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Plotting of activation maps
=====================================
.. currentmodule:: nipy.neurospin.viz_tools.activation_maps
The module :mod:`nipy.neurospin.viz` provides functions to plot
visualization of activation maps in a non-interactive way.
2D cuts of an activation map can be plotted and superimposed on an
anatomical map using matplotlib_. In addition, Mayavi2_ can be used to
plot 3D maps, using volumetric rendering. Some emphasis is made on
automatic choice of default parameters, such as cut coordinates, to give
a sensible view of a map in a purely automatic way, for instance to save
a summary of the output of a calculation.
.. _matplotlib: http://matplotlib.sourceforge.net
.. _Mayavi2: http://code.enthought.com/projects/mayavi
.. warning::
The content of the module will change over time, as neuroimaging
volumetric data structures are used instead of plain numpy arrays.
An example
-----------
::
from nipy.neurospin.viz import plot_map, mni_sform, coord_transform
# First, create a fake activation map: a 3D image in MNI space with
# a large rectangle of activation around Broca Area
import numpy as np
mni_sform_inv = np.linalg.inv(mni_sform)
# Color a asymetric rectangle around Broca area:
x, y, z = -52, 10, 22
x_map, y_map, z_map = coord_transform(x, y, z, mni_sform_inv)
map = np.zeros((182, 218, 182))
map[x_map-30:x_map+30, y_map-3:y_map+3, z_map-10:z_map+10] = 1
# We use a masked array to add transparency to the parts that we are
# not interested in:
thresholded_map = np.ma.masked_less(map, 0.5)
# And now, visualize it:
plot_map(thresholded_map, mni_sform, cut_coords=(x, y, z), vmin=0.5)
This creates the following image:
.. image:: viz.png
The same plot can be obtained fully automaticaly, by letting
:func:`plot_map` find the activation threshold and the cut coordinnates::
auto_plot_map(map, mni_sform, threshold='auto')
In this simple example, the code will easily detect the bar as activation
and position the cut at the center of the bar.
`nipy.neurospin.viz` functions
-------------------------------------------------
.. autosummary::
:toctree: generated
plot_map
3D plotting utilities
---------------------------
.. currentmodule:: nipy.neurospin.viz_tools.maps_3d
The module :mod:`nipy.neurospin.viz3d` can be used as helpers to
represent neuroimaging volumes with Mayavi2_.
.. autosummary::
:toctree: generated
plot_map_3d
plot_anat_3d
More versalite visualizations, the core idea is that given a 3D map
and an affine, the data is exposed in Mayavi as a volumic source, with
world space coordinates corresponding to figure coordinates.
Visualization modules can be applied on this data source as explained in
the `Mayavi manual
<http://code.enthought.com/projects/mayavi/docs/development/html/mayavi/mlab.html#assembling-pipelines-with-mlab>`_
.. autosummary::
:toctree: generated
affine_img_src
|
