Index

A

adjust_axis_range() (in module foa3d.slicing)

analyze_fibers() (in module foa3d.pipeline) analyze_hessian_eigen() (in module foa3d.frangi)

C

ceil_to_multiple() (in module foa3d.utils) check_background() (in module foa3d.slicing) color_text() (in module foa3d.printing) compute_axis_range() (in module foa3d.slicing) compute_dominant_eigen() (in module foa3d.frangi) compute_fiber_angles() (in module foa3d.spharm) compute_fractional_anisotropy() (in module foa3d.frangi) compute_frangi_features() (in module foa3d.frangi) compute_odf_map() (in module foa3d.odf) compute_orientation_dispersion() (in module foa3d.odf) compute_overlap() (in module foa3d.slicing) compute_real_sph_harm() (in module foa3d.spharm) compute_scaled_hessian() (in module foa3d.frangi)

compute_scaled_orientation() (in module foa3d.frangi) compute_scaled_vesselness() (in module foa3d.frangi) compute_slice_range() (in module foa3d.slicing) compute_slice_shape() (in module foa3d.slicing) compute_vec_tensor_eigen() (in module foa3d.odf) config_anisotropy_correction() (in module foa3d.preprocessing) correct_anisotropy() (in module foa3d.preprocessing) create_background_mask() (in module foa3d.utils) create_memory_map() (in module foa3d.utils) create_save_dirs() (in module foa3d.output) crop() (in module foa3d.slicing) crop_img_dict() (in module foa3d.slicing) CustomFormatter (class in foa3d.input)

D

delete_tmp_data() (in module foa3d.utils)

detect_ch_axis() (in module foa3d.utils) divide_nonzero() (in module foa3d.utils)

E

elapsed_time() (in module foa3d.utils)

F

factorial() (in module foa3d.spharm) fiber_angles_to_sph_harm() (in module foa3d.spharm) fiber_vectors_to_sph_harm() (in module foa3d.spharm) foa3d.frangi module foa3d.input module foa3d.odf module foa3d.output module foa3d.pipeline module

foa3d.preprocessing module foa3d.printing module foa3d.slicing module foa3d.spharm module foa3d.utils module frangi_analysis() (in module foa3d.pipeline) frangi_filter() (in module foa3d.frangi) fwhm_to_sigma() (in module foa3d.utils)

G

generate_odf_background() (in module foa3d.odf) generate_slice_ranges() (in module foa3d.slicing) get_available_cores() (in module foa3d.utils) get_cli_parser() (in module foa3d.input) get_config_label() (in module foa3d.utils) get_frangi_config() (in module foa3d.input) get_image_info() (in module foa3d.input)

get_image_size() (in module foa3d.input) get_item_bytes() (in module foa3d.utils) get_item_size() (in module foa3d.utils) get_resolution() (in module foa3d.input) get_resource_config() (in module foa3d.input) get_slicing_config() (in module foa3d.slicing) get_sph_harm_ncoeff() (in module foa3d.spharm) get_sph_harm_norm_factors() (in module foa3d.spharm)

H

hsv_orient_cmap() (in module foa3d.utils)

I

init_frangi_arrays() (in module foa3d.frangi)

init_odf_arrays() (in module foa3d.odf)

L

load_data() (in module foa3d.input)

load_microscopy_image() (in module foa3d.input)

M

mask_background() (in module foa3d.frangi) mask_orientation_dispersion() (in module foa3d.odf) module foa3d.frangi foa3d.input foa3d.odf foa3d.output foa3d.pipeline foa3d.preprocessing foa3d.printing foa3d.slicing foa3d.spharm foa3d.utils

N

norm_factor() (in module foa3d.spharm)

normalize_angle() (in module foa3d.utils) normalize_image() (in module foa3d.utils)

O

odf_analysis() (in module foa3d.pipeline)

P

parallel_frangi_over_slices() (in module foa3d.pipeline) parallel_odf_over_scales() (in module foa3d.pipeline) print_blur() (in module foa3d.printing) print_flsh() (in module foa3d.printing) print_frangi_config() (in module foa3d.printing) print_frangi_progress() (in module foa3d.printing)

print_image_info() (in module foa3d.printing) print_import_time() (in module foa3d.printing) print_odf_info() (in module foa3d.printing) print_pipeline_heading() (in module foa3d.printing) print_prepro_heading() (in module foa3d.printing) print_slicing_info() (in module foa3d.printing)

R

reject_brain_cells() (in module foa3d.pipeline)

reject_vesselness_background() (in module foa3d.frangi) rgb_orient_cmap() (in module foa3d.utils)

S

save_array() (in module foa3d.output) save_frangi_arrays() (in module foa3d.output)

save_odf_arrays() (in module foa3d.output) slice_image() (in module foa3d.slicing) sort_eigen() (in module foa3d.frangi)

T

transform_axes() (in module foa3d.utils)

W

write_frangi_arrays() (in module foa3d.frangi)