# vtk for Python: nii.gz image in 3D reconstruction but no options to set colors

**URL:** https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451
**Category:** Support
**Created:** [October 20, 2020, 5:30am UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451 "2020-10-20T05:30:28Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![lihanhu](https://discourse.vtk.org/letter_avatar_proxy/v4/letter/l/5fc32e/32.png) [@lihanhu](https://discourse.vtk.org/u/lihanhu)
#### Post date: [October 20, 2020, 5:30am UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451/1 "2020-10-20T05:30:28Z")

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I did a cell segmentation program, and the results of the segmentation were marked. But in 3D reconstruction, I don’t know how to mark the result I marked with different colors and color the target object. ☹

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### Author: ![lihanhu](https://discourse.vtk.org/letter_avatar_proxy/v4/letter/l/5fc32e/32.png) [@lihanhu](https://discourse.vtk.org/u/lihanhu)
#### Post date: [October 20, 2020, 5:31am UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451/2 "2020-10-20T05:31:33Z")

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here is my code for 3D reconstruction and ‘path’ is my image folder.

aRenderer = vtk.vtkRenderer()  
renWin = vtk.vtkRenderWindow()  
renWin.AddRenderer(aRenderer)  
iren = vtk.vtkRenderWindowInteractor()  
iren.SetRenderWindow(renWin)  
v16 = vtk.vtkNIFTIImageReader()  
v16.SetDataByteOrderToLittleEndian()  
v16.SetFileName(path)  
mc = vtk.vtkMarchingCubes()  
mc.SetInputConnection(v16.GetOutputPort())  
mc.SetValue(0,2)  
skinMapper = vtk.vtkPolyDataMapper();  
skinMapper.SetInputConnection(mc.GetOutputPort())  
skinMapper.ScalarVisibilityOff()  
skin = vtk.vtkActor()  
skin.SetMapper(skinMapper)  
aRenderer.AddActor(skin)  
iren.Initialize()  
iren.Start()

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<div class="post-metadata">

### Author: ![lihanhu](https://discourse.vtk.org/letter_avatar_proxy/v4/letter/l/5fc32e/32.png) [@lihanhu](https://discourse.vtk.org/u/lihanhu)
#### Post date: [October 20, 2020, 5:41am UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451/3 "2020-10-20T05:41:31Z")

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here is my image of a seg cell…

 ![image](https://discourse.vtk.org/uploads/default/original/2X/7/71c89579567a1851489f941bea42913b6d5f9bfe.jpeg)

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### Author: ![lassoan](https://discourse.vtk.org/user_avatar/discourse.vtk.org/lassoan/32/50_2.png) [@lassoan](https://discourse.vtk.org/u/lassoan)
#### Post date: [October 20, 2020, 1:33pm UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451/4 "2020-10-20T13:33:15Z")

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The example that you have found is for visualizing isosurface of a grayscale volume. To display a labelmap volume in 3D, you need to use discrete marching cubes (or flying edges, for faster operation), set multiple values (`SetValue`), enable `ScalarVisibility`, set an appropriate color lookup table, and apply surface smoothing. See complete example here: [https://lorensen.github.io/VTKExamples/site/Cxx/Medical/GenerateModelsFromLabels/](https://lorensen.github.io/VTKExamples/site/Cxx/Medical/GenerateModelsFromLabels/)

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<div class="post-metadata">

### Author: ![lihanhu](https://discourse.vtk.org/letter_avatar_proxy/v4/letter/l/5fc32e/32.png) [@lihanhu](https://discourse.vtk.org/u/lihanhu)
#### Post date: [October 21, 2020, 8:31am UTC](https://discourse.vtk.org/t/vtk-for-python-nii-gz-image-in-3d-reconstruction-but-no-options-to-set-colors/4451/5 "2020-10-21T08:31:53Z")

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Thanks for your reply!!!  
However, I don’t know how to display the image using Python. The classes in the example just tell users how to write the image into ‘.vtp’ files.

v16 = vtk.vtkNIFTIImageReader()  
v16.SetDataByteOrderToLittleEndian()  
v16.SetFileName(path)

mc = vtk.vtkDiscreteMarchingCubes()  
mc.SetInputConnection(v16.GetOutputPort())  
mc.SetValue(0,1)

smoother = vtk.vtkWindowedSincPolyDataFilter()  
scalarsOff = vtk.vtkMaskFields()  
selector = vtk.vtkThreshold()  
geometry = vtk.vtkGeometryFilter()

smoother.SetInputConnection(mc.GetOutputPort())  
smoother.SetNumberOfIterations(15)  
smoother.BoundarySmoothingOff()  
smoother.SetFeatureAngle(120)  
smoother.Update()

selector.SetInputConnection(smoother.GetOutputPort())  
selector.SetInputArrayToProcess(0,0,0,vtk.vtkDataObject.FIELD\_ASSOCIATION\_CELLS,  
vtk.vtkDataSetAttributes.SCALARS)  
scalarsOff.SetInputConnection(selector.GetOutputPort())  
scalarsOff.CopyAttributeOff(vtk.vtkMaskFields.POINT\_DATA, vtk.vtkDataSetAttributes.SCALARS)  
scalarsOff.CopyAttributeOff(vtk.vtkMaskFields.CELL\_DATA, vtk.vtkDataSetAttributes.SCALARS)  
geometry.SetInputConnection(scalarsOff.GetOutputPort())

I’m using Python to solve the above problem but it doesn’t work…