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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:
__doc__ = """
This examples performs sifferent kinds of (2D and 3D) plots
of a given activation map.
Needs matplotlib.
Author : Bertrand Thirion, 2012
"""
print(__doc__)
from os import path
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
# Local import
from get_data_light import DATA_DIR, get_second_level_dataset
from nibabel import load
from nipy.labs.viz import cm, plot_map
#######################################
# Data and analysis parameters
#######################################
input_image = path.join(DATA_DIR, 'spmT_0029.nii.gz')
if not path.exists(input_image):
get_second_level_dataset()
brain_map = load(input_image)
vmin, vmax = brain_map.get_fdata().min(), brain_map.get_fdata().max()
# make a simple 2D plot
plot_map(brain_map.get_fdata(), brain_map.affine,
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
anat=None,
figure=10,
threshold=3)
# More plots using 3D
if True: # replace with False to skip this
plot_map(brain_map.get_fdata(), brain_map.affine,
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
anat=None,
figure=11,
threshold=3, do3d=True)
from nipy.labs import viz3d
try:
viz3d.plot_map_3d(brain_map.get_fdata(), brain_map.affine,
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
anat=None,
threshold=4)
except ImportError:
print("Need mayavi for 3D visualization")
plt.show()
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