<reponame>acorbin3/derm_ita<gh_stars>0
import math
import numpy as np
from PIL import Image
import skimage
from patchify import patchify

from derm_ita.boarder_removal import get_border_removal_size


def compute_ita_from_lab(lab):
    """
    This function computes the ITA value of the image along with ignore any pixels that are completely black
    """
    # get the luminance and b values wihtin +- 1 std from mean
    l = lab[:, :, 0]
    l = np.where(l != 0, l, np.nan)
    std = np.nanstd(l)
    mean = np.nanmean(l)

    l = np.where(l >= mean - std, l, np.nan)
    l = np.where(l <= mean + std, l, np.nan)

    b = lab[:, :, 2]
    std = np.nanstd(b)
    mean = np.nanmean(b)
    b = np.where(b >= mean - std, b, np.nan)
    b = np.where(b <= mean + std, b, np.nan)

    ita = math.atan2(np.nanmean(l) - 50, np.nanmean(b)) * (180 / np.pi)
    return ita





def format_image_and_get_lab_patches(image: Image, patch_width: int = 8, remove_boarder: bool = True,
                                     border_removal_percentage: float = 0.04):
    """
    This function will remove the boarder, convert the whole image from RGB to LAB and then using Patchify
    tool it will create patches. These patches are non-overlapping that create a grid over the whole image.

    :param image: input image
    :param patch_width: the width size of the patches in pixels.
    :param remove_boarder: The flag to determine if the boarder should be removed
    :param border_removal_percentage: how much of the boarder to remove
    :return: A list of patches that are in a LAB format
    """

    # Crop image to remove the pixels from the boarder
    if remove_boarder:
        w, h = image.size
        removal_size = get_border_removal_size(image, border_removal_percentage, patch_width)
        cropped_area = (removal_size, removal_size, w - removal_size, h - removal_size)
        cropped_image = image.crop(cropped_area)
    else:
        cropped_image = image

    # Convert image to lab values
    lab = np.array(skimage.color.rgb2lab(cropped_image))

    # Get the patches
    return patchify(lab, (patch_width, patch_width, 3), step=patch_width)


def compute_ita_from_lab(lab_image):
    """
    This function computes the ITA value of the image along with ignore any pixels that are completely black
    :param lab_image:  input image formatted in LAB color space
    :return: the ITA value from the input image
    """
    # get the luminance and b values wihtin +- 1 std from mean
    l = lab_image[:, :, 0]
    l = np.where(l != 0, l, np.nan)
    std = np.nanstd(l)
    mean = np.nanmean(l)

    l = np.where(l >= mean - std, l, np.nan)
    l = np.where(l <= mean + std, l, np.nan)

    b = lab_image[:, :, 2]
    std = np.nanstd(b)
    mean = np.nanmean(b)
    b = np.where(b >= mean - std, b, np.nan)
    b = np.where(b <= mean + std, b, np.nan)

    ita = math.atan2(np.nanmean(l) - 50, np.nanmean(b)) * (180 / np.pi)
    return ita

import math
import numpy as np
from PIL import Image
import skimage
from patchify import patchify

from derm_ita.boarder_removal import get_border_removal_size


def compute_ita_from_lab(lab):
    """
    This function computes the ITA value of the image along with ignore any pixels that are completely black
    """
    # get the luminance and b values wihtin +- 1 std from mean
    l = lab[:, :, 0]
    l = np.where(l != 0, l, np.nan)
    std = np.nanstd(l)
    mean = np.nanmean(l)

    l = np.where(l >= mean - std, l, np.nan)
    l = np.where(l <= mean + std, l, np.nan)

    b = lab[:, :, 2]
    std = np.nanstd(b)
    mean = np.nanmean(b)
    b = np.where(b >= mean - std, b, np.nan)
    b = np.where(b <= mean + std, b, np.nan)

    ita = math.atan2(np.nanmean(l) - 50, np.nanmean(b)) * (180 / np.pi)
    return ita





def format_image_and_get_lab_patches(image: Image, patch_width: int = 8, remove_boarder: bool = True,
                                     border_removal_percentage: float = 0.04):
    """
    This function will remove the boarder, convert the whole image from RGB to LAB and then using Patchify
    tool it will create patches. These patches are non-overlapping that create a grid over the whole image.

    :param image: input image
    :param patch_width: the width size of the patches in pixels.
    :param remove_boarder: The flag to determine if the boarder should be removed
    :param border_removal_percentage: how much of the boarder to remove
    :return: A list of patches that are in a LAB format
    """

    # Crop image to remove the pixels from the boarder
    if remove_boarder:
        w, h = image.size
        removal_size = get_border_removal_size(image, border_removal_percentage, patch_width)
        cropped_area = (removal_size, removal_size, w - removal_size, h - removal_size)
        cropped_image = image.crop(cropped_area)
    else:
        cropped_image = image

    # Convert image to lab values
    lab = np.array(skimage.color.rgb2lab(cropped_image))

    # Get the patches
    return patchify(lab, (patch_width, patch_width, 3), step=patch_width)


def compute_ita_from_lab(lab_image):
    """
    This function computes the ITA value of the image along with ignore any pixels that are completely black
    :param lab_image:  input image formatted in LAB color space
    :return: the ITA value from the input image
    """
    # get the luminance and b values wihtin +- 1 std from mean
    l = lab_image[:, :, 0]
    l = np.where(l != 0, l, np.nan)
    std = np.nanstd(l)
    mean = np.nanmean(l)

    l = np.where(l >= mean - std, l, np.nan)
    l = np.where(l <= mean + std, l, np.nan)

    b = lab_image[:, :, 2]
    std = np.nanstd(b)
    mean = np.nanmean(b)
    b = np.where(b >= mean - std, b, np.nan)
    b = np.where(b <= mean + std, b, np.nan)

    ita = math.atan2(np.nanmean(l) - 50, np.nanmean(b)) * (180 / np.pi)
    return ita
This function computes the ITA value of the image along with ignore any pixels that are completely black # get the luminance and b values wihtin +- 1 std from mean This function will remove the boarder, convert the whole image from RGB to LAB and then using Patchify     tool it will create patches. These patches are non-overlapping that create a grid over the whole image.      :param image: input image     :param patch_width: the width size of the patches in pixels.     :param remove_boarder: The flag to determine if the boarder should be removed     :param border_removal_percentage: how much of the boarder to remove     :return: A list of patches that are in a LAB format # Crop image to remove the pixels from the boarder # Convert image to lab values # Get the patches This function computes the ITA value of the image along with ignore any pixels that are completely black     :param lab_image:  input image formatted in LAB color space     :return: the ITA value from the input image # get the luminance and b values wihtin +- 1 std from mean