def show_slices(img, coords=None, threshold=0.1, cmap=None, prefix=None,
show_colorbar=None, formatter='%.2f'):
if cmap is None:
cmap = pylab.cm.hot
data, aff = img.get_data(), img.get_affine()
anatimg = load('/usr/share/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz')
anatdata, anataff = anatimg.get_data(), anatimg.get_affine()
anatdata = anatdata.astype(np.float)
anatdata[anatdata<10.] = np.nan
outfile = 'cluster.svg'
if prefix:
outfile = '_'.join((prefix, outfile))
outfile = os.path.join('figures', outfile)
if coords is None:
osl = viz.plot_map(np.asarray(data), aff, threshold=threshold,
cmap=cmap, black_bg=False)
osl.frame_axes.figure.savefig(outfile, transparent=True)
else:
for idx,coord in enumerate(coords):
outfile = 'cluster%02d' % idx
if prefix:
outfile = '_'.join((prefix, outfile))
outfile = os.path.join('figures', outfile)
osl = viz.plot_map(np.asarray(data), aff, anat=anatdata, anat_affine=anataff,
threshold=threshold, cmap=cmap,
black_bg=False, cut_coords=coord)
if show_colorbar:
cb = colorbar(gca().get_images()[1], cax=axes([0.4, 0.075, 0.2, 0.025]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
show()
osl.frame_axes.figure.savefig(outfile+'.svg', bbox_inches='tight', transparent=True)
osl.frame_axes.figure.savefig(outfile+'.png', dpi=600, bbox_inches='tight', transparent=True)
def plot_map(self, niimg, title):
data = niimg.get_data().squeeze()
params = self.plot_map_params.copy()
fig = pl.figure(facecolor='k', edgecolor='k')
if 'percentile' in self.plot_map_params:
threshold = scoreatpercentile(
data.ravel(), self.plot_map_params['percentile'])
params.pop('percentile')
params['threshold'] = threshold
# vmax = np.abs(data).max()
vmax = np.percentile(np.abs(data), 99)
plot_map(data,
affine=niimg.get_affine(),
vmin=-vmax,
vmax=vmax,
title=title,
figure=fig,
**params)
fname = title.replace(' ', '_').replace('/', '_')
pl.savefig(os.path.join(
self.report_dir, '%s.png' % fname), **self.save_params)
path = os.path.join(self.report_dir, '%s.nii.gz' % fname)
nb.save(niimg, path)
pl.close('all')
return path
def plot_map(self, niimg, title):
data = niimg.get_data().squeeze()
params = self.plot_map_params.copy()
fig = pl.figure(facecolor='k', edgecolor='k')
if 'percentile' in self.plot_map_params:
threshold = scoreatpercentile(data.ravel(),
self.plot_map_params['percentile'])
params.pop('percentile')
params['threshold'] = threshold
# vmax = np.abs(data).max()
vmax = np.percentile(np.abs(data), 99)
plot_map(data,
affine=niimg.get_affine(),
vmin=-vmax,
vmax=vmax,
title=title,
figure=fig,
**params)
fname = title.replace(' ', '_').replace('/', '_')
pl.savefig(os.path.join(self.report_dir, '%s.png' % fname),
**self.save_params)
path = os.path.join(self.report_dir, '%s.nii.gz' % fname)
nb.save(niimg, path)
pl.close('all')
return path
def save_image(nifti, anat, cluster_dict, out_path, f, image_threshold=2,
texcol=1, bgcol=0, iscale=2, text=None, **kwargs):
'''Saves a single nifti image.
Args:
nifti (str or nipy.core.api.image.image.Image): nifti file to visualize.
anat (nipy.core.api.image.image.Image): anatomical nifti file.
cluster_dict (dict): dictionary of clusters.
f (int): index.
image_threshold (float): treshold for `plot_map`.
texcol (float): text color.
bgcol (float): background color.
iscale (float): image scale.
text (Optional[str]): text for figure.
**kwargs: extra keyword arguments
'''
if isinstance(nifti, str):
nifti = load_image(nifti)
feature = nifti.get_data()
elif isinstance(nifti, nipy.core.image.image.Image):
feature = nifti.get_data()
font = {'size': 8}
rc('font', **font)
coords = cluster_dict['top_clust']['coords']
if coords == None:
return
feature /= feature.std()
imax = np.max(np.absolute(feature))
imin = -imax
imshow_args = dict(
vmax=imax,
vmin=imin,
alpha=0.7
)
coords = ([-coords[0], -coords[1], coords[2]])
plt.axis('off')
plt.text(0.05, 0.8, text, horizontalalignment='center',
color=(texcol, texcol, texcol))
try:
plot_map(feature,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=image_threshold,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
return
plt.savefig(out_path, transparent=True, facecolor=(bgcol, bgcol, bgcol))
def show(self, label=None, rcmap=None, **options):
self.P = np.array(self.P)
if label is None:
return viz.plot_map(self.P, self.affine, **options)
else:
color = rcmap or "black"
slicer = viz.plot_map(self.P == label, self.affine, **options)
slicer.contour_map(self.mask, self.affine, levels=[0], colors=(color,))
return slicer
def save_image(nifti,
anat,
cluster_dict,
out_path,
f,
image_threshold=2,
texcol=1,
bgcol=0,
iscale=2,
text=None,
**kwargs):
if isinstance(nifti, str):
nifti = load_image(nifti)
feature = nifti.get_data()
elif isinstance(nifti, nipy.core.image.image.Image):
feature = nifti.get_data()
font = {"size": 8}
rc("font", **font)
coords = cluster_dict["top_clust"]["coords"]
if coords == None:
logger.warning("No cluster found for %s" % nifti_file)
return
feature /= feature.std()
imax = np.max(np.absolute(feature))
imin = -imax
imshow_args = dict(vmax=imax, vmin=imin, alpha=0.7)
coords = ([-coords[0], -coords[1], coords[2]])
#ax = fig.add_subplot(1, 1, 1)
plt.axis("off")
plt.text(0.05,
0.8,
text,
horizontalalignment="center",
color=(texcol, texcol, texcol))
try:
plot_map(feature,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=image_threshold,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
logger.exception(e)
return
plt.savefig(out_path, transparent=True, facecolor=(bgcol, bgcol, bgcol))
def show(self, label=None, rcmap=None, **options):
self.label_image = np.array(self.label_image)
if label is None:
return viz.plot_map(self.label_image, self.affine, **options)
else:
color = rcmap or 'black'
slicer = viz.plot_map(self.label_image == label,
self.affine, **options)
slicer.contour_map(self.mask, self.affine,
levels=[0], colors=(color, ))
return slicer
def save_montage(NIFTI, ANAT, ONAME, SGN):
nifti = load_image(NIFTI)
anat = load_image(ANAT)
imax = nifti.get_data().max()
imin = nifti.get_data().min()
imshow_args = {'vmax': imax, 'vmin': imin}
mcmap = cmaps[SGN + 1]
num_features = nifti.shape[-1]
y = max([1, int(round(sqrt(num_features / 3)))])
x = int(ceil(num_features / y) + 1)
font = {'size': 8}
rc('font', **font)
f = figure(figsize=[iscale * y, iscale * x / 3])
subplots_adjust(left=0.01,
right=0.99,
bottom=0.01,
top=0.99,
wspace=0.1,
hspace=0)
for i in range(0, num_features):
data = nifti.get_data()[:, :, :, i]
data[sign(data) == negative(SGN)] = 0
if max(abs(data.flatten())) > thr + 0.2:
ax = subplot(x, y, i + 1)
max_idx = np.unravel_index(argmax(data), data.shape)
plot_map(data,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
black_bg=True,
threshold=thr,
cut_coords=coord_transform(max_idx[0], max_idx[1],
max_idx[2], xyz_affine(nifti)),
annotate=False,
axes=ax,
cmap=mcmap,
draw_cross=False,
**imshow_args)
text(0.,
0.95,
str(i),
transform=ax.transAxes,
horizontalalignment='center',
color=(1, 1, 1))
savefig(ONAME, facecolor=(0, 0, 0))
def show(self, label=None, rcmap=None, **options):
self.A = np.array(self.A)
if label is not None:
color = rcmap or "black"
slicer = viz.plot_map(self.A[..., label], self.affine, **options)
slicer.contour_map(self.mask, self.affine, levels=[0], colors=(color,))
return slicer
else:
slicer = viz.plot_map(self.mask, self.affine, **options)
for i, label in enumerate(self.labels()):
color = rcmap(1.0 * i / self.size) if rcmap is not None else pl.cm.gist_rainbow(1.0 * i / self.size)
slicer.contour_map(self.A[..., label], self.affine, levels=[0], colors=(color,))
return slicer
def save_image(nifti, anat, cluster_dict, out_path, f, image_threshold=2,
texcol=1, bgcol=0, iscale=2, text=None, **kwargs):
if isinstance(nifti, str):
nifti = load_image(nifti)
feature = nifti.get_data()
elif isinstance(nifti, nipy.core.image.image.Image):
feature = nifti.get_data()
font = {"size":8}
rc("font", **font)
coords = cluster_dict["top_clust"]["coords"]
if coords == None:
logger.warning("No cluster found for %s" % nifti_file)
return
feature /= feature.std()
imax = np.max(np.absolute(feature))
imin = -imax
imshow_args = dict(
vmax=imax,
vmin=imin,
alpha=0.7
)
coords = ([-coords[0], -coords[1], coords[2]])
#ax = fig.add_subplot(1, 1, 1)
plt.axis("off")
plt.text(0.05, 0.8, text, horizontalalignment="center",
color=(texcol, texcol, texcol))
try:
plot_map(feature,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=image_threshold,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
logger.exception(e)
return
plt.savefig(out_path, transparent=True, facecolor=(bgcol, bgcol, bgcol))
def save_image(nifti, anat, cluster_dict, out_path, f, image_threshold=2,
texcol=1, bgcol=0, iscale=2, text=None, **kwargs):
'''
Saves a single nifti image.
'''
if isinstance(nifti, str):
nifti = load_image(nifti)
feature = nifti.get_data()
elif isinstance(nifti, nipy.core.image.image.Image):
feature = nifti.get_data()
font = {'size': 8}
rc('font', **font)
coords = cluster_dict['top_clust']['coords']
if coords == None:
return
feature /= feature.std()
imax = np.max(np.absolute(feature))
imin = -imax
imshow_args = dict(
vmax=imax,
vmin=imin,
alpha=0.7
)
coords = ([-coords[0], -coords[1], coords[2]])
plt.axis('off')
plt.text(0.05, 0.8, text, horizontalalignment='center',
color=(texcol, texcol, texcol))
try:
plot_map(feature,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=image_threshold,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
return
plt.savefig(out_path, transparent=True, facecolor=(bgcol, bgcol, bgcol))
def brainplot(brainmat, savepath):
"""
takes a matrix (e.g. from loading an image file) and plots the activation
the figure is saved at 'savepath'
"""
# savepath should end in .png
plt.figure()
osl = viz.plot_map(np.asarray(brainmat), imgaff, anat=anat_data, anat_affine=anat_aff,
threshold=0.0001, black_bg=True, draw_cross=False)
pylab.savefig(savepath)
def show(self, label=None, rcmap=None, **options):
self.label_image = np.array(self.label_image)
if label is not None:
color = rcmap or 'black'
slicer = viz.plot_map(self.label_image[..., label],
self.affine, **options)
slicer.contour_map(self.mask, self.affine,
levels=[0], colors=(color, ))
return slicer
else:
slicer = viz.plot_map(self.mask, self.affine, **options)
for i, label in enumerate(self.labels()):
color = rcmap(1. * i / self.size) if rcmap is not None \
else pl.cm.gist_rainbow(1. * i / self.size)
slicer.contour_map(
self.label_image[..., label],
self.affine, levels=[0],
colors=(color, ))
return slicer
def show_slices(image_in, anat_file, coordinates, thr):
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as pl
import numpy as np
from nibabel import load
import os
from nipy.labs import viz
anat = anat_file
img = image_in
coords = coordinates[0]
threshold = thr
cmap = pl.cm.jet
prefix = None,
show_colorbar = True
formatter = '%.2f'
img1 = load(img)
data, aff = img1.get_data(), img1.get_affine()
anatimg = load(
anat) #load('/usr/share/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz')
anatdata, anataff = anatimg.get_data(), anatimg.get_affine()
anatdata = anatdata.astype(np.float)
anatdata[anatdata < 10.] = np.nan
outfile1 = os.path.split(img)[1][0:-7]
outfiles = []
for idx, coord in enumerate(coords):
outfile = outfile1 + 'cluster%02d' % idx
osl = viz.plot_map(np.asarray(data),
aff,
anat=anatdata,
anat_affine=anataff,
threshold=threshold,
cmap=cmap,
black_bg=False,
cut_coords=coord)
if show_colorbar:
cb = plt.colorbar(plt.gca().get_images()[1],
cax=plt.axes([0.4, 0.075, 0.2, 0.025]),
orientation='horizontal',
format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
#osl.frame_axes.figure.savefig(outfile+'.svg', bbox_inches='tight', transparent=True)
osl.frame_axes.figure.savefig(os.path.join(os.getcwd(),
outfile + '.png'),
dpi=600,
bbox_inches='tight',
transparent=True)
#pl.savefig(os.path.join(os.getcwd(),outfile+'.png'), dpi=600, bbox_inches='tight', transparent=True)
outfiles.append(os.path.join(os.getcwd(), outfile + '.png'))
return outfiles
def plot_brain(x, affine, template, template_affine, imgfile):
new_brain = x
img = nb.Nifti1Image(new_brain, affine)
nb.save(img, imgfile+".nii.gz")
#title = imgfile.split("/")[-1]
#slicer = plot_map(new_brain, affine, anat=template, anat_affine=template_affine, cmap = plt.cm.jet, title=title)
slicer = plot_map(new_brain, affine, anat=template, anat_affine=template_affine, cmap=cm.cold_hot, black_bg=True)#.cm.jet
slicer.contour_map(template, template_affine, cmap=plt.cm.binary, black_bg=True)# plt.cm.Greys
#plt.show()
#plt.savefig(imgfile+'.png', format='png')
plt.savefig(imgfile+'.pdf', format='pdf', facecolot='k', edgecolor='k')
def plot_bg(cut_coords=None, title=None):
anat, anat_affine, anat_max = anat_cache._AnatCache.get_anat()
figure = pl.figure(figsize=(8, 2.6), facecolor='w', edgecolor='w')
ax = pl.axes([.0, .0, .85, 1], axisbg='w')
slicer = plot_map(anat,
anat_affine,
cmap=pl.cm.gray,
vmin=.1 * anat_max,
vmax=.8 * anat_max,
figure=figure,
cut_coords=cut_coords,
axes=ax, )
slicer.annotate()
slicer.draw_cross()
if title:
slicer.title(title, x=.05, y=.9)
return slicer
def plot_bg(cut_coords=None, title=None):
anat, anat_affine, anat_max = anat_cache._AnatCache.get_anat()
figure = pl.figure(figsize=(8, 2.6), facecolor='w', edgecolor='w')
ax = pl.axes([.0, .0, .85, 1], axisbg='w')
slicer = plot_map(anat,
anat_affine,
cmap=pl.cm.gray,
vmin=.1 * anat_max,
vmax=.8 * anat_max,
figure=figure,
cut_coords=cut_coords,
axes=ax, )
slicer.annotate()
slicer.draw_cross()
if title:
slicer.title(title, x=.05, y=.9)
return slicer
def show_slices(image_in, anat_file, coordinates,thr):
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as pl
import numpy as np
from nibabel import load
import os
from nipy.labs import viz
anat = anat_file
img = image_in
coords = coordinates[0]
threshold=thr
cmap=pl.cm.jet
prefix=None,
show_colorbar=True
formatter='%.2f'
img1 = load(img)
data, aff = img1.get_data(), img1.get_affine()
anatimg = load(anat) #load('/usr/share/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz')
anatdata, anataff = anatimg.get_data(), anatimg.get_affine()
anatdata = anatdata.astype(np.float)
anatdata[anatdata<10.] = np.nan
outfile1 = os.path.split(img)[1][0:-7]
outfiles = []
for idx,coord in enumerate(coords):
outfile = outfile1+'cluster%02d' % idx
osl = viz.plot_map(np.asarray(data), aff, anat=anatdata, anat_affine=anataff,
threshold=threshold, cmap=cmap,
black_bg=False, cut_coords=coord)
if show_colorbar:
cb = plt.colorbar(plt.gca().get_images()[1], cax=plt.axes([0.4, 0.075, 0.2, 0.025]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
#osl.frame_axes.figure.savefig(outfile+'.svg', bbox_inches='tight', transparent=True)
osl.frame_axes.figure.savefig(os.path.join(os.getcwd(),outfile+'.png'), dpi=600, bbox_inches='tight', transparent=True)
#pl.savefig(os.path.join(os.getcwd(),outfile+'.png'), dpi=600, bbox_inches='tight', transparent=True)
outfiles.append(os.path.join(os.getcwd(),outfile+'.png'))
return outfiles
def overlay_new(stat_image,background_image,threshold):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
from pylab import colorbar, gca, axes
import numpy as np
# Second example, with a given anatomical image slicing in the Z
# direction
fnames = [os.path.abspath('z_view.png'),
os.path.abspath('x_view.png'),
os.path.abspath('y_view.png')]
formatter='%.2f'
img = load(stat_image)
data, affine = img.get_data(), img.get_affine()
anat_img = load(background_image)
anat = anat_img.get_data()
anat_affine = anat_img.get_affine()
anat = np.ones(anat.shape) - anat
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='z', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, 0.00, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[0],bbox_inches='tight')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='x', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, -0.06, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[1],bbox_inches='tight')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='y', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, -0.08, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[2],bbox_inches='tight')
pl.close()
return fnames
def overlay_new(stat_image,background_image,threshold):
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
from pylab import colorbar, gca, axes
import numpy as np
# Second example, with a given anatomical image slicing in the Z
# direction
fnames = [os.path.abspath('z_view.png'),
os.path.abspath('x_view.png'),
os.path.abspath('y_view.png')]
formatter='%.2f'
img = load(stat_image)
data, affine = img.get_data(), img.get_affine()
anat_img = load(background_image)
anat = anat_img.get_data()
anat_affine = anat_img.get_affine()
anat = np.ones(anat.shape) - anat
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='z', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, 0.00, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[0],bbox_inches='tight')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='x', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, -0.06, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[1],bbox_inches='tight')
viz.plot_map(data, affine, anat=anat, anat_affine=anat_affine,
slicer='y', threshold=threshold, cmap=viz.cm._cm.hot)
cb = colorbar(gca().get_images()[1], cax=axes([0.3, -0.08, 0.4, 0.07]),
orientation='horizontal', format=formatter)
cb.set_ticks([cb._values.min(), cb._values.max()])
pl.savefig(fnames[2],bbox_inches='tight')
pl.close()
return fnames
from nipy.utils import example_data
# Local import
from get_data_light import get_second_level_dataset
# 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_data()
affine = img.get_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_data()
anat_affine = anat_img.get_affine()
except OSError, e:
# File does not exist: the data package is not installed
print e
anat = None
print('Computing contrasts...')
mean_map = multi_session_model.means[0] # for display
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print(' Contrast % 2i out of %i: %s' %
(index + 1, len(contrasts), contrast_id))
z_image_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
z_map, = multi_session_model.contrast([contrast_val] * 2,
con_id=contrast_id,
output_z=True)
save(z_map, z_image_path)
# make a snapshot of the contrast activation
if contrast_id == 'Effects_of_interest':
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
vmin = -vmax
plot_map(z_map.get_data(),
z_map.get_affine(),
anat=mean_map.get_data(),
anat_affine=mean_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
figure=10,
threshold=2.5,
black_bg=True)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
print("All the results were witten in %s" % write_dir)
plt.show()
contrasts = make_fiac_contrasts()
write_dir = os.getcwd()
print "Computing contrasts..."
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print " Contrast % 2i out of %i: %s" % (index + 1, len(contrasts), contrast_id)
contrast_path = op.join(write_dir, "%s_z_map.nii" % contrast_id)
write_array = mask_array.astype(np.float)
ffx_z_map = (results[0].contrast(contrast_val) + results[1].contrast(contrast_val)).z_score()
write_array[mask_array] = ffx_z_map
contrast_image = Nifti1Image(write_array, affine)
save(contrast_image, contrast_path)
vmax = max(-write_array.min(), write_array.max())
vmin = -vmax
plot_map(
write_array,
affine,
anat=wmean,
anat_affine=affine,
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
figure=10,
threshold=2.5,
black_bg=True,
)
plt.savefig(op.join(write_dir, "%s_z_map.png" % contrast_id))
plt.clf()
print "All the results were witten in %s" % write_dir
#########################################
# Estimate the contrasts
#########################################
print('Computing contrasts...')
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print(' Contrast % 2i out of %i: %s' %
(index + 1, len(contrasts), contrast_id))
# save the z_image
image_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
z_map, = fmri_glm.contrast(contrast_val, con_id=contrast_id, output_z=True)
save(z_map, image_path)
# Create snapshots of the contrasts
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
plot_map(z_map.get_data(),
z_map.get_affine(),
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
slicer='z',
black_bg=True,
threshold=2.5,
title=contrast_id)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
print("All the results were witten in %s" % write_dir)
plt.show()
def montage(nifti,
anat,
roi_dict,
thr=2,
fig=None,
out_file=None,
feature_dict=None,
target_stat=None,
target_value=None):
if isinstance(anat, str):
anat = load_image(anat)
assert nifti is not None
assert anat is not None
assert roi_dict is not None
texcol = 1
bgcol = 0
iscale = 2
weights = nifti.get_data()
#weights = weights / weights.std(axis=3)
features = weights.shape[-1]
indices = [0]
y = 8
x = int(ceil(1.0 * features / y))
font = {"size": 8}
rc("font", **font)
if fig is None:
fig = plt.figure(figsize=[iscale * y, iscale * x / 2.5])
plt.subplots_adjust(left=0.01,
right=0.99,
bottom=0.01,
top=0.99,
wspace=0.1,
hspace=0)
for f in xrange(features):
roi = roi_dict.get(f, None)
if roi is None:
continue
coords = roi["top_clust"]["coords"]
assert coords is not None
feat = weights[:, :, :, f]
feat = feat / feat.std()
imax = np.max(np.absolute(feat))
imin = -imax
imshow_args = {"vmax": imax, "vmin": imin}
coords = ([-coords[0], -coords[1], coords[2]])
ax = fig.add_subplot(x, y, f + 1)
plt.axis("off")
try:
plot_map(feat,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=thr,
figure=fig,
axes=ax,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
logger.exception(e)
plt.text(0.05,
0.8,
str(f),
transform=ax.transAxes,
horizontalalignment="center",
color=(texcol, texcol, texcol))
pos = [(0.05, 0.05), (0.4, 0.05), (0.8, 0.05)]
colors = ["purple", "yellow", "green"]
if feature_dict is not None and feature_dict.get(f, None) is not None:
d = feature_dict[f]
for i, key in enumerate([k for k in d if k != "real_id"]):
plt.text(pos[i][0],
pos[i][1],
"%s=%.2f" % (key, d[key]),
transform=ax.transAxes,
horizontalalignment="left",
color=colors[i])
if key == target_stat:
assert target_value is not None
if d[key] >= target_value:
p_fancy = FancyBboxPatch((0.1, 0.1),
2.5 - .1,
1 - .1,
boxstyle="round,pad=0.1",
ec=(1., 0.5, 1.),
fc="none")
ax.add_patch(p_fancy)
elif d[key] <= -target_value:
p_fancy = FancyBboxPatch((0.1, 0.1),
iscale * 2.5 - .1,
iscale - .1,
boxstyle="round,pad=0.1",
ec=(0., 0.5, 0.),
fc="none")
ax.add_patch(p_fancy)
# stdout.write("\rSaving montage: DONE\n")
if out_file is not None:
plt.savefig(out_file,
transparent=True,
facecolor=(bgcol, bgcol, bgcol))
else:
plt.draw()
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Example of activation image vizualization
with nipy.labs vizualization tools
"""
print __doc__
import os.path
import pylab as pl
from nibabel import load
from nipy.labs import viz
import get_data_light
# get the data
data_dir = get_data_light.get_it()
img = load(os.path.join(data_dir, 'spmT_0029.nii.gz'))
data = img.get_data()
affine = img.get_affine()
viz.plot_map(data, affine, cut_coords=(-52, 10, 22),
threshold=2.0, cmap=viz.cm.cold_hot)
pl.show()
########################################
# Perform a GLM analysis on H1
########################################
fmri_glm = FMRILinearModel(fmri_data,
design_matrix.matrix, mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# Estimate the contrast
z_map, = fmri_glm.contrast(reading_vs_visual, output_z=True)
# Plot the contrast
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
plot_map(z_map.get_data(), z_map.get_affine(),
cmap=cm.cold_hot, vmin=-vmax, vmax=vmax,
slicer='z', black_bg=True, threshold=2.5,
title='Reading vs visual')
# Count all the clusters for |Z| > 2.5
Z = z_map.get_data()
from scipy import ndimage
cluster_map, n_clusters = ndimage.label(np.abs(Z) > 2.5)
cluster_sizes = np.bincount(cluster_map.ravel())[1:]
print "Cluster sizes:"
print np.sort(cluster_sizes)
mask = fmri_glm.mask
########################################
# Perform GLM analysis on H0 (permuted)
print 'Computing contrasts...'
for index, (contrast_id, contrast_val) in enumerate(contrasts.iteritems()):
print ' Contrast % 2i out of %i: %s' % (index + 1, len(contrasts),
contrast_id)
contrast_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
write_array = mask_array.astype(np.float)
write_array[mask_array] = results.contrast(contrast_val).z_score()
contrast_image = Nifti1Image(write_array, affine)
save(contrast_image, contrast_path)
vmax = max(-write_array.min(), write_array.max())
plot_map(write_array,
affine,
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
anat=None,
figure=10,
threshold=2.5)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
plt.clf()
#########################################
# End
#########################################
print "All the results were witten in %s" % write_dir
# make a simple 2D plot
plot_map(write_array,
affine,
from nibabel import load
from nipy.labs import viz
# activation image to look at
img = load('spmT_0029.nii.gz')
data = img.get_data()
affine = img.get_affine()
# visualize the activation on top of MNI template
viz.plot_map(data,
affine,
cut_coords=(-52, 10, 22),
threshold=3.0,
cmap=viz.cm.cold_hot)
plt.show()
#######################################
# 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_data().min(), brain_map.get_data().max()
# make a simple 2D plot
plot_map(brain_map.get_data(),
brain_map.get_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_data(),
brain_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
anat=None,
figure=11,
threshold=3,
do3d=True)
def generate_subject_stats_report(
stats_report_filename,
contrasts,
z_maps,
mask,
design_matrices=None,
subject_id=None,
anat=None,
anat_affine=None,
threshold=2.3,
cluster_th=0,
cmap=viz.cm.cold_hot,
start_time=None,
user_script_name=None,
progress_logger=None,
shutdown_all_reloaders=True,
**glm_kwargs
):
"""Generates a report summarizing the statistical methods and results
Parameters
----------
stats_report_filename: string:
html file to which output (generated html) will be written
contrasts: dict of arrays
contrasts we are interested in; same number of contrasts as zmaps;
same keys
zmaps: dict of image objects or strings (image filenames)
zmaps for contrasts we are interested in; one per contrast id
mask: 'nifti image object'
brain mask for ROI
design_matrix: list of 'DesignMatrix', `numpy.ndarray` objects or of
strings (.png, .npz, etc.) for filenames
design matrices for the experimental conditions
contrasts: dict of arrays
dictionary of contrasts of interest; the keys are the contrast ids,
the values are contrast values (lists)
z_maps: dict of 3D image objects or strings (image filenames)
dict with same keys as 'contrasts'; the values are paths of z-maps
for the respective contrasts
anat: 3D array (optional)
brain image to serve bg unto which activation maps will be plotted;
passed to viz.plot_map API
anat_affine: 2D array (optional)
affine data for the anat
threshold: float (optional)
threshold to be applied to activation maps voxel-wise
cluster_th: int (optional)
minimal voxel count for clusteres declared as 'activated'
cmap: cmap object (default viz.cm.cold_hot)
color-map to use in plotting activation maps
start_time: string (optional)
start time for the stats analysis (useful for the generated
report page)
user_script_name: string (optional, default None)
existing filename, path to user script used in doing the analysis
progress_logger: ProgressLogger object (optional)
handle for logging progress
shutdown_all_reloaders: bool (optional, default True)
if True, all pages connected to the stats report page will
be prevented from reloading after the stats report page
has been completely generated
**glm_kwargs:
kwargs used to specify the control parameters used to specify the
experimental paradigm and the GLM
"""
# prepare for stats reporting
if progress_logger is None:
progress_logger = base_reporter.ProgressReport()
output_dir = os.path.dirname(stats_report_filename)
# copy css and js stuff to output dir
base_reporter.copy_web_conf_files(output_dir)
# initialize gallery of design matrices
design_thumbs = base_reporter.ResultsGallery(
loader_filename=os.path.join(output_dir,
"design.html")
)
# initialize gallery of activation maps
activation_thumbs = base_reporter.ResultsGallery(
loader_filename=os.path.join(output_dir,
"activation.html")
)
# get caller module handle from stack-frame
if user_script_name is None:
user_script_name = sys.argv[0]
user_source_code = base_reporter.get_module_source_code(
user_script_name)
methods = """
GLM and Statistical Inference have been done using the <i>%s</i> script, \
powered by <a href="%s">nipy</a>. Statistic images have been thresholded at \
Z>%s voxel-level.
""" % (user_script_name, base_reporter.NIPY_URL, threshold)
# report the control parameters used in the paradigm and analysis
design_params = ""
if len(glm_kwargs):
design_params += ("The following control parameters were used for "
" specifying the experimental paradigm and fitting the "
"GLM:<br/><ul>")
design_params += base_reporter.dict_to_html_ul(glm_kwargs)
if start_time is None:
start_time = time.ctime()
report_title = "GLM and Statistical Inference"
if not subject_id is None:
report_title += " for subject %s" % subject_id
level1_html_markup = base_reporter.get_subject_report_stats_html_template(
).substitute(
title=report_title,
start_time=start_time,
subject_id=subject_id,
# insert source code stub
source_script_name=user_script_name,
source_code=user_source_code,
design_params=design_params,
methods=methods,
cmap=cmap.name)
with open(stats_report_filename, 'w') as fd:
fd.write(str(level1_html_markup))
fd.close()
progress_logger.log("<b>Level 1 statistics</b><br/><br/>")
# create design matrix thumbs
if not design_matrices is None:
for design_matrix, j in zip(design_matrices,
xrange(len(design_matrices))):
# sanitize design_matrix type
if isinstance(design_matrix, basestring):
if not isinstance(design_matrix, DesignMatrix):
if design_matrix.endswith('.npz'):
npz = np.load(design_matrix)
design_matrix = DesignMatrix(npz['X'],
npz['conditions'],
)
else:
# XXX handle case of .png, jpeg design matrix image
raise TypeError(
"Unsupported design matrix type '%'" % type(
design_matrix))
elif isinstance(design_matrix, np.ndarray) or isinstance(
design_matrix,
list):
X = np.array(design_matrix)
assert len(X.shape) == 2
conditions = ['%i' % i for i in xrange(X.shape[-1])]
design_matrix = DesignMatrix(X, conditions)
# else:
# raise TypeError(
# "Unsupported design matrix type '%s'" % type(
# design_matrix))
# plot design_matrix proper
ax = design_matrix.show(rescale=True)
ax.set_position([.05, .25, .9, .65])
dmat_outfile = os.path.join(output_dir,
'design_matrix_%i.png' % (j + 1),
)
pl.savefig(dmat_outfile, bbox_inches="tight", dpi=200)
thumb = base_reporter.Thumbnail()
thumb.a = base_reporter.a(href=os.path.basename(dmat_outfile))
thumb.img = base_reporter.img(src=os.path.basename(dmat_outfile),
height="500px",
)
thumb.description = "Design Matrix"
thumb.description += " %s" % (j + 1) if len(
design_matrices) > 1 else ""
# commit activation thumbnail into gallery
design_thumbs.commit_thumbnails(thumb)
# make colorbar (place-holder, will be overridden, once we've figured out
# the correct end points) for activations
colorbar_outfile = os.path.join(output_dir,
'activation_colorbar.png')
base_reporter.make_standalone_colorbar(
cmap, threshold, 8., colorbar_outfile)
# create activation thumbs
_vmax = 0
_vmin = threshold
for j in xrange(len(contrasts)):
contrast_id = contrasts.keys()[j]
contrast_val = contrasts[contrast_id]
z_map = z_maps[contrast_id]
# compute cut_coords for viz.plot_map(..) API
# XXX review computation of cut_coords, vmin, and vmax; not clean!!!
if isinstance(z_map, basestring):
z_map = nibabel.load(z_map)
pos_data = z_map.get_data() * (np.abs(z_map.get_data()) > 0)
n_axials = 12
delta_z_axis = 3
z_axis_max = np.unravel_index(
pos_data.argmax(), z_map.shape)[2]
z_axis_min = np.unravel_index(
np.argmax(-pos_data), z_map.shape)[2]
z_axis_min, z_axis_max = (min(z_axis_min, z_axis_max),
max(z_axis_max, z_axis_min))
z_axis_min = min(z_axis_min, z_axis_max - delta_z_axis * n_axials)
cut_coords = np.linspace(z_axis_min, z_axis_max, n_axials)
# compute vmin and vmax
vmax = pos_data.max()
vmin = -vmax
# vmax = max(- z_map.get_data().min(), z_map.get_data().max())
# vmin = - vmax
# # update colorbar endpoints
_vmax = max(_vmax, vmax)
# plot activation proper
viz.plot_map(pos_data, z_map.get_affine(),
cmap=cmap,
anat=anat,
anat_affine=anat_affine,
vmin=vmin,
vmax=vmax,
threshold=threshold,
slicer='z',
cut_coords=cut_coords,
black_bg=True,
)
# store activation plot
z_map_plot = os.path.join(output_dir,
"%s_z_map.png" % contrast_id)
pl.savefig(z_map_plot, dpi=200, bbox_inches='tight',
facecolor="k",
edgecolor="k")
stats_table = os.path.join(output_dir,
"%s_stats_table.html" % contrast_id)
# create thumbnail for activation
thumbnail = base_reporter.Thumbnail()
thumbnail.a = base_reporter.a(href=os.path.basename(stats_table))
thumbnail.img = base_reporter.img(
src=os.path.basename(z_map_plot), height="200px",)
thumbnail.description = "%s contrast: %s" % (contrast_id, contrast_val)
activation_thumbs.commit_thumbnails(thumbnail)
# generate level 1 stats table
title = "Level 1 stats for %s contrast" % contrast_id
generate_level1_stats_table(
z_map, mask,
stats_table,
cluster_th=cluster_th,
z_threshold=threshold,
title=title,
)
# make colorbar for activations
base_reporter.make_standalone_colorbar(
cmap, _vmin, _vmax, colorbar_outfile)
# we're done, shut down re-loaders
progress_logger.log('<hr/>')
# prevent stats report page from reloading henceforth
progress_logger.finish(stats_report_filename)
# prevent any related page from reloading
if shutdown_all_reloaders:
progress_logger.finish_dir(output_dir)
# return generated html
with open(stats_report_filename, 'r') as fd:
stats_report = fd.read()
fd.close()
return stats_report
# GLM fitting
print('Starting fit...')
glms = []
for x, y in zip(X, Y):
glm = GeneralLinearModel(x)
data, mean = data_scaling(y.get_data()[mask_array].T)
glm.fit(data, 'ar1')
glms.append(glm)
# Compute the required contrast
print('Computing test contrast image...')
nregressors = X[0].shape[1]
## should check that all design matrices have the same
c = np.zeros(nregressors)
c[0:4] = cvect
z_vals = (glms[0].contrast(c) + glms[1].contrast(c)).z_score()
# Show Zmap image
z_map = mask_array.astype(np.float)
z_map[mask_array] = z_vals
mean_map = mask_array.astype(np.float)
mean_map[mask_array] = mean
plot_map(z_map,
affine,
anat=mean_map,
anat_affine=affine,
cmap=cm.cold_hot,
threshold=2.5,
black_bg=True)
plt.show()
def montage(nifti, anat, roi_dict, thr=2,
fig=None, out_file=None,
order=None, stats=dict()):
'''
Saves a montage of nifti images.
'''
if isinstance(anat, str):
anat = load_image(anat)
assert nifti is not None
assert anat is not None
assert roi_dict is not None
texcol = 0
bgcol = 1
iscale = 2
if isinstance(nifti, list):
weights = np.array([n.get_data() for n in nifti]).astype('float32')
weights = weights.transpose(1, 2, 3, 0)
nifti = nifti[0]
else:
weights = nifti.get_data(); #weights = weights / weights.std(axis=3)
features = weights.shape[-1]
indices = [0]
y = 8
x = int(ceil(1.0 * features / y))
font = {'size': 8}
rc('font',**font)
if fig is None:
fig = plt.figure(figsize=[iscale * y, (1.5 * iscale) * x / 2.5])
plt.subplots_adjust(left=0.01, right=0.99, bottom=0.05, top=0.99, wspace=0.05, hspace=0.5)
if order is None:
order = range(features)
for i, f in enumerate(order):
roi = roi_dict.get(f, None)
if roi is None:
continue
if 'top_clust' in roi.keys():
coords = roi['top_clust']['coords']
else:
coords = (0., 0., 0.)
assert coords is not None
feat = weights[:, :, :, f]
feat = feat / feat.std()
imax = np.max(np.absolute(feat)); imin = -imax
imshow_args = {'vmax': imax, 'vmin': imin}
coords = ([-coords[0], -coords[1], coords[2]])
ax = fig.add_subplot(x, y, i + 1)
#plt.axis('off')
try:
plot_map(feat,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=thr,
figure=fig,
axes=ax,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
print e
pass
plt.text(0.05, 0.8, str(f),
transform=ax.transAxes,
horizontalalignment='center',
color=(texcol, texcol, texcol))
for j, r in enumerate(roi['top_clust']['rois']):
plt.text(0.05, -0.15 * (.5 + j), r[:35],
transform=ax.transAxes,
horizontalalignment='left',
color=(0, 0, 0))
pos = [(0.05, 0.05), (0.4, 0.05), (0.8, 0.05)]
colors = ['purple', 'blue', 'green']
for i, (k, vs) in enumerate(stats.iteritems()):
v = vs[f]
plt.text(pos[i][0], pos[i][1], '%s=%.2f' % (k, v),
transform=ax.transAxes,
horizontalalignment='left',
color=colors[i])
if out_file is not None:
plt.savefig(out_file, transparent=True, facecolor=(bgcol, bgcol, bgcol))
else:
plt.draw()
print ' Contrast % 2i out of %i: %s' % (index+1,
len(contrasts), contrast_id)
contrast_path = op.join(swd, '%s_z_map.nii'% contrast_id)
write_array = mask_array.astype(np.float)
z_values = st.norm.isf(st.t.sf(output[contrast_id]['t'],result.df_resid))
write_array[mask_array] = z_values
contrast_image = Nifti1Image(write_array, fmri_image.get_affine() )
save(contrast_image, contrast_path)
affine = fmri_image.get_affine()
vmax = max(-write_array.min(), write_array.max())
plot_map(write_array, affine,
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
anat=None,
figure=10,
threshold=2.5)
pylab.savefig(op.join(swd, '%s_z_map.png' % contrast_id))
pylab.clf()
#########################################
# End
#########################################
print "All the results were witten in %s" %swd
plot_map(write_array, affine,
parser.error("Directory Path should be added as argument")
fmri_files = [f for f in listdir(args.path) if isfile(join(args.path, f))]
mask_file = mask_generator.make_mask(args.path, "./Group_Mask")
design_files = design_matrix_generator.make_design(args.path)
multi_session_model = FMRILinearModel(fmri_files, design_files, mask_file)
# GLM fitting
multi_session_model.fit(do_scaling=True, model='ar1')
# Compute the required contrast
print('Computing test contrast image...')
n_regressors = [np.load(f)['arr_0'].shape[1] for f in design_files]
con = [np.hstack((cvect, np.zeros(nr - len(cvect)))) for nr in n_regressors]
z_map, = multi_session_model.contrast(con)
# Show Z-map image
mean_map = multi_session_model.means[0]
print(mean_map)
plot_map(z_map.get_data(),
z_map.get_affine(),
anat=mean_map.get_data(),
anat_affine=mean_map.get_affine(),
cmap=cm.cold_hot,
threshold=2.5,
black_bg=True)
plt.savefig('1st_analiz.png')
def montage(nifti,
anat,
roi_dict,
thr=2,
fig=None,
out_file=None,
order=None,
stats=dict()):
'''Saves a montage of nifti images.
Args:
nifti (list or nipy.core.api.image.image.Image): 4d nifti or list of \
3D niftis.
anat (nipy.core.api.image.image.Image): anatomical nifti image.
roi_dict (dict): dictionary of cluster dictionaries.
out_file (str): output file path.
order (list): List of integers. Order of montage.
stats (Optional[dict]): extra statistics to print on montage as text.
'''
if isinstance(anat, str):
anat = load_image(anat)
assert nifti is not None
assert anat is not None
assert roi_dict is not None
texcol = 0
bgcol = 1
iscale = 2
if isinstance(nifti, list):
weights = np.array([n.get_data() for n in nifti]).astype('float32')
weights = weights.transpose(1, 2, 3, 0)
nifti = nifti[0]
else:
weights = nifti.get_data()
#weights = weights / weights.std(axis=3)
features = weights.shape[-1]
indices = [0]
y = 8
x = int(ceil(1.0 * features / y))
font = {'size': 8}
rc('font', **font)
if fig is None:
fig = plt.figure(figsize=[iscale * y, (1.5 * iscale) * x / 2.5])
plt.subplots_adjust(left=0.01,
right=0.99,
bottom=0.05,
top=0.99,
wspace=0.05,
hspace=0.5)
if order is None:
order = range(features)
for i, f in enumerate(order):
roi = roi_dict.get(f, None)
if roi is None:
continue
if 'top_clust' in roi.keys():
coords = roi['top_clust']['coords']
else:
coords = (0., 0., 0.)
assert coords is not None
feat = weights[:, :, :, f]
feat = feat / feat.std()
imax = np.max(np.absolute(feat))
imin = -imax
imshow_args = {'vmax': imax, 'vmin': imin}
coords = ([-coords[0], -coords[1], coords[2]])
ax = fig.add_subplot(x, y, i + 1)
#plt.axis('off')
try:
plot_map(feat,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=thr,
figure=fig,
axes=ax,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
print e
pass
plt.text(0.05,
0.8,
str(f),
transform=ax.transAxes,
horizontalalignment='center',
color=(texcol, texcol, texcol))
for j, r in enumerate(roi['top_clust']['rois']):
plt.text(0.05,
-0.15 * (.5 + j),
r[:35],
transform=ax.transAxes,
horizontalalignment='left',
color=(0, 0, 0))
pos = [(0.05, 0.05), (0.4, 0.05), (0.8, 0.05)]
colors = ['purple', 'blue', 'green']
for i, (k, vs) in enumerate(stats.iteritems()):
v = vs[f]
plt.text(pos[i][0],
pos[i][1],
'%s=%.2f' % (k, v),
transform=ax.transAxes,
horizontalalignment='left',
color=colors[i])
if out_file is not None:
plt.savefig(out_file,
transparent=True,
facecolor=(bgcol, bgcol, bgcol))
else:
plt.draw()
# concatenate the individual images
first_level_image = concat_images(betas)
# set the model
design_matrix = np.ones(len(betas))[:, np.newaxis] # only the intercept
grp_model = FMRILinearModel(first_level_image, design_matrix, grp_mask)
# GLM fitting using ordinary least_squares
grp_model.fit(do_scaling=False, model='ols')
# specify and estimate the contrast
contrast_val = np.array(([[1]])) # the only possible contrast !
z_map, = grp_model.contrast(contrast_val, con_id='one_sample', output_z=True)
# write the results
save(z_map, path.join(write_dir, 'one_sample_z_map.nii'))
# look at the result
vmax = max(- z_map.get_data().min(), z_map.get_data().max())
vmin = - vmax
plot_map(z_map.get_data(), z_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
threshold=3.,
black_bg=True)
plt.savefig(path.join(write_dir, '%s_z_map.png' % 'one_sample'))
plt.show()
print "Wrote all the results in directory %s" % write_dir
def montage(nifti, anat, roi_dict, thr=2,
fig=None, out_file=None, feature_dict=None,
target_stat=None, target_value=None):
if isinstance(anat, str):
anat = load_image(anat)
assert nifti is not None
assert anat is not None
assert roi_dict is not None
texcol = 1
bgcol = 0
iscale = 2
weights = nifti.get_data(); #weights = weights / weights.std(axis=3)
features = weights.shape[-1]
indices = [0]
y = 8
x = int(ceil(1.0 * features / y))
font = {"size":8}
rc("font",**font)
if fig is None:
fig = plt.figure(figsize=[iscale * y, iscale * x / 2.5])
plt.subplots_adjust(left=0.01, right=0.99, bottom=0.01, top=0.99, wspace=0.1, hspace=0)
for f in xrange(features):
roi = roi_dict.get(f, None)
if roi is None:
continue
coords = roi["top_clust"]["coords"]
assert coords is not None
feat = weights[:, :, :, f]
feat = feat / feat.std()
imax = np.max(np.absolute(feat)); imin = -imax
imshow_args = {"vmax": imax, "vmin": imin}
coords = ([-coords[0], -coords[1], coords[2]])
ax = fig.add_subplot(x, y, f + 1)
plt.axis("off")
try: plot_map(feat,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=thr,
figure=fig,
axes=ax,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
logger.exception(e)
plt.text(0.05, 0.8, str(f),
transform=ax.transAxes,
horizontalalignment="center",
color=(texcol,texcol,texcol))
pos = [(0.05, 0.05), (0.4, 0.05), (0.8, 0.05)]
colors = ["purple", "yellow", "green"]
if feature_dict is not None and feature_dict.get(f, None) is not None:
d = feature_dict[f]
for i, key in enumerate([k for k in d if k != "real_id"]):
plt.text(pos[i][0], pos[i][1], "%s=%.2f" % (key, d[key]) ,transform=ax.transAxes,
horizontalalignment="left", color=colors[i])
if key == target_stat:
assert target_value is not None
if d[key] >= target_value:
p_fancy = FancyBboxPatch((0.1, 0.1), 2.5 - .1, 1 - .1,
boxstyle="round,pad=0.1",
ec=(1., 0.5, 1.),
fc="none")
ax.add_patch(p_fancy)
elif d[key] <= -target_value:
p_fancy = FancyBboxPatch((0.1, 0.1), iscale * 2.5 - .1, iscale - .1,
boxstyle="round,pad=0.1",
ec=(0., 0.5, 0.),
fc="none")
ax.add_patch(p_fancy)
# stdout.write("\rSaving montage: DONE\n")
if out_file is not None:
plt.savefig(out_file, transparent=True, facecolor=(bgcol, bgcol, bgcol))
else:
plt.draw()
if not path.exists(write_dir):
mkdir(write_dir)
print 'Computing contrasts...'
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print ' Contrast % 2i out of %i: %s' % (
index + 1, len(contrasts), contrast_id)
contrast_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
write_array = mask_array.astype(np.float)
ffx_z_map = (results[0].contrast(contrast_val) +
results[1].contrast(contrast_val)).z_score()
write_array[mask_array] = ffx_z_map
contrast_image = Nifti1Image(write_array, affine)
save(contrast_image, contrast_path)
vmax = max(- write_array.min(), write_array.max())
vmin = - vmax
plot_map(write_array, affine,
anat=wmean, anat_affine=affine,
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
figure=10,
threshold=2.5,
black_bg=True)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
print "All the results were witten in %s" % write_dir
plt.show()
z_maps[contrast_id] = map_path
if map_type == 'effects':
effects_maps[contrast_id] = map_path
return subject_id, anat, effects_maps, z_maps, contrasts, fmri_glm.mask
if __name__ == "__maih__":
mem = Memory(os.path.join(output_dir, "cache"))
first_level_glms = map(mem.cache(do_subject_glm), subject_dirs)
# plot stats (per subject)
import matplotlib.pyplot as plt
import nipy.labs.viz as viz
all_masks = []
all_effects_maps = []
for (subject_id, anat, effects_maps, z_maps,
contrasts, mask) in first_level_glms:
all_masks.append(mask)
anat_img = nibabel.load(anat)
z_map = nibabel.load(z_maps.values()[0])
all_effects_maps.append(effects_maps)
for contrast_id, z_map in z_maps.iteritems():
z_map = nibabel.load(z_map)
viz.plot_map(z_map.get_data(), z_map.get_affine(),
anat=anat_img.get_data(),
anat_affine=anat_img.get_affine(), slicer='ortho',
title="%s: %s" % (subject_id, contrast_id),
black_bg=True, cmap=viz.cm.cold_hot, threshold=2.3)
plt.savefig("%s_%s.png" % (subject_id, contrast_id))
# Input files
fmri_files = [example_data.get_filename('fiac', 'fiac0', run)
for run in ['run1.nii.gz', 'run2.nii.gz']]
design_files = [example_data.get_filename('fiac', 'fiac0', run)
for run in ['run1_design.npz', 'run2_design.npz']]
mask_file = example_data.get_filename('fiac', 'fiac0', 'mask.nii.gz')
# Load all the data
multi_session_model = FMRILinearModel(fmri_files, design_files, mask_file)
# GLM fitting
multi_session_model.fit(do_scaling=True, model='ar1')
# Compute the required contrast
print('Computing test contrast image...')
n_regressors = [np.load(f)['X'].shape[1] for f in design_files]
con = [np.hstack((cvect, np.zeros(nr - len(cvect)))) for nr in n_regressors]
z_map, = multi_session_model.contrast(con)
# Show Z-map image
mean_map = multi_session_model.means[0]
plot_map(z_map.get_data(),
z_map.get_affine(),
anat=mean_map.get_data(),
anat_affine=mean_map.get_affine(),
cmap=cm.cold_hot,
threshold=2.5,
black_bg=True)
plt.show()
def plot_cv_tc(epi_data, session_ids, subject_id,
do_plot=True,
write_image=True, mask=True, bg_image=False,
plot_diff=True,
_output_dir=None,
cv_tc_plot_outfile=None):
""" Compute coefficient of variation of the data and plot it
Parameters
----------
epi_data: list of strings, input fMRI 4D images
session_ids: list of strings of the same length as epi_data,
session indexes (for figures)
subject_id: string, id of the subject (for figures)
do_plot: bool, optional,
should we plot the resulting time course
write_image: bool, optional,
should we write the cv image
mask: bool or string, optional,
(string) path of a mask or (bool) should we mask the data
bg_image: bool or string, optional,
(string) pasth of a background image for display or (bool)
should we compute such an image as the mean across inputs.
if no, an MNI template is used (works for normalized data)
"""
if _output_dir is None:
if not cv_tc_plot_outfile is None:
_output_dir = os.path.dirname(cv_tc_plot_outfile)
else:
_output_dir = tempfile.mkdtemp()
cv_tc_ = []
if isinstance(mask, basestring):
mask_array = nibabel.load(mask).get_data() > 0
elif mask == True:
mask_array = compute_mask_files(epi_data[0])
else:
mask_array = None
for (session_id, fmri_file) in zip(session_ids, epi_data):
nim = do_3Dto4D_merge(fmri_file, output_dir=_output_dir)
affine = nim.get_affine()
if len(nim.shape) == 4:
# get the data
data = nim.get_data()
else:
raise TypeError("Expecting 4D image!")
pass
# compute the CV for the session
cache_dir = os.path.join(_output_dir, "CV")
if not os.path.exists(cache_dir):
os.makedirs(cache_dir)
mem = joblib.Memory(cachedir=cache_dir, verbose=5)
cv = mem.cache(compute_cv)(data, mask_array=mask_array)
if write_image:
# write an image
nibabel.save(nibabel.Nifti1Image(cv, affine),
os.path.join(_output_dir, 'cv_%s.nii' % session_id))
if bg_image == False:
try:
viz.plot_map(
cv, affine, threshold=.01, cmap=viz.cm.cold_hot)
except IndexError:
print traceback.format_exc()
else:
if isinstance(bg_image, basestring):
_tmp = nibabel.load(bg_image)
anat, anat_affine = (
_tmp.get_data(),
_tmp.get_affine())
else:
anat, anat_affine = data.mean(-1), affine
try:
viz.plot_map(
cv, affine, threshold=.01, cmap=viz.cm.cold_hot,
anat=anat, anat_affine=anat_affine)
except IndexError:
print traceback.format_exc()
# compute the time course of cv
cv_tc_sess = np.median(
np.sqrt((data[mask_array > 0].T /
data[mask_array > 0].mean(-1) - 1) ** 2), 1)
cv_tc_.append(cv_tc_sess)
cv_tc = np.concatenate(cv_tc_)
if do_plot:
# plot the time course of cv for different subjects
pl.figure()
pl.plot(cv_tc, label=subject_id)
pl.legend()
pl.xlabel('time(scans)')
pl.ylabel('Median coefficient of variation')
pl.axis('tight')
if not cv_tc_plot_outfile is None:
pl.savefig(cv_tc_plot_outfile,
bbox_inches="tight", dpi=200)
return cv_tc
# GLM fitting
print('Starting fit...')
glms = []
for x, y in zip(X, Y):
glm = GeneralLinearModel(x)
data, mean = data_scaling(y.get_data()[mask_array].T)
glm.fit(data, 'ar1')
glms.append(glm)
# Compute the required contrast
print('Computing test contrast image...')
nregressors = X[0].shape[1]
## should check that all design matrices have the same
c = np.zeros(nregressors)
c[0:4] = cvect
z_vals = (glms[0].contrast(c) + glms[1].contrast(c)).z_score()
# Show Zmap image
z_map = mask_array.astype(np.float)
z_map[mask_array] = z_vals
mean_map = mask_array.astype(np.float)
mean_map[mask_array] = mean
plot_map(z_map,
affine,
anat=mean_map,
anat_affine=affine,
cmap=cm.cold_hot,
threshold=2.5,
black_bg=True)
plt.show()
def make_parcels(X,
grp_mask,
contrasts,
affine,
subjects,
write_dir='/tmp/',
method='ward',
n_clusters=500,
do_ttest=False,
do_ftest=False,
do_csv=False,
write_mean=False):
# Define the structure A of the data. Pixels connected to their neighbors.
n_voxels, n_contrasts, n_subjects = X.shape
if len(contrasts) != n_contrasts:
raise ValueError('Incorrect Number of contrasts provided')
# Define a spatial model
shape = grp_mask.shape
connectivity = grid_to_graph(shape[0], shape[1], shape[2],
grp_mask).tocsr()
# concatenate the data spatially
Xv = np.reshape(X, (n_voxels, n_contrasts * n_subjects))
X_ = PCA(n_components=100).fit_transform(Xv)
if method == 'spectral':
i, j = connectivity.nonzero()
sigma = np.sum((Xv[i] - Xv[j])**2, 1).mean()
connectivity.data = np.exp(-np.sum(
(Xv[i] - Xv[j])**2, 1) / (2 * sigma))
connectivity = connectivity.copy() + dia_matrix(
(1.e-3 * np.ones(n_voxels), [0]),
shape=(n_voxels, n_voxels)).tocsr()
# Compute clustering
print "Compute structured hierarchical clustering..."
if method == 'ward':
ward = Ward(n_clusters=n_clusters, connectivity=connectivity).fit(X_)
labels = ward.labels_
elif method == 'spectral':
labels = spectral_clustering(connectivity,
n_clusters=n_clusters,
eigen_solver='arpack',
n_init=5)
elif method in ['k-means', 'kmeans']:
_, labels, _ = k_means(X_,
n_clusters=n_clusters,
n_init=5,
precompute_distances=False,
max_iter=30)
else:
xyz = np.array(np.where(grp_mask)).T
_, labels, _ = k_means(xyz,
n_clusters=n_clusters,
n_init=1,
precompute_distances=False,
max_iter=10)
wlabel = grp_mask.astype(np.int16) - 1
wlabel[wlabel == 0] = labels
save(Nifti1Image(wlabel, affine),
path.join(write_dir, 'parcel_%s_%d.nii' % (method, n_clusters)))
ll, bic = 0, 0
for c, contrast in enumerate(contrasts):
mu_map = np.zeros_like(wlabel).astype(np.float)
s1_map = np.zeros_like(wlabel).astype(np.float)
s2_map = np.zeros_like(wlabel).astype(np.float)
ll_, mu_, sigma1_, sigma2_, bic_ = parameter_map(X[:, c],
labels,
null=False)
ll += ll_.sum()
bic += bic_.sum()
if write_mean:
mu_map[grp_mask == 1] = mu_[labels]
s1_map[grp_mask == 1] = sigma1_[labels]
s2_map[grp_mask == 1] = sigma2_[labels]
save(Nifti1Image(mu_map, affine),
path.join(write_dir, 'mu_%s.nii' % contrast))
save(Nifti1Image(s1_map, affine),
path.join(write_dir, 's1_%s.nii' % contrast))
save(Nifti1Image(s2_map, affine),
path.join(write_dir, 's2_%s.nii' % contrast))
# Get the signals per parcel
mean_X = np.empty((n_clusters, n_contrasts, n_subjects), np.float)
for k in range(n_clusters):
mean_X[k] = X[labels == k].mean(0).reshape(n_subjects, n_contrasts).T
if do_ttest:
# create one-sample t-tests images
wlabel[grp_mask == 1] = labels
active = np.array(np.maximum(0, wlabel.astype(np.float)))
for c, contrast in enumerate(contrasts):
t_test = mean_X[:, c].mean(1) / mean_X[:, c].std(1) *\
np.sqrt(n_subjects)
active[grp_mask == 1] = t_test[(labels).astype(np.int16)]
viz.plot_map(active,
affine,
threshold=4.0,
cmap=viz.cm.cold_hot,
vmin=-20.,
vmax=20)
if do_ftest:
# pseudo F-test
F_test = n_subjects * (mean_X.mean(2)**2 / mean_X.var(2)).sum(1) / 3.
active[grp_mask == 1] = F_test[(labels).astype(np.int16)]
viz.plot_map(active,
affine,
threshold=4.0,
cmap=viz.cm.cold_hot,
vmin=-20.,
vmax=20)
save(Nifti1Image(active, affine), path.join(write_dir, 'F_RFX.nii'))
if do_csv:
# write parcel signals as csv file
hash_ = hashlib.sha224(wlabel).hexdigest()
for c, contrast in enumerate(contrasts):
wpath = path.join(write_dir,
'contrast_%s_%s.csv' % (contrast, hash_))
fid = open(wpath, 'wb')
writer = csv.writer(fid, delimiter=' ')
writer.writerow(subjects)
pdata = mean_X[:, c]
# write pdata
for row in pdata:
writer.writerow(row)
fid.close()
return ll, bic
########################################
# Output beta and variance images
########################################
beta_hat = fmri_glm.glms[0].get_beta() # Least-squares estimates of the beta
variance_hat = fmri_glm.glms[0].get_mse() # Estimates of the variance
mask = fmri_glm.mask.get_data() > 0
# output beta images
beta_map = np.tile(mask.astype(np.float)[..., np.newaxis], dim)
beta_map[mask] = beta_hat.T
beta_image = Nifti1Image(beta_map, fmri_glm.affine)
beta_image.get_header()['descrip'] = (
'Parameter estimates of the localizer dataset')
save(beta_image, path.join(write_dir, 'beta.nii'))
print "Beta image witten in %s" % write_dir
variance_map = mask.astype(np.float)
variance_map[mask] = variance_hat
# Create a snapshots of the variance image contrasts
vmax = np.log(variance_hat.max())
plot_map(np.log(variance_map + .1),
fmri_glm.affine,
cmap=cm.hot_black_bone,
vmin=np.log(0.1),
vmax=vmax,
anat=None,
threshold=.1, alpha=.9)
plt.show()
# concatenate the individual images
first_level_image = concat_images(betas)
# set the model
design_matrix = np.ones(len(betas))[:, np.newaxis] # only the intercept
grp_model = FMRILinearModel(first_level_image, design_matrix, grp_mask)
# GLM fitting using ordinary least_squares
grp_model.fit(do_scaling=False, model='ols')
# specify and estimate the contrast
contrast_val = np.array(([[1]])) # the only possible contrast !
z_map, = grp_model.contrast(contrast_val, con_id='one_sample', output_z=True)
# write the results
save(z_map, path.join(write_dir, 'one_sample_z_map.nii'))
# look at the result
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
vmin = -vmax
plot_map(z_map.get_data(),
z_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
threshold=3.,
black_bg=True)
plt.savefig(path.join(write_dir, '%s_z_map.png' % 'one_sample'))
plt.show()
print("Wrote all the results in directory %s" % write_dir)
def generate_ica_report(
stats_report_filename,
ica_maps,
mask=None,
report_title='ICA Report',
methods_text='ICA',
anat=None,
anat_affine=None,
threshold=2.,
cluster_th=0,
cmap=viz.cm.cold_hot,
start_time=None,
user_script_name=None,
progress_logger=None,
shutdown_all_reloaders=True,
**glm_kwargs
):
"""Generates a report summarizing the statistical methods and results
Parameters
----------
stats_report_filename: string:
html file to which output (generated html) will be written
contrasts: dict of arrays
contrasts we are interested in; same number of contrasts as zmaps;
same keys
zmaps: dict of image objects or strings (image filenames)
zmaps for contrasts we are interested in; one per contrast id
mask: 'nifti image object'
brain mask for ROI
design_matrix: list of 'DesignMatrix', `numpy.ndarray` objects or of
strings (.png, .npz, etc.) for filenames
design matrices for the experimental conditions
contrasts: dict of arrays
dictionary of contrasts of interest; the keys are the contrast ids,
the values are contrast values (lists)
z_maps: dict of 3D image objects or strings (image filenames)
dict with same keys as 'contrasts'; the values are paths of z-maps
for the respective contrasts
anat: 3D array (optional)
brain image to serve bg unto which activation maps will be plotted;
passed to viz.plot_map API
anat_affine: 2D array (optional)
affine data for the anat
threshold: float (optional)
threshold to be applied to activation maps voxel-wise
cluster_th: int (optional)
minimal voxel count for clusteres declared as 'activated'
cmap: cmap object (default viz.cm.cold_hot)
color-map to use in plotting activation maps
start_time: string (optional)
start time for the stats analysis (useful for the generated
report page)
user_script_name: string (optional, default None)
existing filename, path to user script used in doing the analysis
progress_logger: ProgressLogger object (optional)
handle for logging progress
shutdown_all_reloaders: bool (optional, default True)
if True, all pages connected to the stats report page will
be prevented from reloading after the stats report page
has been completely generated
**glm_kwargs:
kwargs used to specify the control parameters used to specify the
experimental paradigm and the GLM
"""
# prepare for stats reporting
if progress_logger is None:
progress_logger = base_reporter.ProgressReport()
output_dir = os.path.dirname(stats_report_filename)
# copy css and js stuff to output dir
base_reporter.copy_web_conf_files(output_dir)
# initialize gallery of activation maps
activation_thumbs = base_reporter.ResultsGallery(
loader_filename=os.path.join(output_dir,
"activation.html")
)
# get caller module handle from stack-frame
if user_script_name is None:
user_script_name = sys.argv[0]
user_source_code = base_reporter.get_module_source_code(
user_script_name)
if start_time is None:
start_time = time.ctime()
ica_html_markup = base_reporter.get_ica_html_template(
).substitute(
title=report_title,
start_time=start_time,
# insert source code stub
source_script_name=user_script_name,
source_code=user_source_code,
methods=methods_text,
cmap=cmap.name)
with open(stats_report_filename, 'w') as fd:
fd.write(str(ica_html_markup))
fd.close()
progress_logger.log("<b>ICA</b><br/><br/>")
# make colorbar (place-holder, will be overridden, once we've figured out
# the correct end points) for activations
colorbar_outfile = os.path.join(output_dir,
'activation_colorbar.png')
base_reporter.make_standalone_colorbar(
cmap, threshold, 8., colorbar_outfile)
# generate thumbs for the gallery
_vmax = 0
_vmin = threshold
for ica_map_id, ica_map in ica_maps.iteritems():
# load the map
if isinstance(ica_map, basestring):
ica_map = nibabel.load(ica_map)
# compute cut_coords for viz.plot_map(..) API
cut_coords = base_reporter.get_cut_coords(
ica_map.get_data(), n_axials=12, delta_z_axis=3)
# compute vmin and vmax
vmin, vmax = base_reporter.compute_vmin_vmax(ica_map.get_data())
# update colorbar endpoints
_vmax = max(_vmax, vmax)
_vmin = min(_vmin, vmin)
# plot activation proper
viz.plot_map(ica_map.get_data(), ica_map.get_affine(),
cmap=cmap,
anat=anat,
anat_affine=anat_affine,
vmin=vmin,
vmax=vmax,
threshold=threshold,
slicer='z',
cut_coords=cut_coords,
black_bg=True,
)
# store activation plot
ica_map_plot = os.path.join(output_dir,
"%s_ica_map.png" % ica_map_id)
pl.savefig(ica_map_plot, dpi=200, bbox_inches='tight',
facecolor="k",
edgecolor="k")
stats_table = ica_map_plot # os.path.join(output_dir,
# "%s_stats_table.html" % ica_map_id)
# create thumbnail for activation
thumbnail = base_reporter.Thumbnail()
thumbnail.a = base_reporter.a(href=os.path.basename(stats_table))
thumbnail.img = base_reporter.img(
src=os.path.basename(ica_map_plot), height="200px",)
thumbnail.description = "Component: %s" % ica_map_id
activation_thumbs.commit_thumbnails(thumbnail)
# make colorbar for activations
base_reporter.make_standalone_colorbar(
cmap, _vmin, _vmax, colorbar_outfile)
# we're done, shut down re-loaders
progress_logger.log('<hr/>')
# prevent stats report page from reloading henceforth
progress_logger.finish(stats_report_filename)
# prevent any related page from reloading
if shutdown_all_reloaders:
progress_logger.finish_dir(output_dir)
# return generated html
with open(stats_report_filename, 'r') as fd:
stats_report = fd.read()
fd.close()
return stats_report
from nipy.labs import viz
from nipy.utils import example_data
# Local import
from get_data_light import get_second_level_dataset
# 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_data()
affine = img.get_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_data()
anat_affine = anat_img.get_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,
def save_image(nifti,
anat,
cluster_dict,
out_path,
f,
image_threshold=2,
texcol=1,
bgcol=0,
iscale=2,
text=None,
**kwargs):
'''Saves a single nifti image.
Args:
nifti (str or nipy.core.api.image.image.Image): nifti file to visualize.
anat (nipy.core.api.image.image.Image): anatomical nifti file.
cluster_dict (dict): dictionary of clusters.
f (int): index.
image_threshold (float): treshold for `plot_map`.
texcol (float): text color.
bgcol (float): background color.
iscale (float): image scale.
text (Optional[str]): text for figure.
**kwargs: extra keyword arguments
'''
if isinstance(nifti, str):
nifti = load_image(nifti)
feature = nifti.get_data()
elif isinstance(nifti, nipy.core.image.image.Image):
feature = nifti.get_data()
font = {'size': 8}
rc('font', **font)
coords = cluster_dict['top_clust']['coords']
if coords == None:
return
feature /= feature.std()
imax = np.max(np.absolute(feature))
imin = -imax
imshow_args = dict(vmax=imax, vmin=imin, alpha=0.7)
coords = ([-coords[0], -coords[1], coords[2]])
plt.axis('off')
plt.text(0.05,
0.8,
text,
horizontalalignment='center',
color=(texcol, texcol, texcol))
try:
plot_map(feature,
xyz_affine(nifti),
anat=anat.get_data(),
anat_affine=xyz_affine(anat),
threshold=image_threshold,
cut_coords=coords,
annotate=False,
cmap=cmap,
draw_cross=False,
**imshow_args)
except Exception as e:
return
plt.savefig(out_path, transparent=True, facecolor=(bgcol, bgcol, bgcol))
def show_slices(
data,
affine,
coords=None,
cmap=None,
show_colorbar=None,
showCross=False,
cluster_thr=0,
annotate=True, ###### KW DOCUMENT
template='../scripts/templates/MNI152_T1_1mm_brain.nii.gz', ####### KW DOCUMENT
dpiRes=300,
suffix='png',
show_title=False):
# Prepare background image
anatimg = nb.load(template)
anatdata, anataff = anatimg.get_data(), anatimg.affine()
anatdata = anatdata.astype(np.float)
anatdata[anatdata < 10.] = np.nan
# Create output figure for each peak coordinate
# (so a different figure for each cluster)
for idx, coord in enumerate(coords):
# Name the output file to include the cluster id,
# the cluster threshold and the minimum cluster extent
outfile = 'Cluster_{}_thr{:04.2f}_minext{:03:0f}'.format(
idx, cluster_thr, cluster_extent)
# If show_title argument has been set to true then print the file name
# and the peak coordinates in the title of the figure
if show_title:
title = '{} {}'.format(outfile + coord)
else:
title = ''
# Woooo plot three orthogonal views of the cluster sliced through the
# peak coordinate
osl = viz.plot_map(np.asarray(data),
affine,
anat=anatdata,
anat_affine=anataff,
threshold=cluster_thr,
cmap=cmap,
annotate=annotate,
black_bg=False,
cut_coords=coord,
draw_cross=showCross,
slicer='ortho',
title=title)
# If the show colorbar option is true then show the color bar on the
# right hand side of the image
if show_colorbar:
cbarLocation = [-0.1, 0.2, 0.015, 0.6]
im = plt.gca().get_images()[1]
cb = plt.colorbar(im,
cax=plt.axes(cbarLocation),
orientation='horizontal',
format='%.2f')
cb.set_ticks([cb._values.min(), cb._values.max()])
# Save the figure!
osl.frame_axes.figure.savefig(opj(output_folder,
'{}.{}'.format(outfile, suffix)),
dpi=dpiRes,
bbox_inches='tight',
transparent=True)
# DONE! Close the plot
plt.close()
# Perform a GLM analysis on H1
########################################
fmri_glm = FMRILinearModel(fmri_data, design_matrix.matrix, mask='compute')
fmri_glm.fit(do_scaling=True, model='ar1')
# Estimate the contrast
z_map, = fmri_glm.contrast(reading_vs_visual, output_z=True)
# Plot the contrast
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
plot_map(z_map.get_data(),
z_map.get_affine(),
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
slicer='z',
black_bg=True,
threshold=2.5,
title='Reading vs visual')
# Count all the clusters for |Z| > 2.5
Z = z_map.get_data()
from scipy import ndimage
cluster_map, n_clusters = ndimage.label(np.abs(Z) > 2.5)
cluster_sizes = np.bincount(cluster_map.ravel())[1:]
print "Cluster sizes:"
print np.sort(cluster_sizes)
mask = fmri_glm.mask
# Estimate the contrasts
#########################################
contrast_id = 'left_right_motor_min'
z_map, effects_map = fmri_glm.contrast(
np.vstack((contrasts['left'], contrasts['right'])),
contrast_type='tmin-conjunction', output_z=True, output_effects=True)
z_image_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
save(z_map, z_image_path)
contrast_path = path.join(write_dir, '%s_con.nii' % contrast_id)
save(effects_map, contrast_path)
# note that the effects_map is two-dimensional:
# these dimensions correspond to 'left' and 'right'
# Create snapshots of the contrasts
vmax = max(- z_map.get_data().min(), z_map.get_data().max())
plot_map(z_map.get_data(), fmri_glm.affine,
cmap=cm.cold_hot,
vmin=- vmax,
vmax=vmax,
anat=None,
figure=10,
threshold=2.5)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
plt.show()
print('All the results were witten in %s' % write_dir)
# Note: fancier visualization of the results are shown
# in the viz3d example
mkdir(write_dir)
print("Computing contrasts...")
mean_map = multi_session_model.means[0] # for display
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print(" Contrast % 2i out of %i: %s" % (index + 1, len(contrasts), contrast_id))
z_image_path = path.join(write_dir, "%s_z_map.nii" % contrast_id)
z_map, = multi_session_model.contrast([contrast_val] * 2, con_id=contrast_id, output_z=True)
save(z_map, z_image_path)
# make a snapshot of the contrast activation
if contrast_id == "Effects_of_interest":
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
vmin = -vmax
plot_map(
z_map.get_data(),
z_map.get_affine(),
anat=mean_map.get_data(),
anat_affine=mean_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
figure=10,
threshold=2.5,
black_bg=True,
)
plt.savefig(path.join(write_dir, "%s_z_map.png" % contrast_id))
print("All the results were witten in %s" % write_dir)
plt.show()
print('Computing contrasts...')
for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
print(' Contrast % 2i out of %i: %s' %
(index + 1, len(contrasts), contrast_id))
# save the z_image
image_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
z_map, = fmri_glm.contrast(contrast_val, con_id=contrast_id, output_z=True)
save(z_map, image_path)
# Create snapshots of the contrasts
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
if index > 0:
plt.clf()
plot_map(
z_map.get_data(),
z_map.get_affine(),
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
anat=None,
cut_coords=None,
slicer='z',
black_bg=True, # looks much better thus
figure=10,
threshold=2.5)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
print("All the results were witten in %s" % write_dir)
plt.show()
contrast_id = 'left_right_motor_min'
z_map, effects_map = fmri_glm.contrast(np.vstack(
(contrasts['left'], contrasts['right'])),
contrast_type='tmin-conjunction',
output_z=True,
output_effects=True)
z_image_path = path.join(write_dir, '%s_z_map.nii' % contrast_id)
save(z_map, z_image_path)
contrast_path = path.join(write_dir, '%s_con.nii' % contrast_id)
save(effects_map, contrast_path)
# note that the effects_map is two-dimensional:
# these dimensions correspond to 'left' and 'right'
# Create snapshots of the contrasts
vmax = max(-z_map.get_data().min(), z_map.get_data().max())
plot_map(z_map.get_data(),
fmri_glm.affine,
cmap=cm.cold_hot,
vmin=-vmax,
vmax=vmax,
anat=None,
figure=10,
threshold=2.5)
plt.savefig(path.join(write_dir, '%s_z_map.png' % contrast_id))
plt.show()
print('All the results were witten in %s' % write_dir)
# Note: fancier visualization of the results are shown
# in the viz3d example
#######################################
# 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_data().min(), brain_map.get_data().max()
# make a simple 2D plot
plot_map(brain_map.get_data(), brain_map.get_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_data(), brain_map.get_affine(),
cmap=cm.cold_hot,
vmin=vmin,
vmax=vmax,
anat=None,
figure=11,
threshold=3, do3d=True)
from nipy.labs import viz3d
########################################
# Output beta and variance images
########################################
beta_hat = fmri_glm.glms[0].get_beta() # Least-squares estimates of the beta
variance_hat = fmri_glm.glms[0].get_mse() # Estimates of the variance
mask = fmri_glm.mask.get_data() > 0
# output beta images
beta_map = np.tile(mask.astype(np.float)[..., np.newaxis], dim)
beta_map[mask] = beta_hat.T
beta_image = Nifti1Image(beta_map, fmri_glm.affine)
beta_image.get_header()['descrip'] = (
'Parameter estimates of the localizer dataset')
save(beta_image, path.join(write_dir, 'beta.nii'))
print("Beta image witten in %s" % write_dir)
variance_map = mask.astype(np.float)
variance_map[mask] = variance_hat
# Create a snapshots of the variance image contrasts
vmax = np.log(variance_hat.max())
plot_map(np.log(variance_map + .1),
fmri_glm.affine,
cmap=cm.hot_black_bone,
vmin=np.log(0.1),
vmax=vmax,
anat=None,
threshold=.1,
alpha=.9)
plt.show()
