I’m using VTK 8.2.0 and OSPRay 1.8.5 from python to show some particle traces (using the Tube filter).
I’m having trouble transferring my colour map to the ray tracer. The particle traces remain black.
Is there a way to transfer the colour properties from my cells to the material OSPRay will use to render?
Or must I have static material properties?
ps: I create a material lookup table (Value Indexed) as follows:
def W_lut(n_Z=74):
import matplotlib
import matplotlib.cm as cm
lut = vtk.vtkLookupTable()
lut.SetNumberOfTableValues(n_Z+1)
lut.Build()
norm = matplotlib.colors.Normalize(vmin=0,vmax=74,clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap=cm.inferno)
ll = []
for i, u in enumerate(range(75)):
lut.SetTableValue(i, mapper.to_rgba(u))
ll.append('W_%d'%(i,))
lut.Annotations = ll
lut.InterpretValuesAsCategories = 1
return lut
and create the materials as:
# Add colormap variables (75 discrete levels)
import matplotlib
import matplotlib.cm as cm
norm = matplotlib.colors.Normalize(vmin=0,vmax=74,clip=True)
mapper = cm.ScalarMappable(norm=norm, cmap=cm.inferno)
for i, u in enumerate(range(75)):
name = 'W_%d'%(i,)
ml.AddMaterial(name, "Alloy")
ml.AddShaderVariable(name, "color", 3, mapper.to_rgba(u)[0:3])
2: Do you need special materials (reflective/refractive/variable appearance)? If not the default OBJMaterial should do color mapping just like a normal VTK render will for any point or cell aligned array. See https://gitlab.kitware.com/vtk/vtk/blob/master/Rendering/RayTracing/Testing/Cxx/TestOSPRayRenderMesh.cxx and run it with the -type and -rep command line arguments to draw the spheres with lines instead of triangle/surfaces.
3: If you do need fancy materials and are aware of 2, then let me know and I’ll look harder at your script to try and see what is going wrong.
Thanks for the quick suggestions. I think I’ll keep the tube filter since it looks better in the OpenGL renderer we use to setup the scenes.
I don’t need any special properties, this was all just trickery to try to get colours.
I’ve just tried with OBJMaterial, which comes out very white instead of coloured.
See the renders below:
Can you share the parts of the code where you set up the mapper and lookup table? In particular, you shouldn’t need to set any material or special color map at all. The way it should work is that if the only thing you do is set the ospray pass, the vtk2ospray code c++ will internally make and setup an ospray::OBJMaterial such that color mapping will work and you will get an image that looks very similar to the gl rendered image you would have without OSPRay.
To demonstrate, open paraview, open the diskoutref.ex2 sample data set, apply streamlines and tube (optionally point to cell filter), color by some array, and turn on ospray.
Try turning off the annotations and categorical nature of the color map please. Either should be OK I think but you could be exercising a code path/bug I haven’t seen yet.
Since the color is too dark it might be something odd like inverted normals on the tube filter but that seems unlikely. In general I find a good trick to debugging things is to insert writers into the code and open the output up in paraview to debug what you are looking at.
I’ve tried the annotations and categorical nature without any difference.
Saving the tubes with a vtkPDataSetWriter and opening in paraview 5.6.0 works,
and there I can OSPRay without any issue and get nice colours. We probably did something wrong in setting up the ray tracer (or in my own build of OSPRay and VTK 8.2.0).
I will try to get our stl files into paraview and render from there.
Hello guys,
I am trying to visualise the particles path in my model and I only have 8 time steps for an unsteady flow. I also have the CSV file with the coordinates of each particles for these time steps. I can read the particles and visualise them, but when I try to use the streaklines Paraview crashes.
I need to see the particle path let say after 2 s, something similar to @Daan_van_Vugt work.
If you add a line at the beginning of the script given in OSPRay colouring materials by scalar so xyz comes from your CSV file you should be able to draw lines between your particle positions.
Something like
import csv
with open('positions_particle_1.csv', 'rb') as csvfile:
reader = csv.reader(csvfile)
for i, row in enumerate(spamreader):
xyz[0,i,0:3] = row
then you can write out the lines to vtk using something like the below:
Thanks Dan,
I tried the following script in paraview as you suggested but it doesn’t work and complaining about the CSV (line2) and return(last line). my csv file has 4 columns (time, X,Y,Z).
Sorry, I am new with Paraview and learning Python, could you please help me with this.
#################################
import csv
with open('para.csv', 'rb') as csvfile:
reader = csv.reader(csvfile)
for i, row in enumerate(spamreader):
xyz[0,i,0:3] = row
vtk_points.poly.SetLines(lines)
writer = vtk.vtkPolyDataWriter()
writer.SetInputData(vtk_points.GetOutput())
writer.SetFileName('lines.vtk')
writer.Update()
# n_p * n_t, 3
pcoords = npvtk.numpy_to_vtk(xyz[:,:,:].reshape(-1,3), deep=True, array_type=vtk.VTK_FLOAT)
self.points = vtk.vtkPoints()
self.points.SetData(pcoords)
# n_p * n_t
q = npvtk.numpy_to_vtk(np.asarray(self.particles.q[0:n_p,:]).ravel(), deep=True, array_type=vtk.VTK_FLOAT)
q.SetName('q')
vtk_points.poly = vtk.vtkPolyData()
vtk_points.poly.SetPoints(self.points)
vtk_points.poly.GetPointData().AddArray(q)
vtk_points.poly.GetPointData().SetActiveScalars('q')
# Set connectivity data per particle
lines = vtk.vtkCellArray()
# See https://vtk.org/Wiki/VTK/Examples/Python/GeometricObjects/Display/PolyLine
for i in range(n_p):
lines.InsertNextCell(n_t, range(n_t*i, n_t*i+n_t))
vtk_points.poly.SetLines(lines)
vtk_points.lut = vtk_lut.W_lut() #as in first post on discourse
tube = vtk.vtkTubeFilter()
tube.SetInputData(vtk_points.poly)
tube.SetNumberOfSides(6)
tube.SetVaryRadiusToVaryRadiusOff()
tube.SetRadius(0.015)
vtk_points.mapper = vtk.vtkPolyDataMapper()
vtk_points.mapper.SetInputConnection(tube.GetOutputPort())
vtk_points.mapper.ScalarVisibilityOn()
vtk_points.mapper.SetScalarRange(vtk_points.poly.GetPointData().GetArray('q').GetRange())
vtk_points.mapper.SetLookupTable(vtk_points.lut)
vtk_points.actor = vtk.vtkActor()
vtk_points.actor.SetMapper(vtk_points.mapper)
#vtk_points.actor.GetProperty().SetMaterialName("Value Indexed")
vtk_points.actor.GetProperty().SetMaterialName("OBJMaterial")
vtk_points.colorbar = vtk_color_bar()
vtk_points.colorbar.SetLookupTable(vtk_points.lut)
vtk_points.colorbar.SetTitle('q')
vtk_points.colorbar.SetPosition(0.05, 0.1)
print(vtk_points)
#########################################
THE CSV FILE CONTENTS:
I would recommend breaking the problem down in smaller chunks, instead of trying to run this entire script in the first try. Perhaps you can see (just by printing the xyz array) if you read your CSV file as expected?
I notice a few things here still: the indentation of for i, row is off, xyz is not defined yet, and n_p also is not defined.
Then once you are sure that you have filled the xyz array correctly you can proceed to making the VTK output.
