Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Adapt Azimuth code for Wilms label transfer #843

Merged
merged 24 commits into from
Nov 5, 2024
Merged

Adapt Azimuth code for Wilms label transfer #843

merged 24 commits into from
Nov 5, 2024
+4,514 −117

Commits on Oct 17, 2024

  1. add functions for label transfer

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    9a28271 View commit details
    Browse the repository at this point in the history

  2. move functions to utils folder

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    70e75ba View commit details
    Browse the repository at this point in the history

  3. Update 02a notebook to use new functions, and style

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    de20e42 View commit details
    Browse the repository at this point in the history

  4. use 0/1 for testing variable

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    2eabc3d View commit details
    Browse the repository at this point in the history

  5. update param usage for label transfer notebooks

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    c3fc4c1 View commit details
    Browse the repository at this point in the history

  6. Update 02b notebook to use new functions, and style

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    9abbee9 View commit details
    Browse the repository at this point in the history

  7. label transfer does not need to be skipped in CI anymore

    @sjspielman
    sjspielman committed Oct 17, 2024
    Configuration menu
    Copy the full SHA
    7693571 View commit details
    Browse the repository at this point in the history

Commits on Oct 18, 2024

  1. merge base

    @sjspielman
    sjspielman committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    6cee2f5 View commit details
    Browse the repository at this point in the history

  2. remove install fetusref code from script

    @sjspielman
    sjspielman committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    788927f View commit details
    Browse the repository at this point in the history

  3. fix notebook name

    @sjspielman
    sjspielman committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    1778edd View commit details
    Browse the repository at this point in the history

Commits on Oct 28, 2024

  1. use separate query variable to prevent feature loss, and rm when done… 

    … for space
    @sjspielman
    sjspielman committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    4aa0eec View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2024

  1. parameter fixes

    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    78dfcdc View commit details
    Browse the repository at this point in the history

  2. use is_ci

    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    d9a6feb View commit details
    Browse the repository at this point in the history

  3. revert testing code

    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    c9b33fc View commit details
    Browse the repository at this point in the history

  4. remove outdated comments

    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    f7f9686 View commit details
    Browse the repository at this point in the history

  5. Add supplemental notebook with results comparing azimuth to adapted a… 

    …zimuth
    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    d4a20f5 View commit details
    Browse the repository at this point in the history

  6. little regex tweak

    @sjspielman
    sjspielman committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    76d9ace View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2024

  1. add query assay arguments to functions

    @sjspielman
    sjspielman committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    0433245 View commit details
    Browse the repository at this point in the history

  2. Update notebook using RNA as the query assay

    @sjspielman
    sjspielman committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    90694c4 View commit details
    Browse the repository at this point in the history

  3. Specify RNA assay in the actual label transfer notebooks

    @sjspielman
    sjspielman committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    69a8a7a View commit details
    Browse the repository at this point in the history

  4. why was s still there? and fix a typo

    @sjspielman
    sjspielman committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    6b3d7ed View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2024

  1. Merge remote-tracking branch 'upstream/feature/wilms-tumor-06-azimuth… 

    …' into sjspielman/wilms-run-azimuth
    @sjspielman
    sjspielman committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    813090a View commit details
    Browse the repository at this point in the history

  2. fix typo - output for 02b needs to be 02b

    @sjspielman
    sjspielman committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    3a0ba1e View commit details
    Browse the repository at this point in the history

  3. names are hard

    @sjspielman
    sjspielman committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    7522c56 View commit details
    Browse the repository at this point in the history