Add application: RACLAHE

[Palollo]

raclahe

Description

RACLAHE (Region-Adaptive Contrast Limited Adaptive Histogram Equalization) is an image enhancement method specifically designed for improving CNN-based segmentation of the prostate and prostatic zones in T2-Weighted MR images.

Usage

jobman submit -i raclahe -- <INPUT_DIR> <OUTPUT_DIR>

The application accepts 2 parameters:

• The input path of a dataset directory.
• The output directory where the results will be saved.

Example:

  jobman submit -i raclahe -- ~/datasets/87f3be56-4725-45c3-9baa-d338de530f73/ ~/persistent-home/results/

Note the output directory path should be any within the persistent-home, which is shared between all desktops and jobs created by the user,
otherwise the results will be lost after the end of the job.

Authors

James Zaridis
FORTH

Contact info

dimzaridis@gmail.com

URL

Quick start:
https://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/blob/main/QUICKSTART.md

Public dockerfile repository:
https://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/tree/main

License

https://github.com/dzaridis/RACLAHE_Image_Enhancement_for_CNN_model_segmentation/blob/main/LICENSE

[Palollo]

@dzaridis, please review the draft but particularly these points...

Usage

Please confirm the parameters accepted by the tool, those which the user can put after the "--" in the jobman submit command (they will be appended to the ENTRYPOINT of your image).
We added the INPUT_DIR and OUTPUT_DIR params to let the user specify them, and you should add them in the source code as currently seems they are fixed to /home/ds/datasets and /home/ds/persistent-home/output, which can work in the UPV reference node but may not work in other federated nodes.

In the dockerfile

• Recommendation: the COPY command with "." is discouraged because it copies all, including files not required in the image like Dockerfile, docker-compose.yml, .dockerignore, .gitignore, Demo Materials, etc. but even personal data which are git configurations for the repo in the directory ".git". I recommend to change your COPY line with this:

COPY --chown=ds:ds __main__.py LICENSE NOTICE requirements.txt utils /home/ds/
COPY --chown=ds:ds utils /home/ds/utils/

• Just to confirm: I see a "weights_path" in the main.py file which does not exist in the image built. Make sure to add if it's required (if not ignore this).

[Palollo]

Just one point more: now there are three levels of visibility for the batch applications (details here).
Which level should be assigned to this application?