Viewer.add_volume: rename parameter dims -> spacing

schlegelp · Apr 16, 2024 · 0cff1cf · 0cff1cf
1 parent d732b35
commit 0cff1cf
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Showing 2 changed files with 15 additions and 13 deletions.
diff --git a/octarine/viewer.py b/octarine/viewer.py
@@ -798,7 +798,9 @@ def add_points(
         elif not isinstance(name, str):
             name = str(name)
 
-        visual = points2gfx(points, color=color, size=size, size_space=size_space, marker=marker)
+        visual = points2gfx(
+            points, color=color, size=size, size_space=size_space, marker=marker
+        )
         visual._object_id = name if name else uuid.uuid4()
 
         self._add_to_scene(visual, center)
@@ -873,7 +875,7 @@ def add_lines(
     def add_volume(
         self,
         volume,
-        dims,
+        spacing=(1, 1, 1),
         name=None,
         color=None,
         offset=(0, 0, 0),
@@ -888,8 +890,8 @@ def add_volume(
         ----------
         volume :    (N, M, K) array
                     Volume to plot.
-        dims :      tuple
-                    Scale factors for the volume.
+        spacing :   tuple
+                    Spacing between voxels.
         name :      str, optional
                     Name for the visual.
         color :     color | list of colors | pygfx.Texture, optional
@@ -933,7 +935,7 @@ def add_volume(
 
         visual = volume2gfx(
             volume,
-            dims=dims,
+            spacing=spacing,
             offset=offset,
             color=color,
             clim=clim,

diff --git a/octarine/visuals.py b/octarine/visuals.py
@@ -107,8 +107,8 @@ def color_to_texture(color, N=256, gamma=1.0, fade=True):
 
 def volume2gfx(
     vol,
-    dims,
     color,
+    spacing=(1, 1, 1),
     offset=(0, 0, 0),
     clim="auto",
     interpolation="linear",
@@ -120,8 +120,8 @@ def volume2gfx(
     ----------
     vol :           np.ndarray
                     3D array representing the volume.
-    dims :          tuple
-                    Dimensions of the volume along the (x, y, z) axes.
+    spacing :       tuple
+                    Spacing between voxels in the volume.
     color :         color | list of colors | pygfx.Texture, optional
                     Colormap to render the volume. This can be:
                       - name of a colormap (e.g. "viridis" or "magma")
@@ -159,10 +159,10 @@ def volume2gfx(
 
     assert isinstance(vol, np.ndarray), "Expected 3D numpy array."
     assert vol.ndim == 3, "Expected 3D numpy array."
-    assert isinstance(dims, (tuple, list, np.ndarray, int, float))
-    if isinstance(dims, (int, float)):
-        dims = [dims] * 3
-    assert len(dims) == 3, "Expected dimensions as tuple of length 3."
+    assert isinstance(spacing, (tuple, list, np.ndarray, int, float))
+    if isinstance(spacing, (int, float)):
+        spacing = [spacing] * 3
+    assert len(spacing) == 3, "Expected spacing as tuple of length 3."
 
     # Similar to vispy, pygfx seems to expect zyx coordinate space
     grid = vol.T
@@ -226,7 +226,7 @@ def volume2gfx(
         vis.local.scale_x,
         vis.local.scale_y,
         vis.local.scale_z,
-    ) = dims
+    ) = spacing
     (vis.local.x, vis.local.y, vis.local.z) = offset
 
     # Add custom attributes