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Committer: ckloss <ckloss@fluid38.(none)>

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On branch master
 Initial commit for lpp, version 2011-10-11
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ckloss
2012-02-03 14:10:31 +01:00
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# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is distributed under
# the GNU General Public License.
# clog tool
oneline = "Read ChemCell and SPPARKS log files and extract time-series data"
docstr = """
c = clog("file1") read in one or more log files
c = clog("log1 log2.gz") can be gzipped
c = clog("file*") wildcard expands to multiple files
c = clog("log.cell","Time") 2nd arg = start string for time section
c = clog("log.cell","",0) 3rd arg = average all runs
incomplete and duplicate thermo entries are deleted
if specify 2nd arg, it delimits a time section
no 2nd arg or empty string, use default which is ChemCell specific
if specify any 3rd arg, average all runs, assume all start at time 0
nvec = c.nvec # of vectors of thermo info
nlen = c.nlen length of each vectors
names = c.names list of vector names
a,b,... = c.get("A","B",...) return one or more vectors of values
c.write("file.txt") write all vectors to a file
c.write("file.txt","A","B",...) write listed vectors to a file
get and write allow abbreviated (uniquely) vector names
"""
# History
# 1/06, Steve Plimpton (SNL): original version
# 2/09, modified to allow different firststr for different log files
# ToDo list
# Variables
# nvec = # of vectors
# nlen = length of each vector
# names = list of vector names
# ptr = dictionary, key = name, value = index into data for which column
# data[i][j] = 2d array of floats, i = 0 to # of entries, j = 0 to nvecs-1
# firststr = string that begins a time-series section in log file
# Imports and external programs
import sys, re, glob
from os import popen
try: tmp = PIZZA_GUNZIP
except: PIZZA_GUNZIP = "gunzip"
# Class definition
class clog:
# --------------------------------------------------------------------
def __init__(self,*list):
self.nvec = 0
self.names = []
self.ptr = {}
self.data = []
self.firststr = "Step Time"
self.ave = 0
# flist = list of all log file names
words = list[0].split()
self.flist = []
for word in words: self.flist += glob.glob(word)
if len(self.flist) == 0 and len(list) == 1:
raise StandardError,"no log file specified"
if len(list) > 1 and len(list[1]): self.firststr = list[1]
if len(list) == 3: self.ave = 1
self.read_all()
# --------------------------------------------------------------------
# read all log data from all files
def read_all(self):
self.read_header(self.flist[0])
if self.nvec == 0: raise StandardError,"log file has no values"
# read all files
for file in self.flist: self.read_one(file)
print
# if no average, sort entries by timestep, cull duplicates
# if average, call self.average()
if self.ave == 0:
self.data.sort(self.compare)
self.cull()
else: self.average()
self.nlen = len(self.data)
print "read %d log entries" % self.nlen
# --------------------------------------------------------------------
def get(self,*keys):
if len(keys) == 0:
raise StandardError, "no log vectors specified"
map = []
for key in keys:
if self.ptr.has_key(key):
map.append(self.ptr[key])
else:
count = 0
for i in range(self.nvec):
if self.names[i].find(key) == 0:
count += 1
index = i
if count == 1:
map.append(index)
else:
raise StandardError, "unique log vector %s not found" % key
vecs = []
for i in range(len(keys)):
vecs.append(self.nlen * [0])
for j in xrange(self.nlen):
vecs[i][j] = self.data[j][map[i]]
if len(keys) == 1: return vecs[0]
else: return vecs
# --------------------------------------------------------------------
def write(self,filename,*keys):
if len(keys):
map = []
for key in keys:
if self.ptr.has_key(key):
map.append(self.ptr[key])
else:
count = 0
for i in range(self.nvec):
if self.names[i].find(key) == 0:
count += 1
index = i
if count == 1:
map.append(index)
else:
raise StandardError, "unique log vector %s not found" % key
else:
map = range(self.nvec)
f = open(filename,"w")
for i in xrange(self.nlen):
for j in xrange(len(map)):
print >>f,self.data[i][map[j]],
print >>f
f.close()
# --------------------------------------------------------------------
def compare(self,a,b):
if a[0] < b[0]:
return -1
elif a[0] > b[0]:
return 1
else:
return 0
# --------------------------------------------------------------------
def cull(self):
i = 1
while i < len(self.data):
if self.data[i][0] == self.data[i-1][0]: del self.data[i]
else: i += 1
# --------------------------------------------------------------------
def average(self):
counts = []
data = []
nlen = 0
i = j = 0
while i < len(self.data):
if self.data[i][0] == 0: j = 0
if j >= nlen:
counts.append(0)
data.append(self.nvec*[0])
nlen += 1
counts[j] += 1
for m in xrange(self.nvec): data[j][m] += self.data[i][m]
j += 1
i += 1
for i in xrange(nlen):
for j in xrange(self.nvec):
data[i][j] /= counts[j]
self.nlen = nlen
self.data = data
# --------------------------------------------------------------------
def read_header(self,file):
if file[-3:] == ".gz":
txt = popen("%s -c %s" % (PIZZA_GUNZIP,file),'r').read()
else:
txt = open(file).read()
s1 = txt.find(self.firststr)
s2 = txt.find("\n",s1)
line = txt[s1:s2]
words = line.split()
for i in range(len(words)):
self.names.append(words[i])
self.ptr[words[i]] = i
self.nvec = len(self.names)
# --------------------------------------------------------------------
def read_one(self,*list):
# if 2nd arg exists set file ptr to that value
# read entire (rest of) file into txt
file = list[0]
if file[-3:] == ".gz":
f = popen("%s -c %s" % (PIZZA_GUNZIP,file),'rb')
else:
f = open(file,'rb')
if len(list) == 2: f.seek(list[1])
txt = f.read()
if file[-3:] == ".gz": eof = 0
else: eof = f.tell()
f.close()
start = last = 0
while not last:
# chunk = contiguous set of concentration entries
# s1 = 1st char on 1st line of chunk
# s2 = 1st char on line after chunk
# set last = 1 if this is last chunk in file, leave 0 otherwise
# set start = position in file to start looking for next chunk
# rewind eof if final entry is incomplete
s1 = txt.find(self.firststr,start)
s2 = txt.find("Loop time of",start+1)
if s1 >= 0 and s2 >= 0 and s1 < s2: # found s1,s2 with s1 before s2
s1 = txt.find("\n",s1) + 1
elif s1 >= 0 and s2 >= 0 and s2 < s1: # found s1,s2 with s2 before s1
s1 = 0
elif s1 == -1 and s2 >= 0: # found s2, but no s1
last = 1
s1 = 0
elif s1 >= 0 and s2 == -1: # found s1, but no s2
last = 1
s1 = txt.find("\n",s1) + 1
s2 = txt.rfind("\n",s1) + 1
eof -= len(txt) - s2
elif s1 == -1 and s2 == -1: # found neither
# could be end-of-file section
# or entire read was one chunk
if txt.find("Loop time of",start) == start: # end of file, so exit
eof -= len(txt) - start # reset eof to "Loop"
break
last = 1 # entire read is a chunk
s1 = 0
s2 = txt.rfind("\n",s1) + 1
eof -= len(txt) - s2
if s1 == s2: break
chunk = txt[s1:s2-1]
start = s2
# split chunk into entries
# parse each entry for numeric fields, append to data
lines = chunk.split("\n")
for line in lines:
words = line.split()
self.data.append(map(float,words))
# print last timestep of chunk
print int(self.data[len(self.data)-1][0]),
sys.stdout.flush()
return eof