Code

Registration V2#102

Code

Merged

ieivanov merged 86 commits intomainczbiohub-sf/shrimPy:mainfrom registration_v2czbiohub-sf/shrimPy:registration_v2Copy head branch name to clipboardJan 19, 2024

+1,807-463

Commits

Commits on Sep 22, 2023

• initial commit adding tools for cropping and registering with ants

  edyoshikun

  committed
  b78a3c3

Commits on Sep 26, 2023

• adding lir crop

  edyoshikun

  committed
  6c1ce18

Commits on Oct 4, 2023

• starting cleanup for registration

  edyoshikun

  committed
  0b71192

Commits on Oct 5, 2023

• converting nan to zero

  edyoshikun

  committed
  f11874d

Commits on Oct 24, 2023

• ants estimate affine

  edyoshikun

  committed
  1df5d66

• adding config file for estimate_transform

  edyoshikun

  committed
  b2e38e1

• cleaning up some redundancies

  edyoshikun

  committed
  7819ec4

• fix edge case of input not being float32

  edyoshikun

  committed
  9fc7df8

• channel is an int

  edyoshikun

  committed
  957fc49

• typo in napari add image for vs ants optimzer

  edyoshikun

  committed
  ccde02e

• adding utils yaml

  edyoshikun

  committed
  ee1845f

Commits on Oct 30, 2023

• separated the manual estimation from the optimizer

  edyoshikun

  committed
  e617ffc

• added ants to numpy and viceversa

  edyoshikun

  committed
  d019bf6

• adding input at the end to prevent from closing

  edyoshikun

  committed
  a76d70c

Commits on Nov 1, 2023

• replacing the reading of .mat to matrix from yaml

  edyoshikun

  committed
  0d39cbe

Commits on Nov 3, 2023

• added changes to ants to numpy from Jordaos input

  edyoshikun

  committed
  362e7a7

• cannot have recOrder as dependency given different pycromanager versions

  edyoshikun

  committed
  9d25d1a

• format

  edyoshikun

  committed
  caa84dc

• add test for optimize_affine and update readme

  edyoshikun

  committed
  6d6504a

• adding docstring

  edyoshikun

  committed
  f2c56fb

• removed the config dependency

  edyoshikun

  committed
  8ed961d

• removing the focus_finding svg

  edyoshikun

  committed
  7a7b20d

• removing the estimate_affine.yml and making flags to choose channels and verbose

  edyoshikun

  committed
  ac4a5fc

• added comment and code to use scipy.

  edyoshikun

  committed
  2d13d4d

• -ls and -lf to -s and -t

  talonchandler

  committed
  58175d0

• document FOCUS_SLICE_ROI_WIDTH

  talonchandler

  committed
  3b9d5eb

• estimate-source-to-target-affine -> estimate-affine

  talonchandler

  committed
  8acad5c

• standardize optimize-affine arguments

  talonchandler

  committed
  3fabc8a

• cleaner docs

  talonchandler

  committed
  52c21ad

• update RegistrationSettings

  talonchandler

  committed
  66d8990

• fix tests

  talonchandler

  committed
  98089b2

• remove duplicate

  talonchandler

  committed
  c34bad0

• write indices to output config

  talonchandler

  committed
  a35153f

• read channels from file

  talonchandler

  committed
  36f0b7e

Commits on Nov 4, 2023

• test fix

  talonchandler

  committed
  9bfbd20

• echo improvments

  talonchandler

  committed
  2ca449c

• black

  talonchandler

  committed
  5bf0ba0

Commits on Nov 9, 2023

• style

  ieivanov

  committed
  3e236f9

• remove duplicate cli call

  ieivanov

  committed
  6226786

Commits on Nov 10, 2023

• more intuitive manual registration

  ieivanov

  committed
  9137527

• Merge branch 'main' into registration_v2

  ieivanov

  committed
  4f709ba

Commits on Nov 13, 2023

• patch for deskewing

  edyoshikun

  committed
  ca75078

Commits on Nov 15, 2023

• testing slurmkit

  edyoshikun

  committed
  df53a74

• fix apply affine example

  ieivanov

  committed
  cd698d6

• matrix multiplication bugfix

  ieivanov

  committed
  fdae716

• updating the lir_crop using new registration

  edyoshikun

  committed
  ebc8b04

Commits on Nov 16, 2023

• adding lir crop to the apply affine and modifying the manual estimation and the optimizer to output the input zyx shape to yaml

  edyoshikun

  committed
  94761c8

• convert nans to zeros

  edyoshikun

  committed
  a29811a

Commits on Dec 12, 2023

• adding test for affine

  edyoshikun

  committed
  4562403

• removed main

  edyoshikun

  committed
  92d54dc

• fix apply_affine docstring

  ieivanov

  committed
  4fd7b6b

• fixing formatting

  edyoshikun

  committed
  4540956

• remove crop-output from cli args

  ieivanov

  committed
  0753c58

• estimate affine cli docstrings

  ieivanov

  committed
  ef4980f

• reverting changes to AnalysisSettings model.

  edyoshikun

  committed
  0e2f8c4

• optimize_affine cli docstrings

  ieivanov

  committed
  7c3c5f9

• Merge branch 'registration_v2' of github.com:czbiohub/mantis_automation into registration_v2

  ieivanov

  committed
  0d30a55

• Revert "reverting changes to AnalysisSettings model."

  Show description for ec56140
  ieivanov

  committed
  ec56140

Commits on Dec 14, 2023

• fix points layer grid mode bug

  ieivanov

  committed
  4172494

• fix tests

  ieivanov

  committed
  7fa9896

Commits on Dec 19, 2023

• combining the croping and merging to the apply-affine

  edyoshikun

  committed
  eb757cb

• removing unnecessary prints()

  edyoshikun

  committed
  af8dd2e

Commits on Jan 5, 2024

• add registration and stabilization modules

  ieivanov

  committed
  5325426

• Merge branch 'main' into registration_v2

  ieivanov

  committed
  538ddee

• style

  ieivanov

  committed
  076f1cb

• flake8

  ieivanov

  committed
  1e8ee8a

• Merge branch 'registration_v2' of github.com:czbiohub/mantis into registration_v2

  edyoshikun

  committed
  59a762d

Commits on Jan 16, 2024

• Registration refator (#118)

  Show description for 6a5f435
  

  ieivanov

  and

  edyoshikun

  authored
  6a5f435

• removing the source n target shape zyx and testing keep overhang

  edyoshikun

  committed
  97d2302

• updating estimate affine with previous commit changes

  edyoshikun

  committed
  ac2dac7

Commits on Jan 17, 2024

• Merge branch 'main' into registration_v2

  ieivanov

  committed
  fde7982

• style

  ieivanov

  committed
  cfd1116

• Update example_apply_affine_settings.yml

  ieivanov

  committed
  5c7fcf5

• Merge branch 'main' into registration_v2

  ieivanov

  committed
  e6ac5f1

• refactor registration and stabilization functions

  ieivanov

  committed
  10277c6

• fixing pytests

  edyoshikun

  committed
  4a54fb7

• more intuitive function names

  ieivanov

  committed
  0b45130

• minor refactor of estimane_affine

  ieivanov

  committed
  83292ad

• Merge branch 'registration_v2' of https://github.com/czbiohub-sf/shrimPy into registration_v2

  ieivanov

  committed
  f358f22

• bugfix

  ieivanov

  committed
  1b78856

• fixing the slurmkit files.

  edyoshikun

  committed
  71eb2c7

• typo

  ieivanov

  committed
  e574675

Commits on Jan 18, 2024

• cleaner processing of additioanal source channels

  ieivanov

  committed
  1957563

• Merge branch 'registration_v2' of github.com:czbiohub/mantis_automation into registration_v2

  ieivanov

  committed
  d62934a

• refactor apply_affine job submission

  ieivanov

  committed
  ab6244f

Commits on Jan 19, 2024

• remove position batch processing

  ieivanov

  committed
  6626aa6