Issues with volume Threshold and Slicer

I have been trying to threshold a volume coming from a VTI image file (structured data). This 3D array contains segmented data, meaning each voxel has a label (0 to 5). I can easily visualize this volume using either show() or Slicer(). I would like to replace classes by 0’s and 1’s depending on the threshold range and visualize the output using Slicer().

Approach 1: using standard vtk

filename = 'test.vti'
vol = load(filename)

# vtkImageThreshold filter
thresholdFilter = vtk.vtkImageThreshold()
thresholdFilter.SetInputData(vol.imagedata())
thresholdFilter.SetInValue(1)
thresholdFilter.SetOutValue(0)
thresholdFilter.ThresholdBetween(0, 2)
thresholdFilter.Update()
thresholdedImage = thresholdFilter.GetOutput()

# Create volume from vtkImageData (output of thresholdFilter.GetOutput())
thresVol = Volume(inputobj=thresholdedImage)

# Show results
show(thresVol)

Result: I see exactly what I expected to see, the right voxels are show in blue color.

Approach 2: using standard vtk, but trying to use Slicer to see the data

filename = 'test.vti'
vol = load(filename)

# vtkImageThreshold filter
thresholdFilter = vtk.vtkImageThreshold()
thresholdFilter.SetInputData(vol.imagedata())
thresholdFilter.SetInValue(1)
thresholdFilter.SetOutValue(0)
thresholdFilter.ThresholdBetween(0, 2)
thresholdFilter.Update()
thresholdedImage = thresholdFilter.GetOutput()

# Create volume from vtkImageData (output of thresholdFilter.GetOutput())
thresVol = Volume(inputobj=thresholdedImage)

# Show results
plt = Slicer(thresVol,
                  bg='white', bg2='lightblue',
                  cmaps=("gist_ncar_r", "jet", "Spectral_r", "hot_r", "bone_r"),
                  useSlider3D=False,
                  showIcon=False,
                  draggable=False)
plt.show()

Result: Slicer comes empty, all the voxels are with label 0. Note that I only changed the way to visualize the data from Approach 1 (Slicer() instead of show())

Approach 3: using vedo Volume thresholding

filename = 'test.vti'
vol = load(filename)

# Thresholding
vol = vol.threshold(above = 0.0, below=2.0, replaceWith=1)

# Show results
show(vol)

Result: I do not see what I expected to see, just some blue voxels, as if the threshold is keeping only few voxels

I honestly do not see what I might be doing wrong…I would appreciate any help.

Thanks! Rafael.

[rafaelmarch3]

Many thanks Marco! Will give it a go now.

[marcomusy]

I close this for the moment, reopen it if needed!