Update dev/main

.github/workflows/docs.yaml

@@ -16,7 +16,8 @@ jobs:
       with:
         fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
     - name: install dacapo
-      run: pip install .[docs]
+      # run: pip install .[docs]
+      run: pip install sphinx-autodoc-typehints sphinx-autoapi sphinx-click sphinx-rtd-theme myst-parser
     - name: Build and Commit
       uses: sphinx-notes/pages@v2
       with:

.gitignore

@@ -29,4 +29,7 @@ tmp/
 # daisy logs
 daisy_logs/
 
-*.csv
+*.csv
+*.private
+
+user_experiments/*

CITATION.cff

@@ -0,0 +1,62 @@
+
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Patton"
+  given-names: "William"
+  orcid: "https://orcid.org/0000-0002-9652-3222"
+- family-names: "Rhoades"
+  given-names: "Jeff L."
+  orcid: "https://orcid.org/0000-0001-5077-2533"
+- family-names: "Zouinkhi"
+  given-names: "Marwan"
+  orcid: "https://orcid.org/0000-0002-9441-2908"
+- family-names: "Funke"
+  given-names: "Jan"
+  orcid: "http://orcid.org/0000-0003-4388-7783"
+title: "DaCapo"
+version: 0.3.0
+doi: 10.48550/arXiv.2408.02834
+date-released: 2024-08-05
+url: "https://github.com/janelia-cellmap/dacapo"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Patton"
+    given-names: "William"
+    orcid: "https://orcid.org/0000-0002-9652-3222"
+  - family-names: "Rhoades"
+    given-names: "Jeff L."
+    orcid: "https://orcid.org/0000-0001-5077-2533"
+  - family-names: "Zouinkhi"
+    given-names: "Marwan"
+    orcid: "https://orcid.org/0000-0002-9441-2908"
+  - family-names: "Ackerman"
+    given-names: "David G."
+    orcid: "http://orcid.org/0000-0003-0172-6594"
+  - family-names: "Malin-Mayor"
+    given-names: "Caroline"
+    orcid: "https://orcid.org/0000-0002-9627-6030"
+  - family-names: "Adjavon"
+    given-names: "Diane"
+  - family-names: "Heinrich"
+    given-names: "Larissa"
+    orcid: "http://orcid.org/0000-0003-2852-6664"
+  - family-names: "Bennett"
+    given-names: "Davis"
+    orcid: "http://orcid.org/0000-0001-7579-2848"
+  - family-names: "Zubov"
+    given-names: "Yurii"
+    orcid: "https://orcid.org/0000-0003-1988-8081"
+  - family-names: "Project Team"
+    given-names: "CellMap"
+  - family-names: "Weigel"
+    given-names: "Aubrey V."
+    orcid: "http://orcid.org/0000-0003-1694-4420"
+  - family-names: "Funke"
+    given-names: "Jan"
+    orcid: "http://orcid.org/0000-0003-4388-7783"
+  doi: 10.48550/arXiv.2408.02834
+  journal: "arXiv-cs.CV"
+  title: "DaCapo: a modular deep learning framework for scalable 3D image segmentation"
+  year: 2024

CONTRIBUTING.md

@@ -22,15 +22,15 @@ This will also be run automatically when a PR is made to master and a codecov re
 
 
 ## Branching and PRs
-- Users that have been added to the CellMap organization and the DaCapo project should be able to develop directly into the CellMap fork of DaCapo. Other users will need to create a fork.
-- For a completely new feature, make a branch off of the `dev/main` branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
-- Currently, you should make your PRs into the `dev/main` branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch should be deleted. 
-- `dev/main` will be regularly merged to `main` when new features are fully implemented and all tests are passing.
+- Users that have been added to the CellMap organization and the DaCapo project should be able to develop directly into the CellMap fork of DaCapo. Other users will need to create a fork or ask to be added as a collaborator.
+- For a completely new feature, make a branch off of the `main` branch of CellMap's fork of DaCapo with a name describing the feature. If you are collaborating on a feature that already has a branch, you can branch off that feature branch.
+- Currently, you should make your PRs into the `main` branch of CellMap's fork, or the feature branch you branched off of. PRs currently require one maintainer's approval before merging. Once the PR is merged, the feature branch will/should be deleted. 
+- `main` will be regularly published to PyPi when new features are fully implemented and all tests are passing.
 
 
 ## Documentation
 Documentation is built using Sphinx. To build the documentation locally, run
 ```bash
 sphinx-build -M html docs/source docs/build
 ```
-This will generate the html files in the `docs/build/html` directory.
+This will generate the html files in the `docs/build/html` directory.

README.md

@@ -72,4 +72,15 @@ Tasks we support and approaches for those tasks:
     - Example of [groundtruth data](https://tinyurl.com/pu8mespz)
  - Visualization
     - [Neuroglancer GitHub Repo](https://github.com/google/neuroglancer)
-
+
+# Citing this repo
+If you use our code, please cite us and spread the news!
+```
+@article{Patton_DaCapo_a_modular_2024,
+author = {Patton, William and Rhoades, Jeff L. and Zouinkhi, Marwan and Ackerman, David G. and Malin-Mayor, Caroline and Adjavon, Diane and Heinrich, Larissa and Bennett, Davis and Zubov, Yurii and Project Team, CellMap and Weigel, Aubrey V. and Funke, Jan},
+doi = {10.48550/arXiv.2408.02834},
+journal = {arXiv-cs.CV},
+title = {{DaCapo: a modular deep learning framework for scalable 3D image segmentation}},
+year = {2024}
+}
+```

dacapo/__init__.py

@@ -5,6 +5,6 @@
 from . import experiments, utils  # noqa
 from .apply import apply  # noqa
 from .train import train  # noqa
-from .validate import validate  # noqa
+from .validate import validate, validate_run  # noqa
 from .predict import predict  # noqa
 from .blockwise import run_blockwise, segment_blockwise  # noqa

dacapo/blockwise/__init__.py

@@ -1,2 +1,3 @@
 from .blockwise_task import DaCapoBlockwiseTask
 from .scheduler import run_blockwise, segment_blockwise
+from . import global_vars

dacapo/blockwise/argmax_worker.py

@@ -54,6 +54,22 @@ def start_worker(
     output_container: Path | str,
     output_dataset: str,
     return_io_loop: bool = False,
+):
+    return start_worker_fn(
+        input_container=input_container,
+        input_dataset=input_dataset,
+        output_container=output_container,
+        output_dataset=output_dataset,
+        return_io_loop=return_io_loop,
+    )
+
+
+def start_worker_fn(
+    input_container: Path | str,
+    input_dataset: str,
+    output_container: Path | str,
+    output_dataset: str,
+    return_io_loop: bool = False,
 ):
     """
     Start the threshold worker.
@@ -111,7 +127,7 @@ def spawn_worker(
     """
     compute_context = create_compute_context()
     if not compute_context.distribute_workers:
-        return start_worker(
+        return start_worker_fn(
             input_array_identifier.container,
             input_array_identifier.dataset,
             output_array_identifier.container,

dacapo/blockwise/empanada_function.py

@@ -50,7 +50,7 @@ def segment_function(input_array, block, **parameters):
 
     Args:
         input_array (np.ndarray): The 3D array to segment.
-        block (dask.array.core.Block): The block object.
+        block (daisy.Block): The block object.
         **parameters: Parameters for the empanada-napari segmenter.
     Returns:
         np.ndarray: The segmented 3D array.

dacapo/blockwise/global_vars.py

@@ -0,0 +1 @@
+current_run = None