panoptica.utils
panoptica.metrics.assd
- panoptica.metrics.assd.__surface_distances(reference, prediction, voxelspacing=None, connectivity=1)
The distances between the surface voxel of binary objects in result and their nearest partner surface voxel of a binary object in reference.
- panoptica.metrics.assd._average_surface_distance(reference, prediction, voxelspacing=None, connectivity=1)
- panoptica.metrics.assd._average_symmetric_surface_distance(reference, prediction, voxelspacing=None, connectivity=1, *args) float
ASSD is computed by computing the average of the bidrectionally computed ASD.
- panoptica.metrics.assd._distance_transform_edt(input_array: ndarray, sampling=None, return_distances=True, return_indices=False)
panoptica.metrics.dice
- panoptica.metrics.dice._compute_dice_coefficient(reference: ndarray, prediction: ndarray, *args) float
Compute the Dice coefficient between two binary masks.
The Dice coefficient measures the similarity or overlap between two binary masks. It is defined as:
Dice = (2 * intersection) / (area_mask1 + area_mask2)
- Parameters:
reference (np.ndarray) – Reference binary mask.
prediction (np.ndarray) – Prediction binary mask.
- Returns:
Dice coefficient between the two binary masks. A value between 0 and 1, where higher values indicate better overlap and similarity between masks.
- Return type:
float
- panoptica.metrics.dice._compute_instance_volumetric_dice(ref_labels: ndarray, pred_labels: ndarray, ref_instance_idx: int, pred_instance_idx: int) float
Compute the Dice coefficient between a specific pair of instances.
The Dice coefficient measures the similarity or overlap between two binary masks representing instances. It is defined as:
Dice = (2 * intersection) / (ref_area + pred_area)
- Parameters:
ref_labels (np.ndarray) – Reference instance labels.
pred_labels (np.ndarray) – Prediction instance labels.
ref_instance_idx (int) – Index of the reference instance.
pred_instance_idx (int) – Index of the prediction instance.
- Returns:
Dice coefficient between the specified instances. A value between 0 and 1, where higher values indicate better overlap and similarity between instances.
- Return type:
float
panoptica.metrics.iou
- panoptica.metrics.iou._compute_instance_iou(reference_arr: ndarray, prediction_arr: ndarray, ref_instance_idx: int, pred_instance_idx: int) float
Compute Intersection over Union (IoU) between a specific pair of reference and prediction instances.
- Parameters:
ref_labels (np.ndarray) – Reference instance labels.
pred_labels (np.ndarray) – Prediction instance labels.
ref_instance_idx (int) – Index of the reference instance.
pred_instance_idx (int) – Index of the prediction instance.
- Returns:
IoU between the specified instances.
- Return type:
float
- panoptica.metrics.iou._compute_iou(reference_arr: ndarray, prediction_arr: ndarray, *args) float
Compute Intersection over Union (IoU) between two masks.
- Parameters:
reference (np.ndarray) – Reference mask.
prediction (np.ndarray) – Prediction mask.
- Returns:
IoU between the two masks. A value between 0 and 1, where higher values indicate better overlap and similarity between masks.
- Return type:
float