eyepy.core.eyeenface

EyeEnface(data, meta)

Parameters:

Name	Type	Description	Default
data	NDArray[int_]		required
meta	'EyeEnfaceMeta'		required

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

def __init__(self, data: npt.NDArray[np.int_],
             meta: 'EyeEnfaceMeta') -> None:
    """

    Args:
        data:
        meta:
    """
    self.data = data
    self._area_maps = []
    self.meta = meta

area_maps: dict[str, EyeEnfacePixelAnnotation] property

Returns:

laterality: str property

Returns:

scale_x: float property

Returns:

scale_y: float property

Returns:

shape: tuple[int, int] property

Returns:

size_x: int property

Returns:

size_y: int property

Returns:

add_area_annotation(area_map=None, meta=None, **kwargs)

Parameters:

Name	Type	Description	Default
area_map	Optional[NDArray[bool_]]		None
meta	Optional[dict]		None
**kwargs			{}

Returns:

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

def add_area_annotation(self,
                        area_map: Optional[npt.NDArray[np.bool_]] = None,
                        meta: Optional[dict] = None,
                        **kwargs) -> EyeEnfacePixelAnnotation:
    """

    Args:
        area_map:
        meta:
        **kwargs:

    Returns:

    """
    if meta is None:
        meta = {}
    meta.update(**kwargs)
    area_annotation = EyeEnfacePixelAnnotation(self, area_map, meta)
    self._area_maps.append(area_annotation)
    return area_annotation

plot(ax=None, region=np.s_[:, :], scalebar='botleft', scalebar_kwargs=None, watermark=True)

Parameters:

Name	Type	Description	Default
ax	Optional[Axes]	Axes to plot on. If not provided plot on the current axes (plt.gca()).	None
region	tuple[slice, slice]	Region of the localizer to plot (default: np.s_[:, :])	s_[:, :]
scalebar	Union[bool, str]	Position of the scalebar, one of "topright", "topleft", "botright", "botleft" or False (default: "botleft"). If True the scalebar is placed in the bottom left corner. You can custumize the scalebar using the scalebar_kwargs argument.	'botleft'
scalebar_kwargs	Optional[dict[str, Any]]	Optional keyword arguments for customizing the scalebar. Check the documentation of plot_scalebar for more information.	None
watermark	bool	If True plot a watermark on the image (default: True). When removing the watermark, please consider to cite eyepy in your publication.	True

Returns: None

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

def plot(
    self,
    ax: Optional[plt.Axes] = None,
    region: tuple[slice, slice] = np.s_[:, :],
    scalebar: Union[bool, str] = 'botleft',
    scalebar_kwargs: Optional[dict[str, Any]] = None,
    watermark: bool = True,
) -> None:
    """

    Args:
        ax: Axes to plot on. If not provided plot on the current axes (plt.gca()).
        region: Region of the localizer to plot (default: `np.s_[:, :]`)
        scalebar: Position of the scalebar, one of "topright", "topleft", "botright", "botleft" or `False` (default: "botleft"). If `True` the scalebar is placed in the bottom left corner. You can custumize the scalebar using the `scalebar_kwargs` argument.
        scalebar_kwargs: Optional keyword arguments for customizing the scalebar. Check the documentation of [plot_scalebar][eyepy.core.plotting.plot_scalebar] for more information.
        watermark: If `True` plot a watermark on the image (default: `True`). When removing the watermark, please consider to cite eyepy in your publication.
    Returns:
        None

    """
    ax = plt.gca() if ax is None else ax
    vmin = np.min(self.data)
    vmax = np.max(self.data)

    ax.imshow(self.data[region], cmap='gray', vmin=vmin, vmax=vmax)

    # Make sure tick labels match the image region
    y_start = region[0].start if region[0].start is not None else 0
    x_start = region[1].start if region[1].start is not None else 0
    y_end = region[0].stop if region[0].stop is not None else self.size_y
    x_end = region[1].stop if region[1].stop is not None else self.size_x

    # Ticks are not clipped to the image region. Clip them here.
    yticks = ax.get_yticks()
    yticks = yticks[np.nonzero(
        np.logical_and(yticks >= 0, yticks <= y_end - y_start - 1))]
    xticks = ax.get_xticks()
    xticks = xticks[np.nonzero(
        np.logical_and(xticks >= 0, xticks <= x_end - x_start - 1))]

    # Set clipped ticks (this is only necessary because we change the labels later)
    ax.set_yticks(yticks)
    ax.set_xticks(xticks)

    # Set labels to ticks + start of the region as an offset
    ax.set_yticklabels([str(int(t + y_start)) for t in yticks])
    ax.set_xticklabels([str(int(t + x_start)) for t in xticks])

    if scalebar:
        if scalebar_kwargs is None:
            scalebar_kwargs = {}

        scale_unit = self.meta['scale_unit']
        scalebar_kwargs = {
            **{
                'scale': (self.scale_x, self.scale_y),
                'scale_unit': scale_unit
            },
            **scalebar_kwargs
        }

        if not 'pos' in scalebar_kwargs:
            sx = x_end - x_start
            sy = y_end - y_start

            if scalebar is True:
                scalebar = 'botleft'

            if scalebar == 'botleft':
                scalebar_kwargs['pos'] = (sx - 0.95 * sx, 0.95 * sy)
            elif scalebar == 'botright':
                scalebar_kwargs['pos'] = (0.95 * sx, 0.95 * sy)
                scalebar_kwargs['flip_x'] = True
            elif scalebar == 'topleft':
                scalebar_kwargs['pos'] = (sx - 0.95 * sx, 0.05 * sy)
                scalebar_kwargs['flip_y'] = True
            elif scalebar == 'topright':
                scalebar_kwargs['pos'] = (0.95 * sx, 0.05 * sy)
                scalebar_kwargs['flip_x'] = True
                scalebar_kwargs['flip_y'] = True

        plot_scalebar(ax=ax, **scalebar_kwargs)

    if watermark:
        plot_watermark(ax)