Index

_

__init__() (pyflowreg.motion_correction.FlowRegLive method) (pyflowreg.motion_correction.parallelization.BaseExecutor method) (pyflowreg.motion_correction.parallelization.MultiprocessingExecutor method), [1] (pyflowreg.motion_correction.parallelization.SequentialExecutor method), [1] (pyflowreg.motion_correction.parallelization.ThreadingExecutor method), [1] (pyflowreg.util.io._arr.ArrayReader method) (pyflowreg.util.io._arr.ArrayWriter method) (pyflowreg.util.io._null.NullVideoWriter method) (pyflowreg.util.io.hdf5.HDF5FileWriter method) (pyflowreg.util.io.mat.MATFileWriter method) (pyflowreg.util.io.mdf.MDFFileReader method) (pyflowreg.util.io.multifile_wrappers.MULTICHANNELFileReader method) (pyflowreg.util.io.multifile_wrappers.MULTIFILEFileWriter method) (pyflowreg.util.io.multifile_wrappers.SUBSETFileReader method) (pyflowreg.util.io.tiff.TIFFFileReader method) (pyflowreg.util.io.tiff.TIFFFileWriter method)

A

a_data (pyflowreg.motion_correction.OFOptions attribute) a_smooth (pyflowreg.motion_correction.OFOptions attribute) add_boundary() (in module pyflowreg.core.optical_flow), [1] alpha (pyflowreg.motion_correction.OFOptions attribute)

apply_gaussian_filter() (in module pyflowreg.util.image_processing) ARRAY (pyflowreg.motion_correction.OF_options.OutputFormat attribute) ArrayReader (class in pyflowreg.util.io._arr) ArrayWriter (class in pyflowreg.util.io._arr)

B

backend_params (pyflowreg.motion_correction.OFOptions attribute) BaseExecutor (class in pyflowreg.motion_correction.parallelization) batches_written (pyflowreg.util.io._null.NullVideoWriter attribute) BatchMotionCorrector (class in pyflowreg.motion_correction.compensate_recording)

BEGONIA (pyflowreg.motion_correction.OF_options.OutputFormat attribute) bin_frames() (pyflowreg.util.io._base.VideoReader method) bin_size (pyflowreg.motion_correction.OFOptions attribute) buffer_size (pyflowreg.motion_correction.OFOptions attribute)

C

CAIMAN_HDF5 (pyflowreg.motion_correction.OF_options.OutputFormat attribute) cc_hw (pyflowreg.motion_correction.OFOptions attribute) cc_initialization (pyflowreg.motion_correction.OFOptions attribute) cc_up (pyflowreg.motion_correction.OFOptions attribute) channel_idx (pyflowreg.motion_correction.OFOptions attribute) channel_normalization (pyflowreg.motion_correction.OFOptions attribute) cleanup() (pyflowreg.motion_correction.parallelization.BaseExecutor method) (pyflowreg.motion_correction.parallelization.MultiprocessingExecutor method), [1] (pyflowreg.motion_correction.parallelization.ThreadingExecutor method), [1] close() (pyflowreg.util.io._arr.ArrayReader method) (pyflowreg.util.io._arr.ArrayWriter method) (pyflowreg.util.io._base.VideoReader method) (pyflowreg.util.io._base.VideoWriter method) (pyflowreg.util.io._null.NullVideoWriter method) (pyflowreg.util.io.hdf5.HDF5FileReader method) (pyflowreg.util.io.hdf5.HDF5FileWriter method) (pyflowreg.util.io.mat.MATFileReader method) (pyflowreg.util.io.mat.MATFileWriter method) (pyflowreg.util.io.mdf.MDFFileReader method) (pyflowreg.util.io.multifile_wrappers.MULTICHANNELFileReader method) (pyflowreg.util.io.multifile_wrappers.MULTIFILEFileWriter method) (pyflowreg.util.io.multifile_wrappers.SUBSETFileReader method) (pyflowreg.util.io.tiff.TIFFFileReader method) (pyflowreg.util.io.tiff.TIFFFileWriter method)

color_map_numpy_2ch() (in module pyflowreg.util.visualization) compensate_arr() (in module pyflowreg.motion_correction) compensate_recording() (in module pyflowreg.motion_correction) compute_flow() (in module pyflowreg.core.level_solver), [1] constancy_assumption (pyflowreg.motion_correction.OFOptions attribute) copy() (pyflowreg.motion_correction.OFOptions method)

D

DisoOF (class in pyflowreg.core.diso_optical_flow) download_data() (in module pyflowreg.util.download)

download_demo_data() (in module pyflowreg.util.download) DSFileReader (class in pyflowreg.util.io._ds_io) DSFileWriter (class in pyflowreg.util.io._ds_io)

E

effective_min_level (pyflowreg.motion_correction.OFOptions property)

estimate_rigid_xcorr_2d() (in module pyflowreg.util.xcorr_prealignment) eta (pyflowreg.motion_correction.OFOptions attribute)

F

flow_backend (pyflowreg.motion_correction.OFOptions attribute) flow_to_color() (in module pyflowreg.util.visualization)

FlowRegLive (class in pyflowreg.motion_correction) format_scanimage_metadata_report() (in module pyflowreg.util.io._scanimage) frames_written (pyflowreg.util.io._null.NullVideoWriter attribute)

G

gaussian_filter_1d_half_kernel() (in module pyflowreg.util.image_processing) get_array() (pyflowreg.util.io._arr.ArrayWriter method) get_current_flow() (pyflowreg.motion_correction.FlowRegLive method) get_displacement() (in module pyflowreg.core.optical_flow), [1] get_displacement_factory (pyflowreg.motion_correction.OFOptions attribute) get_displacement_impl (pyflowreg.motion_correction.OFOptions attribute) get_ds_name() (pyflowreg.util.io._ds_io.DSFileWriter method) get_info() (pyflowreg.motion_correction.parallelization.BaseExecutor method) (pyflowreg.motion_correction.parallelization.MultiprocessingExecutor method), [1] (pyflowreg.motion_correction.parallelization.SequentialExecutor method), [1] (pyflowreg.motion_correction.parallelization.ThreadingExecutor method), [1] get_metadata() (pyflowreg.util.io.mdf.MDFFileReader method) (pyflowreg.util.io.tiff.TIFFFileReader method)

get_motion_tensor_cs() (in module pyflowreg.core.optical_flow) get_motion_tensor_gc() (in module pyflowreg.core.optical_flow), [1] get_motion_tensor_gray() (in module pyflowreg.core.optical_flow) get_params() (pyflowreg.core.diso_optical_flow.DisoOF method) get_reference_frame() (pyflowreg.motion_correction.OFOptions method) get_sigma_at() (pyflowreg.motion_correction.OFOptions method) get_video_file_reader() (in module pyflowreg.util.io.factory) get_video_file_writer() (in module pyflowreg.util.io.factory) get_video_reader() (pyflowreg.motion_correction.OFOptions method) get_video_writer() (pyflowreg.motion_correction.OFOptions method) get_visualization() (in module pyflowreg.util.visualization) get_weight_at() (pyflowreg.motion_correction.OFOptions method)

H

has_batch() (pyflowreg.util.io._base.VideoReader method) HDF5 (pyflowreg.motion_correction.OF_options.OutputFormat attribute)

HDF5FileReader (class in pyflowreg.util.io.hdf5) HDF5FileWriter (class in pyflowreg.util.io.hdf5)

I

imregister_wrapper() (in module pyflowreg.core.optical_flow) imresize_cv2_aa_gauss_sep() (in module pyflowreg.util.resize_util) imresize_fused_gauss_cubic() (in module pyflowreg.util.resize_util) imresize_numba() (in module pyflowreg.util.resize_util) init() (pyflowreg.util.io._arr.ArrayWriter method) (pyflowreg.util.io._base.VideoWriter method) (pyflowreg.util.io._null.NullVideoWriter method)

input_file (pyflowreg.motion_correction.OFOptions attribute) interpolation_method (pyflowreg.motion_correction.OFOptions attribute) interpret_scanimage_dimensions() (in module pyflowreg.util.io._scanimage) iterations (pyflowreg.motion_correction.OFOptions attribute)

L

level_solver() (in module pyflowreg.core.optical_flow)

levels (pyflowreg.motion_correction.OFOptions attribute) load_options() (pyflowreg.motion_correction.OFOptions class method)

M

main() (in module pyflowreg.util.io.factory) (in module pyflowreg.util.io.hdf5) (in module pyflowreg.util.io.mat) (in module pyflowreg.util.io.multifile_wrappers) main2() (in module pyflowreg.util.io.tiff) main3() (in module pyflowreg.util.io.tiff) MAT (pyflowreg.motion_correction.OF_options.OutputFormat attribute) MATFileReader (class in pyflowreg.util.io.mat) MATFileWriter (class in pyflowreg.util.io.mat) MDFFileReader (class in pyflowreg.util.io.mdf) min_frames_per_reference (pyflowreg.motion_correction.OFOptions attribute) min_level (pyflowreg.motion_correction.OFOptions attribute) model_post_init() (pyflowreg.motion_correction.OFOptions method) module pyflowreg.core.diso_optical_flow pyflowreg.core.level_solver pyflowreg.core.optical_flow pyflowreg.motion_correction.parallelization pyflowreg.util.download pyflowreg.util.image_processing pyflowreg.util.io._arr pyflowreg.util.io._base pyflowreg.util.io._ds_io pyflowreg.util.io._null pyflowreg.util.io._scanimage pyflowreg.util.io.factory pyflowreg.util.io.hdf5 pyflowreg.util.io.mat pyflowreg.util.io.mdf pyflowreg.util.io.multifile_wrappers pyflowreg.util.io.tiff pyflowreg.util.resize_util pyflowreg.util.superresolution_helpers pyflowreg.util.visualization pyflowreg.util.xcorr_prealignment

MULTICHANNELFileReader (class in pyflowreg.util.io.multifile_wrappers) MULTIFILE_HDF5 (pyflowreg.motion_correction.OF_options.OutputFormat attribute) MULTIFILE_MAT (pyflowreg.motion_correction.OF_options.OutputFormat attribute) MULTIFILE_TIFF (pyflowreg.motion_correction.OF_options.OutputFormat attribute) MULTIFILEFileWriter (class in pyflowreg.util.io.multifile_wrappers) MultiprocessingExecutor (class in pyflowreg.motion_correction.parallelization), [1] multispectral_mapping() (in module pyflowreg.util.visualization)

N

n_jobs (pyflowreg.motion_correction.compensate_recording.RegistrationConfig attribute) n_references (pyflowreg.motion_correction.OFOptions attribute) naming_convention (pyflowreg.motion_correction.OFOptions attribute) nonlinearity_smoothness_2d() (in module pyflowreg.core.level_solver), [1] normalize() (in module pyflowreg.util.image_processing)

normalize_alpha() (pyflowreg.motion_correction.OFOptions class method) normalize_sigma() (pyflowreg.motion_correction.OFOptions class method) normalize_weight() (pyflowreg.motion_correction.OFOptions class method) NULL (pyflowreg.motion_correction.OF_options.OutputFormat attribute) NullVideoWriter (class in pyflowreg.util.io._null)

O

OFOptions (class in pyflowreg.motion_correction) output_file_name (pyflowreg.motion_correction.OFOptions attribute) output_format (pyflowreg.motion_correction.OFOptions attribute)

output_path (pyflowreg.motion_correction.OFOptions attribute) output_typename (pyflowreg.motion_correction.OFOptions attribute) OutputFormat (class in pyflowreg.motion_correction.OF_options)

P

parallelization (pyflowreg.motion_correction.compensate_recording.RegistrationConfig attribute) parse_scanimage_metadata() (in module pyflowreg.util.io._scanimage) preproc_funct (pyflowreg.motion_correction.OFOptions attribute) process_batch() (pyflowreg.motion_correction.parallelization.BaseExecutor method) (pyflowreg.motion_correction.parallelization.MultiprocessingExecutor method), [1] (pyflowreg.motion_correction.parallelization.SequentialExecutor method), [1] (pyflowreg.motion_correction.parallelization.ThreadingExecutor method), [1] pyflowreg.core.diso_optical_flow module pyflowreg.core.level_solver module pyflowreg.core.optical_flow module pyflowreg.motion_correction.parallelization module pyflowreg.util.download module pyflowreg.util.image_processing module pyflowreg.util.io._arr module pyflowreg.util.io._base module pyflowreg.util.io._ds_io module

pyflowreg.util.io._null module pyflowreg.util.io._scanimage module pyflowreg.util.io.factory module pyflowreg.util.io.hdf5 module pyflowreg.util.io.mat module pyflowreg.util.io.mdf module pyflowreg.util.io.multifile_wrappers module pyflowreg.util.io.tiff module pyflowreg.util.resize_util module pyflowreg.util.superresolution_helpers module pyflowreg.util.visualization module pyflowreg.util.xcorr_prealignment module

Q

quality_setting (pyflowreg.motion_correction.OFOptions attribute)

quiver_visualization() (in module pyflowreg.util.visualization)

R

read_batch() (pyflowreg.util.io._base.VideoReader method) reader_main() (in module pyflowreg.util.io.hdf5) reference_frames (pyflowreg.motion_correction.OFOptions attribute) register_frames() (pyflowreg.motion_correction.FlowRegLive method) register_progress_callback() (pyflowreg.motion_correction.compensate_recording.BatchMotionCorrector method) register_registered_callback() (pyflowreg.motion_correction.compensate_recording.BatchMotionCorrector method) register_w_callback() (pyflowreg.motion_correction.compensate_recording.BatchMotionCorrector method) RegistrationConfig (class in pyflowreg.motion_correction.compensate_recording)

reset() (pyflowreg.util.io._base.VideoReader method) reset_connection() (pyflowreg.util.io.mdf.MDFFileReader method) reset_reference() (pyflowreg.motion_correction.FlowRegLive method) resize_image_cv2() (in module pyflowreg.util.resize_util) resize_image_cv2_aa_blur() (in module pyflowreg.util.resize_util) resize_image_cv2_aa_gauss() (in module pyflowreg.util.resize_util) resize_image_skimage() (in module pyflowreg.util.resize_util) resolve_get_displacement() (pyflowreg.motion_correction.OFOptions method) run() (pyflowreg.motion_correction.compensate_recording.BatchMotionCorrector method)

S

save_meta_info (pyflowreg.motion_correction.OFOptions attribute) save_options() (pyflowreg.motion_correction.OFOptions method) save_valid_idx (pyflowreg.motion_correction.OFOptions attribute) save_valid_mask (pyflowreg.motion_correction.OFOptions attribute) save_w (pyflowreg.motion_correction.OFOptions attribute) SequentialExecutor (class in pyflowreg.motion_correction.parallelization), [1] set_boundary_2d() (in module pyflowreg.core.level_solver), [1] set_flow_init() (pyflowreg.motion_correction.FlowRegLive method) set_params() (pyflowreg.core.diso_optical_flow.DisoOF method)

set_preset() (pyflowreg.core.diso_optical_flow.DisoOF method) set_reference() (pyflowreg.motion_correction.FlowRegLive method) setup() (pyflowreg.motion_correction.parallelization.BaseExecutor method) (pyflowreg.motion_correction.parallelization.MultiprocessingExecutor method), [1] (pyflowreg.motion_correction.parallelization.ThreadingExecutor method), [1] shape (pyflowreg.util.io._base.VideoReader property) sigma (pyflowreg.motion_correction.OFOptions attribute) SUBSETFileReader (class in pyflowreg.util.io.multifile_wrappers) SUITE2P_TIFF (pyflowreg.motion_correction.OF_options.OutputFormat attribute)

T

test_basic_functionality() (in module pyflowreg.util.io.tiff) test_mdf_conversion() (in module pyflowreg.util.io.tiff) ThreadingExecutor (class in pyflowreg.motion_correction.parallelization), [1] TIFF (pyflowreg.motion_correction.OF_options.OutputFormat attribute)

TIFFFileReader (class in pyflowreg.util.io.tiff) TIFFFileWriter (class in pyflowreg.util.io.tiff) to_dict() (pyflowreg.motion_correction.OFOptions method) to_pytorch() (pyflowreg.util.io._base.VideoReader method)

U

unbinned_shape (pyflowreg.util.io._base.VideoReader property) update_initialization_w (pyflowreg.motion_correction.OFOptions attribute)

update_lag (pyflowreg.motion_correction.OFOptions attribute) update_reference (pyflowreg.motion_correction.OFOptions attribute)

V

validate_and_normalize() (pyflowreg.motion_correction.OFOptions method) verbose (pyflowreg.motion_correction.compensate_recording.RegistrationConfig attribute) (pyflowreg.motion_correction.OFOptions attribute)

VideoReader (class in pyflowreg.util.io._base) VideoWriter (class in pyflowreg.util.io._base)

W

warp_image_highres() (in module pyflowreg.util.superresolution_helpers) warpingDepth() (in module pyflowreg.core.optical_flow) weight (pyflowreg.motion_correction.OFOptions attribute) write_frames() (pyflowreg.util.io._arr.ArrayWriter method) (pyflowreg.util.io._base.VideoWriter method) (pyflowreg.util.io._null.NullVideoWriter method) (pyflowreg.util.io.hdf5.HDF5FileWriter method) (pyflowreg.util.io.mat.MATFileWriter method) (pyflowreg.util.io.multifile_wrappers.MULTIFILEFileWriter method) (pyflowreg.util.io.tiff.TIFFFileWriter method)