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Images no longer normalised by default #150

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Merged
timtreis merged 2 commits into from
Aug 29, 2023
Merged

Images no longer normalised by default #150

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b37a710
Disabled default normalisation
timtreis Aug 29, 2023
9ebe0cc
Removed default numeric values from remaining locations
timtreis Aug 29, 2023
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2 changes: 1 addition & 1 deletion src/spatialdata_plot/pl/basic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
"""
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2 changes: 1 addition & 1 deletion src/spatialdata_plot/pl/render.py
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Expand Up @@ -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(
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4 changes: 2 additions & 2 deletions src/spatialdata_plot/pl/utils.py
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Expand Up @@ -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",
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