visualization

ardent.visualization.heatslices(data, title=None, figsize=(10, 5), cmap='gray', n_cuts=5, xcuts=[], ycuts=[], zcuts=[], limit_mode=None, stdevs=4, quantile=0.01, limits=None, vmin=0, vmax=1)

Produce a figure with 3 rows of images, each corresponding to a different orthogonal view of data. Each row can have arbitrarily many parallel views. The data is scaled such that its bulk lies on the interval [0, 1], with the extrema optionally left unaccounted for in determining the scaling. Those values outside the limits saturate at 0 or 1 in the figure.

Parameters:

• data (np.ndarray) -- A 3 or 4 dimensional array containing volumetric intensity data (if 3D) or RGB data (if 4D) to be viewed.
• title (str, optional) -- The figure title. Defaults to None.
• figsize (tuple, optional) -- The width and height of the figure in inches. Defaults to (10, 5).
• cmap (str, optional) -- The name of the chosen color map. Defaults to 'gray'.
• n_cuts (int, optional) -- The number of parallel views to show on each row without a specified list of cuts. Defaults to 5.
• xcuts (list, optional) -- A list of indices at which to display a view in the first row. Defaults to [n_cuts evenly spaced indices. Half the spacing between indices pads each end].
• ycuts (list, optional) -- A list of indices at which to display a view in the second row. Defaults to [n_cuts evenly spaced indices. Half the spacing between indices pads each end].
• zcuts (list, optional) -- A list of indices at which to display a view in the third row. Defaults to [n_cuts evenly spaced indices. Half the spacing between indices pads each end.].
• limit_mode (str, NoneType, optional) --

  A string indicating what mode to use for clipping the extrema of data for determining the scaling to the interval [vmin, vmax].

  Accepted values:

  • None
  • 'stdev'
  • 'quantile'

  Defaults to None.

• stdevs (float, optional) -- Used if limit_mode == 'stdev': The number of standard deviations from the mean that will be scaled to the interval [vmin, vmax]. Defaults to 4.
• quantile (float, optional) -- Used if limit_mode == 'quantile': The proportion of data that will not be considered for scaling to the interval [vmin, vmax]. Defaults to 0.01.
• limits (sequence, optional) -- The lower and upper limits bookmarking which values in data will be considered when scaling to the interval [vmin, vmax]. Overrides limit_mode. Defaults to None.
• vmin (float, optional) -- The smallest value displayed in the figure. Smaller values will saturate to vmin. Defaults to 0.
• vmax (float, optional) -- The largest value displayed in the figure. Larger values will saturate to vmax. Defaults to 1.