imaging-server-kit 0.0.1__tar.gz → 0.0.2__tar.gz

imaging_server_kit-0.0.2/.dockerignore

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

imaging_server_kit-0.0.2/.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-0.0.2/.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-0.0.2}/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-0.0.2}/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-0.0.2/Dockerfile-registry

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

{imaging_server_kit-0.0.1 → imaging_server_kit-0.0.2}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: imaging-server-kit
-Version: 0.0.1
-Summary: Run image processing algorithms in a FastAPI server.
+Version: 0.0.2
+Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
         All rights reserved.
@@ -34,12 +34,15 @@ License: Copyright (c) 2024, EPFL
 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: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Processing
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
@@ -50,6 +53,13 @@ Requires-Dist: python-multipart
 Requires-Dist: tifffile
 Requires-Dist: numpy
 Requires-Dist: scikit-image
+Requires-Dist: geojson
+Requires-Dist: docker
+Requires-Dist: jinja2
+Requires-Dist: pyyaml
+Requires-Dist: dash
+Requires-Dist: dash-bootstrap-components
+Requires-Dist: pytest
 
 ![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
 # 🪐 Imaging Server Kit

imaging_server_kit-0.0.2/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-0.0.2}/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",
+    "docker",  # For the autostartup regsitry
+    "jinja2",  # For the /info route
+    "pyyaml",  # For the /info route
+    "dash",  # For the dash app
+    "dash-bootstrap-components",  # For the dash app
+    "pytest",  # For testing
 ]
 
 [project.urls]

imaging_server_kit-0.0.2/src/imaging_server_kit/__init__.py

@@ -0,0 +1,20 @@
+from imaging_server_kit._version import __version__
+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.autostartup_registry import AutoStartupRegistry
+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-0.0.2}/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 = '0.0.2'
+__version_tuple__ = version_tuple = (0, 0, 2)

imaging_server_kit-0.0.2/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%;
+}

imaging_server_kit-0.0.2/src/imaging_server_kit/autostartup_registry.py

@@ -0,0 +1,58 @@
+from fastapi import FastAPI
+import docker
+
+class AutoStartupRegistry:
+    def __init__(self, algo_servers) -> None:
+        self.algo_servers = algo_servers
+        self.app = FastAPI()
+        self.app.on_event("shutdown")(self.stop_all_algorithm_containers)  # This doesn't work.
+        self.docker_client = docker.from_env()
+        self.services = {}
+        self.register_routes()
+    
+    def register_routes(self):
+        @self.app.get("/")
+        def home():
+            return list_services()
+
+        @self.app.get("/services")
+        def list_services():
+            return {"services": list(self.services.keys())}
+            
+        @self.app.get("/{algorithm}")
+        def get_algorithm_url(algorithm):
+            if algorithm not in self.services.keys():
+                container_url = self.start_algorithm_container(algorithm)
+            else:
+                container_url = self.services.get(algorithm).get("url")
+            return {"url": container_url}
+        
+    def start_algorithm_container(self, algorithm):
+        algorithm_server_image = self.algo_servers[algorithm].get('image')
+
+        port = self.algo_servers[algorithm].get('port')
+
+        container = self.docker_client.containers.run(
+            image=algorithm_server_image,
+            ports={"8000/tcp": port},
+            detach=True,
+            remove=True,
+            name=f"serverkit-server-{algorithm}"
+        )
+
+        container_url = f"http://localhost:{port}"
+
+        self.services[algorithm] = {
+            "container": container,
+            "url": container_url,
+        }
+
+        return container_url
+
+    def stop_algorithm_container(self, algorithm):
+        container = self.services[algorithm].get("container")
+        container.stop()
+    
+    def stop_all_algorithm_containers(self):
+        for algorithm in self.services.keys():
+            self.stop_algorithm_container(algorithm)    

imaging_server_kit-0.0.2/src/imaging_server_kit/client.py

@@ -0,0 +1,131 @@
+import requests
+from typing import List, Dict, Tuple
+import numpy as np
+import imaging_server_kit as serverkit
+from imaging_server_kit.errors import (
+    AlgorithmNotFoundError,
+    AlgorithmServerError,
+    InvalidAlgorithmParametersError,
+    ServerRequestError,
+)
+
+
+class Client:
+    def __init__(self, server_url: str = "") -> None:
+        self._server_url = server_url
+        self._algorithms = {}
+        if server_url != "":
+            self.connect(server_url)
+
+    def connect(self, server_url: str) -> None:
+        self.server_url = server_url
+        endpoint = f"{self.server_url}/services"
+        try:
+            response = requests.get(endpoint)
+        except requests.exceptions.RequestException as e:
+            raise ServerRequestError(endpoint, e)
+
+        if response.status_code == 200:
+            services = response.json().get("services")
+            self.algorithms = services
+        else:
+            raise AlgorithmServerError(response.status_code, response.json())
+
+    @property
+    def server_url(self) -> str:
+        return self._server_url
+
+    @server_url.setter
+    def server_url(self, server_url: str):
+        self._server_url = server_url
+
+    @property
+    def algorithms(self) -> Dict[str, str]:
+        return self._algorithms
+
+    @algorithms.setter
+    def algorithms(self, algorithms: Dict[str, str]):
+        self._algorithms = algorithms
+
+    def run_algorithm(self, algorithm=None, **algo_params) -> List[Tuple]:
+        algorithm = self._validate_algorithm(algorithm)
+        algo_params_encoded = self._encode_numpy_parameters(algo_params)
+
+        try:
+            endpoint = f"{self.server_url}/{algorithm}/"
+            response = requests.post(
+                endpoint,
+                json=algo_params_encoded,
+                headers={
+                    "Content-Type": "application/json",
+                    "accept": "application/json",
+                },
+            )
+        except requests.exceptions.RequestException as e:
+            raise ServerRequestError(endpoint, e)
+
+        if response.status_code == 201:
+            return serverkit.deserialize_result_tuple(response.json())
+        elif response.status_code == 422:
+            raise InvalidAlgorithmParametersError(response.status_code, response.json())
+        else:
+            raise AlgorithmServerError(response.status_code, response.json())
+
+    def get_algorithm_parameters(self, algorithm=None) -> Dict:
+        algorithm = self._validate_algorithm(algorithm)
+
+        endpoint = f"{self.server_url}/{algorithm}/parameters"
+
+        try:
+            response = requests.get(endpoint)
+        except requests.exceptions.RequestException as e:
+            raise ServerRequestError(endpoint, e)
+        
+        if response.status_code == 200:
+            return response.json()
+        else:
+            raise AlgorithmServerError(response.status_code, response.json())
+
+    def get_sample_images(
+        self, algorithm=None, first_only: bool = False
+    ) -> List["np.ndarray"]:
+        algorithm = self._validate_algorithm(algorithm)
+
+        endpoint = f"{self.server_url}/{algorithm}/sample_images"
+        
+        try:
+            response = requests.get(endpoint)
+        except requests.exceptions.RequestException as e:
+            raise ServerRequestError(endpoint, e)
+
+        if response.status_code == 200:
+            images = []
+            for content in response.json().get("sample_images"):
+                encoded_image = content.get("sample_image")
+                image = serverkit.decode_contents(encoded_image)
+                images.append(image)
+                if first_only:
+                    return image
+            return images
+        else:
+            print(
+                f"Error status while attempting to get algorithm sample images: {response.status_code}"
+            )
+            return -1
+
+    def _validate_algorithm(self, algorithm=None) -> str:
+        if algorithm is None:
+            if len(self.algorithms) > 0:
+                algorithm = self.algorithms[0]
+            else:
+                raise AlgorithmNotFoundError(algorithm)
+        else:
+            if algorithm not in self.algorithms:
+                raise AlgorithmNotFoundError(algorithm)
+        return algorithm
+
+    def _encode_numpy_parameters(self, algo_params: dict) -> dict:
+        for param in algo_params:
+            if isinstance(algo_params[param], np.ndarray):
+                algo_params[param] = serverkit.encode_contents(algo_params[param])
+        return algo_params

imaging_server_kit-0.0.2/src/imaging_server_kit/errors.py

@@ -0,0 +1,41 @@
+class AlgorithmNotFoundError(Exception):
+    """Exception raised when a specified algorithm is not found."""
+
+    def __init__(self, algorithm_name, message="Algorithm not found"):
+        self.algorithm_name = algorithm_name
+        self.message = f"{message}: {algorithm_name}"
+        super().__init__(self.message)
+
+
+class AlgorithmServerError(Exception):
+    """Exception raised when a request to an algorithm server returns an unexpected status code."""
+
+    def __init__(self, status_code, response_body, message="Algorithm server returned an unexpected status_code"):
+        self.status_code = status_code
+        self.response_body = response_body
+        self.message = f"{message}: {status_code}\nResponse body: {response_body}"
+        super().__init__(self.message)
+
+
+class InvalidAlgorithmParametersError(Exception):
+    """Exception raised when a request to an algorithm server is made with invalid algorithm parameters."""
+
+    def __init__(self, status_code, response_body, message="Algorithm parameters were invalidated by the server"):
+        self.status_code = status_code
+        self.response_body = response_body
+        pydantic_details = response_body.get("detail")[0]
+        pydantic_validation_msg = pydantic_details.get("msg")
+        pydantic_failing_param = pydantic_details.get("loc")[1]
+        pydantic_failing_param_value = pydantic_details.get("input")
+        self.message = f"{message}: Parameter: {pydantic_failing_param}. {pydantic_validation_msg}. Received: {pydantic_failing_param_value}."
+        super().__init__(self.message)
+
+
+class ServerRequestError(Exception):
+    """Exception raised when HTTP requests fail."""
+
+    def __init__(self, url: str, error: Exception, message="Request to server failed"):
+        self.url = url
+        self.error = error
+        self.message = f"{message} ({url=}): {error}"
+        super().__init__(self.message)