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Add function that loads MetaImage files #98

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vessemer opened this issue Sep 7, 2017 · 2 comments
Closed

Add function that loads MetaImage files #98

vessemer opened this issue Sep 7, 2017 · 2 comments

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@vessemer
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@vessemer vessemer commented Sep 7, 2017

In the field of low-dose CT, not the only DICOM data format is wildly used, but MetaImage (.mhd / .raw) is also taken place. The MetaImage is the text-based tagged file format for medical images. As well as the DICOM format, the MetaImage has descriptors along with the raw data.

Expected Behavior

The .mhd / .raw files may be read via SimpleITK. So load_itk should be provided which takes the itk_path as an input and return the np.ndarray (right now the load_dicom returns the np.ndarray which may be different in the future since MetaImage and DICOM have different metadata and it will be the good decision to build a class which will standardise the metadata by parameters). Furthermore, the orchestrate function load_CT aimed at handling different medical image formats, so the load_CT will take CT_path as an input and will decide whether to return the output of load_dicom or load_itk.

Current Behavior

For now, exists only the possibility to read DICOM file format through load_dicom.

Technical details

This feature should be implemented in the prediction/src/preprocess folder

Acceptance criteria

  • method to load MetaImage (.mhd / .raw) images into memory
  • method to select apropriate loader function
  • tests for the methods
@tdraebing
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@tdraebing tdraebing commented Sep 11, 2017

I would start working on that. Are there any image files in those formats in the larger data set that will be used for model training/testing later on that could be used for tests? Else I would try to find some.

@reubano reubano added minor and removed medium labels Sep 12, 2017
@vessemer vessemer mentioned this issue Sep 18, 2017
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@vessemer
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@vessemer vessemer commented Sep 18, 2017

As far as I can't see any changes for more than the week, I've created a pull request.

@lamby lamby closed this in 91cbff4 Sep 19, 2017
dchansen added a commit to dchansen/concept-to-clinic that referenced this issue Sep 28, 2017
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3 participants