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Move from 2d to 3d array operations#12

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PinkShnack wants to merge 54 commits intomainRI-imaging/qpretrieve:mainfrom 9_feat_br_3d_arraysRI-imaging/qpretrieve:9_feat_br_3d_arraysCopy head branch name to clipboard

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Commits on Jan 7, 2025

• feat: breaking change, process data as 3D zyx array

  

  Eoghan O'Connell

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• tests: ensure new array processing results in identical values

  

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Commits on Jan 14, 2025

• ci: reverse install of libfftw

  

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• ci: try to update first

  

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• ci: fix based on libfftw rename

  

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Commits on Jan 17, 2025

• tests: check to see if there is a difference between win and linux

  

  Eoghan O'Connell

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• clearly deal with user trying to use pyfftw even if it is not installed

  

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• ci: install FFTW extension so that ci actually tests it

  

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• tests: fix pyfftw axes input for fft

  

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Commits on Jan 20, 2025

• fix: for 2d fft and fftshifts, specify axes; tests: FFT checks added

  

  Eoghan O'Connell

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• fix: correctly check for class attr _amplitude within property

  

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• docs: warn the user that a new format will be returned

  

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• tests: data fmt revert method checks

  

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• tests: fix mispelled method name

  

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Commits on Jan 21, 2025

• tests: fix shapes for oah tests

  

  Eoghan O'Connell

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• tests: fix fixture for hologram shape

  

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• tests: allow hologram fixture use with and without param

  

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• enh: use custom error BadFFTFilterError for interfere base input

  

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• tests: use hasattr rather than try except for request fixture

  

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• merging latest main to feat branch

  

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Commits on Jan 22, 2025

• ref: improve naming of modules functions and variables for data and array layout

  

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• enh: interfere base allows str input for getting original data array layout

  

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• tests: add default param to hologram fixture

  

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• tests: test the conversion from 3d data

  

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• tests: ensure old and new uses of fft algorithms are consistent

  

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Commits on Jan 23, 2025

• tests: compare 2d and 3d processing

  

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• docs: add example script for timing the different fft options

  

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• docs: new fft batch example

  

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• docs: add comparison between 2d and 3d transforms

  

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• docs: add new examples to docs

  

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• docs: minor lint changes

  

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• docs: create basic usage guide

  

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Commits on Jan 24, 2025

• docs: create array layout page for the docs

  

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• docs: cleanup the basic usage page and some links

  

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• docs: note on limitations of rgb array layouts

  

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• docs: clearly state allowed input data array layouts in base doctrings

  

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• docs: add type hints for fourier module

  

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• docs: add type hints for interferogram module

  

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• docs: add type hints for array layout module

  

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• docs: add type hints for utils module; ref: make 2d funcs private

  

  Eoghan O'Connell

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Commits on Feb 5, 2025

• ref: minor name changes

  PinkShnack

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• ref: remove warnings from data array input transforms

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• ref, docs: correct docstrings and use of order for padding_3d

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• ref: lint test codebase

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• fix: correct qlsi freq calculation

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• tests: create 3d qlsi pipeline

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• tests: clarify use of hologram data for qlsi utils

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Commits on Feb 10, 2025

• docs: update docstring and code reference with array layout info

  

  Eoghan O'Connell

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• tests: add 3d data tests for different filter names

  

  Eoghan O'Connell

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• tests: test FFTFilter input for both interference algos

  

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• docs: typehints for fftfilters

  

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• update CHANGELOG

  

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Commits on Feb 24, 2025

• docs: improve fft speed example

  

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• docs: minor pipeline fft clarification in example

  

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