Security News
Node.js EOL Versions CVE Dubbed the "Worst CVE of the Year" by Security Experts
Critics call the Node.js EOL CVE a misuse of the system, sparking debate over CVE standards and the growing noise in vulnerability databases.
Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks.
Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks. Writes the results in a csv or json file and can be used both from the terminal or from a Python script. Calculates per-case mean Dice and weighted mean Dice, and per-label mean Dice, weighted mean Dice and Union Dice. The Union Dice for a label is the Dice Score calculated as if all the cases are concatenated into a single big case, aiming to balance out cases in which the Dice Score is 0 but have very few FP voxels or cases in which the Dice Score is 1 but have no positive voxels.
pip install --upgrade dice-score-3d
Simple usage (Python):
from dice_score_3d import dice_metrics
results_dict = dice_metrics(gt_dir, pred_dir, output_path=None, indices={'lung': 1, 'heart': 2}, suffix='.nii.gz')
# Write to csv:
dice_metrics(gt_dir, pred_dir, output_path='results.csv', indices={'lung': 1, 'heart': 2}, suffix='.nii.gz', num_workers=8)
Simple usage (terminal):
dice_score_3d GT.nii.gz PRED.nii.gz -output results.json -indices "{'lung': 1, 'heart': 2}" --console
dice_score_3d GT.nii.gz PRED.nii.gz -output results.json -indices indices.json
Complete documentation:
usage: dice_score_3d [-h] -output OUTPUT -indices INDICES [--reorient] [-dtype {uint8,uint16}] [-prefix PREFIX] [-suffix SUFFIX] [-num_workers NUM_WORKERS] [--console]
ground_truths predictions
DICE Score 3D
positional arguments:
ground_truths Path to Ground Truth. Can be a single file or a folder with all the GT volumes. The number of GT files must match the number of predictions. When passing a
folder of GT files, the name of the GT files must match the name of the predictions. This is not applicable when passing a single file. Supported file
formats: .nii, .nii.gz, .nrrd, .mha, .gipl.
predictions Path to Ground Truth. Can be a single file or a folder with all the predicted volumes. The number of prediction files must match the number of GT files. When
passing a folder of prediction files, the name of the prediction files must match the name of the GT files. This is not applicable when passing a single file.
Supported file formats: .nii, .nii.gz, .nrrd, .mha, .gipl.
options:
-h, --help show this help message and exit
-output OUTPUT The output path to write the computed metrics. Can be a csv or json file, depending on extension. Example: "results.csv", "results.json".
-indices INDICES Path to the json file describing the indices used for calculating the Dice Similarity Coefficient. Can also be a json string. Only the indices present in the
json are considered when evaluating the Dice Score. Example: "{"lung_left": 1, "lung_right": 2}".
--reorient Reorients both the GT and the prediction to the default "LPS" orientation before calculating the Dice Score.
-dtype {uint8,uint16}
Must be either "uint8" when having less than 255 classes, or "uint16" otherwise. Default: uint8.
-prefix PREFIX This parameter is used when the ground truth path is a folder. It filters all the files in the folder and selects only the files with this prefix.
-suffix SUFFIX This parameter is used when the ground truth path is a folder. It filters all the files in the folder and selects only the files with this suffix. Default: .nii.gz.
-num_workers NUM_WORKERS
Number of parallel processes to be used to calculate the Dice Score in parallel. Default: 0.
--console Also prints the Dice metrics to console.
FAQs
Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks.
We found that dice-score-3d demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
Critics call the Node.js EOL CVE a misuse of the system, sparking debate over CVE standards and the growing noise in vulnerability databases.
Security News
cURL and Go security teams are publicly rejecting CVSS as flawed for assessing vulnerabilities and are calling for more accurate, context-aware approaches.
Security News
Bun 1.2 enhances its JavaScript runtime with 90% Node.js compatibility, built-in S3 and Postgres support, HTML Imports, and faster, cloud-first performance.