def main():
# Import a numpy array as the adjacency matrix
home = expanduser('~')
directory_name = join(home, 'Documents', 'data_conn')
data_file_name = join(directory_name, 'func_modeled.npy')
struct_conn = np.load(data_file_name)
# # Generate graph
# G = nx.from_numpy_array(struct_conn)
#
# # Visualize graph - no meaning to position or colour
# plt.figure('Graph')
# n_node = G.number_of_nodes() # number of nodes
# nx.draw(G, node_size=50, node_color=np.arange(n_node), width=0.1, cmap='Blues')
# plt.show()
# Visualise graph with positions specified by brain region coordinates
# # Import node positions from file of (x,y,z) co-ordinates from brain region centers
positions_file_name = join(directory_name, 'region_positions.npy')
region_positions = np.load(positions_file_name)
plotting.plot_connectome(struct_conn,
region_positions - region_positions.mean(0),
title="Structural Connectivity",
display_mode='x',
alpha=0,
node_color='k',
node_size=10,
edge_cmap='jet',
colorbar=True)
plotting.show()
def plot_consistent_edges(all_masks,
tail,
thresh=1.,
color='gray',
coords=None):
edge_frac = (all_masks[tail].sum(axis=0)) / (all_masks[tail].shape[0])
print("For the {} tail, {} edges were selected in at least {}% of folds".
format(tail, (edge_frac >= thresh).sum(), thresh * 100))
edge_frac_square = sp.spatial.distance.squareform(edge_frac)
node_mask = np.amax(
edge_frac_square, axis=0
) >= thresh # find nodes that have at least one edge that passes the threshold
node_size = edge_frac_square.sum(
axis=0
) * node_mask * 20 # size nodes based on how many suprathreshold edges they have
plotting.plot_connectome(adjacency_matrix=edge_frac_square,
edge_threshold=thresh,
node_color=color,
node_coords=coords,
node_size=node_size,
display_mode='lzry',
edge_kwargs={
"linewidth": 1,
'color': color
})
def plot_brain_connections(mat,
power_coords,
mat_name='beta_mat',
thre='99.9%',
save_plot=False,
cache_prefix='r1s1_'):
if mat_name == 'beta_mat':
tit = 'Beta'
elif mat_name == 'wcorr_mat':
tit = 'Weighted Connectivity'
else:
tit = 'Unknown'
# plot
sns.set_style('white')
fig = plt.figure(figsize=(10, 3))
ax = fig.add_subplot(111)
ax.axis("off")
# plot connectome with 80% edge strength in the connectivity
plotting.plot_connectome(
mat,
power_coords,
figure=fig,
edge_threshold=thre,
#node_color=,
colorbar=True,
node_size=0, # size 264
#alpha=.8,
#title='Group analysis: ' + tit,
edge_kwargs={'lw': 8})
if save_plot:
plt.savefig('./bin/' + cache_prefix + mat_name + thre + '.png')
plt.show()
plt.close()
def test_plot_connectome_non_symmetric(node_coords, non_symmetric_matrix):
"""Tests for plot_connectome with non symmetric adjacency matrices."""
ax = plot_connectome(non_symmetric_matrix, node_coords,
display_mode='ortho')
# No thresholding was performed, we should get
# as many arrows as we have edges
for direction in ['x', 'y', 'z']:
assert(len([patch for patch in ax.axes[direction].ax.patches
if isinstance(patch, FancyArrow)])
== np.prod(non_symmetric_matrix.shape))
# Set a few elements of adjacency matrix to zero
non_symmetric_matrix[1, 0] = 0.0
non_symmetric_matrix[2, 3] = 0.0
# Plot with different display mode
ax = plot_connectome(non_symmetric_matrix,
node_coords,
display_mode='lzry')
# No edge in direction 'l' because of node coords
assert(len([patch for patch in ax.axes['l'].ax.patches
if isinstance(patch, FancyArrow)]) == 0)
for direction in ['z', 'r', 'y']:
assert(len([patch for patch in ax.axes[direction].ax.patches
if isinstance(patch, FancyArrow)])
== np.prod(non_symmetric_matrix.shape) - 2)
def CCA_cm_brain_plot(cca, MNIcoords, mode=0, num_edge=200, title=None):
cm = cca.x_weights_mat[:, :, mode]
cm = cm + cm.T
cm_degree = np.sum(abs(cm), axis=1)
cm = matrix_threshold(cm, num_edge=num_edge)
cm_degree_plot = (cm_degree / np.max(cm_degree)) * 75
plotting.plot_connectome(cm,
MNIcoords,
node_size=cm_degree_plot,
node_color='black',
edge_cmap='vlag',
edge_vmin=-1,
edge_vmax=1,
display_mode='lzr',
edge_kwargs={
'Alpha': 0.75,
'lw': 1
},
node_kwargs={
'Alpha': 0,
'lw': 0
},
colorbar=True)
if title is not None:
plt.savefig(title, dpi=600)
plotting.show()
def lesion_dist_cm(cm, MNIcoords, title=None, vmin=-30, vmax=30):
#binarize
cm[cm > 0] = 1
cm = np.sum(cm, axis=2)
#symmetrize
cm = cm + cm.T
cm_degree = np.sum(abs(cm), axis=1)
cm_degree_plot = (cm_degree / np.max(cm_degree)) * 100
plotting.plot_connectome(
cm,
MNIcoords,
node_size=cm_degree_plot,
node_color='black',
edge_cmap='viridis',
edge_vmin=
vmin, # to get same colour echeme as the nifti plot set to opposite
edge_vmax=vmax,
colorbar=True,
display_mode='lzr',
edge_kwargs={
'Alpha': 0.25,
'lw': 1
},
node_kwargs={
'Alpha': 0,
'lw': 0
})
if title is not None:
plt.savefig(title, dpi=600)
plotting.show()
def plot_connectome_edge_thresholding(node_coords, non_symmetric_matrix):
"""Tests for plot_connectome with edge thresholding."""
# Case 1: Threshold is a number
thresh = 1.1
ax = plot_connectome(non_symmetric_matrix,
node_coords,
edge_threshold=thresh)
for direction in ['x', 'y', 'z']:
assert(len([patch for patch in ax.axes[direction].ax.patches
if isinstance(patch, FancyArrow)])
== np.sum(np.abs(non_symmetric_matrix) >= thresh)
)
# Case 2: Threshold is a percentage
thresh = 80
ax = plot_connectome(non_symmetric_matrix,
node_coords,
edge_threshold="{}%".format(thresh))
for direction in ['x', 'y', 'z']:
assert(len([patch for patch in ax.axes[direction].ax.patches
if isinstance(patch, FancyArrow)])
== np.sum(np.abs(non_symmetric_matrix)
>= np.percentile(np.abs(
non_symmetric_matrix.ravel()), thresh))
)
plt.close()
def channel_position_plot(ax, coords, mask=[]):
"""Plot electrode position on brain with nilearn
Plot all electrodes in white and selected electrode in blue.
Output jpeg with several projections
Parameters
----------
ax : pyplot ax
ax where to plot
coords : list
coords of channel to plot
"""
colors = np.array([[0.7, 0.13, 0.13, 1.]] * len(coords))
sizes = 10 * np.ones(len(colors))
if len(mask) > 0 and np.sum(mask) > 0:
sizes[mask] = 0.5 * np.ones(np.sum(mask))
colors[mask] = np.array([[0., 0., 0., .5]] * np.sum(mask))
# nilearn plot
try:
plotting.plot_connectome(np.zeros((len(coords), len(coords))),
coords,
node_color=colors.tolist(),
display_mode='lyrz',
axes=ax,
node_size=sizes)
except:
pass
def plot_ecog_electrodes_mni_from_file_and_labels(mni_coords_fullfile,chan_labels,num_grid_chans=64,colors=list()):
'Plots ECoG electrodes from MNI coordinate file'
#Example code to run it:
#import sys
#sys.path.append('/home/stepeter/AJILE/stepeter_sandbox/ECoG_Preprocessing')
#from plot_ecog_electrodes_mni import *
#mni_coords_fullfile='/data2/users/stepeter/mni_coords/a0f66459/a0f66459_MNI_atlasRegions.xlsx'
#plot_ecog_electrodes_mni_from_file_and_labels(mni_coords_fullfile,chan_num_min=-1,chan_num_max=-1,num_grid_chans=64)
#NOTE: A warning may pop up the first time running it, leading to no output. Rerun this function, and the plots should appear.
#Load in MNI file
mni_file = pd.read_excel(mni_coords_fullfile, delimiter=",")
#Create dataframe for electrode locations
locs=mni_file.loc[mni_file['Electrode'].isin(chan_labels)][['X coor', 'Y coor', 'Z coor']]
print(locs.shape)
#Label strips/depths differently for easier visualization (or use defined color list)
if len(colors)==0:
for s in range(locs.shape[0]):
if s>=num_grid_chans:
colors.append('r')
else:
colors.append('b')
#Plot the result
ni_plt.plot_connectome(np.eye(locs.shape[0]), locs, output_file=None,
node_kwargs={'alpha': 0.5, 'edgecolors': None},
node_size=10, node_color=colors)
def plot_ecog_electrodes_mni_direct(mni_coords,num_grid_chans=64,colors=list()):
'Plots ECoG electrodes from MNI coordinate file'
#Example code to run it:
# import sys
# sys.path.append('/home/stepeter/AJILE/stepeter_sandbox/ECoG_Preprocessing')
# from plot_ecog_electrodes_mni import *
# colors=list()
# cmap = matplotlib.cm.get_cmap('jet')
# for i in range(virtualCoords_pos.shape[1]):
# colors.append(np.asarray(cmap(frac_sbj_virtual_grid[0,i]))[0:3])
# colors = np.asarray(colors)
# colors = list(map(lambda x: x[0], np.array_split(colors, colors.shape[0], axis=0)))
# plot_ecog_electrodes_mni_direct(virtualCoords_pos.T,num_grid_chans=64,colors=colors)
#NOTE: If running in Jupyter, use '%matplotlib inline' instead of '%matplotlib notebook'
#Create dataframe for electrode locations
locs=pd.DataFrame(mni_file.loc[mni_file['Electrode'].isin(chan_labels)]['Coordinates'])
#locs=pd.DataFrame({'x': mni_coords[:,0].T,
# 'y': mni_coords[:,1].T,
# 'z': mni_coords[:,2].T})
#Label strips/depths differently for easier visualization (or use defined color list)
if len(colors)==0:
for s in range(locs.shape[0]):
if s>=num_grid_chans:
colors.append('r')
else:
colors.append('b')
#Plot the result
ni_plt.plot_connectome(np.eye(locs.shape[0]), locs, output_file=None,
node_kwargs={'alpha': 0.5, 'edgecolors': None},
node_size=10, node_color=colors)
def plot_connectivity_glassbrain(subject_id, group, pc, roi_coords,
suffix, session='func1',
preprocessing_folder='pipeline_1',
save=True, msdl=False):
"""Plots connectome of pc
"""
title = '-'.join([suffix, group, subject_id, session])
output_folder = os.path.join(set_figure_base_dir('connectivity'), suffix)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
output_file = os.path.join(output_folder,
'_'.join([suffix, 'connectome', group,
session,
preprocessing_folder, subject_id]))
if msdl:
title += '_msdl'
output_file += '_msdl'
plt.figure(figsize=(10, 20), dpi=90)
if save:
plot_connectome(pc, roi_coords, edge_threshold='90%', title=title,
output_file=output_file)
else:
plot_connectome(pc, roi_coords, edge_threshold='90%', title=title)
def plot_connectome(covs, tv=False):
# g = np.zeros(shape=(160, 160))
g = covs
dos_coords = datasets.fetch_coords_dosenbach_2010()
dos_coords = dos_coords.rois
dos_coords_table = [[x, y, z] for (x, y, z) in dos_coords
] # Reformat the atlas coordinates
f = plt.figure(figsize=(2.3, 3.5)) # 2.2,2.3
if tv:
plotting.plot_connectome(g,
dos_coords_table,
display_mode='z',
output_file='figs/connectome_tv.pdf',
edge_threshold="0.0005%",
annotate=True,
figure=f,
node_size=18)
else:
plotting.plot_connectome(g,
dos_coords_table,
display_mode='z',
output_file='figs/connectome.pdf',
edge_threshold="0.0005%",
annotate=True,
figure=f,
node_size=18)
def save_graphs_models(subj, subj_folder, mnicoor, thresholds):
for i, r in enumerate(thresholds):
correlation_matrix = subj[i]
aux = int(round(thresholds[i] * 100))
if aux < 10:
aux = '0' + str(aux)
else:
aux = str(aux)
print('r=' + aux + ',', end=' ')
SAVEIMAGENAME = subj_folder + "\\" + subj_folder + '_r' + aux + '.png'
plotting.plot_connectome(correlation_matrix,
mnicoor,
colorbar=False,
node_color='black',
edge_vmin=0,
edge_vmax=1,
node_size=10,
display_mode="lzry",
title='r=.' + aux,
output_file=SAVEIMAGENAME)
return None
def test_plot_connectome_with_nans(adjacency, node_coords, base_params):
"""Smoke test for plot_connectome with nans in the adjacency matrix."""
adjacency[0, 1] = np.nan
adjacency[1, 0] = np.nan
base_params["node_color"] = np.array(['green', 'blue', 'k', 'yellow'])
plot_connectome(adjacency, node_coords, **base_params)
plt.close()
def plot_consistent_edges(all_masks,
tail,
thresh=1.,
color='gray',
coords=None,
**plot_kwargs):
"""Plots edges which are consistent in a defined percentage of folds"""
edge_frac = (all_masks[tail].sum(axis=0)) / (all_masks[tail].shape[0])
summary = "{} suprathreshold (>= {} %) edges in {} % of the subjects".format(
(edge_frac >= thresh).sum(), thresh * 100, "TODO")
print("For the {} tail, {} edges were selected in at least {}% of folds".
format(tail, (edge_frac >= thresh).sum(), thresh * 100))
edge_frac_square = sp.spatial.distance.squareform(edge_frac)
node_mask = np.amax(
edge_frac_square, axis=0
) >= thresh # find nodes that have at least one edge that passes the threshold
node_size = edge_frac_square.sum(
axis=0
) * node_mask * 20 # size nodes based on how many suprathreshold edges they have
plotting.plot_connectome(adjacency_matrix=edge_frac_square,
edge_threshold=thresh,
node_color=color,
node_coords=coords,
node_size=node_size,
display_mode='lzry',
edge_kwargs={
"linewidth": 1,
'color': color
},
**plot_kwargs)
return (edge_frac_square >= thresh).astype(int), node_mask
def test_plot_connectome_exceptions_non_symmetric_adjacency(matrix):
"""Tests that warning messages are given when the adjacency matrix ends
up being non symmetric.
"""
node_coords = np.arange(2 * 3).reshape((2, 3))
with pytest.warns(UserWarning, match="A directed graph will be plotted."):
plot_connectome(matrix, node_coords, display_mode='x')
plt.close()
def test_plot_connectome_display_mode(display_mode, node_coords,
adjacency, base_params):
"""Smoke test for plot_connectome with different values
for display_mode.
"""
plot_connectome(adjacency, node_coords, display_mode=display_mode,
**base_params)
plt.close()
def test_plot_connectome_tuple_node_coords(adjacency, node_coords, base_params,
tmpdir):
"""Smoke test for plot_connectome where node_coords is not provided
as an array but as a list of tuples.
"""
plot_connectome(adjacency, [tuple(each) for each in node_coords],
display_mode='x',
**base_params)
plt.close()
def plot_cluster_freqs_on_brain(self, cluster_name, xyz, colormap='viridis', vmin=None, vmax=None, do_3d=False):
"""
Plot the frequencies of single electrode cluster on either a 2d or interactive 2d brain.
Parameters
----------
cluster_name: str
Name of column in self.res['clusters']
xyz: np.ndarray
3 x n array of electrode locations. Should be in MNI space.
colormap: str
matplotlib colormap name
vmin: float
lower limit of colormap values. If not given, lowest value in frequency column will be used
vmax: float
upper limit of colormap values. If not given, highest value in frequency column will be used
do_3d:
Whether to plot an interactive 3d brain, or a 2d brain
Returns
-------
If 2d, returns the matplotlib figure. If 3d, returns the html used to render the brain.
"""
# get frequecies for this cluster
freqs = self.res['clusters'][cluster_name].values
# get color for each frequency. Start with all black
colors = np.stack([[0., 0., 0., 0.]] * len(freqs))
# fill in colors of electrodes with defined frequencies
cm = plt.get_cmap(colormap)
cNorm = clrs.Normalize(vmin=np.nanmin(freqs) if vmin is None else vmin,
vmax=np.nanmax(freqs) if vmax is None else vmax)
colors[~np.isnan(freqs)] = cmx.ScalarMappable(norm=cNorm, cmap=cm).to_rgba(freqs[~np.isnan(freqs)])
# if plotting 2d, use the nilearn glass brain
if not do_3d:
fig, ax = plt.subplots()
ni_plot.plot_connectome(np.eye(xyz.shape[0]), xyz,
node_kwargs={'alpha': 0.7, 'edgecolors': None},
node_size=60, node_color=colors, display_mode='lzr',
axes=ax)
divider = make_axes_locatable(ax)
cax = divider.append_axes('bottom', size='4%', pad=0)
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=colormap,
norm=cNorm,
orientation='horizontal')
cb1.set_label('Frequency', fontsize=20)
cb1.ax.tick_params(labelsize=14)
fig.set_size_inches(15, 10)
return fig
# if plotting 3d use the nilearn 3d brain. Unfortunately this doesn't add a colorbar.
else:
# you need to return the html. If in jupyter, it will automatically render
return ni_plot.view_markers(xyz, colors=colors, marker_size=6)
def plot(connectome, title, axes):
plotting.plot_connectome(connectome,
DesikanAtlas.coordinates(),
title=title,
edge_threshold='90%',
node_size=20,
colorbar=True,
axes=axes,
annotate=True)
def plot_cluster_freqs_on_brain(self, cluster_name, xyz, colormap='viridis', vmin=None, vmax=None, do_3d=False):
"""
Plot the frequencies of single electrode cluster on either a 2d or interactive 2d brain.
Parameters
----------
cluster_name: str
Name of column in self.res['clusters']
xyz: np.ndarray
3 x n array of electrode locations. Should be in MNI space.
colormap: str
matplotlib colormap name
vmin: float
lower limit of colormap values. If not given, lowest value in frequency column will be used
vmax: float
upper limit of colormap values. If not given, highest value in frequency column will be used
do_3d:
Whether to plot an interactive 3d brain, or a 2d brain
Returns
-------
If 2d, returns the matplotlib figure. If 3d, returns the html used to render the brain.
"""
# get frequecies for this cluster
freqs = self.res['clusters'][cluster_name].values
# get color for each frequency. Start with all black
colors = np.stack([[0., 0., 0., 0.]] * len(freqs))
# fill in colors of electrodes with defined frequencies
cm = plt.get_cmap(colormap)
cNorm = clrs.Normalize(vmin=np.nanmin(freqs) if vmin is None else vmin,
vmax=np.nanmax(freqs) if vmax is None else vmax)
colors[~np.isnan(freqs)] = cmx.ScalarMappable(norm=cNorm, cmap=cm).to_rgba(freqs[~np.isnan(freqs)])
# if plotting 2d, use the nilearn glass brain
if not do_3d:
fig, ax = plt.subplots()
ni_plot.plot_connectome(np.eye(xyz.shape[0]), xyz,
node_kwargs={'alpha': 0.7, 'edgecolors': None},
node_size=60, node_color=colors, display_mode='lzr',
axes=ax)
divider = make_axes_locatable(ax)
cax = divider.append_axes('bottom', size='4%', pad=0)
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=colormap,
norm=cNorm,
orientation='horizontal')
cb1.set_label('Frequency', fontsize=20)
cb1.ax.tick_params(labelsize=14)
fig.set_size_inches(15, 10)
return fig
# if plotting 3d use the nilearn 3d brain. Unfortunately this doesn't add a colorbar.
else:
# you need to return the html. If in jupyter, it will automatically render
return ni_plot.view_markers(xyz, colors=colors, marker_size=6)
def test_plot_connectome_exception_wrong_edge_threshold(adjacency, node_coords): # noqa
"""Tests that a TypeError is raised in plot_connectome when edge
threshold is neither a number nor a string.
"""
with pytest.raises(TypeError,
match='should be either a number or a string'):
plot_connectome(
adjacency, node_coords, edge_threshold=object(), display_mode='x'
)
def test_plot_connectome_node_colors(node_color, display_mode, node_coords,
adjacency, base_params, tmpdir):
"""Smoke test for plot_connectome with different values for node_color."""
plot_connectome(adjacency,
node_coords,
node_color=node_color,
display_mode=display_mode,
**base_params)
plt.close()
def test_plot_connectome_node_and_edge_kwargs(adjacency, node_coords):
"""Smoke test for plot_connectome with node_kwargs, edge_kwargs,
and edge_cmap arguments.
"""
plot_connectome(adjacency, node_coords, edge_threshold='70%',
node_size=[10, 20, 30, 40], node_color=np.zeros((4, 3)),
edge_cmap='RdBu', colorbar=True,
node_kwargs={'marker': 'v'},
edge_kwargs={'linewidth': 4})
plt.close()
def test_plot_connectome_exceptions_providing_node_info_with_kwargs(
node_kwargs, adjacency, node_coords, expected_error_node_kwargs):
"""Tests that an error is raised when specifying node parameters
via node_kwargs in plot_connectome.
"""
with pytest.raises(ValueError,
match=expected_error_node_kwargs):
plot_connectome(
adjacency, node_coords, node_kwargs=node_kwargs, display_mode='x'
)
def test_plot_connectome_masked_array_sparse_matrix(node_coords, adjacency,
base_params):
"""Smoke tests for plot_connectome with masked arrays and sparse
matrices as inputs.
"""
masked_adjacency_matrix = np.ma.masked_array(adjacency,
np.abs(adjacency) < 0.5)
plot_connectome(masked_adjacency_matrix, node_coords, **base_params)
sparse_adjacency_matrix = sparse.coo_matrix(adjacency)
plot_connectome(sparse_adjacency_matrix, node_coords, **base_params)
plt.close()
def test_plot_connectome_exceptions_wrong_number_node_colors(node_color,
adjacency,
node_coords):
"""Tests that a wrong number of node colors raises a
ValueError in plot_connectome.
"""
with pytest.raises(ValueError,
match='Mismatch between the number of nodes'):
plot_connectome(
adjacency, node_coords, node_color=node_color, display_mode='x'
)
def test_plot_connectome_exception_wrong_edge_threshold_format(
threshold, adjacency, node_coords):
"""Tests that a ValueError is raised when edge_threshold is an incorrectly
formatted string.
"""
with pytest.raises(ValueError,
match=("should be a number followed "
"by the percent sign")):
plot_connectome(
adjacency, node_coords, edge_threshold=threshold, display_mode='x'
)
def run_mini_pipeline():
atlas = datasets.fetch_atlas_msdl()
atlas_img = atlas['maps']
labels = pd.read_csv(atlas['labels'])['name']
masker = NiftiMapsMasker(maps_img=atlas_img, standardize=True,
memory='/tmp/nilearn', verbose=0)
data = datasets.fetch_adhd(number_subjects)
figures_folder = '../figures/'
count=0
for func_file, confound_file in zip(data.func, data.confounds):
# fit the data to the atlas mask, regress out confounds
time_series = masker.fit_transform(func_file, confounds=confound_file)
correlation = np.corrcoef(time_series.T)
#plotting starts here
plt.figure(figsize=(10, 10))
plt.imshow(correlation, interpolation="nearest")
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
corr_file = figures_folder+'subject_number_' + str(count) + '_correlation.pdf'
plt.savefig(corr_file)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in image.iter_img(atlas_img)]
threshold = 0.6
plotting.plot_connectome(correlation, atlas_region_coords, edge_threshold=threshold)
connectome_file = figures_folder+'subject_number_' + str(count) + '_connectome.pdf'
plt.savefig(connectome_file)
#graph setup
#binarize correlation matrix
correlation[correlation<threshold] = 0
correlation[correlation != 0] = 1
graph = nx.from_numpy_matrix(correlation)
partition=louvain.best_partition(graph)
values = [partition.get(node) for node in graph.nodes()]
plt.figure()
nx.draw_spring(graph, cmap = plt.get_cmap('jet'), node_color = values, node_size=30, with_labels=True)
graph_file = figures_folder+'subject_number_' + str(count) + '_community.pdf'
plt.savefig(graph_file)
count += 1
plt.close('all')
def plot( self, ROIcoord, clusterID, title):
"""
INPUT:
- ROIcoord: MNNI coordinates
- clusterID: which cluster should we plot
"""
ii = np.where( self.W[:, clusterID] !=0 )[0]
RandomMat = np.cov( np.random.random(( 10, len(ii))).T ) # this is just a place holder, we will not plot any of it!
# we just plot the result
plotting.plot_connectome(RandomMat, ROIcoord[ii,:], node_color='black', annotate=False, display_mode='ortho', edge_kwargs = {'alpha':0}, node_size=50, title=title)
def plot_brains(coords, colors, fname):
plt.clf()
adjMat = np.zeros(shape=(len(colors), len(colors)))
bf = plt.figure(figsize=[24, 20])
plot_connectome(adjMat,
coords,
colors,
display_mode='lr',
node_size=900,
figure=bf,
output_file=fname)
def plot_ecog_electrodes_mni_from_file(mni_coords_fullfile,
chan_num_min=-1,
chan_num_max=-1,
num_grid_chans=64,
colors=list()):
'Plots ECoG electrodes from MNI coordinate file'
#Example code to run it:
#import sys
#sys.path.append('/home/stepeter/AJILE/stepeter_sandbox/ECoG_Preprocessing')
#from plot_ecog_electrodes_mni import *
#mni_coords_fullfile='/data2/users/stepeter/mni_coords/a0f66459/294e1c_Trodes_MNIcoords.txt'
#plot_ecog_electrodes_mni(mni_coords_fullfile,chan_num_min=-1,chan_num_max=-1,num_grid_chans=64)
#NOTE: A warning may pop up the first time running it, leading to no output. Rerun this function, and the plots should appear.
#Load in MNI file
mni_file = np.loadtxt(mni_coords_fullfile, delimiter=",")
#Specify which channels to plot (from min to max number)
if chan_num_min == -1:
chan_num_min = 0
if chan_num_max == -1:
chan_num_max = mni_file.shape[0] - 1
slice_inds = slice(chan_num_min, chan_num_max + 1)
#Create dataframe for electrode locations
locs = pd.DataFrame({
'x': mni_file[slice_inds, 0].T,
'y': mni_file[slice_inds, 1].T,
'z': mni_file[slice_inds, 2].T
})
#Label strips/depths differently for easier visualization (or use defined color list)
if len(colors) == 0:
for s in range(locs.shape[0]):
if s >= num_grid_chans:
colors.append('r')
else:
colors.append('b')
#Plot the result
ni_plt.plot_connectome(np.eye(locs.shape[0]),
locs,
output_file=None,
node_kwargs={
'alpha': 0.5,
'edgecolors': None
},
node_size=10,
node_color=colors)
def plotBrains(coords, colors, fname=None):
#Simplified from projUtils version
mpl.rcParams.update(mpl.rcParamsDefault)
numc = len(colors)
adjMat = np.zeros(shape=(numc, numc))
fig = plt.figure(figsize=[24, 12])
plot_connectome(adjMat,
coords,
colors,
display_mode='lr',
node_size=900,
figure=fig,
output_file=fname,
black_bg=False)
def plot_connectome(matrix,
coords,
colors,
size,
threshold,
fname,
cmap=plt.cm.hot,
title='',
max_=None,
min_=None,
display_='ortho'):
"""
Wrapper of the plot_connectome function in nilearn with some fixed
values
"""
from nilearn import plotting
plotting.plot_connectome(adjacency_matrix=matrix,
node_coords=coords,
node_color=colors.tolist(),
node_size=1.5*size,
edge_cmap=cmap,
edge_vmin=min_,
edge_vmax=max_,
edge_threshold=threshold,
output_file=fname,
display_mode=display_,
figure=plt.figure(figsize=(16*1.2,9*1.2)),# facecolor='k', edgecolor='k'),
#axes,
title=title,
#annotate,
black_bg=True,
#alpha,
edge_kwargs={
'alpha':0.8,
'linewidth':9,
},
node_kwargs={
'edgecolors':'k',
},
#colorbar=True
)
###############################################################################
# Plot matrix and graph
# ---------------------
#
# We use `matplotlib` plotting functions to visualize our correlation matrix
# and display the graph of connections with `nilearn.plotting.plot_connectome`.
import matplotlib.pyplot as plt
from nilearn import plotting
plt.imshow(matrix, vmin=-1.0, vmax=1.0, cmap="RdBu_r", interpolation="nearest")
plt.colorbar()
plt.title("Power correlation matrix")
# Tweak edge_threshold to keep only the strongest connections.
plotting.plot_connectome(
matrix, coords, title="Power correlation graph", edge_threshold="99.8%", node_size=20, colorbar=True
)
###############################################################################
# Note the 1. on the matrix diagonal: These are the signals variances, set to
# 1. by the `spheres_masker`. Hence the covariance of the signal is a
# correlation matrix
###############################################################################
# Connectome extracted from Dosenbach's atlas
# -------------------------------------------
#
# We repeat the same steps for Dosenbach's atlas.
dosenbach = datasets.fetch_coords_dosenbach_2010()
coords = np.vstack((dosenbach.rois["x"], dosenbach.rois["y"], dosenbach.rois["z"])).T
from nilearn.group_sparse_covariance import GroupSparseCovarianceCV
gsc = GroupSparseCovarianceCV(verbose=2)
gsc.fit(subject_time_series)
print("-- Computing graph-lasso precision matrices ...")
from sklearn import covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(np.concatenate(subject_time_series))
# Displaying results ##########################################################
atlas_imgs = image.iter_img(msdl_atlas_dataset.maps)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in atlas_imgs]
title = "GraphLasso"
plotting.plot_connectome(-gl.precision_, atlas_region_coords,
edge_threshold='90%',
title="Sparse inverse covariance (GraphLasso)")
plotting.plot_connectome(gl.covariance_,
atlas_region_coords, edge_threshold='90%',
title="Covariance")
plot_matrices(gl.covariance_, gl.precision_, title)
title = "GroupSparseCovariance"
plotting.plot_connectome(-gsc.precisions_[..., 0],
atlas_region_coords, edge_threshold='90%',
title=title)
plot_matrices(gsc.covariances_[..., 0],
gsc.precisions_[..., 0], title)
plt.show()
# The covariance can be found at estimator.covariance_
plt.imshow(estimator.covariance_, interpolation="nearest",
vmax=1, vmin=-1, cmap=plt.cm.RdBu_r)
# And display the labels
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
plt.title('Covariance')
##############################################################################
# And now display the corresponding graph
# ----------------------------------------
from nilearn import plotting
coords = atlas.region_coords
plotting.plot_connectome(estimator.covariance_, coords,
title='Covariance')
##############################################################################
# Display the sparse inverse covariance
# --------------------------------------
# we negate it to get partial correlations
plt.figure(figsize=(10, 10))
plt.imshow(-estimator.precision_, interpolation="nearest",
vmax=1, vmin=-1, cmap=plt.cm.RdBu_r)
# And display the labels
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
plt.title('Sparse inverse covariance')
##############################################################################
# All individual coefficients are stacked in a unique 2D matrix.
print('Correlations of ADHD patients are stacked in an array of shape {0}'
.format(correlation_matrices.shape))
###############################################################################
# as well as the average correlation across all fitted subjects.
mean_correlation_matrix = correlation_measure.mean_
print('Mean correlation has shape {0}.'.format(mean_correlation_matrix.shape))
###############################################################################
# We display the connectomes of the first 3 ADHD subjects and the mean
# correlation matrix over all ADHD patients.
from nilearn import plotting
plot_matrices(correlation_matrices[:4], 'correlation')
plotting.plot_connectome(mean_correlation_matrix, msdl_coords,
title='mean correlation over 13 ADHD subjects')
###############################################################################
# Look at blocks structure, reflecting functional networks.
###############################################################################
# Examine partial correlations
# ----------------------------
# We can also study **direct connections**, revealed by partial correlation
# coefficients. We just change the `ConnectivityMeasure` kind
partial_correlation_measure = ConnectivityMeasure(kind='partial correlation')
###############################################################################
# and repeat the previous operation.
partial_correlation_matrices = partial_correlation_measure.fit_transform(
adhd_subjects)
if "Unknown" not in str(label): # Omit the Unknown label.
# Compute mean location of vertices in label of index k
coordinates.append(np.mean(rr[vert == k], axis=0))
coordinates = np.array(coordinates) # 3D coordinates of parcels
# We now make a synthetic connectivity matrix that connects labels
# between left and right hemispheres.
n_parcels = len(coordinates)
corr = np.zeros((n_parcels, n_parcels))
n_parcels_hemi = n_parcels // 2
corr[np.arange(n_parcels_hemi), np.arange(n_parcels_hemi) + n_parcels_hemi] = 1
corr = corr + corr.T
plotting.plot_connectome(corr, coordinates,
edge_threshold="90%",
title='fsaverage Destrieux atlas')
plotting.show()
##############################################################################
# 3D visualization in a web browser
# ---------------------------------
# An alternative to :func:`nilearn.plotting.plot_surf_roi` is to use
# :func:`nilearn.plotting.view_surf` for more interactive
# visualizations in a web browser. See :ref:`interactive-surface-plotting` for
# more details.
view = plotting.view_surf(fsaverage.infl_left, parcellation,
cmap='gist_ncar', symmetric_cmap=False)
# uncomment this to open the plot in a web browser:
# view.open_in_browser()
from nilearn.connectome import ConnectivityMeasure
connectivity_measure = ConnectivityMeasure(kind='partial correlation')
partial_correlation_matrix = connectivity_measure.fit_transform(
[time_series])[0]
##########################################################################
# Display connectome
# -------------------
#
# We display the graph of connections with `:func: nilearn.plotting.plot_connectome`.
from nilearn import plotting
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Default Mode Network Connectivity")
##########################################################################
# Display connectome with hemispheric projections.
# Notice (0, -52, 18) is included in both hemispheres since x == 0.
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Connectivity projected on hemispheres",
display_mode='lyrz')
plotting.show()
##############################################################################
# 3D visualization in a web browser
# ---------------------------------
gsc.fit(subject_time_series)
from sklearn import covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(np.concatenate(subject_time_series))
##############################################################################
# Displaying results
# -------------------
atlas_imgs = image.iter_img(msdl_atlas_dataset.maps)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in atlas_imgs]
labels = msdl_atlas_dataset.labels
plotting.plot_connectome(gl.covariance_,
atlas_region_coords, edge_threshold='90%',
title="Covariance",
display_mode="lzr")
plotting.plot_connectome(-gl.precision_, atlas_region_coords,
edge_threshold='90%',
title="Sparse inverse covariance (GraphLasso)",
display_mode="lzr",
edge_vmax=.5, edge_vmin=-.5)
plot_matrices(gl.covariance_, gl.precision_, "GraphLasso", labels)
title = "GroupSparseCovariance"
plotting.plot_connectome(-gsc.precisions_[..., 0],
atlas_region_coords, edge_threshold='90%',
title=title,
display_mode="lzr",
edge_vmax=.5, edge_vmin=-.5)
plot_matrices(gsc.covariances_[..., 0],
__author__ = '2d Lt Kyle Palko'
import numpy as np
from nilearn import plotting as plt
# import Pitt 0050013, a young autistic subject
ts = np.genfromtxt('/media/kap/8e22f6f8-c4df-4d97-a388-0adcae3ec1fb/Python/Thesis/C200/ABIDE_pcp/cpac/filt_noglobal/'
'Pitt_0050013_rois_cc200.1D', skip_header=1)
cor = np.corrcoef(ts.T)
# create matrix
x = np.zeros((200, 200))
for i in range(0, np.size(x, axis=0)):
x[i][i] = 1
a = np.genfromtxt('cc200_roi.csv', delimiter=',')
row = np.array([c[0] for c in a])
col = np.array([c[1] for c in a])
del a
for i in range(0, 10):
r = row[i]
c = col[i]
x[r, c] = cor[r, c]
x[c, r] = cor[c, r]
node_coords = np.genfromtxt('cc200_lab_coord.csv', delimiter=',')
plt.plot_connectome(x, node_coords, output_file='corrtest_1.png', node_size=1)
###############################################################################
# Extract and plot correlation matrix
for atlas in ['Power', 'Dosenbach']:
if atlas == 'Power':
timeseries = power_timeseries
coords = power_coords
else:
timeseries = dosenbach_timeseries
coords = dosenbach_coords
connectivity = connectome.ConnectivityMeasure(kind='correlation')
corr_matrix = connectivity.fit_transform([timeseries])[0]
np.fill_diagonal(corr_matrix, 0)
plt.figure()
vmax = np.max(np.abs(corr_matrix))
plt.imshow(corr_matrix, vmin=-vmax, vmax=vmax, cmap='RdBu_r',
interpolation='nearest')
plt.colorbar()
plt.title(atlas + 'correlation matrix')
# Plot the connectome
plotting.plot_connectome(corr_matrix, coords,
edge_threshold='99.8%', node_size=20,
title=atlas + 'correlation connectome')
plotting.show()
if kind == 'tangent':
mean_connectivity_matrix[kind] = conn_measure.mean_
else:
mean_connectivity_matrix[kind] = \
individual_connectivity_matrices[kind].mean(axis=0)
######################################################################
# Plot the mean connectome with hemispheric saggital cuts
import numpy as np
from nilearn import plotting
labels = atlas.labels
region_coords = atlas.region_coords
for kind in kinds:
plotting.plot_connectome(mean_connectivity_matrix[kind],
region_coords, edge_threshold='98%',
title=kind, display_mode='lzry')
######################################################################
# Use the connectivity coefficients to classify ADHD vs controls
from sklearn.svm import LinearSVC
from sklearn.cross_validation import StratifiedKFold, cross_val_score
classes = ['{0}{1}'.format(site, adhd) for site, adhd in zip(sites, adhds)]
print('Classification accuracy:')
mean_scores = []
cv = StratifiedKFold(classes, n_folds=3)
for kind in kinds:
svc = LinearSVC()
# Transform the connectivity matrices to 1D arrays
coonectivity_coefs = connectome.sym_to_vec(
###############################################################################
# as well as the average correlation across all fitted subjects.
mean_correlation_matrix = correlation_measure.mean_
print('Mean correlation has shape {0}.'.format(mean_correlation_matrix.shape))
###############################################################################
# We display the connectome matrices of the first 4 children
from nilearn import plotting
plot_matrices(correlation_matrices[:4], 'correlation')
###############################################################################
# The blocks structure that reflect functional networks are visible.
###############################################################################
# Now we display as a connectome the mean correlation matrix over all children.
plotting.plot_connectome(mean_correlation_matrix, msdl_coords,
title='mean correlation over all children')
###############################################################################
# Studying partial correlations
# -----------------------------
# We can also study **direct connections**, revealed by partial correlation
# coefficients. We just change the `ConnectivityMeasure` kind
partial_correlation_measure = ConnectivityMeasure(kind='partial correlation')
###############################################################################
# and repeat the previous operation.
partial_correlation_matrices = partial_correlation_measure.fit_transform(
children)
###############################################################################
# Most of direct connections are weaker than full connections,
###############################################################################
# Plot resulting connectomes
# ----------------------------
title = 'Correlation between %d regions' % n_regions_extracted
# First plot the matrix
display = plotting.plot_matrix(mean_correlations, vmax=1, vmin=-1,
colorbar=True, title=title)
# Then find the center of the regions and plot a connectome
regions_img = regions_extracted_img
coords_connectome = plotting.find_probabilistic_atlas_cut_coords(regions_img)
plotting.plot_connectome(mean_correlations, coords_connectome,
edge_threshold='90%', title=title)
################################################################################
# Plot regions extracted for only one specific network
# ----------------------------------------------------
# First, we plot a network of index=4 without region extraction (left plot)
from nilearn import image
img = image.index_img(components_img, 4)
coords = plotting.find_xyz_cut_coords(img)
display = plotting.plot_stat_map(img, cut_coords=coords, colorbar=False,
title='Showing one specific network')
################################################################################
# Now, we plot (right side) same network after region extraction to show that
for time_serie, label in zip(time_series.T, labels):
plt.plot(time_serie, label=label)
plt.title("Default Mode Network Time Series")
plt.xlabel("Scan number")
plt.ylabel("Normalized signal")
plt.legend()
plt.tight_layout()
##########################################################################
# Compute precision matrices
from sklearn.covariance import LedoitWolf
cve = LedoitWolf()
cve.fit(time_series)
##########################################################################
# Display connectome
from nilearn import plotting
plotting.plot_connectome(cve.precision_, dmn_coords, title="Default Mode Network Connectivity")
# Display connectome with hemispheric projections.
# Notice (0, -52, 18) is included in both hemispheres since x == 0.
title = "Connectivity projected on hemispheres"
plotting.plot_connectome(cve.precision_, dmn_coords, title=title, display_mode="lyrz")
plotting.show()
w,a = pairwise_classification(Xp, yp, title=output)
print groups[i], groups[j], a
t = np.zeros((len(roi_names), len(roi_names)))
t[ind] = np.abs(w)
t = (t + t.T) / 2.
if msdl:
msdl_str = 'msdl'
else:
msdl_str = 'rois'
output_folder = os.path.join(set_figure_base_dir('classification'),
metric, session, msdl_str)
if not os.path.isdir(output_folder):
os.makedirs(output_folder)
output_file = os.path.join(output_folder, 'connectome_' + output)
plot_connectome(t, roi_coords, title=output,
output_file=output_file,
annotate=True,
edge_threshold='0%')
# 1 vs rest
for i in range(3):
gr_i = dataset.group_indices[groups[i]]
yr = np.zeros(X.shape[0])
yr[gr_i] = 1
output = '_'.join([groups[i] + '_rest', metric, session, msdl_str,
preprocessing_folder])
plt.figure()
w, a = pairwise_classification(X, yr, title=output)
print groups[i] + '_rest', a
if np.sum(w) == 0:
###############################################################################
# Extract and plot correlation matrix
# calculate connectivity and plot Power-264 correlation matrix
connectivity = connectome.ConnectivityMeasure(kind='correlation')
corr_matrix = connectivity.fit_transform([timeseries])[0]
np.fill_diagonal(corr_matrix, 0)
plt.imshow(corr_matrix, vmin=-1., vmax=1., cmap='RdBu_r')
plt.colorbar()
plt.title('Power 264 Connectivity')
# Plot the connectome
plotting.plot_connectome(corr_matrix,
power_coords,
edge_threshold='99.8%',
node_size=20)
###############################################################################
# Extract and plot covariance and sparse covariance
# Compute the sparse inverse covariance
from sklearn.covariance import GraphLassoCV
estimator = GraphLassoCV()
estimator.fit(timeseries)
# Display the covariance
plt.figure(figsize=(5, 5))
plt.imshow(estimator.covariance_, interpolation="nearest",
plt.tight_layout()
##########################################################################
# Compute partial correlation matrix
# -----------------------------------
# Using object :class:`nilearn.connectome.ConnectivityMeasure`: Its
# default covariance estimator is Ledoit-Wolf, allowing to obtain accurate
# partial correlations.
from nilearn.connectome import ConnectivityMeasure
connectivity_measure = ConnectivityMeasure(kind='partial correlation')
partial_correlation_matrix = connectivity_measure.fit_transform(
[time_series])[0]
##########################################################################
# Display connectome
# -------------------
from nilearn import plotting
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Default Mode Network Connectivity")
##########################################################################
# Display connectome with hemispheric projections.
# Notice (0, -52, 18) is included in both hemispheres since x == 0.
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Connectivity projected on hemispheres",
display_mode='lyrz')
plotting.show()
for func, confounds in zip(data.func, data.confounds):
time_series.append(masker.fit_transform(func, confounds=confounds))
# calculate correlation matrices across subjects and display
correlation_matrices = connectome_measure.fit_transform(time_series)
# Mean correlation matrix across 10 subjects can be grabbed like this,
# using connectome measure object
mean_correlation_matrix = connectome_measure.mean_
# grab center coordinates for atlas labels
coordinates = plotting.find_parcellation_cut_coords(labels_img=yeo['thick_17'])
# plot connectome with 80% edge strength in the connectivity
plotting.plot_connectome(mean_correlation_matrix, coordinates,
edge_threshold="80%",
title='Yeo Atlas 17 thick (func)')
##########################################################################
# Load probabilistic atlases - extracting coordinates on brain maps
# -----------------------------------------------------------------
msdl = datasets.fetch_atlas_msdl()
##########################################################################
# Iterate over fetched atlases to extract coordinates - probabilistic
# -------------------------------------------------------------------
from nilearn.input_data import NiftiMapsMasker
# create masker to extract functional data within atlas parcels
masker = NiftiMapsMasker(maps_img=msdl['maps'], standardize=True,
def plot_cluster_stats(self, cluster_name):
"""
Multi panel plot showing:
1. brain map of electrodes in the cluster, color-coded by phase
2. brain map of electrodes in the cluster, color-coded by subsequent memory effect
3. timecourse of resultant vector length of wave direction, averaged across trials
4. timecourse of r^2, averaged across trials
5. polor plot of left-frontal and hippocampal electrode phases
6/7. same as 5, but for recalled and not recalled items only
Data are taken from the timepoint with the highest r-square value.
Figure creation code is so ugly sorry.
"""
############################
# GET TIME TIME FOR X-AXIS #
############################
time_axis = self.res['traveling_waves'][cluster_name]['time']
#####################
# SET UP THE FIGURE #
#####################
gs = gridspec.GridSpec(6, 3)
ax1 = plt.subplot(gs[0, :])
ax2 = plt.subplot(gs[2, :])
ax3 = plt.subplot(gs[3, :])
ax4 = plt.subplot(gs[4, 0], projection='polar')
ax6 = plt.subplot(gs[4, 1], projection='polar')
ax7 = plt.subplot(gs[4, 2], projection='polar')
ax8 = plt.subplot(gs[5, 0], projection='polar')
ax9 = plt.subplot(gs[5, 1], projection='polar')
ax10 = plt.subplot(gs[5, 2], projection='polar')
ax5 = plt.subplot(gs[1, :])
# some figure parameters
fig = plt.gcf()
fig.set_size_inches(15, 30)
mpl.rcParams['xtick.labelsize'] = 18
mpl.rcParams['ytick.labelsize'] = 18
#############################################
# INFO ABOUT THE ELECTRODES IN THIS CLUSTER #
#############################################
cluster_rows = self.res['clusters'][cluster_name].notna()
regions_all = self.get_electrode_roi_by_hemi()
regions = regions_all[cluster_rows]['merged_col'].unique()
regions_str = ', '.join(regions)
xyz = self.res['clusters'][cluster_rows][['x', 'y', 'z']].values
###############################
# ROW 1: electrodes and phase #
###############################
mean_r2 = np.nanmean(self.res['traveling_waves'][cluster_name]['cluster_r2_adj'], axis=1)
argmax_r2 = np.argmax(mean_r2)
print(argmax_r2)
phases = self.res['traveling_waves'][cluster_name]['phase_data'][:, argmax_r2]
# phases = (phases + np.pi) % (2 * np.pi) - np.pi
# phases[phases<0] += np.pi*2
# phases *= 180. / np.pi
# phases -= phases.min() - 1
colors = np.stack([[0., 0., 0., 0.]] * len(phases))
cm = clrs.LinearSegmentedColormap.from_list('cm', cc.cyclic_mrybm_35_75_c68_s25)
cNorm = clrs.Normalize(vmin=0, vmax=np.pi * 2)
colors[~np.isnan(phases)] = cmx.ScalarMappable(norm=cNorm, cmap=cm).to_rgba(phases[~np.isnan(phases)])
ni_plot.plot_connectome(np.eye(xyz.shape[0]), xyz,
node_kwargs={'alpha': 0.7, 'edgecolors': None},
node_size=45, node_color=colors, display_mode='lzr',
axes=ax1)
mean_freq = self.res['traveling_waves'][cluster_name]['mean_freq']
plt.suptitle('{0} ({1:.2f} Hz): {2}'.format(self.subject, mean_freq, regions_str), y=.9)
divider = make_axes_locatable(ax1)
cax = divider.append_axes('right', size='6%', pad=15)
cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cm,
norm=cNorm,
orientation='vertical', ticks=[0, np.pi / 2, np.pi, np.pi * 3 / 2, np.pi * 2])
cb1.ax.yaxis.set_ticklabels(['0°', '90°', '180°', '270°', '360°'])
cb1.ax.tick_params(labelsize=14)
for label in cb1.ax.yaxis.get_majorticklabels():
label.set_transform(label.get_transform() + mpl.transforms.ScaledTranslation(0.15, 0, fig.dpi_scale_trans))
##################################################
# ROW 2: electrodes and subsequent memory effect #
##################################################
sme = self.res['traveling_waves'][cluster_name]['sme_t'][:, argmax_r2]
colors = np.stack([[0., 0., 0., 0.]] * len(sme))
cm = plt.get_cmap('RdBu_r')
clim = np.max(np.abs(sme))
cNorm = clrs.Normalize(vmin=-clim, vmax=clim)
colors[~np.isnan(sme)] = cmx.ScalarMappable(norm=cNorm, cmap=cm).to_rgba(sme[~np.isnan(sme)])
ni_plot.plot_connectome(np.eye(xyz.shape[0]), xyz,
node_kwargs={'alpha': 0.7, 'edgecolors': None},
node_size=45, node_color=colors, display_mode='lzr',
axes=ax5)
divider = make_axes_locatable(ax5)
cax = divider.append_axes('right', size='6%', pad=15)
cb2 = mpl.colorbar.ColorbarBase(cax, cmap='RdBu_r',
norm=cNorm,
orientation='vertical')
cb2.ax.tick_params(labelsize=14)
for label in cb2.ax.yaxis.get_majorticklabels():
label.set_transform(label.get_transform() + mpl.transforms.ScaledTranslation(0.15, 0, fig.dpi_scale_trans))
############################
# ROW 3: timecourse of RVL #
############################
rvl = pycircstat.resultant_vector_length(self.res['traveling_waves'][cluster_name]['cluster_wave_ang'], axis=1)
ax2.plot(time_axis, rvl, lw=2)
ax2.set_ylabel('RVL', fontsize=20)
##################################
# ROW 4: timecourse of r-squared #
##################################
ax3.plot(time_axis, np.nanmean(self.res['traveling_waves'][cluster_name]['cluster_r2_adj'], axis=1), lw=2)
ax3.set_xlabel('Time (ms)', fontsize=20)
ax3.set_ylabel('mean($R^{2}$)', fontsize=20)
############################
# ROW 5a: phase polar plots #
############################
# phases = np.deg2rad(phases)
cluster_regions = regions_all[cluster_rows]['merged_col']
phases_left_front = phases[cluster_regions == 'left-Frontal']
phases_hipp = phases[(cluster_regions == 'left-Hipp') | (cluster_regions == 'right-Hipp')]
phases_other = phases[~cluster_regions.isin(['left-Frontal', 'left-Hipp', 'right-Hipp'])]
for this_phase in phases_left_front:
ax4.plot([this_phase, this_phase], [0, 1], lw=3, c='#67a9cf', alpha=.5)
for this_phase in phases_hipp:
ax4.plot([this_phase, this_phase], [0, 1], lw=3, c='#ef8a62', alpha=.5)
for this_phase in phases_other:
ax4.plot([this_phase, this_phase], [0, .7], lw=2, c='k', alpha=.4, zorder=-1)
ax4.grid()
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax4.plot([r, r], [0, 1.3], lw=1, c=[.7, .7, .7], zorder=-2)
ax4.spines['polar'].set_visible(False)
ax4.set_ylim(0, 1.3)
ax4.set_yticklabels([])
ax4.set_aspect('equal', 'box')
red_patch = mpatches.Patch(color='#67a9cf', label='L. Frontal')
blue_patch = mpatches.Patch(color='#ef8a62', label='Hipp')
_ = ax4.legend(handles=[red_patch, blue_patch], loc='lower left', bbox_to_anchor=(0.9, 0.9),
frameon=False, fontsize=16)
################################################
# ROW 5b: phase polar plots for recalled items #
################################################
phases = self.res['traveling_waves'][cluster_name]['phase_data_recalled'][:, argmax_r2]
# phases = (phases + np.pi) % (2 * np.pi) - np.pi
# phases *= 180. / np.pi
# phases -= phases.min() - 1
# phases = np.deg2rad(phases)
phases_left_front = phases[cluster_regions == 'left-Frontal']
phases_hipp = phases[(cluster_regions == 'left-Hipp') | (cluster_regions == 'right-Hipp')]
phases_other = phases[~cluster_regions.isin(['left-Frontal', 'left-Hipp', 'right-Hipp'])]
for this_phase in phases_left_front:
ax6.plot([this_phase, this_phase], [0, 1], lw=3, c='#67a9cf', alpha=.5)
for this_phase in phases_hipp:
ax6.plot([this_phase, this_phase], [0, 1], lw=3, c='#ef8a62', alpha=.5)
for this_phase in phases_other:
ax6.plot([this_phase, this_phase], [0, .7], lw=2, c='k', alpha=.4, zorder=-1)
ax6.grid()
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax6.plot([r, r], [0, 1.3], lw=1, c=[.7, .7, .7], zorder=-2)
ax6.spines['polar'].set_visible(False)
ax6.set_ylim(0, 1.3)
ax6.set_yticklabels([])
ax6.set_aspect('equal', 'box')
ax6.set_title('Recalled items', y=1.12)
####################################################
# ROW 5c: phase polar plots for not recalled items #
####################################################
phases = self.res['traveling_waves'][cluster_name]['phase_data_not_recalled'][:, argmax_r2]
# phases = (phases + np.pi) % (2 * np.pi) - np.pi
# phases *= 180. / np.pi
# phases -= phases.min() - 1
# phases = np.deg2rad(phases)
phases_left_front = phases[cluster_regions == 'left-Frontal']
phases_hipp = phases[(cluster_regions == 'left-Hipp') | (cluster_regions == 'right-Hipp')]
phases_other = phases[~cluster_regions.isin(['left-Frontal', 'left-Hipp', 'right-Hipp'])]
for this_phase in phases_left_front:
ax7.plot([this_phase, this_phase], [0, 1], lw=3, c='#67a9cf', alpha=.5)
for this_phase in phases_hipp:
ax7.plot([this_phase, this_phase], [0, 1], lw=3, c='#ef8a62', alpha=.5)
for this_phase in phases_other:
ax7.plot([this_phase, this_phase], [0, .7], lw=2, c='k', alpha=.4, zorder=-1)
ax7.grid()
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax7.plot([r, r], [0, 1.3], lw=1, c=[.7, .7, .7], zorder=-2)
ax7.spines['polar'].set_visible(False)
ax7.set_ylim(0, 1.3)
ax7.set_yticklabels([])
ax7.set_aspect('equal', 'box')
ax7.set_title('Not recalled items', y=1.12)
####################################################
# ROW 6:
####################################################
recalled = self.res['traveling_waves']['cluster1']['recalled']
if ('left-Frontal' in self.res['traveling_waves'][cluster_name]['phase_by_roi']) & \
('both-Hipp' in self.res['traveling_waves'][cluster_name]['phase_by_roi']):
phase_by_roi = self.res['traveling_waves'][cluster_name]['phase_by_roi']
phase_left_front_roi = phase_by_roi['left-Frontal'][:, argmax_r2]
# phase_left_front_roi = (phase_left_front_roi + np.pi) % (2 * np.pi)
phase_hipp_roi = phase_by_roi['both-Hipp'][:, argmax_r2]
# phase_hipp_roi = (phase_hipp_roi + np.pi) % (2 * np.pi)
# phase_left_front_roi = (phase_left_front_roi + np.pi) % (2 * np.pi) - np.pi
# phase_left_front_roi *= 180. / np.pi
# phase_left_front_roi -= phase_left_front_roi.min() - 1
# phase_left_front_roi = np.deg2rad(phase_left_front_roi)
# phase_hipp_roi = (phase_hipp_roi + np.pi) % (2 * np.pi) - np.pi
# phase_hipp_roi *= 180. / np.pi
# phase_hipp_roi -= phase_hipp_roi.min() - 1
# phase_hipp_roi = np.deg2rad(phase_hipp_roi)
# LEFT
ax8 = self.rose_plot(phase_left_front_roi, n_bins=30, ax=ax8)
ax8 = self.rose_plot(phase_hipp_roi, n_bins=30, ax=ax8)
ax8.spines['polar'].set_visible(False)
ax8.set_yticks([ax8.get_ylim()[1]])
ax8.set_aspect('equal', 'box')
ax8.tick_params(axis='y', colors=[.7, .7, .7])
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax8.plot([r, r], [0, ax8.get_ylim()[1]], lw=1, c=[.7, .7, .7], zorder=-2)
ax8.grid()
# MIDDLE
ax9 = self.rose_plot(phase_left_front_roi[recalled], n_bins=30, ax=ax9)
ax9 = self.rose_plot(phase_hipp_roi[recalled], n_bins=30, ax=ax9)
ax9.spines['polar'].set_visible(False)
ax9.set_yticks([ax9.get_ylim()[1]])
ax9.set_aspect('equal', 'box')
ax9.tick_params(axis='y', colors=[.7, .7, .7])
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax9.plot([r, r], [0, ax9.get_ylim()[1]], lw=1, c=[.7, .7, .7], zorder=-2)
ax9.grid()
# RIGHT
ax10 = self.rose_plot(phase_left_front_roi[~recalled], n_bins=30, ax=ax10)
ax10 = self.rose_plot(phase_hipp_roi[~recalled], n_bins=30, ax=ax10)
ax10.spines['polar'].set_visible(False)
ax10.set_yticks([ax10.get_ylim()[1]])
ax10.set_aspect('equal', 'box')
ax10.tick_params(axis='y', colors=[.7, .7, .7])
for r in np.linspace(0, 2 * np.pi, 5)[:-1]:
ax10.plot([r, r], [0, ax10.get_ylim()[1]], lw=1, c=[.7, .7, .7], zorder=-2)
ax10.grid()
plt.subplots_adjust(hspace=.5)
return fig
func_filename = adhd_dataset.func[0]
confound_filename = adhd_dataset.confounds[0]
time_series = masker.fit_transform(func_filename,
confounds=[confound_filename])
# Computing precision matrices ################################################
from sklearn.covariance import LedoitWolf
cve = LedoitWolf()
cve.fit(time_series)
# Displaying results ##########################################################
import matplotlib.pyplot as plt
from nilearn import plotting
# Display time series
for time_serie, label in zip(time_series.T, labels):
plt.plot(time_serie, label=label)
plt.title('Default Mode Network Time Series')
plt.xlabel('Scan number')
plt.ylabel('Normalized signal')
plt.legend()
plt.tight_layout()
# Display connectome
title = "Default Mode Network Connectivity"
plotting.plot_connectome(cve.precision_, dmn_coords, title=title)
plotting.show()
############################################################################
# Build and display a correlation matrix
from nilearn.connectome import ConnectivityMeasure
correlation_measure = ConnectivityMeasure(kind='correlation')
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
# Display the correlation matrix
import numpy as np
from matplotlib import pyplot as plt
plt.figure(figsize=(10, 10))
# Mask out the major diagonal
np.fill_diagonal(correlation_matrix, 0)
plt.imshow(correlation_matrix, interpolation="nearest", cmap="RdBu_r",
vmax=0.8, vmin=-0.8)
plt.colorbar()
# And display the labels
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
############################################################################
# And now display the corresponding graph
from nilearn import plotting
coords = atlas.region_coords
# We threshold to keep only the 20% of edges with the highest value
# because the graph is very dense
plotting.plot_connectome(correlation_matrix, coords,
edge_threshold="80%", colorbar=True)
plotting.show()
comp_list=partperm(func_type_list)
with backend_pdf.PdfPages(save_report) as pdf:
for g_index in range(len(func_type_list)+1):
pdf.savefig(at_check[g_index])
plt.close()
#tstats for comparison of metrics accross groups
for kind in kinds:
print('saving report: '+kind)
for func_type in func_type_list :
#average across all subjects
Mean_mat = mean_connectivity_matrix[func_type][kind]
Mean_tot = np.mean(Mean_mat)
#plot connectomes
plotting.plot_connectome(Mean_mat, coords,title= func_type +' '+ kind+' connectome',edge_threshold='90%')
pdf.savefig()
plt.close()
if kind in ['correlation','partial correlation']:
span = [-1,1]
else:
m_span = np.max(np.abs(Mean_mat))
span = [-m_span,m_span]
plot_matrices(Mean_mat,span ,rois, 'Average '+func_type + ' ' + kind+ ' across subjects\nTotal average for '+kind+' = '+str(Mean_tot) ,colmap ="bwr",labelsize=l)
pdf.savefig()
plt.close()
for comp in comps :
paired = Paired
if kind in ['correlation', 'partial correlation']:
# Z-Fisher transform
time_series = masker.fit_transform(func_filename,
confounds=[confound_filename])
##########################################################################
# Display time series
import matplotlib.pyplot as plt
for time_serie, label in zip(time_series.T, labels):
plt.plot(time_serie, label=label)
plt.title('Default Mode Network Time Series')
plt.xlabel('Scan number')
plt.ylabel('Normalized signal')
plt.legend()
plt.tight_layout()
##########################################################################
# Compute precision matrices
from sklearn.covariance import LedoitWolf
cve = LedoitWolf()
cve.fit(time_series)
##########################################################################
# Display connectome
from nilearn import plotting
plotting.plot_connectome(cve.precision_, dmn_coords,
title="Default Mode Network Connectivity")
plotting.show()
masker = NiftiMapsMasker(maps_img=atlas_filename, standardize=True,
memory='nilearn_cache', verbose=5)
data = datasets.fetch_adhd(n_subjects=1)
time_series = masker.fit_transform(data.func[0],
confounds=data.confounds)
correlation_matrix = np.corrcoef(time_series.T)
# Display the correlation matrix
from matplotlib import pyplot as plt
plt.figure(figsize=(10, 10))
plt.imshow(correlation_matrix, interpolation="nearest")
# And display the labels
x_ticks = plt.xticks(range(len(names)), names, rotation=90)
y_ticks = plt.yticks(range(len(names)), names)
# And now display the corresponding graph
from nilearn import plotting
coords = np.vstack((labels['x'], labels['y'], labels['z']))
# We threshold to keep only the 20% of edges with the highest value
# because the graph is very dense
plotting.plot_connectome(correlation_matrix, coords.T,
edge_threshold="80%")
plt.show()
confound_filename = adhd_dataset.confounds[0]
# Computing some confounds
hv_confounds = mem.cache(nilearn.image.high_variance_confounds)(
fmri_filename)
time_series = masker.transform(fmri_filename,
confounds=[hv_confounds, confound_filename])
print("-- Computing graph-lasso inverse matrix ...")
from sklearn import covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(time_series)
# Displaying results ##########################################################
atlas_imgs = image.iter_img(msdl_atlas_dataset.maps)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in atlas_imgs]
title = "GraphLasso"
plotting.plot_connectome(-gl.precision_, atlas_region_coords,
edge_threshold='90%',
title="Sparse inverse covariance")
plotting.plot_connectome(gl.covariance_,
atlas_region_coords, edge_threshold='90%',
title="Covariance")
plot_matrices(gl.covariance_, gl.precision_, title)
plt.show()
roi_names, roi_coords = load_msdl_names_and_coords()
stat_av = read_test('pc', 'av', 'avg')
stat_v = read_test('pc', 'v', 'avg')
stat2 = read_test2('pc', ['av', 'v'], 'avg')
i, j = np.unravel_index(stat2.argmax(), stat2.shape)
print 'av 1sample pval :', stat_av[i, j]
print 'v 1sample pval :', stat_v[i, j]
print roi_names[i], roi_names[j]
print i, j
m = np.eye(2)
m[1,0] = stat2[i, j]
m[0,1] = m[1,0]
plot_connectome(m, [roi_coords[i], roi_coords[j]])
conn = []
behav = []
for i in range(len(dataset.subjects)):
c = load_dynacomp_fc(dataset.subjects[i], session='func1', metric='pc', msdl=True)
conn.append(c[i, j])
b = behav_data[i]['postRT'] - behav_data[i]['preRT']
behav.append(b)
sns.jointplot(np.array(conn), np.array(behav), kind='kde')
sns.axlabel('Connectivity', 'Behavior')