imaging-server-kit 0.0.14__tar.gz → 0.0.16__tar.gz

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/.github/workflows/publish.yml

@@ -5,6 +5,9 @@ on:
     tags:
       - "v*"
 
+permissions:
+  contents: write
+
 jobs:
   publish:
     name: publish

imaging_server_kit-0.0.16/CITATION.cff

@@ -0,0 +1,17 @@
+cff-version: 1.2.0
+message: "If you use this software in the context of scientific publication, please cite it as below."
+authors:
+  - family-names: Wittwer
+    given-names: Mallory
+  - family-names: Andò
+    given-names: Edward
+  - family-names: Barthélemy
+    given-names: Maud
+  - family-names: Aymanns
+    given-names: Florian
+title: "Imaging Server Kit"
+version: 0.0.14
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.15673151
+date-released: 2025-06-16

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.14
+Version: 0.0.16
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -79,6 +79,8 @@ Dynamic: license-file
 
 Deploy image processing algorithms in FastAPI servers and easily run them from Napari, QuPath, and more.
 
+[![DOI](https://zenodo.org/badge/912741131.svg)](https://doi.org/10.5281/zenodo.15673151)
+
 ## Installation
 
 Install the `imaging-server-kit` package with `pip`:

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/README.md

@@ -3,6 +3,8 @@
 
 Deploy image processing algorithms in FastAPI servers and easily run them from Napari, QuPath, and more.
 
+[![DOI](https://zenodo.org/badge/912741131.svg)](https://doi.org/10.5281/zenodo.15673151)
+
 ## Installation
 
 Install the `imaging-server-kit` package with `pip`:

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/docs/index.md

@@ -47,4 +47,21 @@ pip install -e .
 
 ## License
 
-This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+This software is distributed under the terms of the [BSD-3](http://opensource.org/licenses/BSD-3-Clause) license.
+
+## Citing
+
+If you use `imaging-server-kit` in the context of scientific publication, you can cite it as below.
+
+BibTeX:
+
+```
+@software{mallory_wittwer_2025_15673152,
+  author       = {Mallory Wittwer and Edward Andò and Maud Barthélemy and Florian Aymanns},
+  title        = {Imaging-Server-Kit/imaging-server-kit: v0.0.14},
+  url          = {https://doi.org/10.5281/zenodo.15673152},
+  doi          = {10.5281/zenodo.15673152},
+  version      = {v0.0.14},
+  year         = 2025,
+}
+```

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/docs/sections/algorithm_server.md

@@ -50,6 +50,9 @@ The data tuples are inspired from Napari's [LayerDataTuple](https://napari.org/0
 | `"tracks"`        | Array of tracks in the Napari [Tracks](https://napari.org/stable/howtos/layers/tracks.html) format.    |
 | `"class"`         | A class label (for image classification).                                                              |
 | `"text"`          | A string of text (for example, for image captioning).                                                  |
+| `"notification"`  | A notification message (with levels `info`, `warning`, or `error`).                                    |
+| `"scalar"`        | A scalar value (e.g. `42`, `3.14`).                                                                    |
+| `"list"`          | A list of numeric and/or string values (e.g. `[42, 3.14, "cat"]`).                                     |
 
 The function can return multiple outputs, following the pattern:
 

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/examples/servers/serverkit-skimage-log/main.py

@@ -132,7 +132,7 @@ def skimage_log_server(
             (points, points_params, "points"),
         ]
     else:
-        return [("No points were detected.", {}, "text")]
+        return [("No points were detected.", {"level": "info"}, "notification")]
 
 
 if __name__ == "__main__":

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/examples/servers/serverkit-yolo/main.py

@@ -61,7 +61,7 @@ def yolo_detect_server(
 
     probabilities = results[0].boxes.conf.cpu().numpy()
     if len(probabilities) == 0:
-        return [("Nothing was detected", {}, "text")]
+        return [("Nothing was detected", {"level": "info"}, "notification")]
 
     box_results = results[0].boxes.xyxy.cpu().numpy().reshape((-1, 2, 2))
     classes_indeces = results[0].boxes.cls.cpu().numpy()

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.14'
-__version_tuple__ = version_tuple = (0, 0, 14)
+__version__ = version = '0.0.16'
+__version_tuple__ = version_tuple = (0, 0, 16)

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit/core/geometry.py

@@ -38,8 +38,7 @@ def mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
                 )
                 features.append(feature)
             except ValueError:
-                # TODO: not sure what to do when this happens (very occasionally)
-                print("Found an invalid polygon...")
+                print("Invalid polygon geometry.")
 
     return features
 
@@ -90,8 +89,7 @@ def instance_mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
                 )
                 features.append(feature)
             except ValueError:
-                # TODO: not sure what to do when this happens (very occasionally)
-                print("Found an invalid polygon...")
+                print("Invalid polygon geometry.")
 
     return features
 
@@ -175,15 +173,12 @@ def boxes2features(boxes: np.ndarray) -> List[Feature]:
     for i, box in enumerate(boxes):
         coords = np.array(box)[:, ::-1]  # Invert XY
         coords = coords.tolist()
-        coords.append(
-            coords[0]
-        )  # Add the first element at the end to close the Polygon
+        coords.append(coords[0])  # Close the Polygon
         try:
             geom = Polygon(coordinates=[coords], validate=True)
+            features.append(Feature(geometry=geom, properties={"Detection ID": i}))
         except ValueError:
-            print("Invalid box polygon found. Expected an array of shape (N, 4, D) representing the corners of the box.")
-            geom = None  # TODO: should we handle this better?
-        features.append(Feature(geometry=geom, properties={"Detection ID": i}))
+            print("Invalid box polygon geometry. Expected an array of shape (N, 4, D) representing the corners of the box.")
     return features
 
 
@@ -211,8 +206,11 @@ def points2features(points: np.ndarray) -> List[Feature]:
     features = []
     point_coords = np.array(points)[:, ::-1]  # Invert XY
     for i, point in enumerate(point_coords):
-        geom = Point(coordinates=[np.array(point).tolist()])
-        features.append(Feature(geometry=geom, properties={"Detection ID": i}))
+        try:
+            geom = Point(coordinates=[np.array(point).tolist()])
+            features.append(Feature(geometry=geom, properties={"Detection ID": i}))
+        except:
+            print("Invalid point geometry.")
     return features
 
 
@@ -242,8 +240,12 @@ def vectors2features(vectors: np.ndarray) -> List[Feature]:
         point_start = list(vector[0])
         point_end = list(vector[0] + vector[1])
         coords = [point_start, point_end]
-        geom = LineString(coordinates=coords)
-        features.append(Feature(geometry=geom, properties={"Detection ID": i}))
+        try:
+            geom = LineString(coordinates=coords)
+            features.append(Feature(geometry=geom, properties={"Detection ID": i}))
+        except ValueError:
+            print("Invalid line string geometry.")
+
     return features
 
 
@@ -255,6 +257,5 @@ def features2vectors(features):
     displacements = vectors_arr[:, 1] - origins
     vectors = np.stack((origins, displacements))
     vectors = np.rollaxis(vectors, 1)
-    print(f"{vectors.shape=}")
     vectors = vectors[:, :, ::-1]  # Invert XY
     return vectors

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit/core/serialization.py

@@ -106,6 +106,12 @@ def serialize_result_tuple(result_data_tuple: List[Tuple]) -> List[Dict]:
             features = data  # A simple string
         elif data_type == "text":
             features = data  # A text string
+        elif data_type == "notification":
+            features = data
+        elif data_type == "scalar":
+            features = data
+        elif data_type == "list":
+            features = data  # Lists of numeric/string values don't need to be encoded
         else:
             print(f"Unknown data_type: {data_type}")
             features = None
@@ -155,8 +161,15 @@ def deserialize_result_tuple(serialized_results: List[Dict]) -> List[Tuple]:
             data = features  # A simple string
         elif data_type == "text":
             data = features  # A text string
+        elif data_type == "notification":
+            data = features
+        elif data_type == "scalar":
+            data = features
+        elif data_type == "list":
+            data = features
         else:
             print(f"Unknown data_type: {data_type}")
+            data = features
 
         data_tuple = (data, data_params, data_type)
 

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit/core/server.py

@@ -40,7 +40,10 @@ def parse_algo_params_schema(algo_params_schema):
     algo_params = algo_params_schema.get("properties")
     required_params = algo_params_schema.get("required")
     for param in algo_params.keys():
-        algo_params[param]["required"] = param in required_params
+        if required_params is None:
+            algo_params[param]["required"] = False
+        else:
+            algo_params[param]["required"] = param in required_params
     return algo_params
 
 

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit/core/templates/index.html

@@ -11,7 +11,7 @@
 
 <body>
     <div class="container">
-        <h1>Running servers</h1>
+        <h1>Available algorithms</h1>
         {% for service in services %}
         <a href="/{{ service }}/info">
             <div class="card-product">

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.14
+Version: 0.0.16
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL
@@ -79,6 +79,8 @@ Dynamic: license-file
 
 Deploy image processing algorithms in FastAPI servers and easily run them from Napari, QuPath, and more.
 
+[![DOI](https://zenodo.org/badge/912741131.svg)](https://doi.org/10.5281/zenodo.15673151)
+
 ## Installation
 
 Install the `imaging-server-kit` package with `pip`:

{imaging_server_kit-0.0.14 → imaging_server_kit-0.0.16}/src/imaging_server_kit.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 .dockerignore
 .gitattributes
 .gitignore
+CITATION.cff
 Dockerfile
 Dockerfile-GPU
 LICENSE