test pr named axes

napari/_qt/_tests/test_qt_viewer.py

@@ -814,6 +814,11 @@ def test_axes_labels(make_napari_viewer):
     assert tuple(axes_visual.node.text.text) == ('2', '1', '0')
 
 
+def test_axes_visual_corresponds_to_axes_labels():
+    """If we create an axes overlay visual, the text should be corresponding to the axes_labels of the particular layer of
+    which the axes are visualized"""
+
+
 @pytest.fixture()
 def qt_viewer(qtbot):
     qt_viewer = QtViewer(ViewerModel())

napari/components/_tests/test_viewer_model.py

@@ -974,3 +974,36 @@ def test_slice_order_with_mixed_dims():
     assert image_2d._slice.image.view.shape == (4, 5)
     assert image_3d._slice.image.view.shape == (3, 5)
     assert image_4d._slice.image.view.shape == (2, 5)
+
+
+def test_viewer_add_layer_with_axes_labels():
+    "When we add a layer to the viewer model, the axis labels in the dims should be properly updated"
+    viewer = ViewerModel(ndisplay=2)
+    assert viewer.dims.axes_labels == ('-2', '-1')
+    with pytest.raises(ValueError):
+        viewer.add_image(np.zeros((4, 5)), axes_labels=('z', 'y', 'x'))
+    viewer.add_image(np.zeros((4, 5)), axes_labels=('x', 'y'))
+    assert viewer.dims.axes_labels == ('x', 'y')
+
+    # Ensure axes labels stay the same when image with same axes labels are added
+    viewer.add_image(np.zeros((4, 5)), axes_labels=('x', 'y'))
+    assert viewer.dims.axes_labels == ('x', 'y')
+
+    # Ensure axes labels are updated when layer with different axes labels than currently present are added.
+    viewer.add_image(np.zeros((4, 5, 5)), axes_labels=('a', 'b', 'c'))
+    assert viewer.dims.axes_labels == ('a', 'b', 'c', 'x', 'y')
+
+    assert viewer.dims.displayed == ('a', 'b', 'c')
+    assert viewer.dims.not_displayed == ('x', 'y')
+
+
+def test_viewer_multiple_layer_axes_labels():
+    """When adding multiple layers to the viewer with the same axes labels the axes labels of the dims model should stay
+    the same. When layers do not share axes labels, the axes labels in the dims model should be updated. The attribute
+    not_displayed of the dims model should also be properly updated.
+    """
+
+
+def test_viewer_annotation_layer_axes_labels():
+    """When adding a new layer to annotate (for example with shapes layer) an image layer, the axes labels of the parent
+    layer should be inherited."""

napari/layers/_scalar_field/scalar_field.py

@@ -172,6 +172,7 @@ def __init__(
         custom_interpolation_kernel_2d=None,
         depiction='volume',
         experimental_clipping_planes=None,
+        layer_axis_labels=None,
         metadata=None,
         multiscale=None,
         name=None,
@@ -219,6 +220,7 @@ def __init__(
             shear=shear,
             affine=affine,
             opacity=opacity,
+            layer_axis_labels=layer_axis_labels,
             blending=blending,
             visible=visible,
             multiscale=multiscale,

napari/layers/base/_tests/test_named_axes.py

@@ -0,0 +1,52 @@
+import numpy as np
+import pytest
+
+from napari.layers import Image
+
+
+# These tests would be for testing the layers itself
+def test_get_layer_axes_labels():
+    "For a given layer we should be able to retrieve axes labels."
+    shape = (10, 15)
+    np.random.seed(0)
+    data = np.random.random(shape)
+    layer = Image(data, axes_labels=("y", "x"))
+    assert layer.axes_labels == ("y", "x")
+
+
+def test_set_layer_axes_labels():
+    "For a given layer we should be able to set the axes labels."
+    shape = (10, 15)
+    np.random.seed(0)
+    data = np.random.random(shape)
+    layer = Image(data, axes_label=("y", "x"))
+    with pytest.raises(ValueError):
+        layer.axes_labels = ("z", "y", "x")
+
+    layer.axes_labels = ("z", "t")
+    assert layer.axes_labels == ("z", "t")
+
+    # Note: should we give a warning if reversing axes labels for example y,x to x, y
+
+
+def test_default_axes_labels():
+    """If no axes labels are given, default names should be assigned equal to the number of dimensions of a particular
+    layer."""
+    # Note that for broadcasting the default names should be based on negative integers, so ..., -2, -1.
+    shape = (10, 15)
+    data = np.random.random(shape)
+    layer = Image(data)
+    assert layer.axes_labels == (-2, -1)
+
+
+def test_ndim_match_length_axes_labels():
+    """The number of dimensions must match the length of axes labels when creating a layer and should throw an error
+    if not the case"""
+    shape = (10, 15)
+    data = np.random.random(shape)
+    layer = Image(data, axes_labels=("y", "x"))
+    assert layer.dim == 2
+
+
+def test_slice_using_axes_labels():
+    "We should be able to slice based on current axes labels and an interval."

napari/layers/base/base.py

@@ -8,6 +8,7 @@
 import warnings
 from abc import ABC, ABCMeta, abstractmethod
 from collections import defaultdict
+from collections.abc import Iterable
 from contextlib import contextmanager
 from functools import cached_property
 from typing import (
@@ -19,6 +20,7 @@
     Generator,
     List,
     Optional,
+    Sequence,
     Tuple,
     Type,
     Union,
@@ -315,6 +317,7 @@ def __init__(
         experimental_clipping_planes=None,
         mode='pan_zoom',
         projection_mode='none',
+        layer_axis_labels=None,
     ):
         super().__init__()
 
@@ -357,6 +360,10 @@ def __init__(
 
         self._ndim = ndim
 
+        self.layer_axis_labels = self._validate_coerce_axis_labels(
+            layer_axis_labels
+        )
+
         self._slice_input = _SliceInput(
             ndisplay=2,
             world_slice=_ThickNDSlice.make_full(ndim=ndim),
@@ -548,6 +555,40 @@ def _mode_setter_helper(self, mode_in: Union[Mode, str]) -> StringEnum:
 
         return mode
 
+    def _validate_coerce_axis_labels(
+        self, axis_labels: Sequence[str | int] | None
+    ) -> tuple[str]:
+        """Check proper input of axis labels and coerce it to a tuple of strings.
+
+        Paramters
+        ---------
+        axis_labels : Sequence[str | int] | None
+            Axis labels of the layer
+
+        Returns
+        -------
+        tuple[str]
+            Validated axis labels coerced to a tuple of strings
+        """
+        if axis_labels is None:
+            axis_labels = tuple(str(-i) for i in range(self._ndim, 0, -1))
+        elif (
+            isinstance(axis_labels, Iterable)
+            and len(axis_labels) == self._ndim
+        ):
+            axis_labels = tuple(str(i) for i in axis_labels)
+
+        return axis_labels
+
+    @property
+    def axis_labels(self) -> tuple[str]:
+        """The axis labels of the layer."""
+        return self._axis_labels
+
+    @axis_labels.setter
+    def axis_labels(self, axis_labels: Sequence[str | int] | None):
+        self._axis_labels = self._validate_coerce_axis_labels(axis_labels)
+
     @property
     def mode(self) -> str:
         """str: Interactive mode

napari/layers/image/image.py

@@ -224,6 +224,7 @@ def __init__(
         self,
         data,
         *,
+        layer_axis_labels=None,
         affine=None,
         attenuation=0.05,
         blending='translucent',
@@ -279,6 +280,7 @@ def __init__(
             opacity=opacity,
             plane=plane,
             projection_mode=projection_mode,
+            layer_axis_labels=layer_axis_labels,
             rendering=rendering,
             rotate=rotate,
             scale=scale,

napari/layers/labels/labels.py

@@ -279,6 +279,7 @@ def __init__(
         self,
         data,
         *,
+        layer_axis_labels=None,
         affine=None,
         blending='translucent',
         cache=True,
@@ -318,10 +319,9 @@ def __init__(
         self._show_selected_label = False
         self._contour = 0
 
-        data = self._ensure_int_labels(data)
-
         super().__init__(
             data,
+            layer_axis_labels=layer_axis_labels,
             rendering=rendering,
             depiction=depiction,
             name=name,

napari/layers/points/points.py

@@ -373,6 +373,7 @@ def __init__(
         self,
         data=None,
         *,
+        layer_axis_labels=None,
         ndim=None,
         features=None,
         feature_defaults=None,
@@ -450,6 +451,7 @@ def __init__(
         super().__init__(
             data,
             ndim,
+            layer_axis_labels=layer_axis_labels,
             name=name,
             metadata=metadata,
             scale=scale,

napari/layers/shapes/shapes.py

@@ -416,6 +416,7 @@ class Shapes(Layer):
 
     def __init__(
         self,
+        layer_axis_labels=None,
         data=None,
         *,
         ndim=None,
@@ -467,6 +468,7 @@ def __init__(
 
         super().__init__(
             data,
+            layer_axis_labels=layer_axis_labels,
             ndim=ndim,
             name=name,
             metadata=metadata,

napari/layers/surface/surface.py

@@ -189,6 +189,7 @@ class Surface(IntensityVisualizationMixin, Layer):
     def __init__(
         self,
         data,
+        layer_axis_labels=None,
         *,
         features=None,
         feature_defaults=None,
@@ -219,7 +220,8 @@ def __init__(
 
         super().__init__(
             data,
-            ndim,
+            layer_axis_labels=layer_axis_labels,
+            ndim=ndim,
             name=name,
             metadata=metadata,
             scale=scale,

napari/layers/tracks/tracks.py

@@ -97,6 +97,7 @@ class Tracks(Layer):
     def __init__(
         self,
         data,
+        layer_axis_labels=None,
         *,
         features=None,
         properties=None,
@@ -131,6 +132,7 @@ def __init__(
         super().__init__(
             data,
             ndim,
+            layer_axis_labels=layer_axis_labels,
             name=name,
             metadata=metadata,
             scale=scale,