Images no longer normalised by default (#150)

Author: timtreis

src/spatialdata_plot/pl/basic.py

@@ -306,7 +306,7 @@ def render_images(
         na_color: str | tuple[float, ...] | None = (0.0, 0.0, 0.0, 0.0),
         palette: ListedColormap | str | None = None,
         alpha: float = 1.0,
-        quantiles_for_norm: tuple[float | None, float | None] = (3.0, 99.8),  # defaults from CSBDeep
+        quantiles_for_norm: tuple[float | None, float | None] = (None, None),
         **kwargs: Any,
     ) -> sd.SpatialData:
         """

src/spatialdata_plot/pl/render.py

@@ -377,7 +377,7 @@ class ImageRenderParams:
     channel: list[str] | list[int] | int | str | None = None
     palette: ListedColormap | str | None = None
     alpha: float = 1.0
-    quantiles_for_norm: tuple[float | None, float | None] = (3.0, 99.8)  # defaults from CSBDeep
+    quantiles_for_norm: tuple[float | None, float | None] = (None, None)
 
 
 def _render_images(

src/spatialdata_plot/pl/utils.py

@@ -613,8 +613,8 @@ def _get_hex_colors_for_continous_values(values: pd.Series, cmap_name: str = "vi
 
 def _normalize(
     img: xr.DataArray,
-    pmin: float | None = 3.0,
-    pmax: float | None = 99.8,
+    pmin: float | None = None,
+    pmax: float | None = None,
     eps: float = 1e-20,
     clip: bool = False,
     name: str = "normed",