https://github.com/ancestor-mithril/dice-score-3d

Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks
https://github.com/ancestor-mithril/dice-score-3d

dice-score dice-similarity-coefficient medical-imaging-dice

Last synced: 3 months ago
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Utility for calculating the Dice Similarity Coefficient (DSC) for 3D segmentation masks

• Host: GitHub
• URL: https://github.com/ancestor-mithril/dice-score-3d
• Owner: ancestor-mithril
• License: mit
• Created: 2024-07-11T08:45:26.000Z (6 months ago)
• Default Branch: master
• Last Pushed: 2024-08-07T10:59:06.000Z (5 months ago)
• Last Synced: 2024-10-12T05:46:27.232Z (3 months ago)
• Topics: dice-score, dice-similarity-coefficient, medical-imaging-dice
• Language: Python
• Homepage:
• Size: 73.2 KB
• Stars: 3
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# dice-score-3d

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.

## Installation

```

pip install --upgrade dice-score-3d

```

## Usage

Simple usage (Python):

```py

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.

```