diff --git a/docs/source/index.rst b/docs/source/index.rst index 9a354e7a..8861ad60 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -15,8 +15,9 @@ docker aws cosem_starter + roadmap autoapi/index cli .. include:: ../../README.md - :parser: myst_parser.sphinx_ \ No newline at end of file + :parser: myst_parser.sphinx_ diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst new file mode 100644 index 00000000..1582a011 --- /dev/null +++ b/docs/source/roadmap.rst @@ -0,0 +1,77 @@ +.. _sec_roadmap: + +Road Map +======== + +Overview +-------- + ++-----------------------------------+------------------+-------------------------------+ +| Task | Priority | Current State | ++===================================+==================+===============================+ +| Write Documentation | High | Started with a long way to go | ++-----------------------------------+------------------+-------------------------------+ +| Simplify configurations | High | First draft complete | ++-----------------------------------+------------------+-------------------------------+ +| Develop Data Conventions | High | First draft complete | ++-----------------------------------+------------------+-------------------------------+ +| Improve Blockwise Post-Processing | Low | Not Started | ++-----------------------------------+------------------+-------------------------------+ +| Simplify Array handling | High | Almost done (Up/Down sampling)| ++-----------------------------------+------------------+-------------------------------+ + +Detailed Road Map +----------------- + + - [ ] Write Documentation + - [ ] tutorials: not more than three, simple and continuously tested (with Github actions, small U-Net on CPU could work) + - [x] Basic tutorial: train a U-Net on a toy dataset + - [ ] Parametrize the basic tutorial across tasks (instance/semantic segmentation). + - [ ] Improve visualizations. Move some simple plotting functions to DaCapo. + - [ ] Add a pure pytorch implementation to show benefits side-by-side + - [ ] Track performance metrics (e.g., loss, accuracy, etc.) so we can make sure we aren't regressing + - [ ] semantic segmentation (LM and EM) + - [ ] instance segmentation (LM or EM, can be simulated) + - [ ] general documentation of CLI, also API for developers (curate docstrings) + - [x] Simplify configurations + - [x] Depricate old configs + - [x] Add simplified config for simple cases + - [x] can still get rid of `*Config` classes + - [x] Develop Data Conventions + - [x] document conventions + - [ ] convenience scripts to convert dataset into our convention (even starting from directories of PNG files) + - [ ] Improve Blockwise Post-Processing + - [ ] De-duplicate code between “in-memory” and “block-wise” processing + - [ ] have only block-wise algorithms, use those also for “in-memory” + - [ ] no more “in-memory”, this is just a run with a different Compute Context + - [ ] Incorporate `volara` into DaCapo (embargo until January) + - [ ] Improve debugging support (logging of chain of commands for reproducible runs) + - [ ] Split long post-processing steps into several smaller ones for composability (e.g., support running each step independently if we want to support choosing between `waterz` and `mutex_watershed` for fragment generation or agglomeration) + - [x] Incorporate `funlib.persistence` adaptors. + - [x] all of those can be adapters: + - [x] Binarize Labels into Mask + - [x] Scale/Shift intensities + - [ ] Up/Down sample (if easily possible) + - [ ] DVID source + - [x] Datatype conversions + - [x] everything else + - [x] simplify array configs accordingly + +Can Have +-------- + + - [ ] Support other stats stores. Too much time, effort and code was put into the stats and didn’t provide a very nice interface: + - [ ] defining variables to store + - [ ] efficiently batch writing, storing and reading stats to both files and mongodb + - [ ] visualizing stats. + - [ ] Jeff and Marwan suggest MLFlow instead of WandB + - [ ] Support for slurm clusters + - [ ] Support for cloud computing (AWS) + - [ ] Lazy loading of dependencies (import takes too long) + - [ ] Support bioimage model spec for model dissemination + +Non-Goals (for v1.0) +-------------------- + +- custom dash board +- GUI to run experiments \ No newline at end of file