Merge pull request #456 from Carifio24/ipyvolume-axes

Updates for ipyvolume viewer issues

glue_jupyter/common/state3d.py

@@ -85,7 +85,7 @@ def aspect(self):
         # TODO: this could be cached based on the limits, but is not urgent
         aspect = np.array([1, 1, 1], dtype=float)
         if self.native_aspect:
-            aspect[0] = 1.
+            aspect[0] = 1.0
             aspect[1] = (self.z_max - self.z_min) / (self.x_max - self.x_min)
             aspect[2] = (self.y_max - self.y_min) / (self.x_max - self.x_min)
             aspect /= aspect.max()

glue_jupyter/ipyvolume/common/viewer.py

@@ -33,13 +33,13 @@ def __init__(self, *args, **kwargs):
         # FIXME: hack for the movie maker to have access to the figure
         self.state.figure = self.figure
 
-        # note that for ipyvolume, we use axis in the order x, z, y in order to have
+        # note that for ipyvolume, we use axis in the order z, x, y in order to have
         # the z axis of glue pointing up
         def attribute_to_label(attribute):
             return 'null' if attribute is None else attribute.label
 
-        dlink((self.state, 'x_att'), (self.figure, 'xlabel'), attribute_to_label)
-        dlink((self.state, 'y_att'), (self.figure, 'zlabel'), attribute_to_label)
+        dlink((self.state, 'x_att'), (self.figure, 'zlabel'), attribute_to_label)
+        dlink((self.state, 'y_att'), (self.figure, 'xlabel'), attribute_to_label)
         dlink((self.state, 'z_att'), (self.figure, 'ylabel'), attribute_to_label)
 
         self.state.add_callback('x_min', self.limits_to_scales)
@@ -86,12 +86,10 @@ def apply_roi(self, roi, use_current=False):
             self._session.command_stack.do(cmd)
 
     def limits_to_scales(self, *args):
-        if self.state.x_min is not None and self.state.x_max is not None:
-            self.figure.xlim = self.state.x_min, self.state.x_max
         if self.state.y_min is not None and self.state.y_max is not None:
-            self.figure.zlim = self.state.y_min, self.state.y_max
-        # if self.state.z_min is not None and self.state.z_max is not None:
-        #     self.figure.zlim = self.state.z_min, self.state.z_max
+            self.figure.xlim = self.state.y_min, self.state.y_max
+        if self.state.x_min is not None and self.state.x_max is not None:
+            self.figure.zlim = self.state.x_min, self.state.x_max
         if hasattr(self.state, 'z_min'):
             if self.state.z_min is not None and self.state.z_max is not None:
                 self.figure.ylim = self.state.z_min, self.state.z_max

glue_jupyter/ipyvolume/scatter/layer_artist.py

@@ -90,14 +90,25 @@ def _update_color(self, ignore=None):
     def _update_xyz_att(self, *args):
         self.update()
 
+    def _cast_to_float(self, arr):
+        if np.issubdtype(arr.dtype, np.floating):
+            return arr
+
+        # `itemsize` returns the byte size of the dtype
+        size = 8 * arr.dtype.itemsize
+        return arr.astype(f"float{size}")
+
     def redraw(self):
         pass
 
     def update(self):
         # we don't use layer, but layer.data to get everything
-        self.scatter.x = ensure_numerical(self.layer.data[self._viewer_state.x_att]).ravel()
-        self.scatter.z = ensure_numerical(self.layer.data[self._viewer_state.y_att]).ravel()
-        self.scatter.y = ensure_numerical(self.layer.data[self._viewer_state.z_att]).ravel()
+        self.scatter.z = self._cast_to_float(
+                ensure_numerical(self.layer.data[self._viewer_state.x_att]).ravel())
+        self.scatter.y = self._cast_to_float(
+                ensure_numerical(self.layer.data[self._viewer_state.z_att]).ravel())
+        self.scatter.x = self._cast_to_float(
+                ensure_numerical(self.layer.data[self._viewer_state.y_att]).ravel())
         self.quiver.x = self.scatter.x
         self.quiver.z = self.scatter.y
         self.quiver.y = self.scatter.z
@@ -123,9 +134,9 @@ def _clear_selection(self):
 
     def _update_quiver(self):
         with self.quiver.hold_sync():
-            self.quiver.vx = self.layer.data[self.state.vx_att].ravel()
-            self.quiver.vz = self.layer.data[self.state.vy_att].ravel()
+            self.quiver.vz = self.layer.data[self.state.vx_att].ravel()
             self.quiver.vy = self.layer.data[self.state.vz_att].ravel()
+            self.quiver.vx = self.layer.data[self.state.vy_att].ravel()
 
     def _update_size(self):
         size = self.state.size

glue_jupyter/ipyvolume/scatter/tests/test_viewer.py

@@ -39,15 +39,15 @@ def test_labels(app, dataxyz):
     app.add_data(dataxyz)
     scatter = app.scatter3d(data=dataxyz)
     assert str(scatter.state.x_att) == 'x'
-    assert scatter.figure.xlabel == 'x'
+    assert scatter.figure.zlabel == 'x'
     assert str(scatter.state.y_att) == 'y'
-    assert scatter.figure.zlabel == 'y'
+    assert scatter.figure.xlabel == 'y'
     assert str(scatter.state.z_att) == 'z'
     assert scatter.figure.ylabel == 'z'
 
     scatter.state.x_att = dataxyz.id['y']
-    assert scatter.figure.xlabel == 'y'
+    assert scatter.figure.zlabel == 'y'
     scatter.state.y_att = dataxyz.id['z']
-    assert scatter.figure.zlabel == 'z'
+    assert scatter.figure.xlabel == 'z'
     scatter.state.z_att = dataxyz.id['x']
     assert scatter.figure.ylabel == 'x'

glue_jupyter/ipyvolume/tests/test_ipyvolume.py

@@ -36,16 +36,16 @@ def test_scatter3d(app, dataxyz, dataxz):
     assert s.layers[1].layer['y'].tolist() == [4]
     assert s.layers[1].layer['z'].tolist() == [7]
 
-    assert s.layers[1].scatter.x.tolist() == [1, 2, 3]
-    assert s.layers[1].scatter.z.tolist() == [2, 3, 4]
+    assert s.layers[1].scatter.z.tolist() == [1, 2, 3]
+    assert s.layers[1].scatter.x.tolist() == [2, 3, 4]
     assert s.layers[1].scatter.y.tolist() == [5, 6, 7]
     assert s.layers[1].scatter.selected == [2]
 
     s.state.x_att = dataxyz.id['y']
     s.state.y_att = dataxyz.id['z']
     s.state.z_att = dataxyz.id['x']
-    assert s.layers[1].scatter.x.tolist() == [2, 3, 4]
-    assert s.layers[1].scatter.z.tolist() == [5, 6, 7]
+    assert s.layers[1].scatter.z.tolist() == [2, 3, 4]
+    assert s.layers[1].scatter.x.tolist() == [5, 6, 7]
     assert s.layers[1].scatter.y.tolist() == [1, 2, 3]
     assert s.layers[1].scatter.selected == [2]
 

glue_jupyter/ipyvolume/volume/layer_artist.py

@@ -106,6 +106,8 @@ def update(self):
             data *= mask
         else:
             data = self.layer[self.state.attribute]
+
+        data = np.transpose(data, (2, 0, 1))
         finite_mask = np.isfinite(data)
         finite_data = data[finite_mask]
         finite_mask_normalized = finite_data - finite_data.min()