diff --git a/docs/changelog.rst b/docs/changelog.rst
index 103cd80e..f7425bfe 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -1,5 +1,11 @@
Changelog
=========
+1.0.3
+-----
+Bug fixes
+~~~~~~~~~
+- Fixed creating 1D slices of 2D images.
+
1.0.2
-----
Bug fixes
diff --git a/src/napari_matplotlib/slice.py b/src/napari_matplotlib/slice.py
index e3aa80b2..f0d01f3f 100644
--- a/src/napari_matplotlib/slice.py
+++ b/src/napari_matplotlib/slice.py
@@ -1,4 +1,4 @@
-from typing import Any, Dict, Optional, Tuple
+from typing import Any, Dict, List, Optional, Tuple
import matplotlib.ticker as mticker
import napari
@@ -12,7 +12,6 @@
__all__ = ["SliceWidget"]
_dims_sel = ["x", "y"]
-_dims = ["x", "y", "z"]
class SliceWidget(SingleAxesWidget):
@@ -37,7 +36,7 @@ def __init__(
self.dim_selector = QComboBox()
button_layout.addWidget(QLabel("Slice axis:"))
button_layout.addWidget(self.dim_selector)
- self.dim_selector.addItems(_dims)
+ self.dim_selector.addItems(["x", "y", "z"])
self.slice_selectors = {}
for d in _dims_sel:
@@ -61,7 +60,7 @@ def _layer(self) -> napari.layers.Layer:
return self.layers[0]
@property
- def current_dim(self) -> str:
+ def current_dim_name(self) -> str:
"""
Currently selected slice dimension.
"""
@@ -74,12 +73,27 @@ def current_dim_index(self) -> int:
"""
# Note the reversed list because in napari the z-axis is the first
# numpy axis
- return _dims[::-1].index(self.current_dim)
+ return self._dim_names[::-1].index(self.current_dim_name)
+
+ @property
+ def _dim_names(self) -> List[str]:
+ """
+ List of dimension names. This is a property as it varies depending on the
+ dimensionality of the currently selected data.
+ """
+ if self._layer.data.ndim == 2:
+ return ["x", "y"]
+ elif self._layer.data.ndim == 3:
+ return ["x", "y", "z"]
+ else:
+ raise RuntimeError("Don't know how to handle ndim != 2 or 3")
@property
def _selector_values(self) -> Dict[str, int]:
"""
Values of the slice selectors.
+
+ Mapping from dimension name to value.
"""
return {d: self.slice_selectors[d].value() for d in _dims_sel}
@@ -87,19 +101,22 @@ def _get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
"""
Get data for plotting.
"""
- x = np.arange(self._layer.data.shape[self.current_dim_index])
+ dim_index = self.current_dim_index
+ if self._layer.data.ndim == 2:
+ dim_index -= 1
+ x = np.arange(self._layer.data.shape[dim_index])
vals = self._selector_values
vals.update({"z": self.current_z})
slices = []
- for d in _dims:
- if d == self.current_dim:
+ for dim_name in self._dim_names:
+ if dim_name == self.current_dim_name:
# Select all data along this axis
slices.append(slice(None))
else:
# Select specific index
- val = vals[d]
+ val = vals[dim_name]
slices.append(slice(val, val + 1))
# Reverse since z is the first axis in napari
@@ -115,7 +132,7 @@ def draw(self) -> None:
x, y = self._get_xy()
self.axes.plot(x, y)
- self.axes.set_xlabel(self.current_dim)
+ self.axes.set_xlabel(self.current_dim_name)
self.axes.set_title(self._layer.name)
# Make sure all ticks lie on integer values
self.axes.xaxis.set_major_locator(
diff --git a/src/napari_matplotlib/tests/baseline/test_slice_2D.png b/src/napari_matplotlib/tests/baseline/test_slice_2D.png
index 639f25b8..ee3ce3b6 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_slice_2D.png and b/src/napari_matplotlib/tests/baseline/test_slice_2D.png differ
diff --git a/src/napari_matplotlib/tests/baseline/test_slice_3D.png b/src/napari_matplotlib/tests/baseline/test_slice_3D.png
index 43c8c3b6..c30211da 100644
Binary files a/src/napari_matplotlib/tests/baseline/test_slice_3D.png and b/src/napari_matplotlib/tests/baseline/test_slice_3D.png differ
diff --git a/src/napari_matplotlib/tests/test_slice.py b/src/napari_matplotlib/tests/test_slice.py
index 412e71c3..32eb9ad4 100644
--- a/src/napari_matplotlib/tests/test_slice.py
+++ b/src/napari_matplotlib/tests/test_slice.py
@@ -9,9 +9,13 @@
def test_slice_3D(make_napari_viewer, brain_data):
viewer = make_napari_viewer()
viewer.theme = "light"
- viewer.add_image(brain_data[0], **brain_data[1])
+
+ data = brain_data[0]
+ assert data.ndim == 3, data.shape
+ viewer.add_image(data, **brain_data[1])
+
axis = viewer.dims.last_used
- slice_no = brain_data[0].shape[0] - 1
+ slice_no = data.shape[0] - 1
viewer.dims.set_current_step(axis, slice_no)
fig = SliceWidget(viewer).figure
# Need to return a copy, as original figure is too eagerley garbage
@@ -23,7 +27,12 @@ def test_slice_3D(make_napari_viewer, brain_data):
def test_slice_2D(make_napari_viewer, astronaut_data):
viewer = make_napari_viewer()
viewer.theme = "light"
- viewer.add_image(astronaut_data[0], **astronaut_data[1])
+
+ # Take first RGB channel
+ data = astronaut_data[0][:, :, 0]
+ assert data.ndim == 2, data.shape
+ viewer.add_image(data)
+
fig = SliceWidget(viewer).figure
# Need to return a copy, as original figure is too eagerley garbage
# collected by the widget
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