Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
melonora merged 8 commits into from
Feb 26, 2024
Merged

Added validate_table_annotation_target()#468

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
188435a
added validate_table_annotation_target()
LucaMarconato Feb 23, 2024
e2391f3
removed test that is no longer relevant
LucaMarconato Feb 24, 2024
9533410
fix docs
LucaMarconato Feb 24, 2024
fa18c6e
fixed way to test no warnings emitted
LucaMarconato Feb 25, 2024
ff875da
merged validate_table_annotation_target() into validate_table_in_spat…
LucaMarconato Feb 25, 2024
7be6196
fix test
LucaMarconato Feb 25, 2024
ef8f8b4
Merge branch 'main' into dtype_instance_key
LucaMarconato Feb 25, 2024
24ee960
Merge branch 'multi_table' into dtype_instance_key
LucaMarconato Feb 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions src/spatialdata/_core/query/relational_query.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
if match_rows == "left":
warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
regions, region_column_name, instance_key = get_table_keys(table)
groups_df = table.obs.groupby(by=region_column_name)
for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
element_indices = element.index
else:
warnings.warn(
f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
UserWarning,
stacklevel=2,
)
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
element_indices = element.index
else:
warnings.warn(
f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
UserWarning,
stacklevel=2,
)
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
if match_rows == "right":
warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
regions, region_column_name, instance_key = get_table_keys(table)
groups_df = table.obs.groupby(by=region_column_name)
joined_indices = None
Expand Down
58 changes: 36 additions & 22 deletions src/spatialdata/_core/spatialdata.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

self._query = QueryManager(self)

def validate_table_in_spatialdata(self, data: AnnData) -> None:
def validate_table_in_spatialdata(self, table: AnnData) -> None:
"""
Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
in the table and the annotation target do not match. Otherwise, a warning is raised.

Parameters
----------
data
table
The table potentially annotating a SpatialElement

Raises
------
UserWarning
If the table is annotating elements not present in the SpatialData object.
UserWarning
The dtypes of the instance key column in the table and the annotation target do not match.
"""
TableModel().validate(data)
element_names = [
element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
]
if TableModel.ATTRS_KEY in data.uns:
attrs = data.uns[TableModel.ATTRS_KEY]
regions = (
attrs[TableModel.REGION_KEY]
if isinstance(attrs[TableModel.REGION_KEY], list)
else [attrs[TableModel.REGION_KEY]]
)
# TODO: check throwing error
if not all(element_name in element_names for element_name in regions):
warnings.warn(
"The table is annotating an/some element(s) not present in the SpatialData object",
UserWarning,
stacklevel=2,
)
TableModel().validate(table)
if TableModel.ATTRS_KEY in table.uns:
region, _, instance_key = get_table_keys(table)
region = region if isinstance(region, list) else [region]
for r in region:
element = self.get(r)
if element is None:
warnings.warn(
f"The table is annotating {r!r}, which is not present in the SpatialData object.",
UserWarning,
stacklevel=2,
)
else:
if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
dtype = element.dtype
else:
dtype = element.index.dtype
if dtype != table.obs[instance_key].dtype:
warnings.warn(
(
f"Table instance_key column ({instance_key}) has a dtype "
f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
"similar cases may be tolerated in downstream methods, but it is recommended to make "
"the dtypes match."
),
UserWarning,
stacklevel=2,
)

@staticmethod
def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
table = self.tables[table_name]
element_names = {element[1] for element in self._gen_elements()}
if region not in element_names:
raise ValueError(f"Annotation target '{region}' not present as SpatialElement in " f"SpatialData object.")
raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

if table.uns.get(TableModel.ATTRS_KEY):
self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down
48 changes: 41 additions & 7 deletions tests/core/operations/test_spatialdata_operations.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
Image2DModel,
Labels2DModel,
PointsModel,
ShapesModel,
TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
assert are_extents_equal(
data_extent_before, data_extent_after, atol=3
), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
table = full_sdata["table"]
region, region_key, _ = get_table_keys(table)
assert region == "labels2d"

# no warnings
with warnings.catch_warnings():
warnings.simplefilter("error")
full_sdata.validate_table_in_spatialdata(table)

# dtype mismatch
full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
full_sdata.validate_table_in_spatialdata(table)

# region not found
del full_sdata.labels["labels2d"]
with pytest.warns(UserWarning, match="in the SpatialData object"):
full_sdata.validate_table_in_spatialdata(table)

table.obs[region_key] = "points_0"
full_sdata.set_table_annotates_spatialelement("table", region="points_0")

# no warnings
with warnings.catch_warnings():
warnings.simplefilter("error")
full_sdata.validate_table_in_spatialdata(table)

# dtype mismatch
full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
full_sdata.validate_table_in_spatialdata(table)

# region not found
del full_sdata.points["points_0"]
with pytest.warns(UserWarning, match="in the SpatialData object"):
full_sdata.validate_table_in_spatialdata(table)
12 changes: 5 additions & 7 deletions tests/io/test_multi_table.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
def test_set_table_nonexisting_target(self, full_sdata):
with pytest.raises(
ValueError,
match="Annotation target 'non_existing' not present as SpatialElement in " "SpatialData object.",
match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
):
full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
}

if region == "non_existing":
with pytest.warns(
UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
):
# annotation target not present in the SpatialData object
with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
SpatialData(
shapes=shapes_dict,
tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
table = _get_table(region="poly")
table2 = _get_table(region="multipoly")
table3 = _get_table(region="non_existing")
with pytest.warns(
UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
):
# annotation target not present in the SpatialData object
with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
SpatialData(
shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Added validate_table_annotation_target()#468

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Merged

melonora
merged 8 commits into

from

Feb 26, 2024
 Merged


Added validate_table_annotation_target()#468
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


8 commits


Select commit
Hold shift + click to select a range
188435a

added validate_table_annotation_target()


LucaMarconato Feb 23, 2024
e2391f3

removed test that is no longer relevant


LucaMarconato Feb 24, 2024
9533410

fix docs


LucaMarconato Feb 24, 2024
fa18c6e

fixed way to test no warnings emitted


LucaMarconato Feb 25, 2024
ff875da

merged validate_table_annotation_target() into validate_table_in_spat…


LucaMarconato Feb 25, 2024
7be6196

fix test


LucaMarconato Feb 25, 2024
ef8f8b4

Merge branch 'main' into dtype_instance_key


LucaMarconato Feb 25, 2024
24ee960

Merge branch 'multi_table' into dtype_instance_key


LucaMarconato Feb 25, 2024

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


8 changes: 4 additions & 4 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -288,7 +288,7 @@ def _right_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "left":
 warnings.warn("Matching rows ``'left'`` is not supported for ``'right'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'left' is not supported for 'right' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 for element_type, name_element in element_dict.items():
Expand All@@ -300,7 +300,7 @@ def _right_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'right' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -331,7 +331,7 @@ def _inner_join_spatialelement_table(
 element_indices = element.index
 else:
 warnings.warn(
 f"Element type `labels` not supported for left exclusive join. Skipping `{name}`",
 f"Element type `labels` not supported for 'inner' join. Skipping `{name}`",
 UserWarning,
 stacklevel=2,
 )
Expand DownExpand Up@@ -389,7 +389,7 @@ def _left_join_spatialelement_table(
 element_dict: dict[str, dict[str, Any]], table: AnnData, match_rows: Literal["left", "no", "right"]
) -> tuple[dict[str, Any], AnnData]:
 if match_rows == "right":
 warnings.warn("Matching rows ``'right'`` is not supported for ``'left'`` join.", UserWarning, stacklevel=2)
 warnings.warn("Matching rows 'right' is not supported for 'left' join.", UserWarning, stacklevel=2)
 regions, region_column_name, instance_key = get_table_keys(table)
 groups_df = table.obs.groupby(by=region_column_name)
 joined_indices = None
Expand Down

58 changes: 36 additions & 22 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -159,41 +159,55 @@ def __init__(

 self._query = QueryManager(self)

 def validate_table_in_spatialdata(self, data: AnnData) -> None:
 def validate_table_in_spatialdata(self, table: AnnData) -> None:
 """
 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.

 This method validates a table in the SpatialData object to ensure that if annotation metadata is present, the
 annotation target (SpatialElement) is present in the SpatialData object. Otherwise, a warning is raised.
 annotation target (SpatialElement) is present in the SpatialData object, the dtypes of the instance key column
 in the table and the annotation target do not match. Otherwise, a warning is raised.

 Parameters
 ----------
data
table
 The table potentially annotating a SpatialElement

 Raises
 ------
 UserWarning
 If the table is annotating elements not present in the SpatialData object.
 UserWarning
 The dtypes of the instance key column in the table and the annotation target do not match.
 """
 TableModel().validate(data)
 element_names = [
 element_name for element_type, element_name, _ in self._gen_elements() if element_type != "tables"
 ]
 if TableModel.ATTRS_KEY in data.uns:
 attrs = data.uns[TableModel.ATTRS_KEY]
 regions = (
 attrs[TableModel.REGION_KEY]
 if isinstance(attrs[TableModel.REGION_KEY], list)
 else [attrs[TableModel.REGION_KEY]]
 )
 # TODO: check throwing error
 if not all(element_name in element_names for element_name in regions):
 warnings.warn(
 "The table is annotating an/some element(s) not present in the SpatialData object",
 UserWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if TableModel.ATTRS_KEY in table.uns:
 region, _, instance_key = get_table_keys(table)
 region = region if isinstance(region, list) else [region]
 for r in region:
 element = self.get(r)
 if element is None:
 warnings.warn(
 f"The table is annotating {r!r}, which is not present in the SpatialData object.",
 UserWarning,
 stacklevel=2,
 )
 else:
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 dtype = element.dtype
 else:
 dtype = element.index.dtype
 if dtype != table.obs[instance_key].dtype:
 warnings.warn(
 (
 f"Table instance_key column ({instance_key}) has a dtype "
 f"({table.obs[instance_key].dtype}) that does not match the dtype of the indices of "
 f"the annotated element ({dtype}). Please note in the case of int16 vs int32 or "
 "similar cases may be tolerated in downstream methods, but it is recommended to make "
 "the dtypes match."
 ),
 UserWarning,
 stacklevel=2,
 )

 @staticmethod
 def from_elements_dict(elements_dict: dict[str, SpatialElement | AnnData]) -> SpatialData:
Expand DownExpand Up@@ -417,7 +431,7 @@ def set_table_annotates_spatialelement(
 table = self.tables[table_name]
 element_names = {element[1] for element in self._gen_elements()}
 if region not in element_names:
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in  " f"SpatialData object.")
 raise ValueError(f"Annotation target '{region}' not present as SpatialElement in SpatialData object.")

 if table.uns.get(TableModel.ATTRS_KEY):
 self._change_table_annotation_target(table, region, region_key, instance_key)
Expand Down

48 changes: 41 additions & 7 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
from __future__ import annotations

import math
import warnings

import numpy as np
import pytest
Expand All@@ -11,13 +12,7 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._utils import _assert_spatialdata_objects_seem_identical, _assert_tables_seem_identical
from spatialdata.datasets import blobs
from spatialdata.models import (
 Image2DModel,
 Labels2DModel,
 PointsModel,
 ShapesModel,
 TableModel,
)
from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, ShapesModel, TableModel, get_table_keys
from spatialdata.transformations.operations import get_transformation, set_transformation
from spatialdata.transformations.transformations import (
 Affine,
Expand DownExpand Up@@ -417,3 +412,42 @@ def test_transform_to_data_extent(full_sdata: SpatialData, maintain_positioning:
 assert are_extents_equal(
 data_extent_before, data_extent_after, atol=3
 ), f"data_extent_before: {data_extent_before}, data_extent_after: {data_extent_after} for element {element}"


def test_validate_table_in_spatialdata(full_sdata):
 table = full_sdata["table"]
 region, region_key, _ = get_table_keys(table)
 assert region == "labels2d"

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.labels["labels2d"] = Labels2DModel.parse(full_sdata.labels["labels2d"].astype("int16"))
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.labels["labels2d"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

 table.obs[region_key] = "points_0"
 full_sdata.set_table_annotates_spatialelement("table", region="points_0")

 # no warnings
 with warnings.catch_warnings():
 warnings.simplefilter("error")
 full_sdata.validate_table_in_spatialdata(table)

 # dtype mismatch
 full_sdata.points["points_0"].index = full_sdata.points["points_0"].index.astype("int16")
 with pytest.warns(UserWarning, match="that does not match the dtype of the indices of the annotated element"):
 full_sdata.validate_table_in_spatialdata(table)

 # region not found
 del full_sdata.points["points_0"]
 with pytest.warns(UserWarning, match="in the SpatialData object"):
 full_sdata.validate_table_in_spatialdata(table)

12 changes: 5 additions & 7 deletions
tests/io/test_multi_table.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -93,7 +93,7 @@ def test_change_annotation_target(self, full_sdata, region_key, instance_key, er
 def test_set_table_nonexisting_target(self, full_sdata):
 with pytest.raises(
 ValueError,
 match="Annotation target 'non_existing' not present as SpatialElement in  " "SpatialData object.",
 match="Annotation target 'non_existing' not present as SpatialElement in SpatialData object.",
 ):
 full_sdata.set_table_annotates_spatialelement("table", "non_existing")

Expand DownExpand Up@@ -150,9 +150,8 @@ def test_single_table(self, tmp_path: str, region: str):
 }

 if region == "non_existing":
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes=shapes_dict,
 tables={"shape_annotate": table},
Expand DownExpand Up@@ -189,9 +188,8 @@ def test_paired_elements_tables(self, tmp_path: str):
 table = _get_table(region="poly")
 table2 = _get_table(region="multipoly")
 table3 = _get_table(region="non_existing")
 with pytest.warns(
 UserWarning, match=r"The table is annotating an/some element\(s\) not present in the SpatialData object"
 ):
 # annotation target not present in the SpatialData object
 with pytest.warns(UserWarning, match=r", which is not present in the SpatialData object"):
 SpatialData(
 shapes={"poly": test_shapes["poly"], "multipoly": test_shapes["multipoly"]},
 table={"poly_annotate": table, "multipoly_annotate": table3},
Expand Down