eyepy.core.utils

DynamicDefaultDict(factory)

Bases: dict

A defaultdict for which the factory function has access to the missing key.

Source code in src/eyepy/core/utils.py

def __init__(self, factory):
    self.factory = factory

default_intensity_transform(data)

Default intensity transform.

By default intensities are not changed.

Parameters:

Name	Type	Description	Default
data	ndarray	Input data	required

Returns:

Type	Description
ndarray	Input data unchanged

Source code in src/eyepy/core/utils.py

def default_intensity_transform(data: np.ndarray) -> np.ndarray:
    """Default intensity transform.

    By default intensities are not changed.

    Args:
        data: Input data

    Returns:
        Input data unchanged
    """
    return data

drusen(rpe_height, bm_height, volume_shape, minimum_height=2)

Compute drusen from the RPE and BM layer segmentation.

First estimate the ideal RPE based on a histogram of the RPE heights relativ to the BM. Then compute drusen as the area between the RPE and the normal RPE

Parameters:

Name	Type	Description	Default
rpe_height	NDArrayFloat	The RPE height as offset from the lower border of the B-Scan	required
bm_height	NDArrayFloat	The BM height as offset from the lower border of the B-Scan	required
volume_shape	tuple[int, int, int]	Shape of the OCT volume (number of B-Scans, height, width)	required
minimum_height	int	Minimum height of a drusen in pixels	2

Returns:

Type	Description
NDArrayBool	A boolean array with the same shape as the OCT volume. True indicates a
NDArrayBool	voxel beeing part of a drusen.

Source code in src/eyepy/core/utils.py

def drusen(rpe_height: NDArrayFloat,
           bm_height: NDArrayFloat,
           volume_shape: tuple[int, int, int],
           minimum_height: int = 2) -> NDArrayBool:
    """Compute drusen from the RPE and BM layer segmentation.

    First estimate the ideal RPE based on a histogram of the RPE heights relativ
    to the BM. Then compute drusen as the area between the RPE and the normal RPE

    Args:
        rpe_height: The RPE height as offset from the lower border of the B-Scan
        bm_height: The BM height as offset from the lower border of the B-Scan
        volume_shape: Shape of the OCT volume (number of B-Scans, height, width)
        minimum_height: Minimum height of a drusen in pixels

    Returns:
        A boolean array with the same shape as the OCT volume. True indicates a
        voxel beeing part of a drusen.
    """
    # Estimate ideal RPE
    if isinstance(rpe_height, EyeVolumeLayerAnnotation):
        rpe_height = np.copy(rpe_height.data)
    if isinstance(bm_height, EyeVolumeLayerAnnotation):
        bm_height = np.copy(bm_height.data)

    irpe = ideal_rpe(rpe_height, bm_height, volume_shape)
    # Create drusen map
    drusen_map = np.zeros(volume_shape, dtype=bool)
    # Exclude normal RPE and RPE from the drusen area.
    nans = np.isnan(rpe_height + irpe)

    rpe = np.rint(rpe_height + 1)
    rpe[nans] = 0
    rpe = rpe.astype(int)

    irpe = np.rint(irpe)
    irpe[nans] = 0
    irpe = irpe.astype(int)

    for sli in range(drusen_map.shape[0]):
        for col in range(drusen_map.shape[2]):
            if not nans[sli, col]:
                drusen_map[sli, rpe[sli, col]:irpe[sli, col], col] = 1

    drusen_map = filter_by_height_enface(drusen_map, minimum_height)

    return drusen_map

ideal_rpe(rpe_height, bm_height, volume_shape)

Compute the ideal RPE from an RPE with Drusen.

Parameters:

Name	Type	Description	Default
rpe_height	NDArrayFloat	The RPE height as offset from the lower border of the B-Scan	required
bm_height	NDArrayFloat	The BM height as offset from the lower border of the B-Scan	required
volume_shape	tuple[int, int, int]	Shape of the OCT volume (number of B-Scans, height, width)	required

Returns:

Type	Description
NDArrayFloat	The ideal RPE height as offset from the lower border of the B-Scan

Source code in src/eyepy/core/utils.py

def ideal_rpe(rpe_height: NDArrayFloat, bm_height: NDArrayFloat,
              volume_shape: tuple[int, int, int]) -> NDArrayFloat:
    """Compute the ideal RPE from an RPE with Drusen.

    Args:
        rpe_height: The RPE height as offset from the lower border of the B-Scan
        bm_height: The BM height as offset from the lower border of the B-Scan
        volume_shape: Shape of the OCT volume (number of B-Scans, height, width)

    Returns:
        The ideal RPE height as offset from the lower border of the B-Scan
    """
    d, h, w = volume_shape

    # compute shift needed to align the BM to the horizontal center line
    shift = np.empty((d, w), dtype='int')
    shift.fill(h - (h / 2))
    shift = shift - bm_height

    # now shift the RPE location array as well
    shifted_rpe_height = rpe_height + shift

    # Remove all NANs from the shifted RPE data
    clean_shifted = shifted_rpe_height[~np.isnan(shifted_rpe_height)]

    # Compute a histogram with a bin for every pixel height in a B-Scan
    hist, edges = np.histogram(clean_shifted.flatten(),
                               bins=np.arange(volume_shape[1]))

    # Compute the ideal RPE as the mean of the biggest bin and its neighbours
    lower_edge = edges[np.argmax(hist) - 1]
    upper_edge = edges[np.argmax(hist) + 2]
    irpe_height = np.mean(clean_shifted[np.logical_and(
        clean_shifted <= upper_edge, clean_shifted >= lower_edge)])
    ideal_rpe = np.full_like(shifted_rpe_height, irpe_height)

    # Shift back into original image space
    ideal_rpe = np.reshape(ideal_rpe, (d, w)) - shift

    return ideal_rpe

vol_intensity_transform(data)

Wrapper around from_vol_intensity.

Transform intensities from Heyex VOL exports to achieve a constrast similar to the one used in Heyex.

Parameters:

Name	Type	Description	Default
data	NDArrayFloat	Input data	required

Returns:

Type	Description
NDArrayInt	Transformed data

Source code in src/eyepy/core/utils.py

def vol_intensity_transform(data: NDArrayFloat) -> NDArrayInt:
    """Wrapper around from_vol_intensity.

    Transform intensities from Heyex VOL exports to achieve a constrast similar to the one used in Heyex.

    Args:
        data: Input data

    Returns:
        Transformed data
    """
    return from_vol_intensity(data)