partially adreess issue #1066

docs/changes.md

@@ -1,80 +1,15 @@
 
 ## Changes and Fixes
 
-- fixes to `extrude()` thanks to @JeffreyWardman
-- filter out triangle strips in Ribbon and `extrude()`
-- improvements in doc strings
-- add `utils.madcad2vedo` conversion as per #976 by @JeffreyWardman
-- add `utils.camera_to_dict()`
-- add `Axes(title_backface_color=...)` keyword
-- improvements on `plotter.__init__()`
-- fix `labels()` and `labels2d()`
-- add `shapes.plot_scalar()` plot a scalar along a line.
-- add support for `tetgenpy`
-- add `transformations.compute_main_axes()`
-- add `transformations.__call__()` to apply it
-- fix small bug in `pointcloud.distance_to()`
-- add `applications.MorphPlotter()` to morph a polygonal mesh to a target mesh
-- add `smooth_data()` to smooth/diffuse data attributes
-- add `shapes.Tubes()`
-- add `utils.Minimizer()` class
-- add `CellCenters(Points)` class
-- add `core.apply_transform_from_actor()`
-- add `add volume.slab()`
-- add `mesh.generate_random_points()` to generate random points onto a surface
-- add `tetmesh.generate_random_points()` to generate random points in a tet mesh
-- rename `integrate_arrays_over_domain()` to `integrate_data`
-- extend `volume.operation()` to support logic operations as per #1002
-- add `pointcloud.relax_point_positions()` method
-- add `pointcloud.auto_distance()` method calculates the distance to the closest point in the same cloud of points.
-- fixed `mesh.collapse_edges()` after #992
-- add `mesh.cut_closed_surface()`
-- fix `image.clone()` in #1011
-- add `transformations.TransformInterpolator` class
-- add `Line.find_index_at_position()` finds the index of the line vertex that is closest to a point
-- add `visual.LightKit` class which provides "natural" lighting from 4 sources.
-- add `fast-simplification` example by @Louis-Pujol in #992
-- add metadata "shape" to `volume.slice_plane()` in #1018
-- fix `core.mark_boundaries()` method
-- add callbacks for cutters in #1020 and `examples/volumetric/slice_plane3.py`
-- add `utils.andrews_curves()` function.
-- add `transformations.LinearTransform.transpose()` method.
-- add `pointcloud.generate_segments()` to generate a continous line from un-ordered points in 3d
-- fix `assembly.__add__()` by @j042 in #1036
-- small fix to `Ruler3D` class.
-- add `plotter.render_hidden_lines()` method
-- add slot for triangle strips in constructor `Mesh([verts, faces, lines, strips])` in #1019
-- internally use "import vedo.vtkclasses as vtki" instead of "vtk" to avoid confusion
-- add `join_with_strips()` in #1043
-- improvements to `shapes.Ellipsoid()` and bug fixes in #978 by @daniel-a-diaz
-- improvements to `pointcloud.pca_ellipsoid()` and bug fixes
-- improvements to `pointcloud.pca_ellipse()` and bug fixes
-- fix plotter `a` toggle
-- fix viz on jupyter notebook as per #994
-- fix `mesh.imprint()`
-- small fix to `applications.Slicer2DPlotter`
-- automatically apply the actor transform to an object actor that was moved manually (via eg "InteractorStyleTrackballActor") in #1045 and #1046 by @sergei9838
-- add support to `StructuredGrid` data (experimental).
-- improvements to `RayCastPlotter`
-- add `visual.scalar_range()` to control mesh coloring.
-- fix `shapes.Text3D.text()` by @gioda
-- add `volume.isosurface_discrete()` method
-
+- add typing annotations
+- add magic-class example
+- fix bug in `IsosurfaceBrowser` in #1064
+- partial fix of bug in 1066
 
 ## Soft Breaking Changes
 Changes that will break existing code whose fixing is trivial:
 
-- change `clone2d(scale=...)` to `clone2d(size=...)`
-- remove `shapes.StreamLines()` becoming `object.compute_streamlines()`
-- split `mesh.decimate()` into `mesh.decimate()`, `mesh.decimate_pro()` and `mesh.decimate_binned()` as per #992
-- modified `core.clean()` after #992
-- rename `vedo.tetmesh` to `vedo.grids` and support for `RectilinearGrid`
-- remove `import_window()` for obj files and create `load_obj()` by @zhouzq-thu in #891
-- add `smooth_mls_12d(..., n=0)` to fix the number of neighbors in the smoothing
-- modified API for `mesh.binarize()`
-- `plotter.add_hover_legend()` now returns the id of the callback.
-- removed `settings.render_lines_as_tubes` and `settings.hidden_line_removal`, add `plotter.render_hidden_lines()` method
-- fix `close()`, `close_window()` is now obsolete and removed.
+- None
 
 
 ## Hard Breaking Changes
@@ -85,47 +20,7 @@ Changes that will break existing code and need active thinking and work to adapt
 
 ## New/Revised Examples
 ```
-examples/basic/sliders_hsv.py
-examples/basic/buttons1.py
-examples/basic/buttons2.py
-examples/basic/input_box.py
-
-examples/advanced/warp4b.py
-examples/advanced/diffuse_data.py
-examples/advanced/moving_least_squares1D.py
-
-examples/volumetric/slab_vol.py
-examples/volumetric/streamlines1.py
-examples/volumetric/streamlines2.py
-examples/volumetric/streamlines3.py
-examples/volumetric/streamlines4.py
-examples/volumetric/office.py
-examples/volumetric/slice_plane1.py
-examples/volumetric/slice_plane3.py
-examples/volumetric/mesh2volume.py
-examples/volumetric/read_volume3.py
-examples/volumetric/rectl_grid1.py
-examples/volumetric/struc_grid1.py
-examples/volumetric/app_raycaster.py
-examples/volumetric/isosurfaces1.py
-examples/volumetric/isosurfaces2.py
-
-examples/simulations/mag_field1.py
-
-examples/pyplot/plot_stream.py
-examples/pyplot/andrews_cluster.py
-
-examples/other/madcad1.py
-examples/other/tetgen1.py
-examples/other/nelder-mead.py
-examples/other/fast_simpl.py
-
-tests/issues/issue_968.py
-tests/issues/issue_1025.py
-tests/issues/test_force_anim.py
-tests/snippets/test_discourse_1956.py
-tests/snippets/test_ellipsoid_main_axes.py
-tests/snippets/test_compare_fit1.py
+examples/other/magic-class1.py
 ```
 
 ### Broken Examples
@@ -135,20 +30,12 @@ earth_model.py (wrong colormapping?)
 markpoint.py (misplaced leader indicator)
 cut_and_cap.py (incomplete capping)
 gyroscope1.py (broken physics)
-tests/issues/discussion_800.py  (incomplete capping of tube)
+tests/issues/discussion_800.py (incomplete capping of tube)
 ```
 
 #### Broken Projects
 umap_viewer3d
 trackviewer (some problems with removing a track, and z spacing)
-./clone_viewer3d.py and  
-~/Projects/umap_viewer3d
-    [vedo.plotter] INFO: object 'FlagPole' was manually moved. Updated to its current position.
-    [vedo.plotter] INFO: object 'Text3D' was manually moved. Updated to its current position.
-
-rio_organoid
-    too slow??
-
 
 #### Broken Exports to .npz:
 boolean.py

examples/other/magic-class1.py

@@ -0,0 +1,34 @@
+"""Use magicclass to plot\nrandom points and a histogram."""
+import numpy as np
+import vedo
+try:
+    from magicclass import magicclass, field
+    from magicclass.ext.vtk import VedoCanvas
+except ImportError:
+    print("Please install magicclass with: pip install magic-class")
+
+@magicclass
+class ViewerUI:
+    canvas = field(VedoCanvas)
+
+    def plot_random_points(self):
+        """Plot random data."""
+        # create a points object and a set of axes
+        coords = np.random.randn(1000, 3)
+        data = np.cos(coords[:,1])
+        points = vedo.Points(coords)
+        points.cmap("viridis", data).add_scalarbar3d()
+        axes = vedo.Axes(points, c="white")
+        # create a histogram of data
+        histo = vedo.pyplot.histogram(
+            data, c="viridis", title=" ", xtitle="", ytitle="",
+        )
+        histo = histo.clone2d("bottom-right", size=0.25)
+        ui.canvas.plotter.remove("Axes", "Points", "Histogram1D")
+        ui.canvas.plotter.add(points, axes, histo)
+        ui.canvas.plotter.reset_camera().render()
+
+if __name__ == "__main__":
+    ui = ViewerUI()
+    ui.canvas.plotter.add(__doc__)
+    ui.show()

tests/pipeline.txt

@@ -25,6 +25,7 @@ pip install rtree
 pip install trimesh -U
 pip install -q trame==2.5.2
 pip install qtpy
+pip install magic-class -U
 pip install tetgenpy -U
 pip install gustaf -U
 pip install fast-simplification -U
@@ -120,6 +121,7 @@ cd ~/Projects/napari-vedo-bridge
     # python -m pip install "napari[all]"
     conda activate napari-env
     cd $VEDODIR && pip install -q . && cd -
+    pip install -e .
     python $VEDODIR/examples/other/napari1.py # then open plugins ...
     conda deactivate
 ################

vedo/core.py

@@ -231,7 +231,7 @@ def clear(self) -> None:
                 name = data.GetArray(i).GetName()
             data.RemoveArray(name)
 
-    def select(self, key: Union[int,str]) -> Any:
+    def select(self, key: Union[int, str]) -> Any:
         """Select one specific array by its name to make it the `active` one."""
         # Default (ColorModeToDefault): unsigned char scalars are treated as colors,
         # and NOT mapped through the lookup table, while everything else is.
@@ -268,6 +268,8 @@ def select(self, key: Union[int,str]) -> Any:
                 try:
                     # could be a volume mapper
                     self.obj.mapper.SetColorModeToDirectScalars()
+                    data.SetActiveVectors(None) # need this to fix bug in #1066
+                    # print("SetColorModeToDirectScalars for", key)
                 except AttributeError:
                     pass
             else:
@@ -1637,11 +1639,17 @@ def apply_transform(self, LT: Any, concatenate=True, deep_copy=True) -> Any:
         else:
             vedo.logger.error(f"apply_transform(), unknown input type: {[self.dataset]}")
             return self
+
+        # print("================================================", self.name)
+        # print(self.dataset.GetPointData().GetArray("RGBA_TEST3"), flush=True)
+
         tp.SetTransform(tr)
         tp.SetInputData(self.dataset)
         tp.Update()
         out = tp.GetOutput()
 
+        # print(out.GetPointData().GetArray("RGBA_TEST3"), flush=True)
+
         if deep_copy:
             self.dataset.DeepCopy(out)
         else:

vedo/visual.py

@@ -1114,7 +1114,7 @@ def lighting(
 
         return self
 
-    def point_blurring(self, r=1, emissive=False):
+    def point_blurring(self, r=1, alpha=1.0, emissive=False):
         """Set point blurring.
         Apply a gaussian convolution filter to the points.
         In this case the radius `r` is in absolute units of the mesh coordinates.