plotMRI(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)
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Very basic plotting of 3D data with interactive thresholding.
Background/overlay could be nifti files names or NiftiImage
objects, or 3D ndarrays. if no mask provided, only non-0 elements
are plotted
- Available colormaps are presented nicely on
- http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps
- 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
- Parameters:
do_stretch_colors (bool) - Stratch color range to the data (not just to visible data)vlim - 2 element tuple of low/upper bounds of values to plotvlim_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 usednrows (int or None) - Explicit starting number of rows into which position the
slice renderings.
If None, square arrangement would be usedadd_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).
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