Problem with VTKPolyhedron functionality

[Dunckleosteus]

I'm not sure if it's really a problem with the library but when I try to create an unstructured grid using the VTKPolyhedron functionality, only the last polyhedron appears in output. Here is the result in paraview :

Here is the code I wrote :

# points lists defined above
# Construct VTK_QUAD cells with proper point indices
cells = [
    VTKPolyhedron(
        [p1, p2, p3, p4, p5, p6, p7, p8],
            (p1, p2, p3, p4),
            (p5, p6, p7, p8),
            (p1, p2, p6, p5),
            (p2, p3, p7, p6),
            (p3, p4, p8, p7),
        ) for (p1, p2, p3, p4, p5, p6, p7, p8) in zip(points1, points2, points3, points4, points5, points6, points7, points8)
]
# Write to VTK
vtk_grid("test", point_matrix, cells, ascii=true) do vtk
    # You can add cell or point data here, if needed
end

How come only 1 geometry is visible in output, given that I create a list of Polyhedrons ?

[jipolanco]

Hi, could you provide a runnable minimal working example? With the definitions of the points* and point_matrix arrays in particular?

[Dunckleosteus]

Hi sure thing :

using WriteVTK
using CSV
using DataFrames
function roundtuple(tuple, digits = 2)
    return (
        round(tuple[1]; digits=digits), 
        round(tuple[2]; digits=digits), 
        round(tuple[3]; digits=digits)
    )
end
# Load the CSV file into a DataFrame
df = CSV.read("pseudo_circle_square_grid.csv", DataFrame)

# Collect all corner points of quads from DataFrame
nz = 10
z_values::Vector{Float64} = []
for z in 1:nz 
    append!( z_values, fill( z, 4*size(df)[1]));
end

# println(z_values)
points = [(x, y, z) for (x, y, z) in zip(
        repeat([df.x1; df.x2; df.x3; df.x4], nz), 
        repeat([df.y1; df.y2; df.y3; df.y4], nz),
        z_values
    )
]

points_unique = unique(points)

# Create a 2xN matrix of points (required by WriteVTK)
point_matrix = hcat(
    [p[1] for p in points_unique],  # x-coordinates
    [p[2] for p in points_unique],  # y-coordinates
    [p[3] for p in points_unique],
    # zeros(length(points_unique))    # z-coordinates (2D -> 3D)
)'

# Map (x, y) coordinates to a unique index for mesh cell construction
points_dict = Dict{Tuple{Float64, Float64, Float64}, Int64}()
for (idx, pt) in enumerate(points_unique)
    points_dict[pt] = idx
end

# Get cell connectivity using mapped indices
# Convert the Zip iterator to an array using collect
zipped_values1 = collect(zip(repeat(df.x1, nz), repeat(df.y1, nz), z_values))
zipped_values2 = collect(zip(repeat(df.x2, nz), repeat(df.y2, nz), z_values))
zipped_values3 = collect(zip(repeat(df.x3, nz), repeat(df.y3, nz), z_values))
zipped_values4 = collect(zip(repeat(df.x4, nz), repeat(df.y4, nz), z_values))

# Now you can slice the collected arrays
points1 = [points_dict[(x, y, z)] for (x, y, z) in zipped_values1[begin:end-1]]
points2 = [points_dict[(x, y, z)] for (x, y, z) in zipped_values2[begin:end-1]]
points3 = [points_dict[(x, y, z)] for (x, y, z) in zipped_values3[begin:end-1]]
points4 = [points_dict[(x, y, z)] for (x, y, z) in zipped_values4[begin:end-1]]

# Increment z by 1 for the next set of points
points5 = [points_dict[(x, y, z+1)] for (x, y, z) in zipped_values1[begin:end-1]]
points6 = [points_dict[(x, y, z+1)] for (x, y, z) in zipped_values2[begin:end-1]]
points7 = [points_dict[(x, y, z+1)] for (x, y, z) in zipped_values3[begin:end-1]]
points8 = [points_dict[(x, y, z+1)] for (x, y, z) in zipped_values4[begin:end-1]]

cells = [
    VTKPolyhedron(
        [p1, p2, p3, p4, p5, p6, p7, p8],
            (p1, p2, p3, p4),
            (p5, p6, p7, p8),
            (p1, p2, p6, p5),
            (p2, p3, p7, p6),
            (p3, p4, p8, p7),
        ) for (p1, p2, p3, p4, p5, p6, p7, p8) in zip(points1, points2, points3, points4, points5, points6, points7, points8)
]
# Write to VTK
vtk_grid("test", point_matrix, cells, ascii=true) do vtk
    # You can add cell or point data here, if needed
end

And the CSV file :

value,x1,y1,x2,y2,x3,y3,x4,y4
1,100.0,100.0,133.33333333333334,100.0,133.33333333333334,133.33333333333334,100.0,133.33333333333334
2,133.33333333333334,100.0,166.66666666666669,100.0,166.66666666666669,133.33333333333334,133.33333333333334,133.33333333333334
3,166.66666666666669,100.0,200.0,100.0,200.0,133.33333333333334,166.66666666666669,133.33333333333334
4,100.0,133.33333333333334,133.33333333333334,133.33333333333334,133.33333333333334,166.66666666666669,100.0,166.66666666666669
5,133.33333333333334,133.33333333333334,166.66666666666669,133.33333333333334,166.66666666666669,166.66666666666669,133.33333333333334,166.66666666666669
6,166.66666666666669,133.33333333333334,200.0,133.33333333333334,200.0,166.66666666666669,166.66666666666669,166.66666666666669
7,100.0,166.66666666666669,133.33333333333334,166.66666666666669,133.33333333333334,200.0,100.0,200.0
8,133.33333333333334,166.66666666666669,166.66666666666669,166.66666666666669,166.66666666666669,200.0,133.33333333333334,200.0
9,166.66666666666669,166.66666666666669,200.0,166.66666666666669,200.0,200.0,166.66666666666669,200.0
10,100.0,100.0,133.33333333333334,100.0,122.25523828397763,52.55556302831988,71.96699141100893,71.96699141100895
11,71.96699141100893,71.96699141100895,122.25523828397763,52.55556302831988,111.17714323462191,5.111126056639762,43.93398282201785,43.93398282201788
12,133.33333333333334,100.0,166.66666666666669,100.0,177.74476171602237,52.55556302831987,122.25523828397763,52.55556302831988
13,122.25523828397763,52.55556302831988,177.74476171602237,52.55556302831987,188.82285676537805,5.111126056639733,111.17714323462191,5.111126056639762
14,166.66666666666669,100.0,200.0,100.0,228.03300858899104,71.96699141100893,177.74476171602237,52.55556302831987
15,177.74476171602237,52.55556302831987,228.03300858899104,71.96699141100893,256.0660171779821,43.93398282201785,188.82285676537805,5.111126056639733
16,200.0,100.0,200.0,133.33333333333334,247.44443697168012,122.25523828397762,228.03300858899104,71.96699141100893
17,228.03300858899104,71.96699141100893,247.44443697168012,122.25523828397762,294.88887394336024,111.1771432346219,256.0660171779821,43.93398282201785
18,200.0,133.33333333333334,200.0,166.66666666666669,247.44443697168015,177.74476171602237,247.44443697168012,122.25523828397762
19,247.44443697168012,122.25523828397762,247.44443697168015,177.74476171602237,294.8888739433603,188.82285676537805,294.88887394336024,111.1771432346219
20,200.0,166.66666666666669,200.0,200.0,228.03300858899107,228.03300858899104,247.44443697168015,177.74476171602237
21,247.44443697168015,177.74476171602237,228.03300858899107,228.03300858899104,256.06601717798213,256.0660171779821,294.8888739433603,188.82285676537805
22,200.0,200.0,166.66666666666666,200.0,177.74476171602237,247.44443697168012,228.03300858899107,228.03300858899104
23,228.03300858899107,228.03300858899104,177.74476171602237,247.44443697168012,188.8228567653781,294.88887394336024,256.06601717798213,256.0660171779821
24,166.66666666666666,200.0,133.33333333333331,200.0,122.25523828397765,247.44443697168015,177.74476171602237,247.44443697168012
25,177.74476171602237,247.44443697168012,122.25523828397765,247.44443697168015,111.17714323462198,294.8888739433603,188.8228567653781,294.88887394336024
26,133.33333333333331,200.0,100.0,200.0,71.96699141100899,228.03300858899112,122.25523828397765,247.44443697168015
27,122.25523828397765,247.44443697168015,71.96699141100899,228.03300858899112,43.933982822017995,256.06601717798225,111.17714323462198,294.8888739433603
28,100.0,200.0,100.0,166.66666666666666,52.55556302831988,177.74476171602237,71.96699141100899,228.03300858899112
29,71.96699141100899,228.03300858899112,52.55556302831988,177.74476171602237,5.111126056639762,188.8228567653781,43.933982822017995,256.06601717798225
30,100.0,166.66666666666666,100.0,133.33333333333331,52.55556302831987,122.25523828397765,52.55556302831988,177.74476171602237
31,52.55556302831988,177.74476171602237,52.55556302831987,122.25523828397765,5.111126056639733,111.17714323462198,5.111126056639762,188.8228567653781
32,100.0,133.33333333333331,100.0,100.0,71.96699141100896,71.9669914110089,52.55556302831987,122.25523828397765
33,52.55556302831987,122.25523828397765,71.96699141100896,71.9669914110089,43.933982822017924,43.93398282201781,5.111126056639733,111.17714323462198

Thanks for your help !

[jipolanco]

I played a bit with your script and it seems to be an issue with your data. In short, you have repeated cells, and ParaView doesn't seem to like that (but it doesn't complain either...). For example, your cells[34] is identical to your cells[1], and for some reason ParaView simply doesn't show that cell when it's repeated (see hole in screenshot below).

To obtain this image, I just exported cells[1:34]:

cells = [
    VTKPolyhedron(
        [p1, p2, p3, p4, p5, p6, p7, p8],
            (p1, p2, p3, p4),
            (p5, p6, p7, p8),
            (p1, p2, p6, p5),
            (p2, p3, p7, p6),
            (p3, p4, p8, p7),
        ) for (p1, p2, p3, p4, p5, p6, p7, p8) in zip(points1, points2, points3, points4, points5, points6, points7, points8)
]
cells = cells[1:34]
# Write to VTK
vtk_grid("test", point_matrix, cells; append=false, ascii=true) do vtk
    vtk["cell_id"] = 1:length(cells)
    # You can add cell or point data here, if needed
end

[Dunckleosteus]

Right my bad, thanks a lot for your help ! Much appreciated 👍