From 2e0f5b7548a602badb5ef44c71197ba73d0db274 Mon Sep 17 00:00:00 2001 From: William Patton Date: Mon, 11 Nov 2024 10:03:47 -0800 Subject: [PATCH 1/4] Add a roadmap to the docs --- docs/source/index.rst | 1 + docs/source/roadmap.rst | 75 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 docs/source/roadmap.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index 3a94253db..4ac6796fb 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -9,6 +9,7 @@ overview install + roadmap notebooks/minimal_tutorial tutorial docker diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst new file mode 100644 index 000000000..9a58632b5 --- /dev/null +++ b/docs/source/roadmap.rst @@ -0,0 +1,75 @@ +.. _sec_roadmap: + +Road Map +======== + +Overview +-------- + ++-----------------------------------+------------------+-------------------------------+ +| Task | Priority | Current State | ++===================================+==================+===============================+ +| Write Documentation | High | Started with a long way to go | ++-----------------------------------+------------------+-------------------------------+ +| Simplify configurations | High | Not Started | ++-----------------------------------+------------------+-------------------------------+ +| Develop Data Conventions | High | Not Started | ++-----------------------------------+------------------+-------------------------------+ +| Improve Blockwise Post-Processing | Low | Not Started | ++-----------------------------------+------------------+-------------------------------+ +| Simplify Array handling | High | Completed | ++-----------------------------------+------------------+-------------------------------+ + +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) + - [ ] Simplify configurations + - [ ] Depricate old configs + - [ ] Add simplified config for simple cases + - [ ] can still get rid of `*Config` classes + - [ ] Develop Data Conventions + - [ ] 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 + - [ ] 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 From 9df9bbdfa62881277e42758b113cbcf8487734be Mon Sep 17 00:00:00 2001 From: William Patton Date: Mon, 11 Nov 2024 10:07:42 -0800 Subject: [PATCH 2/4] improve formatting --- docs/source/roadmap.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst index 9a58632b5..6a0eeb92a 100644 --- a/docs/source/roadmap.rst +++ b/docs/source/roadmap.rst @@ -57,7 +57,8 @@ Detailed Road Map - [x] everything else - [ ] simplify array configs accordingly -## Can Have +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 @@ -69,7 +70,8 @@ Detailed Road Map - [ ] Lazy loading of dependencies (import takes too long) - [ ] Support bioimage model spec for model dissemination -## Non-Goals (for v1.0) +Non-Goals (for v1.0) +-------------------- - custom dash board - GUI to run experiments \ No newline at end of file From 17b77075e18583d5bd2c14245df1f540550d7c9c Mon Sep 17 00:00:00 2001 From: William Patton Date: Tue, 12 Nov 2024 10:17:24 -0800 Subject: [PATCH 3/4] update roadmap --- docs/source/roadmap.rst | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/source/roadmap.rst b/docs/source/roadmap.rst index 6a0eeb92a..1582a0115 100644 --- a/docs/source/roadmap.rst +++ b/docs/source/roadmap.rst @@ -11,13 +11,13 @@ Overview +===================================+==================+===============================+ | Write Documentation | High | Started with a long way to go | +-----------------------------------+------------------+-------------------------------+ -| Simplify configurations | High | Not Started | +| Simplify configurations | High | First draft complete | +-----------------------------------+------------------+-------------------------------+ -| Develop Data Conventions | High | Not Started | +| Develop Data Conventions | High | First draft complete | +-----------------------------------+------------------+-------------------------------+ | Improve Blockwise Post-Processing | Low | Not Started | +-----------------------------------+------------------+-------------------------------+ -| Simplify Array handling | High | Completed | +| Simplify Array handling | High | Almost done (Up/Down sampling)| +-----------------------------------+------------------+-------------------------------+ Detailed Road Map @@ -33,12 +33,12 @@ Detailed Road Map - [ ] semantic segmentation (LM and EM) - [ ] instance segmentation (LM or EM, can be simulated) - [ ] general documentation of CLI, also API for developers (curate docstrings) - - [ ] Simplify configurations - - [ ] Depricate old configs - - [ ] Add simplified config for simple cases - - [ ] can still get rid of `*Config` classes - - [ ] Develop Data Conventions - - [ ] document conventions + - [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 @@ -55,7 +55,7 @@ Detailed Road Map - [ ] DVID source - [x] Datatype conversions - [x] everything else - - [ ] simplify array configs accordingly + - [x] simplify array configs accordingly Can Have -------- From 637859a9ced256c5d0363bb780e2f6d7868b5a50 Mon Sep 17 00:00:00 2001 From: Marwan Zouinkhi Date: Tue, 12 Nov 2024 14:39:11 -0500 Subject: [PATCH 4/4] Update index.rst --- docs/source/index.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 45739c439..8861ad601 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -9,15 +9,15 @@ overview install - roadmap notebooks/minimal_tutorial unet_architectures tutorial 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_