Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bhklab/readii issues and pull requests

#119 - feat: add image cropping preprocessing

Pull Request - State: closed - Opened by strixy16 8 days ago - 2 comments

#117 - chore: enhance testing CI/CD

Pull Request - State: open - Opened by jjjermiah 12 days ago - 2 comments

#116 - fix: pattern resolver update

Pull Request - State: closed - Opened by strixy16 18 days ago - 3 comments

#115 - fix: axes labelling in plotCrossCorrHeatmap

Pull Request - State: closed - Opened by strixy16 19 days ago - 2 comments

#114 - fix: incorrect correlation heatmap axes labels

Pull Request - State: closed - Opened by strixy16 19 days ago - 1 comment

#113 - feat: add cropping methods from FMCIB pipeline

Pull Request - State: closed - Opened by strixy16 28 days ago - 4 comments

#112 - Introduce process directory, update existing code for ruff check

Pull Request - State: closed - Opened by strixy16 about 1 month ago - 2 comments

#111 - Add FMCIB model setup and inference code

Issue - State: open - Opened by strixy16 about 1 month ago
Labels: enhancement

#110 - Add FMCIB cropping code

Issue - State: open - Opened by strixy16 about 1 month ago
Labels: enhancement

#109 - fix: update toml to fix deprecated "depends_on" key

Pull Request - State: closed - Opened by jjjermiah about 1 month ago - 2 comments

#108 - feat: add overwrite variable to plot self and cross corr functions

Pull Request - State: closed - Opened by strixy16 about 2 months ago - 2 comments

#107 - feat: raise correct error when correlation writer file exists

Pull Request - State: closed - Opened by strixy16 about 2 months ago - 1 comment

#106 - feat: add error for when file output by CorrelationWriter already exists

Pull Request - State: closed - Opened by strixy16 about 2 months ago - 2 comments

#105 - Writer: should have options to handle existing files beyond just failing,

Issue - State: closed - Opened by jjjermiah about 2 months ago - 1 comment

#104 - feat: update plot correlation functions

Pull Request - State: closed - Opened by strixy16 about 2 months ago - 2 comments

#103 - feat: update correlation functions to get subsections of matrix

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#100 - Implement Lasso feature selection

Issue - State: open - Opened by strixy16 2 months ago
Labels: enhancement

#99 - Fill out the testing suite

Issue - State: open - Opened by strixy16 2 months ago

#98 - feat: fix loaders some more

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#97 - fix: look for image type in Path stem as Path is not iterable

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#96 - feat: add CorrelationWriter

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#94 - feat: add io/readers to ruff config

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#92 - feat: add analysis functions

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#91 - feat: expand platform support in pixi and CI/CD workflow

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 1 comment

#90 - feat: add optional segmentationLabel input for singleRadiomifFetaureExtraction

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments
Labels: enhancement

#89 - feat: add data functions used for analysis code

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#88 - fix: Rename argument mata-var in download help CLI

Issue - State: open - Opened by jjjermiah 2 months ago - 1 comment

#87 - Refactor file loading with custom error handling and pathlib support

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 1 comment

#86 - Refactor file loading with custom error handling and pathlib support

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 1 comment

#85 - feat: Initialize documentation

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 2 comments

#84 - feat: Add BaseWriter, and example NIFTIWriter with notebooks documenting them

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 2 comments

#83 - feat: add io/loaders module

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#81 - feat: add abstract and concrete classes for negative controls and regions

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 3 comments

#80 - feat: add readii-datasets CLI command and include orcestra-downloader dependency

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 4 comments

#79 - feat: integrate analyze readii outputs functions

Pull Request - State: closed - Opened by strixy16 2 months ago - 2 comments

#78 - Continuous flag resulting in odd dimensions in pytest

Issue - State: open - Opened by jjjermiah 2 months ago - 1 comment
Labels: bug

#77 - feat: set StructureSetToSegmentation continuous argument to False

Pull Request - State: open - Opened by strixy16 2 months ago - 1 comment

#76 - feat: negative control + NIFTI Writer

Pull Request - State: open - Opened by jjjermiah 2 months ago - 1 comment

#75 - Fix continuous RTSTRUCT index bug

Pull Request - State: closed - Opened by strixy16 2 months ago - 1 comment

#74 - feat: new Negative Controls implementation using strategies and manager

Pull Request - State: closed - Opened by jjjermiah 2 months ago - 3 comments

#73 - Get list of RADCURE series IDs to keep on TCIA

Issue - State: closed - Opened by strixy16 2 months ago

#72 - docs: set up a mkdocs and put basic documentation in

Issue - State: open - Opened by strixy16 2 months ago
Labels: documentation

#71 - style: switch from camelcase

Issue - State: open - Opened by jjjermiah 2 months ago

#70 - Integrate analyze_readii_outputs into package

Issue - State: closed - Opened by strixy16 3 months ago
Labels: enhancement

#68 - refactor: Update Ruff configuration and refactor codebase

Pull Request - State: closed - Opened by jjjermiah 3 months ago - 2 comments

#67 - feat: add slicedim to displayimageslice

Pull Request - State: closed - Opened by strixy16 3 months ago - 2 comments

#66 - feat: add slice dimension specifier to displayImageSlice

Issue - State: closed - Opened by strixy16 3 months ago
Labels: enhancement

#65 - Implement saving negative controls as nifti files for FMCIB use

Issue - State: closed - Opened by strixy16 3 months ago
Labels: enhancement

#64 - Create readii-IDC repository for notebooks

Issue - State: closed - Opened by strixy16 3 months ago - 1 comment

#63 - Fresh run of readii on HNSCC on H4H

Issue - State: closed - Opened by strixy16 3 months ago

#62 - Update randomized_sampled to just be called sampled

Issue - State: open - Opened by strixy16 3 months ago
Labels: enhancement

#61 - Separate the ROI and type for negative control input

Issue - State: open - Opened by strixy16 3 months ago - 1 comment
Labels: enhancement

#60 - need some kind of logger documentation

Issue - State: closed - Opened by strixy16 3 months ago - 4 comments
Labels: documentation, help wanted

#59 - feat: improve logging + make verbose

Pull Request - State: closed - Opened by jjjermiah 3 months ago - 3 comments

#58 - fix: add readii cli entry point to pyproject

Pull Request - State: closed - Opened by jjjermiah 3 months ago - 2 comments

#58 - fix: add readii cli entry point to pyproject

Pull Request - State: closed - Opened by jjjermiah 3 months ago - 2 comments

#55 - Dataset Checklist for READII usage

Issue - State: open - Opened by strixy16 4 months ago

#55 - Dataset Checklist for READII usage

Issue - State: open - Opened by strixy16 4 months ago

#54 - Nothing wrong with getSegmentationType and hasnt caused any issues (i think)

Issue - State: open - Opened by jjjermiah 4 months ago - 1 comment
Labels: good first issue

#54 - Nothing wrong with this function and hasnt caused any issues (i think)

Issue - State: open - Opened by jjjermiah 4 months ago - 1 comment
Labels: good first issue

#52 - Email TCIA about removing RADCURE phase 1

Issue - State: closed - Opened by strixy16 4 months ago

#52 - Email TCIA about removing RADCURE phase 1

Issue - State: open - Opened by strixy16 4 months ago

#51 - feat: remove dicom-parser, update mit, deprecate padSeg

Pull Request - State: closed - Opened by jjjermiah 4 months ago - 2 comments

#51 - feat: remove dicom-parser, update mit, deprecate padSeg

Pull Request - State: closed - Opened by jjjermiah 4 months ago - 2 comments

#50 - IDC notebook B

Issue - State: open - Opened by strixy16 4 months ago
Labels: enhancement

#50 - IDC notebook B

Issue - State: open - Opened by strixy16 4 months ago
Labels: enhancement

#49 - IDC notebook A

Issue - State: open - Opened by strixy16 4 months ago - 1 comment
Labels: enhancement

#49 - IDC notebook A

Issue - State: open - Opened by strixy16 4 months ago - 1 comment
Labels: enhancement

#48 - Update ROI inputs to be dictionary

Issue - State: open - Opened by strixy16 4 months ago
Labels: enhancement

#48 - Update ROI inputs to be dictionary

Issue - State: open - Opened by strixy16 4 months ago
Labels: enhancement

#47 - Submit abstract to ESTRO

Issue - State: closed - Opened by strixy16 4 months ago

#46 - Make radiomic MAE deconstructor

Issue - State: open - Opened by strixy16 4 months ago

#46 - Make radiomic MAE deconstructor

Issue - State: open - Opened by strixy16 4 months ago

#45 - Validate-MIT-nifti

Issue - State: open - Opened by jjjermiah 4 months ago

#44 - Implementing the nifti stuff

Issue - State: open - Opened by jjjermiah 4 months ago - 1 comment
Labels: question

#44 - Implementing the nifti loading stuff

Issue - State: closed - Opened by jjjermiah 4 months ago - 1 comment
Labels: question

#41 - deps: `dicom-parser`

Issue - State: closed - Opened by jjjermiah 4 months ago - 2 comments

#41 - deps: `dicom-parser`

Issue - State: closed - Opened by jjjermiah 4 months ago - 2 comments

#40 - feat: Use Pixi, pyradiomics fork

Pull Request - State: closed - Opened by jjjermiah 4 months ago - 1 comment

#40 - feat: Use Pixi, pyradiomics fork

Pull Request - State: closed - Opened by jjjermiah 4 months ago - 1 comment

#39 - Negative control error handling

Pull Request - State: closed - Opened by strixy16 5 months ago

#39 - Negative control error handling

Pull Request - State: closed - Opened by strixy16 5 months ago

#38 - Negative control error catching and angular commit syntax

Pull Request - State: closed - Opened by strixy16 5 months ago

#38 - Negative control error catching and angular commit syntax

Pull Request - State: closed - Opened by strixy16 5 months ago