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Commit d7e88a9

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dstansbydstansby
authored
Merge pull request #205 from dstansby/slice-test-ndim
Fix slicing 2D images
2 parents cee4975 + 08ee5d0 commit d7e88a9
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‎docs/changelog.rst

Copy file name to clipboardExpand all lines: docs/changelog.rst
+6Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,11 @@
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Changelog
22
=========
3+
1.0.3
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-----
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Bug fixes
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~~~~~~~~~
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- Fixed creating 1D slices of 2D images.
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39
1.0.2
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-----
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Bug fixes

‎src/napari_matplotlib/slice.py

Copy file name to clipboardExpand all lines: src/napari_matplotlib/slice.py
+27-10Lines changed: 27 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
from typing import Any, Dict, Optional, Tuple
1+
from typing import Any, Dict, List, Optional, Tuple
22

33
import matplotlib.ticker as mticker
44
import napari
@@ -12,7 +12,6 @@
1212
__all__ = ["SliceWidget"]
1313

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_dims_sel = ["x", "y"]
15-
_dims = ["x", "y", "z"]
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1716

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class SliceWidget(SingleAxesWidget):
@@ -37,7 +36,7 @@ def __init__(
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self.dim_selector = QComboBox()
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button_layout.addWidget(QLabel("Slice axis:"))
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button_layout.addWidget(self.dim_selector)
40-
self.dim_selector.addItems(_dims)
39+
self.dim_selector.addItems(["x", "y", "z"])
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4241
self.slice_selectors = {}
4342
for d in _dims_sel:
@@ -61,7 +60,7 @@ def _layer(self) -> napari.layers.Layer:
6160
return self.layers[0]
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6362
@property
64-
def current_dim(self) -> str:
63+
def current_dim_name(self) -> str:
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"""
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Currently selected slice dimension.
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"""
@@ -74,32 +73,50 @@ def current_dim_index(self) -> int:
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"""
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# Note the reversed list because in napari the z-axis is the first
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# numpy axis
77-
return _dims[::-1].index(self.current_dim)
76+
return self._dim_names[::-1].index(self.current_dim_name)
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78+
@property
79+
def _dim_names(self) -> List[str]:
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"""
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List of dimension names. This is a property as it varies depending on the
82+
dimensionality of the currently selected data.
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"""
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if self._layer.data.ndim == 2:
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return ["x", "y"]
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elif self._layer.data.ndim == 3:
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return ["x", "y", "z"]
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else:
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raise RuntimeError("Don't know how to handle ndim != 2 or 3")
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@property
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def _selector_values(self) -> Dict[str, int]:
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"""
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Values of the slice selectors.
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Mapping from dimension name to value.
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"""
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return {d: self.slice_selectors[d].value() for d in _dims_sel}
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def _get_xy(self) -> Tuple[npt.NDArray[Any], npt.NDArray[Any]]:
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"""
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Get data for plotting.
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"""
90-
x = np.arange(self._layer.data.shape[self.current_dim_index])
104+
dim_index = self.current_dim_index
105+
if self._layer.data.ndim == 2:
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dim_index -= 1
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x = np.arange(self._layer.data.shape[dim_index])
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vals = self._selector_values
93110
vals.update({"z": self.current_z})
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slices = []
96-
for d in _dims:
97-
if d == self.current_dim:
113+
for dim_name in self._dim_names:
114+
if dim_name == self.current_dim_name:
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# Select all data along this axis
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slices.append(slice(None))
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else:
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# Select specific index
102-
val = vals[d]
119+
val = vals[dim_name]
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slices.append(slice(val, val + 1))
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# Reverse since z is the first axis in napari
@@ -115,7 +132,7 @@ def draw(self) -> None:
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x, y = self._get_xy()
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self.axes.plot(x, y)
118-
self.axes.set_xlabel(self.current_dim)
135+
self.axes.set_xlabel(self.current_dim_name)
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self.axes.set_title(self._layer.name)
120137
# Make sure all ticks lie on integer values
121138
self.axes.xaxis.set_major_locator(

‎src/napari_matplotlib/tests/baseline/test_slice_2D.png

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‎src/napari_matplotlib/tests/baseline/test_slice_3D.png

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‎src/napari_matplotlib/tests/test_slice.py

Copy file name to clipboardExpand all lines: src/napari_matplotlib/tests/test_slice.py
+12-3Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,9 +9,13 @@
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def test_slice_3D(make_napari_viewer, brain_data):
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viewer = make_napari_viewer()
1111
viewer.theme = "light"
12-
viewer.add_image(brain_data[0], **brain_data[1])
12+
13+
data = brain_data[0]
14+
assert data.ndim == 3, data.shape
15+
viewer.add_image(data, **brain_data[1])
16+
1317
axis = viewer.dims.last_used
14-
slice_no = brain_data[0].shape[0] - 1
18+
slice_no = data.shape[0] - 1
1519
viewer.dims.set_current_step(axis, slice_no)
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fig = SliceWidget(viewer).figure
1721
# 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):
2327
def test_slice_2D(make_napari_viewer, astronaut_data):
2428
viewer = make_napari_viewer()
2529
viewer.theme = "light"
26-
viewer.add_image(astronaut_data[0], **astronaut_data[1])
30+
31+
# Take first RGB channel
32+
data = astronaut_data[0][:, :, 0]
33+
assert data.ndim == 2, data.shape
34+
viewer.add_image(data)
35+
2736
fig = SliceWidget(viewer).figure
2837
# Need to return a copy, as original figure is too eagerley garbage
2938
# collected by the widget

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