Added api for renaming coordinate systems

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.10.0
+      rev: 23.10.1
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -27,7 +27,7 @@ repos:
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.1.1
+      rev: v0.1.3
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -10,10 +10,21 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.0.15] - tbd
 
+### Added
+
 ## [0.0.14] - 2023-10-11
 
 ### Added
 
+#### Minor
+
+-   new API: sdata.rename_coordinate_systems()
+
+#### Technical
+
+-   decompose affine transformation into simpler transformations
+-   remove padding for blobs()
+
 #### Major
 
 -   get_extent() function to compute bounding box of the data

src/spatialdata/_core/spatialdata.py

@@ -569,6 +569,62 @@ def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter
 
         return SpatialData(**elements, table=table)
 
+    def rename_coordinate_systems(self, rename_dict: dict[str, str]) -> None:
+        """
+        Rename coordinate systems.
+
+        Parameters
+        ----------
+        rename_dict
+            A dictionary mapping old coordinate system names to new coordinate system names.
+
+        Notes
+        -----
+        The method does not allow to rename a coordinate system into an existing one, unless the existing one is also
+        renamed in the same call.
+        """
+        from spatialdata.transformations.operations import get_transformation, set_transformation
+
+        # check that the rename_dict is valid
+        old_names = self.coordinate_systems
+        new_names = list(set(old_names).difference(set(rename_dict.keys())))
+        for old_cs, new_cs in rename_dict.items():
+            if old_cs not in old_names:
+                raise ValueError(f"Coordinate system {old_cs} does not exist.")
+            if new_cs in new_names:
+                raise ValueError(
+                    "It is not allowed to rename a coordinate system if the new name already exists and "
+                    "if it is not renamed in the same call."
+                )
+            new_names.append(new_cs)
+
+        # rename the coordinate systems
+        for element in self._gen_elements_values():
+            # get the transformations
+            transformations = get_transformation(element, get_all=True)
+            assert isinstance(transformations, dict)
+
+            # appends a random suffix to the coordinate system name to avoid collisions
+            suffixes_to_replace = set()
+            for old_cs, new_cs in rename_dict.items():
+                if old_cs in transformations:
+                    random_suffix = hashlib.sha1(os.urandom(128)).hexdigest()[:8]
+                    transformations[new_cs + random_suffix] = transformations.pop(old_cs)
+                    suffixes_to_replace.add(new_cs + random_suffix)
+
+            # remove the random suffixes
+            new_transformations = {}
+            for cs_with_suffix in transformations:
+                if cs_with_suffix in suffixes_to_replace:
+                    cs = cs_with_suffix[:-8]
+                    new_transformations[cs] = transformations[cs_with_suffix]
+                    suffixes_to_replace.remove(cs_with_suffix)
+                else:
+                    new_transformations[cs_with_suffix] = transformations[cs_with_suffix]
+
+            # set the new transformations
+            set_transformation(element=element, transformation=new_transformations, set_all=True)
+
     def transform_element_to_coordinate_system(
         self, element: SpatialElement, target_coordinate_system: str
     ) -> SpatialElement:

tests/core/operations/test_spatialdata_operations.py

@@ -128,6 +128,59 @@ def test_filter_by_coordinate_system_also_table(full_sdata):
     assert len(filtered_sdata2.table) == len(full_sdata.table)
 
 
+def test_rename_coordinate_systems(full_sdata):
+    # all the elements point to global, add new coordinate systems
+    set_transformation(
+        element=full_sdata.shapes["circles"], transformation=Identity(), to_coordinate_system="my_space0"
+    )
+    set_transformation(element=full_sdata.shapes["poly"], transformation=Identity(), to_coordinate_system="my_space1")
+    set_transformation(
+        element=full_sdata.shapes["multipoly"], transformation=Identity(), to_coordinate_system="my_space2"
+    )
+
+    elements_in_global_before = {
+        name for _, name, _ in full_sdata.filter_by_coordinate_system("global")._gen_elements()
+    }
+
+    # test a renaming without collisions
+    full_sdata.rename_coordinate_systems({"my_space0": "my_space00", "my_space1": "my_space11"})
+    assert {"my_space00", "my_space11", "global", "my_space2"}.issubset(full_sdata.coordinate_systems)
+    assert "my_space0" not in full_sdata.coordinate_systems
+    assert "my_space1" not in full_sdata.coordinate_systems
+
+    # renaming with collisions (my_space2 already exists)
+    with pytest.raises(ValueError):
+        full_sdata.rename_coordinate_systems({"my_space00": "my_space2"})
+
+    # renaming with collisions (my_space3 doesn't exist but it's target of two renamings)
+    with pytest.raises(ValueError):
+        full_sdata.rename_coordinate_systems({"my_space00": "my_space3", "my_space11": "my_space3"})
+
+    # invalid renaming: my_space3 is not a valid coordinate system
+    with pytest.raises(ValueError):
+        full_sdata.rename_coordinate_systems({"my_space3": "my_space4"})
+
+    # invalid renaming: my_space3 is not a valid coordinate system (it doesn't matter if my_space3 is target of one
+    # renaming, as it doesn't exist at the time of the function call)
+    with pytest.raises(ValueError):
+        full_sdata.rename_coordinate_systems(
+            {"my_space00": "my_space3", "my_space11": "my_space3", "my_space3": "my_space4"}
+        )
+
+    # valid renaming with collisions
+    full_sdata.rename_coordinate_systems({"my_space00": "my_space2", "my_space2": "my_space3"})
+    assert get_transformation(full_sdata.shapes["circles"], get_all=True)["my_space2"] == Identity()
+    assert get_transformation(full_sdata.shapes["multipoly"], get_all=True)["my_space3"] == Identity()
+
+    # renaming without effect
+    full_sdata.rename_coordinate_systems({"my_space11": "my_space11"})
+    assert get_transformation(full_sdata.shapes["poly"], get_all=True)["my_space11"] == Identity()
+
+    # check that all the elements with coordinate system global are still there
+    elements_in_global_after = {name for _, name, _ in full_sdata.filter_by_coordinate_system("global")._gen_elements()}
+    assert elements_in_global_before == elements_in_global_after
+
+
 def test_concatenate_tables():
     """
     The concatenation uses AnnData.concatenate(), here we test the

tests/core/test_data_extent.py

@@ -59,8 +59,8 @@ def test_get_extent_points():
     extent = get_extent(sdata["blobs_points"])
     check_test_results0(
         extent,
-        min_coordinates=np.array([12.0, 13.0]),
-        max_coordinates=np.array([500.0, 498.0]),
+        min_coordinates=np.array([3.0, 4.0]),
+        max_coordinates=np.array([509.0, 507.0]),
         axes=("x", "y"),
     )