trace-to-txt

#!/usr/bin/python

import tables as tb
import numpy as np
import os,sys
import pylab as pl

dbfile = sys.argv[1]
burn = int(sys.argv[2])

path, fname = os.path.split(dbfile)
dbname, crap = os.path.splitext(fname)

hf = tb.openFile(dbfile)
hr = hf.root.chain0.PyMCsamples

ind = np.array(np.linspace(burn, len(hr)-1, 500), dtype=int)

os.mkdir(dbname)
os.chdir(dbname)


# Write in longitude, latitude and time
indices_to_keep = hf.root.metadata.ui[:]
(indices_to_keep+1).tofile('indices_to_keep.txt', sep=',')

lpm = hf.root.metadata.logp_mesh
comps = ['lon','lat','t']
for i in xrange(3):
    lpm[:,i].tofile(comps[i]+'.txt',sep=',')

try:
    urb = hf.root.metadata.urb[:][indices_to_keep]
except:
    urb = 0
periurb = hf.root.metadata.periurb[:][indices_to_keep]
urb_cls = 1+periurb+2.*urb
urb_cls.tofile('urb_cls.txt',sep=',')


# Write in the traces
for n in hr.colnames:
    # Exclude step method tuning info
    if n.find('Metropolis')>-1:
        continue
    col = hr.colinstances[n]
    # Vector-valued variables' traces
    if len(col.dtype.shape) > 0:
        f = file(n+'.txt','w')
        for i in ind:
            col[i].tofile(f,sep=',')
            if i != ind[-1]:
                f.write('\n')
        f.close()
    # Scalar-valued variables' traces
    else:
        col[:][ind].tofile(n+'.txt',sep=',')
        
# Zip and return    
os.chdir('..')
os.system('tar -cf %s.tar %s'%(dbname, dbname))
os.system('gzip %s.tar'%dbname)