Index

A

a_on_b() (in module fastpli.tools.rotation) absorption (Layer property) add_crop_tilt_halo() (Simpli method) add_noise() (in module fastpli.simulation.optic) append() (FiberBundle method) (FiberBundles method) apply() (Fiber method) (FiberBundle method) (FiberBundles method) (in module fastpli.analysis.affine_transformation) apply_boundary_conditions() (Solver method) apply_epa() (Simpli method)

apply_optic() (Simpli method) apply_optic_resample() (Simpli method) apply_rofl() (Simpli method) apply_to_points() (Fiber method) (FiberBundle method) (FiberBundles method) apply_to_radii() (Fiber method) (FiberBundle method) (FiberBundles method) apply_untilt() (Simpli method) as_array() (Fiber method) (FiberBundle method) (FiberBundles method)

B

background_absorption (Simpli property)

birefringence (Layer property) bundle() (in module fastpli.model.sandbox.build)

C

calc_matrix() (in module fastpli.analysis.affine_transformation) cast() (Fiber method) (FiberBundle method) (FiberBundles method) close_scene() (Solver method) col_voi (Solver property) copy() (Fiber method) (FiberBundle method) (FiberBundles method) (Layer method) crop_circle() (in module fastpli.model.sandbox.seeds)

crop_rectangle() (in module fastpli.model.sandbox.seeds) crop_tilt_pixel() (Simpli method) crop_tilt_voxel() (Simpli method) cuboid() (in module fastpli.model.sandbox.build) cut() (Fiber method) (FiberBundle method) (FiberBundles method) cut_sphere() (Fiber method) (FiberBundle method) (FiberBundles method) cylinder() (in module fastpli.model.sandbox.build)

D

data() (Layer method) dim (Simpli property) dim_origin (Simpli property) direction() (in module fastpli.analysis.epa)

drag (Solver property) draw_scene() (Solver method) dtype (Fiber property) (FiberBundle property)

E

epa() (in module fastpli.analysis.epa) exec_matrix() (in module fastpli.analysis.affine_transformation)

extend() (FiberBundle method) (FiberBundles method)

F

fastpli.analysis module fastpli.analysis.affine_transformation module fastpli.analysis.epa module fastpli.analysis.images module fastpli.analysis.orientation module fastpli.analysis.rofl module fastpli.io module fastpli.io.fiber_bundles module fastpli.model module fastpli.model.sandbox module fastpli.model.sandbox.build module fastpli.model.sandbox.seeds module fastpli.model.solver module fastpli.model.solver.solver module fastpli.objects module fastpli.objects.fibers module

fastpli.objects.layers module fastpli.simulation module fastpli.simulation.optic module fastpli.simulation.simpli module fastpli.tools module fastpli.tools.helper module fastpli.tools.rotation module Fiber (class in fastpli.objects.fibers) fiber() (in module fastpli.analysis.orientation) fiber_bundle() (in module fastpli.analysis.orientation) fiber_bundles (Simpli property) (Solver property) fiber_bundles() (in module fastpli.analysis.orientation) FiberBundle (class in fastpli.objects.fibers) FiberBundles (class in fastpli.objects.fibers) filter() (in module fastpli.simulation.optic) filter2d() (in module fastpli.simulation.optic) filter_resample() (in module fastpli.simulation.optic) filter_resize() (in module fastpli.simulation.optic) filter_rotations (Simpli property) flip_z_beam (Simpli property) fom_hsv_black() (in module fastpli.analysis.images) fom_rgb() (in module fastpli.analysis.images)

G

generate_tissue() (Simpli method) get_dict() (Simpli method) (Solver method)

get_voi() (Simpli method)

H

histogram() (in module fastpli.analysis.orientation)

hsv_black_sphere() (in module fastpli.analysis.images)

I

interpolate (Simpli property)

L

Layer (class in fastpli.objects.layers) Layers (class in fastpli.objects.layers) layers (FiberBundle property) (FiberBundles property)

light_intensity (Simpli property) load() (in module fastpli.io.fiber_bundles) load_dat() (in module fastpli.io.fiber_bundles) load_h5() (in module fastpli.io.fiber_bundles) (Solver method)

M

memory_usage() (Simpli method) model (Layer property) module fastpli.analysis fastpli.analysis.affine_transformation fastpli.analysis.epa fastpli.analysis.images fastpli.analysis.orientation fastpli.analysis.rofl fastpli.io fastpli.io.fiber_bundles fastpli.model fastpli.model.sandbox fastpli.model.sandbox.build fastpli.model.sandbox.seeds fastpli.model.solver fastpli.model.solver.solver fastpli.objects fastpli.objects.fibers fastpli.objects.layers fastpli.simulation fastpli.simulation.optic fastpli.simulation.simpli fastpli.tools fastpli.tools.helper fastpli.tools.rotation

N

noise_model (Simpli property)

num_steps (Solver property)

O

obj_mean_length (Solver property) obj_min_radius (Solver property)

omp_num_threads (Simpli property) (Solver property) optical_sigma (Simpli property)

P

pip_freeze() (in module fastpli.tools.helper)

pixel_size (Simpli property) points (Fiber property)

R

radii (Fiber property) remap_direction() (in module fastpli.analysis.orientation) remap_half_sphere_x() (in module fastpli.analysis.orientation) remap_half_sphere_z() (in module fastpli.analysis.orientation) remap_sphere() (in module fastpli.analysis.orientation) resample() (in module fastpli.simulation.optic) reset_view() (Solver method) resize() (in module fastpli.simulation.optic) rgb_sphere() (in module fastpli.analysis.images)

rm_crop_tilt_halo() (Simpli method) rofl() (in module fastpli.analysis.rofl) rotate() (Fiber method) (FiberBundle method) (FiberBundles method) run_pipeline() (Simpli method) run_simulation() (Simpli method) run_simulation_pipeline() (Simpli method) run_tissue_pipeline() (Simpli method)

S

save() (in module fastpli.io.fiber_bundles) save_dat() (in module fastpli.io.fiber_bundles) save_h5() (in module fastpli.io.fiber_bundles) (Solver method) save_parameter_h5() (Simpli method) (Solver method) save_ppm() (Solver method) save_stl() (Solver method) scale (Layer property) scale() (Fiber method) (FiberBundle method) (FiberBundles method)

set_dict() (Simpli method) (Solver method) set_view_angles() (Solver method) set_view_center() (Solver method) set_view_distance() (Solver method) set_voi() (Simpli method) shape (Fiber property) Simpli (class in fastpli.simulation.simpli) Solver (class in fastpli.model.solver.solver) step() (Solver method) step_size (Simpli property)

T

tilts (Simpli property) tissue_refrection (Simpli property) to_image_space() (in module fastpli.analysis.images) toggle_axis() (Solver method) toggle_collision_view() (Solver method)

translate() (Fiber method) (FiberBundle method) (FiberBundles method) triangular_circle() (in module fastpli.model.sandbox.seeds) triangular_grid() (in module fastpli.model.sandbox.seeds)

U

unit_vectors() (in module fastpli.analysis.images)

untilt_sensor_view (Simpli property)

V

verbose (Simpli property) version_file_name() (in module fastpli.tools.helper)

version_path() (in module fastpli.tools.helper) voxel_size (Simpli property)

W

wavelength (Simpli property)

X

x() (in module fastpli.tools.rotation)

Y

y() (in module fastpli.tools.rotation)

Z

z() (in module fastpli.tools.rotation) z_2d() (in module fastpli.tools.rotation)

zymz() (in module fastpli.tools.rotation) zyz() (in module fastpli.tools.rotation)