make cmap(on="") work out its default cell or point data

docs/changes.md

@@ -42,7 +42,7 @@ examples/other/pygmsh_cut.py ust cut tetmesh to gen ugrid
 
 #### Broken Projects
 umap_viewer3d
-trackviewer (some problems with removing a track)
+trackviewer (some problems with removing a track, and z spacing)
 
 
 #### Broken Exports to .npz:

docs/documentation.md

@@ -1,16 +1,17 @@
 
 [![license](https://img.shields.io/badge/license-MIT-blue.svg)](https://en.wikipedia.org/wiki/MIT_License)
 [![Anaconda-Server Badge](https://anaconda.org/conda-forge/vedo/badges/version.svg)](https://anaconda.org/conda-forge/vedo)
-[![Ubuntu 23.04 package](https://repology.org/badge/version-for-repo/ubuntu_23_04/vedo.svg)](https://repology.org/project/vedo/versions)
+[![Ubuntu 23.10 package](https://repology.org/badge/version-for-repo/ubuntu_23_10/vedo.svg)](https://repology.org/project/vedo/versions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5842090.svg)](https://doi.org/10.5281/zenodo.5842090)
 
-![](https://user-images.githubusercontent.com/32848391/46815773-dc919500-cd7b-11e8-8e80-8b83f760a303.png)
+![](https://vedo.embl.es/images/feats/teapot_banner.png)
 
 
 A python module for scientific analysis of 3D objects and
 point clouds based on [VTK](https://www.vtk.org/) and [numpy](http://www.numpy.org/).
 
-Check out the [GitHub repository here](https://github.com/marcomusy/vedo).
+Check out the [GitHub repository here](https://github.com/marcomusy/vedo)
+and the [vedo main page here](https://vedo.embl.es).
 
 Find at this [link](https://vedo.embl.es/autodocs/v2023.4.7/vedo.html) the documentation for the older version v2023.4.7.
 
@@ -100,7 +101,8 @@ You can also find online tutorials at:
    - [3D Visualization of STL Files](https://www.youtube.com/watch?v=llq9-oJXepQ)
 
 
-- [Creating an interactive 3D geological model](https://www.youtube.com/watch?v=raiIft8VeRU&t=1s) by A. Pollack (SCRF).
+- [Creating an interactive 3D geological model](https://www.youtube.com/watch?v=raiIft8VeRU&t=1s) by A. Pollack (SCRF). See a more updated example 
+[here](https://github.com/marcomusy/vedo/blob/master/examples/advanced/geological_model.py).
 
 - ["vedo", a python module for scientific analysis and visualization of 3D data](https://www.youtube.com/watch?v=MhIoetdxwc0&t=39s), I2K Conference, by M. Musy (EMBL).
 

examples/advanced/line2mesh_tri.py

@@ -10,7 +10,7 @@
 msh = shape.generate_mesh(invert=True)
 msh.smooth()           # make the triangles more uniform
 msh.compute_quality()  # add a measure of triangle quality
-msh.cmap(cmap, on="cells")
+msh.cmap(cmap)
 
 contour = Line(shape).c("red4").lw(5)
 labels = contour.labels("id")

examples/advanced/measure_curvature.py

@@ -11,8 +11,8 @@
 plt.at(0).show(msh, "Original shape")
 
 # Use built-in curvature method
-msh1 = msh.clone().compute_curvature(method=0).cmap('viridis')
-msh1.add_scalarbar(horizontal=True, size=(100, None))
+msh1 = msh.clone().compute_curvature(method=0)
+msh1.cmap('viridis').add_scalarbar()
 plt.at(1).show(msh1, "Gaussian curvature", azimuth=30, elevation=30)
 
 # Use sphere-fit curvature
@@ -33,14 +33,13 @@
 
 msh2.pointdata['Spherefit_Curvature'] = curvature
 msh2.pointdata['Spherefit_Curvature_Residue'] = residues
-msh2.cmap('viridis', msh2.pointdata['Spherefit_Curvature'])
-msh2.add_scalarbar(horizontal=True, size=(100, None))
+msh2.cmap('viridis', 'Spherefit_Curvature')
+msh2.add_scalarbar()
 plt.at(2).show(msh2, "Sphere-fitted curvature")
 
 # Show fit residues
 msh3 = msh2.clone()
-msh3.cmap('jet', msh2.pointdata['Spherefit_Curvature_Residue'])
-msh3.add_scalarbar(horizontal=True, size=(100, None))
+msh3.cmap('jet', 'Spherefit_Curvature_Residue').add_scalarbar()
 plt.at(3).show(msh3, 'Sphere-fitted curvature\nFit residues')
 
 plt.interactive().close()

examples/advanced/meshquality.py

@@ -8,7 +8,7 @@
 
 # generate a numpy array for mesh quality
 mesh.compute_quality(metric=6)
-mesh.cmap("RdYlBu", on="cells")
+mesh.cmap("RdYlBu")
 
 hist = histogram(mesh.celldata["Quality"], xtitle="mesh quality", ac="w")
 # make it smaller and position it, use_bounds makes the cam

examples/basic/colorlines.py

@@ -17,15 +17,17 @@
 
 # Color the lines based on the scalar value using the 'Accent' colormap,
 #  and add a scalar bar to the plot
-lines = Lines(l1, l2).lw(8).cmap('Accent', dist, on='cells').add_scalarbar('length')
+lines = Lines(l1, l2, lw=8)
+lines.celldata["distance"] = dist
+lines.cmap('Accent').add_scalarbar('length')
 
 # Define a callback function to print the length of the clicked line segment
 def clickfunc(evt):
     if evt.object:
         # Get the ID of the closest point on the clicked line segment
         idl = evt.object.closest_point(evt.picked3d, return_cell_id=True)
         # Print the length of the line segment with 3 decimal places
-        print('clicked line', idl, 'length =', precision(dist[idl],3))
+        print('clicked line', idl, 'length =', dist[idl])
 
 # Create a plotter with the mouse click callback function and show the lines
 plt = Plotter(axes=1, bg2='lightblue')

examples/basic/mesh_coloring.py

@@ -1,33 +1,31 @@
-"""Specify a colors for cells
+"""Specify color mapping for cells
 and points of a Mesh"""
 from vedo import dataurl, Plotter, Mesh
 
 plt = Plotter(N=3, axes=11)
 
 ##################################### add a cell array
 man1 = Mesh(dataurl+"man_low.vtk").linewidth(0.1)
-nv = man1.ncells                           # nr. of cells
-scals = range(nv)                          # coloring by the index of cell
-
+nv = man1.ncells                    # nr. of cells
+scals = range(nv)                   # coloring by the index of cell
 man1.cmap("Paired", scals, on='cells').add_scalarbar("cell nr")
 plt.at(0).show(man1, __doc__, elevation=-60)
 
 
 ##################################### Point coloring
 man2 = Mesh(dataurl+"man_low.vtk")
-scals = man2.vertices[:, 0] + 37           # pick x coordinates of vertices
-
+scals = man2.vertices[:, 0] + 37    # pick x coordinates of vertices
 man2.cmap("hot", scals)
 man2.add_scalarbar(horizontal=True)
 plt.at(1).show(man2, "mesh.cmap()")
 
 
 ##################################### Cell coloring
 man3 = Mesh(dataurl+"man_low.vtk")
-scals = man3.cell_centers[:, 2] + 37     # pick z coordinates of cells
+scals = man3.cell_centers[:, 2] + 37  # pick z coordinates of cells
 man3.cmap("afmhot", scals, on='cells')
 
-# add a fancier 3D scalar bar embedded in the scene
+# Add a fancier 3D scalar bar embedded in the 3d scene
 man3.add_scalarbar3d(size=[0.2,3])
 man3.scalarbar.scale(1.1).rotate_x(90).shift([0,2,0])
 

examples/basic/mesh_custom.py

@@ -9,18 +9,16 @@
 
 # assign color map with specified opacities
 try:
-    import colorcet  # https://colorcet.holoviz.org
+    import colorcet
+    # https://colorcet.holoviz.org
     mycmap = colorcet.bmy
     alphas = np.linspace(0.8, 0.2, num=len(mycmap))
 except ModuleNotFoundError:
     printc("colorcet is not available, use custom cmap", c='y')
+    printc("pip install colorcet", c='y')
     mycmap = ["darkblue", "magenta", (1, 1, 0)]
     alphas = [0.8,              0.6,       0.2]
 
-# - OR by generating a palette between 2 colors:
-#mycmap = makePalette('pink', 'green', N=500, hsv=True)
-#alphas = 1
-
 man.cmap(mycmap, scals, alpha=alphas).add_scalarbar()
 
 show(man, __doc__, viewup="z", axes=7).close()

examples/pyplot/embed_matplotlib.py

@@ -3,7 +3,7 @@
 import matplotlib.pyplot as plt
 from vedo import *
 
-tmsh = TetMesh(dataurl+"limb_ugrid.vtk")
+tmsh = TetMesh(dataurl+"limb.vtu")
 msh = tmsh.tomesh().shrink(0.8)
 
 # Create a histogram with matplotlib

examples/volumetric/tet_astyle.py

@@ -1,13 +1,17 @@
 """Load a tetrahedral mesh and show it in different styles."""
-from vedo import *
+from vedo import TetMesh, show, dataurl
 
-tetm = TetMesh(dataurl+'limb_ugrid.vtk')
+# Load a tetrahedral mesh from file
+tetm = TetMesh(dataurl + 'limb.vtu')
 tetm.compute_cell_size()
 print(tetm)
-tetm.cmap("Blues_r", "chem_0", on="cells").add_scalarbar()
+
+# Assign a color to each tetrahedron based on the value of "chem_0"
+tetm.celldata.select('chem_0').cmap("Blues_r").add_scalarbar()
 
 # Make a copy of tetm and shrink the tets
 msh = tetm.clone().shrink(0.5).tomesh().add_scalarbar()
 
+# Show the two meshes side by side with comments
 show([(tetm, __doc__), (msh, "..shrunk tetrahedra")], N=2).close()
 

examples/volumetric/tet_build.py

@@ -17,19 +17,26 @@
     (2, 5, 5),
 ]
 
+# Cells are defined by a list of 4 vertex indices
+# note that "cells" and "tetrahedrons" are the same thing
 tets = [[0,1,2,3], [4,5,6,7], [8,9,10,11]]
 
-vals = [10.0, 20.0, 30.0] # some cell scalar values
+# Define a scalar value for each cell we have created
+values = np.array([10.0, 20.0, 30.0])
 
-# Create the TeTMesh object
+# Create the TeTMesh object and assign any number of data arrays to it
 tm = TetMesh([points, tets])
-tm.celldata["myscalar"] = vals
+tm.celldata["myscalar1"] = values
+tm.celldata["myscalar2"] = -values / 10
+tm.pointdata["myvector"] = np.random.rand(tm.npoints)
+# ...
 
-tm.cmap('jet', 'myscalar', on='cells').add_scalarbar()
+print(tm)
+
+tm.celldata.select("myscalar2").cmap('jet').add_scalarbar()
 # tm.color('green') # or set a single color
 
-printc("tetmesh.dataset:", type(tm)) # vedo.tetmesh.TetMesh
-printc("#vertices      :", tm.vertices.size)
-printc("#cells         :", len(tm.cells))
+# Create labels for the vertices
+labels = tm.labels2d('id', scale=2)
 
-show(tm, axes=1).close()
+show(tm, labels, __doc__, axes=1).close()

examples/volumetric/tet_cut1.py

@@ -1,9 +1,10 @@
 """Cut a TetMesh with an arbitrary polygonal Mesh"""
 from vedo import *
 
-sphere = Sphere(r=500).x(400).color('green5',0.2).wireframe()
+sphere = Sphere(r=500).x(400)
+sphere.color('green5', 0.2).wireframe()
 
-tmesh = TetMesh(dataurl + 'limb_ugrid.vtk')
+tmesh = TetMesh(dataurl + 'limb.vtu')
 print(tmesh)
 
 ugrid = tmesh.cut_with_mesh(sphere, invert=True).cmap("Reds_r")

examples/volumetric/tet_cut2.py

@@ -6,7 +6,7 @@
 
 sphere = Sphere(r=500).x(400).c('green', 0.1)
 
-tetm1 = TetMesh(dataurl+'limb_ugrid.vtk')
+tetm1 = TetMesh(dataurl+'limb.vtu')
 tetm1.cmap('jet', tetm1.vertices[:, 2], name="ProximoDistal")
 
 # Clone and cut the TetMesh, this returns a UnstructuredGrid:
@@ -21,12 +21,13 @@
 
 # Cut tetm, but the output will keep only the tets on the boundary:
 ugrid3 = tetm1.clone().cut_with_mesh(sphere, on_boundary=True)
-tetm3 = TetMesh(ugrid3).cmap("Reds", "chem_0", on="cells")
+tetm3 = TetMesh(ugrid3)
+tetm3.celldata.select("chem_0").cmap("Reds")
 print(tetm3)
 
 show([
       (ugrid1,sphere,  __doc__),
-      (tetm2, sphere, "Keep only tets that lie\ncompletely outside the Sphere"),
+      (tetm2, sphere, "Keep only tets that lie\ncompletely outside of the Sphere"),
       (tetm3, sphere, "Keep only tets that lie\nexactly on the Sphere"),
      ], 
      N=3, axes=dict(xtitle='x in :mum'),

examples/volumetric/tet_explode.py

@@ -6,7 +6,7 @@
 f1 = 0.005  # control the tetras resolution
 f2 = 0.15   # control the nr of seeds
 
-tmesh = TetMesh(dataurl + "limb_ugrid.vtk")
+tmesh = TetMesh(dataurl + "limb.vtu")
 surf = tmesh.tomesh(fill=False)
 txt = Text2D(__doc__, font="Brachium")
 

examples/volumetric/tet_isos_slice.py

@@ -1,8 +1,11 @@
 # Thresholding and slicing a TetMesh
 from vedo import TetMesh, dataurl, show
 
-tmsh = TetMesh(dataurl+'limb_ugrid.vtk').color('Spectral')
-tmsh.cmap('hot').add_scalarbar3d('chem_0  expression', c='k')
+tmsh = TetMesh(dataurl+'limb.vtu')
+print(tmsh)
+
+tmsh.celldata.select('chem_0').cmap('hot')
+tmsh.add_scalarbar3d('chem_0  expression', c='k')
 
 vals = [0.2, 0.3, 0.8]
 isos = tmsh.isosurface(vals)

examples/volumetric/tet_threshold.py

@@ -1,11 +1,12 @@
 """Threshold a TetMesh with a scalar array"""
 from vedo import *
 
-tetm = TetMesh(dataurl+'limb_ugrid.vtk')
+tetm = TetMesh(dataurl + "limb.vtu")
 
 # Threshold the tetrahedral mesh for values in the range:
 tetm.threshold(above=0.9, below=1)
-tetm.cmap('Accent', 'chem_0', on='cells')
-tetm.add_scalarbar3d('chem_0  expression levels', c='k', italic=1)
+
+tetm.celldata.select("chem_0").cmap("Accent")
+tetm.add_scalarbar3d("chem_0  expression levels", c="k", italic=1)
 
 show(tetm, __doc__, axes=1).close()

tests/test_pipeline.txt

@@ -110,6 +110,7 @@ cd ~/Projects/napari-vedo-bridge
     # conda create -y -n napari-env -c conda-forge python=3.9
     # conda activate napari-env
     # python -m pip install "napari[all]"
+    # cd ../vedo && pip install . && cd -
     conda activate napari-env
     python $VDIR/examples/other/napari1.py
     napari

vedo/colors.py

@@ -1143,8 +1143,11 @@ def printc(
     """
 
     if not vedo.settings.enable_print_color or not _terminal_has_colors:
-        print(*strings, end=end, flush=flush)
-        return
+        if return_string:
+            return ''.join(strings)
+        else:
+            print(*strings, end=end, flush=flush)
+            return
 
     try:  # -------------------------------------------------------------