probepoints

README.md

@@ -7,9 +7,8 @@
 [![gdocs](https://img.shields.io/badge/docs%20by-gendocs-blue.svg)](https://gendocs.readthedocs.io/en/latest)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2561402.svg)](https://doi.org/10.5281/zenodo.2561402)
 
-A 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/).<br>
+A pure 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/).<br>
 
 ## Download and Install:
 Use [pip](https://projects.raspberrypi.org/en/projects/using-pip-on-windows) to install:
@@ -62,24 +61,25 @@ for the all following functionalities:
     - Generate volumetric signed-distance data from an input surface mesh
     - Probe a volume with lines and planes.
   - Add sliders and buttons to interact with the scene and the individual objects.
+  - 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.
   - Integration with the *Qt5* framework.
-  - Support for [FEniCS/dolfin](https://fenicsproject.org/) package.
+  - Support for [FEniCS/Dolfin](https://fenicsproject.org/) package.
 
 
 
 ## Command-line usage
 ```bash
 vtkplotter mesh.obj 
 # valid formats: [vtk,vtu,vts,vtp,vtm,ply,obj,stl,3ds,xml,neutral,
-#                 gmsh,pcd,xyz,txt,byu,tif,off,slc,vti,mhd,png,jpg]
+#                 gmsh,pcd,xyz,txt,byu,tif,off,slc,vti,mhd,dcm,png,jpg]
 ```
 to visualize multiple files or files time-sequences try `-n` or `-s` options. Use `-h` for help.<br> 
 Voxel-data (_vti, slc, tiff_) files can also be visualized with options `-g` and `--slicer`,
 e.g.:
 ```bash
 vtkplotter -g -c blue examples/data/embryo.slc  # (3D scan of a mouse embryo)
-vtkplotter --slicer   examples/data/embryo.slc  # can read a DICOM directory  
+vtkplotter --slicer   examples/data/embryo.slc  # can be used to read DICOM datasets  
 ```
 ![e2](https://user-images.githubusercontent.com/32848391/50738810-58af4380-11d8-11e9-8fc7-6c6959207224.jpg)
 

bin/vtkplotter

@@ -107,6 +107,9 @@ def _showVoxelImage():
         reader.SetFileName(filename)
         reader.Update()
         img = reader.GetOutput()
+
+        if not args.quiet:
+            vc.printHistogram(img, bins=15, minbin=1, logscale=0, height=8, bold=0, c='b')
 
         if args.z_spacing:
             ispa = img.GetSpacing()
@@ -119,13 +122,12 @@ def _showVoxelImage():
         volumeMapper.SetBlendModeToMaximumIntensity()
         volumeMapper.UseJitteringOn()
         volumeMapper.SetInputConnection(reader.GetOutputPort())
-        printc("scalar range is ", img.GetScalarRange(), c="b", bold=0)
         smin, smax = img.GetScalarRange()
         if smax > 1e10:
             print("Warning, high scalar range detected:", smax)
             smax = abs(10 * smin) + 0.1
             print("         reset to:", smax)
-        printc("voxel spacing is", img.GetSpacing(), c="b", bold=0)
+        printc("voxel spacing:", img.GetSpacing(), c="b", bold=0)
 
         # Create transfer mapping scalar value to color
         if args.color is None:

docs/README.rst

@@ -91,6 +91,8 @@ for the all following functionalities:
 - Add sliders and buttons to interact with the scene and the individual objects.
 - Examples with `SHTools <https://shtools.oca.eu/shtools>`_ package for *spherical harmonics* expansion of a mesh shape.
 - Integration with the *Qt5* framework.
+- Draw `latex`-formatted formulas on the rending window.
+- Support for `FEniCS/dolfin <https://fenicsproject.org/>`_ package
 
 
 Hello World example
@@ -113,7 +115,7 @@ Allowed input objects to the ``show()`` command are: \ :raw-html-m2r:`<br>`
 
 Supported ``filename`` extensions are: \ :raw-html-m2r:`<br>`
 `vtk, vtu, vts, vtp, ply, obj, stl, 3ds, xml, neutral, gmsh, pcd, xyz, txt, byu,
-tif, slc, vti, mhd, png, jpg`.
+tif, slc, vti, mhd, dcm, png, jpg`.
 
 
 
@@ -141,7 +143,7 @@ with options ``-g`` or ``--slicer``, e.g.:
 
     vtkplotter            examples/data/embryo.tif  # shows a 3D scan of a mouse embryo
     vtkplotter -g -c blue examples/data/embryo.slc  #  with sliders to control isosurfacing
-    vtkplotter --slicer   examples/data/embryo.slc 
+    vtkplotter --slicer   examples/data/embryo.slc  # can be used to show DICOM files
 
 .. image:: https://user-images.githubusercontent.com/32848391/50738810-58af4380-11d8-11e9-8fc7-6c6959207224.jpg
    :target: https://user-images.githubusercontent.com/32848391/50738810-58af4380-11d8-11e9-8fc7-6c6959207224.jpg

docs/source/conf.py

@@ -36,7 +36,7 @@
 author = 'Marco Musy'
 
 # The short X.Y version
-version = '2019.1.3'
+version = '2019.1.4'
 
 
 # -- General configuration ---------------------------------------------------

examples/README.md

@@ -89,7 +89,7 @@ vp.show(Cylinder(), at=8, legend='cylinder', interactive=1)
 vp = Plotter(shape=(3,3), title='mesh formats') # split window in 3 rows and 3 columns
 vp.sharecam = False                             # each object can be moved independently
 vp.show('data/beethoven.ply', at=0, c=0, axes=0)    # dont show axes
-vp.show('data/cow.g',         at=1, c=1, zoom=1.15) # make it 15% bigger
+vp.show('data/cow.byu',       at=1, c=1, zoom=1.15) # make it 15% bigger
 vp.show('data/limb.pcd',      at=2, c=2)
 vp.show('data/ring.gmsh',     at=3, c=3, wire=1)    # show mesh as wireframe
 vp.show('data/images/dog.jpg',at=4)                 # 2d images can be loaded the same way

examples/advanced/convexHull.py

@@ -7,4 +7,4 @@
 
 ch = convexHull(spid.coordinates()).alpha(0.2)
 
-show([spid, ch, Text(__doc__)], axes=1)
+show(spid, ch, Text(__doc__), axes=1)

examples/advanced/cutAndCap.py

@@ -7,10 +7,10 @@
 
 cutmesh = Hyperboloid().scale(0.4).wire(True).alpha(0.1)
 
-show([p1, cutmesh], at=0, N=2, axes=1, viewup="z")
+show(p1, cutmesh, at=0, N=2, axes=1, viewup="z")
 
 p2 = p1.clone().cutWithMesh(cutmesh)
 
 redcap = p2.cap(returnCap=True).color("r")  # dark red cap only
 
-show([redcap, p2, Text(__doc__)], at=1, interactive=1)
+show(redcap, p2, Text(__doc__), at=1, interactive=1)

examples/advanced/cutWithMesh.py

@@ -14,5 +14,5 @@
 # make a working copy and cut it with the ellipsoid
 cutembryo = embryo.clone().cutWithMesh(msh).backColor("t").phong()
 
-show([embryo, msh, Text(__doc__)], at=0, N=2, axes=1, viewup="z")
+show(embryo, msh, Text(__doc__), at=0, N=2, axes=1, viewup="z")
 show(cutembryo, at=1, interactive=1)

examples/advanced/geodesic.py

@@ -15,4 +15,4 @@
 
 doc = Text(__doc__, c="w")
 
-show([s, Earth(lw=1), doc] + paths, viewup="z", verbose=0)
+show(s, Earth(lw=1), doc, paths, viewup="z", verbose=0)

examples/advanced/interpolateField.py

@@ -62,5 +62,5 @@
 
 vp2 = Plotter(N=2, pos=(200, 300), verbose=0)
 vp2.camera = vp.camera  # share the same camera with previous Plotter
-vp2.show([apos, warped_rbf, src, trs, arr, Text("Radial Basis Function")], at=0)
+vp2.show(apos, warped_rbf, src, trs, arr, Text("Radial Basis Function"), at=0)
 vp2.show(allarr_rbf, at=1, interactive=1)

examples/advanced/meshquality.py

@@ -7,6 +7,8 @@
 
 a1 = meshQuality(Sphere())
 a2 = meshQuality(load(datadir+"shapes/bunny.obj").normalize())
-a3 = meshQuality(load(datadir+"shapes/motor.g").normalize())
+a3 = meshQuality(load(datadir+"shapes/motor.byu").normalize())
 
-show([a1, a2, a3], N=3)
+printHistogram(a2, title='bunny quality', c='g') # histo active scalars
+
+show(a1, a2, a3, N=3)

examples/advanced/moving_least_squares2D.py

@@ -52,5 +52,5 @@
 a0 = Spheres(s1.coordinates(), c=vcols, r=0.03).legend("variance")
 a1 = Spheres(s1.coordinates(), c="red", r=variances).legend("variance")
 
-vp2.show([a0, Text(__doc__, c="k")], at=0)
-vp2.show([a1, act], at=1, zoom=1.3, interactive=1)
+vp2.show(a0, Text(__doc__, c="k"), at=0)
+vp2.show(a1, act, at=1, zoom=1.3, interactive=1)

examples/advanced/projectsphere.py

@@ -7,4 +7,4 @@
 
 ef = projectSphereFilter(e).normalize().wire(True)
 
-show([e, ef, Text(__doc__)])
+show(e, ef, Text(__doc__))

examples/advanced/quadratic_morphing.py

@@ -117,9 +117,9 @@ def draw_shapes(self):
         text2 = Text("morphed vs target", tpos, s=sz / 10, c="dg")
         text3 = Text("deformation", tpos, s=sz / 10, c="dr")
 
-        vp.show([sphere0, sphere1, zero, text3] + hairsacts, at=2)
-        vp.show([self.msource, self.target, text2], at=1)
-        vp.show([self.source, self.target, text1], at=0, zoom=1.2, interactive=1)
+        vp.show(sphere0, sphere1, zero, text3, hairsacts, at=2)
+        vp.show(self.msource, self.target, text2, at=1)
+        vp.show(self.source, self.target, text1, at=0, zoom=1.2, interactive=1)
 
 
 #################################

examples/advanced/thinplate.py

@@ -33,4 +33,4 @@
 
 apts = Points(ptsource, r=15, c="r")
 
-vp.show([act, warped, apts, Text(__doc__)], viewup="z")
+vp.show(act, warped, apts, Text(__doc__), viewup="z")

examples/advanced/thinplate_grid.py

@@ -32,4 +32,4 @@
 apts = Points(ptsource, r=5, c="r")
 arrs = Arrows(ptsource, pttarget)
 
-show([warped, apts, arrs, Text(__doc__)], axes=9, viewup="z", verbose=0, bg="w")
+show(warped, apts, arrs, Text(__doc__), axes=9, viewup="z", verbose=0, bg="w")

examples/advanced/thinplate_morphing.py

@@ -26,4 +26,4 @@
 
 arro = Arrow(sources[0], targets[0])
 
-show([mesh, arro, warp, apts, Text(__doc__)], viewup="z", axes=1)
+show(mesh, arro, warp, apts, Text(__doc__), viewup="z", axes=1)

examples/basic/README.md

@@ -45,6 +45,8 @@ python example.py
 |    |    |
 | [![largestregion](https://user-images.githubusercontent.com/32848391/50738859-bfccf800-11d8-11e9-8c59-17c0ca4d8e06.jpg)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/largestregion.py)<br/> `largestregion.py`    | Extract the mesh region that has the largest connected surface with method `analysis.extractLargestRegion()`. |
 |    |    |
+| [![latex](https://user-images.githubusercontent.com/32848391/55568648-6190b200-5700-11e9-9547-0798c588a7a5.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/latex.py)<br/> `latex.py`                            | Draw latex formatted text on the rendering window. |
+|    |    |
 | [![manyspheres](https://user-images.githubusercontent.com/32848391/50738858-bfccf800-11d8-11e9-9daf-3b11eedf72ac.png)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/manyspheres.py)<br/> `manyspheres.py`          | Draw a very large number of spheres (200.000) with different colors or different radii (for vtk versions before 8.0 this might be slow). |
 |    |    |
 | [![mesh_alphas](https://user-images.githubusercontent.com/32848391/50738857-bf346180-11d8-11e9-80a1-d283aed0b305.jpg)](https://github.com/marcomusy/vtkplotter/blob/master/examples/basic/mesh_alphas.py)<br/> `mesh_alphas.py`          |  Create a set of transparencies which can be passed to method `pointColors()`.|

examples/basic/a_first_example.py

@@ -9,7 +9,7 @@
 
 c.show()        # draw the cube only
 (c+s).show()    # Actor+Actor = Assembly, then show it.
-show([c,s])     # can show list of [Actor, Volume, filename ...]
+show(c,s)       # can show list of [Actor, Volume, filename ...]
 
 vp = Plotter()  # Make a new Plotter() instance and pop up a new window
 vp.add(Torus()) # generate another mesh and add it to the Plotter list
@@ -29,8 +29,8 @@
 print("-> (c+s).show()  # Actor+Actor = Assembly, then show it.")
 (c + s).show()
 
-print("-> show([c,s])   # can show list of [Actor, Volume, filename ...]")
-show([c, s])
+print("-> show(c,s)   # can show list of [Actor, Volume, filename ...]")
+show(c, s)
 
 print("\n-> # Make a new Plotter() instance and pop up a new window\n-> vp = Plotter()")
 vp = Plotter(verbose=0)

examples/basic/align2.py

@@ -19,7 +19,7 @@
 act1 = Points(pts1, r=8, c="b").legend("source")
 act2 = Points(pts2, r=8, c="r").legend("target")
 
-vp.show([act1, act2], at=0)
+vp.show(act1, act2, at=0)
 
 # find best alignment between the 2 sets of Points, e.i. find
 # how to move act1 to best match act2

examples/basic/align3.py

@@ -1,12 +1,12 @@
 """
-Example usage of align() method:
+Example usage of alignProcrustes() method:
  generate 3 random sets of points
  and align them using vtkProcrustesAlignmentFilter.
 """
 from __future__ import division, print_function
 from random import uniform as u
 
-from vtkplotter import Plotter, procrustes, Text, Points
+from vtkplotter import Plotter, alignProcrustes, Text, Points
 
 vp = Plotter(shape=[1, 2], verbose=0, axes=2, sharecam=0, bg="w")
 
@@ -21,12 +21,12 @@
 act2 = Points(pts2, c="g").legend("set2")
 act3 = Points(pts3, c="b").legend("set3")
 
-vp.show([act1, act2, act3], at=0)
+vp.show(act1, act2, act3, at=0)
 
 # find best alignment among the n sets of Points,
 # return an Assembly formed by the aligned sets
-aligned = procrustes([act1, act2, act3])
+aligned = alignProcrustes([act1, act2, act3])
 
 # print(aligned.info['transform'])
 
-vp.show([aligned, Text(__doc__)], at=1, interactive=1)
+vp.show(aligned, Text(__doc__), at=1, interactive=1)

examples/basic/bgImage.py

@@ -12,7 +12,7 @@
 a1 = load(datadir+"shapes/flamingo.3ds").rotateX(-90)
 a2 = Polygon()
 
-vp.show([a1, doc], at=0)
+vp.show(a1, doc, at=0)
 
 vp.backgroundRenderer.GetActiveCamera().Zoom(2.5)
 

examples/basic/boolean.py

@@ -19,7 +19,7 @@
 b3 = booleanOperation(s1, "minus", s2, c=None).legend("minus")
 
 # show the result in 4 different subwindows 0->3
-vp.show([s1, s2], at=0)
+vp.show(s1, s2, at=0)
 vp.show(b1, at=1)
 vp.show(b2, at=2)
 vp.show(b3, at=3)

examples/basic/clustering.py

@@ -22,4 +22,4 @@
 # find back their identity through clustering
 cl = cluster(pts, radius=0.1)  # returns a vtkAssembly
 
-show([cl, Text(__doc__)], axes=1, verbose=0)
+show(cl, Text(__doc__), axes=1, verbose=0)

examples/basic/connVtx.py

@@ -13,4 +13,4 @@
 apt = Point(s.getPoint(index), c="r", r=15)
 cpts = Points(vtxs, c="blue", r=15)
 
-show([s, apt, cpts, Text(__doc__)], verbose=False)
+show(s, apt, cpts, Text(__doc__), verbose=False)

examples/basic/delaunay2d.py

@@ -18,5 +18,5 @@
 cents = d1.cellCenters()
 ap = Points(cents).legend("cell centers")
 
-vp.show([d0, d1], at=0)  # NB: d0 and d1 are slightly different
-vp.show([d1, ap], at=1, interactive=1)
+vp.show(d0, d1, at=0)  # NB: d0 and d1 are slightly different
+vp.show(d1, ap, at=1, interactive=1)

examples/basic/fillholes.py

@@ -13,4 +13,4 @@
 
 doc = Text(__doc__)
 
-show([a, b, doc], elevation=-70)
+show(a, b, doc, elevation=-70)

examples/basic/glyphs.py

@@ -23,12 +23,12 @@
     scaleByVectorSize=True,
 )
 
-show([s, gsphere1, t], at=0, N=2, verbose=0)
+show(s, gsphere1, t, at=0, N=2, verbose=0)
 
 
 #######################################
 gly2 = load(datadir+"shuttle.obj").rotateY(180).scale(0.02)
 
 gsphere2 = Glyph(s, gly2, orientationArray="normals")
 
-show([s, gsphere2], at=1, interactive=1)
+show(s, gsphere2, at=1, interactive=1)

examples/basic/histo2D.py

@@ -2,7 +2,7 @@
 2D histogram with hexagonal binning.
 """
 print(__doc__)
-from vtkplotter import Plotter, histogram2D, Points
+from vtkplotter import Plotter, histogram2D, Points, Latex
 import numpy as np
 
 vp = Plotter(axes=1, verbose=0, bg="w")
@@ -14,8 +14,12 @@
 x = np.random.randn(N) * 1.0
 y = np.random.randn(N) * 1.5
 
-vp.add(histogram2D(x, y, c="dr", bins=15, fill=False))
+histo = histogram2D(x, y, c="dr", bins=15, fill=False)
 
-vp.add(Points([x, y, np.zeros(N)], c="black", alpha=0.1))
+pts = Points([x, y, np.zeros(N)], c="black", alpha=0.1)
 
-vp.show(viewup="z")
+f = r'f(x, y)=A \exp \left(-\left(\frac{\left(x-x_{o}\right)^{2}}{2 \sigma_{x}^{2}}+\frac{\left(y-y_{o}\right)^{2}}{2 \sigma_{y}^{2}}\right)\right)'
+
+formula = Latex(f, c='k', s=2).rotateZ(90).pos(5,-2,1)
+
+vp.show(histo, pts, formula, viewup="z")

examples/basic/largestregion.py

@@ -11,5 +11,5 @@
 act2 = extractLargestRegion(act1).color("b")
 printc("area2 =", act2.area(), c="b")
 
-show([act1, Text(__doc__)], at=0, shape=(2, 1))
+show(act1, Text(__doc__), at=0, shape=(2, 1))
 show(act2, at=1, zoom=1.2, interactive=1)

examples/basic/latex.py

@@ -0,0 +1,18 @@
+from vtkplotter import Latex, Cube, Point, show
+
+# https://matplotlib.org/tutorials/text/mathtext.html
+
+latex1 = r'x= \frac{ - b \pm \sqrt {b^2 - 4ac} }{2a}'
+latex2 = r'$\mathcal{A}\mathrm{sin}(2 \omega t)$'
+latex3 = r'I(Y | X)=\sum_{x \in \mathcal{X}, y \in \mathcal{Y}} p(x, y) \log \left(\frac{p(x)}{p(x, y)}\right)'
+latex4 = r'\Gamma_{\epsilon}(x)=\left[1-e^{-2 \pi \epsilon}\right]^{1-x} \prod_{n=0}^{\infty} \frac{1-\exp (-2 \pi \epsilon(n+1))}{1-\exp (-2 \pi \epsilon(x+n))}'
+latex5 = r'\left( \begin{array}{l}{c t^{\prime}} \\ {x^{\prime}} \\ {y^{\prime}} \\ {z^{\prime}}\end{array}\right)=\left( \begin{array}{cccc}{\gamma} & {-\gamma \beta} & {0} & {0} \\ {-\gamma \beta} & {\gamma} & {0} & {0} \\ {0} & {0} & {1} & {0} \\ {0} & {0} & {0} & {1}\end{array}\right) \left( \begin{array}{l}{c t} \\ {x} \\ {y} \\ {z}\end{array}\right)'
+latex6 = r'\mathrm{CO}_{2}+6 \mathrm{H}_{2} \mathrm{O} \rightarrow \mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}+6 \mathrm{O}_{2}'
+latex7 = r'x~\mathrm{(arb. units)}'
+
+p = Point()
+c = Cube().wire()
+
+l = Latex(latex5, s=1, c='white', bg='', alpha=0.9, fromweb=False).addPos(4,0,-1)
+
+show(p, c, l, axes=8)

examples/basic/lights.py

@@ -2,7 +2,7 @@
 
 vp = Plotter()
 
-cow = vp.load(datadir+"cow.g", c="grey", alpha=0.7)
+cow = vp.load(datadir+"cow.byu", c="grey", alpha=0.7)
 
 vp.add(Plane(pos=[0, -3.6, 0], normal=[0, 1, 0], sx=20, texture="grass"))