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Merge dev for release 1.11.4#1449

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pgunn merged 84 commits intomainflatironinstitute/CaImAn:mainfrom devflatironinstitute/CaImAn:devCopy head branch name to clipboardJan 15, 2025

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Commits on Aug 6, 2024

• VERSION to 1.11.4 in dev after release

  pgunn

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• Changes to wording, readme. Deprecate caiman central (not planning to maintain it, for now)

  pgunn

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• contributing: fix bad formatting

  pgunn

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• README/contributions: finally found where my earlier edits were (dev-logging_cleanup from two weeks ago, post-merge). Syncing them over here correctly.

  pgunn

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Commits on Aug 8, 2024

• Docs: change instructions to use jupyter notebook to instead suggest jupyter lab

  pgunn

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Commits on Aug 9, 2024

• Fix unbound local error in online_cnmf

  ethanbb

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• Fix corr image not validating if it contains nans

  ethanbb

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• Merge pull request #1385 from proektlab/save-nan-fix

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  pgunn

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• Compare kind of dtype rather than dtype itself

  ethanbb

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• Merge pull request #1384 from proektlab/onacid-unbound-fix

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  pgunn

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• Add test for saving/loading HDF5

  ethanbb

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• Merge pull request #1386 from proektlab/save-nan-fix

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  pgunn

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Commits on Aug 10, 2024

• Fix conversion from sparse matrix to dense array

  ethanbb

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Commits on Aug 11, 2024

• Make test_toydata more flexible and add test cases for patch processing

  ethanbb

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• Don't use nb_patch=2 for better fit

  ethanbb

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Commits on Aug 20, 2024

• Update motion_correction.py

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  deMalmazet

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Commits on Aug 21, 2024

• Merge pull request #1392 from deMalmazet/main

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  pgunn

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Commits on Sep 3, 2024

• Merge pull request #1387 from proektlab/lowrank-false-sparse-fix

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  pgunn

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Commits on Sep 15, 2024

• Try to use pytest for tests

  hmaarrfk

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Commits on Sep 18, 2024

• Add winget instructions for dev mode Windows installation

  ethanbb

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Commits on Sep 19, 2024

• Merge pull request #1406 from proektlab/win-installation-winget

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  pgunn

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Commits on Sep 23, 2024

• Merge pull request #1405 from hmaarrfk/pytest

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  pgunn

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Commits on Oct 1, 2024

• update docstring

  kushalkolar

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• Update cnmf.py

  kushalkolar

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• Update estimates.py

  kushalkolar

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• Update cnmf.py

  kushalkolar

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Commits on Oct 11, 2024

• Update cnmf.py

  kushalkolar

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• Update estimates.py

  kushalkolar

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Commits on Oct 12, 2024

• Merge pull request #1410 from flatironinstitute/fix-docs

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  pgunn

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Commits on Nov 20, 2024

• docs: switch to miniforge

  pgunn

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• Conda: assume people are using miniforge; remove defaults channel and don't mention it in docs anymore

  pgunn

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Commits on Dec 6, 2024

• Move dependencies into pyproject

  pgunn

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• Remove skcuda from motion_correction. Implements #1416

  pgunn

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Commits on Dec 10, 2024

• Merge pull request #1432 from flatironinstitute/dev-pyproject

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  pgunn

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• use_cuda deprecation - revise phrasing as per kkolar

  pgunn

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• Fix docs for arguments to tile_and_correct() and tile_and_correct_3d()

  pgunn

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• motion_correction: eliminate the global boolean "opencv".

  pgunn

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• motion_correction: Fix confusing errors from some functions

  pgunn

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• motion_correction: Fix more mistakes in function documentation, other messages

  pgunn

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• motion_correction: Remove some dead code, more docs cleanups

  pgunn

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• Update caiman/motion_correction.py

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  pgunn

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  kushalkolar

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• Update caiman/motion_correction.py

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  pgunn

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  kushalkolar

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Commits on Dec 11, 2024

• Merge pull request #1433 from flatironinstitute/dev-no_skcuda

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  pgunn

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• For now, Windows users should use pip and (sigh) compile caiman. This is a mess.

  pgunn

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• See if the github testrunner is easily fixed

  pgunn

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• Let's switch over to miniforge in CI while we're at it

  pgunn

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• Merge pull request #1434 from flatironinstitute/dev-windows_pip

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  pgunn

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Commits on Dec 12, 2024

• Update readme-gpu.md

  kushalkolar

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• Update movies.py

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  darikoneil

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• Merge pull request #1437 from darikoneil/main

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  pgunn

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Commits on Dec 13, 2024

• Improve get_file_size efficiency for .npy files

  fdeguire03

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• Fix file_name typo

  fdeguire03

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• Improve get_file_size efficiency for .npy files

  

  fdeguire03

  authored and

  Frank DeGuire

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• Merge branch 'dev' of https://github.com/fdeguire03/CaImAn into dev

  

  Frank DeGuire

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  Frank DeGuire

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• Clarify comment in exception

  fdeguire03

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• Merge pull request #1439 from fdeguire03/dev

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  pgunn

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• Merge pull request #1435 from flatironinstitute/update-docs

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  pgunn

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Commits on Jan 6, 2025

• CI: Remove package no longer present

  pgunn

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• Merge pull request #1445 from flatironinstitute/dev-fix_ci_again

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  pgunn

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• Refactor sliding_window and add get_patch_centers

  ethanbb

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• Add interp_shifts_precisely option for tile_and_correct

  ethanbb

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• Implement interp_shifts_precisely for non-opencv and for tile_and_correct_3d

  ethanbb

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• Fix apparent bugs in register_ROIs

  ethanbb

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• Fix incorrectly handling dest indices when interpolating shifts and type of input to cv.remap

  ethanbb

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• Allow inputting parameters to override tile_and_correct defaults in register_ROIs

  ethanbb

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• Make register_ROIs work with rigid correction

  ethanbb

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• Put align_options at the end to avoid messing up positional args

  ethanbb

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• Clarify exception to strides/overlaps for last patch

  ethanbb

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• Add 'interp_shifts_precisely' motion parameter

  ethanbb

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Commits on Jan 7, 2025

• Use new option in apply_shifts_movie and fix apparent inconsistencies

  ethanbb

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• Change interp_shifts_precisely to shifts_interpolate

  ethanbb

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• Merge pull request #1444 from proektlab/register_ROIs-improvements

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  pgunn

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Commits on Jan 9, 2025

• Add npy support to load_memmap

  fdeguire03

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Commits on Jan 10, 2025

• Add data consistency checks to mmapping.py

  fdeguire03

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• Merge pull request #1446 from fdeguire03/dev

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  pgunn

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Commits on Jan 14, 2025

• README: fewer inconsistencies in capitalisation of caiman

  pgunn

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• Add Darcy to dataset thanks, install instructions mention pip now

  pgunn

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• l1_ratio in cnmf.paras.init for call to NMF()

  pgunn

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• Redo l1_ratio because we use splat operator

  pgunn

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• l1_ratio: fix debug message

  pgunn

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• Rename l1_ratio parameter for clarity

  pgunn

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• Notebooks: set default logging level to logging.WARNING, add a blurb.

  pgunn

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• Merge pull request #1448 from flatironinstitute/dev-l1_ratio_threadthrough

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  pgunn

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Commits on Jan 15, 2025

• motion_correction: move some noisy and not too useful messages from info to debug

  pgunn

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