Code

Dev -> Main for release of 1.11.0#1342

Code

Merged

pgunn merged 93 commits intomainflatironinstitute/CaImAn:mainfrom devflatironinstitute/CaImAn:devCopy head branch name to clipboardMay 3, 2024

+1,238-1,350

Commits

Commits on Apr 1, 2024

• Fix SBX functions for older tifffile versions and Windows (close mmaps after using)

  ethanbb

  committed
  98ef067

Commits on Apr 3, 2024

• VERSION: 1.10.10 post-release

  pgunn

  authored
  a5de8bf

Commits on Apr 8, 2024

• Extensions starts with a dot

  marberi

  committed
  0fec0b0

Commits on Apr 10, 2024

• Use memmap to load only indexed parts of files

  ethanbb

  committed
  4a08717

• Simplify by using the same loading code for all time index types

  ethanbb

  committed
  163022f

• Merge branch 'dev' of https://github.com/flatironinstitute/CaImAn into sbxload-update

  ethanbb

  committed
  20bb8ab

Commits on Apr 11, 2024

• Revert tifffile write to what is in dev since it works

  ethanbb

  committed
  2647b59

• Merge pull request #1326 from marberi/dev

  Show description for f5d5295
  pgunn

  authored
  f5d5295

Commits on Apr 12, 2024

• Use del to close memmaps rather than _mmap; reduce code duplication

  ethanbb

  committed
  c75a4f8

• Add comment about not viewing memmap and rename Ns

  ethanbb

  committed
  6c836c0

• Merge pull request #1329 from proektlab/sbxload-update

  Show description for 69772e3
  pgunn

  authored
  69772e3

Commits on Apr 16, 2024

• Trying out a refactor of the basic demo to be less notebook-y, more app-y

  pgunn

  committed
  149d624

• note on single_thread

  pgunn

  committed
  cd64806

• demos get a readme (that caimanmanager will deliver, so it needs to be .txt)

  pgunn

  committed
  4592b43

• Demos readme: format it a little more nicely

  pgunn

  committed
  e17931b

• Smaller cleanups, move logger setup into main(), preparing this to be a model for other demo refactors

  pgunn

  committed
  f30b975

• bringing demo_pipeline and demo_caiman_basic closer together as I refactor demo_pipeline

  pgunn

  committed
  fab66bc

• CLI Demos: Finish re-syncing demo_caiman_basic and demo_pipeline

  pgunn

  committed
  4ff7854

• Rebasing

  pgunn

  committed
  46a15dd

• Work on converting more CLI demos

  pgunn

  committed
  9b56d85

• cli_demos work: convert more, regularise more

  pgunn

  committed
  1315b9a

• cli_demos: Initial conversion of demo_pipeline_cnmfE to "app"

  pgunn

  committed
  2859174

• cli demos: convert demo_pipeline_voltage_imaging to "app"

  pgunn

  committed
  38436e1

• rebasing

  pgunn

  committed
  b882ddd

• cli demos: make amount of parallelism in the backend a CLI parameter

  pgunn

  committed
  21eb57f

• demo_OnACID CLI: Use the new CNMFParams JSON API to let people specify configs as json

  pgunn

  committed
  7ee20e1

• CLI demo_caiman_basic.py: only set params once

  pgunn

  committed
  2ffe070

• demo_caiman_basic CLI demo: move to json config files, only provide one inbuilt config

  pgunn

  committed
  860ea9f

• Demos/jsonconfigs: Fix misuse of params api

  pgunn

  committed
  5a98259

• Revise the three CLI demos that have been refactored to do argument/file-input parsing in the right order

  pgunn

  committed
  3862d71

• Demo revisions: remove inline parameters

  pgunn

  committed
  994773b

• demos_refactor: demo_onacid file load fix

  pgunn

  committed
  13b2730

• demos_refactor: demo_pipeline rework to use json

  pgunn

  committed
  32a6428

• demo_pipeline_NWB conversion work

  pgunn

  committed
  fa065d6

• cli demos json format fix whoops

  pgunn

  committed
  7cfc771

• demos refactor: fixing demos as testing

  pgunn

  committed
  01362a7

• demos_refactor: params files should not try to set quality.decay_time (nothing reads it, not a valid parameter)

  pgunn

  committed
  d04b012

• CLI demos rework: fix demo_onacid_mesoscope's visualisation defaults, match old vals

  pgunn

  committed
  29dcdcf

• demo_behaviour:rebasing

  pgunn

  committed
  2f6291e

• demo refactor: demo_pipeline_voltage_imaging: make method a commandline argument

  pgunn

  committed
  a6bfde2

• demos_refactor: volpy demo import tweaks

  pgunn

  committed
  c27f1a0

• CNMF: Fix some issues from recent CNMFParams refactor

  pgunn

  committed
  ad2533a

• demo_pipeline_cnmfE.py: ready for testing

  pgunn

  committed
  896389a

• remove param temporal.memory_efficient which doesn't seem to do anything

  pgunn

  committed
  1dd6e2a

• Params: Remove doc for temporal.memory_efficient which was documented but not present in code

  pgunn

  committed
  28606d4

• CNMFParams: Remove documented but never-implemented data.mmap_C and data.mmap_F (verified they never were filled in)

  pgunn

  committed
  d607a7c

• Fix bug from 2019 with #030bc6d35

  pgunn

  committed
  0c00f4c

• CNMF: "is True" -> ""

  pgunn

  committed
  bc95a7f

• Remove spatial.block_size_spat

  Show description for dbd8e50
  pgunn

  committed
  dbd8e50

• Remove merging.max_merge_area

  Show description for 378b732
  pgunn

  committed
  378b732

• demo_behavior: more rebase nonsense

  pgunn

  committed
  f8f924b

• demo_behavior: rebase nonsense

  pgunn

  committed
  8f296f6

• After rebase, add demo_behavior back in

  pgunn

  committed
  d87162f

Commits on Apr 18, 2024

• CLI demo refactor: forgot to import os

  pgunn

  committed
  9c36719

• CLI demos refactor: demo_pipeline_cnmfE: Fix a mistake in move to params

  pgunn

  committed
  126ca4a

• Fix paths for more temporary files over a run to land in caiman_data/temp/

  pgunn

  committed
  b607769

Commits on Apr 19, 2024

• Adjust gating, path handling to try harder not to drop temporary files anywhere but caiman_data/temp/

  pgunn

  committed
  97451ba

• Note in docs that caiman.movie.save() returns the filename. Fix a test suite's sloppy path code

  pgunn

  committed
  3ed88c7

• Movie.save(): Always return filename (before it only did it for some target file formats)

  pgunn

  committed
  66ede97

Commits on Apr 23, 2024

• environment.yml: be smarter about alternate builds of conda, set channel-priority to handle if user/distro has set it to something else

  pgunn

  committed
  f78791c

Commits on Apr 24, 2024

• environment.yml: can't actually set channel priority in environment.yml

  pgunn

  committed
  7d5824d

• Try adjusting CI to use environment-minimal.yml

  pgunn

  committed
  53ea964

• minimal environment needs a few more things

  pgunn

  committed
  8b177d5

• environment-minimal hasn't seen enough testing over the years.

  pgunn

  committed
  701c9af

• If we're to use environment-minimal for CI we need to include nose

  pgunn

  committed
  5082983

• prevent old numpy breaking typing

  pgunn

  committed
  b6e67c5

• yaml: Prevent old versions of numpy and associated problems

  pgunn

  committed
  0b81678

• CI's way of managing updating the test environment means lots of minimal version pins

  pgunn

  committed
  14af8d5

• Merge pull request #1334 from flatironinstitute/dev-environment_rework

  Show description for aabb25d
  pgunn

  authored
  aabb25d

• Hotfix: Fix issue in demo_caiman_cnmf_3D from a past refactor to visualization.py

  pgunn

  committed
  73d5721

• cherry-pick 73d572

  pgunn

  committed
  fd24f25

Commits on Apr 26, 2024

• params: better handle if user provides ring_CNN (compensating for a misdesign of CNMFParams)

  pgunn

  committed
  41cd982

• params: better handle if user provides ring_CNN (compensating for a misdesign of CNMFParams)

  pgunn

  committed
  75c95b2

• Fix goof in last hotfix to CNMFParams

  pgunn

  committed
  c45b9aa

• Fix goof in last hotfix to CNMFParams

  pgunn

  committed
  9ea5587

• Remove (broken) support for the old non-hdf5 format of .mat files

  pgunn

  committed
  b8e97f8

• .mat files: give users better messages if they try to open a v1 file

  pgunn

  committed
  fafffce

• mat file revamp: Use consistent phrasing

  pgunn

  committed
  2581815

• Update docs on mat file support

  pgunn

  committed
  29a3a67

• Merge pull request #1337 from flatironinstitute/dev-fix_mat_support

  Show description for df5b487
  pgunn

  authored
  df5b487

Commits on Apr 30, 2024

• CNMFParams: remove some dead code (really just a commit to make CI run, but still a good commit)

  pgunn

  committed
  7943ede

• CLI OnACID demos: correctly handle display of results

  pgunn

  committed
  ac1e2aa

• CLI demo pipeline: get rid of qt errors

  pgunn

  committed
  0fa78a3

• Add note to demo_behaviour that it needs a qt6 build of opencv

  pgunn

  committed
  a5886c4

• demo_behavior and caiman.behavior.behavior: fix ancient calls

  pgunn

  committed
  fe1ad0c

• CLI demo: fix demo_behavior

  pgunn

  committed
  0c80201

Commits on May 1, 2024

• Remove caiman.base.movies.online_NMF() which is unused (and needs the spams library, now hard to package)

  pgunn

  committed
  862dba8

• caiman.behavior.extract_components(): remove method_factorization of dict_learn (which needed spams)

  pgunn

  committed
  887e99e

• Add note about commandline demos to the main README

  pgunn

  committed
  b45633a

• Merge pull request #1211 from flatironinstitute/cli_demos_refactor

  Show description for 6581329
  pgunn

  authored
  6581329

• caimanmanager: don't copy __pycache__ dirs out of the library bundle

  pgunn

  committed
  8e9ad9f

• Merge pull request #1341 from flatironinstitute/dev-fix_pycache_creation

  Show description for 29743f0
  pgunn

  authored
  29743f0

Commits on May 3, 2024

• VERSION: next release will be 1.11.0

  pgunn

  authored
  63c1932