def calculateModularity(adj, labels):
m = np.sum(adj)
N = len(adj)
degrees = bct.strengths_und(adj)
Q = 0
for r in range(N):
for c in range(N):
label_r = labels[r]
label_c = labels[c]
if label_r == label_c: rc = 1
else: rc = 0
Q = Q + adj[r, c] - ((degrees[r] * degrees[c]) / (2 * m) * rc)
Q = Q / (2 * m)
return Q
def compute(self):
weights = bct.strengths_und(self.g)
self.stats['Strength'] = [v for v in weights]
# Lobe grouping
plots.create_bar_lobe_grouped_descending(
"reports/plots/" + self.name + "_weighted_degree_descending.pdf",
self.name + " Weighted Degree Centrality", 'Weighted Degree',
weights)
plt.show()
average = statistics.mean(self.stats['Strength'])
print("Average Strength: " + str(average) + "\n")
return self.stats
def do_opt(adj,mods,option):
if option=='global efficiency':
return bct.efficiency_wei(adj)
elif option=='local efficiency':
return bct.efficiency_wei(adj,local=True)
elif option=='average strength':
return bct.strengths_und(adj)
elif option=='clustering coefficient':
return bct.clustering_coef_wu(adj)
elif option=='eigenvector centrality':
return bct.eigenvector_centrality_und(adj)
elif option=='binary kcore':
return bct.kcoreness_centrality_bu(adj)[0]
elif option=='modularity':
return bct.modularity_und(adj,mods)[1]
elif option=='participation coefficient':
return bct.participation_coef(adj,mods)
elif option=='within-module degree':
return bct.module_degree_zscore(adj,mods)
def do_opt(adj, mods, option):
if option == 'global efficiency':
return bct.efficiency_wei(adj)
elif option == 'local efficiency':
return bct.efficiency_wei(adj, local=True)
elif option == 'average strength':
return bct.strengths_und(adj)
elif option == 'clustering coefficient':
return bct.clustering_coef_wu(adj)
elif option == 'eigenvector centrality':
return bct.eigenvector_centrality_und(adj)
elif option == 'binary kcore':
return bct.kcoreness_centrality_bu(adj)[0]
elif option == 'modularity':
return bct.modularity_und(adj, mods)[1]
elif option == 'participation coefficient':
return bct.participation_coef(adj, mods)
elif option == 'within-module degree':
return bct.module_degree_zscore(adj, mods)
for subject in subjects:
cls = np.load(source_folder +
"graph_data/%s_classic_pow_pln.npy" % subject).item()
pln = np.load(source_folder +
"graph_data/%s_plan_pow_pln.npy" % subject).item()
cls_all.append(cls)
pln_all.append(pln)
for k, band in enumerate(bands.keys()):
data_cls = []
for j in range(len(cls_all)):
tmp = cls_all[j][band]
data_cls.append(
np.asarray([bct.strengths_und(g) for g in tmp]).mean(axis=0))
data_pln = []
for j in range(len(pln_all)):
tmp = pln_all[j][band]
data_pln.append(
np.asarray([bct.strengths_und(g) for g in tmp]).mean(axis=0))
data_cls = np.asarray(data_cls)
data_pln = np.asarray(data_pln)
X = np.vstack([data_cls, data_pln])
y = np.concatenate([np.zeros(len(data_cls)), np.ones(len(data_pln))])
cv = StratifiedKFold(y, n_folds=6, shuffle=True)
model = joblib.load(source_folder +
"graph_data/sk_models/eigen_ada_pln_%s.plk" % band)
def test_strengths_und():
x = load_sample()
s = bct.strengths_und(x)
assert np.allclose(np.sum(x), 38967.38702018)
for subject in subjects:
cls = np.load(source_folder + "graph_data/%s_classic_pow_post.npy" %
subject).item()
pln = np.load(source_folder + "graph_data/%s_plan_pow_post.npy" %
subject).item()
cls_all.append(cls)
pln_all.append(pln)
for k, band in enumerate(bands.keys()):
data_cls = []
for j in range(len(cls_all)):
tmp = cls_all[j][band]
data_cls.append(
np.asarray([bct.strengths_und(g) for g in tmp]).mean(axis=0))
data_pln = []
for j in range(len(pln_all)):
tmp = pln_all[j][band]
data_pln.append(
np.asarray([bct.strengths_und(g) for g in tmp]).mean(axis=0))
data_cls = np.asarray(data_cls)
data_pln = np.asarray(data_pln)
X = np.vstack([data_cls, data_pln])
y = np.concatenate([np.zeros(len(data_cls)), np.ones(len(data_pln))])
cv = StratifiedKFold(y, n_folds=6, shuffle=True)
cv_params = {
#conn_measure = ConnectivityMeasure(kind=kind,vectorize=True)
conn_measure = ConnectivityMeasure(kind=kind)
connectivity_biomarkers[kind] = conn_measure.fit_transform(ts_allsites)
# For each kind, all individual coefficients are stacked in a unique 2D matrix.
print('{0} correlation biomarkers for each subject.'.format(
connectivity_biomarkers['tangent'].shape[1]))
#### Complex graph metrics
eig_cens=[]
clusterings=[]
Node_strengths=[]
for i in range(len(ts_allsites)):
Node_strength=bct.strengths_und(connectivity_biomarkers['tangent'][i])
Node_strengths.append(Node_strength)
eig_cen = bct.centrality.eigenvector_centrality_und(connectivity_biomarkers['tangent'][i])
eig_cens.append(eig_cen)
clustering=bct.clustering_coef_wd(connectivity_biomarkers['tangent'][i])
clusterings.append(clustering)
Node_strengths = np.stack(Node_strengths)
eig_cens=np.stack(eig_cens)
clusterings=np.stack(clusterings)
from nilearn.connectome import sym_matrix_to_vec
mat_connectivity= []
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_length_matrix, args.in_conn_matrix])
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
if not args.append_json:
assert_outputs_exist(parser, args, args.out_json)
else:
logging.debug('Using --append_json, make sure to delete {} '
'before re-launching a group analysis.'.format(
args.out_json))
if args.append_json and args.overwrite:
parser.error('Cannot use the append option at the same time as '
'overwrite.\nAmbiguous behavior, consider deleting the '
'output json file first instead.')
conn_matrix = load_matrix_in_any_format(args.in_conn_matrix)
len_matrix = load_matrix_in_any_format(args.in_length_matrix)
if args.filtering_mask:
mask_matrix = load_matrix_in_any_format(args.filtering_mask)
conn_matrix *= mask_matrix
len_matrix *= mask_matrix
N = len_matrix.shape[0]
if args.avg_node_wise:
func_cast = avg_cast
else:
func_cast = list_cast
gtm_dict = {}
betweenness_centrality = bct.betweenness_wei(len_matrix) / ((N - 1) *
(N - 2))
gtm_dict['betweenness_centrality'] = func_cast(betweenness_centrality)
ci, gtm_dict['modularity'] = bct.modularity_louvain_und(conn_matrix,
seed=0)
gtm_dict['assortativity'] = bct.assortativity_wei(conn_matrix, flag=0)
gtm_dict['participation'] = func_cast(
bct.participation_coef_sign(conn_matrix, ci)[0])
gtm_dict['clustering'] = func_cast(bct.clustering_coef_wu(conn_matrix))
gtm_dict['nodal_strength'] = func_cast(bct.strengths_und(conn_matrix))
gtm_dict['local_efficiency'] = func_cast(
bct.efficiency_wei(len_matrix, local=True))
gtm_dict['global_efficiency'] = func_cast(bct.efficiency_wei(len_matrix))
gtm_dict['density'] = func_cast(bct.density_und(conn_matrix)[0])
# Rich club always gives an error for the matrix rank and gives NaN
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tmp_rich_club = bct.rich_club_wu(conn_matrix)
gtm_dict['rich_club'] = func_cast(tmp_rich_club[~np.isnan(tmp_rich_club)])
# Path length gives an infinite distance for unconnected nodes
# All of this is simply to fix that
empty_connections = np.where(np.sum(len_matrix, axis=1) < 0.001)[0]
if len(empty_connections):
len_matrix = np.delete(len_matrix, empty_connections, axis=0)
len_matrix = np.delete(len_matrix, empty_connections, axis=1)
path_length_tuple = bct.distance_wei(len_matrix)
gtm_dict['path_length'] = func_cast(path_length_tuple[0])
gtm_dict['edge_count'] = func_cast(path_length_tuple[1])
if not args.avg_node_wise:
for i in empty_connections:
gtm_dict['path_length'].insert(i, -1)
gtm_dict['edge_count'].insert(i, -1)
if args.small_world:
gtm_dict['omega'], gtm_dict['sigma'] = omega_sigma(len_matrix)
if os.path.isfile(args.out_json) and args.append_json:
with open(args.out_json) as json_data:
out_dict = json.load(json_data)
for key in gtm_dict.keys():
if isinstance(out_dict[key], list):
out_dict[key].append(gtm_dict[key])
else:
out_dict[key] = [out_dict[key], gtm_dict[key]]
else:
out_dict = {}
for key in gtm_dict.keys():
out_dict[key] = [gtm_dict[key]]
with open(args.out_json, 'w') as outfile:
json.dump(out_dict,
outfile,
indent=args.indent,
sort_keys=args.sort_keys)
threshPos = 0.4
threshNeg = -0.2
pearsonBinary = copy.deepcopy(pearson)
pearsonBinary[ np.abs(pearsonBinary) < threshPos] = 0
pearsonBinaryPos = copy.deepcopy(pearson)
pearsonBinaryPos[ pearsonBinaryPos < threshPos] = 0
pearsonBinaryNeg = copy.deepcopy(pearson)
pearsonBinaryNeg[ pearsonBinaryNeg > threshNeg] = 0
degree = bct.degrees_und(pearsonBinary[:,:,:]).T
degreePos = bct.degrees_und(pearsonBinaryPos[:,:,:]).T
degreeNeg = bct.degrees_und(pearsonBinaryNeg[:,:,:]).T
strength = bct.strengths_und(np.abs( pearson[:,:,:])).T
strengthPos = np.zeros(shape = (windows, nchan))
strengthNeg = np.zeros(shape = (windows, nchan))
for win in range(windows):
strengthPos[win, :], strengthNeg[win, :] , _, _= bct.strengths_und_sign( pearson[:,:,win])
strengthNegAbs = np.abs(strengthNeg)
#normalize
degreeNorm = degree / degree.max(axis=0)
degreePosNorm = degreePos / degreePos.max(axis=0)
degreeNegNorm = degreeNeg / degreeNeg.max(axis=0)
strengthNorm = strength / strength.max(axis=0)
strengthPosNorm = strengthPos / strengthPos.max(axis=0)
if group == 'patient':
participants = ['z1','z2','z3','z4','z5','z6','z8']
elif group == 'control':
participants = ['c1','c2','c3','c5','c6','c7','c8']
all_measures = np.empty(shape=[68,len(participants),5])
adjmats = np.empty(shape=[68,68,len(participants)])
counter = 0
for participant in participants:
adjmat = sio.loadmat(participant + '_FA.mat')
adjmat = adjmat['adjacency_matrix']
labels = get_parcellation_labels(generate_ROI_file(FreeSurfer_ROI_file)).values
labels,adjmat = remove_non_cortical_ROIs(labels,adjmat)
all_measures[:,counter,0] = bct.degrees_und(adjmat)
all_measures[:,counter,1] = bct.strengths_und(adjmat)
all_measures[:,counter,2] = bct.clustering_coef_wu(adjmat)
all_measures[:,counter,3] = bct.betweenness_wei(adjmat)
all_measures[:,counter,4] = bct.efficiency_wei(adjmat,local=True)
adjmats[:,:,counter] = adjmat
counter += 1
mean_measures = np.mean(all_measures,axis=1)
if group == 'patient':
patient = pd.DataFrame(mean_measures, index=labels,columns=['patient.NodeDegree','patient.Strength','patient.ClustCoeff','patient.BetweenCent','patient.LocEff'])
patient_measures = all_measures
patient_adjmats = adjmats
elif group == 'control':
control = pd.DataFrame(mean_measures, index=labels,columns=['control.NodeDegree','control.Strength','control.ClustCoeff','control.BetweenCent','control.LocEff'])
control_measures = all_measures
cls_all.append(cls.mean(axis=0))
pln_all.append(pln.mean(axis=0))
cls_all_2 = np.asarray(cls_all)
pln_all_2 = np.asarray(pln_all)
full_matrix = np.concatenate([cls_all_2, pln_all_2], axis=0)
threshold = np.median(full_matrix[np.nonzero(full_matrix)]) + \
np.std(full_matrix[np.nonzero(full_matrix)])
data_cls_bin = cls_all > threshold
data_pln_bin = pln_all > threshold
data_cls = [np.asarray([bct.strengths_und(g)
for g in data_cls_bin])]
data_pln = [np.asarray([bct.strengths_und(g)
for g in data_pln_bin])]
X = np.vstack([data_cls, data_pln])
y = np.concatenate([np.zeros(len(data_cls)), np.ones(len(data_pln))])
cv = StratifiedKFold(n_splits=6, shuffle=True)
cv_params = {"learning_rate": np.arange(0.1, 1.1, 0.1),
'n_estimators': np.arange(1, 80, 2)}
grid = GridSearchCV(AdaBoostClassifier(),
cv_params,
scoring='roc_auc',
#
# WMD seems relatively fast, maybe 10min per threshold
WMD[i, :] = bct.module_degree_zscore(tmp_matrix, CI)
fn = 'completed WMD calculation for %s at:' % cost
print(fn)
print(datetime.now())
#
# EC[i,:] = bct.eigenvector_centrality_und(tmp_matrix)
# fn = 'completed EC calculation for %s at:' %cost
# print(fn)
# print(datetime.now())
# GC[i,:], _ = bct.gateway_coef_sign(tmp_matrix, CI)
# fn = 'completed GC calculation for %s at:' %cost
# print(fn)
# print(datetime.now())
#
# SC[i,:] = bct.subgraph_centrality(tmp_matrix)
# fn = 'completed SC calculation for %s at:' %cost
# print(fn)
# print(datetime.now())
#
# ST is fast to compute, ~10min per threshold
ST[i, :] = bct.strengths_und(tmp_matrix)
fn = 'completed ST calculation for %s at:' % cost
print(fn)
print(datetime.now())
print("All done at: ")
print(datetime.now())
def process(data):
return bct.strengths_und(data)
participants = ['z1', 'z2', 'z3', 'z4', 'z5', 'z6', 'z8']
elif group == 'control':
participants = ['c1', 'c2', 'c3', 'c5', 'c6', 'c7', 'c8']
all_measures = np.empty(shape=[68, len(participants), 5])
adjmats = np.empty(shape=[68, 68, len(participants)])
counter = 0
for participant in participants:
adjmat = sio.loadmat(participant + '_FA.mat')
adjmat = adjmat['adjacency_matrix']
labels = get_parcellation_labels(
generate_ROI_file(FreeSurfer_ROI_file)).values
labels, adjmat = remove_non_cortical_ROIs(labels, adjmat)
all_measures[:, counter, 0] = bct.degrees_und(adjmat)
all_measures[:, counter, 1] = bct.strengths_und(adjmat)
all_measures[:, counter, 2] = bct.clustering_coef_wu(adjmat)
all_measures[:, counter, 3] = bct.betweenness_wei(adjmat)
all_measures[:, counter, 4] = bct.efficiency_wei(adjmat, local=True)
adjmats[:, :, counter] = adjmat
counter += 1
mean_measures = np.mean(all_measures, axis=1)
if group == 'patient':
patient = pd.DataFrame(mean_measures,
index=labels,
columns=[
'patient.NodeDegree', 'patient.Strength',
'patient.ClustCoeff', 'patient.BetweenCent',
'patient.LocEff'
])