Code

On-the-fly Reconstruction #393

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Commits

Commits on Apr 19, 2023

• pin README links

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• initial cli skeleton

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• first-pass docs

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• first-pass pydantic models

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• improve typing and testing of settings.py

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• full prototype of recorder calculate_transfer_function

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• complete cli draft

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• buttons work via cli

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Commits on Apr 25, 2023

• Merge pull request #347 from mehta-lab/cli-dev

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• connect background corrections

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• update LC_DEVICE_NAME

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• 20220920 -> 20230418

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• document check for "PC software version"

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• remove remaining converter util function

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• Merge pull request #353 from mehta-lab/connect-bg-correction

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• fix syntax error

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• Merge branch '0.4.0dev' into upgrade-mm2

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• improve software+firmware instructions

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• device adapter -> driver

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• direct download link

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• Merge pull request #354 from mehta-lab/upgrade-mm2

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• add regularization settings

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• connect recon params to cli

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• no kwargs

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• invert 2d phase to match

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• more background integration

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• Merge pull request #356 from mehta-lab/connect-reg-params

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• style cleanup

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• eager mode for now

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• fix typo

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• move large overlay info banner

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• avoid repeated updates

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• only use event information

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• bump mm version

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• update instructions

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• Merge pull request #358 from mehta-lab/bump-mm

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• remove acquisition mode suffix from birefringence

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• detect orientation layer and set colormap

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• log

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• increase log level

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• remove copy and test that input is not modified

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• wait until the birefringence layers are spawn

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• "changed" -> "moved" hook

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• Merge pull request #357 from mehta-lab/overlay-hook

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Commits on Apr 28, 2023

• Hot fix for flip + reflection convention

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• reuse variable

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• match repetitive birefringence layers

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• pass overlay name

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• use names with suffices

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• set colormap for multiple orientation layers

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• fix key

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• remove unused function

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• sort once

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Commits on May 12, 2023

• pin upgraded pm

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• update to version compatible with multithreading

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• Merge pull request #373 from mehta-lab/upgrade-pm

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• update waveorder dependency

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• Merge pull request #359 from mehta-lab/multi-overlay

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Commits on Jun 8, 2023

• illumination_wavelength -> wavelength_illumination

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Commits on Jun 9, 2023

• Merge pull request #376 from mehta-lab/rename-wavelength

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Commits on Jun 13, 2023

• added tests for compute-transfer-function and separated function logic

  

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• added documentation for compute-transfer-function

  

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• test

  

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• anisotropic_thin -> oriented_thick

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• changed function names and removed returns

  

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• rename output test and got output-path option working

  

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Commits on Jun 14, 2023

• added a possible template for testing different configurations

  

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• Merge pull request #378 from mehta-lab/rename-anisotropic

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• typo

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• removed test file

  

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• matched function name and fixed typo

  

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• remove unused reconstruction settings class

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• added unit tests, fixed typos

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Commits on Jun 15, 2023

• added tests, fixed docstring, added fixtures

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• cleaned up tests

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• revised settings with examples

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• initial revision of cli

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• document and test model_to_yaml and yaml_to_model

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Commits on Jun 16, 2023

• update compute_transfer_function

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• update apply_inverse_transfer_function

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• doc strings

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• improved names

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• -h for help

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• first pass reconstruct cli

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• rename to prepare for merge

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• Merge branch '0.4.0dev' into testing_compute_transfer

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• remove or "None"

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• fixed docstring parameters

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• cleaned imports and fixtures

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• Merge branch 'testing_compute_transfer' of github.com:mehta-lab/recOrder into testing_compute_transfer

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• complete reconstruct draft

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• add 3d fluorescence compute-tf

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• fluorescence apply_inverse_transfer_function

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• add axial_flip parameter to phase

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• abstracted fixture

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• Merge pull request #377 from mehta-lab/testing_compute_transfer

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• first-pass acquisition_workers.py

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• Merge branch '0.4.0dev' into fluor-cli

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Commits on Jun 17, 2023

• fix bugs and tests

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• simplify tests

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• typo

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• test fluorescence and refactor compute_tf tests

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• Merge branch '0.4.0dev' of github.com:mehta-lab/recOrder into 0.4.0dev

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Commits on Jun 21, 2023

• update default settings

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• typo

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• apply_inverse_transfer_function tests

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• pass birefringence tests

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• whoops

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Commits on Jun 23, 2023

• found image data

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• clean imports

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• fix tests

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• don't accept empty config

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• options -> option

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• validate fov path

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• unused import

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Commits on Jun 27, 2023

• removed iterator, updated to run diff acq orders

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Commits on Jun 28, 2023

• iterates through all dim for every acq order

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Commits on Jun 30, 2023

• grouped together z-stack data

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Commits on Jul 5, 2023

• simplify

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• remove redundant "scheme" parameter

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• fix docs

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• basic test of reconstruct

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• check input channel names

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• index into input dataset

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• document automatic configuration file generation

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• improved instructions

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• better default to match example

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• default 4 states

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• revamped examples folder

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• remove compute module

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• write entire acq into zarr for ptcz, ptzc order

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• simplify examples folder

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• remove unused imports

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• remove old reconstructors

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• remove listener vestiges

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Commits on Jul 6, 2023

• bf fixes

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• integration fixes for phase recon

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• ndtiff to zarr on all acq orders

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• birefringence integration fixes

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• changed acq_mode to str

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• background acquisition integration

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• tidy background recons

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• bkg correction integration fixes

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• Enable phase w/o calibration

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• Add cli_structure documentation

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Commits on Jul 11, 2023

• fix doc....specifiy input.zarr/0/0/0

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• Merge pull request #381 from mehta-lab/fluor-cli

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Commits on Jul 14, 2023

• convert to zarr from ndtiff

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Commits on Jul 19, 2023

• listener works on automaton

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Commits on Jul 21, 2023

• working threaded napari opener

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• to test on hummingbird

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Commits on Jul 22, 2023

• listen and open working on hummingbird

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Commits on Jul 24, 2023

• Merge branch 'mda-listener' of github.com:mehta-lab/recOrder into mda-listener

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• clean up

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• works on hummingbird

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Commits on Jul 25, 2023

• changed initialize zarr store

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• Merge branch '0.4.0dev' of github.com:mehta-lab/recOrder into 0.4.0dev

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• found image data

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• removed iterator, updated to run diff acq orders

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• iterates through all dim for every acq order

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• grouped together z-stack data

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• write entire acq into zarr for ptcz, ptzc order

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• ndtiff to zarr on all acq orders

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• changed acq_mode to str

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• convert to zarr from ndtiff

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• listener works on automaton

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• working threaded napari opener

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• to test on hummingbird

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• listen and open working on hummingbird

  

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• clean up

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• works on hummingbird

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• changed initialize zarr store

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• Merge branch 'mda-listener' of github.com:mehta-lab/recOrder into mda-listener

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• z-stack done logic

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  a0db0ad

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Commits on Jul 26, 2023

• progress towards reconstruction

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  3ba377b

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• Merge 'new-mda-listener' into main-mda-listener

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  2754c8b

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• applying reconstruction but not to all positions

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  b53f7c0

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• reconstruction working

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  2506fcc

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Commits on Jul 27, 2023

• documentation

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  9c162ef

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• fixed offset bug

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  e25765d

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Commits on Jul 28, 2023

• Merge recon-compatibility to main-mda-listener

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  6a5efcd

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• working reconstruction with ReconstructionSettings

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  ddaca6c

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• working reconstruction w ReconstructionSettings

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  572590f

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Commits on Jul 29, 2023

• benchmark

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  84dcb74

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Commits on Aug 2, 2023

• recon works for birefringence

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  e954e40

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• clean up

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  61d81d3

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Commits on Aug 3, 2023

• documentation and comments

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  b2cedbf

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• untracked unnecessary files

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• untracked another file

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  f0f08e0

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• untracked pluginsnap

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  41afe4d

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• merge artifacts

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  80234e2

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