imaging-server-kit 0.0.4__tar.gz → 0.0.5__tar.gz

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: imaging-server-kit
-Version: 0.0.4
+Version: 0.0.5
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -31,8 +31,8 @@ License: Copyright (c) 2024, EPFL
         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
+Project-URL: homepage, https://github.com/Imaging-Server-Kit/imaging-server-kit
+Project-URL: repository, https://github.com/Imaging-Server-Kit/imaging-server-kit
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: BSD License
@@ -53,6 +53,8 @@ Requires-Dist: python-multipart
 Requires-Dist: tifffile
 Requires-Dist: numpy
 Requires-Dist: scikit-image
+Requires-Dist: opencv-contrib-python-headless
+Requires-Dist: imantics
 Requires-Dist: geojson
 Requires-Dist: jinja2
 Requires-Dist: pyyaml
@@ -90,9 +92,10 @@ All of these algorithm servers can be installed locally or built and run with do
 ```{docker-compose.yml}
 services:
   servers_registry:
-    image: mallorywittwerepfl/imaging-server-kit:registry
+    image: mallorywittwerepfl/imaging-server-kit:latest
     ports:
       - "8000:8000"
+    command: python3 start_registry.py
   rembg:
     image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
     depends_on:

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/README.md

@@ -27,9 +27,10 @@ All of these algorithm servers can be installed locally or built and run with do
 ```{docker-compose.yml}
 services:
   servers_registry:
-    image: mallorywittwerepfl/imaging-server-kit:registry
+    image: mallorywittwerepfl/imaging-server-kit:latest
     ports:
       - "8000:8000"
+    command: python3 start_registry.py
   rembg:
     image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
     depends_on:

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/pyproject.toml

@@ -28,6 +28,8 @@ dependencies = [
     "tifffile",
     "numpy",
     "scikit-image",
+    "opencv-contrib-python-headless",
+    "imantics",
     "geojson",
     "jinja2",  # For the /info route
     "pyyaml",  # For the /info route
@@ -38,8 +40,8 @@ dependencies = [
 ]
 
 [project.urls]
-homepage = "https://gitlab.com/epfl-center-for-imaging/imaging-server-kit"
-repository = "https://gitlab.com/epfl-center-for-imaging/imaging-server-kit"
+homepage = "https://github.com/Imaging-Server-Kit/imaging-server-kit"
+repository = "https://github.com/Imaging-Server-Kit/imaging-server-kit"
 
 [build-system]
 requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm"]

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit/__init__.py

@@ -14,7 +14,9 @@ from imaging_server_kit.serialization import (
 )
 from imaging_server_kit.geometry import (
     mask2features,
+    instance_mask2features,
     features2mask,
+    features2instance_mask,
     boxes2features,
     features2boxes,
     points2features,

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit/_version.py

@@ -1,8 +1,13 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
 else:
     VERSION_TUPLE = object
@@ -12,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4'
-__version_tuple__ = version_tuple = (0, 0, 4)
+__version__ = version = '0.0.5'
+__version_tuple__ = version_tuple = (0, 0, 5)

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit/geometry.py

@@ -1,43 +1,83 @@
 from typing import List
-from skimage.measure import find_contours
 from skimage.draw import polygon2mask
 from geojson import Feature, Polygon, Point, LineString
 import numpy as np
+from imantics import Mask
 
 
-def mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
+def instance_mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
     """
     Args:
         segm_mask: Segmentation mask with the background pixels set to zero and the pixels assigned to a segmented
-         object set to an int value
+         object instance set to an int value
 
     Returns:
         A list containing the contours of each object as a geojson.Feature
     """
     features = []
     indices = np.unique(segmentation_mask)
-    indices = np.delete(indices, indices == 0)  # remove background
+    indices = indices[indices != 0] # remove background
 
     if indices.size == 0:
         return features
+    
+    for detection_id in indices:
+        mask = segmentation_mask == int(detection_id)
+        polygons = Mask(mask).polygons()
+        for contour in polygons.points:
+            coords = np.array(contour)
+            coords = np.vstack([coords, coords[0]])  # Close the polygon for QuPath
+            geom = Polygon(coordinates=[coords.tolist()])
+            feature = Feature(
+                geometry=geom, 
+                properties={
+                    "Detection ID": int(detection_id), 
+                    "Class": 1
+                }
+            )
+            features.append(feature)
+
+    return features
+
 
-    # TODO: This is really inefficient for big images! Will need to improve it.
-    for i in indices.tolist():
-        mask = np.array(segmentation_mask == i)
-        mask = np.pad(mask > 0, 1)
-        contours_find = find_contours(mask, 0.5)
-        for detection_id, contour in enumerate(contours_find):
-            contour -= 1  # reset padding
-            contour_as_numpy = contour[:, np.argsort([1, 0])]  # Fix XY
-            geom = Polygon([contour_as_numpy.tolist()])
-            features.append(Feature(geometry=geom, properties={"Detection ID": detection_id, "Class": i}))
+def mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
+    """
+    Args:
+        segm_mask: Segmentation mask with the background pixels set to zero and the pixels assigned to a segmented 
+        class set to an int value
+
+    Returns:
+        A list containing the contours of each object as a geojson.Feature
+    """
+    features = []
+    indices = np.unique(segmentation_mask)
+    indices = indices[indices != 0] # remove background
+
+    if indices.size == 0:
+        return features
+    
+    for pixel_class in indices:
+        mask = segmentation_mask == int(pixel_class)
+        polygons = Mask(mask).polygons()
+        for detection_id, contour in enumerate(polygons.points, start=1):
+            coords = np.array(contour)
+            coords = np.vstack([coords, coords[0]])  # Close the polygon for QuPath
+            geom = Polygon(coordinates=[coords.tolist()])
+            feature = Feature(
+                geometry=geom, 
+                properties={
+                    "Detection ID": detection_id, 
+                    "Class": pixel_class
+                }
+            )
+            features.append(feature)
 
     return features
 
 
 def features2mask(features, image_shape):
     segmentation_mask = np.zeros(image_shape, dtype=np.uint16)
-    for idx, feature in enumerate(features):
+    for feature in features:
         feature_coordinates = np.array(feature["geometry"]["coordinates"])
         feature_coordinates = np.squeeze(feature_coordinates)
         feature_coordinates = feature_coordinates[:, ::-1]  # Invert XY
@@ -48,6 +88,19 @@ def features2mask(features, image_shape):
     return segmentation_mask
 
 
+def features2instance_mask(features, image_shape):
+    segmentation_mask = np.zeros(image_shape, dtype=np.uint16)
+    for feature in features:
+        feature_coordinates = np.array(feature["geometry"]["coordinates"])
+        feature_coordinates = np.squeeze(feature_coordinates)
+        feature_coordinates = feature_coordinates[:, ::-1]  # Invert XY
+        feature_mask = polygon2mask(image_shape, feature_coordinates)
+        feature_properites = feature.get("properties")
+        feature_id = feature_properites.get("Detection ID")
+        segmentation_mask[feature_mask] = feature_id
+    return segmentation_mask
+
+
 def boxes2features(boxes: np.ndarray) -> List[Feature]:
     """
     Convert an array of bounding boxes to a list of geojson-like features.

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit/serialization.py

@@ -72,6 +72,10 @@ def serialize_result_tuple(result_data_tuple: List[Tuple]) -> List[Dict]:
             data = data.astype(np.uint16)
             features = serverkit.mask2features(data)
             data_params['image_shape'] = data.shape
+        elif data_type == "instance_mask":
+            data = data.astype(np.uint16)
+            features = serverkit.instance_mask2features(data)
+            data_params['image_shape'] = data.shape
         elif data_type == "labels3d":
             features = serverkit.encode_contents(data.astype(np.uint16))
         elif data_type == "points":
@@ -85,8 +89,13 @@ def serialize_result_tuple(result_data_tuple: List[Tuple]) -> List[Dict]:
             features = serverkit.vectors2features(data)
         elif data_type == "tracks":
             features = serverkit.encode_contents(data.astype(np.float32))
+        elif data_type == "class":
+            features = data  # A simple string
+        elif data_type == "text":
+            features = data  # A text string
         else:
             print(f"Unknown data_type: {data_type}")
+            features = None
         
         serialized_results.append(
             {
@@ -114,6 +123,9 @@ def deserialize_result_tuple(serialized_results: List[Dict]) -> List[Tuple]:
         elif data_type == "labels":
             image_shape = data_params.pop('image_shape')
             data = serverkit.features2mask(features, image_shape)
+        elif data_type == "instance_mask":
+            image_shape = data_params.pop('image_shape')
+            data = serverkit.features2instance_mask(features, image_shape)
         elif data_type == "labels3d":
             data = serverkit.decode_contents(features).astype(int)
         elif data_type == "points":
@@ -126,6 +138,10 @@ def deserialize_result_tuple(serialized_results: List[Dict]) -> List[Tuple]:
             data = serverkit.features2vectors(features)
         elif data_type == "tracks":
             data = serverkit.decode_contents(features).astype(float)
+        elif data_type == "class":
+            data = features  # A simple string
+        elif data_type == "text":
+            data = features  # A text string
         else:
             print(f"Unknown data_type: {data_type}")
 

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit/server.py

@@ -45,10 +45,20 @@ class Parameters(BaseModel):
 
 
 class Server:
-    def __init__(self, algorithm_name: str, parameters_model: Type[BaseModel]):
+    def __init__(
+        self,
+        algorithm_name: str,
+        parameters_model: Type[BaseModel],
+        metadata_file: str = None,
+    ):
         self.algorithm_name = algorithm_name
         self.parameters_model = parameters_model
 
+        if metadata_file is None:
+            self.metadata_file = "metadata.yaml"
+        else:
+            self.metadata_file = metadata_file
+
         self.app = FastAPI(title=algorithm_name, lifespan=self.lifespan)
         self.app.mount("/static", StaticFiles(directory=str(static_dir)), name="static")
 
@@ -117,7 +127,7 @@ class Server:
 
         @self.app.get(f"/{self.algorithm_name}/info", response_class=HTMLResponse)
         def info(request: Request):
-            algo_info = load_from_yaml("metadata.yaml")
+            algo_info = load_from_yaml(self.metadata_file)
             algo_params_schema = get_algo_params()
             algo_params = parse_algo_params_schema(algo_params_schema)
             return templates.TemplateResponse(
@@ -129,19 +139,30 @@ class Server:
                 },
             )
 
-        @self.app.post(f"/{self.algorithm_name}/process", status_code=status.HTTP_201_CREATED)
+        @self.app.post(
+            f"/{self.algorithm_name}/process", status_code=status.HTTP_201_CREATED
+        )
         async def run_algo(algo_params: self.parameters_model):
             try:
-                result_data_tuple = await asyncio.wait_for(self._run_algorithm(**algo_params.dict()), timeout=60)
-            except asyncio.TimeoutError:  # This works but doesn't actually kill the process... we need something else to terminate it
-                raise HTTPException(status_code=504, detail="Request timeout during processing.")
+                result_data_tuple = await asyncio.wait_for(
+                    self._run_algorithm(**algo_params.dict()), timeout=600
+                )
+            except (
+                asyncio.TimeoutError
+            ):  # This works but doesn't actually kill the process... we need something else to terminate it
+                raise HTTPException(
+                    status_code=504, detail="Request timeout during processing."
+                )
             try:
-                serialized_results = await asyncio.wait_for(self._serialize_result_tuple(result_data_tuple), timeout=10)
+                serialized_results = await asyncio.wait_for(
+                    self._serialize_result_tuple(result_data_tuple), timeout=600
+                )
             except asyncio.TimeoutError:
-                raise HTTPException(status_code=504, detail="Request timeout during serialization.")
-            
-            return serialized_results
+                raise HTTPException(
+                    status_code=504, detail="Request timeout during serialization."
+                )
 
+            return serialized_results
 
         @self.app.get(f"/{self.algorithm_name}/parameters", response_model=dict)
         def get_algo_params():
@@ -156,15 +177,17 @@ class Server:
             return {"sample_images": encoded_images}
 
     async def _serialize_result_tuple(self, result_data_tuple):
-        serialized_results = await asyncio.to_thread(serverkit.serialize_result_tuple, result_data_tuple)
+        serialized_results = await asyncio.to_thread(
+            serverkit.serialize_result_tuple, result_data_tuple
+        )
         return serialized_results
-    
+
     async def _run_algorithm(self, **algo_params):
         result_data_tuple = await asyncio.to_thread(self.run_algorithm, **algo_params)
         return result_data_tuple
-    
+
     def load_sample_images(self) -> List["np.ndarray"]:
         raise NotImplementedError("Subclasses should implement this method")
-    
+
     def run_algorithm(self, **algo_params) -> List[Tuple]:
         raise NotImplementedError("Subclasses should implement this method")

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: imaging-server-kit
-Version: 0.0.4
+Version: 0.0.5
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -31,8 +31,8 @@ License: Copyright (c) 2024, EPFL
         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
+Project-URL: homepage, https://github.com/Imaging-Server-Kit/imaging-server-kit
+Project-URL: repository, https://github.com/Imaging-Server-Kit/imaging-server-kit
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: BSD License
@@ -53,6 +53,8 @@ Requires-Dist: python-multipart
 Requires-Dist: tifffile
 Requires-Dist: numpy
 Requires-Dist: scikit-image
+Requires-Dist: opencv-contrib-python-headless
+Requires-Dist: imantics
 Requires-Dist: geojson
 Requires-Dist: jinja2
 Requires-Dist: pyyaml
@@ -90,9 +92,10 @@ All of these algorithm servers can be installed locally or built and run with do
 ```{docker-compose.yml}
 services:
   servers_registry:
-    image: mallorywittwerepfl/imaging-server-kit:registry
+    image: mallorywittwerepfl/imaging-server-kit:latest
     ports:
       - "8000:8000"
+    command: python3 start_registry.py
   rembg:
     image: registry.rcp.epfl.ch/imaging-server-kit/serverkit-rembg:latest
     depends_on:

{imaging_server_kit-0.0.4 → imaging_server_kit-0.0.5}/src/imaging_server_kit.egg-info/requires.txt

@@ -4,6 +4,8 @@ python-multipart
 tifffile
 numpy
 scikit-image
+opencv-contrib-python-headless
+imantics
 geojson
 jinja2
 pyyaml