To provide the most recent news and documentation www.pymvpa.org reflects the development 2.0 series (renamed 0.6 series) of PyMVPA. If you are interested in the documentation of the previous stable 0.4 series of PyMVPA, please visit v04.pymvpa.org.

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.

NeuroDebian

NITRC-listed