Index

A

AnimImshow (class in cbi_toolbox.utils.plotting)

argsort_tsp() (in module cbi_toolbox.reconstruct.vhf) average_frequency() (in module cbi_toolbox.reconstruct.vhf)

B

ball() (in module cbi_toolbox.simu.primitives)

boccia() (in module cbi_toolbox.simu.primitives) bspline() (in module cbi_toolbox.bsplines)

C

cbi_toolbox module cbi_toolbox.bsplines module cbi_toolbox.parallel module cbi_toolbox.parallel.mpi module cbi_toolbox.reconstruct module cbi_toolbox.reconstruct.fpsopt module cbi_toolbox.reconstruct.preprocess module cbi_toolbox.reconstruct.vhf module cbi_toolbox.simu module cbi_toolbox.simu.dynamic module

cbi_toolbox.simu.imaging module cbi_toolbox.simu.optics module cbi_toolbox.simu.primitives module cbi_toolbox.simu.textures module cbi_toolbox.splineradon module cbi_toolbox.utils module cbi_toolbox.utils.ome module cbi_toolbox.utils.plotting module compute_vector_extent() (in module cbi_toolbox.parallel.mpi) create_slice_view() (in module cbi_toolbox.parallel.mpi) create_vector_type() (in module cbi_toolbox.parallel.mpi) create_wf_1d() (in module cbi_toolbox.simu.optics)

D

deconvolve_sinogram() (in module cbi_toolbox.reconstruct.fpsopt) distribute_bin() (in module cbi_toolbox.parallel)

distribute_bin_all() (in module cbi_toolbox.parallel) distribute_mpi() (in module cbi_toolbox.parallel.mpi) distribute_mpi_all() (in module cbi_toolbox.parallel.mpi)

E

erase_corners() (in module cbi_toolbox.reconstruct.preprocess)

estimate_di() (in module cbi_toolbox.reconstruct.vhf)

F

fft_size() (in module cbi_toolbox.utils) fiber() (in module cbi_toolbox.simu.primitives) forward_ellipse() (in module cbi_toolbox.simu.primitives)

forward_simplex() (in module cbi_toolbox.simu.textures) fps_opt() (in module cbi_toolbox.simu.imaging) fss_opt() (in module cbi_toolbox.simu.imaging)

G

gather_full_shape() (in module cbi_toolbox.parallel.mpi) gaussian_psf() (in module cbi_toolbox.simu.optics)

get_rank() (in module cbi_toolbox.parallel.mpi) get_size() (in module cbi_toolbox.parallel.mpi)

I

inverse_psf_rfft() (in module cbi_toolbox.reconstruct.fpsopt) iradon() (in module cbi_toolbox.splineradon) iradon_inner() (in module cbi_toolbox.splineradon)

iradon_post() (in module cbi_toolbox.splineradon) iradon_pre() (in module cbi_toolbox.splineradon) is_cuda_available() (in module cbi_toolbox.splineradon) is_root_process() (in module cbi_toolbox.parallel.mpi)

L

l_curve() (in module cbi_toolbox.reconstruct.vhf)

load() (in module cbi_toolbox.parallel.mpi) load_ome_tiff() (in module cbi_toolbox.utils.ome)

M

module cbi_toolbox cbi_toolbox.bsplines cbi_toolbox.parallel cbi_toolbox.parallel.mpi cbi_toolbox.reconstruct cbi_toolbox.reconstruct.fpsopt cbi_toolbox.reconstruct.preprocess cbi_toolbox.reconstruct.vhf cbi_toolbox.simu cbi_toolbox.simu.dynamic cbi_toolbox.simu.imaging cbi_toolbox.simu.optics cbi_toolbox.simu.primitives cbi_toolbox.simu.textures cbi_toolbox.splineradon cbi_toolbox.utils cbi_toolbox.utils.ome cbi_toolbox.utils.plotting

mse() (in module cbi_toolbox.reconstruct) mutual_information() (in module cbi_toolbox.reconstruct)

N

noise() (in module cbi_toolbox.simu.imaging)

normalize() (in module cbi_toolbox.reconstruct)

O

openspim_illumination() (in module cbi_toolbox.simu.optics)

opt() (in module cbi_toolbox.simu.imaging) orient_phases() (in module cbi_toolbox.reconstruct.vhf)

P

parallelize() (in module cbi_toolbox.parallel) phantom() (in module cbi_toolbox.simu.primitives) phase_correction() (in module cbi_toolbox.reconstruct.vhf)

phase_diff() (in module cbi_toolbox.reconstruct.vhf) phase_error() (in module cbi_toolbox.reconstruct.vhf) psnr() (in module cbi_toolbox.reconstruct)

Q

quadrant_symmetry() (in module cbi_toolbox.simu.primitives)

quadrant_to_volume() (in module cbi_toolbox.simu.primitives) quantize() (in module cbi_toolbox.simu.imaging)

R

radon() (in module cbi_toolbox.splineradon) radon_inner() (in module cbi_toolbox.splineradon) radon_post() (in module cbi_toolbox.splineradon)

radon_pre() (in module cbi_toolbox.splineradon) redistribute() (in module cbi_toolbox.parallel.mpi) remove_background_illumination() (in module cbi_toolbox.reconstruct.preprocess) resample_wavefront() (in module cbi_toolbox.simu.optics)

S

sample_phases() (in module cbi_toolbox.simu.dynamic) sample_video() (in module cbi_toolbox.reconstruct.vhf) save() (in module cbi_toolbox.parallel.mpi) save_ome_tiff() (in module cbi_toolbox.utils.ome) save_to_gif() (cbi_toolbox.utils.plotting.AnimImshow method)

scale_to_mse() (in module cbi_toolbox.reconstruct) sigsin() (in module cbi_toolbox.simu.dynamic) sigsin_beat() (in module cbi_toolbox.simu.dynamic) simplex() (in module cbi_toolbox.simu.textures) spheres() (in module cbi_toolbox.simu.textures) spim() (in module cbi_toolbox.simu.imaging)

T

to_mpi_datatype() (in module cbi_toolbox.parallel.mpi) torus_boccia() (in module cbi_toolbox.simu.primitives)

trace_points() (in module cbi_toolbox.utils.plotting) transmission_to_absorption() (in module cbi_toolbox.reconstruct.preprocess)

U

unfold_phases() (in module cbi_toolbox.reconstruct.vhf)

V

vhf_phase_naive() (in module cbi_toolbox.reconstruct.vhf)

vhf_phase_uncorrected() (in module cbi_toolbox.reconstruct.vhf)

W

wait_all() (in module cbi_toolbox.parallel.mpi) wf_mix() (in module cbi_toolbox.simu.optics)

wf_to_2d() (in module cbi_toolbox.simu.optics) widefield() (in module cbi_toolbox.simu.imaging)