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#!/usr/bin/env python3
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""A quick and dirty example of using Mayavi to overlay anatomy and activation.
"""
#-----------------------------------------------------------------------------
# Imports
#-----------------------------------------------------------------------------
import numpy as np
try:
from mayavi import mlab
except ImportError:
try:
from enthought.mayavi import mlab
except ImportError:
raise RuntimeError('Need mayavi for this module')
from fiac_util import load_image_fiac
#-----------------------------------------------------------------------------
# Globals
#-----------------------------------------------------------------------------
MASK = load_image_fiac('group', 'mask.nii')
AVGANAT = load_image_fiac('group', 'avganat.nii')
#-----------------------------------------------------------------------------
# Functions
#-----------------------------------------------------------------------------
def view_thresholdedT(design, contrast, threshold, inequality=np.greater):
"""
A mayavi isosurface view of thresholded t-statistics
Parameters
----------
design : {'block', 'event'}
contrast : str
threshold : float
inequality : {np.greater, np.less}, optional
"""
maska = np.asarray(MASK)
tmap = np.array(load_image_fiac('group', design, contrast, 't.nii'))
test = inequality(tmap, threshold)
tval = np.zeros(tmap.shape)
tval[test] = tmap[test]
# XXX make the array axes agree with mayavi2
avganata = np.array(AVGANAT)
avganat_iso = mlab.contour3d(avganata * maska, opacity=0.3, contours=[3600],
color=(0.8,0.8,0.8))
avganat_iso.actor.property.backface_culling = True
avganat_iso.actor.property.ambient = 0.3
tval_iso = mlab.contour3d(tval * MASK, color=(0.8,0.3,0.3),
contours=[threshold])
return avganat_iso, tval_iso
#-----------------------------------------------------------------------------
# Script entry point
#-----------------------------------------------------------------------------
if __name__ == '__main__':
# A simple example use case
design = 'block'
contrast = 'sentence_0'
threshold = 0.3
print('Starting thresholded view with:')
print('Design=', design, 'contrast=', contrast, 'threshold=', threshold)
view_thresholdedT(design, contrast, threshold)
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