[Validate] Fix instance segmentation metrics (#317)

Author: gatli

.circleci/config.yml

@@ -137,17 +137,15 @@ jobs:
           command: |
             pip install --upgrade pip
           name: Upgrade pip
-#        - python/install-packages:
-#            pkg-manager: poetry
       - run:
           command: |
             poetry build
-          name: Test it
+          name: Build the package
       - run:
           command: |
             export FOUND_PKG=$(find ./dist -name "*.tar.gz")
             pip install $FOUND_PKG
-          name: Test it
+          name: Install with Python Version
 workflows:
   nightly_build_test:
     triggers:
@@ -165,7 +163,7 @@ workflows:
       - test_poetry_installation:
           matrix:
             parameters:
-              python_version: ['3.6', '3.7', '3.8', '3.9'] #, '3.10'] Haven't gotten the 3.10 test to work
+              python_version: ['3.6', '3.7', '3.8', '3.9'] #, '3.10'] Haven't gotten the 3.10 poetry install test to work
           context: Nucleus
       - test_client_installation:
           matrix:

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to the [Nucleus Python Client](https://github.com/scaleapi/n
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.14.1](https://github.com/scaleapi/nucleus-python-client/releases/tag/v0.14.1) - 2022-06-20
+
+### Fixed
+- Adapt Segmentation metrics to better support instance segmentation
+- Change Segmentation/Polygon metrics to use new segmentation metrics 
+
 
 ## [0.14.0](https://github.com/scaleapi/nucleus-python-client/releases/tag/v0.14.0) - 2022-06-16
 

nucleus/metrics/cuboid_utils.py

@@ -357,6 +357,4 @@ def detection_iou(
             meter_3d.append(iou_3d[i, j])
             meter_2d.append(iou_2d[i, j])
 
-    meter_3d = np.array(meter_3d)
-    meter_2d = np.array(meter_2d)
-    return meter_3d, meter_2d
+    return np.array(meter_3d), np.array(meter_2d)

nucleus/metrics/segmentation_loader.py

@@ -0,0 +1,34 @@
+from typing import Dict
+
+import numpy as np
+from PIL import Image
+
+try:
+    import fsspec
+except ModuleNotFoundError:
+    from ..package_not_installed import PackageNotInstalled
+
+    fsspec = PackageNotInstalled
+
+
+class SegmentationMaskLoader:
+    def __init__(self, fs: fsspec):
+        self.fs = fs
+
+    def fetch(self, url: str):
+        with self.fs.open(url) as fh:
+            img = Image.open(fh)
+        return np.asarray(img)
+
+
+class InMemoryLoader:
+    """We use this loader in the tests, this allows us to serve images from memory instead of fetching
+    from a filesystem.
+    """
+
+    def __init__(self, url_to_array: Dict[str, np.ndarray]):
+        self.url_to_array = url_to_array
+
+    def fetch(self, url: str):
+        array = self.url_to_array[url]
+        return array