Index

A

A (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute) Ab_matrices() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) add() (zetastitcher.gaussian_stitcher.linear.mapper.MultiDimLinearExpr method) (zetastitcher.gaussian_stitcher.utils.MultiDimLinearExpr method) add_diff_equalities() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method) add_dotprod() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method) add_lb_inequalities() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method) add_orig_equalities() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method) add_quad() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method)

add_sv() (in module zetastitcher.gaussian_stitcher.qp.mapper) add_term() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method) add_ub_inequalities() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method) add_variable() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) aggregate_results() (zetastitcher.align.xcorr_filematrix.XcorrFileMatrix method) align_dog() (in module zetastitcher.align.dog) append() (zetastitcher.gaussian_stitcher.linear.mapper.MultiDimLinearExpr method) (zetastitcher.gaussian_stitcher.utils.MultiDimLinearExpr method) array_size (zetastitcher.io.inputfile_mixin.InputFileMixin property)

B

b (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute)

build() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method)

C

channel (zetastitcher.io.inputfile.InputFile property) clear_absolute_positions() (zetastitcher.align.filematrix.FileMatrix method) close() (zetastitcher.io.inputfile_mixin.InputFileMixin method) (zetastitcher.io.mhdwrapper.MHDWrapper method) compute_end_pos() (zetastitcher.align.filematrix.FileMatrix method)

compute_nominal_positions() (zetastitcher.align.filematrix.FileMatrix method) compute_shift_vectors() (in module zetastitcher.fuse.absolute_positions) ConstraintTuple() (in module zetastitcher.gaussian_stitcher.common) crossCorr() (in module zetastitcher.align.dog) CustomFormatter (class in zetastitcher.scripts.stitch_downscale)

D

data_frame (zetastitcher.align.filematrix.FileMatrix attribute) debug (zetastitcher.fuse.fuse_runner.FuseRunner property)

dog() (in module zetastitcher.align.dog) dtype (zetastitcher.fuse.fuse_runner.FuseRunner property)

E

element_type_to_type_fmt() (zetastitcher.io.mhdwrapper.MHDWrapper static method) Expression (class in zetastitcher.gaussian_stitcher.qp.mapper)

extend() (zetastitcher.gaussian_stitcher.linear.mapper.MultiDimLinearExpr method) (zetastitcher.gaussian_stitcher.utils.MultiDimLinearExpr method)

F

FFMPEGWrapper (class in zetastitcher.io.ffmpeg_wrapper) file (zetastitcher.io.inputfile.InputFile property) file_size (zetastitcher.io.inputfile.InputFile property) (zetastitcher.io.inputfile_mixin.InputFileMixin property) FileMatrix (class in zetastitcher.align.filematrix) flatten() (in module zetastitcher.fuse.fuse) fm (zetastitcher.fuse.fuse_runner.FuseRunner attribute) frame() (zetastitcher.io.inputfile.InputFile method) (zetastitcher.io.pims_wrapper.PimsWrapper method) (zetastitcher.io.zipwrapper.ZipWrapper method)

frame_size (zetastitcher.io.inputfile_mixin.InputFileMixin property) from_data() (zetastitcher.align.xcorr_filematrix.XcorrFileMatrix class method) from_yaml() (zetastitcher.align.xcorr_filematrix.XcorrFileMatrix class method) full_height (zetastitcher.align.filematrix.FileMatrix property) full_thickness (zetastitcher.align.filematrix.FileMatrix property) full_width (zetastitcher.align.filematrix.FileMatrix property) fuse_queue() (in module zetastitcher.fuse.fuse) FuseRunner (class in zetastitcher.fuse.fuse_runner)

G

G (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute) GaussianQPBuilder (class in zetastitcher.gaussian_stitcher.qp.stitching) GaussianStitcher (class in zetastitcher.gaussian_stitcher.linear.stitching) (class in zetastitcher.gaussian_stitcher.stitching) GaussianStitcherQP (class in zetastitcher.gaussian_stitcher.qp.stitching) get_json() (zetastitcher.align.filematrix.FileMatrix method) get_matrices() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianStitcherQP method)

get_node2coordinates() (in module zetastitcher.gaussian_stitcher.linear.stitching) (in module zetastitcher.gaussian_stitcher.qp.stitching) (in module zetastitcher.gaussian_stitcher.stitching) get_typecodes() (in module zetastitcher.io.zipwrapper) get_vars_and_matrices() (zetastitcher.gaussian_stitcher.linear.mapper.MultiDimLinearExpr method) (zetastitcher.gaussian_stitcher.utils.MultiDimLinearExpr method) Gh_matrices() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) global_optimization() (in module zetastitcher.fuse.absolute_positions)

H

h (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute)

I

imread_wrapper() (in module zetastitcher.io.zipwrapper) InputFile (class in zetastitcher.io.inputfile)

InputFileMixin (class in zetastitcher.io.inputfile_mixin) is_multichannel (zetastitcher.fuse.fuse_runner.FuseRunner property)

L

lin_constr2arrays() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) linear_expr() (in module zetastitcher.gaussian_stitcher.linear.mapper) (in module zetastitcher.gaussian_stitcher.utils)

LinearExpr (class in zetastitcher.gaussian_stitcher.linear.mapper) (class in zetastitcher.gaussian_stitcher.utils) load_dir() (zetastitcher.align.filematrix.FileMatrix method) load_yaml() (zetastitcher.align.filematrix.FileMatrix method)

M

main() (in module zetastitcher.gaussian_stitcher.linear.mapper) (in module zetastitcher.gaussian_stitcher.utils) (in module zetastitcher.scripts.stitch_downscale) MHDWrapper (class in zetastitcher.io.mhdwrapper) module zetastitcher zetastitcher.align zetastitcher.align.dog zetastitcher.align.filematrix zetastitcher.align.xcorr_filematrix zetastitcher.fuse zetastitcher.fuse.absolute_positions zetastitcher.fuse.fuse zetastitcher.fuse.fuse_runner zetastitcher.fuse.lcd_numbers zetastitcher.fuse.overlaps zetastitcher.fuse.virtual_fused_volume zetastitcher.gaussian_stitcher zetastitcher.gaussian_stitcher.common zetastitcher.gaussian_stitcher.linear zetastitcher.gaussian_stitcher.linear.mapper zetastitcher.gaussian_stitcher.linear.solver zetastitcher.gaussian_stitcher.linear.stitching zetastitcher.gaussian_stitcher.qp zetastitcher.gaussian_stitcher.qp.mapper zetastitcher.gaussian_stitcher.qp.stitching zetastitcher.gaussian_stitcher.qp.util_debug zetastitcher.gaussian_stitcher.solver zetastitcher.gaussian_stitcher.stitching zetastitcher.gaussian_stitcher.utils zetastitcher.io zetastitcher.io.ffmpeg_wrapper zetastitcher.io.inputfile zetastitcher.io.inputfile_mixin zetastitcher.io.mhdwrapper zetastitcher.io.pims_wrapper zetastitcher.io.tiffwrapper zetastitcher.io.zipwrapper zetastitcher.scripts zetastitcher.scripts.stitch_downscale zetastitcher.version

multidim_lin_expr() (in module zetastitcher.gaussian_stitcher.linear.mapper) (in module zetastitcher.gaussian_stitcher.utils) MultiDimLinearExpr (class in zetastitcher.gaussian_stitcher.linear.mapper) (class in zetastitcher.gaussian_stitcher.utils)

N

new_equality() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) new_inequality() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) new_objective() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method)

new_variable() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) new_vector() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) Nx (zetastitcher.align.filematrix.FileMatrix property) Ny (zetastitcher.align.filematrix.FileMatrix property)

O

one() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method) open() (zetastitcher.io.ffmpeg_wrapper.FFMPEGWrapper method) (zetastitcher.io.inputfile.InputFile method) (zetastitcher.io.mhdwrapper.MHDWrapper method) (zetastitcher.io.pims_wrapper.PimsWrapper method) (zetastitcher.io.tiffwrapper.TiffWrapper method) (zetastitcher.io.zipwrapper.ZipWrapper method)

order() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method) (zetastitcher.gaussian_stitcher.qp.mapper.Term method) output_shape (zetastitcher.fuse.fuse_runner.FuseRunner property) Overlaps (class in zetastitcher.fuse.overlaps) overlay_debug() (in module zetastitcher.fuse.fuse) overlay_debug_enabled (zetastitcher.fuse.virtual_fused_volume.VirtualFusedVolume property)

P

P (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute) parse_and_append() (zetastitcher.align.filematrix.FileMatrix method) parse_args() (in module zetastitcher.scripts.stitch_downscale) parse_file_name() (in module zetastitcher.align.filematrix)

peek (zetastitcher.fuse.virtual_fused_volume.VirtualFusedVolume property) PimsWrapper (class in zetastitcher.io.pims_wrapper) pretty_solver_debug() (in module zetastitcher.gaussian_stitcher.qp.util_debug) print_() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) process_data_frame() (zetastitcher.align.filematrix.FileMatrix method)

Q

q (zetastitcher.gaussian_stitcher.qp.mapper.SolverMatrices attribute)

Qp_matrices() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) QPBuilder (class in zetastitcher.gaussian_stitcher.qp.mapper)

R

run() (zetastitcher.fuse.fuse_runner.FuseRunner method)

S

save_to_yaml() (zetastitcher.align.filematrix.FileMatrix method) set_cache() (in module zetastitcher.io.zipwrapper) set_objective() (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method) shape (zetastitcher.fuse.virtual_fused_volume.VirtualFusedVolume property) (zetastitcher.io.ffmpeg_wrapper.FFMPEGWrapper property) (zetastitcher.io.inputfile.InputFile property) (zetastitcher.io.inputfile_mixin.InputFileMixin property)

slices() (zetastitcher.align.filematrix.FileMatrix method) SolverMatrices (class in zetastitcher.gaussian_stitcher.qp.mapper) sparse_lsqr_solver() (in module zetastitcher.gaussian_stitcher.linear.solver) (in module zetastitcher.gaussian_stitcher.solver) squircle_alpha() (in module zetastitcher.fuse.fuse) stitch() (zetastitcher.gaussian_stitcher.linear.stitching.GaussianStitcher method) (zetastitcher.gaussian_stitcher.qp.stitching.GaussianStitcherQP method) (zetastitcher.gaussian_stitcher.stitching.GaussianStitcher method)

T

Term (class in zetastitcher.gaussian_stitcher.qp.mapper) TiffWrapper (class in zetastitcher.io.tiffwrapper) tiles_along_dir (zetastitcher.align.filematrix.FileMatrix property)

tiles_along_X (zetastitcher.align.filematrix.FileMatrix property) tiles_along_Y (zetastitcher.align.filematrix.FileMatrix property) to_dtype() (in module zetastitcher.fuse.virtual_fused_volume) twoD_gaussian_kernel() (in module zetastitcher.align.dog)

V

var2idx() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) Variable (class in zetastitcher.gaussian_stitcher.qp.mapper) variables() (zetastitcher.gaussian_stitcher.qp.mapper.QPBuilder method) (zetastitcher.gaussian_stitcher.qp.stitching.GaussianQPBuilder method)

variables_set() (zetastitcher.gaussian_stitcher.linear.mapper.LinearExpr method) (zetastitcher.gaussian_stitcher.linear.mapper.MultiDimLinearExpr method) (zetastitcher.gaussian_stitcher.utils.LinearExpr method) (zetastitcher.gaussian_stitcher.utils.MultiDimLinearExpr method) VirtualFusedVolume (class in zetastitcher.fuse.virtual_fused_volume)

W

whole() (zetastitcher.io.inputfile.InputFile method)

X

XcorrFileMatrix (class in zetastitcher.align.xcorr_filematrix)

Z

zero() (zetastitcher.gaussian_stitcher.qp.mapper.Expression method) zetastitcher module zetastitcher.align module zetastitcher.align.dog module zetastitcher.align.filematrix module zetastitcher.align.xcorr_filematrix module zetastitcher.fuse module zetastitcher.fuse.absolute_positions module zetastitcher.fuse.fuse module zetastitcher.fuse.fuse_runner module zetastitcher.fuse.lcd_numbers module zetastitcher.fuse.overlaps module zetastitcher.fuse.virtual_fused_volume module zetastitcher.gaussian_stitcher module zetastitcher.gaussian_stitcher.common module zetastitcher.gaussian_stitcher.linear module zetastitcher.gaussian_stitcher.linear.mapper module zetastitcher.gaussian_stitcher.linear.solver module zetastitcher.gaussian_stitcher.linear.stitching module zetastitcher.gaussian_stitcher.qp module zetastitcher.gaussian_stitcher.qp.mapper module

zetastitcher.gaussian_stitcher.qp.stitching module zetastitcher.gaussian_stitcher.qp.util_debug module zetastitcher.gaussian_stitcher.solver module zetastitcher.gaussian_stitcher.stitching module zetastitcher.gaussian_stitcher.utils module zetastitcher.io module zetastitcher.io.ffmpeg_wrapper module zetastitcher.io.inputfile module zetastitcher.io.inputfile_mixin module zetastitcher.io.mhdwrapper module zetastitcher.io.pims_wrapper module zetastitcher.io.tiffwrapper module zetastitcher.io.zipwrapper module zetastitcher.scripts module zetastitcher.scripts.stitch_downscale module zetastitcher.version module ZipWrapper (class in zetastitcher.io.zipwrapper) zslice() (zetastitcher.io.ffmpeg_wrapper.FFMPEGWrapper method) (zetastitcher.io.inputfile.InputFile method) (zetastitcher.io.mhdwrapper.MHDWrapper method) (zetastitcher.io.tiffwrapper.TiffWrapper method) (zetastitcher.io.zipwrapper.ZipWrapper method) zslice_idx() (zetastitcher.io.inputfile.InputFile method)