def intra_calc_dynamic():
# print(os.getcwd())
atlasobj = path.curatlas()
volumename = '3mm'
nii_path = os.path.join(path.curparent(), 'pBOLD.nii')
outfolder = os.path.join(os.getcwd(), OUTFOLDER_INTRA)
json_path = path.fullfile("intra_attr_dynamic.json")
# print(nii_path)
# print(outfolder)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
intra_ac = IntraAttrCalcDynamic(nii_path,atlasobj,outfolder,json_path)
intra_ac.calc()
def intra_calc():
print(os.getcwd())
atlasobj = path.curatlas()
volumename = '3mm'
nii_path = os.path.join(path.curparent(), 'pBOLD.nii')
outfolder = os.path.join(os.getcwd(), 'bold_net_attr_zzl')
json_path = path.fullfile("intra_attr.json")
print(nii_path)
print(outfolder)
if not os.path.isdir(outfolder):
os.mkdir(outfolder)
intra_ac = IntraAttrCalc(nii_path, atlasobj, outfolder, json_path)
intra_ac.calc()
import os import numpy as np import nibabel as nib from mmdps.proc import atlas # from mmdps.util.loadsave import load_nii, save_csvmat from mmdps.util import path from mmdps.proc import job if __name__ == '__main__': atlasobj = path.curatlas() volumename = '3mm' print(os.path.join(path.curparent(), 'pBOLD.nii')) print(os.getcwd()) outfolder = os.path.join(os.getcwd(), 'bold_net_attr_zzl') print(outfolder)
def function_bnv_nii(net_path, outPath):
edges, vertex = [], []
i = 0
size = 0
netthreshold = 0.4
with open(net_path, 'r') as f:
for row in csv.reader(f.read().splitlines()):
size = len(row)
ifHasEdge = False
for j in range(0, len(row)):
if abs(float(row[j])) > netthreshold and j != i:
if j > i:
edges.append((i, j, 1 / abs(float(row[j]))))
ifHasEdge = True
if not ifHasEdge:
print(i)
vertex.append(i)
i = i + 1
g = igraph.Graph.TupleList(edges,
directed=False,
vertex_name_attr='name',
weights=True)
g.add_vertices(vertex)
# print(vertex)
size = len(g.vs)
# print(size)
louvain_community = g.community_multilevel(weights=g.es['weight'])
member = louvain_community.membership
print(member, louvain_community.modularity)
atl = path.curatlas()
re = [atl.ticks[i] for i in g.vs['name']]
names = g.vs['name']
color_atlas_region(atlasobj=atl,
regions=re,
colors=[member[i] + 1 for i in range(len(member))],
outfilepath=os.path.join(
outPath,
'community_hub_{}.nii'.format(netthreshold)),
resolution="3mm")
curNodeData = atl.bnvnode.nodedata
color = ncolors(louvain_community._len)
visual_style = {}
visual_style["vertex_color"] = [color[member[i]] for i in range(size)]
visual_style["vertex_label"] = g.vs["name"]
# bc_path = os.path.join(outPath,"bold_net_attr","inter-region_bc_hub.csv")
# bc_temp = []
# with open(bc_path,'r') as f:
# for row in csv.reader(f.read().splitlines()):
# for i in row:
# bc_temp.append(int(i))
bc_temp = g.betweenness(weights=g.es['weight'])
temp_np = np.array(bc_temp)
temp_np = (temp_np - temp_np.min()) / (temp_np.max() -
temp_np.min()) * 20 + 15
max_size = temp_np.max()
for i in range(size):
# curNodeData[names[i]][4],curNodeData[names[i]][3] = str(bc_temp[names[i]]),str(member[i]+1)
curNodeData[names[i]][4], curNodeData[names[i]][3] = str(
temp_np[i]), str(member[i] + 1) #bc和curnodedata同顺序
# curNodeData[names[i]][4],curNodeData[names[i]][3] = str(temp_np[names[i]]),str(member[i]+1) #bc和curnodedata同顺序
bc = {}
for i in range(size):
if member[i] not in bc.keys():
bc[member[i]] = {}
bc[member[i]][i] = bc_temp[names[i]]
# print(visual_style['vertex_color'])
for v in bc.values():
visual_style['vertex_color'][max(v, key=lambda s: v[s])] = 'white'
for v in bc.values():
curNodeData[names[max(v, key=lambda s: v[s])]][4] = str(max_size + 5)
with open(
os.path.join(outPath,
'community_hub_{}vis.node'.format(netthreshold)),
'w') as f:
for i in range(size):
content = "\t".join(curNodeData[i]) + "\n"
f.write(content)