3D Pyramid Generator tool based on Argolid

formats/pyramid-generator-3d-tool/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.1-dev0
+commit = True
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/images/formats/pyramid_generator_3d/__init__.py]
+
+[bumpversion:file:pyramidgenerator3d.cwl]
+
+[bumpversion:ict.yml]

formats/pyramid-generator-3d-tool/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/

formats/pyramid-generator-3d-tool/.python-version

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+3.9

formats/pyramid-generator-3d-tool/Dockerfile

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+FROM polusai/bfio:2.4.7
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/pyramid-generator-3d-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
+
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
+ENTRYPOINT ["python3", "-m", "polus.images.formats.pyramid_generator_3d"]
+CMD ["--help"]

formats/pyramid-generator-3d-tool/README.md

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+# pyramid_generator_3d (0.1.1-dev0)
+
+Generate 3D Image Pyramid from an image collection or Zarr directory. This plugin is a wrapper for argolid.
+This tool offers 2 subcommands: `Vol` and `Py3D`, for volume generation and 3D pyramid generation respectively. See [Usage](##usage) section for details.
+
+## Options
+| Name        | Description                                                                 | I/O | Type   |
+|-------------|-----------------------------------------------------------------------------|-----|--------|
+|`--subCmd`   | Subcommand to invoke. Options are `Vol` and `Py3D`.                         |Input|string  |
+|`--zarrDir`  | Directory to Zarr arrays for generating 3D pyramid.                         |Input|collection|
+|`--inpDir`   | Directory to input image collection. Required if `--zarrDir` is unspecified.|Input|collection|
+|`--filePattern` | File pattern for discovering images in `--inpDir`.                       |Input|collection|
+|`--groupBy` | Grouping variable for images. Options are `t`, `z`, `c`.                     |Input|string|
+|`--outDir`  | Path of output directory.                                                    |Output|collection|
+|`--outImgName` | Output name for Zarr arrays when using volume generation.                 |Input|string|
+|`--baseScaleKey`| Base scale key for 3D pyramid generation. Default to 0.                  |Input|integer|
+|`--numLevels` | Number of levels for 3D pyramid.                                           |Input|integer|
+
+## Usage
+### Volume Generation
+Use `Vol` subcommand to generate Zarr arrays from image stacks. It reads images from the input directory, groups them by specific dimension, and writes Zarr array into the output directory.
+The ***required*** options for `Vol` subcommand are `--inpDir`, `--filePattern`, `--groupBy`, `outDir`, `--outImgName`
+Example usage:
+```
+python3 -m polus.images.formats.pyramid_generator_3d --subCmd Vol --inpDir /path/to/input/images --filePattern img_r{r:ddd}_c{c:ddd}.ome.tif --groupBy c --outDir /path/to/output --outImgName output_image
+```
+
+### 3D Pyramid
+Use `Py3D` subcommand to generate 3D pyramid from either <ins>(1) a directory with Zarr array</ins> or <ins>(2) a directory of images</ins>.
+#### From Zarr directory
+When generating from a Zarr directory, the ***required*** options are `--zarrDir`, `--outDir`, and `--numLevels`. `--baseScaleKey` defaults to 0. Since the output will be written into the Zarr directory, use the same directory for `--zarrDir` and `--outDir`.
+Example usage:
+```
+python -m polus.images.formats.pyramid_generator_3d --subCmd Py3D --zarrDir /path/to/zarr/array --outDir /path/to/zarr/array --baseScaleKey 0 --numLevels 2
+```
+
+#### From image collection
+When generating directly from an image collection, the current tool firsts calls the volume generation routine first to generate Zarr array, from which 3D pyramid is subsequently generated. Thus, all options required for `Vol` subcommand are required in addition to the required options of `Py3D` (excluding `--zarrDir`).
+Together, the ***required*** options are `--inpDir`, `--filePattern`, `--groupBy`, `--outDir`, `--outImgName`, `--numLevels`. `--baseScaleKey` defaults to 0.
+Example usage:
+```
+python -m polus.images.formats.pyramid_generator_3d --subCmd Py3D --inpDir /path/to/input/images --filePattern img_r{r:ddd}_c{c:ddd}.ome.tif --groupBy c --outDir /path/to/output --outImgName test_output --baseScaleKey 0 --numLevels 2
+```
+
+## Testing with real data
+
+1. install ome-zarr
+```
+pip install ome-zarr
+```
+
+2. download an example dataset
+```
+cd <input_dir>
+ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/1884807.zarr
+```
+
+More dataset can be found [here](https://www.openmicroscopy.org/2020/11/04/zarr-data.html). To download other dataset, replace the link in the command above with other links copied from the "S3-entrypoint" column from the website.
+
+3. modify .zarray file under `<input_dir>/1884807.zarr/0`, i.e., delete the first element in "chunks" and "shape", which correspond to the T dimension.
+
+4. run the following command:
+```
+python -m polus.images.formats.pyramid_generator_3d --subCmd Py3D --zarrDir <input_path>/1884807.zarr --outDir <input_path>/1884807.zarr --baseScaleKey 0 --numLevels 2
+```
+Pyramid data will be written into the same folder.
+
+## Building
+
+To build the Docker image for the tool, run `./build-docker.sh`.
+
+## Install WIPP Plugin
+
+If WIPP is running, navigate to the plugins page and add a new plugin. Paste the
+contents of `plugin.json` into the pop-up window and submit.

formats/pyramid-generator-3d-tool/VERSION

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+0.1.1-dev0

formats/pyramid-generator-3d-tool/build-docker.sh

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+#!/bin/bash
+
+# Change the name of the tool here
+tool_dir="formats/"
+tool_name="pyramid-generator-3d-tool"
+
+# The version is read from the VERSION file
+version=$(<VERSION)
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+repo_root=$(git rev-parse --show-toplevel)
+echo "Repository root: ${repo_root}"
+
+# The Dockerfile and .dockerignore files are copied to the repository root before building the image
+cd ${repo_root}
+cp ./${tool_dir}/${tool_name}/Dockerfile .
+cp .gitignore .dockerignore
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}