Issues

• feat: implement saving cropped mask for crop and resize negative control generation

  bhklab/readii#137 · Filter by author katy-scott opened on Sep 29, 2025

• bug: string outcome variable handling throwing an attribute error

  bug
  bhklab/readii#135 · Filter by author katy-scott opened on Aug 20, 2025

• bug: numpy ndarray has no attribute 'remove' error from label.py

  bug
  bhklab/readii#134 · Filter by author katy-scott opened on Aug 20, 2025

• feat: add image alignment to flattenImage

  bugfeaturerefactor
  bhklab/readii#133 · Filter by author katy-scott opened on May 27, 2025 · READII 2.0
  

• feat: make constructor class for feature extractor index

  feature
  bhklab/readii#126 · Filter by author katy-scott opened on May 23, 2025 · READII 2.0

• refactor: name negative control elements region, permutation, and crop

  refactor
  bhklab/readii#125 · Filter by author katy-scott opened on May 14, 2025 · READII 2.0

• refactor: add default standard_column_label in outcome column setup functions

  good first issuerefactor
  bhklab/readii#122 · Filter by author katy-scott opened on May 12, 2025 · READII 2.0

• refactor: update divide_by to 365.25 in convertDaysToYears

  good first issuerefactor
  bhklab/readii#121 · Filter by author katy-scott opened on May 12, 2025 · READII 2.0

• Explore compression for saving/loading correlation matrix files

  bhklab/readii#102 · Filter by author katy-scott opened on Dec 19, 2024 · READII 2.0

• Fill out the testing suite

  feature
  bhklab/readii#99 · Filter by author katy-scott opened on Dec 18, 2024 · READII 2.0

• Make function to create nice list of image types from negative control regions and types

  feature
  bhklab/readii#95 · Filter by author katy-scott opened on Dec 18, 2024
  1

  

• Make drop labels function outside of loadFeatureFilesFromImageTypes

  featurerefactor
  bhklab/readii#93 · Filter by author katy-scott opened on Dec 17, 2024
  1

  

• fix: Rename argument mata-var in download help CLI

  bug
  bhklab/readii#88 · Filter by author jjjermiah opened on Dec 13, 2024
  1

• refactor: decide between loadDICOMSITK and read_dicom_series

  refactor
  bhklab/readii#82 · Filter by author jjjermiah opened on Dec 11, 2024

• Continuous flag resulting in odd dimensions in pytest

  bug
  bhklab/readii#78 · Filter by author jjjermiah opened on Dec 9, 2024
  1

• Implement Lasso feature selection

  feature
  bhklab/readii#100 · Filter by author katy-scott opened on Dec 5, 2024
  

• docs: set up a mkdocs and put basic documentation in

  docs
  Feature

  bhklab/readii#72 · Filter by author katy-scott opened on Dec 5, 2024 · READII 2.0

• style: switch from camelcase

  refactor
  bhklab/readii#71 · Filter by author jjjermiah opened on Dec 5, 2024

• Update randomized_sampled to just be called sampled

  refactor
  bhklab/readii#62 · Filter by author katy-scott opened on Nov 18, 2024 · READII 2.0

• Dataset Checklist for READII usage

  bhklab/readii#55 · Filter by author katy-scott opened on Nov 1, 2024 · READII 2.0

• Nothing wrong with getSegmentationType and hasnt caused any issues (i think)

  good first issue
  bhklab/readii#54 · Filter by author jjjermiah opened on Oct 31, 2024
  1

• IDC notebook B

  feature
  Task

  bhklab/readii#50 · Filter by author katy-scott opened on Oct 31, 2024
  

• IDC notebook A

  feature
  bhklab/readii#49 · Filter by author katy-scott opened on Oct 31, 2024
  1

  

• Update ROI inputs to be dictionary

  feature
  bhklab/readii#48 · Filter by author katy-scott opened on Oct 31, 2024 · READII 2.0

• Refactor Feature Extraction Workflow to Modularize Preprocessing, Extraction, and Output Management

  feature
  bhklab/readii#43 · Filter by author jjjermiah opened on Oct 22, 2024 · READII 2.0