meerkat.datasets.siim_cxr package

Module contents

cxr_transform(volume: MedicalVolumeCell)[source]

cxr_transform_pil(volume: MedicalVolumeCell)[source]

download_siim_cxr(dataset_dir: str, kaggle_username: str, kaggle_key: str, download_gaze_data: bool = True, include_mock_reports: bool = True)[source]

Download the dataset from the SIIM-ACR Pneumothorax Segmentation challenge. https://www.kaggle.com/c/siim-acr-pneumothorax- segmentation/data.

Parameters

dataset_dir (str) – Path to directory where the dataset will be downloaded.
kaggle_username (str) – Your kaggle username.
kaggle_key (str) – A kaggle API key. In order to use the Kaggle’s public API, you must first authenticate using an API token. From the site header, click on your user profile picture, then on “My Account” from the dropdown menu. This will take you to your account settings at https://www.kaggle.com/account. Scroll down to the section of the page labelled API: To create a new token, click on the “Create New API Token” button. This will download a json file with a “username” and “key” field. Copy and paste the “key” field and pass it in as kaggle_key. Instructions copied from Kaggle API docs: https://www.kaggle.com/docs/api
download_gaze_data (str) – Download a pkl file containing eye-tracking data collected on a radiologist interpreting the xray.