cortex.quickflat.composite.add_curvature

cortex.quickflat.composite.add_curvature(fig: Axes, dataview: Dataview, extents: tuple[float, float, float, float] | None = None, height: int | None = None, threshold: bool | None = True, contrast: float | None = None, brightness: float | None = None, smooth: float | None = None, cmap: str = 'gray', recache: bool = False, curvature_lims: float = 0.5, legacy_mode: bool = False) → AxesImage

Add curvature layer to figure

Parameters:

figfigure or ax

figure into which to plot image of curvature

dataviewcortex.Dataview object

dataview containing data to be plotted, subject (surface identifier), and transform.

extentstuple[float, float, float, float], optional

(left, right, top, bottom) extents of image plotted. None defaults to extents of images already present in figure.

heightint, optional

Height, in pixels, of the output flatmap image. None defaults to the height of images already present in figure.

thresholdboolean

Whether to apply a threshold to the curvature values to create a binary curvature image (one shade for positive curvature, one shade for negative). None defaults to value specified in the config file

contrastfloat, [0-1] or None

Contrast of curvature image. 1 is maximal contrast (given brightness). If brightness is 0.5 and contrast is 1, and cmap is ‘gray’, curvature will be black and white. None defaults to value in config file.

brightnessfloat, [0-1] or None

How bright to make average value of curvature (0=black, 1=white in gray cmap). None defaults to the value in config file.

curvature_limsfloat

Limits for real curvature values (actual values for cortical curvature are normalized within [-curvature_lims, +`curvature_lims`] before scaling by contrast and shifting by brightness).

smoothscalar or None

Width of smoothing to apply to surface curvature. None defaults to no smoothing, or whatever the default value for curvature is that is stored in <filestore>/<subject>/surface-info/curvature.npz (for some subjects initiated in old versions of pycortex, this may be smoothed too!)

cmapstring

name for colormap of curvature

recacheboolean

Whether or not to recache intermediate files. Takes longer to plot this way, potentially resolves some errors.

Returns:

imgmatplotlib.image.AxesImage

matplotlib axes image object for plotted data