VTK file created using Python API is showing missing elements

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1

Hi,
I’m using the Python API of VTK to convert some Vector data to VTP files. My vector data is in the following format.
(1) A coord.out file, which contains the cell number and the cartesian coordinates of each cell
(2) A vector_data.out file which contains the values of the vectors at each cell point.

I have written a Python script that reads information from these two files and creates a vtp file which can be viewed in Paraview and it is working fine in most cases. However, in some specific cases, the vtp files that are written contain some missing elements. Here is a minimum working example in which I could reproduce the error. I’m also attaching two images to highlight the error. In this

image
image337×575 94.2 KB
the vector data is visualized in our own visualization tool, each sphere indicates a data point with a vector. Here is a screenshot of the same data exported as a vtp file and opened in ParaView
Paraview_image
Paraview_image314×507 78.4 KB
. There is one data point missing, which is indicated with a yellow circle. The Python code, the data files, and the vtp file generated are also attached. Can anyone help me identify the issue here? Thanks.

Python code

"""
16/Feb/2023
* Python script to read the data from the restart
file and to create a VTP file
* Usage: run  this code in the directory which contains the
vector_data.out and coord.out files
* Make sure there are only ONE restart and coord files in
the running directory.
"""

import numpy as np
import vtk

coord_file_name = "coord.out"   # Contains the cartesian coordinates of the cells/points
restart_file_name = "vector_data.out"  # Contains the vector field information at each point/cell
print(f"reading data from: {coord_file_name} and {restart_file_name}")

# read the cord file for cordinates
coord_data = np.loadtxt(coord_file_name)
atom_array = coord_data[:, 0]

file_points = np.column_stack((coord_data[:, 1],
                               coord_data[:, 2],
                               coord_data[:, 3]))

number_of_atoms = len(atom_array)
print(f"number of atoms = {number_of_atoms}")
moment_data = np.loadtxt(restart_file_name)


file_vectors = moment_data[:, 4:]
points = vtk.vtkPoints()
vectors = vtk.vtkFloatArray()
vectors.SetNumberOfComponents(3)
vectors.SetName("vectors")
for point, vector in zip(file_points, file_vectors):
    points.InsertNextPoint(point)
    vectors.InsertNextTuple(vector)
# Create a polydata object and add the points and vectors for the VTK
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.GetPointData().SetVectors(vectors)

# Write the polydata to a VTP file
writer = vtk.vtkXMLPolyDataWriter()
fname = str("restart1")+".vtp"
writer.SetFileName(fname)
writer.SetInputData(polydata)
writer.Write()
print (f"Files written: restart1.vtp")

coord.out

      1    0.000000    0.000000    0.000000     1     1
      2    0.000000    0.000000    1.000000     2     2
      3    0.000000    0.000000    2.000000     3     3
      4    0.000000    0.000000    3.000000     4     4
      5    0.000000    0.000000    4.000000     5     5
      6    0.000000    0.000000    5.000000     6     6
      7    0.000000    0.000000    6.000000     7     7
      8    0.000000    0.000000    7.000000     8     8
      9    0.000000    0.000000    8.000000     9     9
     10    0.000000    0.000000    9.000000    10    10
     11    1.000000    0.000000    0.000000     1     1
     12    1.000000    0.000000    1.000000     2     2
     13    1.000000    0.000000    2.000000     3     3
     14    1.000000    0.000000    3.000000     4     4
     15    1.000000    0.000000    4.000000     5     5
     16    1.000000    0.000000    5.000000     6     6
     17    1.000000    0.000000    6.000000     7     7
     18    1.000000    0.000000    7.000000     8     8
     19    1.000000    0.000000    8.000000     9     9
     20    1.000000    0.000000    9.000000    10    10
     21    2.000000    0.000000    0.000000     1     1
     22    2.000000    0.000000    1.000000     2     2
     23    2.000000    0.000000    2.000000     3     3
     24    2.000000    0.000000    3.000000     4     4
     25    2.000000    0.000000    4.000000     5     5
     26    2.000000    0.000000    5.000000     6     6
     27    2.000000    0.000000    6.000000     7     7
     28    2.000000    0.000000    7.000000     8     8
     29    2.000000    0.000000    8.000000     9     9
     30    2.000000    0.000000    9.000000    10    10
     31    0.000000    1.000000    0.000000     1     1
     32    0.000000    1.000000    1.000000     2     2
     33    0.000000    1.000000    2.000000     3     3
     34    0.000000    1.000000    3.000000     4     4
     35    0.000000    1.000000    4.000000     5     5
     36    0.000000    1.000000    5.000000     6     6
     37    0.000000    1.000000    6.000000     7     7
     38    0.000000    1.000000    7.000000     8     8
     39    0.000000    1.000000    8.000000     9     9
     40    0.000000    1.000000    9.000000    10    10
     41    1.000000    1.000000    0.000000     1     1
     42    1.000000    1.000000    1.000000     2     2
     43    1.000000    1.000000    2.000000     3     3
     44    1.000000    1.000000    3.000000     4     4
     45    1.000000    1.000000    4.000000     5     5
     46    1.000000    1.000000    5.000000     6     6
     47    1.000000    1.000000    6.000000     7     7
     48    1.000000    1.000000    7.000000     8     8
     49    1.000000    1.000000    8.000000     9     9
     50    1.000000    1.000000    9.000000    10    10
     51    2.000000    1.000000    0.000000     1     1
     52    2.000000    1.000000    1.000000     2     2
     53    2.000000    1.000000    2.000000     3     3
     54    2.000000    1.000000    3.000000     4     4
     55    2.000000    1.000000    4.000000     5     5
     56    2.000000    1.000000    5.000000     6     6
     57    2.000000    1.000000    6.000000     7     7
     58    2.000000    1.000000    7.000000     8     8
     59    2.000000    1.000000    8.000000     9     9
     60    2.000000    1.000000    9.000000    10    10
     61    0.000000    2.000000    0.000000     1     1
     62    0.000000    2.000000    1.000000     2     2
     63    0.000000    2.000000    2.000000     3     3
     64    0.000000    2.000000    3.000000     4     4
     65    0.000000    2.000000    4.000000     5     5
     66    0.000000    2.000000    5.000000     6     6
     67    0.000000    2.000000    6.000000     7     7
     68    0.000000    2.000000    7.000000     8     8
     69    0.000000    2.000000    8.000000     9     9
     70    0.000000    2.000000    9.000000    10    10
     71    1.000000    2.000000    0.000000     1     1
     72    1.000000    2.000000    1.000000     2     2
     73    1.000000    2.000000    2.000000     3     3
     74    1.000000    2.000000    3.000000     4     4
     75    1.000000    2.000000    4.000000     5     5
     76    1.000000    2.000000    5.000000     6     6
     77    1.000000    2.000000    6.000000     7     7
     78    1.000000    2.000000    7.000000     8     8
     79    1.000000    2.000000    8.000000     9     9
     80    1.000000    2.000000    9.000000    10    10
     81    2.000000    2.000000    0.000000     1     1
     82    2.000000    2.000000    1.000000     2     2
     83    2.000000    2.000000    2.000000     3     3
     84    2.000000    2.000000    3.000000     4     4
     85    2.000000    2.000000    4.000000     5     5
     86    2.000000    2.000000    5.000000     6     6
     87    2.000000    2.000000    6.000000     7     7
     88    2.000000    2.000000    7.000000     8     8
     89    2.000000    2.000000    8.000000     9     9
     90    2.000000    2.000000    9.000000    10    10

vector_data.out

 #iterens   iatom           |Mom|             M_x             M_y             M_z
      -1       1       1    2.23000000E+00  9.92080191E-01  2.80639967E-02  1.22430821E-01
      -1       1       2    2.23000000E+00  9.89687981E-01  6.32348809E-02  1.28526459E-01
      -1       1       3    2.23000000E+00  9.87507192E-01  6.39845665E-02  1.43998338E-01
      -1       1       4    2.23000000E+00  9.99952001E-01  6.96513257E-03  6.89082640E-03
      -1       1       5    2.23000000E+00  9.99880449E-01  1.39002110E-02  6.77293142E-03
      -1       1       6    2.23000000E+00 -9.99834880E-01  7.08217242E-03 -1.67348472E-02
      -1       1       7    2.23000000E+00  9.99996243E-01  2.39478993E-03  1.33407110E-03
      -1       1       8    2.23000000E+00 -9.99700866E-01 -1.64301910E-02 -1.81170363E-02
      -1       1       9    2.23000000E+00  9.99325556E-01  3.30329379E-02  1.60392887E-02
      -1       1      10    2.23000000E+00  9.99586786E-01 -2.65954204E-02  1.09059596E-02
      -1       1      11    2.23000000E+00  9.89932200E-01  4.87957695E-02  1.32865394E-01
      -1       1      12    2.23000000E+00  9.91690444E-01  5.44111552E-02  1.16573962E-01
      -1       1      13    2.23000000E+00  9.95527733E-01  2.89385757E-02  8.99282532E-02
      -1       1      14    2.23000000E+00  9.99755365E-01  2.18384998E-02  3.50577120E-03
      -1       1      15    2.23000000E+00  9.99735092E-01  1.20853253E-02 -1.95880049E-02
      -1       1      16    2.23000000E+00 -9.99726960E-01 -1.23219757E-03  2.33342441E-02
      -1       1      17    2.23000000E+00  9.99455439E-01  1.94783670E-02 -2.66349298E-02
      -1       1      18    2.23000000E+00 -9.99888318E-01 -1.22907796E-02 -8.50223813E-03
      -1       1      19    2.23000000E+00  9.99978746E-01  2.68412812E-03  5.94160402E-03
      -1       1      20    2.23000000E+00  9.99988894E-01  3.76324073E-03  2.83733760E-03
      -1       1      21    2.23000000E+00  9.95036321E-01  2.87829252E-02  9.52589221E-02
      -1       1      22    2.23000000E+00  9.93204049E-01  7.62520094E-02  8.79280842E-02
      -1       1      23    2.23000000E+00  9.93971103E-01  6.55367179E-02  8.78998528E-02
      -1       1      24    2.23000000E+00  9.99690667E-01 -6.45548874E-03  2.40186759E-02
      -1       1      25    2.23000000E+00  9.99785320E-01  5.22554682E-03  2.00501495E-02
      -1       1      26    2.23000000E+00 -9.99924518E-01 -6.70090382E-03 -1.02983768E-02
      -1       1      27    2.23000000E+00  9.99980548E-01 -2.98448497E-03  5.47698377E-03
      -1       1      28    2.23000000E+00 -9.99664911E-01  2.54815790E-02 -4.55569720E-03
      -1       1      29    2.23000000E+00  9.99984272E-01 -4.71425411E-03  3.03823812E-03
      -1       1      30    2.23000000E+00  9.99439569E-01  2.11730912E-02  2.59277639E-02
      -1       1      31    2.23000000E+00  9.90037592E-01  5.73724139E-02  1.28584497E-01
      -1       1      32    2.23000000E+00  9.89611065E-01  8.09521689E-02  1.18813659E-01
      -1       1      33    2.23000000E+00  9.93309258E-01  5.14838057E-02  1.03373764E-01
      -1       1      34    2.23000000E+00  9.99223061E-01  3.31665733E-02  2.12897174E-02
      -1       1      35    2.23000000E+00  9.99944778E-01 -5.65687514E-03 -8.85670437E-03
      -1       1      36    2.23000000E+00 -9.99465099E-01  1.80636901E-02  2.72620579E-02
      -1       1      37    2.23000000E+00  9.99898438E-01  1.29073296E-02 -6.04271363E-03
      -1       1      38    2.23000000E+00 -9.99947201E-01  2.26567431E-03  1.00230385E-02
      -1       1      39    2.23000000E+00  9.99942664E-01 -3.02681571E-03  1.02716434E-02
      -1       1      40    2.23000000E+00  9.99880687E-01  1.49532705E-02 -3.87444333E-03
      -1       1      41    2.23000000E+00  9.90874406E-01  2.55661141E-02  1.32341551E-01
      -1       1      42    2.23000000E+00  9.92052315E-01  6.27654185E-02  1.09053688E-01
      -1       1      43    2.23000000E+00  9.94883276E-01  6.74650287E-02  7.52046344E-02
      -1       1      44    2.23000000E+00  9.99893419E-01  6.79238013E-03  1.29233731E-02
      -1       1      45    2.23000000E+00  9.99686412E-01 -1.00579277E-04 -2.50413090E-02
      -1       1      46    2.23000000E+00 -9.99980683E-01  5.57174008E-03 -2.75482373E-03
      -1       1      47    2.23000000E+00  9.99906753E-01  3.58188085E-03 -1.31778168E-02
      -1       1      48    2.23000000E+00 -9.99855227E-01 -2.12095563E-03 -1.68827522E-02
      -1       1      49    2.23000000E+00  9.99706295E-01 -2.39902336E-02 -3.43406882E-03
      -1       1      50    2.23000000E+00  9.98128991E-01 -5.46842778E-02  2.73522717E-02
      -1       1      51    2.23000000E+00  9.96348479E-01  2.33877637E-02  8.21140714E-02
      -1       1      52    2.23000000E+00  9.92999504E-01  6.96498382E-02  9.53985595E-02
      -1       1      53    2.23000000E+00  9.95985592E-01  3.50434104E-02  8.23690484E-02
      -1       1      54    2.23000000E+00  9.99264819E-01  1.31135280E-02  3.60257893E-02
      -1       1      55    2.23000000E+00  9.99996119E-01  2.49960196E-03  1.23039883E-03
      -1       1      56    2.23000000E+00 -9.99617953E-01 -1.27405831E-02 -2.45280576E-02
      -1       1      57    2.23000000E+00  9.99972325E-01  5.70090622E-03  4.78009693E-03
      -1       1      58    2.23000000E+00 -9.99967341E-01 -5.28749961E-03 -6.11215615E-03
      -1       1      59    2.23000000E+00  9.99708532E-01 -1.77261436E-02  1.63900717E-02
      -1       1      60    2.23000000E+00  9.99852518E-01 -1.36503624E-02 -1.04216383E-02
      -1       1      61    2.23000000E+00  9.95671770E-01  5.07067878E-02  7.78880548E-02
      -1       1      62    2.23000000E+00  9.94660253E-01  5.47749131E-02  8.74682245E-02
      -1       1      63    2.23000000E+00  9.94054341E-01  7.57436935E-02  7.82231477E-02
      -1       1      64    2.23000000E+00  9.99436762E-01  3.10893935E-02  1.26336215E-02
      -1       1      65    2.23000000E+00  9.99991416E-01 -3.61005299E-03  2.03346374E-03
      -1       1      66    2.23000000E+00 -9.99771710E-01  2.09079020E-02  4.40307559E-03
      -1       1      67    2.23000000E+00  9.99562300E-01 -1.97757566E-02 -2.20029017E-02
      -1       1      68    2.23000000E+00 -9.99464383E-01  2.26819824E-02  2.35897119E-02
      -1       1      69    2.23000000E+00  9.99789709E-01  1.03860938E-02 -1.76824007E-02
      -1       1      70    2.23000000E+00  9.99504758E-01  2.40226923E-02 -2.03260684E-02
      -1       1      71    2.23000000E+00  9.96582552E-01  8.27045884E-03  8.21876969E-02
      -1       1      72    2.23000000E+00  9.96198224E-01  6.55064037E-02  5.74283079E-02
      -1       1      73    2.23000000E+00  9.93404889E-01  6.23305584E-02  9.62373494E-02
      -1       1      74    2.23000000E+00  9.98917893E-01  2.80054655E-02 -3.71313569E-02
      -1       1      75    2.23000000E+00  9.99923524E-01 -7.14435545E-05 -1.23669380E-02
      -1       1      76    2.23000000E+00 -9.99420244E-01 -2.48519825E-02  2.32713346E-02
      -1       1      77    2.23000000E+00  9.99963789E-01 -7.51129149E-03 -4.00026584E-03
      -1       1      78    2.23000000E+00 -9.99372517E-01  3.49810018E-02 -5.55889274E-03
      -1       1      79    2.23000000E+00  9.99376345E-01  3.31224097E-02 -1.22404150E-02
      -1       1      80    2.23000000E+00  9.98700392E-01 -2.72946713E-02 -4.30410046E-02
      -1       1      81    2.23000000E+00  9.95686561E-01  1.97075118E-02  9.06635870E-02
      -1       1      82    2.23000000E+00  9.93794735E-01  6.09751549E-02  9.30271708E-02
      -1       1      83    2.23000000E+00  9.91160113E-01  8.20697130E-02  1.04241035E-01
      -1       1      84    2.23000000E+00  9.99990167E-01  4.31856347E-03  1.00775365E-03
      -1       1      85    2.23000000E+00  9.99406164E-01  2.39964743E-02 -2.47283003E-02
      -1       1      86    2.23000000E+00 -9.99887431E-01 -1.39303533E-02  5.57403669E-03
      -1       1      87    2.23000000E+00  9.99934245E-01 -2.68869047E-03 -1.11479042E-02
      -1       1      88    2.23000000E+00 -9.99971920E-01  6.49882384E-03  3.73144785E-03
      -1       1      89    2.23000000E+00  9.99945078E-01  9.82881943E-03 -3.63814442E-03
      -1       1      90    2.23000000E+00  9.99556516E-01 -2.77188054E-02 -1.08829705E-02

restart1.vtp

<?xml version="1.0"?>
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
  <PolyData>
    <Piece NumberOfPoints="90"                   NumberOfVerts="0"                    NumberOfLines="0"                    NumberOfStrips="0"                    NumberOfPolys="0"                   >
      <PointData Vectors="vectors">
        <DataArray type="Float32" Name="vectors" NumberOfComponents="3" format="appended" RangeMin="0.99999997185"        RangeMax="1.0000000297"         offset="0"                   />
      </PointData>
      <CellData>
      </CellData>
      <Points>
        <DataArray type="Float32" Name="Points" NumberOfComponents="3" format="appended" RangeMin="0"                    RangeMax="9.4339811321"         offset="1436"                />
      </Points>
      <Verts>
        <DataArray type="Int64" Name="connectivity" format="appended" RangeMin=""                     RangeMax=""                     offset="1708"                />
        <DataArray type="Int64" Name="offsets" format="appended" RangeMin=""                     RangeMax=""                     offset="1724"                />
      </Verts>
      <Lines>
        <DataArray type="Int64" Name="connectivity" format="appended" RangeMin=""                     RangeMax=""                     offset="1740"                />
        <DataArray type="Int64" Name="offsets" format="appended" RangeMin=""                     RangeMax=""                     offset="1756"                />
      </Lines>
      <Strips>
        <DataArray type="Int64" Name="connectivity" format="appended" RangeMin=""                     RangeMax=""                     offset="1772"                />
        <DataArray type="Int64" Name="offsets" format="appended" RangeMin=""                     RangeMax=""                     offset="1788"                />
      </Strips>
      <Polys>
        <DataArray type="Int64" Name="connectivity" format="appended" RangeMin=""                     RangeMax=""                     offset="1804"                />
        <DataArray type="Int64" Name="offsets" format="appended" RangeMin=""                     RangeMax=""                     offset="1820"                />
      </Polys>
    </Piece>
  </PolyData>
  <AppendedData encoding="base64">
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2

The vtp file is missing. You can paste it as text if discourse doesn’t allow you to upload it.

3

I have added the VTP files.

4

The ,vtp file looks fine. You might have uncovered a bug in the glyph filter (either in ParaView or in VTK itself).

To see that all the points are there, add vert cells so that you can see the points without glyphing:

cells = vtk.vtkCellArray()
for point, vector in zip(file_points, file_vectors):
    i = points.InsertNextPoint(point)
    cells.InsertNextCell(1)
    cells.InsertCellPoint(i)
    vectors.InsertNextTuple(vector)

# Create a polydata object and add the points and vectors for the VTK
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetVerts(cells)
polydata.GetPointData().SetVectors(vectors)
1 Like
5

Hi,
Thanks. This modification is working fine. Do you think it is helpful to report this bug? Should I make another post for that?

6

I’ve checked the .vtp file and it contains all the points and vectors, the vtkGlyph3D filter doesn’t have any problem with it either. So you can try posting the .vtp and your screenshot to the ParaView issue tracker to see what they think.