2020.0.1

.circleci/config.yml

@@ -5,7 +5,35 @@
 version: 2
 
 jobs:
-  build-real:
+
+  build-dolfin-stable:
+    docker:
+      - image: quay.io/fenicsproject/dolfinx:dev-env-real
+    environment:
+      MPLBACKEND: "agg"
+      DEBIAN_FRONTEND: "noninteractive"
+
+    steps:
+      - checkout
+
+      - run:
+          name: install vtkplotter
+          command: |
+            pip3 install vtk
+            pip3 install .
+
+      - run:
+          name: Run tests
+          command: |
+            cd
+            cd project/tests/dolfin
+            source run_all.sh
+
+      - store_artifacts:
+          path: test-reports
+          destination: test-reports
+
+  build-dolfinx:
     docker:
       - image: quay.io/fenicsproject/dolfinx:dev-env-real
     environment:
@@ -42,17 +70,16 @@ jobs:
           name: Run tests
           command: |
             cd
-            cd project/tests
-            pwd
-            ls
+            cd project/tests/dolfinx
             source run_all.sh
 
       - store_artifacts:
           path: test-reports
           destination: test-reports
 
+######################################################
 workflows:
   version: 2
   build-stuff:
     jobs:
-      - build-real
+      - build-dolfinx

MANIFEST.in

@@ -2,6 +2,3 @@ include vtkplotter/*
 include vtkplotter/textures/*
 include vtkplotter/fonts/*
 include vtkplotter/fonts/licenses/*
-include vtkplotter/data/*
-include vtkplotter/data/images/*
-include vtkplotter/data/timecourse1d/*

README.md

@@ -59,52 +59,52 @@ in a program, whilst mantaining access to the full range of VTK native classes.
 It includes a [**large set of working examples**](https://github.com/marcomusy/vtkplotter-examples/tree/master/vtkplotter_examples)
 for all the following functionalities:
 
-  - Import meshes from VTK format, STL, Wavefront OBJ, 3DS, XML, Neutral, GMSH, OFF, PCD (PointCloud), volumetric TIFF stacks, DICOM, SLC, MHD, 2D images PNG, JPEG.
+  - Import meshes from VTK format, STL, Wavefront OBJ, 3DS, Dolfin-XML, Neutral, GMSH, OFF, PCD (PointCloud), volumetric TIFF stacks, DICOM, SLC, MHD, 2D images PNG, JPEG.
   - Export meshes as ASCII or binary to VTK, STL, OBJ, PLY formats.
-  - Mesh analysis through the built-in methods of VTK package. Additional analysis tools like *Moving Least Squares*, mesh morphing.
-  - Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..). Interactive cutter widget.
+  - Mesh analysis through the built-in methods of VTK. Additional analysis tools like *Moving Least Squares*, mesh morphing and more..
+  - Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..).
   - Split mesh based on surface connectivity. Extract the largest connected area.
-  - Calculate mass properties, like area, volume, center of mass, average size etc.
+  - Calculate areas, volumes, center of mass, average sizes etc.
   - Calculate vertex and face normals, curvatures, feature edges. Fill mesh holes.
   - Subdivide faces of a mesh, increasing the number of vertex points. Mesh simplification.
   - Coloring and thresholding of meshes based on associated scalar or vectorial data.
-  - Point-surface operations: find nearest points, determine if a point lies inside or outside a mesh.
-  - Create primitive objects like: spheres, arrows, cubes, torus, ellipsoids...
-  - Generate *glyphs* (associating a mesh to each vertex of a source mesh).
-  - Create animations easily by just defining the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is also supported.
+  - Point-surface operations: find nearest points, determine if a point lies inside or outside of a mesh.
+  - Create primitive shapes: spheres, arrows, cubes, torus, ellipsoids...
+  - Generate *glyphs* (associate a mesh to every vertex of a source mesh).
+  - Create animations easily by just setting the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is supported.
   - Straightforward support for multiple *sync-ed* or independent renderers in  the same window.
   - Registration (alignment) of meshes with different techniques.
-  - Mesh smoothing with *Laplacian* and *WindowedSinc* algorithms.
+  - Mesh smoothing.
   - Delaunay triangulation in 2D and 3D.
   - Generate meshes by joining nearby lines in space.
   - Find the closest path from one point to another, travelling along the edges of a mesh.
-  - Find the intersection of a mesh with a line (or with another mesh).
+  - Find the intersection of a mesh with lines, planes or other meshes.
   - Analysis of *Point Clouds*:
 	 - *Moving Least Squares* smoothing of 2D, 3D and 4D clouds
-    - Fit lines, planes and spheres and ellipses in space
+    - Fit lines, planes, spheres and ellipses in space
     - Identify outliers in a distribution of points
     - Decimate a cloud to a uniform distribution.
   - Histogramming and function plotting in 1D and 2D.
   - Interpolate scalar and vectorial fields with *Radial Basis Functions* and *Thin Plate Splines*.
   - Analysis of volumetric datasets:
     - Isosurfacing of volumes
-    - Direct maximum projection rendering
+    - Composite and maximum projection volumetric rendering
     - Generate volumetric signed-distance data from an input surface mesh
     - Probe a volume with lines and planes
     - Generate stream-lines and stream-tubes from vectorial fields
   - Add sliders and buttons to interact with the scene and the individual objects.
   - Fully customizable axis style.
-  - Draw `latex`-formatted formulas on the rending window.
-  - Examples using [SHTools](https://shtools.oca.eu/shtools) package for *spherical harmonics* expansion of a mesh shape.
+  - Visualization of tensors.
+  - Draw `latex`-formatted formulas in the rending window.
   - Integration with the *Qt5* framework.
+  - Examples using [SHTools](https://shtools.oca.eu/shtools) package for *spherical harmonics* expansion of a mesh shape.
   - Support for [FEniCS/Dolfin](https://fenicsproject.org/) platform for visualization of finite-element calculations.
-  - Visualization of tensors.
+  - Interoperability with the [trimesh](https://trimsh.org/) library.
   - Export a 3D scene and embed it into a [web page](https://vtkplotter.embl.es/examples/fenics_elasticity.html).
   - Embed the 3D rendering in a *jupyter* notebook with [K3D](https://github.com/K3D-tools/K3D-jupyter) (can export an interactive 3D-snapshot page [here](https://vtkplotter.embl.es/examples/K3D_snapshot.html)).
-  - Interoperability with the [trimesh](https://trimsh.org/) library.
 
 
-### Command Line Interface
+### ➜ Command Line Interface
 Visualize a mesh from a terminal window with:
 ```bash
 vtkplotter mesh.obj
@@ -123,7 +123,7 @@ To visualize multiple files or files time-sequences try `-n` or `-s` options. Us
 |`vtkplotter head.vti` |`vtkplotter -s *.vtk` |`vtkplotter `<br>`--slicer embr.slc` |   `vtkplotter --lego embryo.slc`|
 |![isohead](https://user-images.githubusercontent.com/32848391/56972083-a7f3f800-6b6a-11e9-9cb3-1047b69dcad2.gif)|   ![viz_raycast](https://user-images.githubusercontent.com/32848391/58336919-f7b1a080-7e44-11e9-9106-f574371093a8.gif)  | ![viz_slicer](https://user-images.githubusercontent.com/32848391/56972084-a7f3f800-6b6a-11e9-98c4-dc4ffec70a5e.png)  |![lego](https://user-images.githubusercontent.com/32848391/56969949-71b47980-6b66-11e9-8251-4bbdb275cb22.jpg) |
 
-### Graphic User Interface
+### ➜ Graphic User Interface
 A Graphic User Interface is available (mainly useful to *Windows 10* users):
 
 ![gui](https://user-images.githubusercontent.com/32848391/63259840-c861d280-c27f-11e9-9c2a-99d0fae85313.png)

bin/vtkplotter

@@ -1,7 +1,9 @@
 #!/usr/bin/env python
 #
 from __future__ import division, print_function
-from vtkplotter import Actor, Volume, Plotter, ProgressBar
+from vtkplotter import Plotter, ProgressBar
+from vtkplotter.mesh import Mesh
+from vtkplotter.volume import Volume
 from vtkplotter import settings, printc, getColor, humansort, __version__
 from vtkplotter import vtkio, utils, datadir
 import vtk
@@ -418,7 +420,7 @@ def draw_scene():
                     ic = args.color
             cf.SetValue(0, threshold)
             cf.Update()
-            act = Actor(cf.GetOutput(), c=ic, alpha=args.alpha).wireframe(args.wireframe)
+            act = Mesh(cf.GetOutput(), c=ic, alpha=args.alpha).wireframe(args.wireframe)
             if args.flat:
                 act.flat()
             else:
@@ -448,7 +450,7 @@ def draw_scene():
                     cf.ComputeScalarsOff()
                     cf.SetValue(0, wval)
                     cf.Update()
-                    a = Actor(cf.GetOutput(), ic, alpha=act.alpha())
+                    a = Mesh(cf.GetOutput(), ic, alpha=act.alpha())
                 bacts.update({wval_2: a}) # store it
                 #print('generated', wval_2, wval, len(bacts.keys()))
 
@@ -517,7 +519,7 @@ def draw_scene():
 
             if isinstance(actor, vtk.vtkActor):
 
-                if isinstance(actor, Actor):
+                if isinstance(actor, Mesh):
                     actors.append(actor)
                     actor.wireframe(wire)
                     actor.lighting(args.lighting)
@@ -960,64 +962,120 @@ else:  #########################################################################
     pr.add_argument("--lego",                       help="Voxel rendering for 3D image files", action="store_true")
     pr.add_argument("--cmap",                       help="Voxel rendering color map name", default='jet', metavar='')
     pr.add_argument("--mode",                       help="Voxel rendering composite mode", default=0, metavar='')
-    pr.add_argument("--run",                        help="Run example from vtkplotter-examples", default='', metavar='')
+    pr.add_argument("-r", "--run",                  help="Run example from vtkplotter-examples", metavar='')
     pr.add_argument("--list",                       help="List examples in vtkplotter-examples", action="store_true")
     args = pr.parse_args()
 
     if args.run:
         import glob
         exfiles = [f for f in glob.glob(datadir.replace('data','') + "**/*.py", recursive=True)]
-        matching = [s for s in exfiles if (args.run in s and "__" not in s and "version.py" not in s)]
-        if len(matching) > 1:
-            printc("Matching scripts are:", matching[:10], 'Running first only.', c='y', bold=0, italic=1)
-        if len(matching) == 0:
-            printc("No matching example found containing:", args.run, c=1)
-            printc("Use vtkplotter --list to show available scripts.", c=1)
+        matching = [s for s in exfiles if (args.run.lower() in os.path.basename(s).lower() and "__" not in s)]
+        matching = list(sorted(matching))
+        nmat = len(matching)
+        if nmat == 0:
+            printc("No matching example found containing string:", args.run, c=1)
+            printc(" Use vtkplotter --list to show available scripts.", c=1)
+            printc(" Current datadir is:", datadir, c=1)
             exit(1)
-        print("Running", matching[0])
-        os.system('python ' + matching[0])
+
+        if nmat > 1:
+            printc("\nSelect one of", nmat, "matching scripts:", c='y', italic=1)
+
+        for mat in matching[:25]:
+            printc(os.path.basename(mat).replace('.py',''), c='y', italic=1, end=' ')
+            with open(mat) as fm:
+                lline = ''.join(fm.readlines(60))
+                lline = lline.replace('\n','').replace('\'','').replace('\"','').replace('-','')
+                line = lline[:56] #cut
+                if line.startswith('from'): line=''
+                if line.startswith('import'): line=''
+                if len(lline) > len(line):
+                    line += '..'
+                if len(line)>5:
+                    printc('-', line,  c='y', bold=0, italic=1)
+                else:
+                    print()
+
+        if nmat>25:
+            printc('...', c='y')
+
+        if nmat > 1:
+            exit(0)
+
+        if args.no_camera_share: # -i option to dump the full code
+            print()
+            with open(matching[0]) as fm:
+                codedump = fm.readlines()
+            for line in codedump:
+                printc(line.strip(), c='cyan', italic=1, bold=0)
+            print()
+
+        printc("(in", os.path.dirname(matching[0])+')', c='y', bold=0, italic=1)
+        os.system('python3 ' + matching[0])
 
     elif args.list:
+        print()
         printc("Available examples are:", box='-')
         expath = datadir.replace('data','')
 
         import glob
-        exfiles = [(f, os.path.basename(f)) for f in glob.glob(expath + "**/*.py", recursive=True)]
+        exfiles = [(f, os.path.basename(f))
+                    for f in glob.glob(expath + "**/*.py", recursive=True)]
+        nl = 4
+
+        if not len(exfiles):
+            printc("vtkplotter-example not installed?")
+            printc("> pip install -U git+https://github.com/marcomusy/vtkplotter-examples")
+            exit()
 
-        printc("basic examples:", c='g', bold=1)
+        printc("Basic examples:", c='g', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
             if "basic" in f:
-                printc(bn, c='g', bold=0, end=' ')
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='g', bold=0)
 
-        printc("\nadvanced examples:", c='y', bold=1)
+        printc("Advanced examples:", c='y', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
             if "advanced" in f:
-                printc(bn, c='y', bold=0, end=' ')
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='y', bold=0)
 
-        printc("\nvolumetric examples:", c='b', bold=1)
+        printc("Volumetric examples:", c='b', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
             if "volumetric" in f:
-                printc(bn, c='b', bold=0, end=' ')
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='b', bold=0)
 
-        printc("\ndolfin examples:", c='r', bold=1)
+        printc("Other examples:", c='cyan', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
-            if "dolfin" in f:
-                printc(bn, c='r', bold=0, end=' ')
+            if "other" in f and "dolfin" not in f and "trimesh" not in f:
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='cyan', bold=0)
 
-        printc("\ntrimesh examples:", c='m', bold=1)
+        printc("      Dolfin examples:", c='r', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
-            if "trimesh" in f:
-                printc(bn, c='m', bold=0, end=' ')
+            if "dolfin" in f:
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='r', bold=0)
 
-        printc("\nother examples:", c='w', bold=1)
+        printc("      Trimesh examples:", c='m', bold=1, underline=1)
+        scs = []
         for f,bn in exfiles:
-            if "other" in f and "dolfin" not in f and "trimesh" not in f:
-                printc(bn, c='w', bold=0, end=' ')
+            if "trimesh" in f:
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='m', bold=0)
         print()
+
     else:
         draw_scene()
-
-
-
-
-

docs/news.txt

@@ -1,4 +1,4 @@
-20xx/xx/xx
+2020/01/08
 - added type axes=11 (horizontal grid)
 - fix bug by @m-albert on Volume from numpy object
 - fix typos in docs
@@ -7,9 +7,15 @@
 - add testing directory with circleCI
 - examples and package are now split into two separate repos
 - added possibility to run any example from CLI `vtkplotter --run shrink.py`
+  or list them all with `vtkplotter --list`
+- reshuffled methods by splitting actors.py module
+- general improvements and stability
+- some methods are now deprecated: getPoints becomes points() etc.
+- Actor() becomes Mesh()
+- added advanced/centerline.py examples
+- bump version to 2020.0.1
 
-
-2019/21/19
+2019/11/19
 - added PDV paraview file reading.
 - PDB protein data bank file reader
 - added error bars in plotxy()