fix tests

Author: LucaMarconato

notebooks/transformations_demo.ipynb

@@ -7,16 +7,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import zarr\n",
+    "from pathlib import Path\n",
+    "\n",
     "import numpy as np\n",
+    "import zarr\n",
+    "from ome_zarr_models._v06.collection import Collection\n",
+    "from ome_zarr_models._v06.image import Image\n",
     "\n",
     "import ngff_transformations.graph\n",
     "import ngff_transformations.transform as ngt\n",
-    "\n",
-    "from pathlib import Path\n",
-    "from ome_zarr_models._v06.image import Image\n",
-    "from ome_zarr_models._v06.collection import Collection\n",
-    "from ngff_transformations.graph import transform_graph_to_networkx, draw_graph"
+    "from ngff_transformations.graph import draw_graph, transform_graph_to_networkx"
    ]
   },
   {
@@ -44,9 +44,7 @@
     }
    ],
    "source": [
-    "EXAMPLE_PATH = (\n",
-    "    Path(\"../data/ngff-rfc5-coordinate-transformation-examples\")\n",
-    ")\n",
+    "EXAMPLE_PATH = Path(\"../data/ngff-rfc5-coordinate-transformation-examples\")\n",
     "\n",
     "\n",
     "def get_all_zarrs(directory: Path) -> list[Path]:\n",
@@ -69,7 +67,7 @@
     "for zarr_path in get_all_zarrs(EXAMPLE_PATH):\n",
     "    relative_path = zarr_path.relative_to(EXAMPLE_PATH)\n",
     "\n",
-    "    if 'organ' not in str(relative_path):\n",
+    "    if \"organ\" not in str(relative_path):\n",
     "        continue\n",
     "\n",
     "    group: Collection | Image\n",
@@ -78,7 +76,7 @@
     "            group = Collection.from_zarr(zarr.open_group(zarr_path, mode=\"r\"))\n",
     "        else:\n",
     "            group = Image.from_zarr(zarr.open_group(zarr_path, mode=\"r\"))\n",
-    "    except Exception as e:\n",
+    "    except Exception:\n",
     "        # raise e\n",
     "        # print(str(e))\n",
     "        # continue\n",
@@ -97,7 +95,11 @@
    "id": "72648a07-c8d1-4078-80ef-2b7fb4758451",
    "metadata": {},
    "outputs": [],
-   "source": "transformation_path, (src_coord_system, tgt_coord_system) = ngff_transformations.graph.find_walks_in_graph(nx_graph, 'VOI-01.ome.zarr/1', None, 'overview.ome.zarr', 'anatomical')"
+   "source": [
+    "transformation_path, (src_coord_system, tgt_coord_system) = ngff_transformations.graph.find_walks_in_graph(\n",
+    "    nx_graph, \"VOI-01.ome.zarr/1\", None, \"overview.ome.zarr\", \"anatomical\"\n",
+    ")"
+   ]
   },
   {
    "cell_type": "code",
@@ -137,7 +139,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "transformed_data = ngt.transform_with_sequence3D(data, ['y', 'x', 'z', 'c'], transformation_path, ['y', 'x', 'z', 'c'])"
+    "transformed_data = ngt.transform_with_sequence3D(data, [\"y\", \"x\", \"z\", \"c\"], transformation_path, [\"y\", \"x\", \"z\", \"c\"])"
    ]
   },
   {

src/ngff_transformations/__init__.py

@@ -3,8 +3,8 @@
 __version__ = version("ngff-transformations")
 
 from ngff_transformations.graph import (
-    find_walks_in_graph,
     draw_graph,
+    find_walks_in_graph,
     get_relative_path,
     transform_graph_to_networkx,
 )

src/ngff_transformations/graph.py

@@ -1,18 +1,17 @@
-from typing import Any
+import logging
 
 import matplotlib.pyplot as plt
 import networkx as nx
 from ome_zarr_models._utils import TransformGraph
 from ome_zarr_models._v06.coordinate_transforms import (
     CoordinateSystemIdentifier,
-    Transform,
     Sequence,
+    Transform,
 )
-from pydantic import ValidationError
-import logging
 from ome_zarr_models._v06.coordinate_transforms import (
     Sequence as SequenceTransformation,
 )
+from pydantic import ValidationError
 
 
 def transform_graph_to_networkx(tgraph: TransformGraph) -> nx.DiGraph:
@@ -125,9 +124,7 @@ def _get_name_of_subgraph(
             f"Ambiguous coordinate system name '{cs_identifier}' found in both root and subgraph '{path_name}'. Use full identifier."
         )
     if cs_identifier not in nodes and cs_path_name not in nodes:
-        raise ValueError(
-            f"Coordinate system '{cs_identifier}' not found in graph nodes."
-        )
+        raise ValueError(f"Coordinate system '{cs_identifier}' not found in graph nodes.")
     if cs_path_name in nodes:
         return cs_path_name
     return cs_identifier
@@ -159,9 +156,7 @@ def _add_transform_and_inverse_transformation_edges(
         pass
 
 
-def draw_graph(
-    g: nx.DiGraph, figsize: tuple[int, int] = (12, 8), with_edge_labels: bool = True
-) -> None:
+def draw_graph(g: nx.DiGraph, figsize: tuple[int, int] = (12, 8), with_edge_labels: bool = True) -> None:
     """
     Draw a NetworkX graph showing all nodes and edges with their names.
 
@@ -219,9 +214,7 @@ def draw_graph(
     plt.show()
 
 
-def get_relative_path(
-    graph: nx.DiGraph, source_coordinate_system: str, target_coordinate_system: str
-) -> list[str]:
+def get_relative_path(graph: nx.DiGraph, source_coordinate_system: str, target_coordinate_system: str) -> list[str]:
     cost_key = "cost"
     """
     Get the relative path from one node to another in the transformation graph.
@@ -270,14 +263,10 @@ def create_sequence_transformation_from_graph_walk(
         edge_transformation = graph.get_edge_data(source, target)["transformation"]
         transformations.append(edge_transformation)
 
-    return Sequence(
-        input=walk[0], output=walk[-1], transformations=tuple(transformations)
-    )
+    return Sequence(input=walk[0], output=walk[-1], transformations=tuple(transformations))
 
 
-def get_node(
-    path: str | None = None, name: str | None = None
-) -> str | CoordinateSystemIdentifier:
+def get_node(path: str | None = None, name: str | None = None) -> str | CoordinateSystemIdentifier:
     if path is None and name is None:
         raise ValueError("Both path and name of the coordinate system cannot be None")
     if path is None:
@@ -287,17 +276,13 @@ def get_node(
     return CoordinateSystemIdentifier(path=path, name=name)
 
 
-def find_walks_in_graph(
-    graph, src_path, src_name, tgt_path, tgt_name
-) -> list[str | CoordinateSystemIdentifier]:
+def find_walks_in_graph(graph, src_path, src_name, tgt_path, tgt_name) -> list[str | CoordinateSystemIdentifier]:
     src_node = get_node(src_path, src_name)
     tgt_node = get_node(tgt_path, tgt_name)
 
     graph_walk = list(nx.all_shortest_paths(graph, src_node, tgt_node))
     if not graph_walk:
-        raise ValueError(
-            f"No path found from {src_node} to {tgt_node} in the transformation graph."
-        )
+        raise ValueError(f"No path found from {src_node} to {tgt_node} in the transformation graph.")
     if len(graph_walk) > 1:
         logging.warning(
             f"Multiple paths found from {src_node} to {tgt_node} in the transformation graph. Using the first one."

tests/test_graph.py

@@ -8,12 +8,16 @@
 from ome_zarr_models._v06.image import Image
 
 from ngff_transformations.graph import (
-    find_walks_in_graph,
     get_relative_path,
     transform_graph_to_networkx,
+    create_sequence_transformation_from_graph_walk,
 )
 
-EXAMPLE_PATH = Path(__file__).parent.parent / "data" / "ngff-rfc5-coordinate-transformation-examples"
+EXAMPLE_PATH = (
+    Path(__file__).parent.parent
+    / "data"
+    / "ngff-rfc5-coordinate-transformation-examples"
+)
 
 
 def get_test_zarr_paths(data_dir: Path = EXAMPLE_PATH) -> list[Path]:
@@ -67,7 +71,8 @@ def test_graph(zarr_path: Path):
 
     example_edge = list(nx_graph.edges)[0]
     path = get_relative_path(nx_graph, example_edge[0], example_edge[1])
-    sequence_transformation = find_walks_in_graph(
-        graph=nx_graph, path)
+    sequence_transformation = create_sequence_transformation_from_graph_walk(
+        graph=nx_graph, walk=path
+    )
 
     assert isinstance(sequence_transformation, Sequence)