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fix wrong point size when affine specified #193

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merged 1 commit into from
Mar 14, 2024
Merged

fix wrong point size when affine specified #193

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28 changes: 25 additions & 3 deletions src/napari_spatialdata/_viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@
from qtpy.QtCore import QObject, Signal
from shapely import Polygon
from spatialdata.models import PointsModel, ShapesModel
from spatialdata.transformations import Identity
from spatialdata.transformations import Affine, Identity
from spatialdata.transformations._utils import scale_radii

from napari_spatialdata.utils._utils import (
_adjust_channels_order,
Expand Down Expand Up @@ -307,7 +308,7 @@ def add_sdata_circles(self, sdata: SpatialData, key: str, selected_cs: str, mult
radii = df.radius.to_numpy()
adata = _get_metadata_adata(sdata, original_name)

self.viewer.add_points(
layer = self.viewer.add_points(
xy,
name=key,
affine=affine,
Expand All @@ -324,6 +325,8 @@ def add_sdata_circles(self, sdata: SpatialData, key: str, selected_cs: str, mult
"indices": df.index.to_list(),
},
)
assert affine is not None
self._adjust_radii_of_points_layer(layer=layer, affine=affine)

def add_sdata_shapes(self, sdata: SpatialData, key: str, selected_cs: str, multi: bool) -> None:
original_name = key
Expand Down Expand Up @@ -405,7 +408,7 @@ def add_sdata_points(self, sdata: SpatialData, key: str, selected_cs: str, multi

xy = points[["y", "x"]].values[subsample]
np.fliplr(xy)
self.viewer.add_points(
layer = self.viewer.add_points(
xy,
name=key,
size=20,
Expand All @@ -421,6 +424,23 @@ def add_sdata_points(self, sdata: SpatialData, key: str, selected_cs: str, multi
"indices": subsample.tolist(),
},
)
assert affine is not None
self._adjust_radii_of_points_layer(layer=layer, affine=affine)

def _adjust_radii_of_points_layer(self, layer: Layer, affine: npt.ArrayLike) -> None:
assert isinstance(affine, np.ndarray)
axes: tuple[str, ...]
if affine.shape == (3, 3):
axes = ("y", "x")
elif affine.shape == (4, 4):
axes = ("z", "y", "x")
else:
raise ValueError(f"Invalid affine shape: {affine.shape}")
affine_transformation = Affine(affine, input_axes=axes, output_axes=axes)
metadata = layer.metadata
radii = metadata["sdata"][metadata["name"]].radius.to_numpy()
new_radii = scale_radii(radii=radii, affine=affine_transformation, axes=axes)
layer.size = new_radii * 2

def _affine_transform_layers(self, coordinate_system: str) -> None:
for layer in self.viewer.layers:
Expand All @@ -432,3 +452,5 @@ def _affine_transform_layers(self, coordinate_system: str) -> None:
affine = _get_transform(element_data, coordinate_system)
if affine is not None:
layer.affine = affine
if layer._type_string == "points":
self._adjust_radii_of_points_layer(layer, affine)
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