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Merged
LucaMarconato merged 5 commits into from
Jan 17, 2024
Merged

Made _locate_spatial_element public, renamed to locate_element() #427

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9200dae
made _locate_spatial_element public, renamed to locate_element()
LucaMarconato Jan 9, 2024
99dd10b
Merge branch 'main' into locate_element
LucaMarconato Jan 16, 2024
cc8d173
returning path instead of tuple in locate_element()
LucaMarconato Jan 16, 2024
3d50252
updated changelog
LucaMarconato Jan 16, 2024
615bd79
locate_elements() now returns a list
LucaMarconato Jan 17, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down
87 changes: 29 additions & 58 deletions src/spatialdata/_core/spatialdata.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
return elem_group
return root

def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
def locate_element(self, element: SpatialElement) -> list[str] | None:
"""
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

Parameters
----------
element
The queried SpatialElement


Returns
-------
name and type of the element

Raises
------
ValueError
the element is not found or found multiple times in the SpatialData object
A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
None if the element is not found.
"""
found: list[SpatialElement] = []
found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
found_element_type.append(element_type)
found_element_name.append(element_name)
if len(found) == 0:
raise ValueError("Element not found in the SpatialData object.")
if len(found) > 1:
raise ValueError(
f"Element found multiple times in the SpatialData object."
f"Found {len(found)} elements with names: {found_element_name},"
f" and types: {found_element_type}"
)
assert len(found_element_name) == 1
assert len(found_element_type) == 1
return found_element_name[0], found_element_type[0]

def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
"""
Check if the SpatialElement is contained in the SpatialData object.

Parameters
----------
element
The SpatialElement to check
raise_exception
If True, raise an exception if the element is not found. If False, return False if the element is not found.

Returns
-------
True if the element is found; False otherwise (if raise_exception is False).
"""
try:
self._locate_spatial_element(element)
return True
except ValueError as e:
if raise_exception:
raise e
return False
return None
Comment thread
LucaMarconato marked this conversation as resolved.
return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

def _write_transformations_to_disk(self, element: SpatialElement) -> None:
"""
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

transformations = get_transformation(element, get_all=True)
assert isinstance(transformations, dict)
found_element_name, found_element_type = self._locate_spatial_element(element)

located = self.locate_element(element)
if located is None:
raise ValueError(
"Cannot save the transformation to the element as it has not been found in the SpatialData object"
)
if self.path is not None:
group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
axes = get_axes_names(element)
if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_raster,
)
for path in located:
found_element_type, found_element_name = path.split("/")
group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
axes = get_axes_names(element)
if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_raster,
)

overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
else:
raise ValueError("Unknown element type")
overwrite_coordinate_transformations_non_raster(
group=group, axes=axes, transformations=transformations
)
else:
raise ValueError("Unknown element type")

def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
"""
Expand Down
8 changes: 4 additions & 4 deletions src/spatialdata/transformations/operations.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
assert to_coordinate_system is None
_set_transformations(element, transformation)
else:
if not write_to_sdata.contains_element(element, raise_exception=True):
raise RuntimeError("contains_element() failed without raising an exception.")
if write_to_sdata.locate_element(element) is None:
raise RuntimeError("The element is not found in the SpatialData object.")
if not write_to_sdata.is_backed():
raise ValueError(
"The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
assert to_coordinate_system is None
_set_transformations(element, {})
else:
if not write_to_sdata.contains_element(element, raise_exception=True):
raise RuntimeError("contains_element() failed without raising an exception.")
if write_to_sdata.locate_element(element) is None:
raise RuntimeError("The element is not found in the SpatialData object.")
if not write_to_sdata.is_backed():
raise ValueError(
"The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down
9 changes: 4 additions & 5 deletions tests/core/operations/test_spatialdata_operations.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
im = full_sdata.images["image2d"]
del full_sdata.images["image2d"]
with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
full_sdata._locate_spatial_element(im)
assert full_sdata.locate_element(im) is None
full_sdata.images["image2d"] = im
full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
Expand Down
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
Skip to content
Made _locate_spatial_element public, renamed to locate_element()#427

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 Merged

LucaMarconato
merged 5 commits into

from

Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

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1 change: 1 addition & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
Expand Down

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// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
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.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
Skip to content
Made _locate_spatial_element public, renamed to locate_element()#427

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to your account

 Merged

LucaMarconato
merged 5 commits into

from

Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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Commits

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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

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1 change: 1 addition & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
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Made _locate_spatial_element public, renamed to locate_element()#427

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LucaMarconato
merged 5 commits into

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Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

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1 change: 1 addition & 0 deletions
CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
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" + '
Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
Skip to content
Made _locate_spatial_element public, renamed to locate_element()#427

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 Merged

LucaMarconato
merged 5 commits into

from

Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

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1 change: 1 addition & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
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('^' + ".*" + '
Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
Skip to content
Made _locate_spatial_element public, renamed to locate_element()#427

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

LucaMarconato
merged 5 commits into

from

Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

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CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
Expand Down

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Made _locate_spatial_element public, renamed to locate_element() by LucaMarconato · Pull Request #427 · scverse/spatialdata · GitHub
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LucaMarconato
merged 5 commits into

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Jan 17, 2024
 Merged


Made _locate_spatial_element public, renamed to locate_element()
#427
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9200dae

made _locate_spatial_element public, renamed to locate_element()


LucaMarconato Jan 9, 2024
99dd10b

Merge branch 'main' into locate_element


LucaMarconato Jan 16, 2024
cc8d173

returning path instead of tuple in locate_element()


LucaMarconato Jan 16, 2024
3d50252

updated changelog


LucaMarconato Jan 16, 2024
615bd79

locate_elements() now returns a list


LucaMarconato Jan 17, 2024

File filter

Filter by extension
Filter by extension
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Loading
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1 change: 1 addition & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning][].
### Added

- added SpatialData.subset() API
- added SpatialData.locate_element() API

### Fixed

Expand Down

87 changes: 29 additions & 58 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -312,24 +312,19 @@ def _init_add_element(self, name: str, element_type: str, overwrite: bool) -> za
 return elem_group
 return root

 def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 def locate_element(self, element: SpatialElement) -> list[str] | None:
 """
Find the SpatialElement within the SpatialData object.
Locate a SpatialElement within the SpatialData object and, if found, returns its Zarr path relative to the root.

 Parameters
 ----------
 element
 The queried SpatialElement


 Returns
 -------
 name and type of the element

 Raises
 ------
 ValueError
 the element is not found or found multiple times in the SpatialData object
 A list of Zarr paths of the element relative to the root (multiple copies of the same element are allowed), or
 None if the element is not found.
 """
 found: list[SpatialElement] = []
 found_element_type: list[str] = []
Expand All@@ -341,39 +336,8 @@ def _locate_spatial_element(self, element: SpatialElement) -> tuple[str, str]:
 found_element_type.append(element_type)
 found_element_name.append(element_name)
 if len(found) == 0:
 raise ValueError("Element not found in the SpatialData object.")
 if len(found) > 1:
 raise ValueError(
 f"Element found multiple times in the SpatialData object."
 f"Found {len(found)} elements with names: {found_element_name},"
 f" and types: {found_element_type}"
 )
 assert len(found_element_name) == 1
 assert len(found_element_type) == 1
 return found_element_name[0], found_element_type[0]

 def contains_element(self, element: SpatialElement, raise_exception: bool = False) -> bool:
 """
 Check if the SpatialElement is contained in the SpatialData object.

 Parameters
 ----------
 element
 The SpatialElement to check
 raise_exception
 If True, raise an exception if the element is not found. If False, return False if the element is not found.

 Returns
 -------
 True if the element is found; False otherwise (if raise_exception is False).
 """
 try:
 self._locate_spatial_element(element)
 return True
 except ValueError as e:
 if raise_exception:
 raise e
 return False
 return None
Comment thread
LucaMarconato marked this conversation as resolved.

 return [f"{found_element_type[i]}/{found_element_name[i]}" for i in range(len(found))]

 def _write_transformations_to_disk(self, element: SpatialElement) -> None:
 """
Expand All@@ -388,25 +352,32 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:

 transformations = get_transformation(element, get_all=True)
 assert isinstance(transformations, dict)
 found_element_name, found_element_type = self._locate_spatial_element(element)

 located = self.locate_element(element)
 if located is None:
 raise ValueError(
 "Cannot save the transformation to the element as it has not been found in the SpatialData object"
 )
 if self.path is not None:
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )
 for path in located:
 found_element_type, found_element_name = path.split("/")
 group = self._get_group_for_element(name=found_element_name, element_type=found_element_type)
 axes = get_axes_names(element)
 if isinstance(element, (SpatialImage, MultiscaleSpatialImage)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_raster,
 )

 overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
 elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
 from spatialdata._io._utils import (
 overwrite_coordinate_transformations_non_raster,
 )
overwrite_coordinate_transformations_raster(group=group, axes=axes, transformations=transformations)
elif isinstance(element, (DaskDataFrame, GeoDataFrame, AnnData)):
from spatialdata._io._utils import (
overwrite_coordinate_transformations_non_raster,
)

 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
 else:
 raise ValueError("Unknown element type")
 overwrite_coordinate_transformations_non_raster(
 group=group, axes=axes, transformations=transformations
 )
 else:
 raise ValueError("Unknown element type")

 def filter_by_coordinate_system(self, coordinate_system: str | list[str], filter_table: bool = True) -> SpatialData:
 """
Expand Down

8 changes: 4 additions & 4 deletions
src/spatialdata/transformations/operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,8 +68,8 @@ def set_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, transformation)
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either set a transformation to an element "
Expand DownExpand Up@@ -164,8 +164,8 @@ def remove_transformation(
 assert to_coordinate_system is None
 _set_transformations(element, {})
 else:
 if not write_to_sdata.contains_element(element, raise_exception=True):
 raise RuntimeError("contains_element() failed without raising an exception.")
 if write_to_sdata.locate_element(element) is None:
 raise RuntimeError("The element is not found in the SpatialData object.")
 if not write_to_sdata.is_backed():
 raise ValueError(
 "The SpatialData object is not backed. You can either remove a transformation from an "
Expand Down

9 changes: 4 additions & 5 deletions
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -310,15 +310,14 @@ def test_concatenate_sdatas(full_sdata: SpatialData) -> None:


def test_locate_spatial_element(full_sdata: SpatialData) -> None:
 assert full_sdata._locate_spatial_element(full_sdata.images["image2d"]) == ("image2d", "images")
 assert full_sdata.locate_element(full_sdata.images["image2d"])[0] == "images/image2d"
 im = full_sdata.images["image2d"]
 del full_sdata.images["image2d"]
 with pytest.raises(ValueError, match="Element not found in the SpatialData object."):
 full_sdata._locate_spatial_element(im)
 assert full_sdata.locate_element(im) is None
 full_sdata.images["image2d"] = im
 full_sdata.images["image2d_again"] = im
with pytest.raises(ValueError):
 full_sdata._locate_spatial_element(im)
paths = full_sdata.locate_element(im)
assert len(paths) == 2


def test_get_item(points: SpatialData) -> None:
Expand Down