def metrics(a,
appVal,
degenName="NoModel",
pcLoss="0",
edgePCCons = [v for v in range(1,11)],
dVal = "2",
thresholdtype = "local"
):
appValW = appVal
appValT = appVal
# # prepare matrices for weighted measures
# pcCent = mbt.np.zeros((len(a.G.nodes()), 10))
# betCentT = mbt.np.zeros((len(a.G.nodes()), 10))
# nM = mbt.np.zeros((10))
# wmd = mbt.np.zeros((len(a.G.nodes()), 10))
# pcCentNm = mbt.np.zeros((len(a.G.nodes()), 10))
# nMNm = mbt.np.zeros((10))
# wmdNm = mbt.np.zeros((len(a.G.nodes()), 10))
# QNm = mbt.np.zeros((10))
# unweighted measures
for n,e in enumerate(edgePCCons):
ofb = '_'.join(["brain", degenName, thresholdtype, str(e), "d"+dVal+"_"])
a.localThresholding(edgePC=e)
a.makebctmat()
a.weightToDistance()
propDict = {"edgePC":str(a.edgePC),
"pcLoss":pcLoss}
degs = a.G.degree(weight='weight')
extras.writeResults(degs, "degreeWt", ofb, propDict=propDict,
append=appVal)
# weighted betweenness centrality
# bcT = mbt.centrality.betweenness_centrality(a.G, weight='distance')
# betCentT[:,n] = [bcT[v] for v in a.G.nodes()]
# # weighted modularity metrics
# ci = bct.modularity_louvain_und_sign(a.bctmat)
# Q = ci[1]
# ciN = a.assignbctResult(ci[0])
# extras.writeResults(Q, "QWt", ofb, propDict=propDict, append=appValT)
# extras.writeResults(ciN, "ciWt", ofb, propDict=propDict, append=appValT)
#
# nMWt = len(mbt.np.unique(ci[0]))
# nM[n] = nMWt
# extras.writeResults(nMWt, "nMWt", ofb, propDict=propDict, append=appValT)
# del(nMWt)
#
# wmdWt = extras.withinModuleDegree(a.G, ciN, weight='weight')
# wmd[:,n] = [wmdWt[v] for v in a.G.nodes()]
# extras.writeResults(wmdWt, "wmdWt", ofb, propDict=propDict, append=appValT)
# del wmdWt
#
# pcCentWt = bct.participation_coef_sign(a.bctmat,ci[0])
# pcCent[:,n] = pcCentWt
# pcCentWt = a.assignbctResult(pcCentWt)
# extras.writeResults(pcCentWt, "pcCentWt", ofb, propDict=propDict, append=appValT)
#
# # infomap partitioning
# bIM = infomap.nx2infomap(a.G)
# del(bIM)
# try:
# f = open("nxdigraph.clu", "r") # recapture results from output file
# modules = mbt.np.array([int(v.strip('\n')) for v in f.readlines()[1:]])
# f.close()
# remove("nxdigraph.clu")
#
# ciNIM = a.assignbctResult(modules)
# QIM = community.modularity(ciNIM, a.G)
#
# pcCentIM = bct.participation_coef_sign(a.bctmat, modules)
# pcCentIM = a.assignbctResult(pcCentIM)
# wmdIM = extras.withinModuleDegree(a.G, ciNIM, weight='weight')
# nMIM = len(np.unique(ciNIM[0]))
#
# except:
# modules = np.array((np.repeat(np.nan, len(a.G.nodes()))))
# QIM = "NA"
# pcCentIM = {v:"NA" for v in a.G.nodes()}
# wmdIM = {v:"NA" for v in a.G.nodes()}
# ciNIM = {v:"NA" for v in a.G.nodes()}
# nMIM = 0
#
# extras.writeResults(QIM, "QIM", ofbT, propDict=propDict, append=appValT)
# extras.writeResults(ciNIM, "ciIM", ofbT, propDict=propDict, append=appValT)
# del QIM
#
# extras.writeResults(nMIM, "nMIM", ofbT, propDict=propDict, append=appValT)
# del nMIM
#
# extras.writeResults(pcCentIM, "pcCentIM", ofbT, propDict=propDict, append=appValT)
# del pcCentIM
#
# extras.writeResults(wmdIM, "wmdIM", ofbT, propDict=propDict, append=appValT)
# del(wmdIM, ciNIM)
#
#
# # infomap partitioning
# bIM = infomap.nx2infomap(a.G)
# del(bIM)
# f = open("nxdigraph.clu", "r") # recapture results from output file
# modules = mbt.np.array([int(v.strip('\n')) for v in f.readlines()[1:]])
# f.close()
# remove("nxdigraph.clu")
#
# ciNIM = a.assignbctResult(modules)
# QIMWt = community.modularity(ciNIM, a.G)
# QIM[n] = QIMWt
# extras.writeResults(QIMWt, "QIMWt", ofbT, propDict=propDict,append=appValT)
# extras.writeResults(ciNIM, "ciIMWt", ofbT, propDict=propDict, append=appValT)
# del(QIMWt)
#
# nMIMWt = len(np.unique(modules))
# nMIM[n] = nMIMWt
# extras.writeResults(nMIMWt, "nMIMWt", ofbT, propDict=propDict, append=appValT)
# del(nMIMWt)
#
# pcCentIMWt = bct.participation_coef_sign(a.bctmat, modules)
# pcCentIM[:,n] = pcCentIMWt
# pcCentIMWt = a.assignbctResult(pcCentIMWt)
# extras.writeResults(pcCentIMWt, "pcCentIMWt", ofbT, propDict=propDict, append=appValT)
# del(pcCentIMWt)
#
# wmdIMWt = extras.withinModuleDegree(a.G, ciNIM, weight='weight')
# wmdIM[:,n] = [wmdIMWt[v] for v in a.G.nodes()]
# extras.writeResults(wmdIMWt, "wmdIMWt", ofbT, propDict=propDict, append=appValT)
# del wmdIMWt
# # Newman partitioning
# ciNm = bct.modularity_und(a.bctmat)
# QNmWt = ciNm[1]
# QNm[n] = QNmWt
# ciNNm = a.assignbctResult(ciNm[0])
# extras.writeResults(QNmWt, "QNmWt", ofb, propDict=propDict, append=appValT)
# extras.writeResults(ciNNm, "ciNmWt", ofb, propDict=propDict, append=appValT)
#
# nMNmWt = len(mbt.np.unique(ciNm[0]))
# nMNm[n] = nMNmWt
# extras.writeResults(nMNmWt, "nMNmWt", ofb, propDict=propDict, append=appValT)
# del(nMNmWt)
#
# pcCentNmWt = bct.participation_coef_sign(a.bctmat,ciNm[0])
# pcCentNm[:,n] = pcCentNmWt
# pcCentNmWt = a.assignbctResult(pcCentNmWt)
# extras.writeResults(pcCentNmWt, "pcCentNmWt", ofb, propDict=propDict, append=appValT)
#
# wmdNmWt = extras.withinModuleDegree(a.G, ciNNm, weight='weight')
# wmdNm[:,n] = [wmdNmWt[v] for v in a.G.nodes()]
# extras.writeResults(wmdNmWt, "wmdNmWt", ofb, propDict=propDict, append=appValT)
# del wmdNmWt
appValT=True
# now to collect measures in a binary graph
a.binarise()
a.weightToDistance()
a.makebctmat()
#### small worldness metrics ####
degs = mbt.nx.degree(a.G)
extras.writeResults(degs, "degree", ofb, propDict=propDict,
append=appVal)
# clustCoeff = mbt.nx.average_clustering(a.G)
# extras.writeResults(clustCoeff, "clusterCoeff", ofb, propDict=propDict,
# append=appVal)
# del(clustCoeff)
#
# pl = mbt.nx.average_shortest_path_length(a.G)
# extras.writeResults(pl, "pl", ofb, propDict=propDict, append=appVal)
# del(pl)
#
# ge = extras.globalefficiency(a.G)
# extras.writeResults(ge, "ge", ofb, propDict=propDict, append=appVal)
# del(ge)
#
# le = extras.localefficiency(a.G)
# extras.writeResults(le, "le", ofb, propDict=propDict, append=appVal)
# del(le)
#
# # hub metrics
# betCent = mbt.centrality.betweenness_centrality(a.G)
# extras.writeResults(betCent, "betCent", ofb, propDict=propDict,
# append=appVal)
#
# closeCent = mbt.centrality.closeness_centrality(a.G)
# extras.writeResults(closeCent, "closeCent", ofb, propDict=propDict,
# append=appVal)
#
# hs = extras.hubscore(a.G, bc=betCent, cc=closeCent, degs=degs,
# weighted=False)
# extras.writeResults(hs, "hs", ofb, propDict=propDict, append=appVal)
# del(hs, betCent, closeCent, degs)
#
# try:
# eigCent = mbt.centrality.eigenvector_centrality_numpy(a.G)
# except:
# eigCent = dict(zip(a.G.nodes(), ['NA' for n in a.G.nodes()]))
# extras.writeResults(eigCent, "eigCentNP", ofb, propDict=propDict,
# append=appVal)
# del(eigCent)
#
# eln = extras.edgeLengths(a.G, nodeWise=True)
# extras.writeResults(eln, "eln", ofb, propDict=propDict, append=appVal)
# del(eln)
#
# el = extras.edgeLengths(a.G)
# meanEL = mbt.np.mean(mbt.np.array((el.values()), dtype=float))
# extras.writeResults(meanEL, "meanEL", ofb, propDict=propDict,
# append=appVal)
#
# medianEL = mbt.np.median(mbt.np.array((el.values()), dtype=float))
# extras.writeResults(medianEL, "medianEL", ofb, propDict=propDict,
# append=appVal)
#
# del(el, meanEL, medianEL)
# # 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, propDict=propDict, append=appVal)
# del wmd
#
# nM = len(mbt.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)
# extras.writeResults(rc, "rcCoeff", ofb, propDict=propDict, append=appVal)
# del(rc)
# # robustness
# rbt = a.robustness()
# extras.writeResults(rbt, "robustness", ofb, propDict=propDict,
# append=appVal)
#
# # infomap partitioning
# bIM = infomap.nx2infomap(a.G)
# del(bIM)
# try:
# f = open("nxdigraph.clu", "r") # recapture results from output file
# modules = mbt.np.array([int(v.strip('\n')) for v in f.readlines()[1:]])
# f.close()
# remove("nxdigraph.clu")
#
# ciNIM = a.assignbctResult(modules)
# QIM = community.modularity(ciNIM, a.G)
#
# pcCentIM = bct.participation_coef_sign(a.bctmat, modules)
# pcCentIM = a.assignbctResult(pcCentIM)
# wmdIM = extras.withinModuleDegree(a.G, ciNIM, weight='weight')
# nMIM = len(np.unique(ciNIM[0]))
#
# except:
# modules = np.array((np.repeat(np.nan, len(a.G.nodes()))))
# QIM = "NA"
# pcCentIM = {v:"NA" for v in a.G.nodes()}
# wmdIM = {v:"NA" for v in a.G.nodes()}
# ciNIM = {v:"NA" for v in a.G.nodes()}
# nMIM = 0
#
# extras.writeResults(QIM, "QIM", ofbT, propDict=propDict, append=appValT)
# extras.writeResults(ciNIM, "ciIM", ofbT, propDict=propDict, append=appValT)
# del QIM
#
# extras.writeResults(nMIM, "nMIM", ofbT, propDict=propDict, append=appValT)
# del nMIM
#
# extras.writeResults(pcCentIM, "pcCentIM", ofbT, propDict=propDict, append=appValT)
# del pcCentIM
#
# extras.writeResults(wmdIM, "wmdIM", ofbT, propDict=propDict, append=appValT)
# del(wmdIM, ciNIM)
#
# # Newman partitioning
# ciNm = bct.modularity_und(a.bctmat)
# QNm= ciNm[1]
# ciNNm = a.assignbctResult(ciNm[0])
# extras.writeResults(QNm, "QNm", ofb, propDict=propDict, append=appValT)
# extras.writeResults(ciNNm, "ciNm", ofb, propDict=propDict, append=appValT)
# del QNm
#
# nMNm = len(mbt.np.unique(ciNm[0]))
# extras.writeResults(nMNm, "nMNm", ofb, propDict=propDict, append=appValT)
# del nMNm
#
# pcCentNm = bct.participation_coef_sign(a.bctmat,ciNm[0])
# pcCentNm = a.assignbctResult(pcCentNm)
# extras.writeResults(pcCentNm, "pcCentNm", ofb, propDict=propDict, append=appValT)
# del pcCentNm
#
# wmdNm = extras.withinModuleDegree(a.G, ciNNm, weight='weight')
# extras.writeResults(wmdNm, "wmdNm", ofb, propDict=propDict, append=appValT)
# del(wmdNm,ciNNm,ciNm)
# append any further iterations
appVal = True
# propDict = {"pcLoss":pcLoss}
# # weighted measures
# a.adjMatThresholding(MST=False)
# a.weightToDistance()
# ofb = '_'.join(["brain", degenName, "d"+dVal+"_"])
# a.makebctmat()
#
# # weighted hub metrics
# degs = a.G.degree(weight='weight')
# extras.writeResults(degs, "degree_wt", ofb, propDict=propDict, append=appValW)
#
# betCent = mbt.centrality.betweenness_centrality(a.G, weight='distance')
# extras.writeResults(betCent, "betCent_wt", ofb, propDict=propDict, append=appValW)
#
# closeCent = mbt.centrality.closeness_centrality(a.G, distance='distance')
# extras.writeResults(closeCent, "closeCent_wt", ofb, propDict=propDict, append=appValW)
#
# eigCent = mbt.centrality.eigenvector_centrality_numpy(a.G)
# extras.writeResults(eigCent, "eigCentNP_wt", ofb, propDict=propDict, append=appValW)
# del(eigCent)
# # weighted modularity metrics
# ci = bct.modularity_louvain_und_sign(a.bctmat)
# Q = ci[1]
# ciN = a.assignbctResult(ci[0])
# extras.writeResults(Q, "Q_wt", ofb, propDict=propDict, append=appValW)
# extras.writeResults(ciN, "ci_wt", ofb, propDict=propDict, append=appValW)
#
# nM = len(mbt.np.unique(ci[0]))
# extras.writeResults(nM, "nM_wt", ofb, propDict=propDict, append=appValW)
# del(nM)
#
# wmd = extras.withinModuleDegree(a.G, ciN, weight='weight')
# extras.writeResults(wmd, "wmd_wt", ofb, propDict=propDict, append=appValW)
# del wmd
#
appValT=False
# pcCent = a.assignbctResult(mbt.np.mean(pcCent, axis=1))
# extras.writeResults(pcCent, "pcCentWt_wt", ofb, propDict=propDict, append=appValW)
# del(pcCent,ci)
#
# betCentT = a.assignbctResult(mbt.np.mean(betCentT, axis=1))
# extras.writeResults(betCentT, "betCentWtT_wt", ofb, propDict=propDict, append=appValW)
#
# nM = mbt.np.mean(nM)
# extras.writeResults(nM, "nMWt_wt", ofb, propDict=propDict, append=appValW)
# del(nM)
#
# wmd = a.assignbctResult(mbt.np.mean(wmd, axis=1))
# extras.writeResults(wmd, "wmdWt_wt", ofb, propDict=propDict, append=appValW)
# del(wmd)
#
#
# # Infomap
# QIM = np.mean(QIM)
# extras.writeResults(QIM, "QIMWt_wt", ofb, append=appVal)
# del(QIM)
#
# pcCentIM = a.assignbctResult(np.mean(pcCentIM, axis=1))
# extras.writeResults(pcCentIM, "pcCentIMWt_wt", ofb, append=appVal)
# del(pcCentIM)
#
# wmdIM = a.assignbctResult(np.mean(wmdIM, axis=1))
# extras.writeResults(wmdIM, "wmdIMWt_wt", ofb, append=appVal)
# del(wmdIM)
#
# nMIM = np.mean(nMIM)
# extras.writeResults(nMIM, "nMIMWt_wt", ofb, append=appVal)
# del(nMIM)
#
# # Newman
# QNm = mbt.np.mean(QNm)
# extras.writeResults(QNm, "QNmWt_wt", ofb, append=appValW)
# del(QNm)
#
# pcCentNm = a.assignbctResult(mbt.np.mean(pcCentNm, axis=1))
# extras.writeResults(pcCentNm, "pcCentNmWt_wt", ofb, append=appValW)
# del(pcCentNm)
#
# wmdNm = a.assignbctResult(mbt.np.mean(wmdNm, axis=1))
# extras.writeResults(wmdNm, "wmdNmWt_wt", ofb, append=appValW)
# del(wmdNm)
#
# nMNm = mbt.np.mean(nMNm)
# extras.writeResults(nMNm, "nMNmWt_wt", ofb, append=appValW)
# del(nMNm)
a.applyThreshold()
a = mbt.brainObj()
appVal = False
appValT = False
# unweighted measures
# iterate through thresholds
for e in edgePCCons:
ofb = '_'.join(["brain", thresholdtype, str(e), "d"+dVal+"_"])
propDict = {"edgePC":str(e)} # added properties for results files
a.importAdjFile(adjMatFile, delimiter=delim)
a.localThresholding(edgePC=e) # apply a threshold
a.removeUnconnectedNodes() # remove unconnected nodes
degs = a.G.degree(weight='weight')
extras.writeResults(degs, "degreeWt", ofb, append=appVal)
a.binarise() # binarise the graph
a.importSpatialInfo(parcelFile) # read spatial information
a.weightToDistance() # convert weights to distance (for closeness centrality function)
a.makebctmat() # create an array to be used by the brain connectivity toolbox functions
ofbT = '_'.join(["brain", thresholdtype, str(e), "d"+dVal+"_"])
#### small worldness metrics ####
degs = mbt.nx.degree(a.G) # measure degree
extras.writeResults(degs, "degree", ofb, propDict=propDict, append=appVal) # write the results to a file
clustCoeff = mbt.nx.average_clustering(a.G)
extras.writeResults(clustCoeff, "clusterCoeff", ofb, propDict=propDict, append=appVal)
del(clustCoeff)