envs/kitoverlay/skimage/feature/_basic_features.py

from itertools import combinations_with_replacement
import itertools
import numpy as np
from skimage import filters, feature
from skimage.util.dtype import img_as_float32
from .._shared._dependency_checks import is_wasm

if not is_wasm:
    from concurrent.futures import ThreadPoolExecutor as PoolExecutor
else:
    from contextlib import AbstractContextManager

    # Threading isn't supported on WASM, mock ThreadPoolExecutor as a fallback
    class PoolExecutor(AbstractContextManager):
        def __init__(self, *_, **__):
            pass

        def __exit__(self, exc_type, exc_val, exc_tb):
            pass

        def map(self, fn, iterables):
            return map(fn, iterables)


def _texture_filter(gaussian_filtered):
    H_elems = [
        np.gradient(np.gradient(gaussian_filtered)[ax0], axis=ax1)
        for ax0, ax1 in combinations_with_replacement(range(gaussian_filtered.ndim), 2)
    ]
    eigvals = feature.hessian_matrix_eigvals(H_elems)
    return eigvals


def _singlescale_basic_features_singlechannel(
    img, sigma, intensity=True, edges=True, texture=True
):
    results = ()
    gaussian_filtered = filters.gaussian(img, sigma=sigma, preserve_range=False)
    if intensity:
        results += (gaussian_filtered,)
    if edges:
        results += (filters.sobel(gaussian_filtered),)
    if texture:
        results += (*_texture_filter(gaussian_filtered),)
    return results


def _mutiscale_basic_features_singlechannel(
    img,
    intensity=True,
    edges=True,
    texture=True,
    sigma_min=0.5,
    sigma_max=16,
    num_sigma=None,
    workers=None,
):
    """Features for a single channel nd image.

    Parameters
    ----------
    img : ndarray
        Input image, which can be grayscale or multichannel.
    intensity : bool, default True
        If True, pixel intensities averaged over the different scales
        are added to the feature set.
    edges : bool, default True
        If True, intensities of local gradients averaged over the different
        scales are added to the feature set.
    texture : bool, default True
        If True, eigenvalues of the Hessian matrix after Gaussian blurring
        at different scales are added to the feature set.
    sigma_min : float, optional
        Smallest value of the Gaussian kernel used to average local
        neighborhoods before extracting features.
    sigma_max : float, optional
        Largest value of the Gaussian kernel used to average local
        neighborhoods before extracting features.
    num_sigma : int, optional
        Number of values of the Gaussian kernel between sigma_min and sigma_max.
        If None, sigma_min multiplied by powers of 2 are used.
    workers : int or None, optional
        The number of parallel threads to use. If set to ``None``, the full
        set of available cores are used.

    Returns
    -------
    features : list
        List of features, each element of the list is an array of shape as img.
    """
    # computations are faster as float32
    img = np.ascontiguousarray(img_as_float32(img))
    if num_sigma is None:
        num_sigma = int(np.log2(sigma_max) - np.log2(sigma_min) + 1)
    sigmas = np.logspace(
        np.log2(sigma_min),
        np.log2(sigma_max),
        num=num_sigma,
        base=2,
        endpoint=True,
    )
    with PoolExecutor(max_workers=workers) as ex:
        out_sigmas = list(
            ex.map(
                lambda s: _singlescale_basic_features_singlechannel(
                    img, s, intensity=intensity, edges=edges, texture=texture
                ),
                sigmas,
            )
        )
    features = itertools.chain.from_iterable(out_sigmas)
    return features


def multiscale_basic_features(
    image,
    intensity=True,
    edges=True,
    texture=True,
    sigma_min=0.5,
    sigma_max=16,
    num_sigma=None,
    workers=None,
    *,
    channel_axis=None,
):
    """Local features for a single- or multi-channel nd image.

    Intensity, gradient intensity and local structure are computed at
    different scales thanks to Gaussian blurring.

    Parameters
    ----------
    image : ndarray
        Input image, which can be grayscale or multichannel.
    intensity : bool, default True
        If True, pixel intensities averaged over the different scales
        are added to the feature set.
    edges : bool, default True
        If True, intensities of local gradients averaged over the different
        scales are added to the feature set.
    texture : bool, default True
        If True, eigenvalues of the Hessian matrix after Gaussian blurring
        at different scales are added to the feature set.
    sigma_min : float, optional
        Smallest value of the Gaussian kernel used to average local
        neighborhoods before extracting features.
    sigma_max : float, optional
        Largest value of the Gaussian kernel used to average local
        neighborhoods before extracting features.
    num_sigma : int, optional
        Number of values of the Gaussian kernel between sigma_min and sigma_max.
        If None, sigma_min multiplied by powers of 2 are used.
    workers : int or None, optional
        The number of parallel threads to use. If set to ``None``, the full
        set of available cores are used.
    channel_axis : int or None, optional
        If None, the image is assumed to be a grayscale (single channel) image.
        Otherwise, this parameter indicates which axis of the array corresponds
        to channels.

        .. versionadded:: 0.19
           ``channel_axis`` was added in 0.19.

    Returns
    -------
    features : np.ndarray
        Array of shape ``image.shape + (n_features,)``. When `channel_axis` is
        not None, all channels are concatenated along the features dimension.
        (i.e. ``n_features == n_features_singlechannel * n_channels``)
    """
    if not any([intensity, edges, texture]):
        raise ValueError(
            "At least one of `intensity`, `edges` or `textures`"
            "must be True for features to be computed."
        )
    if channel_axis is None:
        image = image[..., np.newaxis]
        channel_axis = -1
    elif channel_axis != -1:
        image = np.moveaxis(image, channel_axis, -1)

    all_results = (
        _mutiscale_basic_features_singlechannel(
            image[..., dim],
            intensity=intensity,
            edges=edges,
            texture=texture,
            sigma_min=sigma_min,
            sigma_max=sigma_max,
            num_sigma=num_sigma,
            workers=workers,
        )
        for dim in range(image.shape[-1])
    )
    features = list(itertools.chain.from_iterable(all_results))
    out = np.stack(features, axis=-1)
    return out