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Merged
timtreis merged 8 commits into from
Aug 7, 2023
Merged

handle empty points in the image #133

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43b6b3e
handle empty points in the image
Aug 3, 2023
5b4d1cb
Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image
timtreis Aug 3, 2023
73fd58c
Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image
timtreis Aug 3, 2023
3948928
fix _get_collection_shape for when data contains empty points
Sonja-Stockhaus Aug 3, 2023
447ab2f
add unit test for empty geometry in shapes
Aug 5, 2023
0476f91
baseline image empty geometry
Aug 5, 2023
f1af679
changelog update
Aug 7, 2023
a19eb42
Update basic.py
timtreis Aug 7, 2023
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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@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down
4 changes: 4 additions & 0 deletions src/spatialdata_plot/pl/basic.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
kwargs
Additional arguments to be passed to cmap and norm.

Notes
-------
- Empty geometries will be removed at the time of plotting.

Returns
-------
None
Expand Down
2 changes: 2 additions & 0 deletions src/spatialdata_plot/pl/render.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
) -> PatchCollection:
patches = []
for shape in shapes:
# remove empty points/polygons
shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
# We assume that all elements in one collection are of the same type
if shape["geometry"].iloc[0].geom_type == "Polygon":
patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down
6 changes: 4 additions & 2 deletions src/spatialdata_plot/pl/utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

# Split by Point and Polygon:
tmp_points = sdata.shapes[e_id][
sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
sdata.shapes[e_id]["geometry"].apply(
lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
)
]
tmp_polygons = sdata.shapes[e_id][
sdata.shapes[e_id]["geometry"].apply(
lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
)
]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png
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5 changes: 5 additions & 0 deletions tests/pl/test_render_shapes.py
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Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
sdata_blobs.pl.render_shapes(
elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
).pl.show()

def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
sdata_blobs.pl.render_shapes().pl.show()
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

from

Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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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@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

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Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

, 'i');
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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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';
document.head.appendChild(style);
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} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

from

Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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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@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

, 'i');
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// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
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handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

from

Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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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@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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Sorry, this file is invalid so it cannot be displayed.

5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

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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" + '
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
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handle empty points in the image#133

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handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
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5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

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Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

, '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"]');
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btn.click();
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}
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if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
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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('^' + ".*" + '
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

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Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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CHANGELOG.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

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Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

, 'i');
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// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

from

Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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1 change: 1 addition & 0 deletions
CHANGELOG.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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Sorry, this file is invalid so it cannot be displayed.

5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
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} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
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applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
handle empty points in the image by Sonja-Stockhaus · Pull Request #133 · scverse/spatialdata-plot · GitHub
Skip to content
handle empty points in the image#133

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 Merged

timtreis
merged 8 commits into

from

Aug 7, 2023
 Merged


handle empty points in the image
#133
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43b6b3e

handle empty points in the image

Aug 3, 2023
5b4d1cb

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
73fd58c

Merge branch 'main' into bugfix/issue128-reading-highly-resolved-image


timtreis Aug 3, 2023
3948928

fix _get_collection_shape for when data contains empty points


Sonja-Stockhaus Aug 3, 2023
447ab2f

add unit test for empty geometry in shapes

Aug 5, 2023
0476f91

baseline image empty geometry

Aug 5, 2023
f1af679

changelog update

Aug 7, 2023
a19eb42

Update basic.py


timtreis Aug 7, 2023

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1 change: 1 addition & 0 deletions
CHANGELOG.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning][].
### Fixed

- Multi-scale images/labels are now correctly substituted and the action is logged (#131).
- Empty geometries among the shapes can be handeled (#133).

## [0.0.2] - 2023-06-25

Expand Down

4 changes: 4 additions & 0 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -195,6 +195,10 @@ def render_shapes(
 kwargs
 Additional arguments to be passed to cmap and norm.

 Notes
 -------
 - Empty geometries will be removed at the time of plotting.

 Returns
 -------
 None
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata_plot/pl/render.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -121,6 +121,8 @@ def _get_collection_shape(
 ) -> PatchCollection:
 patches = []
 for shape in shapes:
 # remove empty points/polygons
 shape = shape[shape["geometry"].apply(lambda geom: not geom.is_empty)]
 # We assume that all elements in one collection are of the same type
 if shape["geometry"].iloc[0].geom_type == "Polygon":
 patches += [Polygon(p.exterior.coords, closed=True) for p in shape["geometry"]]
Expand Down

6 changes: 4 additions & 2 deletions
src/spatialdata_plot/pl/utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -314,11 +314,13 @@ def get_point_bb(

 # Split by Point and Polygon:
 tmp_points = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(lambda geom: geom.geom_type == "Point")
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: (geom.geom_type == "Point" and not geom.is_empty)
 )
 ]
 tmp_polygons = sdata.shapes[e_id][
 sdata.shapes[e_id]["geometry"].apply(
 lambda geom: geom.geom_type in ["Polygon", "MultiPolygon"]
 lambda geom: (geom.geom_type in ["Polygon", "MultiPolygon"] and not geom.is_empty)
 )
 ]

Expand Down
Binary file addedtests/_images/Shapes_can_render_empty_geometry.png

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Sorry, this file is invalid so it cannot be displayed.

5 changes: 5 additions & 0 deletions
tests/pl/test_render_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,3 +1,4 @@
import geopandas as gpd
import matplotlib
import scanpy as sc
import spatialdata_plot # noqa: F401
Expand DownExpand Up@@ -46,3 +47,7 @@ def test_plot_can_render_polygons_with_rgba_colored_outline(self, sdata_blobs: S
 sdata_blobs.pl.render_shapes(
 elements="blobs_polygons", outline=True, outline_color=(0.0, 1.0, 0.0, 1.0)
 ).pl.show()

 def test_plot_can_render_empty_geometry(self, sdata_blobs: SpatialData):
 sdata_blobs.shapes["blobs_circles"].at[0, "geometry"] = gpd.points_from_xy([None], [None])[0]
 sdata_blobs.pl.render_shapes().pl.show()