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Fix HistogramWidget for multiscale data #252

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Merged
merged 2 commits into from
Jan 23, 2024
Merged

Fix HistogramWidget for multiscale data #252

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34c9e2c
Fix HistogramWidget for multiscale
dstansby Jan 23, 2024
31c8fac
Fix pandas deprecation warning
dstansby Jan 23, 2024
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5 changes: 3 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,15 @@ build-backend = "setuptools.build_meta"
write_to = "src/napari_matplotlib/_version.py"

[tool.pytest.ini_options]
qt_api = "pyqt6"
addopts = "--mpl --mpl-baseline-relative"
filterwarnings = [
"error",
"ignore:(?s).*Pyarrow will become a required dependency of pandas",
# Coming from vispy
"ignore:distutils Version classes are deprecated:DeprecationWarning",
"ignore:`np.bool8` is a deprecated alias for `np.bool_`:DeprecationWarning",
]
qt_api = "pyqt6"
addopts = "--mpl --mpl-baseline-relative"

[tool.black]
line-length = 79
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16 changes: 11 additions & 5 deletions src/napari_matplotlib/histogram.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
import numpy as np
import numpy.typing as npt
from matplotlib.container import BarContainer
from napari.layers import Image
from napari.layers._multiscale_data import MultiScaleData
from qtpy.QtWidgets import (
QComboBox,
QLabel,
Expand Down Expand Up @@ -67,14 +69,18 @@ def draw(self) -> None:
"""
Clear the axes and histogram the currently selected layer/slice.
"""
layer = self.layers[0]
layer: Image = self.layers[0]
data = layer.data

if layer.data.ndim - layer.rgb == 3:
if isinstance(layer.data, MultiScaleData):
data = data[layer.data_level]

if layer.ndim - layer.rgb == 3:
# 3D data, can be single channel or RGB
data = layer.data[self.current_z]
# Slice in z dimension
data = data[self.current_z]
self.axes.set_title(f"z={self.current_z}")
else:
data = layer.data

# Read data into memory if it's a dask array
data = np.asarray(data)

Expand Down