mvpa2.misc.plot.lightbox.plot_lightbox¶
- mvpa2.misc.plot.lightbox.plot_lightbox(background=None, background_mask=None, cmap_bg='gray', overlay=None, overlay_mask=None, cmap_overlay='autumn', vlim=(0.0, None), vlim_type=None, do_stretch_colors=False, add_info=True, add_hist=True, add_colorbar=True, fig=None, interactive=None, nrows=None, ncolumns=None, slices=None, slice_title='k=%(islice)s')¶
Very basic plotting of 3D data with interactive thresholding.
background/overlay and corresponding masks could be nifti files names or SpatialImage objects, or 3D ndarrays. If no mask is provided, only non-0 elements are plotted.
Parameters: do_stretch_colors : bool, optional
Stratch color range to the data (not just to visible data)
vlim : tuple, optional
2 element tuple of low/upper bounds of values to plot
vlim_type : None or ‘symneg_z’
- If not None, then vlim would be treated accordingly:
- symneg_z
z-score values of symmetric normal around 0, estimated by symmetrizing negative part of the distribution, which often could be assumed when total distribution is a mixture of by-chance performance normal around 0, and some other in the positive tail
ncolumns : int or None
Explicit starting number of columns into which position the slice renderings. If None, square arrangement would be used
nrows : int or None
Explicit starting number of rows into which position the slice renderings. If None, square arrangement would be used
add_hist : bool or tuple (int, int)
If True, add histogram and position automagically. If a tuple – use as (row, column)
add_info : bool or tuple (int, int)
If True, add information and position automagically. If a tuple – use as (row, column).
slices : None or list of int
If not to plot whole volume, what slices to plot.
slice_title : None or str
Desired title of slices. Use string comprehension and assume islice variable present with current slice index.
Available colormaps are presented nicely on :
TODO: :
- Make interface more attractive/usable
- allow multiple overlays... or just unify for them all to be just a list of entries
- handle cases properly when there is only one - background/overlay
Notes
No care is taken to deduce the orientation (e.g. Left-to-Right, Posterior-to-Anterior) of fMRI volumes. Therefore all input volumes should be in the same orientation.
