2.4

notebooks/basic/fitline.ipynb → notebooks/advanced/fitline.ipynb

@@ -32,14 +32,7 @@
     "# 'data' still contains the last iteration points\n",
     "vp += Points(data, r=2, c=\"yellow\")\n",
     "\n",
-    "# the first fitted slope direction is stored\n",
-    "# in mesh.info['slope] and mesh.info['normal]\n",
-    "print(\"Line Fit slope = \", vp.actors[0].info[\"slope\"])\n",
-    "\n",
-    "plane = fitPlane(data)  # fit a plane\n",
-    "print(\"Plan Fit normal=\", plane.info[\"normal\"])\n",
-    "\n",
-    "vp += plane\n",
+    "vp += fitPlane(data)  # fit a plane\n",
     "\n",
     "vp.show()"
    ]

notebooks/basic/pca.ipynb

@@ -2,35 +2,9 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\u001b[1m\u001b[32minside  points # 249\u001b[0m\n",
-      "\u001b[1m\u001b[31moutside points # 251\u001b[0m\n",
-      "\u001b[1ma-sphericity: 0.010310868419372739\u001b[0m\n",
-      "\u001b[1mError in triangulate()\u001b[0m\n",
-      "\u001b[1mError in triangulate()\u001b[0m\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a3837ca4488f4c97900adfae6f30cade",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Plot(antialias=3, axes=['x', 'y', 'z'], axes_helper=1.0, background_color=16777215, camera=[0.5632771544478462…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "\"\"\"\n",
     "Draw the PCA (Principal Component Analysis) ellipsoid that contains\n",
@@ -52,27 +26,20 @@
     "vp += Points(ipts, c=\"g\")\n",
     "vp += Points(opts, c=\"r\")\n",
     "\n",
-    "printc(\"inside  points #\", len(ipts), c='g')\n",
-    "printc(\"outside points #\", len(opts), c='r')\n",
+    "printc(\"inside  points #\", ipts.N(), c='g')\n",
+    "printc(\"outside points #\", opts.N(), c='r')\n",
     "printc(\"a-sphericity:\", elli.asphericity())\n",
     "vp.show()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "closePlotter()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

setup.py

@@ -83,6 +83,8 @@
 # rm examples/other/voronoi3d.txt examples/other/voronoi3d.txt.vol
 # rm examples/other/embryo.html examples/other/embryo.x3d
 
+# comment out defs in docs.py
+
 # git status
 # git add [files]
 # git commit -a -m 'comment'
@@ -98,6 +100,7 @@
 # release examples
 
 ## to generate documentation:
+# comment in defs in docs.py
 # Install the dependencies in docs/requirements.txt
 #  pip install -r docs/requirements.txt
 #

tests/dolfinx/test_aaa.py

@@ -13,13 +13,13 @@
 import numpy as np
 from petsc4py import PETSc
 
-import dolfin
-from dolfin import (MPI, BoxMesh, DirichletBC, Function, VectorFunctionSpace,
-                    cpp)
-from dolfin.cpp.mesh import CellType
-from dolfin.fem import apply_lifting, assemble_matrix, assemble_vector, set_bc
+import dolfinx
+from dolfinx import (MPI, UnitCubeMesh, 
+                     DirichletBC, Function, VectorFunctionSpace, cpp)
+from dolfinx.cpp.mesh import CellType
+from dolfinx.fem import apply_lifting, assemble_matrix, assemble_vector, set_bc
 #from dolfin.io import XDMFFile
-from dolfin.la import VectorSpaceBasis
+from dolfinx.la import VectorSpaceBasis
 from ufl import (Identity, SpatialCoordinate, TestFunction, TrialFunction,
                  as_vector, dx, grad, inner, sym, tr)
 
@@ -67,7 +67,7 @@ def build_nullspace(V):
 #    MPI.comm_world, [np.array([0.0, 0.0, 0.0]),
 #                     np.array([2.0, 1.0, 1.0])], [12, 12, 12],
 #    CellType.tetrahedron, dolfin.cpp.mesh.GhostMode.none)
-cmap = dolfin.fem.create_coordinate_map(mesh.ufl_domain())
+cmap = dolfinx.fem.create_coordinate_map(mesh.ufl_domain())
 mesh.geometry.coord_mapping = cmap
 
 def boundary(x):
@@ -168,7 +168,6 @@ def sigma(v):
      offscreen=1)
 
 #################################################################################
-import numpy as np
 from vtkplotter import settings, screenshot
 actor = settings.plotter_instance.actors[0]
 solution = actor.scalars(0)
@@ -179,8 +178,6 @@ def sigma(v):
 print('min', 'mean', 'max, N:')
 print(np.min(solution), np.mean(solution), np.max(solution), len(solution))
 
-
-
 # Plot solution
 # import matplotlib.pyplot as plt
 # import dolfin.plotting

vtkplotter/addons.py

@@ -139,6 +139,7 @@ def addScalarBar(mesh,
         titprop.ShadowOff()
         titprop.SetColor(c)
         titprop.SetVerticalJustificationToTop()
+        titprop.SetFontSize(titleFontSize)
         sb.SetTitle(title)
         sb.SetVerticalTitleSeparation(titleYOffset)
         sb.SetTitleTextProperty(titprop)