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Adding phase retrieval #130

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tobias-liaudat wants to merge 159 commits intodevelopCosmoStat/wf-psf:developfrom u/tobias-liaudat/feature-phase_retrievalCosmoStat/wf-psf:u/tobias-liaudat/feature-phase_retrievalCopy head branch name to clipboard

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Commits

Commits on Jan 8, 2024

• add dev configs

  tobias-liaudat

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  625d135

• config for fast test

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  6e88956

• fix configs

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• update (fix) configs

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• try again

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  d16cd72

• fix config problem

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• Merge branch 'develop' of https://github.com/CosmoStat/wf-psf into u/tobias-liaudat/feature-phase_retrieval

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  e45df03

Commits on Jan 9, 2024

• Add new Zernike projection function with obscurations

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• Add new Zk projection algorithm

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• Add default behaviour

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• Improve comments and doc

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  7838cca

Commits on Jan 11, 2024

• Fix problem with repeating seed for S init after projection

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  5ee00bc

Commits on Jan 12, 2024

• Fix small bug when random seed is not defined

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  08c0aad

• Add phase retrieval test configs

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  20dcfdb

• update dev configs

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• Add job for PR validation

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  51e8b65

• Add log dir

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  9b5e817

• Update configs

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  e03a34f

• update job

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• Add new configs and job in new dir

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• debug lines

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• try bug fix

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• add new test

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• fix paths

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• erase debug lines

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• fix another path

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• update paths

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• remove unused configs

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  d200f07

Commits on Jan 15, 2024

• Add plot all config

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  d50b647

• fix job

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  a5b3f5c

• fix conf

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  d55f46e

• Fix config file

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  652d504

• Fix path

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• Fix path

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  d066fc3

• fix path

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  1716bfa

• Update configs and job for standard sanity check run

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  ac8d578

• update name

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  3bb5779

• Remove projections

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  b2e5032

Commits on Jan 16, 2024

• Update model with new projection procedure

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  092198d

• Small bug fix when reset is True and project is False

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  256aa3c

• Remove repeated line (probably a typo)

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  abfe770

• Reproducibility change

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  0b19f88

• Add PR validation configs

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  2167eaa

• Add PR validation job

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  f8f6ccf

Commits on Mar 6, 2024

• Merge branch 'develop' of https://github.com/CosmoStat/wf-psf into u/tobias-liaudat/feature-phase_retrieval

  tobias-liaudat

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  e8c2634

• Merge branch 'develop' of https://github.com/CosmoStat/wf-psf into u/tobias-liaudat/feature-phase_retrieval

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  dcf6918

• remove duplicated comment

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• add unit test for obscured zernike projection

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• apply black

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• add unit test for PI_zernikes

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• black file

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  af59920

Commits on Mar 11, 2024

• Merge branch 'develop' of https://github.com/CosmoStat/wf-psf into u/tobias-liaudat/feature-phase_retrieval

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  a2121eb

• clean dev and validation files

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  b8a661c

• remove TODO comment as it is already done

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  d07e72d

Commits on Mar 13, 2024

• clean comment

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  ffe365d

• clean comments

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• clean more comments

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• black formatting

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  8fed999

Commits on Mar 18, 2024

• improve comment

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  7aaea30

• specify exception

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  48217ea

• add comment

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• improve messages

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  09d881b

• add more descriptive name for PI_zernikes

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  93e0fec

• add comment

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  ea09bf3

• improve comments

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• remove unused import

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• remove unused imports

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• remove unused import

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• black formatting

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• remove unnecessary dependency

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• apply black formatting

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  44e55c8

• fix docstring

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  17d9a45

• Modified to use PSF Factory Class

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• Added Factory class and rm duplicate

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• Refactored with DataHandler class and updated docstrings

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  657f1d7

• Updated to DataHandler class

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• Reduced to single DataHandler class

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• Updated docstring

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• Updated docstring

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• Reformatted with black

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• Removed attribute from class

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• Added refactored v1 SpatialVaryingPSF module

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  3cedf69

• Updated docstring and comment

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• Added unit test package for sims

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• Unit tests for spatial_varying_psf module

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• Added spatial_varying_psf module

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• Added fixtures

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• Reformatted module

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• Renamed module following pep8

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• Added logger and changed arg names

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• Updated module description with new name of sim.spatial_varying_psf module

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• Added missing doc strings

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• Formatting and updated unit tests to check logging

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• Renamed dict key training -> train

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• Fix run_config_name typo and DataHandler obj creation

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• Reformat with black

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• Changed name to grid_size

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• Change to correct psf_factory_class method name

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• Reformatted with black

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• Refactored to generic DataHandler

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• Change dataset name to

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• Revert "Change dataset name to"

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• Added pytest-mock dependency to create mock api calls in unit tests

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• Updated module with new data object

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  a081817

• Updated conftest with new data key

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• Changed to absolute path

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  452abb9

• Added mock fixtures and unit tests for Data and TrainingHandlers

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• Updated with new training_data and test_data namespaces

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  238100d

• Corrected missing args due to new data_conf object

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  352ef42

• add black formatter to check/format the code to the ci.yml file

  

  nada moukaddem

  authored and

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  c83e7bd

• Refactored with DataHandler class and updated docstrings

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  0edc700

• Removed print() from unit test

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  38091c3

• Corrected name of arg

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  a4bab87

• Added missing args

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• Updated fixture for data_conf

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• Changed key train to training

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  2cef6a6

• Moved build_psf_models() to psf_models.psf_models

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  d4faaee

• Updated import build_psf_models from psf_models.psf_models

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• Removed duplicated parametric model class

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  f140870

• Refactor: Updated class, variable, and function names to comply with PEP8

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• Modify class names to comply with PEP8

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• Change name of TestClass to RegisterConfigClass

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• Add module for psf physical model

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• Update doc strings

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  10021d0

Commits on Mar 19, 2024

• Move get_obs_positions utility function to data package

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• Add test_data unit test package

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  956b2e7

• Rename tf_zernike_cube method to generate_zernike_maps_3d

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Commits on Mar 20, 2024

• Refactor: Rename ground_truth_psf_model function to create_ground_truth_psf_model

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• Refactor: Remove methods, Improve docstrings, Set attributes in appropriate functions

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  9b1dccd

• Fix model_params.pupil_diameter typo

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• Remove interpolation attributes from class

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  18d34b3

• Add test_psf_models unit test package

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  160e45f

• Add get_zernike_prior method to retrieve zernike prior from a dataset

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  37f2053

• Add fixture and unit tests for get_zernike_prior method

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  5c1c973

• Modify to use get_zernike_prior() to retrieve zernike_prior info

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• Refactor: Change/Add fixture and mocks for get_zernike_prior, fix mocker.patch path

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• Correct formatting with black

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• Change zks_pad function name to pad_zernikes

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• Format with black

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Commits on Mar 21, 2024

• Refactor: Remove unused attributes, Add predict_zernikes, Improve docstrings and variable names

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  bb27ce4

• Add unit tests for pad_zernikes

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  db844be

• Refactor: Remove nzernikes attribute, Improve function names, Use zk_param and zk_prior directly to determine num of Zernikes

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Commits on Mar 22, 2024

• Update to new class name TFPhysicalLayer

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• Replace compute_zernike with predict_zernike in methods predict_step, predict_opd, predict_mono_psfs

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• Update call() docstring for TFPhysicalLayer for clarity

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• Reformat with black

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  9d76f55

• Refactor: Added conditionals for pad_zernike and corrected typo in compute_zernikes

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• Add unit test for compute_zernikes

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Commits on Mar 25, 2024

• Refactor: Add conditional to pad_zernikes() to check shapes match

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• Change tensors to same length in unit test, Add unit test to check mismatch shapes

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Commits on Mar 27, 2024

• Merge branch 'feature/issues-116-and-123/psf-model-and-sims' into u/tobias-liaudat/feature-phase_retrieval

  

  Jennifer Pollack

  committed
  7410ed2

• Update class name to PSFSimulator

  

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  b48f780

• Correct format with black

  

  Jennifer Pollack

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• Remove unwanted text

  

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• Remove unused import

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  faea59a

• Change new funcs names to improve readability

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  8e3dc09

• Remove Duplicate Black formatter step from ci

  

  Jennifer Pollack

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  4dfeca2

• Reformat file with black

  

  Jennifer Pollack

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  68aad3f

• Change names to improve readability; Correct typo

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