Merge branch 'master' of https://github.com/sdorkenw/MeshParty

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.16.11
+current_version = 1.16.13
 commit = True
 tag = True
 

docs/guide/skeletons.rst

@@ -15,7 +15,7 @@ Again assuming you have a mesh object loaded, the key function is :func:`meshpar
 
 ::
 
-    from trimesh_io import skeletonize
+    from meshparty import skeletonize
 
     # skeletonize the mesh using a 12 um invalidation radius
     # assuming units of mesh.vertices is in nm

meshparty/__init__.py

@@ -1 +1 @@
-__version__ = "1.16.11"
+__version__ = "1.16.13"

meshparty/trimesh_io.py

@@ -361,13 +361,15 @@ def _download_meshes_thread_precomputed(args):
 
     while len(download_segids):
         download_now = download_segids[:100]
-        download_segids = download_segids[len(download_now):]
-
-        cv_meshes = cv.mesh.get(
-            download_now,
-            remove_duplicate_vertices=remove_duplicate_vertices,
-            fuse=False
-        )
+        download_segids = download_segids[len(download_now):]    
+        if isinstance(cv.mesh, ShardedMultiLevelPrecomputedMeshSource):
+            cv_meshes = cv.mesh.get(download_now)
+        else:     
+            cv_meshes = cv.mesh.get(
+                download_now,
+                remove_duplicate_vertices=remove_duplicate_vertices,
+                fuse=False
+            )
 
         for segid, cv_mesh in cv_meshes.items():
             mesh = Mesh(

meshparty/trimesh_vtk.py

@@ -276,22 +276,18 @@ def render_actors(actors, camera=None, do_save=False, filename=None,
     if VIDEO_WIDTH is not None:
         logging.warning('VIDEO_WIDTH is deprecated, please use VIDEO_WIDTH')
         video_width=VIDEO_WIDTH
-    print('setting up renderer')
     # create a rendering window and renderer
     ren, renWin, iren = _setup_renderer(
         video_width, video_height, back_color, camera=camera)
-    print('done setting up')
     for a in actors:
         # assign actor to the renderer
         ren.AddActor(a)
-    print('actors added')
     # render
     if camera is None:
         ren.ResetCamera()
     else:
         ren.ResetCameraClippingRange()
         camera.ViewingRaysModified()
-    print('camera set')
     if return_keyframes:
         key_frame_cameras = []
 
@@ -304,7 +300,6 @@ def vtkKeyPress(obj, event):
             return
         iren.AddObserver("KeyPressEvent", vtkKeyPress)
     renWin.Render()
-    print('render done')
     if do_save is False:
         trackCamera = vtk.vtkInteractorStyleTrackballCamera()
         iren.SetInteractorStyle(trackCamera)
@@ -324,7 +319,6 @@ def vtkKeyPress(obj, event):
         writer.SetFileName(filename)
         writer.SetInputData(w2if.GetOutput())
         writer.Write()
-    print('finalizing..')
     renWin.Finalize()
 
     if return_keyframes:
@@ -609,15 +603,17 @@ def skeleton_actor(sk,
         data = vertex_data
 
     if data is not None:
-        if normalize_property:
-            data = data / np.nanmax(data)
-        sk_mesh.GetPointData().SetScalars(numpy_to_vtk(data))
-        lut = vtk.vtkLookupTable()
-        if lut_map is not None:
-            lut_map(lut)
-        lut.Build()
+        colors, map_colors = process_colors(data, sk.vertices)
+        vtk_colors = numpy_to_vtk(colors)
+        vtk_colors.SetName('colors')   
+        sk_mesh.GetPointData().SetScalars(vtk_colors)
+        if map_colors:
+            lut = vtk.vtkLookupTable()
+            if lut_map is not None:
+                lut_map(lut)
+            lut.Build()
+            mapper.SetLookupTable(lut)
         mapper.ScalarVisibilityOn()
-        mapper.SetLookupTable(lut)
 
     actor = vtk.vtkActor()
     actor.SetMapper(mapper)