data/pathml/utils.py

"""
Copyright 2021, Dana-Farber Cancer Institute and Weill Cornell Medicine
License: GNU GPL 2.0
"""

import os
import shutil
import tarfile
import urllib
from pathlib import Path

import cv2
import matplotlib.pyplot as plt
import numpy as np
from loguru import logger
from matplotlib.colors import TABLEAU_COLORS


def download_from_url(url, download_dir, name=None):
    """
    Download a file from a url to destination directory.
    If the file already exists, does not download.

    Args:
        url (str): Url of file to download
        download_dir (str): Directory where file will be downloaded
        name (str, optional): Name of saved file. If ``None``, uses base name of url argument. Defaults to ``None``.

    See: https://stackoverflow.com/questions/7243750/download-file-from-web-in-python-3
    """
    if name is None:
        name = os.path.basename(url)

    path = os.path.join(download_dir, name)

    if os.path.exists(path):
        print(f"File {name} already exists, skipping download.")
        return
    else:
        os.makedirs(download_dir, exist_ok=True)

        # Download the file from `url` and save it locally under `file_name`:
        with urllib.request.urlopen(url) as response, open(path, "wb") as out_file:
            shutil.copyfileobj(response, out_file)
        return path  # added when including qupath utils


def parse_file_size(fs):
    """
    Parse a file size string into bytes.
    """
    units = {"B": 1, "KB": 10**3, "MB": 10**6, "GB": 10**9, "TB": 10**12}
    number, unit = [s.strip() for s in fs.split()]
    return int(float(number) * units[unit.upper()])


def upsample_array(arr, factor):
    """
    Upsample array by a factor. Each element in input array will become a CxC block in the upsampled array, where
    C is the constant upsampling factor. From https://stackoverflow.com/a/32848377

    :param arr: input array to be upsampled
    :type arr: np.ndarray
    :param factor: Upsampling factor
    :type factor: int
    :return: np.ndarray
    """
    r, c = arr.shape  # number of rows/columns
    rs, cs = arr.strides  # row/column strides
    x = np.lib.stride_tricks.as_strided(
        arr, (r, factor, c, factor), (rs, 0, cs, 0)
    )  # view a as larger 4D array
    return x.reshape(r * factor, c * factor)  # create new 2D array


def pil_to_rgb(image_array_pil):
    """
    Convert PIL RGBA Image to numpy RGB array
    """
    image_array_rgba = np.asarray(image_array_pil)
    image_array = cv2.cvtColor(image_array_rgba, cv2.COLOR_RGBA2RGB).astype(np.uint8)
    return image_array


def segmentation_lines(mask_in):
    """
    Generate coords of points bordering segmentations from a given mask.
    Useful for plotting results of tissue detection or other segmentation.
    """
    assert (
        mask_in.dtype == np.uint8
    ), f"Input mask dtype {mask_in.dtype} must be np.uint8"
    kernel = np.ones((3, 3), np.uint8)
    dilated = cv2.dilate(mask_in, kernel)
    diff = np.logical_xor(dilated.astype(bool), mask_in.astype(bool))
    y, x = np.nonzero(diff)
    return x, y


def plot_mask(im, mask_in, ax=None, color="red", downsample_factor=None):
    """
    plot results of segmentation, overlaying on original image_ref

    :param im: Original RGB image_ref
    :type im: np.ndarray
    :param mask_in: Boolean array of segmentation mask, with True values for masked pixels. Must be same shape as im.
    :type mask_in: np.ndarray
    :param ax: Matplotlib axes object to plot on. If None, creates a new plot. Defaults to None.
    :param color: Color to plot outlines of mask. Defaults to "red". Must be recognized by matplotlib.
    :param downsample_factor: Downsample factor for image_ref and mask to speed up plotting for big images
    """
    if downsample_factor:
        mask_in = mask_in[::downsample_factor, ::downsample_factor]
        im = im[::downsample_factor, ::downsample_factor]

    x, y = segmentation_lines(mask_in)
    if ax is None:
        fig, ax = plt.subplots()
    ax.imshow(im)
    ax.scatter(x, y, color=color, marker=".", s=1)
    ax.axis("off")
    return ax


def contour_centroid(contour):
    """
    Return the centroid of a contour, calculated using moments.
    From `OpenCV implementation <https://docs.opencv.org/3.4/d0/d49/tutorial_moments.html>`_

    :param contour: Contour array as returned by cv2.findContours
    :type contour: np.array
    :return: (x, y) coordinates of centroid.
    :rtype: tuple
    """
    # from the docs: "Note that the numpy type for the input array should be either np.int32 or np.float32"
    assert contour.dtype == np.float32
    # get the moments
    mu = cv2.moments(contour)
    # get the centers of mass
    # add 1e-5 to avoid division by zero
    i, j = (mu["m10"] / (mu["m00"] + 1e-5), mu["m01"] / (mu["m00"] + 1e-5))
    return i, j


def sort_points_clockwise(points):
    """
    Sort a list of points into clockwise order around centroid, ordering by angle with centroid and x-axis.
    After sorting, we can pass the points to cv2 as a contour.
    Centroid is defined as center of bounding box around points.

    :param points: Array of points (N x 2)
    :type points: np.ndarray
    :return: Array of points, sorted in order by angle with centroid (N x 2)
    :rtype: np.ndarray

    Return sorted points
    """
    # identify centroid as point in center of box bounding all points
    x, y, w, h = cv2.boundingRect(points)
    centroid = (x + w // 2, y + h // 2)
    # get angle of vector between point and centroid
    diffs = [point - centroid for point in points]
    angles = [np.arctan2(d[0], d[1]) for d in diffs]
    # sort by angle to order points around the circle
    return points[np.argsort(angles)]


def _pad_or_crop_1d(array, axis, target_dim):
    """
    Modify shape of input array at target axis by zero-padding or cropping.

    :param array: Input array
    :type array: np.ndarray
    :param axis: Index of target axis
    :type axis: int
    :param target_dim: target size of specified axis
    :return: np.ndarray
    """
    in_dim = array.shape[axis]
    if in_dim == target_dim:
        # no action needed
        return array
    diff = target_dim - in_dim
    offset = (int(np.floor(abs(diff) / 2)), int(np.ceil(abs(diff) / 2)))
    if diff > 0:
        # pad
        n_pad = [(0, 0)] * array.ndim
        n_pad[axis] = offset
        return np.pad(array, pad_width=n_pad, mode="constant", constant_values=0)
    else:
        # crop
        # need to use slice(none) to access only target dimension
        slc = [slice(None)] * array.ndim
        slc[axis] = slice(offset[0], -offset[1])
        array = array[tuple(slc)]
        return array


def pad_or_crop(array, target_shape):
    """
    Make dimensions of input array match target shape by either zero-padding or cropping each axis.

    :param array: Input array
    :type array: np.ndarray
    :param target_shape: Target shape of output
    :type target_shape: tuple
    :return: Input array cropped/padded to match target_shape
    :rtype: np.ndarray
    """
    if array.shape == target_shape:
        # no need to do anything
        return array

    for axis, target in enumerate(target_shape):
        array = _pad_or_crop_1d(array, axis=axis, target_dim=target)
    return array


def RGB_to_HSI(imarr):
    """
    Convert imarr from RGB to HSI colorspace.

    :param imarr: numpy array of RGB image_ref (m, n, 3)
    :type imarr: np.ndarray
    :return: numpy array of HSI image_ref (m, n, 3)
    :rtype: np.ndarray

    References:
        http://eng.usf.edu/~hady/courses/cap5400/rgb-to-hsi.pdf
    """
    assert imarr.dtype == np.uint8, f"Input image dtype {imarr.dtype} must be np.uint8"
    R = imarr[:, :, 0]
    G = imarr[:, :, 1]
    B = imarr[:, :, 2]
    # add some noise to avoid divide by zero
    eps = 1e-6
    patch_sum = np.sum(imarr, axis=2) + eps
    r = R / patch_sum
    g = G / patch_sum
    b = B / patch_sum
    h = np.zeros_like(r, dtype=np.float32)
    # when R=G=B, we need to assign h=0 otherwise we get divide by 0
    h_0 = np.logical_and(R == G, G == B)
    num_h = 0.5 * ((r[~h_0] - g[~h_0]) + (r[~h_0] - b[~h_0]))
    denom_h = np.sqrt(
        (r[~h_0] - g[~h_0]) ** 2 + (r[~h_0] - b[~h_0]) * (g[~h_0] - b[~h_0])
    )
    h[~h_0] = np.arccos(num_h / denom_h)
    h[B > G] = 2 * np.pi - h[B > G]
    h = h / (2.0 * np.pi)
    patch_norm = np.stack([r, g, b], axis=2)
    s = 1 - 3 * np.amin(patch_norm, axis=2)
    patchsum = np.sum(imarr, axis=2)
    i = patchsum / (3 * 255)
    out = np.stack([h, s, i], axis=2)
    return out


def RGB_to_OD(imarr):
    """
    Convert input image from RGB space to optical density (OD) space.
    `OD = -log(I)`, where I is the input image in RGB space.

    :param imarr: Image array, RGB format
    :type imarr: numpy.ndarray
    :return: Image array, OD format
    :rtype: numpy.ndarray
    """
    assert imarr.dtype == np.uint8, f"Input image dtype {imarr.dtype} must be np.uint8"
    # need to account for possible zero values
    OD = -np.log((imarr.astype(np.float32) + 1) / 255.0)
    return OD


def RGB_to_HSV(imarr):
    """convert image from RGB to HSV"""
    assert imarr.dtype == np.uint8, f"Input image dtype {imarr.dtype} must be np.uint8"
    hsv = cv2.cvtColor(imarr, cv2.COLOR_RGB2HSV)
    return hsv


def RGB_to_LAB(imarr):
    """convert image from RGB to LAB color space"""
    assert imarr.dtype == np.uint8, f"Input image dtype {imarr.dtype} must be np.uint8"
    imarr_float32 = imarr.astype(np.float32) / 255
    lab = cv2.cvtColor(imarr_float32, cv2.COLOR_RGB2Lab)
    return lab


def RGB_to_GREY(imarr):
    """convert image_ref from RGB to HSV"""
    assert imarr.dtype == np.uint8, f"Input image dtype {imarr.dtype} must be np.uint8"
    grey = cv2.cvtColor(imarr, cv2.COLOR_RGB2GRAY)
    return grey


def normalize_matrix_rows(A):
    """
    Normalize the rows of an array.

    :param A: Input array.
    :type A: np.ndarray
    :return: Array with rows normalized.
    :rtype: np.ndarray
    """
    return A / np.linalg.norm(A, axis=1)[:, None]


def normalize_matrix_cols(A):
    """
    Normalize the columns of an array.

    :param A: An array
    :type A: np.ndarray
    :return: Array with columns normalized
    :rtype: np.ndarray
    """
    return A / np.linalg.norm(A, axis=0)[None, :]


def plot_segmentation(ax, masks, palette=None, markersize=5):
    """
    Plot segmentation contours. Supports multi-class masks.

    Args:
        ax: matplotlib axis
        masks (np.ndarray): Mask array of shape (n_masks, H, W). Zeroes are background pixels.
        palette: color palette to use. if None, defaults to matplotlib.colors.TABLEAU_COLORS
        markersize (int): Size of markers used on plot. Defaults to 5
    """
    assert masks.ndim == 3
    n_channels = masks.shape[0]

    if palette is None:
        palette = list(TABLEAU_COLORS.values())

    nucleus_labels = list(np.unique(masks))
    if 0 in nucleus_labels:
        nucleus_labels.remove(0)  # background
    # plot each individual nucleus
    for label in nucleus_labels:
        for i in range(n_channels):
            nuclei_mask = masks[i, ...] == label
            x, y = segmentation_lines(nuclei_mask.astype(np.uint8))
            ax.scatter(x, y, color=palette[i], marker=".", s=markersize)


def _test_log(msg):
    # passes thru message to pathml logger
    # used for testing logging
    logger.info(msg)


def find_qupath_home(start_path):
    """
    Search for the QuPath home directory by looking for .jar files within the given start path.

    Args:
        start_path (str): The starting directory path from which to begin the search.

    Returns:
        str or None: The absolute path of the QuPath home directory if found; otherwise, None.
    """

    for root, dirs, files in os.walk(start_path):
        if any("qupath" in file.lower() and file.endswith(".jar") for file in files):
            return str(Path(root).parent.parent)
    return None


def setup_qupath(qupath_home=None):
    """
    Set up the QuPath environment by downloading and extracting it if not already installed.

    This function checks for an existing QuPath installation in the specified directory.
    If not found, it downloads QuPath from its official release page and extracts it.

    Args:
        qupath_home (str, optional): The directory path where QuPath is or will be installed.
                                     Defaults to '~/tools/qupath' if None.

    Returns:
        str: The path to the QuPath home directory after setting it up.
    """

    default_path = str(Path.home() / "tools/qupath")
    qupath_home = qupath_home if qupath_home is not None else default_path
    Path(qupath_home).mkdir(parents=True, exist_ok=True)

    # Check for existing QuPath installation
    existing_qupath_home = find_qupath_home(qupath_home)
    if existing_qupath_home:
        return existing_qupath_home

    print("Downloading")
    # URL and name of QuPath tarball
    # qupath_url = "https://github.com/qupath/qupath/releases/download/v0.3.0/QuPath-0.3.0-Linux.tar.xz"
    qupath_url = "https://github.com/qupath/qupath/releases/download/v0.4.3/QuPath-0.4.3-Linux.tar.xz"
    qupath_tar_name = "QuPath-0.4.3-Linux.tar.xz"
    tar_path = download_from_url(qupath_url, qupath_home, qupath_tar_name)

    # Extract QuPath if the tarball was downloaded
    if tar_path:
        print("Extracting QuPath...")
        with tarfile.open(tar_path) as tar:
            tar.extractall(path=qupath_home)
        os.remove(tar_path)

    # Find the QuPath home by searching for jar files
    return find_qupath_home(qupath_home)