Source code for AFQ.tractography.utils

import logging
import dipy.tracking.utils as dtu
import numpy as np


logger = logging.getLogger('AFQ')


def get_percentile_threshold(mask, threshold):
    zero_mask = mask == 0
    mask[zero_mask] = np.nan
    new_threshold = np.nanpercentile(
        mask,
        100 - threshold)
    mask[zero_mask] = 0
    return new_threshold


def gen_seeds(seed_mask, seed_threshold,
              n_seeds, thresholds_as_percentages,
              random_seeds, rng_seed, affine):
    """
    Generate seeds for tracking. For parameters, see
    :func:`AFQ.tractography.tractography.track`.
    """
    logger.info("Generating Seeds...")
    if isinstance(n_seeds, int):
        if len(np.unique(seed_mask)) > 2:
            if thresholds_as_percentages:
                seed_threshold = get_percentile_threshold(
                    seed_mask, seed_threshold)
            seed_mask = seed_mask > seed_threshold
        if random_seeds:
            seeds = dtu.random_seeds_from_mask(seed_mask, seeds_count=n_seeds,
                                               seed_count_per_voxel=False,
                                               affine=affine,
                                               random_seed=rng_seed)
        else:
            seeds = dtu.seeds_from_mask(seed_mask,
                                        density=n_seeds,
                                        affine=affine)
    else:
        # If user provided an array, we'll use n_seeds as the seeds:
        seeds = n_seeds
    return seeds