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zinfolhs.py
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zinfolhs.py
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from zhdf import new,loaddump,pool,ncores,da,progressbar,h5py
import numpy as np
import pandas as pd
import os,json,re,sys
import multiprocessing as mp
import networkx as nx
print ''
print ncores
from collections import Counter
import networkx as nx
from infomap import infomap
import community
np.warnings.filterwarnings('ignore')
print 'load libs'
os.system('rm centrality/lhsgroup/*')
filename = 'lhs.h5'
groups = new(filename).groups
mcm = list(pd.read_csv('src/background/smiles_mined.csv').name)
cs = [i.split(',')[-1].replace('\n','') for i in tuple(open('carbons.csv'))]
#cs.extend('RO2')
def getedge(num,allspecs,prodloss,flux,tsps):#,allspecs,a,tsps):
edges = []
print len(num)
print ''
import progressbar,re
import numpy as np
bar = progressbar.ProgressBar()
for j in bar(list(num)):
spec = allspecs[j]
for i in allspecs:
fluxes = set(prodloss[spec]['prod']) & set(prodloss[i]['loss'])
if len(fluxes) > 0 :
arr = 20 + np.log10(np.array(flux.loc[tsps,flux.columns[list(fluxes)]].sum(axis=1)))
edges.append([i,spec,arr])
return edges
def mapinfomap(e):
try:
g= e[0]
t= e[1]
print 'Infomap'
G = infomap.Infomap("-d -N 100")
Gnx = nx.DiGraph()
jval = np.array([float(k[2][t]) for k in edgelist if (len(k[-1])>0 and len(k[-3])>0 and k[2][t]!='')])
#if len(jval)<1: continue
jval = jval[jval>0]
jmin = np.min(jval)
jmax = np.max(jval)-jmin
for j in edgelist:
jedge = j[2][t]
if str(jedge) not in ['','-inf']:
jedge = float(jedge)
jedge -= jmin
jedge /= jmax
try:
Gnx.add_edge(j[0],j[1],weight=abs(jedge))
G.addLink(toindex[j[0]],toindex[j[1]],weight=abs(jedge))
except Exception as e:
print 'fail' , e
G.run();
tree = G.tree
partition = {}
for node in tree.leafIter():
partition[node.originalLeafIndex] = node.moduleIndex()
groups = [[] for i in np.empty(np.array(partition.values()).max())]
for i,j in enumerate(speclist):
try:
groups[partition[i]].append(j)
except:
print 'no node', i,j
groups = sorted(groups,key=lambda x : len(x),reverse=True)
with open('centrality/lhsgroup/%04d_%04d.gps'%(g,t),'w') as f:
for i in groups:#filter(lambda x : len(x) in range(2,11),groups)
f.write('-'.join(set(i))+'\n')
return ['-'.join(set(i)) for i in groups]
except Exception as e:
print 'failed',e
return ''
pool.close()
pool = mp.Pool(ncores)
for g in groups.values():
print 'gogogo '+str(g)
run = new(filename,groupid=g)
allspecs = filter(lambda x: x not in ['LAT', 'LON','PRESS', 'TEMP', 'H2O', 'M','NA', 'O1D', 'R','O','O1D',
'O3', 'O2', 'NO2', 'NO3', 'N2O5', 'H2O2', 'TEMP', 'NO', 'NA',
'KMT05', 'KMT04', 'KMT07', 'KMT06', 'KMT01', 'HO2NO2', 'KMT03',
'KMT02', 'HO2', 'KMT09', 'RO2', 'KMT08', 'CO', 'HNO3', 'SO3', 'SO2',
'N2', 'OH', 'H2', 'HONO', 'HSO3', 'H2O', 'KMT12', 'KMT11', 'SA'],run.spec.columns)
speclist = list(allspecs)
toindex = dict(zip(speclist,range(len(speclist))))
fromindex = dict(zip(range(len(speclist)),speclist))
tsps = run.ts[range(24,len(run.spec),24)]
edgelist=[]
bar = progressbar.ProgressBar()
results = [pool.apply_async(getedge, args=(x,allspecs,run.prodloss,run.flux.compute(),tsps)) for x in np.array_split(range(len(allspecs)),ncores)]
[edgelist.extend(p.get()) for p in bar(results)]
print 'edgelist ready'
pool.close()
pool = mp.Pool(ncores)
words = pool.map(mapinfomap,zip([g]*len(tsps),xrange(len(tsps))))
l =[]
for i in words:
l.extend(i)
print 'save collections'
with open('centrality/lhsgroup/collected.txt','w') as f:
items = Counter(l).items()
items = sorted(items,key=lambda x:x[1],reverse=True)
for i in items:
f.write('%d,%s\n'%(i[1],i[0]))
os.system('/opt/pbs/bin/qdel $PBS_JOBID')
os.system('pkill screen')