Code

Add extractor for BioFormats (CXD)#338

Code

Draft

weiglszonja wants to merge 24 commits intomaincatalystneuro/roiextractors:mainfrom add_bioformatscatalystneuro/roiextractors:add_bioformatsCopy head branch name to clipboard

+618

Commits

Commits on May 30, 2024

• add base extractor class for BioFormats

  weiglszonja

  committed
  d6a7fed

  Copy full SHA for d6a7fed

• add CxdImagingExtractor

  weiglszonja

  committed
  5da3988

  Copy full SHA for 5da3988

• add aicsimageio to requirements-full.txt

  weiglszonja

  committed
  871c371

  Copy full SHA for 871c371

• add utils

  weiglszonja

  committed
  69b99d9

  Copy full SHA for 69b99d9

• renamed module

  weiglszonja

  committed
  894dfef

  Copy full SHA for 894dfef

• move import utils locally

  weiglszonja

  committed
  3722f6d

  Copy full SHA for 3722f6d

Commits on Jun 1, 2024

• try add to api docs

  weiglszonja

  committed
  663d4be

  Copy full SHA for 663d4be

• rename module to bioformatsimagingextractors

  weiglszonja

  committed
  eb33c30

  Copy full SHA for eb33c30

• try again

  weiglszonja

  committed
  aa7c97f

  Copy full SHA for aa7c97f

• add BioFormatsImagingExtractor to api docs

  weiglszonja

  committed
  641d871

  Copy full SHA for 641d871

Commits on Jun 2, 2024

• sampling frequency as optional argument

  weiglszonja

  committed
  224c78d

  Copy full SHA for 224c78d

• update parsed_metadata with sampling frequency

  weiglszonja

  committed
  bf1b80d

  Copy full SHA for bf1b80d

Commits on Jun 4, 2024

• Merge branch 'main' into add_bioformats

  weiglszonja

  authored
  cb55905

  Copy full SHA for cb55905

• add first tests

  weiglszonja

  committed
  45065f8

  Copy full SHA for 45065f8

Commits on Jun 5, 2024

• Merge branch 'main' into add_bioformats

  weiglszonja

  authored
  29e3385

  Copy full SHA for 29e3385

• try skip tests when bioformats dependencies are missing

  weiglszonja

  committed
  46c0672

  Copy full SHA for 46c0672

• fix import

  weiglszonja

  committed
  3133de2

  Copy full SHA for 3133de2

• remove JAVA_HOME environment variable setting

  weiglszonja

  committed
  baf9123

  Copy full SHA for baf9123

• try add new workflow for testing BioFormats

  weiglszonja

  committed
  635cfe1

  Copy full SHA for 635cfe1

• add run-bioformats-tests.yml to deploy_pr_tests.yaml

  weiglszonja

  committed
  ff54c9a

  Copy full SHA for ff54c9a

• try install dependencies directly in yml first

  weiglszonja

  committed
  48ddfa8

  Copy full SHA for 48ddfa8

• try activate conda env in every step

  weiglszonja

  committed
  376a3ef

  Copy full SHA for 376a3ef

• try activate conda env in every step

  weiglszonja

  committed
  d3c5d14

  Copy full SHA for d3c5d14

• Update requirements-full.txt

  weiglszonja

  authored
  309da64

  Copy full SHA for 309da64