Merge pull request #36 from khanlab/new-indexing

New indexing

.flake8

@@ -1,2 +1,3 @@
 [flake8]
 max-line-length = 79
+extend-ignore = W503

.github/release-drafter.yml

@@ -8,22 +8,15 @@ template: |
   $CHANGES
 categories:
   - title: 🚀 Features
-    labels:
-      - breaking
-      - enhancement
+    labels: [breaking, enhancement]
   - title: 🐛 Bug Fixes
-    labels:
-      - bug
+    labels: [bug]
   - title: 🧰 Maintenance
-    labels:
-      - maintenance
-      - test
+    labels: [maintenance, test]
   - title: 📝 Documentation
-    labels:
-      - documentation
+    labels: [documentation]
 
-exclude-labels:
-  - skip_changelog
+exclude-labels: [skip_changelog]
 
 change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
 change-title-escapes: \<*_&    # You can add  # and @ to disable mentions, and add ` to disable code blocks.
@@ -33,13 +26,7 @@ version-resolver:
   #   labels:
   #     - 'breaking'
   minor:
-    labels:
-      - breaking
-      - enhancement
+    labels: [breaking, enhancement]
   patch:
-    labels:
-      - maintenance
-      - bug
-      - test
-      - documentation
+    labels: [maintenance, bug, test, documentation]
   default: patch

.github/workflows/deploy.yml

@@ -91,9 +91,9 @@ jobs:
   #       with:
   #         python-version: '3.9'
 
-  #     #----------------------------------------------
-  #     #  -----  install & configure poetry  -----
-  #     #----------------------------------------------
+  #  #----------------------------------------------
+  #  #  -----  install & configure poetry  -----
+  #  #----------------------------------------------
   #     - name: Install Poetry
   #       uses: snok/install-poetry@v1
   #       with:

.github/workflows/quality.yml

@@ -3,13 +3,9 @@ name: Lint workflow
 
 on:
   push:
-    branches:
-      - '*'
-      - '!push-action/*'
+    branches: ['*', '!push-action/*']
   pull_request:
-    branches:
-      - '*'
-      - '!push-action/*'
+    branches: ['*', '!push-action/*']
 
 jobs:
   quality:

.gitignore

@@ -1,2 +1,3 @@
 # Local poetry config
 poetry.toml
+**/__pycache__

labelmerge/workflow/scripts/labelmerge.py

@@ -16,7 +16,7 @@
 def load_atlas(atlas_path: PathLike):
     """Loading relevant atlas data"""
     atlas = nib.load(atlas_path)
-    data = atlas.get_fdata().astype(np.ushort)
+    data = atlas.get_fdata().astype(np.int_)
     header = atlas.header
     affine = atlas.affine
 
@@ -58,6 +58,15 @@ def split_labels(
     if drops is None:
         drops = []
     unique_vals = np.unique(atlas[atlas > 0])
+    all_labels: pd.Series[int] = metadata["index"]
+    if not set(unique_vals) <= set(all_labels):
+        unlabeled_vals = ", ".join(
+            str(val) for val in set(unique_vals) - set(all_labels)
+        )
+        raise MetadataError(
+            f"Labels with indices {unlabeled_vals} from {prefix}atlas not "
+            "found in metadata table"
+        )
     normal_ds = xr.Dataset(
         dict(
             [
@@ -73,7 +82,7 @@ def split_labels(
         dict(
             [
                 assemble_mask(atlas, metadata, label, prefix)
-                for label in unique_vals
+                for label in all_labels
                 if label in exceptions
             ]
         )