How to improve noises of displaying 2D DICOM slices with rendering vtk and make it more clear ?

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#1

Here is my code to display 2d slices of DICOM volume using vtk renderer with python :

    # Read DICOM images
    self.reader = vtk.vtkDICOMImageReader()
    self.reader.SetDirectoryName(folder)
    self.reader.Update()
   
    #Create Sagittal Slice Matrix
    sagittal = vtk.vtkMatrix4x4()
    sagittal.DeepCopy((0, 0, -1, center[0],
                       1, 0, 0, center[1],
                       0, -1, 0, center[2],
                       0, 0, 0, 1))

    # Reslice image
    widget = QVTKRenderWindowInteractor()
    slice = vtk.vtkImageReslice()
    slice.SetInputConnection(self.reader.GetOutputPort())
    slice.SetOutputDimensionality(2)
    slice.SetResliceAxes(sagittal)
    slice.SetInterpolationModeToLinear()

    # Display the image
    actor = vtk.vtkImageActor()
    actor.GetMapper().SetInputConnection(slice.GetOutputPort())

    renderer = vtk.vtkRenderer()

    # Remove Renderer And Reset
    renderer.RemoveAllViewProps()
    renderer.ResetCamera()
    widget.GetRenderWindow().Render()
    renderer.AddActor(actor)

    widget.GetRenderWindow().AddRenderer(renderer)
    # Set up the interaction
    slice_interactorStyle = vtk.vtkInteractorStyleImage()
    slice_interactor = widget.GetRenderWindow().GetInteractor()
    slice_interactor.SetInteractorStyle(slice_interactorStyle)
    widget.GetRenderWindow().SetInteractor(slice_interactor)
    widget.GetRenderWindow().Render()

    # Start interaction
    slice_interactor.Start()

This is also my output :

Screenshot%20from%202019-09-30%2014-47-05
Screenshot from 2019-09-30 14-47-05.jpg758Ă—544 129 KB

#2

The vtkImageProperty can be used to adjust the contrast. For a 16 bit CT you can use the following as a starting point:

actor.GetProperty().SetLevel(0.0)
actor.GetProperty().SetWindow(2000.0)
2 Likes
#3

Woooow !!
incredible
This is exactly what I wanted :slight_smile:
Thank You very much for your answering

#4

could you please explain a little about color window and color level ?
what are they changing and effecting on?

#5

VTK’s “ColorWindow” and “ColorLevel” correspond to what radiologists usually call the “window level” and “window width”, e.g.:

To make a long story short, the image mapper has a lookup table (grayscale by default), and the ColorWindow and ColorLevel in the image property control the range of image values that are mapped through the lookup table.

#7

for volume is it also the same way or is different?

#8

You mean volume rendering, i.e. vtkVolumeProperty? Completely different.

#9

Yes, vtkVolumeProperty
I mean for adjusting the volume contrast too what should I do?
as you see my volume has lots of noise too.

#10

as I searched , only understand that I have to use vtkPiecewiseFunction with vtkVolumeProperty.setColor()
but I’m not sure about t it

I’m first in vtk.

#11

Here is an example with explanations:
https://lorensen.github.io/VTKExamples/site/Python/Medical/MedicalDemo4/

And the chapter in the VTK textbook (though it is out of date now):
https://lorensen.github.io/VTKExamples/site/VTKBook/07Chapter7/#73-volume-rendering

#13

Thank you so much for all your helpful responses.:pray:

#14

I have exactly similar project but I am new to python. I need to ask some basics. How can I contact with you?

#16

You can message me here.

#17

Im working on a same project but on pelvis. I need to add implant to some pictures and move them to find the best position. Since last time I messaged I had succeeded a lot. Do you find any way to make a 3D stl file from CT-Images?

#18

I think you can use https://vtk.org/doc/nightly/html/classvtkSTLWriter.html for that. You can find here a little sample:https://vtk.org/Wiki/VTK/Examples/Cxx/IO/WriteSTL