dacapo-toolbox 1.0.0__tar.gz

dacapo_toolbox-1.0.0/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

dacapo_toolbox-1.0.0/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

dacapo_toolbox-1.0.0/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,26 @@
+* {{ cookiecutter.project_name }} version:
+* Python version:
+* Operating System:
+
+### Bug or feature?
+
+Are you reporting a bug or adding a new feature? Perhaps you want more documentation? 
+Please tell us here and tag the issue appropriately.
+
+### Description
+
+Describe the bug you want fixed, the feature you want to see, etc. 
+If you are requesting a new feature, please say why you think that feature is important and belongs in this library, and any guesses on how to implement it.
+
+### What I Did/What I Would Like to Do
+
+For a bug:
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```
+
+For a feature:
+```
+Provide sample code that you would hope to run and what it would output.
+```

dacapo_toolbox-1.0.0/.github/workflows/docs.yaml

@@ -0,0 +1,37 @@
+name: Generate Pages
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  id-token: write
+  contents: write
+  pages: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 180
+    steps:
+    - name: Setup checkout
+      uses: actions/checkout@master
+    - name: Install uv
+      uses: astral-sh/setup-uv@main
+    - uses: extractions/setup-just@v3
+    - name: Install pandoc
+      uses: pandoc/actions/setup@v1
+      with:
+        version: 2.19
+    - name: install ffmpeg
+      run: sudo apt-get install ffmpeg
+    - name: build docs
+      run: just docs
+    - name: Set permissions
+      run: chmod -R a+rX ./docs/build/html
+    - name: Update gh branch
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

dacapo_toolbox-1.0.0/.github/workflows/publish.yaml

@@ -0,0 +1,37 @@
+name: Publish
+
+permissions:
+  id-token: write
+
+on:
+  push:
+    tags: ["*"]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+      - name: Publish distribution 📦 to PyPI
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

dacapo_toolbox-1.0.0/.github/workflows/ruff.yaml

@@ -0,0 +1,22 @@
+name: ruff
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  static-analysis:
+    name: ruff
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup checkout
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: ruff
+        run: |
+          uv run --extra dev ruff check src tests

dacapo_toolbox-1.0.0/.github/workflows/tests.yaml

@@ -0,0 +1,36 @@
+name: Test
+
+on:
+  pull_request:
+    branches:
+      - main
+      - dev/main
+  push:
+    branches:
+      - main
+      - dev/main
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [ubuntu-latest]
+        python-version: ['3.11', '3.12']
+    timeout-minutes: 20
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Test
+        run: uv run --pre --extra dev --python ${{ matrix.python-version }} pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+      
+      - name: Coverage
+        uses: codecov/codecov-action@v3

dacapo_toolbox-1.0.0/.github/workflows/ty.yaml

@@ -0,0 +1,22 @@
+name: type-check
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  static-analysis:
+    name: ty
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup checkout
+        uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: ty
+        run: |
+          uv run --pre --all-extras ty check src/dacapo_toolbox

dacapo_toolbox-1.0.0/.gitignore

@@ -0,0 +1,17 @@
+__pycache__
+*.egg-info
+docs/build
+docs/source/tutorials
+tutorials/**/*.zarr
+tutorials/**/_static
+*.hdf
+*.gif
+*.jpg
+.coverage
+coverage.xml
+uv.lock
+.vscode
+build
+volara_logs
+lightning_logs
+*.ipynb

dacapo_toolbox-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: dacapo-toolbox
+Version: 1.0.0
+Summary: A suite of tools for large scale ND training.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+Requires-Dist: edt>=3.0.0
+Requires-Dist: funlib-persistence>=0.6
+Requires-Dist: gunpowder>=1.4.2
+Requires-Dist: scikit-learn>=1.7.1
+Requires-Dist: torch>=2.6.0
+Provides-Extra: postprocessing
+Requires-Dist: volara-torch>=1.0.1; extra == "postprocessing"
+Requires-Dist: volara>=1.0.2; extra == "postprocessing"
+Provides-Extra: vis
+Requires-Dist: matplotlib>=3.10.5; extra == "vis"
+Provides-Extra: dev
+Requires-Dist: pytest>=8.3.4; extra == "dev"
+Requires-Dist: pytest-cov>=6.0.0; extra == "dev"
+Requires-Dist: ruff>=0.9.6; extra == "dev"
+Requires-Dist: pytest-xdist>=3.6.1; extra == "dev"
+Requires-Dist: ty>=0.0.1a18; extra == "dev"
+Provides-Extra: accelerators
+Requires-Dist: accelerate>=1.10.0; extra == "accelerators"
+Requires-Dist: lightning>=2.5.3; extra == "accelerators"
+Provides-Extra: sample-datasets
+Requires-Dist: wget>=3.2; extra == "sample-datasets"
+Provides-Extra: examples
+Requires-Dist: torchvision>=0.22.0; extra == "examples"
+Provides-Extra: docs
+Requires-Dist: h5py>=3.13.0; extra == "docs"
+Requires-Dist: ipykernel>=6.29.5; extra == "docs"
+Requires-Dist: matplotlib>=3.10.3; extra == "docs"
+Requires-Dist: mwatershed>=0.5.3; extra == "docs"
+Requires-Dist: tems>=1.0.3; extra == "docs"
+Requires-Dist: torchvision>=0.22.0; extra == "docs"
+Requires-Dist: volara>=1.0.1; extra == "docs"
+Requires-Dist: volara-torch>=1.0.0; extra == "docs"
+Requires-Dist: wget>=3.2; extra == "docs"
+Requires-Dist: jupytext>=1.17.2; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=2.0; extra == "docs"
+Requires-Dist: sphinx-material>=0.0.36; extra == "docs"
+Requires-Dist: sphinx-click>=6.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2.0; extra == "docs"
+Requires-Dist: nbsphinx>=0.9.7; extra == "docs"
+Requires-Dist: myst-parser>=4.0; extra == "docs"
+
+![dacapo-toolbox](docs/source/_static/dacapo-toolbox-logo.png)
+[![tests](https://github.com/pattonw/dacapo-toolbox/actions/workflows/tests.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/tests.yaml)
+[![ruff](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ruff.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ruff.yaml)
+[![ty](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ty.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ty.yaml)
+[![pypi](https://github.com/pattonw/dacapo-toolbox/actions/workflows/publish.yaml/badge.svg)](https://pypi.org/project/dacapo-toolbox/)
+[![docs](https://github.com/pattonw/dacapo-toolbox/actions/workflows/docs.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/docs.yaml)
+
+# DaCapo-Toolbox
+
+> A simple interface for large scale microscopy training and post processing
+
+## What is DaCapo-Toolbox?
+
+DaCapo-Toolbox wraps powerful tools for large scale microscopy training and evaluation such as:
+[gunpowder](https://github.com/funkelab/gunpowder), [daisy](https://github.com/funkelab/daisy), and
+[volara](https://github.com/e11bio/volara) in simple interfaces that abstract away the intricacies
+of the specific tools and just provides interfaces in common formats such as
+[zarr](https://zarr.readthedocs.io/en/stable/), [torch](https://pytorch.org), [dask](https://dask.org),
+and [numpy](https://numpy.org).
+
+## Installation
+
+`pip install dacapo-toolbox`
+
+## Usage
+
+See the [DaCapo-Toolbox docs](https://pattonw.github.io/dacapo-toolbox)

dacapo_toolbox-1.0.0/README.md

@@ -0,0 +1,27 @@
+![dacapo-toolbox](docs/source/_static/dacapo-toolbox-logo.png)
+[![tests](https://github.com/pattonw/dacapo-toolbox/actions/workflows/tests.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/tests.yaml)
+[![ruff](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ruff.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ruff.yaml)
+[![ty](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ty.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/ty.yaml)
+[![pypi](https://github.com/pattonw/dacapo-toolbox/actions/workflows/publish.yaml/badge.svg)](https://pypi.org/project/dacapo-toolbox/)
+[![docs](https://github.com/pattonw/dacapo-toolbox/actions/workflows/docs.yaml/badge.svg)](https://github.com/pattonw/dacapo-toolbox/actions/workflows/docs.yaml)
+
+# DaCapo-Toolbox
+
+> A simple interface for large scale microscopy training and post processing
+
+## What is DaCapo-Toolbox?
+
+DaCapo-Toolbox wraps powerful tools for large scale microscopy training and evaluation such as:
+[gunpowder](https://github.com/funkelab/gunpowder), [daisy](https://github.com/funkelab/daisy), and
+[volara](https://github.com/e11bio/volara) in simple interfaces that abstract away the intricacies
+of the specific tools and just provides interfaces in common formats such as
+[zarr](https://zarr.readthedocs.io/en/stable/), [torch](https://pytorch.org), [dask](https://dask.org),
+and [numpy](https://numpy.org).
+
+## Installation
+
+`pip install dacapo-toolbox`
+
+## Usage
+
+See the [DaCapo-Toolbox docs](https://pattonw.github.io/dacapo-toolbox)

dacapo_toolbox-1.0.0/docs/source/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

dacapo_toolbox-1.0.0/docs/source/api.rst

@@ -0,0 +1,79 @@
+.. _sec_api:
+
+API Reference
+=============
+
+.. automodule:: dacapo_toolbox
+   :no-index:
+
+Dataset
+=======
+
+    .. autoclass:: dacapo_toolbox.dataset.iterable_dataset
+        :members:
+
+    .. autoclass:: dacapo_toolbox.dataset.SimpleAugmentConfig
+        :members:
+
+    .. autoclass:: dacapo_toolbox.dataset.DeformAugmentConfig
+        :members:
+    
+    .. autoclass:: dacapo_toolbox.dataset.MaskedSampling
+        :members:
+
+    .. autoclass:: dacapo_toolbox.dataset.PointSampling
+        :members:
+
+Transforms
+==========
+
+Affinities
+----------
+
+    .. autoclass:: dacapo_toolbox.transforms.affs.Affs
+        :members:
+    
+    .. autoclass:: dacapo_toolbox.transforms.affs.AffsMask
+        :members:
+
+    .. autofunction:: dacapo_toolbox.transforms.affs.compute_affs
+        :members:
+
+Distances
+---------
+
+    .. autoclass:: dacapo_toolbox.transforms.distances.SignedDistanceTransform
+        :members:
+
+    .. autoclass:: dacapo_toolbox.transforms.distances.SDTBoundaryMask
+        :members:
+
+LSDS
+----
+
+    .. autoclass:: dacapo_toolbox.transforms.lsds.LSD
+        :members:
+
+    .. autofunction:: dacapo_toolbox.transforms.lsds.get_local_shape_descriptors
+    
+Weight Balancing
+----------------
+
+    .. autoclass:: dacapo_toolbox.transforms.weight_balancing.BalanceLabels
+        :members:
+
+    .. autofunction:: dacapo_toolbox.transforms.weight_balancing.balance_weights
+
+Visualizations
+==============
+
+    .. autofunction:: dacapo_toolbox.vis.preview.gif_2d
+
+    .. autofunction:: dacapo_toolbox.vis.preview.cube
+
+Sample Data
+===========
+
+    .. autofunction:: dacapo_toolbox.sample_datasets.cremi
+
+

dacapo_toolbox-1.0.0/docs/source/conf.py

@@ -0,0 +1,65 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "DaCapo"
+copyright = "2024, William Patton, Jeff Rhoades, Marwan Zouinkhi,  David Ackerman, Caroline Malin-Mayor, Jan Funke"
+author = " William Patton, Jeff Rhoades, Marwan Zouinkhi, David Ackerman, Caroline Malin-Mayor, Jan Funke"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "nbsphinx",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx_autodoc_typehints",
+    "sphinx_click",  # auto document cli
+    "myst_parser",  # include md files in rst files
+]
+
+nbsphinx_custom_formats = {
+    ".py": ["jupytext.reads", {"fmt", "py:percent"}],
+}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+html_css_files = [
+    "css/custom.css",
+]

dacapo_toolbox-1.0.0/docs/source/index.rst

@@ -0,0 +1,17 @@
+.. DaCapo documentation master file, created by
+   sphinx-quickstart on Tue Aug  2 16:34:19 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: DaCapo Toolbox:
+
+   overview
+   install
+   api
+   tutorials/dataset/dataset_overview
+   tutorials/dataset/cremi
+
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_

dacapo_toolbox-1.0.0/docs/source/install.rst

@@ -0,0 +1,16 @@
+.. _sec_install:
+
+Installation
+============
+
+For the most recent release:
+
+.. code-block:: bash
+
+   pip install dacapo-toolbox
+
+For the latest version:
+
+.. code-block:: bash
+
+   pip install git+https://github.com/pattonw/dacapo-toolbox

dacapo_toolbox-1.0.0/docs/source/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

dacapo_toolbox-1.0.0/docs/source/overview.rst

@@ -0,0 +1,13 @@
+.. _sec_overview:
+
+Overview
+========
+
+What is the DaCapo Toolbox?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The DaCapo Toolbox contains a set of convenient tools for training neural networks on large microscopy datasets.
+Specifically it focuses on providing a simple interface to many tools and techniques with an emphasis on
+common interfaces such as torch/numpy/dask and other common scientific computing packages.
+The main exception to this is the `funlib.persistence.Array` object. A thin wrapper around a `dask` array with
+added metadata necessary for reliable training on diverse microscopy datasets.