Develop Reference

Why Gmsh create more surfaces than expected when I use "gmhs.model.occ.cut()" command?

I am trying to create a volume in Gmsh (using Python API) by cutting some small cylinders from a bigger one.
When I do that, I expect to have one surface for each cutted region, instead, I get the result in the figure. I have highlighted in red the surfaces that give me the problem (some cutted regions behave as expected), as you can see, instead of one surface I get two, that sometimes aren't even equal.
gmsh creates more surfaces than expected:
So, my questions are:
Why gmsh behaves like that?
How can I fix this as I need predictable behavior?
Below is the code I used to generate the geometry.
The code to work requires some parameters such as core_height, core_inner_radius and core_outer_radius, the number of small cylinders and their radius.
gmsh.initialize(sys.argv)
#gmsh.initialize()
gmsh.clear()
gmsh.model.add("circle_extrusion")
inner_cyl_tag = 1
outer_cyl_tag = 2
inner_cyl = gmsh.model.occ.addCylinder(0,0,0, 0, 0, core_height, core_inner_radius, tag = inner_cyl_tag)
outer_cyl = gmsh.model.occ.addCylinder(0,0,0, 0, 0, core_height, core_outer_radius, tag = outer_cyl_tag)
core_tag = 3
cut1 = gmsh.model.occ.cut([(3,outer_cyl)],[(3,inner_cyl)], tag = core_tag)
#create a set of filled cylinders
#set position
angle_vector = np.linspace(0,2*np.pi,number_of_hp+1)
pos_x = hp_radial_position*np.cos(angle_vector)
pos_y = hp_radial_position*np.sin(angle_vector)
pos_z = 0.0
#cut one cylinder at the time and assign the new core tag
for ii in range(0,len(angle_vector)):
old_core_tag = core_tag
heat_pipe = gmsh.model.occ.addCylinder(pos_x[ii], pos_y[ii], pos_z, 0, 0, core_height,hp_outer_radius, tag =-1)
core_tag = heat_pipe+1
core = gmsh.model.occ.cut([(3,old_core_tag)],[(3,heat_pipe)], tag = core_tag)
gmsh.model.occ.synchronize()
#get volume entities and assign physical groups
volumes = gmsh.model.getEntities(dim=3)
solid_marker = 1
gmsh.model.addPhysicalGroup(volumes[0][0], [volumes[0][1]],solid_marker)
gmsh.model.setPhysicalName(volumes[0][0],solid_marker, "solid_volume")
#get surfaces entities and apply physical groups
surfaces = gmsh.model.getEntities(dim=2)
surface_markers= np.arange(1,len(surfaces)+1,1)
for ii in range(0,len(surfaces)):
gmsh.model.addPhysicalGroup(2,[surfaces[ii][1]],tag = surface_markers[ii])
#We finally generate and save the mesh:
gmsh.model.mesh.generate(3)
gmsh.model.mesh.refine()
gmsh.model.mesh.refine()
gmsh.option.setNumber("Mesh.MshFileVersion", 2.2) #save in ASCII 2 format
gmsh.write(mesh_name+".msh")
# Launch the GUI to see the results:
#if '-nopopup' not in sys.argv:
# gmsh.fltk.run()
gmsh.finalize()

I do not think that you have additional surfaces in the sense of gmsh.model.occ surfaces. To me this looks like your volume mesh is sticking out of your surface mesh, i.e. volume and surface mesh do not fit together.
Here is what I did to check your case:
First I added the following lines at the beginning of our code to get a minimum working example:
import gmsh
import sys
import numpy as np
inner_cyl_tag = 1
outer_cyl_tag = 2
core_height = 1
core_inner_radius = 0.1
core_outer_radius = 0.2
number_of_hp = 5
hp_radial_position = 0.1
hp_outer_radius = 0.05
What I get with this code is the following:
To visualize it like this go to "Tools"-->"Options"-->"Mesh" and check "2D element faces", "3D element edges" and "3D element faces".
You can see that there are some purple triangles sticking out of the green/yellowish surfaces triangles of the inner surfaces.
You could try to visualize your case the same way and check <--> uncheck the "3D element faces" a few times.
So here is the solution for this behaviour, I did not know that gmsh behaves like this myself. It seems that when you create your mesh and refine it the refinement will be applied on the 2D surface mesh and the 3D volume mesh seperately, which means that those two meshes are not connected after the refinement anymore. What I did next was to try what happens if you create the 2D mesh only, refine it, and then create the 3D mesh, i.e.:
replace:
gmsh.model.mesh.generate(3)
gmsh.model.mesh.refine()
gmsh.model.mesh.refine()
by:
gmsh.model.mesh.generate(2)
gmsh.model.mesh.refine()
gmsh.model.mesh.refine()
gmsh.model.mesh.generate(3)
The result then looks like this:
I hope that this was actually your problem. But in future it would be good if you could provide us a minimum working example of code that we can copy-paste and get the same visualization you showed us in your image.

Blender Bevel tool on selected edges scripting problem

In Blender, my attempt (see code below) to python script BEVEL on selected edges with the BEVEL tool (not the modifier) fails: All selected and non-selected edges are beveled.
What I want :
What I get:
Question 1: why?
Question 2: Is there a way to apply the beveler by script without using operators (ops) depending on the context?
Thank you.
Code that does not work:
def selectEdgesAlongX(mesh):
"""Select all edges of an object directed along X"""
bm = bmesh.new()
bm.from_mesh(mesh)
edges, verts = bm.edges, bm.verts
verts.ensure_lookup_table()
for edge in bm.edges:
indices = (edge.verts[0].index, edge.verts[1].index)
vs=[verts[index].co for index in indices]
edge.select = abs((vs[1]-vs[0])[0])>1e-4
bm.to_mesh(mesh)
bm.free()
def printSelectedEdges(mesh):
print([edge.select for edge in mesh.edges])
# box
dims = (depth,height, width) = (0.4,0.6,1)
thickness, radius = 0.05, 0.05
center =(0,0,0)
bpy.ops.mesh.primitive_cube_add(size=1,enter_editmode=False, align='WORLD', location=center, scale=np.array(dims)/2-thickness)
interior = bpy.context.view_layer.objects.active
interior.name='interior'
printSelectedEdges(interior.data)
selectEdgesAlongX(interior.data)
printSelectedEdges(interior.data)
bpy.ops.object.editmode_toggle()
bpy.ops.mesh.bevel(offset=0.03, offset_pct=0,segments=10, affect='EDGES')
print outputs:

Snapping an object to another object vertex in Maya over Python Script

I want to snap / align an object A to vertex of object B. I have tried using below script but its not snapping exactly to the vertex but snapping with an offset. Can any one suggest me a solution. Here are the snapshots.
import maya.cmds as cmds
vertices = [];
srcObj = "pCone1";
def snapToVertex(vertex,object):
cmds.select(vertex);
x,y,z = cmds.pointPosition();
cmds.select(object);
cmds.duplicate();
cmds.move(x,y,z);
def processTask():
cmds.select( cmds.polyListComponentConversion( tv=True ) );
vertices = cmds.ls(sl = True);
print vertices;
for vrtx in vertices:
snapToVertex(vrtx,srcObj);
processTask();
Snapped with my above Script, Which didn't snap exactly to vertex.
But it should be snapped exactly to the Vervex's as below image.

It's better not to use Reset Transformations command for your Cone from Modify main menu, 'cause pivot point goes back to its initial place. The analog for useful Freeze Transformations command in Python is cmds.makeIdentity(). Even if you've moved you pivot point by 1 unit (for example) along +Y axis, do not forget to subtract that 1 from variable y cause Maya somehow remembers pivot's position. Offset of the Cone's pivot point (for snapping pivot to a vertex) depends on the Cone's size itself. By default it's 1.
Add this snippet to your code to move the duplicates in World Space:
# cmds.makeIdentity( 'pCone1', apply=True )
pivSnap = 1
cmds.xform( 'pCone1', piv=[ 0, pivSnap, 0 ] )
cmds.move( x, y-pivSnap, z, a=True, ws=True, wd=True )
You can test this code (here I moved pivot up by 0.5):
import maya.cmds as cmds
cmds.polyCube( sx=1, sy=15, sz=1, w=1, h=15, d=1 )
cmds.polyCone( r=.5, h=1, sx=10 )
cmds.move( 10, x=True )
pivSnap = .5
cmds.xform( 'pCone1', piv=[ 0, pivSnap, 0 ] )
cmds.rotate( 0, 0, '45deg' )
cmds.select( 'pCube1.e[33]','pCube1.e[37]','pCube1.e[41]','pCube1.e[45]','pCube1.e[49]','pCube1.e[53]','pCube1.e[57]','pCube1.e[61]' )
vertices = []
srcObj = "pCone1"
def snapToVertex( vertex, object ):
cmds.select( vertex )
x,y,z = cmds.pointPosition()
print( x,y,z )
cmds.select( object )
cmds.manipMoveContext( m=2 )
cmds.delete( 'pCube1', ch=True )
cmds.duplicate()
cmds.move( x, y-pivSnap, z, a=True, ws=True, wd=True )
def processTask():
cmds.select( cmds.polyListComponentConversion( tv=True ) )
vertices = cmds.ls( sl=True )
print( vertices )
for vrtx in vertices:
snapToVertex( vrtx, srcObj )
processTask()

you could greatly simplify your code and only use a few commands
import maya.cmds as mc
verts = mc.ls(os=True)
src = 'pCone1'
base_name = 'fancy_cone'
for i, vert in enumerate(verts):
dup = mc.duplicate(src, n='%s_%s' %(base_name, i))[0]
mc.xform(dup, ws=True, t=mc.xform(vert, q=True, ws=True, t=True))
keep in mind a few caveats:
1) this is assuming that the pivot of your source cone is at the tip with the tip at the origin... so it requires setting up that source cone the way you want it as if the origin point is a vertex you will be snapping it to. This would also be beneficial if the object you're 'pinning' to is rotated (no need to do any kind of vector math to determine the positional offset that way)
2) to use the orderedSelection (os) flag in the ls command, you need to be sure track selection order is turned on in your maya preferences under the selection sub section - this way you can select the verts you want in the order you want them to be created (top-down, bottum-up, whatever) instead of the vert index order
This should also be significantly faster - by tracking any created objects, you don't actually need to select anything and can manipulate the objects directly. I also put it all into one loop without any function calls which would be faster (although, you probably won't notice it unless you're making a LOOOOOOT of these).
Depending on your needs though, you may actually want to utilize a snapping function multiple places; However, I would suggest keeping the duplication out of it in case there are situations you want to snap without duplicating.
Something like this (subject to same caveats as above):
import maya.cmds as mc
def snapToVertex(vertex, object):
pos = mc.xform(vertex, q=True, ws=True, t=True)
mc.xform(object, ws=True, t=pos) # combine to single line if prefered
def processTask():
verts = mc.ls(os=True)
src = 'pCone1'
base_name = 'fancy_cone'
for i, vert in enumerate(verts):
dup = mc.duplicate(src, n='%s_%s' %(base_name, i))[0]
snapToVertex(vert, dup)
processTask()

Vtk inserts incorrect color between nodes when mapping texture to mesh

Hi I am trying to map a texture to 3d mesh using Mayavi and Python bindings of vtk. I am visualising an .obj wavefront. This obj is 3D photograph of a face. The texture image is a composite of three 2D photographs.
Each node in the mesh has an (uv) co-ordinate in the image, which defines its color. Different regions of the mesh draw their colours from different sections of the image. To illustrate this I have replaced the actual texture image with this one:
And mapped this to the mesh instead.
The problem I am having is illustrated around the nose. At the border between red and green there is an outline of blue. Closer inspection of this region in wireframe mode shows that it is not a problem with the uv mapping, but with how vtk is interpolating colour between two nodes. For some reason it is adding a piece of blue in between two nodes where one is red and one is green.
This causes serious problems when visualising using the real texture
Is there a way to force vtk to choose the colour of one or the other neighbouring nodes for the colour between them? I tried turning "edge-clamping" on, but this did not achieve anything.
The code that I am using is below and you can access the files in question from here https://www.dropbox.com/sh/ipel0avsdiokr10/AADmUn1-qmsB3vX7BZObrASPa?dl=0
but I hope this is a simple solution.
from numpy import *
from mayavi import mlab
from tvtk.api import tvtk
import os
from vtk.util import numpy_support
def obj2array(f):
"""function for reading a Wavefront obj"""
if type(f)==str:
if os.path.isfile(f)==False:
raise ValueError('obj2array: unable to locate file ' + str(f))
f =open(f)
vertices = list()
connectivity = list()
uv = list()
vt = list()
fcount = 0
for l in f:
line = l.rstrip('\n')
data = line.split()
if len(data)==0:
pass
else:
if data[0] == 'v':
vertices.append(atleast_2d(array([float(item) for item in data[1:4]])))
elif data[0]=='vt':
uv.append(atleast_2d(array([float(item) for item in data[1:3]])))
elif data[0]=='f':
nverts = len(data)-1 # number of vertices comprising each face
if fcount == 0: #on first face establish face format
fcount = fcount + 1
if data[1].find('/')==-1: #Case 1
case = 1
elif data[1].find('//')==True:
case = 4
elif len(data[1].split('/'))==2:
case = 2
elif len(data[1].split('/'))==3:
case = 3
if case == 1:
f = atleast_2d([int(item) for item in data[1:len(data)]])
connectivity.append(f)
if case == 2:
splitdata = [item.split('/') for item in data[1:len(data)]]
f = atleast_2d([int(item[0]) for item in splitdata])
connectivity.append(f)
if case == 3:
splitdata = [item.split('/') for item in data[1:len(data)]]
f = atleast_2d([int(item[0]) for item in splitdata])
connectivity.append(f)
if case == 4:
splitdata = [item.split('//') for item in data[1:len(data)]]
f = atleast_2d([int(item[0]) for item in splitdata])
connectivity.append(f)
vertices = concatenate(vertices, axis = 0)
if len(uv)==0:
uv=None
else:
uv = concatenate(uv, axis = 0)
if len(connectivity) !=0:
try:
conarray = concatenate(connectivity, axis=0)
except ValueError:
if triangulate==True:
conarray=triangulate_mesh(connectivity,vertices)
else:
raise ValueError('obj2array: not all faces triangles?')
if conarray.shape[1]==4:
if triangulate==True:
conarray=triangulate_mesh(connectivity,vertices)
return vertices, conarray,uv
# load texture image
texture_img = tvtk.Texture(interpolate = 1,edge_clamp=1)
texture_img.input = tvtk.BMPReader(file_name='HM_1_repose.bmp').output
#load obj
verts, triangles, uv = obj2array('HM_1_repose.obj')
# make 0-indexed
triangles = triangles-1
surf = mlab.triangular_mesh(verts[:,0],verts[:,1],verts[:,2],triangles)
tc=numpy_support.numpy_to_vtk(uv)
pd = surf.mlab_source.dataset._vtk_obj.GetPointData()
pd.SetTCoords(tc)
surf.actor.actor.mapper.scalar_visibility=False
surf.actor.enable_texture = True
surf.actor.actor.texture = texture_img
mlab.show(stop=True)

You can turn off all interpolation (change interpolate = 1 to interpolate = 0 in your example), but there is not a way to turn off interpolation at just the places where it would interpolate across sub-images of the texture – at least not without writing your own fragment shader. This will likely look crude.
Another solution would be to create 3 texture images with transparent texels at each location that is not part of the actor's face. Then render the same geometry with the same texture coordinates but a different image each time (i.e., have 3 actors each with the same polydata but a different texture image).

I just ran into this exact problem as well and found that the reason this happens is because VTK assumes there's a 1-to-1 relationship between points in the polydata and uv coordinates when rendering the actor and associated vtkTexture. However, in my case and the case of OP, there are neighboring triangles that are mapped to different sections the the image, so they have very different uv coordinates. The points that share these neighboring faces can only have one uv coordinate (or Tcoord) associated with it, but they actually need 2 (or more, depending on your case).
My solution was to loop through and duplicate these points that lie on the the seams/borders and create a new vtkCellArray with triangles with these duplicated pointIds. Then I simply replaced the vtkPolyData Polys() list with the new triangles. It would have been much easier to duplicate the points and update the existing pointIds for each of the triangles that needed it, but I couldn't find a way to update the cells properly.

Change color depending on height in Mayavi iso_surface

Is is possible to change the colour of an iso-surface depending on height of the points (in python / mayavi) ?
I can create an iso-surface visualization with my script, but I don't know how to make the iso_surface change colour with z axis so that it will be let's say black at the bottom and white at the top of the plot.
I need this in order to make sense of the visualization when it is viewed from directly above the graph.
If you know any other way to achieve this, please let me know as well.
I only want to show one iso_surface plot.

I managed to do this by combining some code from examples http://docs.enthought.com/mayavi/mayavi/auto/example_atomic_orbital.html#example-atomic-orbital and http://docs.enthought.com/mayavi/mayavi/auto/example_custom_colormap.html . Basically you must create a surface as in atomic-orbital example and then make it change colour depending on x. You must create an array of values for x. My code is (the relevant part) :
#src.image_data.point_data.add_array(np.indices(list(self.data.shape)[self.nx,self.ny,self.nz])[2].T.ravel())
src.image_data.point_data.add_array(np.indices(list(self.data.shape))[0].T.ravel())
src.image_data.point_data.get_array(1).name = 'z'
# Make sure that the dataset is up to date with the different arrays:
src.image_data.point_data.update()
# We select the 'scalar' attribute, ie the norm of Phi
src2 = mlab.pipeline.set_active_attribute(src, point_scalars='scalar')
# Cut isosurfaces of the norm
contour = mlab.pipeline.contour(src2)
# contour.filter.contours=[plotIsoSurfaceContours]
# contour.filter.contours=[plotIsoSurfaceContours[0]]
min_c = min(contour.filter._data_min * 1.05,contour.filter._data_max)
max_c = max(contour.filter._data_max * 0.95,contour.filter._data_min)
plotIsoSurfaceContours = [ max(min(max_c,x),min_c) for x in plotIsoSurfaceContours ]
contour.filter.contours= plotIsoSurfaceContours
# Now we select the 'angle' attribute, ie the phase of Phi
contour2 = mlab.pipeline.set_active_attribute(contour, point_scalars='z')
# And we display the surface. The colormap is the current attribute: the phase.
# mlab.pipeline.surface(contour2, colormap='hsv')
xxx = mlab.pipeline.surface(contour2, colormap='gist_ncar')
colorbar = xxx.module_manager.scalar_lut_manager
colorbar.reverse_lut = True
lut = xxx.module_manager.scalar_lut_manager.lut.table.to_array()
lut[:,-1] = int(plotIsoSurfaceOpacity * 254)
xxx.module_manager.scalar_lut_manager.lut.table = lut
# mlab.colorbar(title='Phase', orientation='vertical', nb_labels=3)
self.data is my data, and for unknown reasons if you want to set opacity of your surface you must reverse the lut first and then set the opacity. Multiplication by 254 instead of 255 is done to avoid a possible bug in mayavi.
I hope this helps someone.