Update preprocessing API for experiment 0.1 #7
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
iamamutt
pushed a commit
that referenced
this pull request
Aug 3, 2021
Quality control tables prototype
iamamutt
pushed a commit
that referenced
this pull request
Feb 2, 2022
* Allow load to resolve priority list of paths Fixes #42 * Add support for parsing multianimal position data Fixes #55 * add plot for experiment-level average time spent at different locations of the arena * update docker stuff * Merge remote-tracking branch 'origin/datajoint_pipeline' * python package changes for docker install * docker updates * fix context path * fix dockerfile path * docker ghcr.io PAT instructions for private repo * use datajoint_pipeline for actions branch * pull latest conda/mamba image * Docker updates (#7) * new branch avoid build * changes to docker dev yml * user group settings * minor updates * update docker image * docker container paths permissions fixes * minor rename * refactor docker for aeon_db worker * incorporate thinhs changes * get env for linux amd64 * image updates * add script for sudo * process root dirs separately then concat * some keys not in json file * docker env updates * update sciviz deployment * confirm API works, revert back the temporary changes in `chunkdata` * gh actions github context * change cache type * remove old cache * devcontainer updates * dockerfile updates * docker updates * docker updates * Docker updates (#61) Updates to docker and trigger gh actions * test action * env instructions * fix repo owner * add locked envs * Docker updates Updates to docker and trigger gh actions * docker updates * docker updates * rm tmp dir gh actions * rm tmp dir gh actions * add back api fix * gh action * none path * docker updates * Docker ingestion tested (#64) * docker updates * try without cache * debug buildx * ingestion updates Co-authored-by: glopesdev <glopesdev@users.noreply.github.com> Co-authored-by: Thinh Nguyen <thinh@vathes.com> Co-authored-by: Jai Bhagat <jkbhagatio@gmail.com>
iamamutt
pushed a commit
that referenced
this pull request
Feb 2, 2022
* new branch avoid build * changes to docker dev yml * user group settings * minor updates * update docker image
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This pull request makes changes to the preprocessing API to work on data from experiment 0.1. Specifically it adds support for reading out binary tracking position data, annotations, and support for multiple patches.
The current form of the API is not backwards compatible yet with the old experiment 0. This forms part of a broader discussion we could/should have about backwards compatibility of the analysis pipelines with experimental data. My opinion atm is that version control is enough to take care of this specific situation: Experiment 0 was a prototype run at a particular moment in time which will almost certainly never be repeated again in its original form.
Because of this, I believe just tagging a version from this repo which is compatible with Experiment 0 will be enough for whoever wants to analyze that data, and there is no need to compromise current improvements yet with the added complication of maintaining back-compatibility.
Once we have multiple arenas with multiple versions of acquisition software this will change, but for now I think we can/should keep our lifes simpler.