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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__ = """
Example of activation image visualization with nipy.labs visualization tools
Needs *example data* package.
Needs matplotlib
"""
print(__doc__)
import os.path
try:
import matplotlib.pyplot as plt
except ImportError:
raise RuntimeError("This script needs the matplotlib library")
# Local import
from get_data_light import get_second_level_dataset
from nibabel import load
from nipy.labs import viz
from nipy.utils import example_data
# get the data
data_dir = get_second_level_dataset()
# First example, with a anatomical template
img = load(os.path.join(data_dir, 'spmT_0029.nii.gz'))
data = img.get_fdata()
affine = img.affine
viz.plot_map(data, affine, cut_coords=(-52, 10, 22),
threshold=2.0, cmap=viz.cm.cold_hot)
plt.savefig('ortho_view.png')
# Second example, with a given anatomical image slicing in the Z direction
try:
anat_img = load(example_data.get_filename('neurospin', 'sulcal2000',
'nobias_anubis.nii.gz'))
anat = anat_img.get_fdata()
anat_affine = anat_img.affine
except OSError as e:
# File does not exist: the data package is not installed
print(e)
anat = None
anat_affine = None
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='z', threshold=2, cmap=viz.cm.cold_hot, black_bg=True)
plt.savefig('z_view.png')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='x', threshold=2, cmap=viz.cm.cold_hot, black_bg=True)
plt.savefig('x_view.png')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='y', threshold=2, cmap=viz.cm.cold_hot, black_bg=True)
plt.savefig('y_view.png')
plt.show()
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