login.py

def apply_mask(
    img: Union[np.ndarray, pv.Image], mask: Union[np.ndarray, pv.Image]
) -> Union[np.ndarray, pv.Image]:
    """
    Applies a binary mask to an image using PyVips.

    Parameters
    ----------
    img : np.ndarray
        Image as a NumPy array.
    mask : np.ndarray
        Binary mask as a NumPy array (same dimensions as img).

    Returns
    -------
    np.ndarray
        Image with the mask applied.
    """
    if isinstance(img, np.ndarray):
        # Convert numpy array to pyvips Image
        vips_img = pv.Image.new_from_array(img)
    else:
        vips_img = img
    if isinstance(mask, np.ndarray):
        # Convert numpy array to pyvips Image
        vips_mask = pv.Image.new_from_array(mask)
    else:
        vips_mask = mask

    # Convert numpy arrays to pyvips images
    vips_img = pv.Image.new_from_array(img)
    vips_mask = pv.Image.new_from_array(mask)

    # Create a masked image using PyVips
    masked_img = vips_img * vips_mask

    # Convert the PyVips image back to a numpy array
    if isinstance(img, np.ndarray):
        return masked_img.numpy()
    return masked_img

def dicomread(
    image_path: Union[os.PathLike, str], as_dataset=False
) -> Union[np.ndarray, pydicom.Dataset]:
    """Reads a dicom from a file.

    Parameters
    ----------
    image_path : os.PathLike or str
        Path to a dicom file.

    Returns
    -------
    np.ndarray or pydicom.Dataset
        Array of pixel values, or Dataset if as_dataset=True.
    """
    if as_dataset:
        return pydicom.dcmread(image_path)
    return pydicom.dcmread(image_path).pixel_array

def dicomread_volume(
    dicom_dir: Union[os.PathLike, str, list[Union[io.BytesIO, os.PathLike, str]]],
    as_sequence=False,
) -> Union[np.ndarray, pydicom.Sequence]:
    """Reads a dicom series from a directory.

    Parameters
    ----------
    dicom_dir : os.PathLike or str or list[io.BytesIO or os.PathLike or str]
        Path to directory with the dicoms or list of dicoms as path or bytes.
    as_sequence : bool, optional
        If True, returns a pydicom sequence of pydicom datasets, by default False.

    Returns
    -------
    np.ndarray or pydicom.Sequence
        Dicom series as numpy volume, or Sequence if as_sequence=True.
    """

    # Get a list of all DICOM files in the directory
    if isinstance(dicom_dir, list):
        dicom_files = dicom_dir
    else:
        dicom_files = [
            os.path.join(dicom_dir, filename)
            for filename in os.listdir(dicom_dir)
            if filename.endswith(".dcm")
        ]
        if not dicom_files:
            dicom_files = [
                os.path.join(dicom_dir, filename) for filename in os.listdir(dicom_dir)
            ]

    dicoms = []
    for file in dicom_files:
        try:
            dicoms.append(pydicom.dcmread(file))
        except InvalidDicomError:
            LOGGER.warning(f"Invalid DICOM file: {file}")

    if len(dicoms) == 0:
        raise ValueError("No valid DICOM files found in the directory.")
    if len({ds.SeriesInstanceUID for ds in dicoms}) != 1:
        raise ValueError("All DICOM files must belong to the same series.")

    dicoms.sort(key=lambda x: x.InstanceNumber)
    if as_sequence:
        return pydicom.Sequence(dicoms)

    # Read the first DICOM file to get image dimensions
    first_ds = dicoms[0]
    rows = int(first_ds.Rows)
    columns = int(first_ds.Columns)
    slices = len(dicoms)

    # Initialize a 3D array to store pixel data
    volume = np.zeros((rows, columns, slices), dtype=np.uint16)

    # Read each DICOM file and store pixel data in the volume array
    for i, ds in enumerate(dicoms):
        volume[:, :, i] = ds.pixel_array
    return volume

def dicomseg_to_nifti_vol(dicom_seg_ds: hd.seg.Segmentation) -> np.ndarray:
    """
    Converts a DICOM Segmentation object to a 3D numpy array.

    Parameters
    ----------
    dicom_seg_ds : hd.seg.Segmentation
        DICOM Segmentation object.

    Returns
    -------
    np.ndarray
        3D numpy array of the segmentation.
    """
    rows, cols = dicom_seg_ds.Rows, dicom_seg_ds.Columns
    slice_count = len(
        dicom_seg_ds.ReferencedSeriesSequence[0].ReferencedInstanceSequence
    )
    full_dims = (slice_count, rows, cols)
    full_vol = np.zeros(full_dims)

    for i, frame in enumerate(dicom_seg_ds.PerFrameFunctionalGroupsSequence):
        slice_idx = frame.FrameContentSequence[0].DimensionIndexValues[1]
        full_vol[slice_idx] = dicom_seg_ds.pixel_array[i]
    # lps to ras
    full_vol = np.flip(full_vol, axis=0)
    full_vol = np.flip(full_vol, axis=1)
    full_vol = full_vol.transpose((2, 1, 0))
    return full_vol

def dicomsegread(
    image_path: Union[os.PathLike, str], as_volume: True
) -> Union[np.ndarray, hd.seg.Segmentation]:
    """Reads a dicom segmentation from a file.

    Parameters
    ----------
    image_path : os.PathLike or str
        Path to a dicom segmentation file.

    Returns
    -------
    np.ndarray
        Array of pixel values.
    """
    dicom_seg = hd.seg.segread(image_path)
    if as_volume:
        return dicomseg_to_nifti_vol(dicom_seg)
    return dicom_seg.pixel_array

def dicomwrite(
    img: Union[np.ndarray, pydicom.Dataset],
    path: Union[os.PathLike, str],
    write_like_original: bool = False,
) -> str:
    """Writes an image to path. kwargs are passthrough to wrapped function.

    Parameters
    ----------
    img : np.ndarray or pydicom.Dataset
        Numpy array or Dicom dataset. If array, Dicom dataset is created.
    path : os.PathLike or str
        Path to desired file.
    kwargs : dict
        Additional arguments to pass to pydicom.dcmwrite.

    Returns
    -------
    str
        Path of newly created file.
    """
    path = str(path)
    if not path.endswith(".dcm"):
        LOGGER.warning(
            "Dicom extension not detected in path! Dicoms should end in .dcm! Appending .dcm..."
        )
        path += ".dcm"
    if isinstance(img, np.ndarray):
        LOGGER.warning(
            "Chances are you won't be adding all the metadata you want and need by passing a numpy array to dicomwrite! Use pydicom.Dataset instead! Converting to a Dataset and continuing"  # pylint: disable=line-too-long
        )
        img = pydicom.Dataset()
        img.PixelData = img.tobytes()
        img.Rows, img.Columns = img.shape
    pydicom.dcmwrite(path, img, write_like_original)
    return path

def draw_shapes(
    img: Union[np.ndarray, pv.Image],
    shape_points: list[tuple[int, tuple[int, int, int], list[tuple[int, int]]]],
) -> Union[np.ndarray, pv.Image]:
    """
    Draws a list of shape points onto the input image using PyVips with SVG xml.

    Warnings
    --------
       No safety checks! Make sure img and shape_points are for the same downsample factor!

    Parameters
    ----------
    img : Union[np.ndarray, pyvips.Image]
        Input image as a NumPy array or pyvips Image.
    shape_points : List[Tuple[int, Tuple[int, int, int], List[Tuple[int, int]]]]
        List of tuples containing shape ID, RGB color, and list of points.
        Expected to use output from lavlab.omero_util.getShapesAsPoints.

    Returns
    -------
    Union[np.ndarray, pyvips.Image]
        Modified image with shapes drawn, same type as input.
    """
    if isinstance(img, np.ndarray):
        # Convert numpy array to pyvips Image
        pv_img = pv.Image.new_from_array(img)
    else:
        pv_img = img

    width = pv_img.width
    height = pv_img.height
    svg_header = (
        f'<svg viewBox="0 0 {width} {height}" '
        f'xmlns="http://www.w3.org/2000/svg" '
        f'shape-rendering="crispEdges">'
    )
    svg_shapes = ""

    for _, rgb, xy in shape_points:
        hex_color = f"#{rgb[0]:02x}{rgb[1]:02x}{rgb[2]:02x}"
        points = " ".join([f"{x},{y}" for y, x in xy])
        svg_shapes += f'<polygon points="{points}" fill="{hex_color}"/>'

    svg_footer = "</svg>"
    svg = svg_header + svg_shapes + svg_footer
    svg_img = pv.Image.svgload_buffer(svg.encode("utf-8"))

    # Composite the SVG image over the original image
    composite_img = pv_img.composite2(svg_img, "over", x=0, y=0)

    # Return the modified image in the same type as the input
    if isinstance(img, np.ndarray):
        return composite_img.numpy()
    return composite_img

def edge(img_arr: np.ndarray, method: str = "SOBEL", **kwargs) -> np.ndarray:
    """Edge detection.

    Parameters
    ----------
    img_arr : np.ndarray
        Input image as a numpy array.
    method : str, optional
        One of the enumerated methods: SOBEL, PREWITT, ROBERTS, CANNY. Defaults to SOBEL.

    Returns
    -------
    np.ndarray
        Edge map.
    """
    function = getattr(EdgeDetectionMethods, method, None)
    if function is None:
        raise KeyError(f"{method} is not a valid edge detection method!")
    return function(img_arr, **kwargs)

def get_color_region_contours(
    img_arr: np.ndarray, rgb_val: tuple[int, int, int], axis=-1
) -> np.ndarray:
    """
    Finds the contours of all areas with a given rgb value. Useful for finding drawn ROIs.

    Parameters
    ----------
    img_arr: np.ndarray or PIL.Image
        Image with ROIs. Converts PIL Image to np array for processing.
    rgb_val: tuple[int,int,int]
        Red, Green, and Blue values for the roi color.
    axis: int, Default: -1
        Which axis is the color channel. Default is the last axis [:,:,color]

    Returns
    -------
    list[ tuple[int(None), rgb_val, contours] ]
        Returns list of lavlab shapes.
    """
    assert isinstance(img_arr, np.ndarray)
    mask_bin = np.all(img_arr == rgb_val, axis=axis)
    contours = skimage.measure.find_contours(mask_bin, level=0.5)
    del mask_bin
    # wrap in lavlab shape convention
    for i, contour in enumerate(contours):
        contour = [(x, y) for y, x in contour]
        contours[i] = (None, rgb_val, contour)
    return contours

def get_downsample_from_dimensions(
    base_shape: tuple[int, ...], sample_shape: tuple[int, ...]
) -> tuple[float, ...]:
    """
    Essentially an alias for np.divide().

    Finds the ratio between a base array shape and a sample array shape by dividing each axis.

    Parameters
    ----------
    base_shape: tuple(int)*x
        Shape of the larger image. (Image.size / base_nparray.shape)
    sample_shape: tuple(int)*x
        Shape of the smaller image. (Image.size / sample_nparray.shape)

    Raises
    ------
    AssertionError
        Asserts that the input shapes have the same amount of axes

    Returns
    -------
    tuple(int)*x
        Returns a tuple containing the downsample factor of each axis for the sample array.

    """
    assert len(base_shape) == len(sample_shape)
    return tuple(np.divide(base_shape, sample_shape))

def imadjust(
    img_arr: np.ndarray,
    tol: int = 1,
    vin: tuple[int, int] = (0, 255),
    vout: tuple[int, int] = (0, 255),
) -> np.ndarray:
    """
    Matlab's imadjust in Python.

    Parameters
    ----------
    img_arr : np.ndarray
        Grayscale image.
    tol : int, optional
        Tolerance, from 0 to 100, defaults to 1.
    vin : tuple[int, int], optional
        Input image bounds, defaults to (0,255).
    vout : tuple[int, int], optional
        Output image bounds, defaults to (0,255).

    Returns
    -------
    np.ndarray
        Intensity adjusted image.
    """
    assert len(img_arr.shape) == 2, "Input image should be 2-dims"

    tol = max(0, min(100, tol))

    if tol > 0:
        # Compute in and out limits
        hist = np.histogram(img_arr, bins=256, range=(0, 255))[0]

        # Cumulative histogram
        cum = hist.cumsum()

        # Compute bounds
        total = img_arr.size
        low_bound = total * tol / 100
        upp_bound = total * (100 - tol) / 100
        vin = (bisect.bisect_left(cum, low_bound), bisect.bisect_left(cum, upp_bound))

    # Avoid division by zero by setting vin[1] if it's the same as vin[0]
    if vin[0] == vin[1]:
        vin = (vin[0], vin[0] + 1)

    # Stretching
    scale = (vout[1] - vout[0]) / (vin[1] - vin[0])
    vs = img_arr - vin[0]
    vs[img_arr < vin[0]] = 0
    vd = vs * scale + 0.5 + vout[0]
    vd[vd > vout[1]] = vout[1]
    dst = vd

    return dst.astype(np.uint8)

def imbinarize(image):
    """
    Generates a binary image from a grayscale image using Otsu's thresholding.

    Parameters
    ----------
    image : np.ndarray
        numpy array

    Returns
    -------
    np.ndarray
        binary image
    """
    if len(image.shape) == 3:
        image = rgb2gray(image)

    # Apply Otsu's thresholding
    thresh = skimage.filters.threshold_otsu(image)
    binary_image = image > thresh
    return binary_image

def imcomplement(img_arr: np.ndarray) -> np.ndarray:
    """Generates the image's complement (inverts the image).

    Parameters
    ----------
    img_arr : np.ndarray
        Input image.

    Returns
    -------
    np.ndarray
        Inverted image.
    """
    return ~img_arr

def imcrop(
    img_arr: Union[np.ndarray, pv.Image], dims: tuple[int, int, int, int]
) -> Union[np.ndarray, pv.Image]:
    """Crops a region from an image using pyvips

    Parameters
    ----------
    img_arr : Union[np.ndarray, pv.Image]
        Input image as a NumPy array or pyvips Image.
    dims : tuple[int,int,int,int]
        Desired dimensions: left, top, width, height.

    Returns
    -------
    Union[np.ndarray, pv.Image]
        Cropped image.
    """
    img = img_arr
    if not isinstance(img, pv.Image):
        assert isinstance(img, np.ndarray)
        img_arr = pv.Image.new_from_array(img)
    assert isinstance(img_arr, pv.Image)

    rotated_img = img_arr.crop(*dims)
    assert isinstance(rotated_img, pv.Image)

    # Retain the input type in the output
    if isinstance(img, np.ndarray):
        return rotated_img.numpy()
    return rotated_img

def imhist(img_arr: np.ndarray, bins=256) -> None:
    """Plots and displays histogram of image intensity values

    Parameters
    ----------
    img_arr : np.ndarray
        Input image.
    bins : int, optional
        Number of bins, defaults to 256.

    Returns
    -------
    None
    """
    # Calculate the histogram
    matplotlib.pyplot.hist(img_arr.ravel(), bins=bins, range=(0.0, 256.0))

    # Set the title and labels
    matplotlib.pyplot.title("Histogram of Image Intensity Values")
    matplotlib.pyplot.xlabel("Intensity Value")
    matplotlib.pyplot.ylabel("Frequency")

    # Show the histogram
    matplotlib.pyplot.show()

def imread(image_path: Union[os.PathLike, BinaryIO, str], wild=False) -> np.ndarray:
    """
    Loads an image from a file.

    Parameters
    ----------
    image_path : Union[os.PathLike, BinaryIO]
        Path to image.
    wild : bool, optional
        If True, will not warn about niche formats, by default False.

    Returns
    -------
    np.ndarray
        Array of pixel values.

    Warnings
    --------
    This function can cause an OOM error if the image is too large!
    Use wsiread if your image is large.
    """
    if isinstance(image_path, BinaryIO):
        return pv.Image.new_from_buffer(image_path, "").numpy()
    image_path = str(image_path)
    if image_path.endswith(".nii") or image_path.endswith(".nii.gz"):
        if not wild:
            LOGGER.warning(
                "Nifti detected, use niftiread() for clarity if possible otherwise enable wild. Using niftiread..."  # pylint: disable=line-too-long
            )
        nii = niftiread(image_path)
        assert isinstance(nii, np.ndarray)
        return nii
    if image_path.endswith(".dcm"):
        if not wild:
            LOGGER.warning(
                "Dicom detected, use dicomread() for clarity if possible otherwise enable wild. Using dicomread..."  # pylint: disable=line-too-long
            )
        dcm = dicomread(image_path)
        assert isinstance(dcm, np.ndarray)
        return dcm
    if os.path.isdir(image_path):
        if not wild:
            LOGGER.warning(
                "Dicom directory detected, use dicomread_volume() for clarity if possible otherwise enable wild. Using dicomread_volume"  # pylint: disable=line-too-long
            )
        dcm_vol = dicomread_volume(image_path)
        assert isinstance(dcm_vol, np.ndarray)
        return dcm_vol

    img = pv.Image.new_from_file(str(image_path))
    assert isinstance(img, pv.Image)
    if not is_memsafe_pvimg(img):
        LOGGER.warning("Image is too large for memory! Use wsiread() for large images.")
        return wsiread(image_path)
    return img.numpy()

def imresize(
    img: Union[np.ndarray, pv.Image], factor: Union[int, float, tuple[int, ...]]
) -> Union[np.ndarray, pv.Image]:
    """
    Convenience wrapper for resize functions. Uses pyvips for 2D and skimage for 3D.

    Parameters
    ----------
    img : Union[np.ndarray, pv.Image]
        Input image as a NumPy array or pyvips Image.
    factor : Union[int, float, Tuple[int, ...]]
        Scale factor (if int or float) or desired dimensions (if tuple).

    Returns
    -------
    Union[np.ndarray, pv.Image]
        Resized image as a NumPy array or pyvips Image.
    """
    if isinstance(img, np.ndarray):
        dimensions = len(img.shape)
        if dimensions == 3 and img.shape[2] == 3:
            dimensions = 2
            width, height = img.shape[1], img.shape[0]
        elif dimensions == 2:
            height, width = img.shape
    elif isinstance(img, pv.Image):
        dimensions = 2
        width, height = img.width, img.height
    else:
        raise TypeError(
            "Unsupported image type. Only np.ndarray and pyvips.Image are supported."
        )

    if dimensions == 2:
        if isinstance(factor, (int, float)):
            factor_tuple = (float(factor), float(factor))
        elif isinstance(factor, tuple) and len(factor) == 2:
            factor_tuple = (factor[1] / width, factor[0] / height)

        if isinstance(img, np.ndarray):
            pv_img = pv.Image.new_from_array(img)
            return imresize2d(pv_img, factor_tuple).numpy()
        return imresize2d(img, factor_tuple)
    if dimensions == 3:
        assert isinstance(factor, tuple)
        return imresize3d(img, (factor[0], factor[1], factor[2]))
    raise ValueError(
        "Unsupported image dimensions. Only 2D and 3D images are supported."
    )

def imresize2d(img: pv.Image, scale: tuple[float, float]) -> pv.Image:
    """
    Resizes a 2D image using pyvips' resize function.

    Parameters
    ----------
    img : pv.Image
        Input 2D image.
    target_size : Tuple[int, int]
        Scale factor h and v.

    Returns
    -------
    pv.Image
        Resized image as a pyvips Image.
    """
    return img.resize(scale[0], vscale=scale[1])

def imresize3d(img: np.ndarray, target_size: tuple[int, int, int]) -> np.ndarray:
    """
    Resizes a 3D image using skimage's resize function.

    Parameters
    ----------
    img : np.ndarray
        Input 3D image.
    target_size : Tuple[int, int, int]
        Desired dimensions as a tuple of (depth, height, width).

    Returns
    -------
    np.ndarray
        Resized image as a NumPy array.
    """
    return skimage.transform.resize(img, target_size)

def imrotate(
    img_arr: Union[np.ndarray, pv.Image], degrees: Union[int, float]
) -> Union[np.ndarray, pv.Image]:
    """Rotates an input image using pyvips.

    Parameters
    ----------
    img_arr : Union[np.ndarray, pv.Image]
        Input image as a NumPy array or pyvips Image.
    degrees : int or float
        Rotation in degrees.

    Returns
    -------
    Union[np.ndarray, pv.Image]
        Rotated image.
    """
    img = img_arr
    if not isinstance(img, pv.Image):
        assert isinstance(img, np.ndarray)
        img_arr = pv.Image.new_from_array(img)
    assert isinstance(img_arr, pv.Image)

    rotated_img = img_arr.rotate(degrees, interpolate=pv.Interpolate.new("nearest"))
    assert isinstance(rotated_img, pv.Image)

    # Retain the input type in the output
    if isinstance(img, np.ndarray):
        return rotated_img.numpy()
    return rotated_img

def imshow(image, **kwargs):
    """Just matplotlib.pyplot.imshow() see docs for more"""
    matplotlib.pyplot.figure()
    matplotlib.pyplot.imshow(image, **kwargs)

def imwarp(
    img_arr: Union[np.ndarray, pv.Image],
    affine_matrix: tuple[float, float, float, float],
) -> Union[np.ndarray, pv.Image]:
    """Affine warps a region from an image using pyvips

    Parameters
    ----------
    img_arr : Union[np.ndarray, pv.Image]
        Input image as a NumPy array or pyvips Image.
    affine : tuple[float,float,float,float]
        4 element affine transform matrix

    Returns
    -------
    Union[np.ndarray, pv.Image]
        Warped image
    """
    img = img_arr
    if not isinstance(img, pv.Image):
        assert isinstance(img, np.ndarray)
        img_arr = pv.Image.new_from_array(img)
    assert isinstance(img_arr, pv.Image)

    rotated_img = img_arr.affine(
        affine_matrix, interpolate=pv.Interpolate.new("nearest")
    )
    assert isinstance(rotated_img, pv.Image)

    # Retain the input type in the output
    if isinstance(img, np.ndarray):
        return rotated_img.numpy()
    return rotated_img

def imwrite(
    img: Union[np.ndarray, pv.Image], path: Union[os.PathLike, str], **kwargs
) -> str:
    """Writes an image to path. kwargs are passthrough to wrapped function.

    Parameters
    ----------
    img : Union[np.ndarray, pv.Image]
        Numpy array or PyVips image.
    path : os.PathLike or str
        Path to desired file.

    Returns
    -------
    str
        Path of newly created file.
    """
    path = str(path)
    if path.endswith(".nii") or path.endswith(".nii.gz"):
        LOGGER.warning(
            "Nifti detected, use niftiwrite() for clarity! Using niftiwrite..."
        )
        return niftiwrite(img, path, **kwargs)
    if path.endswith(".dcm"):
        LOGGER.warning(
            "Dicom detected, use dicomwrite() for clarity! Using dicomwrite..."
        )
        return dicomwrite(img, path, **kwargs)
    if not isinstance(img, pv.Image):
        assert isinstance(img, np.ndarray)
        img = pv.Image.new_from_array(img)
    assert isinstance(img, pv.Image)
    img.write_to_file(path, **kwargs)
    return path

def niftiread(
    image_path: Union[os.PathLike, str, io.BytesIO], as_nib=False
) -> Union[np.ndarray, FileBasedImage]:
    """Loads a nifti from a file.

    Parameters
    ----------
    image_path : os.PathLike or str
        Path to nifti.
    as_nib : bool, optional
        If True, returns a nibabel image class, by default False.

    Returns
    -------
    np.ndarray or FileBasedImage
        Array of pixel values or appropriate Nifti image class when as_nib=True.
    """
    if isinstance(image_path, io.BytesIO):
        return nib.Nifti1Image.from_stream(image_path)
    image_path = str(image_path)
    if as_nib:
        return nib.load(image_path)  # type: ignore
    return nib.load(image_path).get_fdata()  # type: ignore

def niftiwrite(
    img: Union[np.ndarray, nib.Nifti1Image, nib.Nifti2Image],
    path: Union[os.PathLike, str],
    affine=None,
    **kwargs,
) -> str:
    """Writes an image to path. kwargs are passthrough to wrapped function.

    Parameters
    ----------
    img : np.ndarray or nib.Nifti1Image or nib.Nifti2Image
        Numpy array or Nifti image. If array, Nifti image is created.
    path : os.PathLike or str
        Path to desired file.
    affine : np.ndarray, optional
        Affine matrix for the image, by default uses nibabel's default.
    kwargs : dict
        Additional arguments to pass to nib.save.

    Returns
    -------
    str
        Path of newly created file.
    """
    path = str(path)
    if not path.endswith(".nii") and not path.endswith(".nii.gz"):
        LOGGER.warning(
            "Nifti extension not detected in path! Niftis should end in .nii or .nii.gz! Appending .nii.gz..."  # pylint: disable=line-too-long
        )
        path += ".nii.gz"
    if isinstance(img, np.ndarray):
        img = nib.Nifti1Image(img, affine)
    nib.save(img, path, **kwargs)
    return path

def wsiread(image_path: Union[os.PathLike, str]) -> pv.Image:
    """Reads a Whole Slide Image from a file.

    Allows operations on images larger than memory.
    wrapper for pyvips.Image.new_from_file()

    Warnings
    --------
    This function does not return a numpy array!
    You'll need to use proper WSI workflows (like tilewise operations) to do analyses on this!
    See the pyvips documentation for more information.

    Parameters
    ----------
    image_path : os.PathLike or string representing a file
        Path to WSI.

    Returns
    -------
    pv.Image
        PyVips Image, see documentation for usage.
    """
    return pv.Image.new_from_file(str(image_path))

def wsiwrite(
    img: pv.Image, path: Union[os.PathLike, str], use_fast_compression=None, **kwargs
) -> str:
    """Writes an image to path. kwargs are passthrough to wrapped function.

    Parameters
    ----------
    img : pv.Image
        PyVips image.
    path : os.PathLike or str
        Path to desired file.
    use_fast_compression : bool, optional
        Use fast compression as configured in context, by default uses bool from config.

    Returns
    -------
    str
        Path of newly created file.
    """
    path = str(path)
    if use_fast_compression is None:
        use_fast_compression = lavlab.ctx.histology.use_fast_compression
    if not kwargs:
        kwargs = (
            lavlab.ctx.histology.fast_compression_options
            if use_fast_compression
            else lavlab.ctx.histology.slow_compression_options
        )
    img.write_to_file(path, **kwargs)
    return path