Index

_

__getitem__() (jnormcorre.utils.lazy_array.lazy_data_loader method) __init__() (jnormcorre.motion_correction.FrameCorrector method) (jnormcorre.motion_correction.MotionCorrect method), [1] (jnormcorre.motion_correction.tile_and_correct_dataset method) (jnormcorre.simulation.SimData method) (jnormcorre.utils.registrationarrays.FilteredArray method), [1] (jnormcorre.utils.registrationarrays.Hdf5Array method), [1] (jnormcorre.utils.registrationarrays.RegistrationArray method), [1] (jnormcorre.utils.registrationarrays.TiffArray method), [1]

_compute_at_indices() (jnormcorre.utils.lazy_array.lazy_data_loader method)

A

apply_shifts_dft_fast_1() (in module jnormcorre.motion_correction)

B

batching (jnormcorre.motion_correction.FrameCorrector property) (jnormcorre.utils.registrationarrays.FilteredArray property) (jnormcorre.utils.registrationarrays.RegistrationArray property)

bin_median() (in module jnormcorre.motion_correction)

C

calculate_padding() (jnormcorre.simulation.SimData method) calculate_splits() (in module jnormcorre.motion_correction)

ceil_max() (in module jnormcorre.motion_correction) crop_image() (in module jnormcorre.motion_correction) crop_image_vmap() (in module jnormcorre.motion_correction)

D

dtype (jnormcorre.utils.lazy_array.lazy_data_loader property), [1] (jnormcorre.utils.registrationarrays.FilteredArray property) (jnormcorre.utils.registrationarrays.Hdf5Array property) (jnormcorre.utils.registrationarrays.RegistrationArray property) (jnormcorre.utils.registrationarrays.TiffArray property)

dtype() (jnormcorre.utils.lazy_array.lazy_data_loader method)

F

fill_maxh() (in module jnormcorre.motion_correction) fill_maxw() (in module jnormcorre.motion_correction) fill_minh() (in module jnormcorre.motion_correction) fill_minw() (in module jnormcorre.motion_correction)

filter_function (jnormcorre.utils.registrationarrays.FilteredArray property) FilteredArray (class in jnormcorre.utils.registrationarrays), [1] first_value() (in module jnormcorre.motion_correction) floor_min() (in module jnormcorre.motion_correction) FrameCorrector (class in jnormcorre.motion_correction)

G

generate_base_image() (jnormcorre.simulation.SimData method) generate_gaussian_blob() (jnormcorre.simulation.SimData method) generate_template_chunk() (in module jnormcorre.motion_correction) get_freq_comps_jax() (in module jnormcorre.motion_correction)

get_indices() (in module jnormcorre.motion_correction) get_patch_start_and_end_coords() (in module jnormcorre.motion_correction) get_patches_jax() (in module jnormcorre.motion_correction) get_xy_grid() (in module jnormcorre.motion_correction)

H

Hdf5Array (class in jnormcorre.utils.registrationarrays), [1]

J

jnormcorre module jnormcorre.motion_correction module jnormcorre.simulation module

jnormcorre.utils module jnormcorre.utils.lazy_array module jnormcorre.utils.registrationarrays module

L

lazy_data_loader (class in jnormcorre.utils.lazy_array), [1]

load_split_heuristic() (in module jnormcorre.motion_correction)

M

module jnormcorre jnormcorre.motion_correction jnormcorre.simulation jnormcorre.utils jnormcorre.utils.lazy_array jnormcorre.utils.registrationarrays

motion_correct() (jnormcorre.motion_correction.MotionCorrect method), [1] MotionCorrect (class in jnormcorre.motion_correction), [1]

N

nan_processing() (in module jnormcorre.motion_correction) ndim (jnormcorre.utils.lazy_array.lazy_data_loader property), [1] (jnormcorre.utils.registrationarrays.FilteredArray property) (jnormcorre.utils.registrationarrays.Hdf5Array property) (jnormcorre.utils.registrationarrays.RegistrationArray property) (jnormcorre.utils.registrationarrays.TiffArray property)

ndim() (jnormcorre.utils.lazy_array.lazy_data_loader method)

P

plot_overview() (jnormcorre.simulation.SimData method)

pwrigid_function (jnormcorre.motion_correction.FrameCorrector property)

R

raw_data_loader (jnormcorre.utils.registrationarrays.FilteredArray property) register_frames() (jnormcorre.motion_correction.FrameCorrector method) register_frames_and_transfer() (jnormcorre.motion_correction.FrameCorrector method) register_frames_to_template_pwrigid() (in module jnormcorre.motion_correction), [1] register_frames_to_template_rigid() (in module jnormcorre.motion_correction), [1] register_to_template_and_transfer_pwrigid() (in module jnormcorre.motion_correction), [1] register_to_template_and_transfer_rigid() (in module jnormcorre.motion_correction), [1]

register_translation_jax_full() (in module jnormcorre.motion_correction) register_translation_jax_simple() (in module jnormcorre.motion_correction) RegistrationArray (class in jnormcorre.utils.registrationarrays), [1] regular_collate() (in module jnormcorre.motion_correction) return_identity() (in module jnormcorre.motion_correction) return_identity_mins() (in module jnormcorre.motion_correction) rigid_function (jnormcorre.motion_correction.FrameCorrector property)

S

save() (jnormcorre.simulation.SimData method) second_value() (in module jnormcorre.motion_correction) shape (jnormcorre.utils.lazy_array.lazy_data_loader property), [1] (jnormcorre.utils.registrationarrays.FilteredArray property) (jnormcorre.utils.registrationarrays.Hdf5Array property) (jnormcorre.utils.registrationarrays.RegistrationArray property) (jnormcorre.utils.registrationarrays.TiffArray property)

shape() (jnormcorre.utils.lazy_array.lazy_data_loader method) SimData (class in jnormcorre.simulation) simulate() (jnormcorre.simulation.SimData method) subtract_values() (in module jnormcorre.motion_correction)

T

template (jnormcorre.motion_correction.FrameCorrector property) (jnormcorre.utils.registrationarrays.RegistrationArray property) threshold_dim1() (in module jnormcorre.motion_correction) threshold_dim2() (in module jnormcorre.motion_correction) threshold_shifts_0_else() (in module jnormcorre.motion_correction)

threshold_shifts_0_if() (in module jnormcorre.motion_correction) threshold_shifts_1_else() (in module jnormcorre.motion_correction) threshold_shifts_1_if() (in module jnormcorre.motion_correction) TiffArray (class in jnormcorre.utils.registrationarrays), [1] tile_and_correct_dataset (class in jnormcorre.motion_correction)

U

update_src_freq_flag() (in module jnormcorre.motion_correction)

update_src_freq_identity() (in module jnormcorre.motion_correction) update_src_freq_jax() (in module jnormcorre.motion_correction)

V

verify_strides_and_overlaps() (in module jnormcorre.motion_correction)

vmap_register_translation() (in module jnormcorre.motion_correction)