imaging-server-kit 0.0.11__tar.gz → 0.0.13__tar.gz

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: imaging-server-kit
-Version: 0.0.11
+Version: 0.0.13
 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-0.0.13}/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-0.0.13}/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 = '0.0.13'
+__version_tuple__ = version_tuple = (0, 0, 13)

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.13}/src/imaging_server_kit/core/geometry.py

@@ -29,17 +29,17 @@ def mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
             coords = np.vstack([coords, coords[0]])  # Close the polygon for QuPath
             try:
                 geom = Polygon(coordinates=[coords.tolist()], validate=True)
+                feature = Feature(
+                    geometry=geom, 
+                    properties={
+                        "Detection ID": detection_id, 
+                        "Class": int(pixel_class),  # the int() casting solves a bug with json serialization
+                    }
+                )
+                features.append(feature)
             except ValueError:
                 # TODO: not sure what to do when this happens (very occasionally)
                 print("Found an invalid polygon...")
-            feature = Feature(
-                geometry=geom, 
-                properties={
-                    "Detection ID": detection_id, 
-                    "Class": int(pixel_class),  # the int() casting solves a bug with json serialization
-                }
-            )
-            features.append(feature)
 
     return features
 
@@ -81,17 +81,17 @@ def instance_mask2features(segmentation_mask: np.ndarray) -> List[Feature]:
             coords = np.vstack([coords, coords[0]])  # Close the polygon for QuPath
             try:
                 geom = Polygon(coordinates=[coords.tolist()], validate=True)
+                feature = Feature(
+                    geometry=geom, 
+                    properties={
+                        "Detection ID": int(detection_id), 
+                        "Class": 1
+                    }
+                )
+                features.append(feature)
             except ValueError:
                 # TODO: not sure what to do when this happens (very occasionally)
                 print("Found an invalid polygon...")
-            feature = Feature(
-                geometry=geom, 
-                properties={
-                    "Detection ID": int(detection_id), 
-                    "Class": 1
-                }
-            )
-            features.append(feature)
 
     return features
 
@@ -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-0.0.13}/src/imaging_server_kit/demo/threshold.py

@@ -2,8 +2,7 @@ from pathlib import Path
 import numpy as np
 import uvicorn
 from imaging_server_kit import algorithm_server, ImageUI, FloatSpinBoxUI
-from skimage.util import img_as_float
-
+from skimage.exposure import rescale_intensity
 
 @algorithm_server(
     algorithm_name="intensity-threshold",
@@ -29,7 +28,7 @@ def threshold_algo_server(
     threshold: float,
 ):
     """Implements a simple intensity threshold algorithm."""
-    mask = img_as_float(image) > threshold
+    mask = rescale_intensity(image, out_range=(0, 1)) > threshold
     return [(mask, {"name": "Threshold result"}, "mask")]
 
 

{imaging_server_kit-0.0.11 → imaging_server_kit-0.0.13}/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: 0.0.13
 Summary: Deploy image processing algorithms in FastAPI servers. 
 Author-email: Mallory Wittwer <mallory.wittwer@epfl.ch>
 License: Copyright (c) 2024, EPFL