from __future__ import division
import struct
from optparse import OptionParser
import numpy
import matplotlib.pyplot
import readInfo
parser = OptionParser()
parser.add_option("--dir", dest="dir", default="./")
(options, args) = parser.parse_args()
dir = options.dir
info = readInfo.read(dir)
#if (info['absStopTime'] - info['absStartTime']) != 10000000:
# print "-1"
# exit()
equilibrationTime = (info['absStartTime'] + info['absStopTime']) / 2
minimumClusterSize = 3
"""
weightedClusterCount=0
weightedImpureCount=0
f=open(dir+"/aliveness.txt","r")
for line in f:
q=line.split()
parser.add_option("--motileFraction", dest="motileFraction", default="0.5")
(options, args) = parser.parse_args()
dir = options.dir
startTime = options.startTime
stopTime = options.stopTime
analysisFrameSkip = options.analysisFrameSkip
debug = options.debug
allTime = options.allTime
endTimeFraction = options.endTimeFraction
fakeAlivePrefix = options.fakeAlive
boxes = options.boxes
motileFraction = options.motileFraction
info = readInfo.read(dir, False)
startSl = info['startSl']
rodLength = info['rodLength']
frameSkip = info['frameSkip']
absStartTime = info['absStartTime']
absStopTime = info['absStopTime']
partNum = info['partNum']
timeStep = info['timeStep']
if allTime:
#print "All time."
startTime = absStartTime
stopTime = absStopTime
elif endTimeFraction != 0.0:
#print "Fraction of time."
stopTime = absStopTime
noPBC = options.noPBC
resolution = options.resolution
rerun = options.rerun
fakeAlivePrefix = options.fakeAlive
aliveFraction = options.aliveFraction
baseDir = os.path.expanduser(baseDir)
import matplotlib
if save:
matplotlib.use("PDF")
import matplotlib.pyplot as plt
matplotlib.rc('font', family='serif')
info = readInfo.read(baseDir, True)
startSl = info['startSl']
rodLength = info['rodLength']
frameSkip = info['frameSkip']
absStartTime = info['absStartTime']
absStopTime = info['absStopTime']
partNum = info['partNum']
timeStep = info['timeStep']
if (imWidth == 0):
imWidth = numpy.floor(startSl / numpy.sqrt(8.0) - rodLength / 2.0)
if (imHeight == 0):
imHeight = numpy.floor(startSl / numpy.sqrt(8.0) - rodLength / 2.0)
if allTime: