imaging-server-kit 0.1.0__tar.gz → 0.1.2__tar.gz

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.1.0
+Version: 0.1.2
 Summary: Convert image processing functions to GUIs, FastAPI servers, and more.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -52,10 +52,11 @@ Requires-Dist: numpy
 Requires-Dist: tifffile
 Requires-Dist: tqdm
 Requires-Dist: pydantic>=2.0
-Requires-Dist: scikit-image
+Requires-Dist: scikit-image[optional]
 Requires-Dist: jinja2
 Requires-Dist: PyYAML
 Requires-Dist: cookiecutter
+Requires-Dist: opencv-contrib-python-headless
 Requires-Dist: imantics
 Requires-Dist: geojson
 Requires-Dist: fastapi

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/docs/sections/04_multialgo.ipynb

@@ -80,8 +80,14 @@
     "\n",
     "## Next steps\n",
     "\n",
-    "In the next section, we will explore the concept of streamed inference in Imaging Server Kit."
+    "In the next section, we will explore the concept of *live updates* in Imaging Server Kit."
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "57909c69",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/docs/sections/05_streams.ipynb

@@ -5,9 +5,9 @@
    "id": "9ec31672",
    "metadata": {},
    "source": [
-    "# Streamed inference\n",
+    "# Live updates\n",
     "\n",
-    "Streamed inference allows an algorithm to send **intermediate outputs** to the client application before it has finished running. This makes it possible for user interfaces, such as the Napari Viewer, to update in real time.\n",
+    "Algorithms can send **intermediate outputs** to the client application before they have finished running. This makes it possible for user interfaces, such as the Napari Viewer, to update in real time.\n",
     "\n",
     "For example, you might \"stream\":\n",
     "\n",
@@ -56,7 +56,7 @@
    "id": "c5f4b3d1",
    "metadata": {},
    "source": [
-    "Running this algorithm in Napari results in a \"streamed output\" showcasing a segmentation mask progressively updating as the threshold value increases.\n",
+    "When running this algorithm in Napari, the displayed segmentation mask progressively gets updated as the threshold value increases.\n",
     "\n",
     "<video width=512 controls loop autoplay>\n",
     "  <source src=\"../_static/progressive_threshold.mp4\" type=\"video/mp4\">\n",

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/pyproject.toml

@@ -27,11 +27,12 @@ dependencies = [
     "tifffile",  # To encode/decode
     "tqdm",
     "pydantic>=2.0",
-    "scikit-image",  # To imread samples and run demo examples
+    "scikit-image[optional]",  # To imread samples and run demo examples
     "jinja2",  # To template the info endpoint
     "PyYAML",  # To load the metadata yaml file
     "cookiecutter",  # To start from a template
-    "imantics",  # To convert masks to features for QuPath
+    "opencv-contrib-python-headless",  # We need this instead of opencv-python to be able to run servers in docker.
+    "imantics",  # To convert masks to features for QuPath. Comes with opencv-python.
     "geojson",  # To convert masks and points to features for QuPath 
     # Used in app
     "fastapi",

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.1.0'
-__version_tuple__ = version_tuple = (0, 1, 0)
+__version__ = version = '0.1.2'
+__version_tuple__ = version_tuple = (0, 1, 2)
 
-__commit_id__ = commit_id = 'g9cf654ced'
+__commit_id__ = commit_id = 'g7132691fd'

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/client.py

@@ -22,6 +22,9 @@ from imaging_server_kit.core.results import Results
 from imaging_server_kit.core.serialization import deserialize_results
 
 
+TIMEOUT_SEC = 3600  # Timeout for the /process route (in seconds)
+
+
 class Client(AlgorithmRunner):
     """Client to connect to and interact with algorithm servers.
     
@@ -181,7 +184,7 @@ class Client(AlgorithmRunner):
 
     def _run(self, algorithm: str, param_results: Results) -> Results:
         endpoint = f"{self.server_url}/{algorithm}/process"
-        with httpx.Client(base_url=self.server_url) as client:
+        with httpx.Client(base_url=self.server_url, timeout=TIMEOUT_SEC) as client:
             try:
                 response = client.post(
                     endpoint,

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/core/results.py

@@ -234,7 +234,7 @@ class Results(LayerStackBase):
                 return layer
 
     def update(
-        self, layer_name: str, updated_data: np.ndarray, updated_meta: Dict
+        self, layer_name: str, updated_data: Any, updated_meta: Dict
     ) -> Optional[DataLayer]:
         """Update the data and meta attributes of a layer."""
         layer = self.read(layer_name)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/demo/examples.py

@@ -50,7 +50,7 @@ def threshold_algo(image, threshold, dark_background):
         mask = image > thresh_rel
     else:
         mask = image <= thresh_rel
-    return sk.Mask(mask, name="Binary mask (manual)")
+    return sk.Mask(mask, name="Binarized image")
 
 
 ## Automatic threshold

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/template/cookiecutter.json

@@ -1,5 +1,5 @@
 {
-  "name": "Threshold",
+  "name": "threshold",
   "project_url": "https://github.com/scikit-image/scikit-image",
   "python_version": "3.9"
 }

imaging_server_kit-0.1.0/src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py → imaging_server_kit-0.1.2/src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/main.py

@@ -15,20 +15,20 @@ import imaging_server_kit as sk
     project_url="{{ cookiecutter.project_url }}",
     tags=["Segmentation"],
     parameters={
-        "image": sk.Image(dimensionality=[2, 3]),
+        "image": sk.Image(),
         "threshold": sk.Float(
             name="Threshold",
-            default=0.5,
-            min=0.0,
-            max=1.0,
-            step=0.1,
-            auto_call=True,
+            default=128,
+            min=0,
+            max=255,
+            step=1,
+            auto_call=False,
         ),
     },
     samples=[
         {
             "image": Path(__file__).parent / "samples" / "blobs.tif",
-            "threshold": 0.7,
+            "threshold": 140,
         }
     ],
 )

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_bool.py

@@ -36,9 +36,11 @@ class Bool(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return bool(data)
+    def serialize(cls, data: Optional[bool], client_origin: str):
+        if data is not None:
+            return bool(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return bool(serialized_data)
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str):
+        if serialized_data is not None:
+            return bool(serialized_data)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_boxes.py

@@ -1,4 +1,4 @@
-from typing import Dict, List, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 import numpy as np
 from geojson import Feature, Polygon
 
@@ -133,9 +133,12 @@ class Boxes(DataLayer):
         self.meta = merged_boxes_meta
 
     @classmethod
-    def serialize(cls, data, client_origin):
+    def serialize(cls, boxes: Optional[np.ndarray], client_origin: str) -> Optional[List[Feature]]:
+        if boxes is None:
+            return None
+        
         features = []
-        for i, box in enumerate(data):
+        for i, box in enumerate(boxes):
             coords = np.array(box)[:, ::-1]  # Invert XY
             coords = coords.tolist()
             coords.append(coords[0])  # Close the Polygon
@@ -149,15 +152,18 @@ class Boxes(DataLayer):
         return features
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
+    def deserialize(cls, serialized_data: Optional[List[Dict[str, Any]]], client_origin: str) -> Optional[np.ndarray]:
+        if serialized_data is None:
+            return None
         boxes = np.array(
             [feature["geometry"]["coordinates"] for feature in serialized_data]
         )
         boxes = np.array(
             [box[0] for box in boxes]
         )  # We get back a shape of (N, 1, 5, 2) - so we remove dim. 1
-        boxes = boxes[:, :-1]  # Remove the last element
-        boxes = boxes[:, :, ::-1]  # Invert XY
+        if len(boxes) > 0:
+            boxes = boxes[:, :-1]  # Remove the last element
+            boxes = boxes[:, :, ::-1]  # Invert XY
         return boxes
 
     @classmethod
@@ -175,4 +181,5 @@ class Boxes(DataLayer):
         assert isinstance(
             data, np.ndarray
         ), f"Boxes data ({type(data)}) is not a Numpy array"
+        
         assert len(data.shape) == 3, "Boxes data should have shape (N, 4, D)"

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_choice.py

@@ -51,9 +51,11 @@ class Choice(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return str(data)
+    def serialize(cls, data: Optional[str], client_origin: str):
+        if data is not None:
+            return str(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return str(serialized_data)
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str):
+        if serialized_data is not None:
+            return str(serialized_data)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_float.py

@@ -49,9 +49,11 @@ class Float(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return float(data)
+    def serialize(cls, data: Optional[float], client_origin: str):
+        if data is not None:
+            return float(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return float(serialized_data)
+    def deserialize(cls, serialized_data: Optional[float], client_origin: str):
+        if serialized_data is not None:
+            return float(serialized_data)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_image.py

@@ -94,11 +94,14 @@ class Image(DataLayer):
         # so that we can compute a running average.
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return encode_contents(data.astype(np.float32))
+    def serialize(cls, data: Optional[np.ndarray], client_origin: str):
+        if data is not None:
+            return encode_contents(data.astype(np.float32))
 
     @classmethod
-    def deserialize(cls, serialized_data: Union[np.ndarray, str], client_origin):
+    def deserialize(cls, serialized_data: Optional[Union[np.ndarray, str]], client_origin:str):
+        if serialized_data is None:
+            return None
         if isinstance(serialized_data, str):
             serialized_data = decode_contents(serialized_data)
         return serialized_data.astype(float)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_integer.py

@@ -50,9 +50,11 @@ class Integer(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return int(data)
+    def serialize(cls, data: Optional[int], client_origin: str):
+        if data is not None:
+            return int(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return int(serialized_data)
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str):
+        if serialized_data is not None:
+            return int(serialized_data)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_mask.py

@@ -242,17 +242,21 @@ class Mask(DataLayer):
             self.data[tile_slices] = mask_tile
 
     @classmethod
-    def serialize(cls, data, client_origin):
+    def serialize(cls, mask: Optional[np.ndarray], client_origin: str) -> Optional[Union[List[Feature], str]]:
+        if mask is None:
+            return None
         if client_origin == "Python/Napari":
-            features = encode_contents(data.astype(np.uint16))
+            features = encode_contents(mask.astype(np.uint16))
         elif client_origin == "Java/QuPath":
-            features = mask2features(data)
+            features = mask2features(mask)
         else:
             raise ValueError(f"Unrecognized client origin: {client_origin}")
         return features
 
     @classmethod
-    def deserialize(cls, serialized_data: Union[np.ndarray, str], client_origin):
+    def deserialize(cls, serialized_data: Optional[Union[np.ndarray, str]], client_origin: str) -> Optional[np.ndarray]:
+        if serialized_data is None:
+            return None
         if isinstance(serialized_data, str):
             if client_origin == "Python/Napari":
                 data = decode_contents(serialized_data).astype(int)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_notification.py

@@ -40,12 +40,14 @@ class Notification(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return str(data)
+    def serialize(cls, data: Optional[str], client_origin: str) -> Optional[str]:
+        if data is not None:
+            return str(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return str(serialized_data)
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str) -> Optional[str]:
+        if serialized_data is not None:
+            return str(serialized_data)
 
     def __str__(self) -> str:
         level = self.meta.get("level", "info")

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_null.py

@@ -35,11 +35,11 @@ class Null(DataLayer):
             self.validate_data(data, self.meta, self.constraints)
 
     @classmethod
-    def serialize(cls, data, client_origin):
+    def serialize(cls, data, client_origin: str):
         if data is not None:
             raise ValueError(f"Cannot serialize this object: {data}")
         return None
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
+    def deserialize(cls, serialized_data, client_origin: str):
         return None

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_paths.py

@@ -60,11 +60,14 @@ class Paths(DataLayer):
         return pixel_domain
 
     @classmethod
-    def serialize(cls, data: List[np.ndarray], client_origin):
-        return [encode_contents(arr.astype(np.float32)) for arr in data]
+    def serialize(cls, data: Optional[List[np.ndarray]], client_origin:str):
+        if data is not None:
+            return [encode_contents(arr.astype(np.float32)) for arr in data]
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str) -> Optional[List[np.ndarray]]:
+        if serialized_data is None:
+            return None
         data = []
         for f in serialized_data:
             if isinstance(f, str):

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_points.py

@@ -160,7 +160,9 @@ class Points(DataLayer):
         self.meta = merged_points_meta
 
     @classmethod
-    def serialize(cls, points: np.ndarray, client_origin: str):
+    def serialize(cls, points: Optional[np.ndarray], client_origin: str) -> Optional[Union[str, List[Feature]]]:
+        if points is None:
+            return None
         if client_origin == "Python/Napari":
             point_features = encode_contents(points.astype(np.float32))
         elif client_origin == "Java/QuPath":
@@ -170,12 +172,16 @@ class Points(DataLayer):
         return point_features
 
     @classmethod
-    def deserialize(cls, serialized_points: Union[np.ndarray, str], client_origin: str) -> np.ndarray:
+    def deserialize(cls, serialized_points: Optional[Union[np.ndarray, str]], client_origin: str) -> Optional[np.ndarray]:
+        if serialized_points is None:
+            return None
         if isinstance(serialized_points, str):
             if client_origin == "Python/Napari":
                 points = decode_contents(serialized_points).astype(float)
             else:
                 raise ValueError(f"Unrecognized client origin: {client_origin}")
+        else:
+            points = serialized_points
         return points
 
     @classmethod

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_string.py

@@ -36,9 +36,11 @@ class String(DataLayer):
         # TODO: implement string-specific properties, for example: max_length (could be validated).
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return str(data)
+    def serialize(cls, data: Optional[str], client_origin: str) -> Optional[str]:
+        if data is not None:
+            return str(data)
 
     @classmethod
-    def deserialize(cls, serialized_data, client_origin):
-        return str(serialized_data)
+    def deserialize(cls, serialized_data: Optional[str], client_origin: str) -> Optional[str]:
+        if serialized_data is not None:
+            return str(serialized_data)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_tracks.py

@@ -49,11 +49,14 @@ class Tracks(DataLayer):
         # TODO: Implement object-specific properties, like max_objects or min_track_length (could be validated).
 
     @classmethod
-    def serialize(cls, data, client_origin):
-        return encode_contents(data.astype(np.float32))
+    def serialize(cls, data, client_origin: str) -> Optional[str]:
+        if data is not None:
+            return encode_contents(data.astype(np.float32))
 
     @classmethod
-    def deserialize(cls, serialized_data: Union[np.ndarray, str], client_origin):
+    def deserialize(cls, serialized_data: Optional[Union[np.ndarray, str]], client_origin: str) -> Optional[np.ndarray]:
+        if serialized_data is None:
+            return None
         if isinstance(serialized_data, str):
             serialized_data = decode_contents(serialized_data)
         return serialized_data.astype(float)

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit/types/_vectors.py

@@ -1,4 +1,4 @@
-from typing import Dict, List, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 import numpy as np
 from geojson import Feature, LineString
 
@@ -141,7 +141,9 @@ class Vectors(DataLayer):
         self.meta = merged_vectors_meta
 
     @classmethod
-    def serialize(cls, vectors, client_origin):
+    def serialize(cls, vectors: Optional[np.ndarray], client_origin: str) -> Optional[List[Feature]]:
+        if vectors is None:
+            return None
         serialized_vectors = []
         vectors = vectors[:, :, ::-1]  # Invert XY
         for i, vector in enumerate(vectors):
@@ -158,7 +160,10 @@ class Vectors(DataLayer):
         return serialized_vectors
 
     @classmethod
-    def deserialize(cls, serialized_vectors, client_origin: str) -> np.ndarray:
+    def deserialize(cls, serialized_vectors: Optional[List[Dict[str, Any]]], client_origin: str) -> Optional[np.ndarray]:
+        if serialized_vectors is None:
+            return None
+        
         vectors_arr = np.array(
             [feature["geometry"]["coordinates"] for feature in serialized_vectors]
         )

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.1.0
+Version: 0.1.2
 Summary: Convert image processing functions to GUIs, FastAPI servers, and more.
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -52,10 +52,11 @@ Requires-Dist: numpy
 Requires-Dist: tifffile
 Requires-Dist: tqdm
 Requires-Dist: pydantic>=2.0
-Requires-Dist: scikit-image
+Requires-Dist: scikit-image[optional]
 Requires-Dist: jinja2
 Requires-Dist: PyYAML
 Requires-Dist: cookiecutter
+Requires-Dist: opencv-contrib-python-headless
 Requires-Dist: imantics
 Requires-Dist: geojson
 Requires-Dist: fastapi

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/SOURCES.txt

@@ -73,14 +73,14 @@ src/imaging_server_kit/demo/examples.py
 src/imaging_server_kit/demo/sample_images/blobs.tif
 src/imaging_server_kit/demo/sample_images/tracks.tif
 src/imaging_server_kit/template/cookiecutter.json
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.dockerignore
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/.gitignore
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/Dockerfile
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/README.md
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/docker-compose.yml
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/main.py
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/requirements.txt
-src/imaging_server_kit/template/serverkit-{{ cookiecutter.project_slug }}/samples/blobs.tif
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/.dockerignore
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/.gitignore
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/Dockerfile
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/README.md
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/docker-compose.yml
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/main.py
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/requirements.txt
+src/imaging_server_kit/template/serverkit-{{cookiecutter.name}}/samples/blobs.tif
 src/imaging_server_kit/types/__init__.py
 src/imaging_server_kit/types/_bool.py
 src/imaging_server_kit/types/_boxes.py

{imaging_server_kit-0.1.0 → imaging_server_kit-0.1.2}/src/imaging_server_kit.egg-info/requires.txt

@@ -2,10 +2,11 @@ numpy
 tifffile
 tqdm
 pydantic>=2.0
-scikit-image
+scikit-image[optional]
 jinja2
 PyYAML
 cookiecutter
+opencv-contrib-python-headless
 imantics
 geojson
 fastapi