hoa-tools 1.0.2b1__tar.gz → 1.0.4__tar.gz

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.8
+    rev: v0.11.9
     hooks:
       - id: ruff
       - id: ruff-format

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/.vscode/settings.json

@@ -1,5 +1,6 @@
 {
   "python.testing.pytestArgs": ["tests"],
   "python.testing.unittestEnabled": false,
-  "python.testing.pytestEnabled": true
+  "python.testing.pytestEnabled": true,
+  "python.analysis.typeCheckingMode": "strict"
 }

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/PKG-INFO

@@ -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 → hoa_tools-1.0.4}/docs/how_to.md

@@ -4,3 +4,7 @@
 
 Download the private metadata JSON files to a directory on your computer,
 then use [hoa_tools.dataset.change_metadata_directory][].
+
+## Find all datasets registered to a given dataset?
+
+Use [hoa_tools.dataset.Dataset.get_registered][].

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/docs/release-notes.md

@@ -1,5 +1,17 @@
 # Release notes
 
+## 1.0.4
+
+- Fixed a bug that prevented transforming VOIs between two datasets that
+  are indirectly registered.
+
+## 1.0.3
+
+- Added the ability to transform between datasets that are indirectly registered,
+  for example two zoom datasets that are registered to the same common overview dataset.
+- Added [hoa_tools.dataset.Dataset.get_registered][] to get all datasets registered
+  (directly or indirectly) to a given dataset.
+
 ## 1.0.2
 
 - Fixed the inclusion of the metadata inventory in the distribution on PyPI.

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/docs/tutorial/registration.py

@@ -12,11 +12,15 @@ import hoa_tools.voi
 
 # -
 
-# Lets start by getting an overview dataset, a zoom dataset, and defining a VOI in the zoom dataset.
+# Lets start by getting an overview dataset, and seeing what datasets are registered to it.
 
 overview_dataset = hoa_tools.dataset.get_dataset(
     "S-20-29_brain_complete-organ_25.33um_bm05"
 )
+sorted([d.name for d in overview_dataset.get_registered()])
+
+# From these we'll take a zoom dataset, and define a VOI in the zoom dataset.
+
 zoom_dataset = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
 zoom_voi = hoa_tools.voi.VOI(
     dataset=zoom_dataset,

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/pyproject.toml

@@ -26,6 +26,7 @@ classifiers = [
 dependencies = [
   "dask[array]",
   "gcsfs>2023",
+  "networkx>=3",
   "pandas>=2",
   "pydantic>=2",
   "simpleitk",
@@ -43,6 +44,7 @@ optional-dependencies = { dev = [
   "ruff",
   "jupyterlab",
   "jupytext",
+  "types-networkx",
   "pandas-stubs",
   "datamodel-code-generator",
 ], docs = [
@@ -76,11 +78,22 @@ skip = 'schemas/*'
 minversion = "6.0"
 testpaths = ["tests"]
 addopts = [
+  "-ra",
   "--color=yes",
   "--cov=hoa_tools",
   "--cov-report=xml",
   "--verbose",
   "--doctest-rst",
+  "-vv",
+  "--strict-config",
+  "--strict-markers",
+]
+xfail_strict = true
+log_cli_level = "INFO"
+filterwarnings = [
+  "error",
+  # coming from simpleITK
+  "ignore:builtin type Swig.* has no __module__ attribute:DeprecationWarning",
 ]
 
 [tool.coverage]

{hoa_tools-1.0.2b1 → hoa_tools-1.0.4}/src/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-1.0.2b1 → hoa_tools-1.0.4}/src/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-1.0.2b1 → hoa_tools-1.0.4}/src/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 → hoa_tools-1.0.4}/src/hoa_tools.egg-info/PKG-INFO

@@ -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 → hoa_tools-1.0.4}/src/hoa_tools.egg-info/requires.txt

@@ -1,5 +1,6 @@
 dask[array]
 gcsfs>2023
+networkx>=3
 pandas>=2
 pydantic>=2
 simpleitk
@@ -13,6 +14,7 @@ pre-commit
 ruff
 jupyterlab
 jupytext
+types-networkx
 pandas-stubs
 datamodel-code-generator
 

hoa_tools-1.0.4/tests/test_registration.py

@@ -0,0 +1,119 @@
+import pytest
+
+import hoa_tools.dataset
+import hoa_tools.registration
+import hoa_tools.voi
+from hoa_tools.types import ArrayCoordinate
+
+
+def test_transform_voi() -> None:
+    overview = hoa_tools.dataset.get_dataset(
+        "S-20-29_brain_complete-organ_25.33um_bm05"
+    )
+    child = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
+
+    child_voi = hoa_tools.voi.VOI(
+        dataset=child,
+        downsample_level=0,
+        lower_corner=ArrayCoordinate(x=3434, y=2060, z=2656),
+        size=ArrayCoordinate(x=256, y=256, z=128),
+    )
+
+    overview_voi = child_voi.transform_to(overview)
+    assert overview_voi.dataset.name == "S-20-29_brain_complete-organ_25.33um_bm05"
+    assert overview_voi.downsample_level == 0
+    assert overview_voi.lower_corner == ArrayCoordinate(x=2975, y=1689, z=4316)
+    assert overview_voi.size == ArrayCoordinate(x=69, y=69, z=33)
+
+
+def test_inverse_registration() -> None:
+    overview = hoa_tools.dataset.get_dataset(
+        "S-20-29_brain_complete-organ_25.33um_bm05"
+    )
+    zoom = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
+
+    transform = hoa_tools.registration.Inventory.get_registration(
+        source_dataset=zoom, target_dataset=overview
+    )
+    transform_inv = hoa_tools.registration.Inventory.get_registration(
+        source_dataset=overview, target_dataset=zoom
+    )
+
+    assert transform.GetParameters() == (
+        0.020069870800809003,
+        0.0,
+        0.0,
+        92062.68586067778,
+        30372.305582420606,
+        52529.27516774854,
+        1.0000012996591003,
+    )
+
+    # Check transform roundtrip
+    point = (0, 0, 0)
+    assert transform_inv.TransformPoint(transform.TransformPoint(point)) == point
+
+
+def test_transform_path() -> None:
+    # Test getting transform between two datasets that aren't directly registered
+    zoom1 = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
+    zoom2 = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-05_6.5um_bm05")
+
+    hoa_tools.registration.Inventory.get_registration(
+        source_dataset=zoom1, target_dataset=zoom2
+    )
+
+
+def test_no_transform_path() -> None:
+    # Test getting transform between two datasets that aren't directly registered
+    d1 = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
+    d2 = hoa_tools.dataset.get_dataset(
+        "LADAF-2020-27_spleen_complete-organ_25.08um_bm05"
+    )
+
+    assert (d1, d2) not in hoa_tools.registration.Inventory
+
+    with pytest.raises(
+        ValueError,
+        match=(
+            "No registration path between S-20-29_brain_VOI-04_6.5um_bm05 and "
+            "LADAF-2020-27_spleen_complete-organ_25.08um_bm05"
+        ),
+    ):
+        hoa_tools.registration.Inventory.get_registration(
+            source_dataset=d1, target_dataset=d2
+        )
+
+
+def test_registered() -> None:
+    # Test getting transform between two datasets that aren't directly registered
+    d = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
+    registered = d.get_registered()
+    assert {d.name for d in registered} == {
+        "S-20-29_brain_complete-organ_25.33um_bm05",
+        "S-20-29_brain_VOI-04_2.5um_bm05",
+        "S-20-29_brain_VOI-03_6.5um_bm05",
+        "S-20-29_brain_VOI-01_2.5um_bm05",
+        "S-20-29_brain_VOI-03_2.5um_bm05",
+        "S-20-29_brain_VOI-01b_6.5um_bm05",
+        "S-20-29_brain_VOI-02_2.5um_bm05",
+        "S-20-29_brain_VOI-01_6.5um_bm05",
+        "S-20-29_brain_VOI-02_6.5um_bm05",
+        "S-20-29_brain_VOI-05_2.5um_bm05",
+        "S-20-29_brain_VOI-04_6.5um_bm05",
+        "S-20-29_brain_VOI-05_6.5um_bm05",
+    }
+
+
+def test_transform_zoom_to_zoom() -> None:
+    zoom1 = hoa_tools.dataset.get_dataset("LADAF-2021-64_heart_VOI-07_6.51um_bm18")
+    zoom2 = hoa_tools.dataset.get_dataset("LADAF-2021-64_heart_VOI-7.1_2.26um_bm18")
+
+    voi = hoa_tools.voi.VOI(
+        dataset=zoom1,
+        downsample_level=0,
+        lower_corner={"x": 3434, "y": 2060, "z": 2656},
+        size={"x": 256, "y": 256, "z": 128},
+    )
+
+    voi.transform_to(zoom2)

hoa_tools-1.0.2b1/tests/test_registration.py

@@ -1,24 +0,0 @@
-import hoa_tools.dataset
-import hoa_tools.registration
-import hoa_tools.voi
-from hoa_tools.types import ArrayCoordinate
-
-
-def test_transform_voi() -> None:
-    overview = hoa_tools.dataset.get_dataset(
-        "S-20-29_brain_complete-organ_25.33um_bm05"
-    )
-    child = hoa_tools.dataset.get_dataset("S-20-29_brain_VOI-04_6.5um_bm05")
-
-    child_voi = hoa_tools.voi.VOI(
-        dataset=child,
-        downsample_level=0,
-        lower_corner=ArrayCoordinate(x=3434, y=2060, z=2656),
-        size=ArrayCoordinate(x=256, y=256, z=128),
-    )
-
-    overview_voi = child_voi.transform_to(overview)
-    assert overview_voi.dataset.name == "S-20-29_brain_complete-organ_25.33um_bm05"
-    assert overview_voi.downsample_level == 0
-    assert overview_voi.lower_corner == ArrayCoordinate(x=2975, y=1689, z=4316)
-    assert overview_voi.size == ArrayCoordinate(x=69, y=69, z=33)