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Fix color future warning #308

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merged 10 commits into from
Aug 13, 2024
Merged

Fix color future warning #308

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65083d9
Fix FutureWarning: Labels.color is deprecated
zoccoler Mar 26, 2024
00a7eeb
Fix bug when viewer is closed from code
zoccoler Mar 26, 2024
be58dc0
Fix opacity attribution (again)
zoccoler Mar 26, 2024
7d463a7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 26, 2024
aa06562
update requirements
zoccoler Mar 28, 2024
c6fc41d
Revert "Fix opacity attribution (again)"
zoccoler Apr 12, 2024
9f777ea
revert checking image layer type
zoccoler Apr 12, 2024
1ddbffb
remove unused layer type
zoccoler Apr 12, 2024
c734987
Merge branch 'main' into fix_color_future_warning
zoccoler Aug 12, 2024
7cdf261
remove unused variable
zoccoler Aug 12, 2024
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12 changes: 6 additions & 6 deletions napari_clusters_plotter/_plotter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import pandas as pd
from matplotlib.figure import Figure
from napari.layers import Image, Labels, Layer, Points, Surface
from napari.utils import DirectLabelColormap
from napari.utils.colormaps import ALL_COLORMAPS
from napari_tools_menu import register_dock_widget
from qtpy import QtWidgets
Expand Down Expand Up @@ -719,7 +720,7 @@
for prediction in np.unique(self.cluster_ids)
}
# take care of background label
cmap_dict[0] = [0, 0, 0, 0]
cmap_dict[None] = [0, 0, 0, 0]

keep_selection = list(self.viewer.layers.selection)

Expand Down Expand Up @@ -820,7 +821,7 @@
layer_in_viewer.colormap = self.visualized_layer.colormap
layer_in_viewer.contrast_limits = self.visualized_layer.contrast_limits
elif isinstance(self.visualized_layer, Labels):
layer_in_viewer.color = self.visualized_layer.color
layer_in_viewer.colormap = self.visualized_layer.colormap

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else:
print("Update failed")

Expand Down Expand Up @@ -856,11 +857,10 @@
cluster_data = generate_cluster_4d_labels(
self.analysed_layer, plot_cluster_name
)

cluster_layer = Layer.create(
cluster_data,
{
"color": cmap_dict,
"colormap": DirectLabelColormap(color_dict=cmap_dict),
"name": "cluster_ids_in_space",
"scale": self.layer_select.value.scale,
},
Expand All @@ -878,7 +878,7 @@
cluster_layer = Layer.create(
cluster_data,
{
"color": cmap_dict,
"colormap": DirectLabelColormap(color_dict=cmap_dict),
"name": "cluster_ids_in_space",
"scale": self.layer_select.value.scale,
},
Expand Down Expand Up @@ -919,7 +919,7 @@
cluster_layer = Layer.create(
cluster_data,
{
"color": cmap_dict,
"colormap": DirectLabelColormap(color_dict=cmap_dict),
"name": "cluster_ids_in_space",
"scale": self.layer_select.value.scale,
},
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -10,7 +10,7 @@ tornado~=6.2
numpy~=1.23.5
docutils~=0.17.1
pandas~=1.5.3
napari~=0.4.17
napari~=0.4.19
matplotlib~=3.7.1
magicgui~=0.7.2
qtpy~=2.3.0
Expand Down
2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -49,7 +49,7 @@ install_requires =
hdbscan
qtpy
dask
napari
napari>=0.4.19
magicgui
scikit-image
superqt
Expand Down
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