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Merged
LucaMarconato merged 6 commits into from
Feb 19, 2024
Merged

Update locate values #460

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de7da2b
add possibility for custom table name
melonora Feb 18, 2024
a167a59
change docstring
melonora Feb 18, 2024
1c9e69d
updated changelog
melonora Feb 18, 2024
bff1353
added table_name parameter
melonora Feb 18, 2024
7dc2c02
update changelog
melonora Feb 18, 2024
250fbc3
Merge branch 'multi_table' into update_locate_values
LucaMarconato Feb 19, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down
20 changes: 14 additions & 6 deletions src/spatialdata/_core/query/relational_query.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
"""
Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
SpatialData object
element_name
The name of the spatial elements to be joined with the table.
table_name
The name of the table to match to the element.

Returns
-------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
# table_name = "table"
# _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
# return table
assert sdata.table is not None, "No table found in the SpatialData"
assert sdata[table_name] is not None, "No table found in the SpatialData"
element_type, _, element = sdata._find_element(element_name)
assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
elements_dict = {element_type: {element_name: element}}
return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
element: SpatialElement | None = None,
sdata: SpatialData | None = None,
element_name: str | None = None,
table_name: str = "table",
) -> list[_ValueOrigin]:
el = _get_element(element=element, sdata=sdata, element_name=element_name)
origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

# adding from the obs columns or var
if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
table = sdata.table
table = sdata[table_name]
if table is not None:
# check if the table is annotating the element
region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
element: SpatialElement | None = None,
sdata: SpatialData | None = None,
element_name: str | None = None,
table_name: str = "table",
) -> pd.DataFrame:
"""
Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
SpatialData object; either element or (sdata, element_name) must be provided
element_name
Name of the element; either element or (sdata, element_name) must be provided
table_name
Name of the table to get the values from.

Returns
-------
Expand All@@ -674,7 +680,9 @@ def get_values(
value_keys = [value_key] if isinstance(value_key, str) else value_key
locations = []
for vk in value_keys:
origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
origins = _locate_value(
value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
)
if len(origins) > 1:
raise ValueError(
f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
return df
if sdata is not None:
assert element_name is not None
matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
obs = matched_table.obs
Expand Down
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Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
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Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

from

Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

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if (__m === '*' || __re.test(location.href)) {
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Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
Skip to content
Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

from

Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

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Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
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Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

from

Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
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Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

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Feb 19, 2024
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Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
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Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

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Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
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el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
Skip to content
Update locate values#460

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 Merged

LucaMarconato
merged 6 commits into

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Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down

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Update locate values by melonora · Pull Request #460 · scverse/spatialdata · GitHub
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 Merged

LucaMarconato
merged 6 commits into

from

Feb 19, 2024
 Merged


Update locate values
#460
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de7da2b

add possibility for custom table name


melonora Feb 18, 2024
a167a59

change docstring


melonora Feb 18, 2024
1c9e69d

updated changelog


melonora Feb 18, 2024
bff1353

added table_name parameter


melonora Feb 18, 2024
7dc2c02

update changelog


melonora Feb 18, 2024
250fbc3

Merge branch 'multi_table' into update_locate_values


LucaMarconato Feb 19, 2024

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3 changes: 2 additions & 1 deletion
CHANGELOG.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -38,8 +38,9 @@ and this project adheres to [Semantic Versioning][].
- Added function get_instance_key_column in SpatialData to get the instance_key column in table.obs.
- Added function set_table_annotates_spatialelement in SpatialData to either set or change the annotation metadata of
 a table in a given SpatialData object.
- Added table_name parameter to the aggegate function to allow users to give a custom table name to table resulting
- Added table_name parameter to the aggregate function to allow users to give a custom table name to table resulting
 from aggregation.
- Added table_name parameter to the get_values function.
- Added tables property in SpatialData.
- Added tables setter in SpatialData.
- Added gen_spatial_elements generator in SpatialData to generate the SpatialElements in a given SpatialData object.
Expand Down

20 changes: 14 additions & 6 deletions
src/spatialdata/_core/query/relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -533,7 +533,7 @@ def join_sdata_spatialelement_table(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -543,6 +543,8 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 SpatialData object
 element_name
 The name of the spatial elements to be joined with the table.
 table_name
 The name of the table to match to the element.

 Returns
 -------
Expand All@@ -559,11 +561,11 @@ def match_table_to_element(sdata: SpatialData, element_name: str) -> AnnData:
 # table_name = "table"
 # _, table = join_sdata_spatialelement_table(sdata, element_name, table_name, "left", match_rows="left")
 # return table
 assert sdata.table is not None, "No table found in the SpatialData"
 assert sdata[table_name] is not None, "No table found in the SpatialData"
 element_type, _, element = sdata._find_element(element_name)
 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
 elements_dict = {element_type: {element_name: element}}
 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
 return _filter_table_by_elements(sdata[table_name], elements_dict, match_rows=True)


def match_element_to_table(
Expand DownExpand Up@@ -611,6 +613,7 @@ def _locate_value(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> list[_ValueOrigin]:
 el = _get_element(element=element, sdata=sdata, element_name=element_name)
 origins = []
Expand All@@ -625,7 +628,7 @@ def _locate_value(

 # adding from the obs columns or var
 if model in [ShapesModel, Labels2DModel, Labels3DModel] and sdata is not None:
 table = sdata.table
 table = sdata[table_name]
 if table is not None:
 # check if the table is annotating the element
 region = table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY]
Expand All@@ -646,6 +649,7 @@ def get_values(
 element: SpatialElement | None = None,
 sdata: SpatialData | None = None,
 element_name: str | None = None,
 table_name: str = "table",
) -> pd.DataFrame:
 """
 Get the values from the element, from any location: df columns, obs or var columns (table).
Expand All@@ -660,6 +664,8 @@ def get_values(
 SpatialData object; either element or (sdata, element_name) must be provided
 element_name
 Name of the element; either element or (sdata, element_name) must be provided
 table_name
 Name of the table to get the values from.

 Returns
 -------
Expand All@@ -674,7 +680,9 @@ def get_values(
 value_keys = [value_key] if isinstance(value_key, str) else value_key
 locations = []
 for vk in value_keys:
 origins = _locate_value(value_key=vk, element=element, sdata=sdata, element_name=element_name)
 origins = _locate_value(
 value_key=vk, element=element, sdata=sdata, element_name=element_name, table_name=table_name
 )
 if len(origins) > 1:
 raise ValueError(
 f"{vk} has been found in multiple locations of (element, sdata, element_name) = "
Expand DownExpand Up@@ -706,7 +714,7 @@ def get_values(
 return df
 if sdata is not None:
 assert element_name is not None
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
 matched_table = match_table_to_element(sdata=sdata, element_name=element_name, table_name=table_name)
 region_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.REGION_KEY_KEY]
 instance_key = matched_table.uns[TableModel.ATTRS_KEY][TableModel.INSTANCE_KEY]
 obs = matched_table.obs
Expand Down