imaging-server-kit 0.0.1__tar.gz → 0.0.3__tar.gz

imaging_server_kit-0.0.3/.dockerignore

@@ -0,0 +1,2 @@
+reference_deployment/
+examples/

imaging_server_kit-0.0.3/.gitattributes

@@ -0,0 +1,35 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text

imaging_server_kit-0.0.3/.gitignore

@@ -0,0 +1,28 @@
+__pycache__/
+*.py[cod]
+*$py.class
+old/
+data/
+env/
+build/
+dist/
+downloads/
+eggs/
+.eggs/
+*.egg-info/
+.installed.cfg
+*.egg
+.tox/
+.coverage
+.coverage.*
+.cache
+docs/_build/
+.idea/
+venv/
+.vscode/
+.ipynb_checkpoints
+.python-version
+.DS_Store
+**/_version.py
+
+push.sh

{imaging_server_kit-0.0.1 → imaging_server_kit-0.0.3}/Dockerfile

@@ -1,6 +1,10 @@
+# Doc: https://github.com/conda-forge/miniforge-images
 FROM condaforge/miniforge3:latest
 
-RUN conda install python=3.9 -y
+ARG PYTHON_VERSION=3.9
+RUN conda install python=$PYTHON_VERSION -y
+
+WORKDIR /app
 
 COPY . .
 
@@ -8,4 +12,4 @@ RUN python -m pip install -e .
 
 EXPOSE 8000
 
-CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "300"]
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000"]

{imaging_server_kit-0.0.1 → imaging_server_kit-0.0.3}/Dockerfile-GPU

@@ -1,5 +1,8 @@
+# Doc: https://github.com/iot-salzburg/gpu-jupyter
 FROM cschranz/gpu-jupyter:v1.6_cuda-12.0_ubuntu-22.04_python-only
+
 ENV DEBIAN_FRONTEND=noninteractive
+
 USER root
 
 COPY . .
@@ -8,4 +11,4 @@ RUN python -m pip install -e .
 
 EXPOSE 8000
 
-CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000", "--timeout-keep-alive", "300"]
+CMD ["uvicorn", "main:app", "--host", "0.0.0.0", "--port", "8000"]

imaging_server_kit-0.0.3/Dockerfile-registry

@@ -0,0 +1,5 @@
+FROM mallorywittwerepfl/imaging-server-kit:3.9
+
+COPY start_registry.py .
+
+CMD ["uvicorn", "start_registry:app", "--host", "0.0.0.0", "--port", "8000"]

imaging_server_kit-0.0.3/PKG-INFO

@@ -0,0 +1,184 @@
+Metadata-Version: 2.2
+Name: imaging-server-kit
+Version: 0.0.3
+Summary: Deploy image processing algorithms in FastAPI servers. 
+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: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+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
+Requires-Dist: geojson
+Requires-Dist: jinja2
+Requires-Dist: pyyaml
+Requires-Dist: dash
+Requires-Dist: dash-bootstrap-components
+Requires-Dist: a2wsgi
+Requires-Dist: pytest
+
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Imaging Server Kit
+
+Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
+
+## Usage
+
+### Algorithm servers
+
+Set up and run a server with one, or multiple algorithms from the Imaging Server Kit collection (or your own):
+
+- [StarDist](https://github.com/Imaging-Server-Kit/serverkit-stardist)
+- [CellPose](https://github.com/Imaging-Server-Kit/serverkit-cellpose)
+- [Spotiflow](https://github.com/Imaging-Server-Kit/serverkit-spotiflow)
+- [Rembg](https://github.com/Imaging-Server-Kit/serverkit-rembg)
+- [Scikit-image LoG detector](https://github.com/Imaging-Server-Kit/serverkit-skimage-LoG)
+- [Orientationpy](https://github.com/Imaging-Server-Kit/serverkit-orientationpy)
+<!-- - [Tau Fibrils Detector](https://github.com/Imaging-Server-Kit/serverkit-tau-fibrils-yolo) -->
+
+To do that, the recommended way is to edit a `docker-compose.yml` file and pull server images from `registry.rcp.epfl.ch` (EPFL users only):
+
+```{docker-compose.yml}
+services:
+  servers_registry:
+    image: mallorywittwerepfl/imaging-server-kit:registry
+    ports:
+      - "8000:8000"
+  rembg:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
+    depends_on:
+      - servers_registry
+  skimage-log:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-skimage-log:latest
+    depends_on:
+      - servers_registry
+```
+
+Start the server with
+
+```
+docker compose up
+```
+
+The server should be accessible at http://localhost:8000.
+
+**Build the docker images yourself**
+
+To build the algorithm server images yourself (e.g. if you are not from EPFL), see [Reference Deployment](https://github.com/Imaging-Server-Kit/serverkit-deploy-docker).
+
+**Create a server for your project**
+
+To learn how to create a server for your project, see [Algorithm Server Template](https://github.com/Imaging-Server-Kit/cookiecutter-serverkit).
+
+### Python client
+
+Once the server is running, connect to it and run algorithms from Python:
+
+```python
+from imaging_server_kit import Client
+
+client = Client("http://localhost:8000")
+
+print(client.algorithms)
+# [`rembg`, `stardist`, `cellpose`]
+
+algo_output = client.run_algorithm(
+    algorithm="rembg",
+    image=(...),
+    rembg_model_name="silueta",
+)
+```
+
+### Napari plugin
+
+Once the server is running, use the [Napari Server Kit](https://github.com/Imaging-Server-Kit/napari-serverkit) plugin to connect to it and run algorithms in Napari.
+
+### QuPath extension
+
+Once the server is running, use the [QuPath Extension Server Kit](https://github.com/Imaging-Server-Kit/qupath-extension-serverkit) to connect to it and run algorithms from within QuPath.
+
+## Install locally
+
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install imaging-server-kit
+```
+
+or clone the project and install the development version:
+
+```
+git clone https://github.com/Imaging-Server-Kit/imaging-server-kit.git
+cd imaging-server-kit
+pip install -e .
+```
+
+## Build with `docker`
+
+Build the `imaging-server-kit` docker image for a specific Python version:
+
+```
+docker build --build-arg PYTHON_VERSION=3.9 -t imaging-server-kit:3.9 .
+```
+
+Run [build.sh](./build.sh) to build docker images for Python 3.9, 3.10, 3.11, GPU and the server kit registry:
+
+```
+bash ./build.sh
+```
+
+## 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-0.0.3/README.md

@@ -0,0 +1,121 @@
+![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
+# 🪐 Imaging Server Kit
+
+Deploy image processing algorithms in FastAPI servers and easily run them in Napari, QuPath, and more.
+
+## Usage
+
+### Algorithm servers
+
+Set up and run a server with one, or multiple algorithms from the Imaging Server Kit collection (or your own):
+
+- [StarDist](https://github.com/Imaging-Server-Kit/serverkit-stardist)
+- [CellPose](https://github.com/Imaging-Server-Kit/serverkit-cellpose)
+- [Spotiflow](https://github.com/Imaging-Server-Kit/serverkit-spotiflow)
+- [Rembg](https://github.com/Imaging-Server-Kit/serverkit-rembg)
+- [Scikit-image LoG detector](https://github.com/Imaging-Server-Kit/serverkit-skimage-LoG)
+- [Orientationpy](https://github.com/Imaging-Server-Kit/serverkit-orientationpy)
+<!-- - [Tau Fibrils Detector](https://github.com/Imaging-Server-Kit/serverkit-tau-fibrils-yolo) -->
+
+To do that, the recommended way is to edit a `docker-compose.yml` file and pull server images from `registry.rcp.epfl.ch` (EPFL users only):
+
+```{docker-compose.yml}
+services:
+  servers_registry:
+    image: mallorywittwerepfl/imaging-server-kit:registry
+    ports:
+      - "8000:8000"
+  rembg:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
+    depends_on:
+      - servers_registry
+  skimage-log:
+    image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-skimage-log:latest
+    depends_on:
+      - servers_registry
+```
+
+Start the server with
+
+```
+docker compose up
+```
+
+The server should be accessible at http://localhost:8000.
+
+**Build the docker images yourself**
+
+To build the algorithm server images yourself (e.g. if you are not from EPFL), see [Reference Deployment](https://github.com/Imaging-Server-Kit/serverkit-deploy-docker).
+
+**Create a server for your project**
+
+To learn how to create a server for your project, see [Algorithm Server Template](https://github.com/Imaging-Server-Kit/cookiecutter-serverkit).
+
+### Python client
+
+Once the server is running, connect to it and run algorithms from Python:
+
+```python
+from imaging_server_kit import Client
+
+client = Client("http://localhost:8000")
+
+print(client.algorithms)
+# [`rembg`, `stardist`, `cellpose`]
+
+algo_output = client.run_algorithm(
+    algorithm="rembg",
+    image=(...),
+    rembg_model_name="silueta",
+)
+```
+
+### Napari plugin
+
+Once the server is running, use the [Napari Server Kit](https://github.com/Imaging-Server-Kit/napari-serverkit) plugin to connect to it and run algorithms in Napari.
+
+### QuPath extension
+
+Once the server is running, use the [QuPath Extension Server Kit](https://github.com/Imaging-Server-Kit/qupath-extension-serverkit) to connect to it and run algorithms from within QuPath.
+
+## Install locally
+
+Install the `imaging-server-kit` package with `pip`:
+
+```
+pip install imaging-server-kit
+```
+
+or clone the project and install the development version:
+
+```
+git clone https://github.com/Imaging-Server-Kit/imaging-server-kit.git
+cd imaging-server-kit
+pip install -e .
+```
+
+## Build with `docker`
+
+Build the `imaging-server-kit` docker image for a specific Python version:
+
+```
+docker build --build-arg PYTHON_VERSION=3.9 -t imaging-server-kit:3.9 .
+```
+
+Run [build.sh](./build.sh) to build docker images for Python 3.9, 3.10, 3.11, GPU and the server kit registry:
+
+```
+bash ./build.sh
+```
+
+## 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-0.0.3/build.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+PYTHON_VERSIONS=("3.9" "3.10" "3.11")
+
+for version in "${PYTHON_VERSIONS[@]}"; do
+  echo "Building image for Python $version..."
+  docker build --build-arg PYTHON_VERSION=$version -t imaging-server-kit:$version .
+done
+
+# echo "Building image for Python 3.9, GPU-compatible..."
+# docker build -t imaging-server-kit:gpu --file Dockerfile-GPU .
+
+echo "Building image for Python 3.9, serverkit registry..."
+docker build -t imaging-server-kit:registry --file Dockerfile-registry .

{imaging_server_kit-0.0.1 → imaging_server_kit-0.0.3}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "imaging-server-kit"
 dynamic = ["version"]
-description = "Run image processing algorithms in a FastAPI server."
+description = "Deploy image processing algorithms in FastAPI servers. "
 readme = "README.md"
 requires-python = ">=3.9"
 license = { file = "LICENSE" }
@@ -9,12 +9,15 @@ authors = [{ name = "Mallory Wittwer", email = "mallory.wittwer@epfl.ch" }]
 
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
     "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
     "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
     "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",
 ]
 
@@ -25,6 +28,13 @@ dependencies = [
     "tifffile",
     "numpy",
     "scikit-image",
+    "geojson",
+    "jinja2",  # For the /info route
+    "pyyaml",  # For the /info route
+    "dash",  # For the dash app
+    "dash-bootstrap-components",  # For the dash app
+    "a2wsgi",  # For the dash app
+    "pytest",  # For testing
 ]
 
 [project.urls]

imaging_server_kit-0.0.3/src/imaging_server_kit/__init__.py

@@ -0,0 +1,24 @@
+from ._version import version as __version__
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+from imaging_server_kit.client import Client
+from imaging_server_kit.server import Server, Parameters
+from imaging_server_kit.registry import Registry
+from imaging_server_kit.encoding import encode_contents, decode_contents
+from imaging_server_kit.serialization import (
+    serialize_result_tuple,
+    deserialize_result_tuple,
+)
+from imaging_server_kit.geometry import (
+    mask2features,
+    features2mask,
+    boxes2features,
+    features2boxes,
+    points2features,
+    features2points,
+    vectors2features,
+    features2vectors,
+)

{imaging_server_kit-0.0.1 → imaging_server_kit-0.0.3}/src/imaging_server_kit/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.1'
-__version_tuple__ = version_tuple = (0, 0, 1)
+__version__ = version = '0.0.3'
+__version_tuple__ = version_tuple = (0, 0, 3)

imaging_server_kit-0.0.3/src/imaging_server_kit/assets/style.css

@@ -0,0 +1,108 @@
+body {
+    padding: 0;
+    margin: 0;
+    background-color: rgb(40, 40, 40);
+    color: white;
+    height: 100vh;
+    display: flex;
+    flex-direction: column;
+}
+
+.main-container {
+    height: 100vh;
+    display: flex;
+    flex-direction: column;
+    /* background-color: orange; */
+}
+
+header {
+    margin: 10px 0px;
+    text-align: center;
+    height: 120px;
+    line-height: 120px;
+}
+
+footer {
+    margin: 10px 0px;
+    text-align: center;
+    height: 120px;
+    line-height: 120px;
+}
+
+.main-row {
+    display: flex;
+    flex: 1 1;
+    overflow: auto;
+    width: 100%;
+    margin: 10px;
+    margin-left: 0px;
+    /* background-color: purple; */
+}
+
+.col {
+    padding: 0;
+}
+
+.parameters-column,
+.layer-column,
+.graph-column {
+    margin: 0 !important;
+    padding: 15px;
+    background-color: rgb(50, 50, 50);
+    margin-bottom: 0px;
+    height: 100%;
+    overflow: auto;
+}
+
+.layer-column {
+    /* flex: 0 1 400px; */
+    /* background-color: blue; */
+}
+
+.parameters-column {
+    /* flex: 0 1 400px; */
+    min-width: 400px;
+    /* background-color: green; */
+}
+
+.graph-column {
+    padding: 0px;
+    margin: 0;
+    flex: 1;
+    min-width: 800px;
+    /* background-color: orange; */
+}
+
+
+.layer-column .btn-secondary,
+.parameters-column .btn-primary {
+    width: 100%;
+    margin-top: 10px;
+}
+
+.dash-dropdown * {
+    background-color: rgb(70, 70, 70);
+    color: white;
+}
+
+.dash-dropdown .Select-value-label {
+    color: white !important;
+}
+
+.upload-data {
+    background-color: rgb(0, 0, 0);
+    border: 1px dashed rgb(240, 240, 240);
+    padding: 10px;
+    text-align: center;
+}
+
+.graph-container {
+    background-color: burlywood;
+    flex: 1;
+    height: 90%;
+}
+
+#graph {
+    background-color: rgb(0, 0, 0);
+    height: 100%;
+}