New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add function that loads MetaImage files #98

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

Comments

Projects
None yet
3 participants
@vessemer
Copy link
Contributor

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

@vessemer vessemer referenced this issue Sep 7, 2017

Merged

Calculate tumor volume #78

1 of 1 task complete

@reubano reubano added this to the 2-feature-building milestone Sep 11, 2017

@tdraebing

This comment has been minimized.

Copy link
Contributor

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 referenced this issue Sep 18, 2017

Merged

Add function that loads MetaImage files #119

1 of 1 task complete
@vessemer

This comment has been minimized.

Copy link
Contributor

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment