def test_participation():
W = np.eye(3)
ci = np.array([1, 1, 2])
assert np.allclose(bct.participation_coef(W, ci), [0, 0, 0])
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [0, 0, 0])
W = np.ones((3, 3))
assert np.allclose(bct.participation_coef(W, ci), [
0.44444444, 0.44444444, 0.44444444])
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [
0.44444444, 0.44444444, 0.44444444])
W = np.eye(3)
W[0, 1] = 1
W[0, 2] = 1
assert np.allclose(bct.participation_coef(W, ci), [0.44444444, 0, 0])
assert np.allclose(bct.participation_coef_sign(W, ci)
[0], [0.44444444, 0, 0])
W = np.eye(3)
W[0, 1] = -1
W[0, 2] = -1
W[1, 2] = 1
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [0., 0.5, 0.])
def participation_test():
W = np.eye(3)
ci = np.array([1, 1, 2])
assert np.allclose(bct.participation_coef(W, ci), [0, 0, 0])
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [0, 0, 0])
W = np.ones((3, 3))
assert np.allclose(bct.participation_coef(W, ci), [
0.44444444, 0.44444444, 0.44444444])
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [
0.44444444, 0.44444444, 0.44444444])
W = np.eye(3)
W[0, 1] = 1
W[0, 2] = 1
assert np.allclose(bct.participation_coef(W, ci), [0.44444444, 0, 0])
assert np.allclose(bct.participation_coef_sign(W, ci)
[0], [0.44444444, 0, 0])
W = np.eye(3)
W[0, 1] = -1
W[0, 2] = -1
W[1, 2] = 1
assert np.allclose(bct.participation_coef_sign(W, ci)[0], [0., 0.5, 0.])
def calculate_communities(self, reorder=False, **kwargs):
assert self.community_alg is not None, \
print("Community algorithm has not been set!")
G = self.G
graph_mat = self.graph_mat
# calculate community structure
comm, mod = self.community_alg(graph_mat, **kwargs)
# if there is a reference, relabel communities based on their closest association
if self.ref_community:
comm = self._relabel_community(comm, self.ref_community)
# label vertices of G
G.vs['community'] = comm
G.vs['within_module_degree'] = bct.module_degree_zscore(
graph_mat, comm)
if np.min(graph_mat) < 0:
participation_pos, participation_neg = bct.participation_coef_sign(
graph_mat, comm)
G.vs['part_coef_pos'] = participation_pos
G.vs['part_coef_neg'] = participation_neg
else:
G.vs['part_coef'] = bct.participation_coef(graph_mat, comm)
if reorder:
self.reorder()
# calculate subgraph (within-community) characteristics
self._subgraph_analysis()
return mod
def run_graph(sub):
'''run graph analysis, get PC/WMD/Q'''
for condition in Conditions:
for atlas in Atlases:
matrix = []
for direction in Directions:
fn = datapath + str(
sub) + '_' + condition + direction + atlas + '.corrmat'
try:
matrix += [np.loadtxt(fn)]
except:
break
PCs = []
WMDs = []
Qs = []
if np.shape(matrix)[0] > 1:
matrix = np.sum(matrix, axis=0) / np.shape(matrix)[0]
for c in np.arange(0.05, 0.16, 0.01):
mat_th = threshold(matrix.copy(), c)
graph = matrix_to_igraph(matrix.copy(), c)
i = graph.community_infomap(edge_weights='weight')
CI = np.asarray(i.membership) + 1
PCs += [bct.participation_coef(mat_th, CI)]
WMDs += [bct.module_degree_zscore(mat_th, CI)]
Qs += [i.modularity]
fn = datapath + str(sub) + '_' + condition + atlas + '.PC'
np.save(fn, PCs)
fn = datapath + str(sub) + '_' + condition + atlas + '.WMD'
np.save(fn, WMDs)
fn = datapath + str(sub) + '_' + condition + atlas + '.Q'
np.save(fn, Qs)
def calc_particip(G, partition, A, C):
# Calculate participation coefficient for each node
P = participation_coef(A, C)
# Create a dictionary keyed by RSN, values are lists of particip coef of every node in RSN
particip = collections.defaultdict(list)
for ind, p in enumerate(P):
particip[partition[list(G.nodes())[ind]]].append(p)
return particip
def compute(self):
try:
name = "Results/Communities/" + self.name + "_" + self.communities_algorithm + "_communities.node"
print('Trying', name)
last_results = pd.read_csv(
name,
" ",
names=['X', 'Y', 'Z', 'Community', 'Degree', 'RegionName'])
print('Loading communities...')
communities = last_results['Community']
region_names = last_results['RegionName']
except Exception:
print('Divinding communities...')
communities = NM(self.g, self.name, self.stats,
self.communities_algorithm).compute()
region_names = pd.read_csv("data/lobes.node", " ",
header='infer')['RegionName']
participations = bct.participation_coef(self.g, communities,
'undirected')
within_degrees = bct.module_degree_zscore(self.g, communities, 0)
connectors, provincials = [], []
for node in zip(participations, within_degrees, region_names):
if node[1] > 1:
if node[0] > 0.6:
connectors.append((node[2], node[1], node[0]))
if node[0] < 0.4:
provincials.append((node[2], node[1], node[0]))
print("Connectors", connectors)
print("Provincials", provincials)
self.stats['RegionName'] = region_names
self.stats['Community'] = communities
self.stats['wMD'] = within_degrees
self.stats['PC'] = participations
plots.create_box_plot_nodes('PC', self.stats, self.name)
plots.create_plot_communitycolored(
"reports/plots/ParticipationCoeff/" + str(self.name) + '_' +
str(self.communities_algorithm) + ".pdf",
('fMRI' if self.name == 'fmri' else 'EEG-' + self.name),
'Within-module Degree Z-score',
within_degrees,
'Participation Coefficient',
participations,
communities=communities,
xticks=[-3, -2, -1, 0, 1, 2, 3],
yticks=[0, 0.2, 0.4, 0.6, 0.8, 1.0])
return self.stats
def test_pc():
x = load_sample(thres=.4)
# ci,q = bct.modularity_und(x)
ci = np.load(mat_path('sample_partition.npy'))
pc = np.load(mat_path('sample_pc.npy'))
pc_ = bct.participation_coef(x, ci)
print(list(zip(pc, pc_)))
assert np.allclose(pc, pc_, atol=0.02)
def test_pc():
x = load_sample(thres=.4)
# ci,q = bct.modularity_und(x)
ci = np.load(mat_path('sample_partition.npy'))
pc = np.load(mat_path('sample_pc.npy'))
pc_ = bct.participation_coef(x, ci)
print(list(zip(pc, pc_)))
assert np.allclose(pc, pc_, atol=0.02)
def cal_dynamic_graph(MTD, impose=False, threshold=False):
'''calculate graph metrics across time(dynamic)'''
#setup outputs
time_points = MTD.shape[0]
ci = np.zeros([MTD.shape[1], MTD.shape[0]])
q = np.zeros([MTD.shape[0]])
WMD = np.zeros([MTD.shape[1], MTD.shape[0]])
PC = np.zeros([MTD.shape[1], MTD.shape[0]])
WW = np.zeros([MTD.shape[1], MTD.shape[0]])
BW = np.zeros([MTD.shape[1], MTD.shape[0]])
#modularity
if impose:
ci = np.tile(
np.loadtxt(
'/home/despoB/kaihwang/Rest/ThaGate/ROIs/Morel_Striatum_Gordon_CI'
), [time_points, 1]).T
for i, t in enumerate(range(0, time_points)):
matrix = MTD[i, :, :]
#need to deal with NANs because of coverage (no signal in some ROIs)
matrix[np.isnan(matrix)] = 0
#threshold here
if threshold:
matrix = bct.threshold_proportional(matrix, threshold)
#modularity
if impose == False:
ci[:, i], q[i] = bct.modularity_louvain_und_sign(matrix)
#PC
# for now, no negative weights
matrix[matrix < 0] = 0
PC[:, i] = bct.participation_coef(matrix, ci[:, i])
#WMD
WMD[:, i] = bct.module_degree_zscore(matrix, ci[:, i])
## within weight
WW[:, i] = cal_within_weight(matrix, ci[:, i])
## between Weight
BW[:, i] = cal_between_weight(matrix, ci[:, i])
# cal q using impsose CI partition
if impose:
q[i] = cal_modularity_w_imposed_community(matrix, ci[:, i])
return ci, q, PC, WMD, WW, BW
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)
def test_pipline():
''' A run thorugh test using a csv input from Aaron'''
# load matrix
matrix = np.genfromtxt('HCP_MMP1_roi-pair_corr.csv',
delimiter=',',
dtype=None)
matrix[np.isnan(matrix)] = 0.0
# step through costs, do infomap, return final infomap across cost
max_cost = .15
min_cost = .01
# ave consensus across costs
partition = ave_consensus_costs_parition(matrix, min_cost, max_cost)
partition = np.array(partition) + 1
# import thresholded matrix to BCT, import partition, run WMD/PC
PCs = np.zeros((len(np.arange(min_cost, max_cost + 0.01,
0.01)), matrix.shape[0]))
WMDs = np.zeros((len(np.arange(min_cost, max_cost + 0.01,
0.01)), matrix.shape[0]))
for i, cost in enumerate(np.arange(min_cost, max_cost, 0.01)):
tmp_matrix = threshold(matrix.copy(), cost)
#PC
PCs[i, :] = bct.participation_coef(tmp_matrix, partition)
#WMD
WMDs[i, :] = bct.module_degree_zscore(matrix, partition)
np.save("partition", partition)
np.save("PCs", PCs)
np.save("WMDs", WMDs)
#altantively, merge consensus using the power method
recursive_partition = power_recursive_partition(matrix, min_cost, max_cost)
recursive_partition = recursive_partition + 1
np.save('rescursive_partition', recursive_partition)
def cal_sFC_graph(subject, sequence, roi, impose=False, threshold=1.0):
''' load TS and run static FC'''
ts_path = '/home/despoB/kaihwang/Rest/ThaGate/NotBackedUp/'
fn = ts_path + str(subject) + '_%s_%s_000.netts' % (roi, sequence)
ts = np.loadtxt(fn)
matrix = np.corrcoef(ts)
matrix[np.isnan(matrix)] = 0
matrix = bct.threshold_proportional(matrix, threshold)
num_iter = 200
consensus = np.zeros((num_iter, matrix.shape[0], matrix.shape[1]))
for i in np.arange(0, num_iter):
ci, _ = bct.modularity_louvain_und_sign(matrix, qtype='sta')
consensus[i, :, :] = community_matrix(ci)
mean_matrix = np.nanmean(consensus, axis=0)
mean_matrix[np.isnan(mean_matrix)] = 0
CI, Q = bct.modularity_louvain_und_sign(mean_matrix, qtype='sta')
#no negative weights
matrix[matrix < 0] = 0
PC = bct.participation_coef(matrix, CI)
#WMD
WMD = bct.module_degree_zscore(matrix, CI)
## within weight
WW = cal_within_weight(matrix, CI)
## between Weight
BW = cal_between_weight(matrix, CI)
return CI, Q, PC, WMD, WW, BW
def calculate_communities(self, reorder=False, **kwargs):
assert self.community_alg is not None, \
print("Community algorithm has not been set!")
G = self.G
graph_mat = self.graph_mat
# calculate community structure
comm, mod = self.community_alg(graph_mat, **kwargs)
# if there is a reference, relabel communities based on their closest association
if self.ref_community:
comm = self._relabel_community(comm,self.ref_community)
# label vertices of G
G.vs['community'] = comm
G.vs['within_module_degree'] = bct.module_degree_zscore(graph_mat,comm)
if np.min(graph_mat) < 0:
participation_pos, participation_neg = bct.participation_coef_sign(graph_mat, comm)
G.vs['part_coef_pos'] = participation_pos
G.vs['part_coef_neg'] = participation_neg
else:
G.vs['part_coef'] = bct.participation_coef(graph_mat, comm)
if reorder:
self.reorder()
# calculate subgraph (within-community) characteristics
self._subgraph_analysis()
return mod
def load_network(kind,
parcel,
data="lau",
weights='log',
hemi="both",
version=1,
subset="all",
path=None):
'''
Function to load a dictionary containing information about the specified
brain network.
Parameters
----------
kind : string
Either 'SC' or 'FC'.
hemi : string
Either "both", "L" or "R".
weights " string
The weights of the edges. The options "normal", "log" or "binary".
The default is "log".
data : string
Either "HCP" or "lau".
parcel : string
Either "68", "114", ... [if 'lau'] / "s400", "s800" [if "HCP"]
version : int
Version of the network.
subset : string
Either 'discov', 'valid' or 'all'
path : string
path to the "data" folder in which the data will be stored. If
none, then assumes that path is current folder.
Returns
-------
Network : dictionary
Dictionary storing relevant attributes about the network
'''
# Initialize dictionary + store basic information about the network
Network = {}
Network["info"] = {}
Network["info"]["kind"] = kind
Network["info"]["parcel"] = parcel
Network["info"]["data"] = data
Network["info"]["hemi"] = hemi
Network["info"]["weights"] = weights
Network["info"]["version"] = version
Network["info"]["subset"] = subset
# Modify parameter names to what they are in file names
version = '' if version == 1 else '_v' + str(version)
subset = '' if subset == 'all' else subset
hemi = '' if hemi == 'both' else hemi
# Store important paths for loading the relevant data
main_path = path + "/brainNetworks/" + data + "/"
network_path = (main_path + "matrices/consensus/" + subset + kind +
parcel + hemi + version + "/")
matrix_path = network_path + "/" + weights
# Store general information about the network's parcellation
parcel_info = get_general_parcellation_info(parcel)
Network['order'] = parcel_info[0]
Network['noplot'] = parcel_info[1]
Network['lhannot'] = parcel_info[2]
Network['rhannot'] = parcel_info[3]
Network['atlas'] = parcel_info[4]
# Load the cammoun_id of the parcellation, if Cammoun (i.e. 033, 060, etc.)
if parcel[0] != 's':
Network['cammoun_id'] = parcel_to_n(parcel)
# masks
masks = get_node_masks(Network, path=main_path)
Network['node_mask'] = masks[0]
Network['hemi_mask'] = masks[1]
Network['subcortex_mask'] = masks[2]
# hemisphere
Network['hemi'] = get_hemi(Network, path=main_path)
# coordinates
Network['coords'] = get_coordinates(Network, path=main_path)
# Adjacency matrix
Network['adj'], last_modified = get_adjacency(Network,
matrix_path,
minimal_processing=True,
return_last_modified=True)
# Test whether the network is connected. Raise a warning if not...
if not np.all(bct.reachdist(Network['adj'])[0]):
warnings.warn(("This brain network appears to be disconnected. This "
"might cause problem for the computation of the other "
"measures"))
# node strength
Network["str"] = np.sum(Network['adj'], axis=0)
# Inverse of adjacency matrix
inv = Network['adj'].copy()
inv[Network['adj'] > 0] = 1 / inv[Network['adj'] > 0]
Network["inv_adj"] = inv
# distance
Network["dist"] = cdist(Network["coords"], Network["coords"])
# clustering coefficient
Network["cc"] = bct.clustering_coef_wu(Network['adj'])
# shortest path
Network['sp'] = get_shortest_path(Network,
matrix_path=matrix_path,
last_modified=last_modified)
# diffusion embedding
de = compute_diffusion_map(Network['adj'],
n_components=10,
return_result=True,
skip_checks=True)
Network["de"] = de[0]
Network["de_extra"] = de[1]
# Principal components
Network['PCs'], Network['PCs_ev'] = getPCs(Network['adj'])
# eigenvector centrality
Network["ec"] = bct.eigenvector_centrality_und(Network['adj'])
# mean first passage time
Network["mfpt"] = bct.mean_first_passage_time(Network['adj'])
# betweenness centrality
Network['bc'] = get_betweenness(Network,
matrix_path=matrix_path,
last_modified=last_modified)
# routing efficiency
Network["r_eff"] = efficiency(Network)
# diffusion efficiency
Network["d_eff"] = efficiency_diffusion(Network)
# subgraph centrality
Network["subc"] = bct.subgraph_centrality(Network["adj"])
# closeness centrality
Network['clo'] = 1 / np.mean(Network['sp'], axis=0)
# communities + participation coefficient
path = matrix_path + "/communities/"
if os.path.exists(path):
files = []
for i in os.listdir(path):
if os.path.isfile(os.path.join(path, i)) and 'ci_' in i:
files.append(i)
if len(files) > 0:
Network["ci"] = []
for file in files:
Network["ci"].append(np.load(os.path.join(path, file)))
Network["ppc"] = []
for i in range(len(files)):
ppc = bct.participation_coef(Network['adj'], Network["ci"][i])
Network["ppc"].append(ppc)
# Edge lengths
if (data == "HCP") and (kind == "SC"):
path = main_path + "matrices/" + subset + kind + parcel + hemi + "_lengths.npy"
if os.path.exists(path):
Network["lengths"] = np.load(path)
# streamline connection lengths
path = network_path + "/len.npy"
if os.path.exists(path):
Network['len'] = np.load(path)
# ROI names
if parcel[0] != "s":
Network['ROInames'] = get_ROInames(Network)
# geodesic distances between nodes
if parcel[0] == "s":
n = parcel[1:]
fname_l = n + "Parcels7Networks_lh_dist.csv"
fname_r = n + "Parcels7Networks_rh_dist.csv"
else:
fname_l = "scale" + Network['cammoun_id'] + "_lh_dist.csv"
fname_r = "scale" + Network['cammoun_id'] + "_rh_dist.csv"
Network['geo_dist_L'] = pd.read_csv(main_path + "/geodesic/medial/" +
fname_l,
header=None).values
Network['geo_dist_R'] = pd.read_csv(main_path + "/geodesic/medial/" +
fname_r,
header=None).values
return Network
#
# medianEL = np.median(np.array((el.values()), dtype=float))
# medianELNorm = np.median(np.array((elNorm), dtype=float))
# extras.writeResults(medianEL, "medianEL", ofb, propDict=propDict, append=appVal)
# extras.writeResults(medianELNorm, "medianELNorm", ofb, propDict=propDict, append=appVal)
#
# del(el, elNorm, meanEL, meanELNorm, medianEL, medianELNorm)
# modularity metrics
ci = bct.modularity_louvain_und(a.bctmat)
Q = ci[1]
ciN = a.assignbctResult(ci[0])
extras.writeResults(Q, "Q", ofb, propDict=propDict, append=appVal)
extras.writeResults(ciN, "ci", ofb , propDict=propDict, append=appVal)
pcCent = bct.participation_coef(a.bctmat,ci[0])
pcCent = a.assignbctResult(pcCent)
extras.writeResults(pcCent, "pcCent", ofb, propDict=propDict, append=appVal)
del pcCent
wmd = extras.withinModuleDegree(a.G, ciN)
extras.writeResults(wmd, "wmd", ofb, append=appVal)
del wmd
nM = len(np.unique(ci[0]))
extras.writeResults(nM, "nM", ofb, propDict=propDict, append=appVal)
del(nM)
del(ci, ciN, Q)
# # rich club measures
# rc = mbt.nx.rich_club_coefficient(a.G, normalized=False)
def centrality(self,
sbj_number,
nodes_number,
atlas,
make_symmetric=True,
upper_threshold=None,
lower_threshold=None,
binarize=False):
'''
Computing centrality measures of the adjencency matrix
Parameters
----------
sbj_number: int |
number of subjects
nodes_number: int|
number of nodes
atlas: excel file |
please se example available in the repo (e.g. new_atlas_coords.xlsx)
make_symmetric: Boolean|
True indicate that the matrix is either upper
or lower triangular and need to be symmetrize
False indicate that the matrix is a full matrix already
upper_threshold: int |
an integer value ranging from 0 to 100 representing the
percentage of values as respect to maximum. The value
under that threshold will be 0 (Default is None)
lower_threshold: int |
an integer value ranging from 0 to 100 representing the
percentage of values as respect to maximum. The value
above that threshold will be 0 (Default is None)
binarize= Boolean|
True will make the connectivity matrix binary
Default is False
Returns
-------
dict: : dictonary with the following keys |
edge_betweeness_bin: | np.ndarray
Edge betweenness centrality is the fraction of all
shortest paths in the network that contain a given
edge. Edges with high values of betweenness centrality
participate in a large number of shortest paths.
It will return node betweenness centrality vector.
edge_betweeness_wei: | np.ndarray
Edge betweenness centrality is the fraction of all
shortest paths in the network that contain a given
edge. Edges with high values of betweenness centrality
participate in a large number of shortest paths.
It will return node betweenness centrality vector.
eigenvector_centrality_und: | np.ndarray
Eigenector centrality is a self-referential measure
of centrality: nodes have high eigenvector centrality
if they connect to other nodes that have high
eigenvector centrality. The eigenvector centrality of
node i is equivalent to the ith element in the eigenvector
corresponding to the largest eigenvalue of the adjacency matrix.
It will return the eigenvector associated with the
largest eigenvalue of the matrix
coreness_kcoreness_centrality_bu: | np.ndarray
The k-core is the largest subgraph comprising nodes
of degree at least k. The coreness of a node is k if
the node belongs to the k-core but not to the (k+1)-core.
This function computes the coreness of all nodes for a
given binary undirected connection matrix.
It will return the node coreness.
kn_kcoreness_centrality_bu: | np.ndarray
The k-core is the largest subgraph comprising nodes
of degree at least k. The coreness of a node is k if
the node belongs to the k-core but not to the (k+1)-core.
This function computes the coreness of all nodes for a
given binary undirected connection matrix.
It will return the size of k-core
module_degree_zscore: | np.ndarray
The within-module degree z-score is a within-module
version of degree centrality. It will return
within-module degree Z-score
participation_coef: | np.ndarray
Participation coefficient is a measure of diversity
of intermodular connections of individual nodes.
It will return the participation coefficient
subgraph_centrality: | np.ndarray
The subgraph centrality of a node is a weighted sum
of closed walks of different lengths in the network
starting and ending at the node. This function returns
a vector of subgraph centralities for each node of the
network. It will return the subgraph centrality
'''
with open(self.net_label_txt) as f:
net = f.read().splitlines()
self.atlas = pd.read_excel(atlas, header=None)
self.atlas = np.array(self.atlas)
self.ci_original = self.atlas[:, 8]
self.centrality = {
"edge_betweeness_bin":
np.zeros([sbj_number, nodes_number]),
"edge_betweeness_wei":
np.zeros([sbj_number, nodes_number]),
"eigenvector_centrality_und":
np.zeros([sbj_number, nodes_number]),
"coreness_kcoreness_centrality_bu":
np.zeros([sbj_number, nodes_number]),
"kn_kcoreness_centrality_bu":
np.zeros([sbj_number, nodes_number]),
"module_degree_zscore":
np.zeros([sbj_number, nodes_number]),
"participation_coef":
np.zeros([sbj_number, nodes_number]),
"subgraph_centrality":
np.zeros([sbj_number, nodes_number])
}
for subj in range(len(self.matrices_files)):
self.matrix = pd.read_csv(self.matrices_files[subj],
sep=' ',
header=None)
self.matrix = np.array(self.matrix)
if make_symmetric == True:
self.matrix = self.matrix + self.matrix.T - np.diag(
self.matrix.diagonal())
else:
self.matrix = self.matrix
self.max = np.max(self.matrix.flatten())
if upper_threshold == None:
self.matrix = self.matrix
else:
self.matrix[self.matrix < upper_threshold * self.max / 100] = 0
if lower_threshold == None:
self.matrix = self.matrix
else:
self.matrix[self.matrix > lower_threshold * self.max / 100] = 0
self.matrix_bin = bct.algorithms.binarize(self.matrix)
self.matrix_weight = self.matrix
if binarize == True:
self.matrix = bct.algorithms.binarize(self.matrix)
else:
self.matrix = self.matrix
np.fill_diagonal(self.matrix, 0)
np.fill_diagonal(self.matrix_bin, 0)
np.fill_diagonal(self.matrix_weight, 0)
self.BC = bct.betweenness_bin(self.matrix_bin)
self.centrality['edge_betweeness_bin'][subj] = self.BC
self.BC_w = bct.betweenness_wei(self.matrix_weight)
self.centrality['edge_betweeness_wei'][subj] = self.BC_w
self.v = bct.eigenvector_centrality_und(self.matrix)
self.centrality['eigenvector_centrality_und'][subj] = self.v
self.coreness, self.kn = bct.kcoreness_centrality_bu(
self.matrix_bin)
self.centrality['coreness_kcoreness_centrality_bu'][
subj] = self.coreness
self.centrality['kn_kcoreness_centrality_bu'][subj] = self.kn
self.Z = bct.module_degree_zscore(self.matrix, ci=self.ci_original)
self.centrality['module_degree_zscore'][subj] = self.Z
self.P = bct.participation_coef(self.matrix, ci=self.ci_original)
self.centrality['participation_coef'][subj] = self.P
self.Cs = bct.subgraph_centrality(self.matrix_bin)
self.centrality['subgraph_centrality'][subj] = self.Cs
return self.centrality
def figure_4(data, specify, t_ids_b, method='laplacian', panels='all',
show=True, save=False, save_path=None):
'''
Function to create Figure 4
Parameters
----------
data : dict
Dictionary of the data to be used to generate the figures. If the
required data is not found in this dictionary, the item of figure
1 that requires this data will not be created and a message
will be printed.
specify : dict
Dictionary containing information about the trajectories that will be
shown in panel a (see main_script.py for an example).
t_ids_b: List
List of time points indices indicating the time points at which
the centrality slope distributions will be plotted on the surface
of the brain (panel b).
method : str
Method used to compute the transition probabilities. The purpose of
this parameter is to choose whether the x_scale of our figures should
be linear or logarithmic.
panels : str or list
List of the panels of Figure 1 that we want to create. If we want
to create all of them, use 'all'. Otherwise, individual panels can
be specified. For example, we could have panels=['a'] or
panels=['a', 'b'].
show : Boolean
If True, the figures will be displayed. If not, the figures will
bot be displayed.
save : Boolean
If True, the figures will be saved in the folder specified by the
save_path parameter.
save_path : str
Path of the folder in which the figures will be saved.
'''
if show is False:
plt.ioff()
if panels == 'all':
panels = ['a', 'b', 'c']
n = len(data['sc'])
k = len(data['t_points'])
# Slopes of the closeness centrality trajectories
slopes = np.gradient(data['cmulti'], axis=0)
if 'a' in panels:
required_entries = ['t_points', 'cmulti']
requirements = check_requirements(data, required_entries)
if requirements:
node_ids = specify['ID']
fig = plt.figure(figsize=(9, 3))
ax = fig.add_subplot(111)
for i in range(n):
ax.plot(data['t_points'],
data['cmulti'][:, i],
c='lightgray')
abs_max_color = max(-1 * np.amin(slopes), np.amax(slopes))
for i, id in enumerate(node_ids):
norm = plt.Normalize(-abs_max_color, abs_max_color)
slope_colors = RdBu_11_r.mpl_colormap(norm(slopes[:, id]))
for ii in range(k-1):
plt.plot([data['t_points'][ii],
data['t_points'][ii+1]],
[data['cmulti'][ii, id],
data['cmulti'][ii+1, id]],
c=slope_colors[ii, :],
linewidth=3)
if method == 'laplacian':
plt.xscale('log')
plt.xlabel('t')
plt.ylabel("c_multi")
if save:
figure_name = 'cmulti_with_gradient.png'
fig.savefig(os.path.join(save_path, figure_name))
if 'b' in panels:
required_entries = ['t_points', 'lhannot', 'rhannot', 'noplot',
'order']
requirements = check_requirements(data, required_entries)
if requirements:
fig = plt.figure(figsize=(9, 3))
ax = fig.add_subplot(111)
for i in range(n):
ax.plot(data['t_points'],
slopes[:, i],
c='lightgray',
zorder=0)
for t_id in t_ids_b:
plt.scatter(np.zeros((n))+data['t_points'][t_id],
slopes[t_id, :],
marker='s', c=slopes[t_id, :],
cmap=RdBu_11_r.mpl_colormap, rasterized=True,
zorder=1)
if method == 'laplacian':
plt.xscale('log')
plt.xlabel('t')
plt.ylabel("slope")
if save:
figure_name = 'slopes.png'
fig.savefig(os.path.join(save_path, figure_name))
for t_id in t_ids_b:
im = plot_fsaverage(slopes[t_id, :],
lhannot=data['lhannot'],
rhannot=data['rhannot'],
noplot=data['noplot'],
order=data['order'],
views=['lateral', 'm'],
vmin=np.amin(slopes[t_id, :]),
vmax=np.amax(slopes[t_id, :]),
colormap=RdBu_11_r.mpl_colormap)
if save:
figure_name = ('slopes_brain_surface_' +
str(int(round(data['t_points'][t_id]))) +
'.png')
im.save_image(os.path.join(save_path, figure_name),
mode='rgba')
if 'c' in panels:
required_entries = ['sc', 't_points', 'ci']
requirements = check_requirements(data, required_entries)
if requirements:
measures = []
labels = []
measures.append(np.sum(data['sc'], axis=0))
labels.append("strength")
measures.append(-bct.clustering_coef_wu(data['sc']))
labels.append("clustering(-)")
for ci in data['ci']:
measures.append(bct.participation_coef(data['sc'], ci))
labels.append(("participation (" +
str(int(round(ci.max()))) +
")"))
k = len(data['t_points'])
m = len(measures)
corrs = np.zeros((m, k))
for i in range(m):
for j in range(k):
corrs[i, j] = pearsonr(slopes[j, :], measures[i])[0]
corr_min = np.amin(corrs)
corr_max = np.amax(corrs)
for i in range(m):
plt.figure()
plt.imshow(corrs[i, :][np.newaxis, :],
cmap=Spectral_4_r.mpl_colormap,
vmin=corr_min,
vmax=corr_max,
aspect=0.1 * k)
plt.axis('off')
plt.title(labels[i])
if save is True:
figure_name = "correlations_" + labels[i] + ".png"
plt.savefig(os.path.join(save_path, figure_name))
if show is False:
plt.close('all')
plt.ion()
def cal_thalamus_and_cortical_ROIs_nodal_properties(Thalamocortical_corrmat, Cortical_adj, \
Cortical_plus_thalamus_CI, Thalamus_CIs, Cortical_CI, Cortical_ROIs_positions, Thalamus_voxel_positions, cost_thresholds):
'''Function to calculate voxel-wise nodal properties of the thalamus, and nodal properties of cortical ROIs.
Metrics to be calculated include:
Participation Coefficient (PC)
Between network connectivity weiight (BNWR)
Ratio of connection weight devoted to between network interactions
Number of network/modules/components connected (NNC)
Within module degree zscore (WMD)
For WMD, matrices will be binarzied, and normalized to corticocortical connections' mean and SD
usage: PCs, BNWRs, NNCs, WMDs, bPCs, mean_NNC, mean_BNWR, mean_PC, mean_bPC, mean_WMD = cal_thalamus_and_cortical_ROIs_nodal_properties(Thalamocor_adj,
Cortical_adj,
Cortical_plus_thalamus_CI,
Thalamus_CIs,
Cortical_CI,
Cortical_ROIs_positions,
Thalamus_voxel_positions,
cost_thresholds)
----
Parameters
----
Thalamocor_adj: Thalamocortical adj matrix
Cortical_adj: corticocortical adj matrix
Cortical_plus_thalamus_CI: A vector of community/module/network assignment of all nodes, cortical ROIs + thalamic voxels
Thalamus_CIs: A vector of network assignements for thalamic voxels
Cortical_CI: A vector of network assignments for cortical ROIs
Cortical_ROIs_positions: a position vector indicating in the thalamocortical adj matrix which rows/columns are cortical ROIs
Thalamus_voxel_posistions: a position vector indicating in the thalamocortical adj matrix which rows/columns are thalamic voxels
cost_thresholds: the thoresholds that can threshold the thalamocortical edges at density .01 to .15.
return variables are graph metrics across thresholds (with "s"), or averaged across thresholds "mean"
'''
##Thalamus nodal roles
Thalamocortical_corrmat[np.isnan(Thalamocortical_corrmat)] = 0
#PC
PCs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
bPCs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
#BNWR between network connectivity weight
BNWRs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
#get number of networks/communities connected
NNCs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
#loop through costs
for c in cost_thresholds:
#copy adj matrix and then threshold
Par_adj = Thalamocortical_corrmat.copy()
#remove weights connected to low SNR communities (CI==0, orbital frontal, inferior temporal)
Par_adj[Cortical_ROIs_positions[Cortical_CI == 0], :] = 0
Par_adj[:, Cortical_ROIs_positions[Cortical_CI == 0]] = 0
Par_adj[Par_adj < c] = 0
#binary
bPar_adj = Par_adj.copy()
bPar_adj = bPar_adj > c
#PC
PCs += [bct.participation_coef(Par_adj, Cortical_plus_thalamus_CI)]
bPCs += [bct.participation_coef(bPar_adj, Cortical_plus_thalamus_CI)]
#aPCs += [bct.participation_coef(Par_adj, Cortical_plus_thalamus_CI)]
#BNWR and NNCs
Tha_BNWR = np.zeros(Cortical_plus_thalamus_CI.size)
Tha_NNCs = np.zeros(Cortical_plus_thalamus_CI.size)
for ix, i in enumerate(Thalamus_voxel_positions):
sum_between_weight = np.nansum(
Par_adj[i, Cortical_plus_thalamus_CI != Thalamus_CIs[ix]])
sum_total = np.nansum(Par_adj[i, :])
Tha_BNWR[i] = sum_between_weight / sum_total
Tha_BNWR[i] = np.nan_to_num(Tha_BNWR[i])
Tha_NNCs[i] = len(
np.unique(Cortical_plus_thalamus_CI[Par_adj[i, ] != 0]))
BNWRs += [Tha_BNWR]
NNCs += [Tha_NNCs]
##Cortical nodal roles
Cortical_adj[np.isnan(Cortical_adj)] = 0
Cortical_PCs = [] #np.zeros(Cortical_CI.size)
Cortical_bPCs = [] #np.zeros(Cortical_CI.size)
Cortical_BNWR = [] #np.zeros(Cortical_CI.size)
Cortical_NNCs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
for ix, c in enumerate(np.arange(0.01, 0.16, 0.01)):
M = bct.threshold_proportional(Cortical_adj, c, copy=True)
bM = bct.weight_conversion(M, 'binarize', copy=True)
#PC
Cortical_PCs += [bct.participation_coef(M, Cortical_CI)]
Cortical_bPCs += [bct.participation_coef(bM, Cortical_CI)]
#BNWR and NNC
BNWR = np.zeros(Cortical_CI.size)
Cor_NNCs = np.zeros(Cortical_plus_thalamus_CI.size)
for i in range(len(Cortical_CI)):
sum_between_weight = np.nansum(M[i, Cortical_CI != Cortical_CI[i]])
sum_total = np.nansum(M[i, :])
BNWR[i] = sum_between_weight / sum_total
BNWR[i] = np.nan_to_num(BNWR[i])
Cor_NNCs[i] = len(np.unique(Cortical_CI[M[i, ] != 0]))
Cortical_BNWR += [BNWR]
Cortical_NNCs += [Cor_NNCs]
#do WMD, first convert matrices to binary, then calcuate z score using mean and std of "corticocortical degrees"
Cortical_wm_mean = {}
Cortical_wm_std = {}
Cortical_WMDs = [] #np.zeros(Cortical_CI.size)
WMDs = [] #np.zeros(Cortical_plus_thalamus_CI.size)
for ix, c in enumerate(np.arange(0.01, 0.16, 0.01)):
#threshold by density
bM = bct.weight_conversion(
bct.threshold_proportional(Cortical_adj, c, copy=True), 'binarize')
Cortical_WMDs += [bct.module_degree_zscore(bM, Cortical_CI)]
#return mean and degree
for CI in np.unique(Cortical_CI):
Cortical_wm_mean[ix + 1, CI] = np.nanmean(
np.sum(bM[Cortical_CI == CI, :][:, Cortical_CI == CI], 1))
Cortical_wm_std[ix + 1, CI] = np.nanstd(
np.sum(bM[Cortical_CI == CI, :][:, Cortical_CI == CI], 1))
#thalamic WMD, threshold by density
M = bct.weight_conversion(
bct.threshold_absolute(Thalamocortical_corrmat,
cost_thresholds[ix],
copy=True), 'binarize')
tha_wmd = np.zeros(Cortical_plus_thalamus_CI.size)
for i in np.unique(Cortical_CI):
tha_wmd[Cortical_plus_thalamus_CI==i] = (np.sum(M[Cortical_plus_thalamus_CI==i][:, Cortical_plus_thalamus_CI==i],1)\
- Cortical_wm_mean[ix+1,i])/Cortical_wm_std[ix+1,i]
tha_wmd = np.nan_to_num(tha_wmd)
WMDs += [tha_wmd]
# organize output
NNCs = np.array(NNCs)
BNWRs = np.array(BNWRs)
PCs = np.array(PCs)
bPCs = np.array(bPCs)
WMDs = np.array(WMDs)
NNCs[:, Cortical_ROIs_positions] = np.array(
Cortical_NNCs)[:, Cortical_ROIs_positions]
BNWRs[:, Cortical_ROIs_positions] = np.array(
Cortical_BNWR)[:, Cortical_ROIs_positions]
PCs[:, Cortical_ROIs_positions] = np.array(
Cortical_PCs)[:, Cortical_ROIs_positions]
bPCs[:, Cortical_ROIs_positions] = np.array(
Cortical_bPCs)[:, Cortical_ROIs_positions]
WMDs[:, Cortical_ROIs_positions] = np.array(
Cortical_WMDs)[:, Cortical_ROIs_positions]
# average across thresholds, convert into percentage
mean_NNC = (np.sum(NNCs, axis=0) / 15.0) * 100
mean_BNWR = (np.sum(BNWRs, axis=0) / 15.0) * 100
mean_PC = (np.sum(PCs, axis=0) /
13.5) * 100 #this is the thoretical upperbound
mean_bPC = (np.sum(bPCs, axis=0) /
13.5) * 100 #this is the thoretical upperbound
mean_WMD = (np.sum(WMDs, axis=0) / 15.0) * 100
return PCs, BNWRs, NNCs, WMDs, bPCs, mean_NNC, mean_BNWR, mean_PC, mean_bPC, mean_WMD
def __init__(self,
kind,
parcel,
data='lau',
hemi='both',
binary=False,
version=1,
subset='all',
path=None):
mainPath = path + "/brainNetworks/" + data + "/"
home = os.path.expanduser("~")
self.info = {}
self.info["kind"] = kind
self.info["parcel"] = parcel
self.info["data"] = data
self.info["hemi"] = hemi
self.info["binary"] = binary
self.info["version"] = version
self.info["subset"] = subset
if version == 1:
version = ''
else:
version = "_v2"
if binary is True:
binary = "b"
else:
binary = ''
if subset == "all":
subset = ''
if hemi == "both":
hemi = ''
matrxPath = mainPath + "matrices/" + subset + kind + parcel + hemi + binary + version
# hemisphere
self.hemi = np.load(matrxPath + "/hemi.npy")
# Adjacency matrix
path = matrxPath + ".npy"
A = np.load(path)
# Look at time when file was last modified
last_modified = os.path.getmtime(path)
# set negative values to 0, fill diagonal, make symmetric
A[A < 0] = 0
np.fill_diagonal(A, 0)
A = (A + A.T) / 2
self.adj = A
# Number of nodes in the network
self.n = len(self.adj)
# coordinates
path = mainPath + "coords/coords" + parcel + hemi + ".npy"
self.coords = np.load(path)
# Inverse of adjacency matrix
inv = A.copy()
inv[A > 0] = 1 / inv[A > 0]
self.inv_adj = inv
# distance
self.dist = cdist(self.coords, self.coords)
# shortest path
#
# Loaded from saved file...
# IF file not found OR Adjacency was modified after creation,
# then recompute measure
path = matrxPath + "/sp.npy"
if os.path.exists(path) is False:
print("shortest path not found")
print("computing shortest path...")
self.sp = bct.distance_wei(self.inv_adj)[0]
np.save(matrxPath + "/sp.npy", self.sp)
elif os.path.getmtime(path) < last_modified:
print("new adjacency matrix was found")
print("computing shortest paths...")
self.sp = bct.distance_wei(self.inv_adj)[0]
np.save(matrxPath + "/sp.npy", self.sp)
else:
self.sp = np.load(path)
# diffusion embedding
de = compute_diffusion_map(A, n_components=10, return_result=True)
self.de = de[0]
self.de_extra = de[1]
# Principal components
self.PCs, self.PCs_ev = load_data.getPCs(self.adj)
# betweenness centrality
#
# Loaded from saved file...
# IF file not found OR Adjacency was modified after creation,
# then recompute measure
path = matrxPath + "/bc.npy"
if os.path.exists(path) is False:
print("betweenness centrality not found")
print("computing betweenness centrality...")
self.bc = bct.betweenness_wei(self.inv_adj)
np.save(matrxPath + "/bc.npy", self.bc)
elif os.path.getmtime(path) < last_modified:
print("new adjacency matrix was found")
print("recomputing betweeness centrality...")
self.bc = bct.betweenness_wei(self.inv_adj)
np.save(matrxPath + "/bc.npy", self.bc)
else:
self.bc = np.load(path)
# communities + participation coefficient
path = matrxPath + "/communities/"
if os.path.exists(path):
files = []
for i in os.listdir(path):
if os.path.isfile(os.path.join(path, i)) and 'ci_' in i:
files.append(i)
if len(files) > 0:
self.ci = []
for file in files:
self.ci.append(np.load(os.path.join(path, file)))
self.ppc = []
for i in range(len(files)):
ppc = bct.participation_coef(A, self.ci[i])
self.ppc.append(ppc)
if (data == "HCP") and (kind == "SC"):
path = mainPath + "matrices/" + subset + kind + parcel + hemi + "_lengths.npy"
self.lengths = np.load(path)
# streamline connection lengths
path = matrxPath + "/len.npy"
if os.path.exists(path) is True:
self.len = np.load(path)
# network information
if parcel[0] == "s":
nb = parcel[1:]
self.order = "LR"
self.noplot = [b'Background+FreeSurfer_Defined_Medial_Wall', b'']
self.lhannot = (home + "/"
"nnt-data/"
"atl-schaefer2018/"
"fsaverage/"
"atl-Schaefer2018_space-fsaverage_"
"hemi-L_desc-" + nb + "Parcels7Networks_"
"deterministic.annot")
self.rhannot = (home + "/"
"nnt-data/"
"atl-schaefer2018/"
"fsaverage/"
"atl-Schaefer2018_space-fsaverage_"
"hemi-R_desc-" + nb + "Parcels7Networks_"
"deterministic.annot")
else:
nb = _parcel_to_n(parcel)
self.order = "RL"
self.noplot = None
self.lhannot = (home + "/"
"nnt-data/"
"atl-cammoun2012/"
"fsaverage/"
"atl-Cammoun2012_space-fsaverage_"
"res-" + nb + "_hemi-L_deterministic.annot")
self.rhannot = (home + "/"
"nnt-data/"
"atl-cammoun2012/"
"fsaverage/"
"atl-Cammoun2012_space-fsaverage_"
"res-" + nb + "_hemi-R_deterministic.annot")
self.cammoun_id = nb
dsets = ['MGH']
# import thresholded matrix to BCT, import partition, run WMD/PC
PC = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
WMD = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
EC = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
GC = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
SC = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
ST = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 18166))
for ix, matrix in enumerate(MATS):
for i, cost in enumerate(np.arange(min_cost, max_cost, 0.01)):
tmp_matrix = threshold(matrix.copy(), cost)
PC[i, :] = bct.participation_coef(tmp_matrix, CI)
#WMD[i,:] = bct.module_degree_zscore(tmp_matrix,CI)
#EC[i,:] = bct.eigenvector_centrality_und(tmp_matrix)
#GC[i,:], _ = bct.gateway_coef_sign(tmp_matrix, CI)
#SC[i,:] = bct.subgraph_centrality(tmp_matrix)
#ST[i,:] = bct.strengths_und(tmp_matrix)
mes = 'finished running cost:%s' % cost
print(mes)
# fn = 'images/Voxelwise_4mm_%s_WMD.nii' %dsets[ix]
# write_graph_to_vol_yeo_template_nifti(np.nanmean(WMD,axis=0), fn, 'voxelwise')
#
# fn = 'images/Voxelwise_4mm_%s_WeightedDegree.nii' %dsets[ix]
# write_graph_to_vol_yeo_template_nifti(np.nanmean(ST,axis=0), fn, 'voxelwise')
#
def cal_indiv_graph():
'''loop through subjects and get PC/WMD/Q/eG/CI'''
### loop through subjects, 1 to 156
gordon_files = glob.glob("Data/*Gordon*.netcc")
yeo_files = glob.glob("Data/*Yeo*.netcc")
files = gordon_files + yeo_files
for f in files:
if f in gordon_files:
cmd = "cat %s | tail -n 352 > Data/test" %f
roi='gordon'
if f in yeo_files:
cmd = "cat %s | tail -n 422 > Data/test" %f #422 for Yeo
roi='yeo'
sub = f[5:8]
os.system(cmd)
# load matrix
matrix = np.genfromtxt('Data/test',delimiter='\t',dtype=None)
matrix[np.isnan(matrix)] = 0.0
matrix[matrix<0]=0.0
# step through costs, do infomap, return final infomap across cost
max_cost = .15
min_cost = .01
partition = ave_consensus_costs_parition(matrix, min_cost, max_cost)
partition = np.array(partition) + 1
# calculate modularity, efficiency?
Q = cal_modularity_w_imposed_community(matrix,partition)
Eg = bct.efficiency_wei(matrix)
# import thresholded matrix to BCT, import partition, run WMD/PC
PCs = np.zeros((len(np.arange(min_cost, max_cost+0.01, 0.01)), matrix.shape[0]))
WMDs = np.zeros((len(np.arange(min_cost, max_cost+0.01, 0.01)), matrix.shape[0]))
for i, cost in enumerate(np.arange(min_cost, max_cost, 0.01)):
tmp_matrix = threshold(matrix.copy(), cost)
#PC
PCs[i,:] = bct.participation_coef(tmp_matrix, partition)
#WMD
WMDs[i,:] = bct.module_degree_zscore(matrix, partition)
PC = np.mean(PCs, axis=0) # ave across thresholds
WMD = np.mean(WMDs, axis=0)
fn = "Graph_output/%s_%s_PC" %(sub, roi)
np.savetxt(fn, PC)
fn = "Graph_output/%s_%s_WMD" %(sub, roi)
np.savetxt(fn, WMD)
fn = "Graph_output/%s_%s_Q" %(sub, roi)
np.savetxt(fn, np.array(Q, ndmin=1))
fn = "Graph_output/%s_%s_Eg" %(sub, roi)
np.savetxt(fn, np.array(Eg, ndmin=1))
fn = "Graph_output/%s_%s_Partition" %(sub, roi)
np.savetxt(fn, partition)
s, s)
Yeo17ci = nib.load(fn)
fn = '/data/backed_up/kahwang/ECoG_fMRI/%s/infomap/%s_Infomap_to_7Network_2mm.nii' % (
s, s)
Yeo7ci = nib.load(fn)
Yeo7ci = np.round(masker.fit_transform(Yeo7ci))
Yeo17ci = np.round(masker.fit_transform(Yeo17ci))
ts = masker.fit_transform(ffiles)
mat = np.nan_to_num(np.corrcoef(ts.T))
min_cost = .02
max_cost = .10
PC_7 = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 400))
PC_17 = np.zeros((len(np.arange(min_cost, max_cost + 0.01, 0.01)), 400))
for i, cost in enumerate(np.arange(min_cost, max_cost, 0.01)):
tmp_matrix = threshold(mat.copy(), cost)
PC_7[i, :] = bct.participation_coef(tmp_matrix, Yeo7ci)
PC_17[i, :] = bct.participation_coef(tmp_matrix, Yeo17ci)
fn = '/home/kahwang/bin/example_graph_pipeline/phub_images/%s_PC_7network.nii.gz' % s
write_graph_to_vol_sch400_template_nifti(np.nanmean(PC_7, axis=0),
fn,
resolution=400)
fn = '/home/kahwang/bin/example_graph_pipeline/phub_images/%s_PC_17network.nii.gz' % s
write_graph_to_vol_sch400_template_nifti(np.nanmean(PC_17, axis=0),
fn,
resolution=400)
#end of line
def get_true_network_metrics(A):
#control centrality
c_c = control_centrality(A)
cc_fake = np.zeros((100, 1))
for i in range(0, 100):
cc_fake[i] = np.mean(control_centrality(generate_fake_graph(A)))
m_cc_fake = np.mean(cc_fake)
cc_norm = c_c / m_cc_fake
# Get identity of node with lowest control centrality
min_cc_true = np.where(c_c == np.amin(c_c))[0]
# get synchronizability
sync = synchronizability(A)
# normalized sync
sync_fake = np.zeros((100, 1))
for i in range(0, 100):
sync_fake[i] = synchronizability(generate_fake_graph(A))
m_sync_fake = np.mean(sync_fake)
sync_norm = sync / m_sync_fake
# get betweeness centrality
bc = betweenness_centrality(A)
bc_fake = np.zeros((100, 1))
for i in range(0, 100):
bc_fake[i] = np.mean(betweenness_centrality(generate_fake_graph(A)))
m_bc_fake = np.mean(bc_fake)
bc_norm = bc / m_bc_fake
# Get identity of node with max bc
max_bc_true = np.where(bc == np.amax(bc))[0]
# get eigenvector centrality
ec = bct.eigenvector_centrality_und(A)
ec_fake = np.zeros((100, 1))
for i in range(0, 100):
ec_fake[i] = np.mean(
bct.eigenvector_centrality_und(generate_fake_graph(A)))
m_ec_fake = np.mean(ec_fake)
ec_norm = ec / m_ec_fake
# Get identity of node with max ec
max_ec_true = np.where(ec == np.amax(ec))[0]
# get edge betweeness centrality
edge_bc, ignore = bct.edge_betweenness_wei(A)
edge_bc_fake = np.zeros((100, 1))
for i in range(0, 100):
edge_bc_fake[i] = np.mean(
bct.edge_betweenness_wei(generate_fake_graph(A))[0])
m_edge_bc_fake = np.mean(edge_bc_fake)
edge_bc_norm = edge_bc / m_edge_bc_fake
# get clustering coeff
clust = bct.clustering_coef_wu(A)
clust_fake = np.zeros((100, 1))
for i in range(0, 100):
clust_fake[i] = np.mean(bct.clustering_coef_wu(generate_fake_graph(A)))
m_clust_fake = np.mean(clust_fake)
clust_norm = clust / m_clust_fake
# Get identity of node with max clust
max_clust_true = np.where(clust == np.amax(clust))[0]
# get node strength
ns = node_strength(A)
ns_fake = np.zeros((100, 1))
for i in range(0, 100):
ns_fake[i] = np.mean(node_strength(generate_fake_graph(A)))
m_ns_fake = np.mean(ns_fake)
ns_norm = ns / m_ns_fake
# Get identity of node with max clust
max_ns_true = np.where(ns == np.amax(ns))[0]
#Get true efficiency
Ci, ignore = bct.modularity_und(A)
par = bct.participation_coef(A, Ci)
eff = bct.efficiency_wei(A, 0)
eff_fake = np.zeros((100, 1))
for i in range(0, 100):
eff_fake[i] = (bct.efficiency_wei(generate_fake_graph(A)))
m_eff_fake = np.mean(eff_fake)
eff_norm = eff / m_eff_fake
# Get true transistivity
trans = bct.transitivity_wu(A)
trans_fake = np.zeros((100, 1))
for i in range(0, 100):
trans_fake[i] = (bct.transitivity_wu(generate_fake_graph(A)))
m_trans_fake = np.mean(trans_fake)
trans_norm = trans / m_trans_fake
# store output results in a dictionary
#nodal
results = {}
results['control_centrality'] = c_c
results['control_centrality_norm'] = cc_norm
results['min_cc_node'] = min_cc_true
# global measure
results['sync'] = sync
results['sync_norm'] = sync_norm
# nodal
results['bc'] = bc
results['bc_norm'] = bc_norm
results['max_bc_node'] = max_bc_true
# nodal
results['ec'] = ec
results['ec_norm'] = ec_norm
results['max_ec_node'] = max_ec_true
# nodal
results['clust'] = clust
results['clust_norm'] = clust_norm
results['max_clust_node'] = max_clust_true
# nodal
results['ns'] = ns
results['ns_norm'] = ns_norm
results['max_ns_node'] = max_ns_true
# global
results['eff'] = eff
results['eff_norm'] = eff_norm
# global
results['trans'] = trans
results['trans_norm'] = trans_norm
# nodal
results['par'] = par
# edge
results['edge_bc'] = edge_bc
results['edge_bc_norm'] = edge_bc_norm
return (results)
def resample_network(A, n_perm, e_f, type_to_remove, final_electrodes):
# type to remove : 1 for white matter, 0 for grey matter
# e_f : Following Erin + John convention. This is the fraction of nodes to
# keep in the network (ex.. ef=.2 means we remove 80% of the nodes)
e_f = np.array(e_f)
nch = A.shape[0]
n_f = e_f.shape[0]
# create sub dataframes for only the grey and white matter elec
wm = final_electrodes[final_electrodes.iloc[:, 2] > 0]
gm = final_electrodes[final_electrodes.iloc[:, 2] == 0]
# numbers of each electrode type
numWhite = wm.shape[0]
numGrey = gm.shape[0]
# fraction to remove
if (type_to_remove == 1):
e_n = numWhite - np.ceil(e_f * numWhite)
else:
e_n = numGrey - np.ceil(e_f * numGrey)
# control centrality
all_c_c = np.zeros((nch, n_f, n_perm))
all_c_c[:] = np.nan
cc_reg = np.zeros((nch, n_f, n_perm))
cc_reg[:] = np.nan
all_cc_norm = np.zeros((nch, n_f, n_perm))
all_cc_norm[:] = np.nan
#init node strengths
all_ns = np.zeros((nch, n_f, n_perm))
all_ns[:] = np.nan
all_ns_norm = np.zeros((nch, n_f, n_perm))
all_ns_norm[:] = np.nan
# init betweenness centrality
all_bc = np.zeros((nch, n_f, n_perm))
all_bc[:] = np.nan
all_bc_norm = np.zeros((nch, n_f, n_perm))
all_bc_norm[:] = np.nan
# synch
all_sync = np.zeros((n_f, n_perm))
all_sync[:] = np.nan
all_sync_norm = np.zeros((n_f, n_perm))
all_sync_norm[:] = np.nan
# efficiency
all_eff = np.zeros((n_f, n_perm))
all_eff[:] = np.nan
all_eff_norm = np.zeros((n_f, n_perm))
all_eff_norm[:] = np.nan
# eigenvector centrality
all_ec = np.zeros((nch, n_f, n_perm))
all_ec[:] = np.nan
all_ec_norm = np.zeros((nch, n_f, n_perm))
all_ec_norm[:] = np.nan
# clustering coeff
all_clust = np.zeros((nch, n_f, n_perm))
all_clust[:] = np.nan
all_clust_norm = np.zeros((nch, n_f, n_perm))
all_clust_norm[:] = np.nan
# participation coeff
all_par = np.zeros((nch, n_f, n_perm))
all_par[:] = np.nan
# transistivity
all_trans = np.zeros((n_f, n_perm))
all_trans[:] = np.nan
all_trans_norm = np.zeros((n_f, n_perm))
all_trans_norm[:] = np.nan
# edge bc
all_edge_bc = []
all_edge_bc_norm = []
# get true particpation
Ci, ignore = bct.modularity_und(A)
true_par = bct.participation_coef(A, Ci)
avg_par_removed = np.zeros((n_f, n_perm))
avg_par_removed[:] = np.nan
# get the true bc
true_bc = betweenness_centrality(A)
avg_bc_removed = np.zeros((n_f, n_perm))
avg_bc_removed[:] = np.nan
# loop over all removal fractions and permutations
for f in range(0, n_f):
all_edge_bc_cur_fraction = []
all_edge_bc_norm_cur_fraction = []
for i_p in range(0, n_perm):
if (i_p % 100 == 0):
print(
"Doing permutation {0} for removal of fraction {1}".format(
i_p, f))
# make a copy of the adjacency matrix (we will edit this each time)
A_tmp = A.copy()
# picking the nodes to remove
if (type_to_remove == 1):
to_remove = wm.sample(int(e_n[f])).iloc[:, 0]
else:
to_remove = gm.sample(int(e_n[f])).iloc[:, 0]
# take these electrodes out of the adjacency matrix
A_tmp = np.delete(A_tmp, to_remove, axis=0)
A_tmp = np.delete(A_tmp, to_remove, axis=1)
# create a new array to hold the identity of the channels
ch_ids = np.arange(0, nch)
ch_ids = np.delete(ch_ids, to_remove)
# get the new metrics from A_tmp
r = get_true_network_metrics(A_tmp)
# edge metric
all_edge_bc_cur_fraction.append(r['edge_bc'])
all_edge_bc_norm_cur_fraction.append(r['edge_bc_norm'])
# populate the nodal measures
for i in range(0, ch_ids.shape[0]):
all_c_c[ch_ids[i], f, i_p] = r['control_centrality'][i]
all_ns[ch_ids[i], f, i_p] = r['ns'][i]
all_bc[ch_ids[i], f, i_p] = r['bc'][i]
all_par[ch_ids[i], f, i_p] = r['par'][i]
all_ec[ch_ids[i], f, i_p] = r['ec'][i]
all_clust[ch_ids[i], f, i_p] = r['clust'][i]
all_cc_norm[ch_ids[i], f,
i_p] = r['control_centrality_norm'][i]
all_ns_norm[ch_ids[i], f, i_p] = r['ns_norm'][i]
all_bc_norm[ch_ids[i], f, i_p] = r['bc_norm'][i]
all_ec_norm[ch_ids[i], f, i_p] = r['ec_norm'][i]
all_clust_norm[ch_ids[i], f, i_p] = r['clust_norm'][i]
# populate the global measures
all_sync[f, i_p] = r['sync']
all_sync_norm[f, i_p] = r['sync_norm']
all_eff[f, i_p] = r['eff']
all_eff_norm[f, i_p] = r['eff_norm']
all_trans[f, i_p] = r['trans']
all_trans_norm[f, i_p] = r['trans_norm']
all_edge_bc.append(all_edge_bc_cur_fraction)
all_edge_bc_norm.append(all_edge_bc_norm_cur_fraction)
# construct the output dictionary from a resampling
#nodal
results = {}
results['control_centrality'] = all_c_c
results['control_centrality_norm'] = all_cc_norm
# global measure
results['sync'] = all_sync
results['sync_norm'] = all_sync_norm
# nodal
results['bc'] = all_bc
results['bc_norm'] = all_bc_norm
# nodal
results['ec'] = all_ec
results['ec_norm'] = all_ec_norm
# nodal
results['clust'] = all_clust
results['clust_norm'] = all_clust_norm
# nodal
results['ns'] = all_ns
results['ns_norm'] = all_ns_norm
# global
results['eff'] = all_eff
results['eff_norm'] = all_eff_norm
# global
results['trans'] = all_trans
results['trans_norm'] = all_trans_norm
# nodal
results['par'] = all_par
#edge
results['edge_bc'] = all_edge_bc
results['edge_bc_norm'] = all_edge_bc_norm
return (results)
ylab = 'node score PC%s' % (ncomp+1)
xlab = 'evolutionary expansion'
hctsa_utils.scatterregplot(y, x, title, xlab, ylab, pointsize=50)
####################################
# Participation coefficient
####################################
# tsn and participation coefficient
uniqlabels, uniqidx = np.unique(rsnlabels, return_index=True)
uniqlabels = uniqlabels[np.argsort(uniqidx)]
rsnidx = np.zeros((400, 1))
for n, rsn in enumerate(uniqlabels):
idx = np.where(np.array(rsnlabels) == rsn)[0]
rsnidx[idx] = n
participCoef = bct.participation_coef(fc_average_discov, rsnidx)
toplot = participCoef
brains = plotting.plot_conte69(toplot, lhlabels, rhlabels,
vmin=np.percentile(toplot, 2.5),
vmax=np.percentile(toplot, 97.5),
colormap='viridis',
colorbartitle=('fc participation coefficient'),
surf='inflated')
# plot and correlate
ncomp = 0
x = participCoef
y = node_score[:, ncomp]
corr = scipy.stats.spearmanr(x, y)
pvalspin = hctsa_utils.get_spinp(x, y, corrval=corr[0], nspin=10000,
if __name__ == '__main__':
dat_dir = os.environ['pnd']
graph_dir = dat_dir+'/graphs/'
modularity_dir = dat_dir+'/modularity/'
role_dir = dat_dir+'/node_roles'
if not os.path.exists(role_dir):
os.makedirs(role_dir)
nnodes = 148
for subjid in ['pandit', 'ctrl']:
thresh_dens = '0.1'
qscores = '%s.dens_%s.Qval' % (subjid, thresh_dens)
df = np.loadtxt(os.path.join(modularity_dir, qscores))
maxiter = df.argmax()
trees_name = '%s.dens_%s.trees' % (subjid, thresh_dens)
trees_in = os.path.join(modularity_dir, trees_name)
coms = np.loadtxt(trees_in)[:, maxiter]
graph_name = '%s.dens_%s.edgelist.gz' % (subjid, thresh_dens)
g = make_networkx_graph(nnodes, os.path.join(graph_dir, graph_name))
ga = nx.adjacency_matrix(g).toarray()
pc = bct.participation_coef(ga, coms)
wz = bct.module_degree_zscore(ga, coms)
pc_out_name = '%s.dens_%s_part_coef.txt' % (subjid, thresh_dens)
np.savetxt(os.path.join(role_dir, pc_out_name), pc, fmt='%.4f')
wz_out_name = '%s.dens_%s_within_mod_Z.txt' % (subjid, thresh_dens)
np.savetxt(os.path.join(role_dir, wz_out_name), wz, fmt='%.4f')
def Graph_Analysis(data,
weight=True,
thresh_func=bct.threshold_proportional,
threshold=.15,
plot_threshold=None,
community_alg=bct.community_louvain,
ref_community=None,
reorder=False,
display=True,
layout='kk',
print_options={},
plot_options={}):
"""
Creates and displays graphs of a data matrix.
Parameters
----------
data: pandas DataFrame
data to use to create the graph
thresh_func: function that takes in a connectivity matrix and thresholds
any algorithm that returns a connectivity matrix of the same size as the original may be used.
intended to be used with bct.threshold_proportional or bct.threshold_absolute
community_alg: function that takes in a connectivity matrix and returns community assignment
intended to use algorithms from brain connectivity toolbox like commnity_louvain or
modularity_und. Must return a list of community assignments followed by Q, the modularity
index
edge_metric: str: 'pearson', 'separman' or 'MI'
relationship metric between nodes. MI stands for mutual information. "abs_"
may be used in front of "pearson" or "spearman" to get the absolute value
of the correlations, e.g. abs_pearson
threshold: float 0 <= x <= 1, optional
the proportion of weights to keep (to be passed to bct.threshold_proportion)
weight: bool, optional
if True, creates a weighted graph (vs. a binary)
reorder: bool, optional
if True, reorder vertices based on community assignment
display: bool, optinal
if True, display the graph and print node membership
layout: str: 'kk', 'circle', 'grid' or other igraph layouts, optional
Determines how the graph is displayed
avg_num_edges: int > 1
thresholds the edges on the graph so each node has, on average, avg_num_edges
print_options: dict, optional
dictionary of arguments to be passed to print_community_members
plot_options: dict, optional
dictionary of arguments to be passed to plot_graph
Returns
----------
G: igraph Graph
the graph object created by the function
graph_mat: numpy matrix
the matrix used to create the graph
"""
#threshold and remove diagonal
graph_mat = thresh_func(data.as_matrix(), threshold)
# make a binary version if not weighted
if not weight:
graph_mat = np.ceil(graph_mat)
G = igraph.Graph.Adjacency(graph_mat.tolist(), mode='undirected')
else:
G = igraph.Graph.Weighted_Adjacency(graph_mat.tolist(),
mode='undirected')
column_names = data.columns
# community detection
# using louvain but also bct.modularity_und which is "Newman's spectral community detection"
# bct.modularity_louvain_und_sign
comm, mod = community_alg(graph_mat)
# if there is a reference, relbale communities based on their closest association
if ref_community:
comm = relabel_community(comm, ref_community)
G.vs['community'] = comm
G.vs['id'] = range(len(G.vs))
G.vs['name'] = column_names
G.vs['within_module_degree'] = bct.module_degree_zscore(graph_mat, comm)
G.vs['part_coef'] = bct.participation_coef(graph_mat, comm)
if weight:
G.vs['eigen_centrality'] = G.eigenvector_centrality(
directed=False, weights=G.es['weight'])
else:
G.vs['eigen_centrality'] = G.eigenvector_centrality(directed=False)
#if reorder, reorder vertices by community membership
if reorder:
G = community_reorder(G)
# get connectivity matrix used to make the graph
connectivity_matrix = graph_to_dataframe(G)
# calculate subgraph (within-community) characteristics
subgraph_analysis(G, community_alg=community_alg)
# visualize
layout_graph = None
if plot_threshold:
layout_mat = thresh_func(data.as_matrix(), plot_threshold)
layout_graph = igraph.Graph.Weighted_Adjacency(layout_mat.tolist(),
mode='undirected')
visual_style = {}
visual_style = get_visual_style(G,
layout_graph,
layout=layout,
vertex_size='eigen_centrality',
labels=G.vs['id'],
size=1000)
if display:
# plot community structure
print_community_members(G, **print_options)
plot_graph(G, visual_style=visual_style, **plot_options)
return (G, connectivity_matrix, visual_style)