hoa-tools 1.0.2b1__py3-none-any.whl → 1.0.4__py3-none-any.whl

hoa_tools/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.2b1'
-__version_tuple__ = version_tuple = (1, 0, 2, 'b1')
+__version__ = version = '1.0.4'
+__version_tuple__ = version_tuple = (1, 0, 4)

hoa_tools/dataset.py

@@ -17,6 +17,7 @@ from typing import Literal
 
 import dask.array.core
 import gcsfs
+import networkx as nx
 import numpy as np
 import xarray as xr
 import zarr.core
@@ -41,6 +42,9 @@ class Dataset(HOAMetadata):
     def __str__(self) -> str:
         return f"Dataset(name={self.name})"
 
+    def __hash__(self) -> int:
+        return hash(self.name)
+
     def _organ_str(self) -> str:
         """
         Get name of organ, with organ context appended if present.
@@ -114,6 +118,18 @@ class Dataset(HOAMetadata):
         ]
         return sorted(parents, key=lambda c: c.name)
 
+    def get_registered(self) -> set["Dataset"]:
+        """
+        Get a set of all datasets that are registered (even indirectly) to this dataset.
+        """
+        import hoa_tools.registration
+
+        dataset_names = nx.node_connected_component(
+            hoa_tools.registration.Inventory._graph.to_undirected(),  # noqa: SLF001
+            self.name,
+        )
+        return {get_dataset(name) for name in dataset_names}
+
     @property
     def _remote_fmt(self) -> Literal["n5", "zarr"]:
         if self.data.gcs_url.startswith("n5://"):

hoa_tools/registration.py

@@ -8,6 +8,10 @@ in units of micro-meters (μm).
 Transforms are defined using the `SimpleITK` library.
 """
 
+import itertools
+from typing import Any
+
+import networkx as nx
 import numpy as np
 import SimpleITK as sitk
 
@@ -28,13 +32,18 @@ class RegistrationInventory:
         """
         Create registration inventory.
         """
-        self._registrations: dict[tuple[str, str], sitk.Transform] = {}
+        self._graph: nx.DiGraph[Any] = nx.DiGraph()
 
     def __contains__(self, item: tuple[Dataset, Dataset]) -> bool:
         """
         Check for existence of registration between two datasets.
         """
-        return (item[0].name, item[1].name) in self._registrations
+        try:
+            nx.shortest_path(self._graph, item[0].name, item[1].name)
+        except nx.exception.NetworkXNoPath:
+            return False
+        else:
+            return True
 
     def get_registration(
         self, *, source_dataset: Dataset, target_dataset: Dataset
@@ -42,7 +51,28 @@ class RegistrationInventory:
         """
         Get a registration.
         """
-        return self._registrations[(source_dataset.name, target_dataset.name)]
+        try:
+            path = nx.shortest_path(
+                self._graph, source_dataset.name, target_dataset.name
+            )
+        except nx.exception.NetworkXNoPath:
+            msg = (
+                f"No registration path between {source_dataset.name} and "
+                f"{target_dataset.name}"
+            )
+            raise ValueError(msg) from None
+
+        transforms: list[sitk.Transform] = [
+            self._graph[p1][p2]["transform"] for p1, p2 in itertools.pairwise(path)
+        ]
+        if len(transforms) == 1:
+            return transforms[0]
+
+        ndim = 3
+        t = sitk.CompositeTransform(ndim)  # type: ignore[no-untyped-call]
+        for transform in transforms:
+            t.AddTransform(transform)  # type: ignore[no-untyped-call]
+        return t
 
     def add_registration(
         self,
@@ -59,16 +89,20 @@ class RegistrationInventory:
         This will override any already defined transforms for these two datasets.
 
         """
-        self._registrations[(source_dataset.name, target_dataset.name)] = transform
-        self._registrations[(target_dataset.name, source_dataset.name)] = (
-            transform.GetInverse()  # type: ignore[no-untyped-call]
+        self._graph.add_edge(
+            source_dataset.name, target_dataset.name, transform=transform
+        )
+        self._graph.add_edge(
+            target_dataset.name,
+            source_dataset.name,
+            transform=transform.GetInverse(),  # type: ignore[no-untyped-call]
         )
 
     def _clear(self) -> None:
         """
         Remove all registrations.
         """
-        self._registrations = {}
+        self._graph = nx.DiGraph()
 
 
 def build_transform(

{hoa_tools-1.0.2b1.dist-info → hoa_tools-1.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: hoa-tools
-Version: 1.0.2b1
+Version: 1.0.4
 Summary: Tools for working with the Human Organ Atlas
 Author-email: David Stansby <d.stansby@ucl.ac.uk>
 License: Copyright (c) 2024, David Stansby
@@ -44,6 +44,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Requires-Dist: dask[array]
 Requires-Dist: gcsfs>2023
+Requires-Dist: networkx>=3
 Requires-Dist: pandas>=2
 Requires-Dist: pydantic>=2
 Requires-Dist: simpleitk
@@ -56,6 +57,7 @@ Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: jupyterlab; extra == "dev"
 Requires-Dist: jupytext; extra == "dev"
+Requires-Dist: types-networkx; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
 Requires-Dist: datamodel-code-generator; extra == "dev"
 Provides-Extra: docs

{hoa_tools-1.0.2b1.dist-info → hoa_tools-1.0.4.dist-info}/RECORD

@@ -1,11 +1,11 @@
 hoa_tools/__init__.py,sha256=wc7Yn5CXR3hxr2JyV3eEyCx3p8UZdknXDFJPSthKE_g,87
 hoa_tools/_n5.py,sha256=NGDJBbuyp1scGZ9fjuH7QqAQBpax9nxg2MhwhnV698M,310
-hoa_tools/_version.py,sha256=w7r5zi_L5eXXI6Dl3_kMp_3jBUG5p94YT5f5H78ZElY,519
-hoa_tools/dataset.py,sha256=tZtC-DhFTptzo8F_LkMgcoW0EIHnMEe1I3zW-pJOEEk,9086
+hoa_tools/_version.py,sha256=rXTOeD0YpRo_kJ2LqUiMnTKEFf43sO_PBvJHDh0SQUA,511
+hoa_tools/dataset.py,sha256=0pIuht5wePO0OXxRhj8ylgncf9PcwsfJJsl5uYXLcNo,9604
 hoa_tools/inventory.py,sha256=44IbE1eLFTetAeCadpBFYXXIwcX5fagq76zSMLWBOmE,613
 hoa_tools/metadata.py,sha256=HGdhjoaUZ2oW9EguO7iuoSU22XLPvPZyIUPvvjoNtbE,22851
 hoa_tools/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-hoa_tools/registration.py,sha256=EXnSrwLgxm5fpxTqCKWXNV0fbKOLWHP-Dt8Yb0-v4oY,2535
+hoa_tools/registration.py,sha256=BXxJYMHh6pngwTnjcx7phryWb_b0LHsXxsOvUk_es7k,3481
 hoa_tools/types.py,sha256=X8GzZXknwgmtTLWR2d_JxEfoavXAQ1zVrf8BaNdevSw,1452
 hoa_tools/voi.py,sha256=t6XAPMpS70W5OphWr3U4j8eXMVElR1OuuzJCoDLs7zc,7868
 hoa_tools/data/metadata/metadata/A186_lung_right_VOI-3_4.26um_bm18.json,sha256=XsMNYpnxvwqUt0h56gfhoXW5XCgBOXdiWzaIxJ_qov8,7550
@@ -191,8 +191,8 @@ hoa_tools/data/metadata/metadata/S-20-29_lung_left_VOI-02_6.5um_bm05.json,sha256
 hoa_tools/data/metadata/metadata/S-20-29_lung_left_VOI-04_6.5um_bm05.json,sha256=BncVFzcPaqrGiBWSEo46L_xbkr-od21Vr7j4XqZUEE8,6116
 hoa_tools/data/metadata/metadata/S-20-29_lung_left_VOI-05_6.5um_bm05.json,sha256=iseb551Vq9B-sHCYWprmbso4XXeb-o2-bFsMlyTyjE8,6118
 hoa_tools/data/metadata/metadata/S-20-29_lung_left_complete-organ_25.31um_bm05.json,sha256=sjNcr9XX7aDDjFMf8yScq4CU53mudSwsExZV7pqXBxQ,5875
-hoa_tools-1.0.2b1.dist-info/licenses/LICENSE.md,sha256=CU-KGODbkoeDUXYPeLgpicDrFTffLQECao-wTKJrXFU,1480
-hoa_tools-1.0.2b1.dist-info/METADATA,sha256=LLBx6e9uTgSjJfWvrVcbbvno3V7EBSx5Rr--hYE2_lw,5065
-hoa_tools-1.0.2b1.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
-hoa_tools-1.0.2b1.dist-info/top_level.txt,sha256=NkWbNX-2byZN6hcVyowOVv0aiRNdH0uXpOkA0SFHDgY,10
-hoa_tools-1.0.2b1.dist-info/RECORD,,
+hoa_tools-1.0.4.dist-info/licenses/LICENSE.md,sha256=CU-KGODbkoeDUXYPeLgpicDrFTffLQECao-wTKJrXFU,1480
+hoa_tools-1.0.4.dist-info/METADATA,sha256=YhOFzXOVcCBMfeJRyphYn7mCHJN0EJOWsQ7zDMb4CjA,5136
+hoa_tools-1.0.4.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+hoa_tools-1.0.4.dist-info/top_level.txt,sha256=NkWbNX-2byZN6hcVyowOVv0aiRNdH0uXpOkA0SFHDgY,10
+hoa_tools-1.0.4.dist-info/RECORD,,

{hoa_tools-1.0.2b1.dist-info → hoa_tools-1.0.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.3.1)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any