[Validate[ Add semantic segmentation metrics (#302)

* Add real semseg metrics

* Fix SegmentationIOU

* Fix aggregation

* Support segment field and metadata filtering

* Add confusion masking

* Cleaning up mypy type inference

* Fix segmentation filtering

* Convert RGB masks to L

* Fix pivoted confusion

* Pivot precision

* Bump beta to 0.13b

* Add test coverage and remove average precision (as we have no probability thresholds)

* Make rasterio optional

* Apply suggestions from code review

Co-authored-by: Sasha Harrison <70984140+sasha-scale@users.noreply.github.com>

* Improve documentation and output new lock file

Co-authored-by: Sasha Harrison <70984140+sasha-scale@users.noreply.github.com>

Author: gatli

.circleci/config.yml

@@ -21,7 +21,7 @@ jobs:
             apt-get -y install curl libgeos-dev
             pip install --upgrade pip
             pip install poetry
-            poetry install -E shapely
+            poetry install -E metrics
 
       - run:
           name: Black Formatting Check # Only validation, without re-formatting

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).
 
+## [0.13.0](https://github.com/scaleapi/nucleus-python-client/releases/tag/v0.13.0) - 2022-06-08
+
+### Added
+
+- Segmentation functions to Validate API
+ 
 ## [0.12.4](https://github.com/scaleapi/nucleus-python-client/releases/tag/v0.12.4) - 2022-06-02
 
 ### Fixed

README.md

@@ -188,7 +188,7 @@ sphinx-autobuild . ./_build/html --watch ../nucleus
 
 ## Custom Metrics using Shapely in scale-validate
 
-Certain metrics use `shapely` which is added as an optional dependency.
+Certain metrics use `Shapely` and `rasterio` which is added as optional dependencies.
 
 ```bash
 pip install scale-nucleus[metrics]
@@ -205,4 +205,4 @@ apt-get install libgeos-dev
 
 To develop it locally use
 
-`poetry install --extras shapely`
+`poetry install --extras metrics`

nucleus/metrics/__init__.py

@@ -5,6 +5,8 @@
     FieldFilter,
     ListOfOrAndFilters,
     MetadataFilter,
+    SegmentFieldFilter,
+    SegmentMetadataFilter,
     apply_filters,
 )
 from .polygon_metrics import (
@@ -16,6 +18,14 @@
     PolygonRecall,
 )
 from .segmentation_metrics import (
+    SegmentationFWAVACC,
+    SegmentationIOU,
+    SegmentationMAP,
+    SegmentationMaskMetric,
+    SegmentationPrecision,
+    SegmentationRecall,
+)
+from .segmentation_to_poly_metrics import (
     SegmentationMaskToPolyMetric,
     SegmentationToPolyAveragePrecision,
     SegmentationToPolyIOU,

nucleus/metrics/cuboid_utils.py

@@ -6,9 +6,9 @@
 try:
     from shapely.geometry import Polygon
 except ModuleNotFoundError:
-    from ..shapely_not_installed import ShapelyNotInstalled
+    from ..package_not_installed import PackageNotInstalled
 
-    Polygon = ShapelyNotInstalled
+    Polygon = PackageNotInstalled
 
 
 from nucleus.annotation import CuboidAnnotation