Utilizing the vtk python library I am trying to color vtk polydata by a defined attribute (atype). So far I did not succeed. The renderer does not color by the specified attribute (atype) but instead by other date specified (position_and_radii).

Checking with paraview, all the data is around, and in paraview I can easily color by the requested attribute.

There is something I miss and I cannot figure out what ...

This is a simple code example.

# libraries
import vtk
import pandas as pd

# generate data
df_cell = pd.DataFrame(
    [[1,1,1,1,0.1,'abc'],[2,2,2,2,0.2,'def'],[3,3,3,3,0.3,'def'],[4,4,4,4,0.4,'abc']],
    columns=['ID','position_x','position_y','position_z','radius','atype'],
)

# generate VTK instances to fill for positions and radii
vp_points = vtk.vtkPoints()
vfa_radii = vtk.vtkFloatArray()
vfa_radii.SetName('radius')

# fill VTK instance with positions and radii
for i in df_cell.index:
    vp_points.InsertNextPoint(
        df_cell.loc[i, 'position_x'],
        df_cell.loc[i, 'position_y'],
        df_cell.loc[i, 'position_z']
    )
    vfa_radii.InsertNextValue(df_cell.loc[i, 'radius'])

# generate data instances
vfa_data = vtk.vtkFloatArray()
vfa_data.SetNumberOfComponents(2)
vfa_data.SetNumberOfTuples(df_cell.shape[0])
vfa_data.CopyComponent(0, vfa_radii, 0)
vfa_data.SetName('positions_and_radii')

# generate unstructred grid for data
vug_data = vtk.vtkUnstructuredGrid()
vug_data.SetPoints(vp_points)
vug_data.GetPointData().AddArray(vfa_data)
vug_data.GetPointData().SetActiveScalars('positions_and_radii')

# fill this grid with given attributes
voa_data = vtk.vtkStringArray()
voa_data.SetName('atype')
for i in df_cell.index:
    voa_data.InsertNextValue(df_cell.loc[i, 'atype'])
vug_data.GetPointData().AddArray(voa_data)

# generate sphere source
vss_data = vtk.vtkSphereSource()
vss_data.SetRadius(1.0)
vss_data.SetPhiResolution(16)
vss_data.SetThetaResolution(32)

# generate Glyph to save
vg_data = vtk.vtkGlyph3D()
vg_data.SetInputData(vug_data)
vg_data.SetSourceConnection(vss_data.GetOutputPort())

# define important preferences for VTK
vg_data.ClampingOff()
vg_data.SetScaleModeToScaleByScalar()
vg_data.SetScaleFactor(1.0)
vg_data.SetColorModeToColorByScalar()
vg_data.Update()

# build VTKLooktupTable (color scheme)
vlt_color = vtk.vtkLookupTable()
vlt_color.SetNumberOfTableValues(256)
vlt_color.SetHueRange(9/12, 0/12)  # rainbow heat map
vlt_color.Build()

# set up the mapper
vpdm_data = vtk.vtkPolyDataMapper()
vpdm_data.SetInputConnection(vg_data.GetOutputPort())
vpdm_data.ScalarVisibilityOn()
vpdm_data.SetLookupTable(vlt_color)
vpdm_data.ColorByArrayComponent('atype', 1)

# set up the actor
actor = vtk.vtkActor()
actor.SetMapper(vpdm_data)

# do renderer setup
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(800, 600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)

# add the actor to the renderer
#ren.ResetCamera()
ren.SetBackground(1/3, 1/3, 1/3) # gray
ren.AddActor(actor)

# render
iren.Initialize()
renWin.Render()
iren.Start()

# write VTK
vw_writer = vtk.vtkXMLPolyDataWriter()
vw_writer.SetFileName('vtkpoly.vtp')
vw_writer.SetInputData(vg_data.GetOutput())
vw_writer.Write()

This is the output I get:

And this is the output I would expect, displayed by paraview.

Additionaly, does anyone know by heart, how it is possible to add a colorbar with legend to the rendered image (as viewable in the paraview image)?

Thank you, Elmar

Utilizing the vtk python library I am trying to color vtk polydata by a defined attribute (atype). So far I did not succeed. The renderer does not color by the specified attribute (atype) but instead by other date specified (position_and_radii).

Checking with paraview, all the data is around, and in paraview I can easily color by the requested attribute.

There is something I miss and I cannot figure out what ...

This is a simple code example.

# libraries
import vtk
import pandas as pd

# generate data
df_cell = pd.DataFrame(
    [[1,1,1,1,0.1,'abc'],[2,2,2,2,0.2,'def'],[3,3,3,3,0.3,'def'],[4,4,4,4,0.4,'abc']],
    columns=['ID','position_x','position_y','position_z','radius','atype'],
)

# generate VTK instances to fill for positions and radii
vp_points = vtk.vtkPoints()
vfa_radii = vtk.vtkFloatArray()
vfa_radii.SetName('radius')

# fill VTK instance with positions and radii
for i in df_cell.index:
    vp_points.InsertNextPoint(
        df_cell.loc[i, 'position_x'],
        df_cell.loc[i, 'position_y'],
        df_cell.loc[i, 'position_z']
    )
    vfa_radii.InsertNextValue(df_cell.loc[i, 'radius'])

# generate data instances
vfa_data = vtk.vtkFloatArray()
vfa_data.SetNumberOfComponents(2)
vfa_data.SetNumberOfTuples(df_cell.shape[0])
vfa_data.CopyComponent(0, vfa_radii, 0)
vfa_data.SetName('positions_and_radii')

# generate unstructred grid for data
vug_data = vtk.vtkUnstructuredGrid()
vug_data.SetPoints(vp_points)
vug_data.GetPointData().AddArray(vfa_data)
vug_data.GetPointData().SetActiveScalars('positions_and_radii')

# fill this grid with given attributes
voa_data = vtk.vtkStringArray()
voa_data.SetName('atype')
for i in df_cell.index:
    voa_data.InsertNextValue(df_cell.loc[i, 'atype'])
vug_data.GetPointData().AddArray(voa_data)

# generate sphere source
vss_data = vtk.vtkSphereSource()
vss_data.SetRadius(1.0)
vss_data.SetPhiResolution(16)
vss_data.SetThetaResolution(32)

# generate Glyph to save
vg_data = vtk.vtkGlyph3D()
vg_data.SetInputData(vug_data)
vg_data.SetSourceConnection(vss_data.GetOutputPort())

# define important preferences for VTK
vg_data.ClampingOff()
vg_data.SetScaleModeToScaleByScalar()
vg_data.SetScaleFactor(1.0)
vg_data.SetColorModeToColorByScalar()
vg_data.Update()

# build VTKLooktupTable (color scheme)
vlt_color = vtk.vtkLookupTable()
vlt_color.SetNumberOfTableValues(256)
vlt_color.SetHueRange(9/12, 0/12)  # rainbow heat map
vlt_color.Build()

# set up the mapper
vpdm_data = vtk.vtkPolyDataMapper()
vpdm_data.SetInputConnection(vg_data.GetOutputPort())
vpdm_data.ScalarVisibilityOn()
vpdm_data.SetLookupTable(vlt_color)
vpdm_data.ColorByArrayComponent('atype', 1)

# set up the actor
actor = vtk.vtkActor()
actor.SetMapper(vpdm_data)

# do renderer setup
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(800, 600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)

# add the actor to the renderer
#ren.ResetCamera()
ren.SetBackground(1/3, 1/3, 1/3) # gray
ren.AddActor(actor)

# render
iren.Initialize()
renWin.Render()
iren.Start()

# write VTK
vw_writer = vtk.vtkXMLPolyDataWriter()
vw_writer.SetFileName('vtkpoly.vtp')
vw_writer.SetInputData(vg_data.GetOutput())
vw_writer.Write()

This is the output I get:

And this is the output I would expect, displayed by paraview.

Additionaly, does anyone know by heart, how it is possible to add a colorbar with legend to the rendered image (as viewable in the paraview image)?

Thank you, Elmar

• python
• vtk

1 Answer 1

To solve the coloring issue map the atype string values to numeric values. then configure the vtk mapper to use this numeric array. I highlighted the changes in the code bellow using ####:

# libraries
import vtk
import pandas as pd

# generate data
df_cell = pd.DataFrame(
    [[1,1,1,1,0.1,'abc'],[2,2,2,2,0.2,'def'],[3,3,3,3,0.3,'def'],[4,4,4,4,0.4,'abc']],
    columns=['ID','position_x','position_y','position_z','radius','atype'],
)

# generate VTK instances to fill for positions and radii
vp_points = vtk.vtkPoints()
vfa_radii = vtk.vtkFloatArray()
vfa_radii.SetName('radius')

# fill VTK instance with positions and radii
for i in df_cell.index:
    vp_points.InsertNextPoint(
        df_cell.loc[i, 'position_x'],
        df_cell.loc[i, 'position_y'],
        df_cell.loc[i, 'position_z']
    )
    vfa_radii.InsertNextValue(df_cell.loc[i, 'radius'])

# generate data instances
vfa_data = vtk.vtkFloatArray()
vfa_data.SetNumberOfComponents(2)
vfa_data.SetNumberOfTuples(df_cell.shape[0])
vfa_data.CopyComponent(0, vfa_radii, 0)
vfa_data.SetName('positions_and_radii')

# generate unstructred grid for data
vug_data = vtk.vtkUnstructuredGrid()
vug_data.SetPoints(vp_points)
vug_data.GetPointData().AddArray(vfa_data)
vug_data.GetPointData().SetActiveScalars('positions_and_radii')

# fill this grid with given attributes
voa_data = vtk.vtkStringArray()
voa_data.SetName('atype')

#################################################################################
atype_mapping = {atype: idx for idx, atype in enumerate(df_cell['atype'].unique())}
numeric_atype = vtk.vtkIntArray()
numeric_atype.SetName('atype_numeric')

for atype in df_cell['atype']:
    numeric_atype.InsertNextValue(atype_mapping[atype])

vug_data.GetPointData().AddArray(numeric_atype)
################################################################################

# generate sphere source
vss_data = vtk.vtkSphereSource()
vss_data.SetRadius(1.0)
vss_data.SetPhiResolution(16)
vss_data.SetThetaResolution(32)

# generate Glyph to save
vg_data = vtk.vtkGlyph3D()
vg_data.SetInputData(vug_data)
vg_data.SetSourceConnection(vss_data.GetOutputPort())

# define important preferences for VTK
vg_data.ClampingOff()
vg_data.SetScaleModeToScaleByScalar()
vg_data.SetScaleFactor(1.0)
vg_data.SetColorModeToColorByScalar()
vg_data.Update()


# build VTKLooktupTable (color scheme)
vlt_color = vtk.vtkLookupTable()
vlt_color.SetNumberOfTableValues(256)
vlt_color.SetHueRange(9/12, 0/12)  # rainbow heat map
vlt_color.Build()

# set up the mapper
vpdm_data = vtk.vtkPolyDataMapper()
vpdm_data.SetInputConnection(vg_data.GetOutputPort())
vpdm_data.ScalarVisibilityOn()
vpdm_data.SetLookupTable(vlt_color)


###############################################################
vpdm_data.SetScalarModeToUsePointFieldData()
vpdm_data.SelectColorArray('atype_numeric')
vpdm_data.SetScalarRange(0, 1)
###############################################################


# set up the actor
actor = vtk.vtkActor()
actor.SetMapper(vpdm_data)

# do renderer setup
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(800, 600)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)

# add the actor to the renderer
#ren.ResetCamera()
ren.SetBackground(1/3, 1/3, 1/3) # gray
ren.AddActor(actor)

# render
iren.Initialize()
renWin.Render()
iren.Start()

# write VTK
vw_writer = vtk.vtkXMLPolyDataWriter()
vw_writer.SetFileName('vtkpoly.vtp')
vw_writer.SetInputData(vg_data.GetOutput())
vw_writer.Write()