CODEWITHSUNDEEP
pythonimage-processingsimpleitkimage-thresholding
stu dent
stu dent

Reputation: 5

How to perform thresholding?

When I apply thresholding I'm getting an error:

import SimpleITK as sitk
img = sitk.ReadImage("Sub1.png")
img=img>20

The error is:

RuntimeError                              Traceback (most recent call last)
<ipython-input-48-a1d4494dca15> in <module>()
      1 #img = sitk.Image(img.GetSize(), sitk.sitkUInt8)
----> 2 img=img>20

~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in __gt__(self, other)
   4424            return Greater( self, other )
   4425         try:
-> 4426            return Greater( self, float(other) )
   4427         except (ValueError, TypeError):
   4428            return NotImplemented

~/sitkpy/lib/python3.5/site-packages/SimpleITK/SimpleITK.py in Greater(*args)
  34345 
  34346     """
> 34347     return _SimpleITK.Greater(*args)
  34348 class GridImageSource(ImageFilter_0):
  34349     """

RuntimeError: Exception thrown in SimpleITK Greater: /tmp/SimpleITK/Code/Common/include/sitkMemberFunctionFactory.hxx:209:
sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not supported in 2D byN3itk6simple18GreaterImageFilterE

I applied img = sitk.Image(img.GetSize(), sitk.sitkUInt8) but I'm getting a black image.

Is there any option like double(img) or im2bw in Python? Will normalize work? print(img) gives the following

VectorImage (0x2f57af0) RTTI typeinfo: itk::VectorImage Reference Count: 1 Modified Time: 1289 Debug: Off Object Name: Observers: none Source: (none) Source output name: (none) Release Data: Off Data Released: False Global Release Data: Off PipelineMTime: 1278 UpdateMTime: 1288 RealTimeStamp: 0 seconds LargestPossibleRegion: Dimension: 2 Index: [0, 0] Size: [305, 305] BufferedRegion: Dimension: 2 Index: [0, 0] Size: [305, 305] RequestedRegion: Dimension: 2 Index: [0, 0] Size: [305, 305] Spacing: [1, 1] Origin: [0, 0] Direction: 1 0 0 1

IndexToPointMatrix: 1 0 0 1

PointToIndexMatrix: 1 0 0 1

Inverse Direction: 1 0 0 1

VectorLength: 4 PixelContainer: ImportImageContainer (0x24ba950) RTTI typeinfo: itk::ImportImageContainer Reference Count: 1 Modified Time: 1285 Debug: Off Object Name: Observers: none Pointer: 0x30bb390 Container manages memory: true Size: 372100 Capacity: 372100

​

Upvotes: 0

Views: 484

Answers (1)

blowekamp
blowekamp

Reputation: 1431

Your exception reads: RuntimeError: Exception thrown in SimpleITK Greater: /tmp/SimpleITK/Code/Common/include/sitkMemberFunctionFactory.hxx:209: sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not supported in 2D byN3itk6simple18GreaterImageFilterE

Try running: import SimpleITK as sitk img = sitk.ReadImage("Sub1.png") print img

This means that your input image is NOT a scalar image it is an image with multiple components. The ">" or sitk.GraterThan does not support vector images. It only support scalar images.

The question is: is your image suppose to be a RGB image? And how do you want to deal with "thresholding" the multi-channel image?

Upvotes: 2

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