2020.0.2

marcomusy · Jan 20, 2020 · a3f187b · a3f187b
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diff --git a/README.md b/README.md
@@ -39,14 +39,14 @@ pip install -U vtkplotter
 *Windows-10 users* can place this file
 [vtkplotter.bat](https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter.bat)
 on the desktop to *drag&drop* files to visualize.
-(Need to edit the path of the local Anaconda installation).
+(Need to edit the path of the local python installation).
 
 
 ## 📙 Documentation
 Automatically generated documentation can be found [**here**](https://vtkplotter.embl.es).
 
 
-#### 📌 Need help?
+##### 📌 Need help?
 Have any question, or wish to suggest or ask for a missing feature?
 Do not hesitate to open a [**issue**](https://github.com/marcomusy/vtkplotter-examples/issues)
 or send an [email](mailto:[email protected]).
@@ -56,12 +56,13 @@ or send an [email](mailto:[email protected]).
 Intuitive and straightforward API which can be combined with VTK seamlessly
 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, 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. Additional analysis tools like *Moving Least Squares*, mesh morphing and more..
+It includes a **[large set of working examples](https://github.com/marcomusy/vtkplotter-examples/tree/master/vtkplotter_examples)**
+for a wide range of functionalities *(click triangle to expand...)*:
+<details>
+<summary>*working with polygonal meshes and point clouds*</summary>
+  - Import meshes from VTK format, STL, Wavefront OBJ, 3DS, Dolfin-XML, Neutral, GMSH, OFF, PCD (PointCloud),
+  - Export meshes as ASCII or binary to VTK, STL, OBJ, PLY ... formats.
+  - 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 areas, volumes, center of mass, average sizes etc.
@@ -79,40 +80,61 @@ for all the following functionalities:
   - 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 lines, planes or other meshes.
+  - Interpolate scalar and vectorial fields with *Radial Basis Functions* and *Thin Plate Splines*.
+  - Add sliders and buttons to interact with the scene and the individual objects.
+  - Visualization of tensors.
   - Analysis of *Point Clouds*:
 	 - *Moving Least Squares* smoothing of 2D, 3D and 4D clouds
     - 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
-    - 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.
-  - 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.
-  - 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)).
-
-
-### ➜ Command Line Interface
+</details>
+<details>
+<summary>*working with volumetric data*</summary>
+  - Import data from VTK format volumetric TIFF stacks, DICOM, SLC, MHD and more
+  - Import 2D images as PNG, JPEG, BMP
+  - Isosurfacing of volumes
+  - 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
+  - Slice and crop volumes
+  - Support for other volumetric structures (structured and grid data)
+</details>
+<details>
+<summary>*plotting and histogramming*</summary>
+  - Fully customizable axis styles
+  - 'donut' plots and pie charts
+  - Scatter plots in 2D and 3D
+  - Surface function plotting
+  - 1D customizable histograms
+  - 2D hexagonal histograms
+  - Polar plots and histogramming
+  - Draw `latex`-formatted formulas in the rendering window.
+  - Quiver plots
+  - Point markers analogous to `matplotlib`
+
+</details>
+
+
+Moreover:
+- 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.
+- 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)).
+
+
+## ⌨ Command Line Interface
 Visualize a mesh from a terminal window with:
 ```bash
 vtkplotter mesh.obj
 # valid formats: [vtk,vtu,vts,vtp,vtm,ply,obj,stl,3ds,dolfin-xml,neutral,gmsh,
 #                 pcd,xyz,txt,byu,tif,off,slc,vti,mhd,dcm,dem,nrrd,nii,bmp,png,jpg]
 ```
 Voxel-data (_mhd, vti, slc, tiff, dicom etc.._) files can be visualized with options `-g`. E.g.:<br>
-`vtkplotter -g examples/data/embryo.slc`<br>
+`vtkplotter -g embryo.slc`<br>
 
 ![isohead](https://user-images.githubusercontent.com/32848391/58336107-5a09a180-7e43-11e9-8c4e-b50e4e95ae71.gif)
 
@@ -123,7 +145,7 @@ 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)
@@ -135,7 +157,7 @@ pip install -U git+https://github.com/marcomusy/vtkplotter-examples
 vtkplotter --list
 vtkplotter --run tube.py
 ```
-**More than 280 working examples can be found in directories** _(scroll down to see thumbnails):_ <br>
+**More than 300 working examples can be found in directories** _(scroll down to see thumbnails):_ <br>
 [**examples/basic**](https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/basic)<br>
 [**examples/advanced**](https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/advanced)<br>
 [**examples/volumetric**](https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/volumetric)<br>

diff --git a/bin/vtkplotter b/bin/vtkplotter
@@ -1044,6 +1044,22 @@ else:  #########################################################################
                 scs.append(lb+bn.replace('.py',''))
         printc("".join(scs), c='y', bold=0)
 
+        printc("Simulation examples:", c='m', bold=1, underline=1)
+        scs = []
+        for f,bn in exfiles:
+            if "simulation" in f:
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='m', bold=0)
+
+        printc("Plotting 2D examples:", c='w', bold=1, underline=1)
+        scs = []
+        for f,bn in exfiles:
+            if "plotting2d" in f:
+                lb = ' ' if (len(scs)+1)%nl else '\n'
+                scs.append(lb+bn.replace('.py',''))
+        printc("".join(scs), c='w', bold=0)
+
         printc("Volumetric examples:", c='b', bold=1, underline=1)
         scs = []
         for f,bn in exfiles:

diff --git a/docs/README.rst b/docs/README.rst
@@ -20,13 +20,13 @@
 .. image:: https://img.shields.io/badge/docs%20by-gendocs-blue.svg
    :target: https://gendocs.readthedocs.io/en/latest/
    :alt: Documentation Built by gendocs
-   
+
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.2561402.svg
    :target: https://doi.org/10.5281/zenodo.2561402
-   
+
 ---------------------
 
-A lightweight python module for scientific visualization, analysis and animation of 3D objects 
+A lightweight python module for scientific visualization, analysis and animation of 3D objects
 and `point clouds` based on `VTK <https://www.vtk.org/>`_
 and `numpy <http://www.numpy.org/>`_.
 
@@ -52,18 +52,18 @@ Check out the **Git repository** here: https://github.com/marcomusy/vtkplotter-e
 
 *Windows-10 users* can manually place this file
 `vtkplotter.bat <https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter.bat>`_
-on the desktop to *drag&drop* files to visualize. 
+on the desktop to *drag&drop* files to visualize.
 (Need to edit the path of their local Anaconda installation).
 
 
 Features:
 ---------
 
-Intuitive and straightforward API which can be combined with VTK seamlessly 
+Intuitive and straightforward API which can be combined with VTK seamlessly
 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>`_ 
+It includes a
+`large set of working examples <https://github.com/marcomusy/vtkplotter-examples/tree/master/vtkplotter_examples>`_
 for the all following functionalities:
 
 - Import meshes from VTK format, STL, Wavefront OBJ, 3DS, XML, Neutral, GMSH, PCD (PointCloud), volumetric TIFF stacks, SLC, MHD, 2D images PNG, JPEG.
@@ -76,7 +76,7 @@ for the all following functionalities:
 - 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, check if a point lies inside or outside a mesh.
-- Create primitive objects like: spheres, arrows, cubes, torus, ellipsoids... 
+- 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 to moving objects automatically.
 - Straightforward support for multiple `sync-ed` or independent renderers in  the same window.
@@ -87,7 +87,7 @@ for the all following functionalities:
 - 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).
 - Analysis of `Point Clouds`:
-    
+
     - `Moving Least Squares` smoothing of 2D, 3D and 4D clouds
     - Fit lines, planes and spheres in space
     - Perform PCA (Principal Component Analysis) on point coordinates
@@ -122,14 +122,14 @@ In your python script, load a simple ``3DS`` file and display it:
 .. code-block:: python
 
     from vtkplotter import show
-    
-    show('flamingo.3ds') 
+
+    show('flamingo.3ds')
 
 .. image:: https://user-images.githubusercontent.com/32848391/50738813-58af4380-11d8-11e9-84ce-53579c1dba65.png
    :alt: flam
 
 Allowed input objects to the ``show()`` command are: \ :raw-html-m2r:`<br>`
-``filename``, ``vtkPolyData``, ``vtkActor``, 
+``filename``, ``vtkPolyData``, ``vtkActor``,
 ``vtkActor2D``, ``vtkImageActor``, ``vtkAssembly`` or ``vtkVolume``.
 
 
@@ -167,7 +167,7 @@ Load and browse a sequence of meshes:
 
 .. code-block:: bash
 
-    vtkplotter -s examples/data/timecourse1d/*.vtk   
+    vtkplotter -s examples/data/timecourse1d/*.vtk
 
 .. image:: https://user-images.githubusercontent.com/32848391/58336919-f7b1a080-7e44-11e9-9106-f574371093a8.gif
 
@@ -203,23 +203,23 @@ More than 280 examples can be found in directories:
 
 
 Apply a *Moving Least Squares* algorithm to obtain a smooth surface from a to a
-large cloud of scattered points in space 
+large cloud of scattered points in space
 (`moving_least_squares2D.py <https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/advanced/moving_least_squares2D.py>`_):
 
 .. image:: https://user-images.githubusercontent.com/32848391/50738808-5816ad00-11d8-11e9-9854-c952be6fb941.jpg
    :target: https://user-images.githubusercontent.com/32848391/50738808-5816ad00-11d8-11e9-9854-c952be6fb941.jpg
    :alt: rabbit
 
 
-Simulation of a gyroscope hanging from a spring 
+Simulation of a gyroscope hanging from a spring
 (`gyroscope1.py <https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/simulations/gyroscope1.py>`_):
 
 .. image:: https://user-images.githubusercontent.com/32848391/39766016-85c1c1d6-52e3-11e8-8575-d167b7ce5217.gif
    :target: https://user-images.githubusercontent.com/32848391/39766016-85c1c1d6-52e3-11e8-8575-d167b7ce5217.gif
    :alt: gyro
 
 
-Quantum-tunnelling effect integrating the Schroedinger equation with 4th order Runge-Kutta method. 
+Quantum-tunnelling effect integrating the Schroedinger equation with 4th order Runge-Kutta method.
 The animation shows the evolution of a particle in a box hitting a sinusoidal potential barrier
 (`tunnelling2.py <https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/simulations/tunnelling2.py>`_):
 
@@ -238,7 +238,7 @@ Visualizing a Turing system of reaction-diffusion between two molecules
 
 
 
-Support for the `FEniCS/dolfin <https://fenicsproject.org/>`_ platform for visualization of PDE and 
+Support for the `FEniCS/dolfin <https://fenicsproject.org/>`_ platform for visualization of PDE and
 finite element solutions
 (`see here <https://github.com/marcomusy/vtkplotter-examples/blob/master/vtkplotter_examples/other/dolfin>`_.
 
@@ -249,13 +249,11 @@ finite element solutions
 Mesh format conversion
 ^^^^^^^^^^^^^^^^^^^^^^
 
-The command ``vtkconvert`` can be used to convert multiple files from a format to a different one:
+The command ``vtkplotter-convert`` can be used to convert multiple files from a format to a different one:
 
 .. code-block:: bash
 
-   Usage: vtkconvert [-h] [-to] [files [files ...]]
+   Usage: vtkplotter-convert [-h] [-to] [files [files ...]]
    allowed targets formats: [vtk, vtp, vtu, vts, ply, stl, byu, xml]
 
-   Example: > vtkconvert myfile.vtk -to ply
-
-
+   Example: > vtkplotter-convert myfile.vtk -to ply
diff --git a/docs/logos/fenics_mesh.py b/docs/logos/fenics_mesh.py
@@ -9,12 +9,12 @@
 show(tf, bx)
 
 printc('implicitModeller', mytext, "this takes time")
-imp = implicitModeller(mergeActors(tf, bx), 
+imp = implicitModeller(mergeActors(tf, bx),
                        distance=0.04,
-                       outer=True, 
-#                       res=[50,20,10], 
+                       outer=True,
+#                       res=[50,20,10],
                        res=[110,40,20],
-                       bounds=[-1.0, 10.0, -1.0, 2.0, -.5, .5], 
+                       bounds=[-1.0, 10.0, -1.0, 2.0, -.5, .5],
                        maxdist=0.25,
         )
 

diff --git a/docs/news.txt b/docs/news.txt
@@ -1,3 +1,22 @@
+2020/01/20
+- added shapes Arrow2D and Arrows2D, SphericGrid, CubicGrid
+- completely revised customizable axes=1 type
+  - axes can be created for each object independently
+- quiver plots, scatter plots, error bands plots
+- plotting in spherical coordinates
+- '2d' backend to plot static images in notebooks.
+Available backends:
+```python
+from vtkplotter import *
+# embedWindow('2d')
+# embedWindow('k3d')
+# embedWindow('itk')
+# embedWindow('panel')
+# embedWindow(False)
+```
+- Added wavefront format .OBJ writer
+
+
 2020/01/08
 - added type axes=11 (horizontal grid)
 - fix bug by @m-albert on Volume from numpy object
@@ -15,6 +34,7 @@
 - added advanced/centerline.py examples
 - bump version to 2020.0.1
 
+
 2019/11/19
 - added PDV paraview file reading.
 - PDB protein data bank file reader

diff --git a/setup.py b/setup.py
@@ -36,8 +36,8 @@
                 'Programming Language :: Python :: 2.7',
                 'Programming Language :: Python :: 3.5',
                 'Programming Language :: Python :: 3.6',
-                'Programming Language :: Python :: 3.7'
-                'Programming Language :: Python :: 3.8'
+                'Programming Language :: Python :: 3.7',
+                'Programming Language :: Python :: 3.8',
                 ],
     include_package_data=True
 )
@@ -56,10 +56,14 @@
 
 # cd ~/Projects/vtkplotter-examples/vtkplotter_examples
 # ./run_all.sh
+# cd ~/Projects/vtkplotter/
 # python prove/test_filetypes.py
 
+# cd ~/Projects/vtkplotter/tests/common
+# ./run_all.sh
+
 # check vtkconvert:
-# vtkconvert data/290.vtk -to ply; vtkplotter data/290.ply
+# vtkplotter-convert data/290.vtk -to ply; vtkplotter data/290.ply
 
 # check on python2 the same stuff is ok
 # cd ~/Projects/vtkplotter/
@@ -119,7 +123,7 @@
 #    git clone https://github.com/marcomusy/vtkplotter.git
 #    cd vtkplotter
 #    pip3 -v install . --user
-#    
+#
 #    cd
 #    pip3 install git+https://github.com/FEniCS/fiat.git --upgrade
 #    pip3 install git+https://github.com/FEniCS/ufl.git  --upgrade