_weighted_gray_alpha() (in module microscopy_data_analysis.image_processing) img_add_weighted_gray_alpha_numba() (in module microscopy_data_analysis.image_processing) img_add_weighted_rgba() (in module microscopy_data_analysis.image_processing) img_anms() (in module microscopy_data_analysis.image_processing) img_autoclip() (in module microscopy_data_analysis.image_processing) img_correlation() (in module microscopy_data_analysis.image_aligning) img_gammaCorrection() (in module microscopy_data_analysis.image_processing) img_gray_to_rgba() (in module microscopy_data_analysis.image_processing) img_make_square() (in module microscopy_data_analysis.image_processing) img_morphLaplace() (in module microscopy_data_analysis.image_processing) img_noise_line_suppression() (in module microscopy_data_analysis.image_processing) img_normalize() (in module microscopy_data_analysis.image_processing) img_normalize_fast() (in module microscopy_data_analysis.image_processing) img_normalize_numba() (in module microscopy_data_analysis.image_processing) img_padding_attenuation() (in module microscopy_data_analysis.image_processing) img_periodic_tiling() (in module microscopy_data_analysis.image_processing) img_rebin_by_mean() (in module microscopy_data_analysis.image_processing)

img_rotate_back() (in module microscopy_data_analysis.image_processing) img_rotate_bound() (in module microscopy_data_analysis.image_processing) img_single_to_double_channel() (in module microscopy_data_analysis.image_processing) img_to_half_int16() (in module microscopy_data_analysis.image_processing) img_to_half_int8() (in module microscopy_data_analysis.image_processing) img_to_int16() (in module microscopy_data_analysis.image_processing) img_to_int8() (in module microscopy_data_analysis.image_processing) img_to_uint16() (in module microscopy_data_analysis.image_processing) img_to_uint8() (in module microscopy_data_analysis.image_processing) img_to_uint8_fast() (in module microscopy_data_analysis.image_processing) img_to_uint8_numba() (in module microscopy_data_analysis.image_processing) img_transform() (in module microscopy_data_analysis.image_processing) img_transform_minimal() (in module microscopy_data_analysis.image_processing) imgs_from_datacube() (microscopy_data_analysis.stacks.image_stack method) imsave() (in module microscopy_data_analysis.data_formats_io) imsave_multi() (in module microscopy_data_analysis.data_formats_io) info() (microscopy_data_analysis.stacks.image_stack method) intersect() (in module microscopy_data_analysis.general_util) isleft() (in module microscopy_data_analysis.general_util)

L

length (microscopy_data_analysis.visualisation.line_object attribute) line_analysis_object (class in microscopy_data_analysis.line_analysis) line_check_angle() (in module microscopy_data_analysis.line_detection) line_check_angle_s() (in module microscopy_data_analysis.line_detection) line_enhance_horizontal() (in module microscopy_data_analysis.line_detection) line_object (class in microscopy_data_analysis.visualisation) line_process() (in module microscopy_data_analysis.line_detection)

line_process_partial() (in module microscopy_data_analysis.line_detection) line_process_vis() (in module microscopy_data_analysis.line_detection) lineIntersection() (in module microscopy_data_analysis.general_util) load_cmap() (in module microscopy_data_analysis.general_util) lorentzian() (in module microscopy_data_analysis.peak_fitting) lorentzian_A() (in module microscopy_data_analysis.peak_fitting) lorentzian_parameter_bounds() (in module microscopy_data_analysis.peak_fitting) lorentzian_peakheight() (in module microscopy_data_analysis.peak_fitting)

M

make_circular_mask() (in module microscopy_data_analysis.general_util) make_line_overview() (in module microscopy_data_analysis.line_analysis) (microscopy_data_analysis.line_analysis.line_analysis_object method) make_mask() (in module microscopy_data_analysis.general_util) make_polygons() (microscopy_data_analysis.stacks.image_stack method) map_from_polygons() (microscopy_data_analysis.stacks.image_stack method) map_from_polygons_h5() (microscopy_data_analysis.stacks.image_stack method) max_from_2d() (in module microscopy_data_analysis.general_util) merge_conpoi() (microscopy_data_analysis.line_analysis.line_analysis_object method) microscopy_data_analysis.data_formats_io module microscopy_data_analysis.general_util module microscopy_data_analysis.image_aligning module microscopy_data_analysis.image_processing module microscopy_data_analysis.line_analysis module

microscopy_data_analysis.line_detection module microscopy_data_analysis.peak_fitting module microscopy_data_analysis.stacks module microscopy_data_analysis.visualisation module module microscopy_data_analysis.data_formats_io microscopy_data_analysis.general_util microscopy_data_analysis.image_aligning microscopy_data_analysis.image_processing microscopy_data_analysis.line_analysis microscopy_data_analysis.line_detection microscopy_data_analysis.peak_fitting microscopy_data_analysis.stacks microscopy_data_analysis.visualisation multi_ident_func_fit() (in module microscopy_data_analysis.peak_fitting)

N

normalize() (microscopy_data_analysis.stacks.image_stack method)

O

obtain_maps() (in module microscopy_data_analysis.line_detection)

optimize_positions() (microscopy_data_analysis.stacks.image_stack method) overwrite_modifiable_datasets() (microscopy_data_analysis.stacks.image_stack method)

P

peak_com2d() (in module microscopy_data_analysis.general_util) peak_fit() (in module microscopy_data_analysis.peak_fitting) phase_correlation() (in module microscopy_data_analysis.image_aligning) pinpoint_crossings() (microscopy_data_analysis.line_analysis.line_analysis_object method) pixel_to_real() (microscopy_data_analysis.stacks.image_stack method) plot_connection_network() (microscopy_data_analysis.stacks.image_stack method)

point_in_convex_ccw_roi() (in module microscopy_data_analysis.general_util) points_on_image() (in module microscopy_data_analysis.image_aligning) polygon_roi() (in module microscopy_data_analysis.general_util) print_number_of_lines() (microscopy_data_analysis.line_analysis.line_analysis_object method) pseudo_voigt() (in module microscopy_data_analysis.peak_fitting) pseudo_voigt_parameter_bounds() (in module microscopy_data_analysis.peak_fitting) pseudo_voigt_peakheight() (in module microscopy_data_analysis.peak_fitting)

R

read_in_json() (in module microscopy_data_analysis.visualisation) read_in_json_old() (in module microscopy_data_analysis.visualisation) readable_names() (in module microscopy_data_analysis.data_formats_io) real_to_pixel() (microscopy_data_analysis.stacks.image_stack method)

refine_positions() (microscopy_data_analysis.stacks.image_stack method) rfft_circ_mask() (in module microscopy_data_analysis.general_util) rfft_starmask() (in module microscopy_data_analysis.general_util) rfft_to_fft() (in module microscopy_data_analysis.general_util)

S

save_as_json() (in module microscopy_data_analysis.visualisation) save_cmap() (in module microscopy_data_analysis.general_util) save_dm4_spectra_as_csv() (in module microscopy_data_analysis.data_formats_io) sequential_peak_fit() (in module microscopy_data_analysis.peak_fitting) set_directory_path() (microscopy_data_analysis.stacks.image_stack method) set_img() (microscopy_data_analysis.stacks.image_stack method) set_img_list() (microscopy_data_analysis.stacks.image_stack method) set_positions() (microscopy_data_analysis.stacks.image_stack method) set_print_mode() (microscopy_data_analysis.stacks.image_stack method) set_units_per_pixel() (microscopy_data_analysis.stacks.image_stack method) show() (microscopy_data_analysis.visualisation.image_plotting method) shrink_extend_line() (microscopy_data_analysis.line_analysis.line_analysis_object method) sift_align_matches() (in module microscopy_data_analysis.image_aligning) smoothbox_kernel() (in module microscopy_data_analysis.general_util) sniff_dimensions() (microscopy_data_analysis.stacks.image_stack method) snip() (in module microscopy_data_analysis.peak_fitting) snip_pure() (in module microscopy_data_analysis.peak_fitting) sort_ids_out() (microscopy_data_analysis.line_analysis.line_analysis_object method) sort_tuples_close_repetition() (microscopy_data_analysis.stacks.image_stack static method)

sortout_by_angle() (microscopy_data_analysis.line_analysis.line_analysis_object method) sortout_by_confidence() (microscopy_data_analysis.line_analysis.line_analysis_object method) sortout_by_value() (microscopy_data_analysis.line_analysis.line_analysis_object method) sortout_short() (microscopy_data_analysis.line_analysis.line_analysis_object method) sortout_zero_connections() (microscopy_data_analysis.line_analysis.line_analysis_object method) split_function_into_equal_area_parts() (in module microscopy_data_analysis.general_util) stack_align() (in module microscopy_data_analysis.image_aligning) stack_align_com_precise() (in module microscopy_data_analysis.image_aligning) stack_align_from_matrices() (in module microscopy_data_analysis.image_aligning) stack_crop_shifts() (in module microscopy_data_analysis.image_aligning) stack_shift_precise() (in module microscopy_data_analysis.image_aligning) stack_shifting() (in module microscopy_data_analysis.image_aligning) stack_sift_align_to_first() (in module microscopy_data_analysis.image_aligning) stats() (microscopy_data_analysis.stacks.image_stack method) stitch() (in module microscopy_data_analysis.image_aligning) stitch_1d_overlap() (in module microscopy_data_analysis.general_util) stitch_given_shift() (in module microscopy_data_analysis.image_aligning) stitch_pair() (in module microscopy_data_analysis.image_aligning) subtract_dark_field() (microscopy_data_analysis.stacks.image_stack method)

T

take_map() (in module microscopy_data_analysis.general_util)

V

vis_make_mp4() (in module microscopy_data_analysis.visualisation) vis_make_scale_bar() (in module microscopy_data_analysis.visualisation)

vis_plot_line_ids() (in module microscopy_data_analysis.visualisation) vis_zoom() (in module microscopy_data_analysis.visualisation)

X

x (microscopy_data_analysis.visualisation.line_object attribute)

Y

y (microscopy_data_analysis.visualisation.line_object attribute)

Z

z_transform_images() (microscopy_data_analysis.stacks.image_stack method)