Index

_

__call__() (peri.interpolation.BarnesInterpolation1D method) (peri.interpolation.ChebyshevInterpolation1D method)

_kwargs (LMParticleGroupCollection attribute) _num_iter (LMEngine attribute)

A

add_handler() (peri.logger.Logger method) add_particle() (peri.comp.objs.PlatonicSpheresCollection method) add_subtract() (in module peri.opt.addsubtract)

add_subtract_locally() (in module peri.opt.addsubtract) aN() (in module peri.util) AnisotropicGaussian (class in peri.comp.psfs) AnisotropicGaussianXYZ (class in peri.comp.psfs)

B

BarnesInterpolation1D (class in peri.interpolation) BarnesStreakLegPoly2P1D (class in peri.comp.ilms)

boundingtile() (peri.util.Tile static method) build_funcs() (peri.states.State method) burn() (in module peri.opt.optimize)

C

calc_accel_correction() (LMEngine method) (peri.opt.optimize.LMEngine method) calc_grad() (LMEngine method) (peri.opt.optimize.LMEngine method) calc_J() (peri.opt.optimize.LMEngine method) calc_model_cosine() (LMEngine method) (peri.opt.optimize.LMEngine method) calc_residuals() (peri.opt.optimize.LMEngine method) center (peri.util.Tile attribute) characterize_psf() (peri.comp.exactpsf.ExactPSF method) (peri.comp.exactpsf.FixedSSChebPSF method) ChebyshevInterpolation1D (class in peri.interpolation) ChebyshevPSF (class in peri.comp.exactpsf) check_completion() (LMEngine method) (peri.opt.optimize.LMEngine method)

check_consistency() (peri.models.Model method) check_inputs() (peri.models.Model method) check_terminate() (peri.opt.optimize.LMEngine method) check_termination() (LMEngine method) check_update_J() (peri.opt.optimize.LMEngine method) Component (class in peri.comp.comp) ComponentCollection (class in peri.comp.comp) ConfocalImageModel (class in peri.models) contains() (peri.util.Tile method) coords() (peri.util.Tile method) corners (peri.util.Tile attribute) crb() (peri.states.State method) create_default_conf() (in module peri.conf)

D

damping (LMEngine attribute) data (peri.states.ImageState attribute) (peri.states.State attribute) decrease_damping() (LMEngine method) delistify() (in module peri.util) diffname() (peri.models.Model method) do_internal_run() (LMEngine method) (LMParticleGroupCollection method) (peri.opt.optimize.LMEngine method)

do_levmarq() (in module peri.opt.optimize) do_levmarq_all_particle_groups() (in module peri.opt.optimize) do_levmarq_particles() (in module peri.opt.optimize) do_run_1() (LMEngine method) (LMParticleGroupCollection method) (peri.opt.optimize.LMEngine method) do_run_2() (LMEngine method) (LMParticleGroupCollection method) (peri.opt.optimize.LMEngine method) drift() (peri.comp.exactpsf.ExactPSF method)

E

error (peri.states.State attribute) evaluate() (peri.models.Model method) ExactLineScanConfocalPSF (class in peri.comp.exactpsf)

ExactPinholeConfocalPSF (class in peri.comp.exactpsf) ExactPSF (class in peri.comp.exactpsf) execute() (peri.comp.comp.Component method) exports() (peri.comp.comp.Component method)

F

feature_guess() (in module peri.opt.addsubtract) filtered_image() (peri.util.Image method) find_expected_error() (peri.opt.optimize.LMEngine method) find_LM_updates() (LMEngine method) (peri.opt.optimize.LMEngine method)

finish() (in module peri.opt.optimize) finish_state() (in module peri.runner) FixedSSChebPSF (class in peri.comp.exactpsf) FromArray (class in peri.comp.psfs)

G

Gaussian4D (class in peri.comp.psfs) get() (peri.comp.comp.Component method) (peri.comp.comp.ComponentCollection method) (peri.states.ImageState method) get_base_model() (peri.models.Model method) get_conf_filename() (in module peri.conf) get_difference_model() (peri.models.Model method)

get_padding_size() (peri.comp.comp.Component method) get_scale() (peri.util.RawImage method) get_scale_from_raw() (peri.util.RawImage static method) get_termination_stats() (LMEngine method) (peri.opt.optimize.LMEngine method) get_update_io_tiles() (peri.states.ImageState method) get_update_tile() (peri.comp.comp.Component method) get_values() (peri.comp.comp.ParameterGroup method)

I

IdentityPSF (class in peri.comp.psfs) Image (class in peri.util) ImageState (class in peri.states) increase_damping() (LMEngine method)

indir() (in module peri.util) initargs() (peri.comp.comp.ComponentCollection method) (peri.comp.comp.ParameterGroup method) initialize() (peri.comp.comp.Component method) intersection() (peri.util.Tile static method)

J

J (LMEngine attribute)

JTJ (LMEngine attribute)

K

kcenter (peri.util.Tile attribute)

kvectors() (peri.util.Tile method)

L

LegendrePoly2P1D (class in peri.comp.ilms) link_zscale() (in module peri.runner) listify() (in module peri.util) LMAugmentedState (class in peri.opt.optimize) LMEngine (class in peri.opt.optimize) LMGlobals (class in peri.opt.optimize) LMParticleGroupCollection (class in peri.opt.optimize) LMParticles (class in peri.opt.optimize)

load() (in module peri.states) load_conf() (in module peri.conf) load_image() (peri.util.RawImage method) load_wisdom() (in module peri.fft) locate_spheres() (in module peri.runner) Logger (class in peri.logger) loglikelihood (peri.states.State attribute) logposterior (peri.states.State attribute) logprior (peri.states.State attribute)

M

map_vars() (peri.models.Model method) measure_size_drift() (peri.comp.exactpsf.ExactPSF method) Model (class in peri.models)

model (peri.states.ImageState attribute) (peri.states.State attribute) model_to_data() (peri.states.ImageState method)

N

noformat() (peri.logger.Logger method) nopickle() (peri.comp.comp.Component method) (peri.comp.comp.ParameterGroup method)

NullImage (class in peri.util) num_pix (LMAugmentedState attribute) (LMGlobals attribute)

O

oddify() (in module peri.util) optimize_from_initial() (in module peri.runner) OrthoManipulator (class in peri.viz.interaction)

OrthoPrefeature (class in peri.viz.interaction) OrthoViewer (class in peri.viz.interaction) oslicer() (peri.util.Tile method) overhang() (peri.util.Tile method)

P

pack_args() (peri.comp.exactpsf.ExactLineScanConfocalPSF method) (peri.comp.exactpsf.ExactPSF method) (peri.comp.exactpsf.ExactPinholeConfocalPSF method) pad() (peri.util.Tile method) param_names (LMParticles attribute) param_particle() (peri.comp.objs.PlatonicSpheresCollection method) param_particle_pos() (peri.comp.objs.PlatonicSpheresCollection method) param_particle_rad() (peri.comp.objs.PlatonicSpheresCollection method) param_radii() (peri.comp.objs.PlatonicSpheresCollection method) ParameterGroup (class in peri.comp.comp) params (peri.comp.comp.ParameterGroup attribute) particle_groups (LMParticleGroupCollection attribute) patch_docs() (in module peri.util) peri.conf (module)

peri.fft (module) peri.logger (module) PlatonicSpheresCollection (class in peri.comp.objs) Polynomial2P1D (class in peri.comp.ilms) Polynomial3D (class in peri.comp.ilms) pop_update() (peri.states.State method) ProgressBar (class in peri.util) PSF (class in peri.comp.psfs) PSF4D (class in peri.comp.psfs) psf_slice() (peri.comp.exactpsf.ExactPSF method) psffunc() (peri.comp.exactpsf.ExactLineScanConfocalPSF method) (peri.comp.exactpsf.ExactPSF method) (peri.comp.exactpsf.ExactPinholeConfocalPSF method) push_update() (peri.states.State method)

R

randomize_parameters() (peri.comp.ilms.BarnesStreakLegPoly2P1D method) RawImage (class in peri.util) read_environment() (in module peri.conf) reflect_overhang() (peri.util.Tile method) region_size (LMParticleGroupCollection attribute) register() (peri.comp.comp.Component method) remove_handler() (peri.logger.Logger method) remove_particle() (peri.comp.objs.PlatonicSpheresCollection method) reset() (LMAugmentedState method) (LMEngine method) (LMGlobals method) (LMParticleGroupCollection method) (LMParticles method) (peri.opt.optimize.LMEngine method)

residuals (peri.states.State attribute) rmatrix() (peri.comp.objs.Slab method) rpsf_xy() (peri.comp.psfs.PSF4D method) rpsf_z() (peri.comp.psfs.PSF4D method)

S

save() (in module peri.states) save_wisdom() (in module peri.fft) set_filter() (peri.util.Image method) set_formatter() (peri.logger.Logger method) set_image() (peri.states.ImageState method) set_level() (peri.logger.Logger method) set_mem_level() (peri.states.ImageState method) set_model() (peri.states.ImageState method) set_params() (LMGlobals method) set_particles() (LMParticles method) set_scale() (peri.util.RawImage method) set_shape() (peri.comp.comp.Component method) (peri.comp.comp.ComponentCollection method)

set_tile() (peri.comp.comp.Component method) (peri.comp.comp.ComponentCollection method) (peri.util.Image method) set_values() (peri.comp.comp.ParameterGroup method) set_verbosity() (peri.logger.Logger method) setup_passthroughs() (peri.comp.comp.ComponentCollection method) Slab (class in peri.comp.objs) slicer (peri.util.Tile attribute) split_params() (peri.comp.comp.ComponentCollection method) State (class in peri.states) stats (LMParticleGroupCollection attribute) sync_params() (peri.comp.comp.ComponentCollection method)

T

temp_update() (peri.states.State method) Tile (class in peri.util) transform() (in module peri.conf)

translate() (peri.util.Tile method) trigger_parameter_change() (peri.comp.comp.Component method) trigger_update() (peri.comp.comp.Component method)

U

update() (peri.comp.comp.ParameterGroup method) (peri.comp.objs.PlatonicSpheresCollection method) (peri.states.ImageState method) (peri.states.State method) update_Broyden_J() (LMEngine method) (peri.opt.optimize.LMEngine method) update_eig_J() (LMEngine method) (peri.opt.optimize.LMEngine method) update_from_model_change() (peri.states.ImageState method)

update_function() (peri.opt.optimize.LMEngine method) update_hyper() (peri.states.State method) update_J() (LMEngine method) (peri.opt.optimize.LMEngine method) update_param_vals() (LMEngine method) (peri.opt.optimize.LMEngine method) update_select_J() (LMEngine method) (peri.opt.optimize.LMEngine method) update_sigma() (peri.states.State method)

V

values (peri.comp.comp.ParameterGroup attribute)

volume (peri.util.Tile attribute)