[ITK-users] How to using SimpleITK to access and change the voxel value without touch the metadata

[Po-Yu Kao]

Hello,

I am using SimpleITK library in python 2.7.

I want to do some basic preprocessing on CT scans with nii.gz. format. For
example, I use img = sitk.ReadImage(ct_scan_path) to read the image, and
then use nda = sitk.GetArrayFromImage(ct_img) to access n-dimensional numpy
array. Then, I do some preprocessing steps on this n-dimensional numpy, and
save it back to the image format by using img_preprocessed =
sitk.GetImageFromArray(nda_preprocessed). However, when I check the
metadata of these two images, it gives me different values which are showed
below.

Does anyone know how to copy all the metadata from the original image to
another image? or Does anyone know how to access and change the voxel value
of the image without touching the metadata?

Original Image:
print img

Image (0x4237b40)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3601
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 3578
  UpdateMTime: 3600
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [0.488281, 0.488281, 5]
  Origin: [-114, 294.012, 21.82]
  Direction:
1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix:
0.488281 0 0
0 -0.488281 0
0 0 5

  PointToIndexMatrix:
2.048 0 0
0 -2.048 0
0 0 0.2

  Inverse Direction:
1 0 0
0 -1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x398e780)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3597
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef9225010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328

Preprocessed Image:

Image (0x3857e60)
  RTTI typeinfo:   itk::Image<float, 3u>
  Reference Count: 1
  Modified Time: 3605
  Debug: Off
  Object Name:
  Observers:
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 0
  RealTimeStamp: 0 seconds
  LargestPossibleRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  BufferedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  RequestedRegion:
    Dimension: 3
    Index: [0, 0, 0]
    Size: [512, 512, 37]
  Spacing: [1, 1, 1]
  Origin: [0, 0, 0]
  Direction:
1 0 0
0 1 0
0 0 1

  IndexToPointMatrix:
1 0 0
0 1 0
0 0 1

  PointToIndexMatrix:
1 0 0
0 1 0
0 0 1

  Inverse Direction:
1 0 0
0 1 0
0 0 1

  PixelContainer:
    ImportImageContainer (0x39856c0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, float>
      Reference Count: 1
      Modified Time: 3606
      Debug: Off
      Object Name:
      Observers:
        none
      Pointer: 0x7f6ef4823010
      Container manages memory: true
      Size: 9699328
      Capacity: 9699328
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