Code

Incorporate napari btrack internally#246

Code

Merged

paddyroddy merged 138 commits intomainquantumjot/btrack:mainfrom incorporate-napari-btrack-internallyquantumjot/btrack:incorporate-napari-btrack-internallyCopy head branch name to clipboardMar 22, 2023

+1,397-69

Commits

Commits on May 12, 2021

• Initial commit

  quantumjot

  committed
  380ce0c

Commits on May 17, 2021

• updated requirements

  quantumjot

  committed
  d27befd

Commits on Jan 21, 2022

• Update requirements.txt

  quantumjot

  authored
  b039f8e

Commits on Mar 9, 2022

• automated conversion to NPE2

  alessandrofelder

  committed
  975fa77

• manually remove obsolete decorator

  alessandrofelder

  committed
  aae6716

• implement basic tracking widget

  alessandrofelder

  committed
  935663a

• update test to function widget

  Show description for d1d4108
  alessandrofelder

  committed
  d1d4108

Commits on Mar 16, 2022

• Update QT setup on github actions

  dstansby

  committed
  4ed4634

• Comment out test that isn't yet working

  dstansby

  committed
  e9890e7

• Merge pull request #16 from dstansby/test-qt-setup

  dpshelio

  authored
  eee509b

• Merge branch 'main' into initial-tracking-widget

  dpshelio

  committed
  78ecb21

• 💄 Blackify it

  dpshelio

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  123a5a1

• test number of widgets

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  dpshelio

  and

  dstansby

  authored
  a106903

• Names output layer using segmentation input

  dpshelio

  committed
  3471fa3

• 💄 Blackify

  dpshelio

  committed
  813a0ff

• 💄 Remove tabs from the automated conversion

  dpshelio

  committed
  5004d8e

• Merge pull request #15 from lowe-lab-ucl/initial-tracking-widget

  dpshelio

  authored
  9323552

Commits on Mar 30, 2022

• Add and run pre-commit

  paddyroddy

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  bbc2bf4

• Remove references to cython

  paddyroddy

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  6aaf601

• Merge branch 'main' into add-pre-commit

  paddyroddy

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  226464c

• Final run of pre-commit

  paddyroddy

  committed
  b87d83d

• Merge pull request #21 from lowe-lab-ucl/add-pre-commit

  Show description for 00cc1a9
  paddyroddy

  authored
  00cc1a9

Commits on Apr 19, 2022

• Use v2 of codecov action

  dstansby

  committed
  5504092

Commits on Apr 20, 2022

• Merge pull request #12 from dstansby/codeov

  Show description for 0c5bd6d
  paddyroddy

  authored
  0c5bd6d

Commits on May 12, 2022

• add example script that opens widget

  Show description for 3e46a86
  alessandrofelder

  committed
  3e46a86

• Add dt to widget GUI

  dstansby

  committed
  5a80b3b

• wip:making the tracker config into widgets

  alessandrofelder

  committed
  fbb0b8f

• Add vscode

  paddyroddy

  committed
  c808af3

• Being creating widgets programmatically from pydantic

  paddyroddy

  committed
  2084b8b

• add widgets for segmentation image, and config save/load

  alessandrofelder

  committed
  6b508c5

Commits on May 13, 2022

• Ignore vscode

  paddyroddy

  committed
  299a551

• Add pre-commit workflow

  paddyroddy

  committed
  97142ef

• address review comments

  Show description for 037d542
  alessandrofelder

  committed
  037d542

• fix example docstring

  alessandrofelder

  committed
  9ecf6d2

• Merge pull request #23 from lowe-lab-ucl/add-example

  Show description for 6945264
  dstansby

  authored
  6945264

• Move workflow to correct place

  paddyroddy

  committed
  6b9c824

Commits on May 16, 2022

• Change to all PRs and pushes to main

  paddyroddy

  committed
  009809e

• Fix CI

  paddyroddy

  committed
  a100e51

• Merge pull request #25 from lowe-lab-ucl/add-pre-commit-ci

  Show description for 15c999b
  dstansby

  authored
  15c999b

Commits on May 23, 2022

• Merge branch 'main' into prog-make-widgets-from-pydantic

  paddyroddy

  committed
  a6b63e9

• Tidy up and simplify widget creation

  paddyroddy

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  74f68e8

• Use extend instead of append

  paddyroddy

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  7361bb3

• Remove unnecessary initialisation

  paddyroddy

  committed
  c4e1d94

• Use two lists and zip

  paddyroddy

  committed
  682b660

Commits on May 24, 2022

• Create separate widget methods

  paddyroddy

  committed
  6aa01c5

• Simplify names for widgets

  paddyroddy

  committed
  6347789

• Create custom widget

  paddyroddy

  committed
  a812c07

Commits on May 25, 2022

• add dummy callbacks, naive implementation of reset defaults

  alessandrofelder

  committed
  b61234a

• naive implementation of run button, uses only default config

  alessandrofelder

  committed
  c60ed0d

Commits on May 31, 2022

• import some useful modules and define some global variables

  alessandrofelder

  committed
  c41fc72

• flesh out load + save, added matrix helper functionality, make widget scrollable

  alessandrofelder

  committed
  42d6ab0

• fix adaptation from pydantic to widgets and back

  alessandrofelder

  committed
  573e3b4

• Fix typing issue

  paddyroddy

  committed
  4c2feba

• Fix typing for tests?

  paddyroddy

  committed
  753b40e

• Revert "Fix typing for tests?"

  Show description for a1cc910
  paddyroddy

  committed
  a1cc910

• Fix tests

  paddyroddy

  committed
  6fe9a42

Commits on Jun 9, 2022

• write widget-config roundtrip test

  alessandrofelder

  committed
  272b546

• implement naive mode (cell/particle) feature

  alessandrofelder

  committed
  a219460

• derive tracker volume from segmentation size

  alessandrofelder

  committed
  8feea64

Commits on Jun 15, 2022

• make example use labels instead of image layer

  alessandrofelder

  committed
  89249a5

• flesh out button tests

  alessandrofelder

  committed
  4f2830a

• document tests

  alessandrofelder

  committed
  d9ec8ce

• make tests py3.7 compatible

  alessandrofelder

  committed
  dd3c54c

• make matrices easier to read

  alessandrofelder

  committed
  0fd8768

• Update/add docstrings to track.py

  alessandrofelder

  committed
  0d1500e

• add tooltip help for segmentation

  alessandrofelder

  committed
  1010d60

• wip

  alessandrofelder

  committed
  9c9d790

• revert change to pre-commit config

  alessandrofelder

  committed
  ae3cad8

• fix formatting

  alessandrofelder

  committed
  f1591c0

• expose max_search_radius to user

  alessandrofelder

  committed
  2352438

• improve comment

  alessandrofelder

  committed
  dbf5d6c

• fix tracker.volume computation

  alessandrofelder

  committed
  f1762b6

• Apply suggestions from code review

  Show description for 818c868
  

  alessandrofelder

  and

  dstansby

  committed
  818c868

• improve variable names

  alessandrofelder

  committed
  58e9b38

• add more complete type hints to test

  alessandrofelder

  committed
  8d9d1f0

• add assertion to test_run_button

  alessandrofelder

  committed
  01b331a

• call get_scaled_matrix with kwargs, fix E501 in docstring

  alessandrofelder

  committed
  11b5245

• store matrices as np.arrays instead of lists

  alessandrofelder

  committed
  0588ce3

• rely on same viewer reference (initalised once) in the widget and tests

  alessandrofelder

  committed
  5d92099

• small improvements from code review

  alessandrofelder

  committed
  e53b15b

• extend() -> append() where possible

  alessandrofelder

  committed
  6d51599

• fix a problem with segmentation choices

  alessandrofelder

  committed
  f001f95

Commits on Jun 16, 2022

• small more-pythonic reformulations

  alessandrofelder

  committed
  2df8389

• make intent of hypothesis widget creation clearer

  alessandrofelder

  committed
  5b9e051

Commits on Jun 17, 2022

• Merge pull request #26 from lowe-lab-ucl/prog-make-widgets-from-pydantic

  Show description for 1601210
  dstansby

  authored
  1601210

Commits on Jun 22, 2022

• Add napari and fix magicgui bug

  paddyroddy

  committed
  4f07df0

Commits on Jun 23, 2022

• Merge pull request #34 from lowe-lab-ucl/fix-issue-24

  Show description for 31b28e8
  alessandrofelder

  authored
  31b28e8

Commits on Jun 24, 2022

• Adds isort and black configuration as part of the project

  dpshelio

  committed
  51d4487

• Removes isort arguments from pre-commit as they are in pyproject

  dpshelio

  committed
  80d3410

• Changed the line-length value and removed isort properties controlled by black

  dpshelio

  committed
  94ae4b4

• isort-ing the project as per the rules defined

  dpshelio

  committed
  21233e7

Commits on Jun 29, 2022

• Merge pull request #30 from lowe-lab-ucl/isort

  Show description for 6305171
  paddyroddy

  authored
  6305171

Commits on Mar 1, 2023

• correctly pass DISPLAY and XAUTHORITY env variables to tox (#41)

  p-j-smith

  authored
  642c213

• Add Q matrix to list of Matrices.names to create widgets for

  p-j-smith

  committed
  eba5511

• Add improved linting

  paddyroddy

  committed
  33e6113

• Run pre-commit as is

  paddyroddy

  committed
  0ce7a98

• Don't create the MotionModel widgets twice

  p-j-smith

  committed
  2a8176d

• Satisfy pre-commit

  paddyroddy

  committed
  8a6028b

• Merge pull request #38 from lowe-lab-ucl/fix/add-widget-for-Q-matrix

  Show description for 135f8ea
  paddyroddy

  authored
  135f8ea

• Merge branch 'main' into fix-pre-commit

  paddyroddy

  authored
  7908ef1

• Fix linting

  paddyroddy

  committed
  0052e8c

Commits on Mar 2, 2023

• Import annotations from __future__

  p-j-smith

  committed
  d5741f9

• Don't set strict=True when call zip.

  Show description for 6c7a3e2
  p-j-smith

  committed
  6c7a3e2

• More sparing use of ignore

  paddyroddy

  committed
  520e2fc

• Merge pull request #43 from lowe-lab-ucl/fix-pre-commit

  Show description for d315982
  paddyroddy

  authored
  d315982

• Remove flake8 file (#45)

  Show description for aa9157e
  paddyroddy

  authored
  aa9157e

• Add issues to project board automatically (#39)

  Show description for 7b1c33b
  paddyroddy

  authored
  7b1c33b

• Fix failing tests (#47)

  Show description for 66ea027
  p-j-smith

  authored
  66ea027

• Forgot toml all flag (#48)

  Show description for 99d9a2b
  paddyroddy

  authored
  99d9a2b

• Make the btrack widget scrollable (#51)

  Show description for 331ecfc
  p-j-smith

  authored
  331ecfc

Commits on Mar 9, 2023

• Move to pyproject.toml format (#58)

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  paddyroddy

  authored
  60d4182

• Use qtpy instead of pyqt5 (#59)

  Show description for d6a2406
  p-j-smith

  authored
  d6a2406

Commits on Mar 13, 2023

• Fix links for readme badges (#62)

  Show description for 173a8c8
  p-j-smith

  authored
  173a8c8

Commits on Mar 22, 2023

• Remove cell and particle modes to support arbitrary TrackerConfig configs (#64)

  Show description for 11e61ad
  

  p-j-smith

  and

  paddyroddy

  authored
  11e61ad

• Move everything into a btrack/napari folder to mirror the parent

  paddyroddy

  committed
  e4e39b8

• Forgot to move the hidden files

  paddyroddy

  committed
  8afcebb

• Remove reference to the old plugin

  paddyroddy

  committed
  dc0c68a

• Incorporate parts of pyproject.toml from napari-btrack

  paddyroddy

  committed
  c6fd3be

• Borrow stuff from napari-btrack

  paddyroddy

  committed
  02817ab

• Update linting.yml

  paddyroddy

  committed
  4a54644

• Add qt to CI for tests

  paddyroddy

  committed
  add0009

• Removing napari_btrack folder

  paddyroddy

  committed
  d26b31e

• Add examples about the plugin

  paddyroddy

  committed
  d5d90ca

• Delete unrequired files

  paddyroddy

  committed
  dd931d0

• Merge remote-tracking branch 'napari-btrack/prepare-for-incorporation-with-btrack' into incorporate-napari-btrack-internally

  paddyroddy

  committed
  2ac88cc

• Ignore .envrc

  paddyroddy

  committed
  4a3be76

• Add track making widget to repo

  paddyroddy

  committed
  b7ed40c

• Rename napari_btrack to btrack.napari

  paddyroddy

  committed
  2c2b4fb

• Make black 79 characters

  paddyroddy

  committed
  961b79e

• Delete napari.yml

  paddyroddy

  committed
  0eb1cf7

• Merge remote-tracking branch 'napari-btrack/prepare-for-incorporation-with-btrack' into incorporate-napari-btrack-internally

  paddyroddy

  committed
  b934d6a

• Fix linting

  paddyroddy

  committed
  752ae04

• Move napari-btrack test to the correct plac

  paddyroddy

  committed
  9021629

• Always run the reader test

  paddyroddy

  committed
  a093d4b

• Remove numpy as in requirements.txt

  paddyroddy

  committed
  0eac064

• Fix napari test referring to old plugin name

  paddyroddy

  committed
  decca33

• Merge branch 'main' into incorporate-napari-btrack-internally

  paddyroddy

  committed
  39fd8b8

• Fix tests badge

  paddyroddy

  committed
  a088ba5