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

[Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]]

Hello Po-Yu Kao,

The step you are missing is that you need to explicitly copy the meta-data information from your original image, the function is CopyInformation(). This assumes that you did not change any spatial information (padded the numpy array as part of your processing which implies a change in the spatial region occupied by the image etc.).

Your code should look something like this:

ct_img = sitk.ReadImage(ct_scan_path)
nda = sitk.GetArrayFromImage(ct_img)

# Do some work on the numpy array nda

img_preprocessed = sitk.GetImageFromArray(nda_preprocessed)
img_preprocessed.CopyInformation(ct_img)

If you did change some spatial aspects of the image in your numpy code then you will need to set them manually:
img_preprocessed.SetSpacing(new_spacing)
img_preprocessed.SetOrigin(new_origin)
img_preprocessed.SetDirection(new_direction)

We are moving away from the mailing to a discourse forum: https://discourse.itk.org/
Please post future questions on that forum.

     regards
          Ziv


From: Po-Yu Kao <poyu_kao at ucsb.edu>
Date: Tuesday, November 28, 2017 at 9:41 PM
To: "community at itk.org" <community at itk.org>
Subject: [ITK] How to using SimpleITK to access and change the voxel value without touch the metadata

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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