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Merged
LucaMarconato merged 4 commits into from
Jul 18, 2024
Merged

Fix setting vmin vmax #307

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668831f
fix vmin vmax
melonora Jul 15, 2024
7823d90
add tests
melonora Jul 15, 2024
179951b
add to changelog
melonora Jul 15, 2024
88c018b
add baseline to test
melonora Jul 16, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning][].
- scale parameter was ignored for single-scale images (#301)
- Changes to support for dask-expr (#283)
- Added error handling for non-existent elements (#305)
- Specifying vmin and vmax properly clips image data (#307)

## [0.2.3] - 2024-07-03

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4 changes: 2 additions & 2 deletions src/spatialdata_plot/pl/utils.py
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Expand Up@@ -375,11 +375,11 @@ def _prepare_cmap_norm(
cmap.set_bad("lightgray" if na_color is None else na_color)

if norm is None:
norm = Normalize(vmin=vmin, vmax=vmax)
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
elif isinstance(norm, Normalize) or not norm:
pass # TODO
elif vcenter is None:
norm = Normalize(vmin=vmin, vmax=vmax)
norm = Normalize(vmin=vmin, vmax=vmax, clip=True)
else:
norm = TwoSlopeNorm(vmin=vmin, vmax=vmax, vcenter=vcenter)

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Binary file addedtests/_images/Images_can_pass_normalize.png
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Binary file addedtests/_images/Images_can_pass_vmin_vmax.png
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13 changes: 13 additions & 0 deletions tests/pl/test_render_images.py
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Expand Up@@ -3,6 +3,8 @@
import numpy as np
import scanpy as sc
import spatialdata_plot # noqa: F401
from matplotlib import pyplot as plt
from matplotlib.colors import Normalize
from spatial_image import to_spatial_image
from spatialdata import SpatialData

Expand DownExpand Up@@ -68,6 +70,17 @@ def test_plot_can_render_two_channels_str_from_image(self, sdata_blobs_str: Spat
def test_plot_can_render_two_channels_str_from_multiscale_image(self, sdata_blobs_str: SpatialData):
sdata_blobs_str.pl.render_images(element="blobs_multiscale_image", channel=["c1", "c2"]).pl.show()

def test_plot_can_pass_vmin_vmax(self, sdata_blobs: SpatialData):
fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
sdata_blobs.pl.render_images(element="blobs_image", channel=1).pl.show(ax=axs[0])
sdata_blobs.pl.render_images(element="blobs_image", channel=1, vmin=0, vmax=0.4).pl.show(ax=axs[1])

def test_plot_can_pass_normalize(self, sdata_blobs: SpatialData):
fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
norm = Normalize(vmin=0, vmax=0.4, clip=True)
sdata_blobs.pl.render_images(element="blobs_image", channel=1).pl.show(ax=axs[0])
sdata_blobs.pl.render_images(element="blobs_image", channel=1, norm=norm).pl.show(ax=axs[1])

def test_plot_can_pass_color_to_single_channel(self, sdata_blobs: SpatialData):
sdata_blobs.pl.render_images(element="blobs_image", channel=1, palette="red").pl.show()

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