imaging-server-kit 0.0.1__tar.gz

imaging_server_kit-0.0.1/.dockerignore

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+deployment/
+examples/
+build/
+LICENSE

imaging_server_kit-0.0.1/.github/workflows/publish.yml

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+# Build the package and publish it to PyPI on tag push.
+name: Publish to PyPI
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  publish:
+    name: publish
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Build package
+        run: |
+          python -m pip install -U pip build
+          python -m build
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.TWINE_API_KEY }}

imaging_server_kit-0.0.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py
+
+old/
+data/

imaging_server_kit-0.0.1/Dockerfile

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+FROM condaforge/miniforge3:latest
+
+RUN conda install python=3.9 -y
+
+COPY . .
+
+RUN python -m pip install -e .
+
+EXPOSE 8000
+
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "300"]

imaging_server_kit-0.0.1/Dockerfile-3.10

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+FROM condaforge/miniforge3:latest
+
+RUN conda install python=3.10 -y
+
+COPY . .
+
+RUN python -m pip install -e .
+
+EXPOSE 8000
+
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "300"]

imaging_server_kit-0.0.1/Dockerfile-GPU

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+FROM cschranz/gpu-jupyter:v1.6_cuda-12.0_ubuntu-22.04_python-only
+ENV DEBIAN_FRONTEND=noninteractive
+USER root
+
+COPY . .
+
+RUN python -m pip install -e .
+
+EXPOSE 8000
+
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "300"]

imaging_server_kit-0.0.1/LICENSE

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+Copyright (c) 2024, EPFL
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

imaging_server_kit-0.0.1/MANIFEST.in

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+include LICENSE
+include README.md
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

imaging_server_kit-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: imaging-server-kit
+Version: 0.0.1
+Summary: Run image processing algorithms in a FastAPI server.
+Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
+License: Copyright (c) 2024, EPFL
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: homepage, https://gitlab.com/epfl-center-for-imaging/imaging-server-kit
+Project-URL: repository, https://gitlab.com/epfl-center-for-imaging/imaging-server-kit
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastapi
+Requires-Dist: uvicorn[standard]
+Requires-Dist: python-multipart
+Requires-Dist: tifffile
+Requires-Dist: numpy
+Requires-Dist: scikit-image
+
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Imaging Server Kit
+
+Run seamlessly interoperable algorithms on images using FastAPI.
+
+## Setup
+
+Build the `imaging-server-kit` image with `docker`:
+
+```
+docker build -t imaging-server-kit:3.9 .
+```
+
+or build specific images:
+
+```
+docker build -t imaging-server-kit:3.10 --file Dockerfile-3.10 .
+docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
+```
+
+**Run an algorithm server**
+
+The server will be running on `http://localhost:8000`.
+
+```bash
+docker build -t serverkit/rembg .
+docker run -it --rm -p 8000:8000 serverkit/rembg
+```
+
+**Run an algorithm server with multiple algorithms**
+
+See [deployment](./reference_deployment/README.md). The server will be running on `http://localhost:7000`.
+
+## Usage
+
+**Python client**
+
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install git+https://gitlab.com/epfl-center-for-imaging/imaging-server-kit.git
+```
+
+Connect to an algorithm server and run algorithms from Python:
+
+```python
+from imaging_server_kit import Client
+
+client = Client()
+
+client.connect("http://localhost:7000")
+
+print(client.algorithms)
+# [`rembg`, `stardist`, `sam2`]
+
+data_tuple = client.run_algorithm(
+    algorithm="rembg",
+    image=(...),
+    rembg_model_name="silueta",
+)
+```
+
+More [examples](./examples/).
+
+**Napari client**
+
+Coming soon.
+
+**Web client**
+
+Coming soon.
+
+**QuPath client**
+
+Coming soon.
+
+**Fiji plugin**
+
+Coming soon.
+
+## Contributing
+
+Contributions are very welcome.
+
+## License
+
+This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.

imaging_server_kit-0.0.1/README.md

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+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Imaging Server Kit
+
+Run seamlessly interoperable algorithms on images using FastAPI.
+
+## Setup
+
+Build the `imaging-server-kit` image with `docker`:
+
+```
+docker build -t imaging-server-kit:3.9 .
+```
+
+or build specific images:
+
+```
+docker build -t imaging-server-kit:3.10 --file Dockerfile-3.10 .
+docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
+```
+
+**Run an algorithm server**
+
+The server will be running on `http://localhost:8000`.
+
+```bash
+docker build -t serverkit/rembg .
+docker run -it --rm -p 8000:8000 serverkit/rembg
+```
+
+**Run an algorithm server with multiple algorithms**
+
+See [deployment](./reference_deployment/README.md). The server will be running on `http://localhost:7000`.
+
+## Usage
+
+**Python client**
+
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install git+https://gitlab.com/epfl-center-for-imaging/imaging-server-kit.git
+```
+
+Connect to an algorithm server and run algorithms from Python:
+
+```python
+from imaging_server_kit import Client
+
+client = Client()
+
+client.connect("http://localhost:7000")
+
+print(client.algorithms)
+# [`rembg`, `stardist`, `sam2`]
+
+data_tuple = client.run_algorithm(
+    algorithm="rembg",
+    image=(...),
+    rembg_model_name="silueta",
+)
+```
+
+More [examples](./examples/).
+
+**Napari client**
+
+Coming soon.
+
+**Web client**
+
+Coming soon.
+
+**QuPath client**
+
+Coming soon.
+
+**Fiji plugin**
+
+Coming soon.
+
+## Contributing
+
+Contributions are very welcome.
+
+## License
+
+This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.

imaging_server_kit-0.0.1/examples/example.py

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+"""
+Demo: Running an algorithm.
+"""
+
+import imaging_server_kit as serverkit
+
+
+def main():
+    client = serverkit.Client()
+    status_code = client.connect("http://localhost:7000")
+    print(f"{status_code=}")
+    print(f"{client.algorithms=}")
+
+    algo = client.algorithms[0]  # e.g. `rembg`
+
+    # Get the algo params
+    rembg_params = client.get_algorithm_parameters(algo)
+    print(f"{rembg_params=}")
+
+    # Get the algo sample image
+    rembg_sample_images = client.get_sample_images(algo)
+    for image in rembg_sample_images:
+        print(f"{image.shape=}")
+    sample_image = rembg_sample_images[0]
+
+    # Run the algo (return type is a `LayerDataTuple`)
+    algo_output = client.run_algorithm(
+        algorithm=algo, image=sample_image, rembg_model_name="silueta"
+    )
+    for data, data_params, data_type in algo_output:
+        print(f"Algo returned: {data_type=} ({data.shape=})")
+
+
+if __name__ == "__main__":
+    main()

imaging_server_kit-0.0.1/main.py

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+import imaging_server_kit as serverkit
+
+server = serverkit.Server(algorithm_name="foo", parameters_model=serverkit.Parameters)
+app = server.app

imaging_server_kit-0.0.1/pyproject.toml

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+[project]
+name = "imaging-server-kit"
+dynamic = ["version"]
+description = "Run image processing algorithms in a FastAPI server."
+readme = "README.md"
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+authors = [{ name = "Mallory Wittwer", email = "mallory.wittwer@epfl.ch" }]
+
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Image Processing",
+]
+
+dependencies = [
+    "fastapi",
+    "uvicorn[standard]",
+    "python-multipart",
+    "tifffile",
+    "numpy",
+    "scikit-image",
+]
+
+[project.urls]
+homepage = "https://gitlab.com/epfl-center-for-imaging/imaging-server-kit"
+repository = "https://gitlab.com/epfl-center-for-imaging/imaging-server-kit"
+
+[build-system]
+requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
+
+[tool.setuptools_scm]
+write_to = "src/imaging_server_kit/_version.py"
+version_scheme = "guess-next-dev"
+local_scheme = "no-local-version"

imaging_server_kit-0.0.1/reference_deployment/LICENSE

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+Copyright (c) 2024, EPFL
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

imaging_server_kit-0.0.1/reference_deployment/README.md

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+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Deployment
+
+Start the server:
+
+```
+docker compose up -d
+```
+
+**Add a new algorithm**
+
+Start from the template:
+
+```
+cookiecutter cookiecutter_template/
+```
+
+Edit the `Parameters` and `Server` in your `main.py` to your liking.
+
+Move your `serverkit-my-algo` folder to `./servers`.
+
+Add an entry to `docker-compose.yml`:
+
+```
+my-algo:
+  build:
+    context: ./servers/serverkit-my-algo
+  depends_on:
+    - servers_registry
+```
+
+Restart the server:
+
+```
+docker compose restart
+```
+
+## Contributing
+
+Contributions are very welcome.
+
+## License
+
+This project is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+
+## Issues
+
+If you encounter any problems, please file an issue along with a detailed description.

imaging_server_kit-0.0.1/reference_deployment/cookiecutter_template/README.md

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+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# Imaging Server Kit - Algorithm Template

imaging_server_kit-0.0.1/reference_deployment/cookiecutter_template/cookiecutter.json

@@ -0,0 +1,5 @@
+{
+  "package": "skimage",
+  "project_url": "https://scikit-image.org/",
+  "author": "EPFL Center for Imaging"
+}

imaging_server_kit-0.0.1/reference_deployment/cookiecutter_template/requirements.txt

@@ -0,0 +1 @@
+cookiecutter

imaging_server_kit-0.0.1/reference_deployment/cookiecutter_template/serverkit-{{ cookiecutter.package }}/Dockerfile

@@ -0,0 +1,5 @@
+FROM imaging-server-kit:3.9
+
+COPY . .
+
+RUN python -m pip install -r requirements.txt

imaging_server_kit-0.0.1/reference_deployment/cookiecutter_template/serverkit-{{ cookiecutter.package }}/README.md

@@ -0,0 +1,6 @@
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# {{ cookiecutter.package }} API in docker
+
+Implementation of a web API server for [{{ cookiecutter.package }}]({{ cookiecutter.project_url }}).
+
+Author: {{ cookiecutter.author }}