4.10

README.md

@@ -23,6 +23,11 @@ on the desktop to *drag&drop* files to visualize.
 ## Documentation
 Automatically generated documentation can be found [**here**](https://vtkplotter.embl.es).
 
+#### 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/issues)
+or send an [email](mailto:marco.musy@embl.es).
+
 ## Features
 
 Intuitive and straightforward API which can be combined with VTK seamlessly 

docs/news.txt

@@ -0,0 +1,16 @@
+2019/11/19
+- added PDV paraview file reading.
+- PDB protein data bank file reader
+- added error bars in plotxy()
+- fast fitting of 2d circles with utils.fitCircle2D()
+- added flag-style pop-up labels for meshes and volumes
+- added settings for resolving polygonal clashes with mesh edges
+- built in set of parametric surfaces in shapes.py module
+- improved plotting2d with error bars
+- added warpMeshToPoint() method
+- improved texture control, can pass texture coords explicitly
+- fix trimesh problem with coloring vertices
+- can use "panel" backend in notebooks
+
+
+

examples/advanced/fitspheres2.py

@@ -29,7 +29,7 @@
 
 vp += Points(pts1, c=cols)
 vp += Lines(pts1, pts2, c="black 0.2")
-vp += histogram(vals, title="values", bins=20, vrange=[0, 1])
+vp += histogram(vals, bins=20, vrange=[0, 1]).pos(-1,1,-1)
 vp += Text(__doc__, pos=1)
 
-vp.show()
+vp.show(axes=1)

examples/basic/acollection.ipynb

@@ -8,7 +8,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a833f7c22dc942edbe873727193e0c22",
+       "model_id": "4639a002733847bd8674f05b70c0cadb",
        "version_major": 2,
        "version_minor": 0
       },

examples/basic/align1.py

@@ -8,7 +8,8 @@
 
 vp = Plotter()
 
-limb = vp.load(datadir + "270.vtk")
+# flag() shows the filename when hovering with mouse
+limb = vp.load(datadir + "270.vtk").flag()
 rim  = vp.load(datadir + "270_rim.vtk").c("r").lw(4)
 
 arim = alignICP(rim, limb, rigid=True).c("g").lw(5)

examples/basic/mirror.py

@@ -1,12 +1,14 @@
 """
 Mirror a mesh along one of the Cartesian axes.
+
+Hover mouse to see original and mirrored.
 """
 from vtkplotter import Plotter, Text, datadir
 
 vp = Plotter(axes=2)
 
-myted1 = vp.load(datadir+"teddy.vtk")
+myted1 = vp.load(datadir+"teddy.vtk").flag('original')
 
-myted2 = myted1.clone().mirror("y").pos([0, 3, 0]).color("green")
+myted2 = myted1.clone().mirror("y").pos([0, 3, 0]).c("green").flag('mirrored')
 
 vp.show(myted1, myted2, Text(__doc__), viewup="z")

examples/basic/run_all.sh

@@ -170,6 +170,9 @@ python cutter.py
 echo Running texturecubes.py
 python texturecubes.py
 
+echo Running texture_coords.py
+python texture_coords.py
+
 echo Running ribbon.py
 python ribbon.py
 

examples/basic/texture_coords.py

@@ -0,0 +1,26 @@
+"""Assign texture coordinates to a polygon
+"""
+from vtkplotter import Actor, Text, datadir, show
+
+# define a polygon of 4 vertices:
+polygon_a = [
+    [(82, 92, 47), (87, 88, 47), # x,y,z of vertices
+     (93, 95, 47), (88, 99, 47)],
+    [[0, 1, 2, 3]],              # vertex connectivity
+]
+
+# texture coordinates, one (u,v) pair for each vertex:
+tc = [(0,0), (1,0), (1,1), (0,1)]
+#tc = [(0,0), (2,0), (2,2), (0,2)]
+
+# create the vtkActor
+a = Actor(polygon_a)
+
+a.texture(datadir+"images/dog.jpg",
+          tcoords=tc,
+          interpolate=True,
+          repeat=True,      # when tcoords extend beyond [0,1]
+          edgeClamp=False,  #  only used when repeat is False
+         )
+
+show(a, Text(__doc__), axes=8)

examples/other/flag_labels.py

@@ -0,0 +1,23 @@
+"""Hover mouse onto an object
+to pop a flag-style label
+"""
+from vtkplotter import *
+
+# Can modify default behaviour through settings:
+#settings.flagDelay = 0          # popup delay in milliseconds
+#settings.flagFont = "Courier"   # font type ("Arial", "Courier", "Times")
+#settings.flagFontSize = 18
+#settings.flagJustification = 0
+#settings.flagAngle = 0
+#settings.flagBold = False
+#settings.flagItalic = True
+#settings.flagShadow = False
+#settings.flagColor = 'black'
+#settings.flagBackgroundColor = 'white'
+
+s = load(datadir+'/bunny.obj').flag() # picks filename by default
+c = Cube(side=0.2).x(0.3).flag('my cube\nlabel')
+
+#s.flag(False) #disable
+
+show(s, c, Text(__doc__))

examples/other/run_all.sh

@@ -15,6 +15,9 @@ python colorpalette.py
 echo Running printc.py
 python printc.py
 
+echo Running flag_labels.py
+python flag_labels.py
+
 echo Running icon.py
 python icon.py
 

examples/other/trimesh/ray.py

@@ -1,6 +1,8 @@
 import trimesh
 import numpy as np
-from vtkplotter import show
+from vtkplotter import show, settings
+
+settings.useDepthPeeling = True
 
 # test on a sphere mesh
 mesh = trimesh.creation.icosphere()

examples/plotting2d/README.md

@@ -17,7 +17,9 @@ python example.py
 |    |    |
 | [![fxy](https://user-images.githubusercontent.com/32848391/50738863-bfccf800-11d8-11e9-882d-7b217aceb55a.jpg)](https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d/fxy.py)<br/> `fxy.py`                       | Draw a surface representing a function _f(x, y)_ defined as a string/formula or as a reference to an external already existing function. <br/>Red points indicate where the function does not exist. |
 |    |    |
-| [![histo](https://user-images.githubusercontent.com/32848391/68141260-77cc4e00-ff2d-11e9-9280-0efc5b87314d.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d/histogram.py)<br/> `histogram.py`         | Draw a 2D histogram with error bars. |
+| [![plotxy](https://user-images.githubusercontent.com/32848391/69158509-d6c1c380-0ae6-11ea-9dbf-ff5cd396a9a6.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d/plotxy.py)<br/> `plotxy.py`              | Draw a _x_ vs _y_ plot with optional error bars. |
+|    |    |
+| [![histo](https://user-images.githubusercontent.com/32848391/68141260-77cc4e00-ff2d-11e9-9280-0efc5b87314d.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d/histogram.py)<br/> `histogram.py`         | Draw a 2D histogram with optional error bars. |
 |    |    |
 | [![histo2d](https://user-images.githubusercontent.com/32848391/50738861-bfccf800-11d8-11e9-9698-c0b9dccdba4d.jpg)](https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d/histoHexagonal.py)<br/> `histoHexagonal.py`    | Make a histogram of two variables with hexagonal binning. |
 |    |    |

examples/plotting2d/axesStyle.py

@@ -0,0 +1,8 @@
+from vtkplotter import *
+
+Earth(r=1).x(3)  # set position x=3
+
+Sphere(r=.3).x(-3).texture('marble2')
+
+printc('press keypad 1-9 to change axes style', box='-', invert=1)
+show(..., axes=11, bg='db', bg2='k', verbose=0)

examples/plotting2d/plotxy.py

@@ -1,27 +1,36 @@
 from vtkplotter import plotxy, show
 import numpy as np
 
-x = np.arange(0, 10, 1)
-y = np.sin(x)
+x  = np.arange(0, 10, 1)
+y  = np.sin(x)
 
+# assign errors to both x and y
+ye = np.random.rand(10)/2
+xe = np.random.rand(10)
+
+##############
 plt1 = plotxy(
-    [x, y],
-    yscale=3, # set an optional scaling factor
+    [x, y],       # accepts different formats
+    yscale=3,     # set an optional y-scaling factor
     xlimits=(-1, 11),
     splined=False,
-    lc="r",
-    marker="*",
-    mc="dr",
+    lc="r",       # line color
+    marker="*",   # marker style
+    mc="dr",      # marker color
 )
 
+##############
 plt2 = plotxy(
     [x+1, y+0.2],
-    yscale=3, # choose the same y-scale as above
+    xerrors=xe,   # show error bars
+    yerrors=ye,
+    yscale=3,     # choose the same y-scale as above!
     splined=True,
     xtitle="x variable (mm)",
     ytitle="y(x)",
     lc="b",
-    marker="D",
+    marker="s",   # o, p, *, h, D, d , v, ^, s, x, a
 )
 
+##############
 show(plt1, plt2, bg="w", axes=1)

examples/plotting2d/run_all.sh

@@ -12,6 +12,9 @@ echo
 echo Running annotations.py
 python annotations.py    
 
+echo Running axesStyle.py
+python axesStyle.py
+
 echo Running customAxes.py
 python customAxes.py
 

examples/run_all.sh

@@ -88,10 +88,10 @@ vtkplotter
 
 
 ##################################### not run/ignored:
-#basic/lights.py
-#plotting2d/text_just.py
-#other/makeVideo.py
-#other/spherical_harmonics2.py
-#other/remesh_ACVD.py
-#other/tf_learn_embryo.py
-#other/self_org_maps3d.py
+# examples/basic/lights.py
+# examples/plotting2d/text_just.py
+# examples/other/makeVideo.py
+# examples/other/spherical_harmonics2.py
+# examples/other/remesh_ACVD.py
+# examples/other/tf_learn_embryo.py
+# examples/other/self_org_maps3d.py

examples/simulations/hanoi3d.py

@@ -79,7 +79,7 @@ def demo3d_hanoi(**kwargs):
     }
     for k in disks:
         vp += disks[k]
-    vp += Box(pos=(3.0, 0, -0.05), length=12.0, width=4.0, height=0.1)
+    vp += Box(pos=(3.0, 0, -.5), length=12.0, width=4.0, height=0.1)
     vp.show(zoom=1.2)
 
     printc("\n Press q to continue, Esc to exit. ", c="y", invert=1)

examples/volumetric/numpy2volume.ipynb

@@ -15,7 +15,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e2c9bea738bf4d44834a41fb1213eacb",
+       "model_id": "884bf91fb6dc4413add52b6dc0574aba",
        "version_major": 2,
        "version_minor": 0
       },

setup.py

@@ -5,7 +5,7 @@
     verstrline = open(VERSIONFILE, "rt").read()
     verstr = verstrline.split('=')[1].replace('\n','').replace("'","")
 except:
-    verstr='unknown_version'
+    verstr='unknown'
 
 ##############################################################
 setup(
@@ -50,11 +50,12 @@
 # pip install .
 
 # cd examples && ./run_all.sh
+# python tutorial.py
 # cd ~/Projects/vtkplotter/
 # python tests/test_filetypes.py
 
 # check vtkconvert:
-# vtkconvert vtkplotter/data/290.vtk -to ply
+# vtkconvert vtkplotter/data/290.vtk -to ply; vtkplotter vtkplotter/data/290.ply
 
 # check on python2 the same stuff is ok
 # cd ~/Projects/vtkplotter/
@@ -63,7 +64,7 @@
 
 # check notebooks:
 # cd ~/Projects/vtkplotter/
-# jupyter notebook &
+# jupyter notebook > /dev/null 2>&1
 # remove trailing spaces
 
 # cd ~/Projects/vtkplotter/
@@ -72,7 +73,7 @@
 # rm examples/other/trimesh/featuretype.STL examples/other/trimesh/machinist.XAML
 # rm examples/other/scene.npy examples/other/timecourse1d.npy vtkplotter/data/290.ply
 # rm examples/other/voronoi3d.txt examples/other/voronoi3d.txt.vol
-# rm examples/other/embryo.html examples/other/embryo.x3d timecourse1d.npy
+# rm examples/other/embryo.html examples/other/embryo.x3d 
 
 # git status
 # git add [files]

vtkplotter/__init__.py

@@ -12,7 +12,10 @@
     - `examples/advanced <https://github.com/marcomusy/vtkplotter/blob/master/examples/advanced>`_ ,
     - `examples/volumetric <https://github.com/marcomusy/vtkplotter/blob/master/examples/volumetric>`_,
     - `examples/simulations <https://github.com/marcomusy/vtkplotter/blob/master/examples/simulations>`_
+    - `examples/plotting2d <https://github.com/marcomusy/vtkplotter/blob/master/examples/plotting2d>`_
     - `examples/others <https://github.com/marcomusy/vtkplotter/blob/master/examples/other>`_.
+    - `examples/others/dolfin <https://github.com/marcomusy/vtkplotter/blob/master/examples/other/dolfin>`_.
+    - `examples/others/trimesh <https://github.com/marcomusy/vtkplotter/blob/master/examples/other/trimesh>`_.
 
 
 Publications where ``vtkplotter`` has been used so far: