imaging-server-kit 0.0.11__tar.gz → 0.0.12__tar.gz

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.11
+Version: 0.0.12
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.12}/docs/sections/algorithm_server.md

@@ -45,7 +45,7 @@ The data tuples are inspired from Napari's [LayerDataTuple](https://napari.org/0
 | `"mask"`          | A segmentation mask (2D, 3D) as integer numpy array. Integers represent the **object class**.            |
 | `"instance_mask"` | A segmentation mask (2D, 3D) as integer nD array. Integers represent **object instances**.            |
 | `"points"`        | A collection of point coordinates (array of shape (N, 2) or (N, 3)).                                  |
-| `"boxes"`         | A collection of boxes (array of shape (N, 4) representing the top-left and bottom-right box corners). |
+| `"boxes"`         | A collection of boxes (array of shape (N, 4, 2) representing the box corners). |
 | `"vectors"`       | Array of vectors in the Napari [Vectors](https://napari.org/stable/howtos/layers/vectors.html) format.|
 | `"tracks"`        | Array of tracks in the Napari [Tracks](https://napari.org/stable/howtos/layers/tracks.html) format.   |
 | `"class"`         | A class label (for image classification).                                                             |

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.12}/src/imaging_server_kit/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.11'
-__version_tuple__ = version_tuple = (0, 0, 11)
+__version__ = version = '0.0.12'
+__version_tuple__ = version_tuple = (0, 0, 12)

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.12}/src/imaging_server_kit/core/geometry.py

@@ -181,14 +181,15 @@ def boxes2features(boxes: np.ndarray) -> List[Feature]:
         try:
             geom = Polygon(coordinates=[coords], validate=True)
         except ValueError:
-            print("Invalid box polygon found.")
+            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}))
     return features
 
 
 def features2boxes(features):
     boxes = np.array([feature["geometry"]["coordinates"] for feature in features])
-    boxes = np.squeeze(boxes)
+    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
     return boxes

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.12}/src/imaging_server_kit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.11
+Version: 0.0.12
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL