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This example uses vtkDiscreteFlyingEdges3D or vtkDiscreteMarchingCubes to create vtkPolyData models from a 3D volume that contains discrete labels. These volumes are normally the output of a segmentation algorithm. The polydata for each label will be output into a separate file.

You can load these files into ParaView, where they will appear as a series of time steps. You can then single step through displaying the polydate from each file making up the series.

If you want to see the segmentation results as cube models, see the example GenerateCubesFromLabels

The input volume must be in MetaIO format.

Once you generate the models, you can view them with Paraview


This original source code for this example is here.

Other languages

See (Cxx), (Python)


If you have a question about this example, please use the VTK Discourse Forum


#!/usr/bin/env python3

import os
import sys

# noinspection PyUnresolvedReferences
import vtkmodules.vtkInteractionStyle
# noinspection PyUnresolvedReferences
import vtkmodules.vtkRenderingOpenGL2
from vtkmodules.vtkCommonDataModel import (
from vtkmodules.vtkFiltersCore import (
from vtkmodules.vtkFiltersGeneral import (
from vtkmodules.vtkFiltersGeometry import vtkGeometryFilter
from vtkmodules.vtkIOImage import vtkMetaImageReader
from vtkmodules.vtkIOXML import vtkXMLPolyDataWriter
from vtkmodules.vtkImagingStatistics import vtkImageAccumulate

def get_program_parameters():
    import argparse
    description = 'Creates vtkPolyData models from a 3D volume that contains discrete labels.'
    epilogue = '''
These volumes are normally the output of a segmentation algorithm.
The polydata for each label will be output into a separate file.
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
    parser.add_argument('filename', help='Input volume e.g. Frog/frogtissue.mhd.')
    parser.add_argument('startlabel', type=int, help='The starting label in the input volume, e,g, 1.')
    parser.add_argument('endlabel', type=int, help='The ending label in the input volume e.g. 29')
    parser.add_argument('-m', '--marching_cubes', action='store_false',
                        help='Use Marching Cubes instead of Flying Edges.')
    args = parser.parse_args()
    return args.filename, args.startlabel, args.endlabel, args.marching_cubes

def main():
    Generate models from labels.
    1) Read the meta file
    2) Generate a histogram of the labels
    3) Generate models from the labeled volume
    4) Smooth the models
    5) Output each model into a separate file


    file_name, start_label, end_label, use_flying_edges = get_program_parameters()

    if start_label > end_label:
        end_label, start_label = start_label, end_label

    reader = vtkMetaImageReader(file_name=file_name)

    if use_flying_edges:
        discrete_cubes = vtkDiscreteFlyingEdges3D()
        discrete_cubes = vtkDiscreteMarchingCubes()
    discrete_cubes.GenerateValues(end_label - start_label + 1, start_label, end_label)

    smoothing_iterations = 15
    pass_band = 0.001
    feature_angle = 120.0
    smoother = vtkWindowedSincPolyDataFilter(number_of_iterations=smoothing_iterations, boundary_smoothing=False,
                                             feature_edge_smoothing=False, feature_angle=feature_angle,
                                             non_manifold_smoothing=True, normalize_coordinates=True

    selector = vtkThreshold()
    if use_flying_edges:
        selector.SetInputArrayToProcess(0, 0, 0, vtkDataObject.FIELD_ASSOCIATION_POINTS,
        selector.SetInputArrayToProcess(0, 0, 0, vtkDataObject.FIELD_ASSOCIATION_CELLS,

    # Strip the scalars from the output.
    scalars_off = vtkMaskFields()
    scalars_off.CopyAttributeOff(vtkMaskFields.POINT_DATA, vtkDataSetAttributes().SCALARS)
    scalars_off.CopyAttributeOff(vtkMaskFields.CELL_DATA, vtkDataSetAttributes().SCALARS)

    histogram = vtkImageAccumulate(component_extent=(0, end_label, 0, 0, 0, 0),
                                   component_origin=(0, 0, 0), component_spacing=(1, 1, 1))
    (reader >> histogram).update()

    geometry = vtkGeometryFilter()
    writer = vtkXMLPolyDataWriter()
    reader >> discrete_cubes >> smoother >> selector >> scalars_off >> geometry >> writer

    file_prefix = 'Label'
    for i in range(start_label, end_label + 1):
        # See if the label exists, if not skip it.
        frequency = histogram.output.point_data.scalars.GetTuple1(i)
        if frequency == 0.0:

        # Select the cells for a given label.
        selector.lower_threshold = i
        selector.upper_threshold = i

        # Output the polydata.
        output_fn = f'{file_prefix:s}{i:d}.vtp'
        print(f'{os.path.basename(sys.argv[0]):s} writing {output_fn:s}')

        writer.file_name = output_fn

if __name__ == '__main__':