Project-MONAI / Project-MONAI/MONAI
Save individual normalization modes (multi-channel) in Auto3dSeg's model config
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Description
Is your feature request related to a problem? Please describe.
I trained a model with the Auto3dSeg Autorunner and was trying to run inference using the SlicerMONAIAuto3DSeg extension (https://github.com/lassoan/SlicerMONAIAuto3DSeg).
modality: mri
extra_modalities: {image2 : none} # a second modality is a label which should NOT be normalized
The model expects multiple input images (image1: mri, image2: label --> no normalization).
The following .yaml file is an example of the use of multiple input images for a model: https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/tasks/hecktor22/input.yaml
Currently, no matter how many input modalities (imageModality and extra_modalities) were provided, only a single value for normalize_mode is saved in the model's `config'.
Describe the solution you'd like
- When multiple input images were provided and the same normalization mode was used for all of them, then a single value for
normalize_modeis valid - When multiple input images of different types/modalities were provided, then a list of normalization modes corresponding to the number of input images should be used for
normalize_mode.
Additional context
https://github.com/lassoan/SlicerMONAIAuto3DSeg/issues/32
https://github.com/JolleyLab/Internal/issues/194
Contributor guide
First steps
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- Comment on the issue to say you are picking it up — it saves two people doing the same work.
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- Open a pull request that references the issue number.
Research direction
Start with the Auto3dSeg Autorunner path that writes the model config and compare its handling with the tutorials' auto3dseg/tasks/hecktor22/input.yaml example. Trace how imageModality and extra_modalities become normalize_mode values. Done means identical modes remain a single value, while differing modes are saved in input order as a list, including an unnormalized label modality.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100