Index

A

align() (motion_correction.algorithms.Morphic method) (motion_correction.algorithms.OpticalILK method) (motion_correction.algorithms.OpticalPoly method) (motion_correction.algorithms.OpticalTVL1 method) (motion_correction.algorithms.Phase method)

align_morphic_cpu() (motion_correction.algorithms.Morphic method) align_morphic_gpu() (motion_correction.algorithms.Morphic method) apply_correction_flim() (in module motion_correction.motion_correction) (motion_correction.desktop.flim_aligner.FlimAligner method) apply_correction_intensity() (motion_correction.desktop.flim_aligner.FlimAligner method)

C

calculate_correction() (in module motion_correction.motion_correction) centers_to_edges() (in module motion_correction.image_registration.iterative_zoom) chi2_shift() (in module motion_correction.image_registration.chi2_shifts) chi2_shift_iterzoom() (in module motion_correction.image_registration.chi2_shifts) chi2n_map() (in module motion_correction.image_registration.chi2_shifts) coarse_to_fine() (in module motion_correction.pyimof.util) color_wheel() (in module motion_correction.pyimof.display)

combined_transforms (motion_correction.motion_correction.CorrectionResults attribute) corrected (motion_correction.motion_correction.Metric attribute) corrected_intensity_data_stack (motion_correction.motion_correction.CorrectionResults attribute) CorrectionResults (class in motion_correction.motion_correction) correlate2d() (in module motion_correction.image_registration.fft_tools.correlate2d) cross_correlation_shifts() (in module motion_correction.image_registration.cross_correlation_shifts) cross_correlation_shifts_FITS() (in module motion_correction.image_registration.cross_correlation_shifts)

D

dftups() (in module motion_correction.image_registration.fft_tools.upsample) dftups1d() (in module motion_correction.image_registration.fft_tools.upsample) display_images() (in module motion_correction.desktop.utility)

downsample() (in module motion_correction.image_registration.fft_tools.downsample) downsample_1d() (in module motion_correction.image_registration.fft_tools.downsample) downsample_axis() (in module motion_correction.image_registration.fft_tools.downsample) downsample_cube() (in module motion_correction.image_registration.fft_tools.downsample)

E

export_results() (motion_correction.desktop.flim_aligner.FlimAligner method)

F

fits_overlap() (in module motion_correction.image_registration.FITS_tools.fits_overlap) FlimAligner (class in motion_correction.desktop.flim_aligner) floread() (in module motion_correction.pyimof.io) flow_to_color() (in module motion_correction.pyimof.display)

flowrite() (in module motion_correction.pyimof.io) fourier_interp1d() (in module motion_correction.image_registration.fft_tools.scale) fourier_interp2d() (in module motion_correction.image_registration.fft_tools.scale) fourier_interpnd() (in module motion_correction.image_registration.fft_tools.scale)

G

gaussian() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) gaussian_centered() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) get_aggregated_intensity_image() (in module motion_correction.motion_correction) get_cd() (in module motion_correction.image_registration.FITS_tools.load_header) get_ffts() (in module motion_correction.image_registration.fft_tools.fast_ffts) get_intensity_stack() (in module motion_correction.motion_correction) (motion_correction.desktop.flim_aligner.FlimAligner method)

get_pyramid() (in module motion_correction.pyimof.util) get_tight_figsize() (in module motion_correction.pyimof.display) global_corrected (motion_correction.motion_correction.Metric attribute) global_corrected_intensity_data_stack (motion_correction.motion_correction.CorrectionResults attribute) global_transforms (motion_correction.motion_correction.CorrectionResults attribute)

H

header_overlap() (in module motion_correction.image_registration.FITS_tools.fits_overlap)

I

ilk() (in module motion_correction.pyimof.solvers)

iterative_zoom() (in module motion_correction.image_registration.iterative_zoom) iterative_zoom_1d() (in module motion_correction.image_registration.iterative_zoom)

J

join_path() (in module motion_correction.desktop.utility)

L

load_data() (in module motion_correction.image_registration.FITS_tools.load_header) load_header() (in module motion_correction.image_registration.FITS_tools.load_header)

load_ptfile() (in module motion_correction.pqreader) local_transforms (motion_correction.motion_correction.CorrectionResults attribute)

M

make_kernel() (in module motion_correction.image_registration.fft_tools.smooth_tools) match_fits() (in module motion_correction.image_registration.FITS_tools.match_images) Metric (class in motion_correction.motion_correction) Metrics (class in motion_correction.motion_correction) metrics (motion_correction.motion_correction.CorrectionResults attribute) module motion_correction motion_correction.algorithms motion_correction.desktop motion_correction.desktop.flim_aligner motion_correction.desktop.utility motion_correction.image_registration motion_correction.image_registration.chi2_shifts motion_correction.image_registration.conftest motion_correction.image_registration.cross_correlation_shifts motion_correction.image_registration.fft_tools motion_correction.image_registration.fft_tools.correlate2d motion_correction.image_registration.fft_tools.downsample motion_correction.image_registration.fft_tools.fast_ffts motion_correction.image_registration.fft_tools.scale motion_correction.image_registration.fft_tools.shift motion_correction.image_registration.fft_tools.smooth_tools motion_correction.image_registration.fft_tools.tests motion_correction.image_registration.fft_tools.tests.test_downsample motion_correction.image_registration.fft_tools.tests.test_upsample motion_correction.image_registration.fft_tools.upsample motion_correction.image_registration.fft_tools.zoom motion_correction.image_registration.FITS_tools motion_correction.image_registration.FITS_tools.fits_overlap motion_correction.image_registration.FITS_tools.load_header motion_correction.image_registration.FITS_tools.match_images motion_correction.image_registration.iterative_zoom motion_correction.image_registration.register_images motion_correction.image_registration.version motion_correction.motion_correction motion_correction.pqreader motion_correction.pqwriter motion_correction.pyimof motion_correction.pyimof.display motion_correction.pyimof.io motion_correction.pyimof.solvers motion_correction.pyimof.util Morphic (class in motion_correction.algorithms) motion_correction module motion_correction.algorithms module motion_correction.desktop module motion_correction.desktop.flim_aligner module motion_correction.desktop.utility module motion_correction.image_registration module motion_correction.image_registration.chi2_shifts module motion_correction.image_registration.conftest module

motion_correction.image_registration.cross_correlation_shifts module motion_correction.image_registration.fft_tools module motion_correction.image_registration.fft_tools.correlate2d module motion_correction.image_registration.fft_tools.downsample module motion_correction.image_registration.fft_tools.fast_ffts module motion_correction.image_registration.fft_tools.scale module motion_correction.image_registration.fft_tools.shift module motion_correction.image_registration.fft_tools.smooth_tools module motion_correction.image_registration.fft_tools.tests module motion_correction.image_registration.fft_tools.tests.test_downsample module motion_correction.image_registration.fft_tools.tests.test_upsample module motion_correction.image_registration.fft_tools.upsample module motion_correction.image_registration.fft_tools.zoom module motion_correction.image_registration.FITS_tools module motion_correction.image_registration.FITS_tools.fits_overlap module motion_correction.image_registration.FITS_tools.load_header module motion_correction.image_registration.FITS_tools.match_images module motion_correction.image_registration.iterative_zoom module motion_correction.image_registration.register_images module motion_correction.image_registration.version module motion_correction.motion_correction module motion_correction.pqreader module motion_correction.pqwriter module motion_correction.pyimof module motion_correction.pyimof.display module motion_correction.pyimof.io module motion_correction.pyimof.solvers module motion_correction.pyimof.util module MSE (motion_correction.desktop.flim_aligner.SimMetric attribute) mse (motion_correction.motion_correction.Metrics attribute)

N

NCC (motion_correction.desktop.flim_aligner.SimMetric attribute) ncc (motion_correction.motion_correction.Metrics attribute)

ncc() (in module motion_correction.desktop.utility) NRM (motion_correction.desktop.flim_aligner.SimMetric attribute) nrm (motion_correction.motion_correction.Metrics attribute)

O

obsolete_test_center_zoom_even() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) obsolete_test_center_zoom_simple2() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) obsolete_test_center_zoom_simple3() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) odddftups() (in module motion_correction.image_registration.fft_tools.upsample)

OpticalILK (class in motion_correction.algorithms) OpticalPoly (class in motion_correction.algorithms) OpticalTVL1 (class in motion_correction.algorithms) original (motion_correction.motion_correction.Metric attribute)

P

Phase (class in motion_correction.algorithms) plot() (in module motion_correction.pyimof.display) plot_grids() (in module motion_correction.desktop.utility) plot_sequence_images() (in module motion_correction.desktop.utility) (in module motion_correction.pqreader)

plotthings() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) project_to_header() (in module motion_correction.image_registration.FITS_tools.match_images) pytest_configure() (in module motion_correction.image_registration.conftest)

Q

quiver() (in module motion_correction.pyimof.display)

R

register_fits() (in module motion_correction.image_registration.FITS_tools.match_images)

register_images() (in module motion_correction.image_registration.register_images) resize_flow() (in module motion_correction.pyimof.util)

S

save_sequence_images() (in module motion_correction.desktop.utility) set_channel() (motion_correction.desktop.flim_aligner.FlimAligner method) set_methods() (motion_correction.desktop.flim_aligner.FlimAligner method) set_sim_metric() (motion_correction.desktop.flim_aligner.FlimAligner method) shift2d() (in module motion_correction.image_registration.fft_tools.shift) shiftnd() (in module motion_correction.image_registration.fft_tools.shift)

SimMetric (class in motion_correction.desktop.flim_aligner) smooth() (in module motion_correction.image_registration.fft_tools.smooth_tools) SPM (motion_correction.desktop.flim_aligner.SimMetric attribute) spm (motion_correction.motion_correction.Metrics attribute) SSI (motion_correction.desktop.flim_aligner.SimMetric attribute) ssi (motion_correction.motion_correction.Metrics attribute)

T

test_downsample_matched() (in module motion_correction.image_registration.fft_tools.tests.test_downsample) test_downsample_nodownsample() (in module motion_correction.image_registration.fft_tools.tests.test_downsample) test_downsample_padded() (in module motion_correction.image_registration.fft_tools.tests.test_downsample)

test_issue6_regression() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) tv_regularize() (in module motion_correction.pyimof.util) tvl1() (in module motion_correction.pyimof.solvers)

U

upsample_image() (in module motion_correction.image_registration.fft_tools.upsample)

W

write_pt3() (in module motion_correction.pqwriter)

Z

zoom1d() (in module motion_correction.image_registration.fft_tools.zoom) zoom_on_pixel() (in module motion_correction.image_registration.fft_tools.zoom)

zoomed_gaussian() (in module motion_correction.image_registration.fft_tools.tests.test_upsample) zoomnd() (in module motion_correction.image_registration.fft_tools.zoom)