add argument return_background for get_centroids and get_element_instances in the case of labels#621

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Merged
giovp merged 7 commits into from
Jul 9, 2024
Merged

add argument return_background for get_centroids and get_element_instances in the case of labels #621

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45f1195
add argument for and
giovp Jul 8, 2024
c539c56
fix join tests
giovp Jul 8, 2024
89e62eb
cleanup
giovp Jul 8, 2024
69aaf74
add docs
giovp Jul 9, 2024
f2a65df
add note regardign the background label
giovp Jul 9, 2024
b531255
try fixing docs
giovp Jul 9, 2024
3b7026e
add release note
giovp Jul 9, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down
8 changes: 7 additions & 1 deletion src/spatialdata/_core/centroids.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
e: SpatialElement,
coordinate_system: str = "global",
return_background: bool = False,
) -> DaskDataFrame:
"""
Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
coordinate_system
The coordinate system in which the centroids are computed.
return_background
If True, the centroid of the background label (0) is included in the output.

Notes
-----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
-------
pd.DataFrame
A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
The index of the DataFrame is the collection of label values, sorted ascendingly.
The index of the DataFrame is the collection of label values, sorted in ascending order.
"""
centroids: dict[int, float] = defaultdict(float)
for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
e: DataArray | DataTree,
coordinate_system: str = "global",
return_background: bool = False,
) -> DaskDataFrame:
"""Get the centroids of a Labels element (2D or 3D)."""
model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
for axis in get_axes_names(e):
dfs.append(_get_centroids_for_axis(e, axis))
df = pd.concat(dfs, axis=1)
if not return_background and 0 in df.index:
df = df.drop(index=0) # drop the background label
t = get_transformation(e, coordinate_system)
centroids = PointsModel.parse(df, transformations={coordinate_system: t})
return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down
12 changes: 10 additions & 2 deletions src/spatialdata/_core/query/relational_query.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
element: SpatialElement,
return_background: bool = False,
) -> pd.Index:
"""
Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
----------
element
The SpatialElement.
return_background
If True, the background label (0) is included in the output.

Returns
-------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
element: DataArray | DataTree,
return_background: bool = False,
) -> pd.Index:
model = get_model(element)
assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
xdata = next(iter(v))
# can be slow
instances = da.unique(xdata.data).compute()
return pd.Index(np.sort(instances))
index = pd.Index(np.sort(instances))
if not return_background and 0 in index:
return index.drop(0) # drop the background label
return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
both the SpatialElement and table.

For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
the ``'left'`` and ``'right_exclusive'`` joins are supported.
the ``'left'`` and ``'right_exclusive'`` joins are supported.
For Labels, the background label (0) is not included in the output and it will not be returned.

Parameters
----------
Expand Down
8 changes: 5 additions & 3 deletions tests/core/query/test_relational_query.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
table_name="table",
how="left",
)
assert all(table.obs["instance_id"] == range(100))

assert all(table.obs["instance_id"] == range(1, 100))

@giovpgiovpJul 8, 2024

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here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.


full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

element_dict, table = join_spatialelement_table(
sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
)
assert all(table.obs["instance_id"] == range(100))
assert all(table.obs["instance_id"] == range(1, 100))

with pytest.warns(UserWarning, match="Element type"):
join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
)
assert element_dict["labels2d"] is None
assert table is None
assert len(table) == 1
assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down
14 changes: 11 additions & 3 deletions tests/core/test_centroids.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
scale_factors = [2] if is_multiscale else None
if is_3d:
model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
},
index=[0, 1, 2],
)
if not return_background:
expected_centroids = expected_centroids.drop(index=0)
else:
array = np.array(
[
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

if coordinate_system == "aligned":
set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
centroids = get_centroids(element, coordinate_system=coordinate_system)
centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

labels_indices = get_element_instances(element)
labels_indices = get_element_instances(element, return_background=return_background)
assert np.array_equal(centroids.index.values, labels_indices)

if not return_background:
assert 0 not in centroids.index

if coordinate_system == "global":
assert np.array_equal(centroids.compute().values, expected_centroids.values)
else:
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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add argument return_background for get_centroids and get_element_instances in the case of labels#621

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 Merged

giovp
merged 7 commits into

from

Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

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add argument return_background for get_centroids and get_element_instances in the case of labels#621

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 Merged

giovp
merged 7 commits into

from

Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

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add argument return_background for get_centroids and get_element_instances in the case of labels#621

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 Merged

giovp
merged 7 commits into

from

Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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MemberAuthor
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

Skip to content
add argument return_background for get_centroids and get_element_instances in the case of labels#621

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

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to your account

 Merged

giovp
merged 7 commits into

from

Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

Copy link


Copy Markdown

MemberAuthor
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

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add argument return_background for get_centroids and get_element_instances in the case of labels#621

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 Merged

giovp
merged 7 commits into

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Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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MemberAuthor
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The reason will be displayed to describe this comment to others. Learn more.

here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

Skip to content
add argument return_background for get_centroids and get_element_instances in the case of labels#621

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

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 Merged

giovp
merged 7 commits into

from

Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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MemberAuthor
Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down

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

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add argument return_background for get_centroids and get_element_instances in the case of labels#621

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 Merged

giovp
merged 7 commits into

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Jul 9, 2024
 Merged


add argument return_background for get_centroids and get_element_instances in the case of labels
#621
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45f1195

add argument for and


giovp Jul 8, 2024
c539c56

fix join tests


giovp Jul 8, 2024
89e62eb

cleanup


giovp Jul 8, 2024
69aaf74

add docs


giovp Jul 9, 2024
f2a65df

add note regardign the background label


giovp Jul 9, 2024
b531255

try fixing docs


giovp Jul 9, 2024
3b7026e

add release note


giovp Jul 9, 2024

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2 changes: 2 additions & 0 deletions
CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning][].

## [0.x.x] - 2024-xx-xx

- Add `return_background` as argument to `get_centroids` and `get_element_instances` #621

## [0.2.1] - 2024-07-04

### Minor
Expand Down

8 changes: 7 additions & 1 deletion
src/spatialdata/_core/centroids.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -35,6 +35,7 @@ def _validate_coordinate_system(e: SpatialElement, coordinate_system: str) -> No
def get_centroids(
 e: SpatialElement,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """
 Get the centroids of the geometries contained in a SpatialElement, as a new Points element.
Expand All@@ -45,6 +46,8 @@ def get_centroids(
 The SpatialElement. Only points, shapes (circles, polygons and multipolygons) and labels are supported.
 coordinate_system
 The coordinate system in which the centroids are computed.
 return_background
 If True, the centroid of the background label (0) is included in the output.

 Notes
 -----
Expand All@@ -69,7 +72,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
 -------
 pd.DataFrame
 A DataFrame containing one column, named after "axis", with the centroids of the labels along that axis.
 The index of the DataFrame is the collection of label values, sorted ascendingly.
 The index of the DataFrame is the collection of label values, sorted in ascending order.
 """
 centroids: dict[int, float] = defaultdict(float)
 for i in xdata[axis]:
Expand All@@ -95,6 +98,7 @@ def _get_centroids_for_axis(xdata: xr.DataArray, axis: str) -> pd.DataFrame:
def _(
 e: DataArray | DataTree,
 coordinate_system: str = "global",
 return_background: bool = False,
) -> DaskDataFrame:
 """Get the centroids of a Labels element (2D or 3D)."""
 model = get_model(e)
Expand All@@ -110,6 +114,8 @@ def _(
 for axis in get_axes_names(e):
 dfs.append(_get_centroids_for_axis(e, axis))
 df = pd.concat(dfs, axis=1)
 if not return_background and 0 in df.index:
 df = df.drop(index=0) # drop the background label
 t = get_transformation(e, coordinate_system)
 centroids = PointsModel.parse(df, transformations={coordinate_system: t})
 return transform(centroids, to_coordinate_system=coordinate_system)
Expand Down

12 changes: 10 additions & 2 deletions
src/spatialdata/_core/query/relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -86,6 +86,7 @@ def _filter_table_by_element_names(table: AnnData | None, element_names: str | l
@singledispatch
def get_element_instances(
 element: SpatialElement,
 return_background: bool = False,
) -> pd.Index:
 """
 Get the instances (index values) of the SpatialElement.
Expand All@@ -94,6 +95,8 @@ def get_element_instances(
 ----------
 element
 The SpatialElement.
 return_background
 If True, the background label (0) is included in the output.

 Returns
 -------
Expand All@@ -106,6 +109,7 @@ def get_element_instances(
@get_element_instances.register(DataTree)
def _(
 element: DataArray | DataTree,
 return_background: bool = False,
) -> pd.Index:
 model = get_model(element)
 assert model in [Labels2DModel, Labels3DModel], "Expected a `Labels` element. Found an `Image` instead."
Expand All@@ -119,7 +123,10 @@ def _(
 xdata = next(iter(v))
 # can be slow
 instances = da.unique(xdata.data).compute()
 return pd.Index(np.sort(instances))
 index = pd.Index(np.sort(instances))
 if not return_background and 0 in index:
 return index.drop(0) # drop the background label
 return index


@get_element_instances.register(GeoDataFrame)
Expand DownExpand Up@@ -568,7 +575,8 @@ def join_spatialelement_table(
 both the SpatialElement and table.

 For Points and Shapes elements every valid join for argument how is supported. For Labels elements only
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 the ``'left'`` and ``'right_exclusive'`` joins are supported.
 For Labels, the background label (0) is not included in the output and it will not be returned.

 Parameters
 ----------
Expand Down

8 changes: 5 additions & 3 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -699,14 +699,15 @@ def test_labels_table_joins(full_sdata):
 table_name="table",
 how="left",
 )
 assert all(table.obs["instance_id"] == range(100))

 assert all(table.obs["instance_id"] == range(1, 100))
@giovpgiovpJul 8, 2024

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here the labels has values 0,100 but the 0 element is background, so is effectively filtered in the left/right joins when get_element_instances is called on labels. Hence the indices of the instances are different.

 full_sdata["table"].obs["instance_id"] = list(reversed(range(100)))

 element_dict, table = join_spatialelement_table(
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="left", match_rows="left"
 )
 assert all(table.obs["instance_id"] == range(100))
 assert all(table.obs["instance_id"] == range(1, 100))

 with pytest.warns(UserWarning, match="Element type"):
 join_spatialelement_table(
Expand All@@ -724,7 +725,8 @@ def test_labels_table_joins(full_sdata):
 sdata=full_sdata, spatial_element_names="labels2d", table_name="table", how="right_exclusive"
 )
 assert element_dict["labels2d"] is None
 assert table is None
 assert len(table) == 1
 assert all(table.obs["instance_id"] == 0) # the background value, which is filtered out effectively


def test_points_table_joins(full_sdata):
Expand Down

14 changes: 11 additions & 3 deletions
tests/core/test_centroids.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -100,7 +100,10 @@ def test_get_centroids_shapes(shapes, coordinate_system: str, shapes_name: str):
@pytest.mark.parametrize("coordinate_system", ["global", "aligned"])
@pytest.mark.parametrize("is_multiscale", [False, True])
@pytest.mark.parametrize("is_3d", [False, True])
def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: bool, is_3d: bool):
@pytest.mark.parametrize("return_background", [False, True])
def test_get_centroids_labels(
 labels, coordinate_system: str, is_multiscale: bool, is_3d: bool, return_background: bool
):
 scale_factors = [2] if is_multiscale else None
 if is_3d:
 model = Labels3DModel
Expand All@@ -124,6 +127,8 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo
 },
 index=[0, 1, 2],
 )
 if not return_background:
 expected_centroids = expected_centroids.drop(index=0)
 else:
 array = np.array(
 [
Expand All@@ -145,11 +150,14 @@ def test_get_centroids_labels(labels, coordinate_system: str, is_multiscale: boo

 if coordinate_system == "aligned":
 set_transformation(element, transformation=affine, to_coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system)
 centroids = get_centroids(element, coordinate_system=coordinate_system, return_background=return_background)

 labels_indices = get_element_instances(element)
 labels_indices = get_element_instances(element, return_background=return_background)
 assert np.array_equal(centroids.index.values, labels_indices)

 if not return_background:
 assert 0 not in centroids.index

 if coordinate_system == "global":
 assert np.array_equal(centroids.compute().values, expected_centroids.values)
 else:
Expand Down