Skip to content

README.md

Latest commit

 

History

History
53 lines (39 loc) · 2.32 KB

README.md

File metadata and controls

53 lines (39 loc) · 2.32 KB

Kaggle Second Annual Data Science Bowl

The Kaggle cardiac MRI dataset dataset consists of 1140 cine-MRI images, split into 500 training, 200 validation, and 440 test images. The images are stored in DICOM format. Only the left ventricle volume for the ED and ES phases is provided. Labels on test images are not available. The EF can be derived. In the original competition, the Continuous Ranked Probability Score (CRPS) is used for evaluation.

Download

Note

It is recommended to download the dataset to download the data under ~/.cache/cinema_datasets/kaggle as the integration tests uses this path. Otherwise define the path using environment variable CINEMA_DATA_DIR.

If you see 403 - Forbidden - You must accept this competition's rules before you'll be able to download files error, you need to join the competition and accept the rules on the Kaggle website. You may need to verify your Kaggle account.

This data set can be downloaded from Kaggle using kaggle API.

  1. The authentication token shall be obtained and stored under ~/.kaggle/kaggle.json. Run the following command to change the permissions.

    ```bash
chmod 600 ~/.kaggle/kaggle.json
```

  2. Then, execute the following commands to download and unzip files, the unzip command will not print any output.

    pip install kaggle
kaggle competitions download -c second-annual-data-science-bowl
unzip -q second-annual-data-science-bowl.zip -d second-annual-data-science-bowl

Preprocessing

Warning

DICOM images contain lots of files. This may hit the limit of the number of files that can be stored.

Use the kaggle_preprocess entrypoint to preprocess the data with the following steps:

  • resampling LAX 2C/4C images to 1.0 x 1.0 mm and SAX images to 1.0 x 1.0 x 10.0 mm.
  • cropping the images to 256 x 256 for LAX and 192 x 192 for SAX, based on 2C/4C/SAX intersection center.
  • normalizing the values to [0, 1].
kaggle_preprocess

The CLI requires to install the cinema package at the root of repository with pip install -e ..