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plotLCurveModel.py
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plotLCurveModel.py
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#!/usr/bin/env python
import sys, os
import numpy, math
import argparse
import astropy.io.fits
import astropy.stats
import loadingSavingUtils, statsUtils
import spectrumClasses, timeClasses
import scipy.optimize
import copy
import ppgplot
import scipy.signal as signal
def quad(x, a1, a2, a3):
y = a1 * x * x + a2 *x + a3
return y
class object:
def __init__(self, id):
self.id = id
self.MJD = []
self.mag = []
self.err = []
self.ephemeris = None
self.data = []
self.hasEphemeris = False
def appendData(self, dataDict):
# self.MJD.append(data['MJD'])
# self.mag.append(data['mag'])
# self.err.append(data['err'])
self.data.append(dataDict)
def getColumn(self, columnName):
return [d[columnName] for d in self.data]
def loadEphemeris(self):
# Look in the local directory for a file called 'id'-ephem.dat and load it
filename = self.id + "-ephem.dat"
if os.path.exists(filename):
self.ephemeris = timeClasses.ephemerisObject()
self.ephemeris.loadFromFile(filename)
self.hasEphemeris = True
return True
return False
def computePhases(self):
if not self.hasEphemeris: return
for d in self.data:
d['phase'] = self.ephemeris.getPhase(d['HJD'])
print d['HJD'], d['phase']
def setHJDs(self, MJD, HJD):
keys = [d['MJD'] for d in self.data]
dates = zip(MJD, HJD)
for index, d in enumerate(dates):
self.data[index]['HJD'] = d[1]
def convertFluxMagnitude(self):
fudge = 10
for d in self.data:
d['mag'] = -2.5 * numpy.log10(d['flux'])
d['err'] = -2.5 * d['flux_err'] / numpy.log(10) / d['flux'] /fudge
# print d['mag'], d['err']
def filterData(self, columnName, limit1, limit2):
newData = []
if limit1>limit2:
temp = limit1
limit1 = limit2
limit2 = temp
for d in self.data:
value = d[columnName]
if value>limit1 and value<limit2:
newData.append(d)
else:
print "Filtering out a point: %s %f not between %f and %f"%(columnName, value, limit1, limit2)
self.data = newData
def writeData(self, filename):
outputFile = open(filename, 'wt')
for d in self.data:
date = d['HJD']
phase = d['phase']
flux = 10**(d['mag'] / -2.5)
flux_error = flux * numpy.log(10) * d['err']
print date, phase, d['mag'], flux, flux_error
outputFile.write("%f 0 %E %E 1 1\n"%(phase, flux, flux_error))
outputFile.close()
def sortData(self, columnName):
print "Sorting data by:", columnName
sortedData = self.data.sort(key=lambda x:x[columnName])
def computeHJDs(self):
if self.hasEphemeris:
print o.id, o.ephemeris
MJD = o.getColumn('MJD')
correctHelio = timeClasses.heliocentric()
correctHelio.setTelescope('CSS')
correctHelio.setTarget(o.ephemeris.ra, o.ephemeris.dec)
BMJD = correctHelio.convertMJD(MJD)
HJD = [b + 2400000.5 for b in BMJD]
self.setHJDs(MJD, HJD)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Plots lcurve model alongside observed data.')
parser.add_argument('observed', type=str, help='Observed data.')
parser.add_argument('model', type=str, help='Modelled data.')
parser.add_argument('name', type=str, help='Object name.')
parser.add_argument('--ps', action='store_true', help = "Dump plots to ps files instead of the screen.")
arg = parser.parse_args()
print "Astropy version:", astropy.__version__
objects = []
observedData = object('observed')
dataFile = open(arg.observed, 'rt')
for line in dataFile:
fields = line.strip().split(' ')
data = {}
data['phase'] = float(fields[0])
data['observedtime'] = float(fields[1])
data['flux'] = float(fields[2])
data['flux_err'] = float(fields[3])
# print data
observedData.appendData(data)
dataFile.close()
objects.append(observedData)
modelledData = object('modelled')
dataFile = open(arg.model, 'rt')
for line in dataFile:
fields = line.strip().split(' ')
data = {}
data['phase'] = float(fields[0])
data['observedtime'] = float(fields[1])
data['flux'] = float(fields[2])
data['flux_err'] = float(fields[3])
print data
modelledData.appendData(data)
dataFile.close()
print "%d targets loaded"%len(objects)
observedData.convertFluxMagnitude()
modelledData.convertFluxMagnitude()
if arg.ps: device = arg.name + "_lcurve.ps/ps"
else: device = "/xs"
PGPlotWindow = ppgplot.pgopen(device)
ppgplot.pgask(True)
pgPlotTransform = [0, 1, 0, 0, 0, 1]
ppgplot.pgslct(PGPlotWindow)
ppgplot.pgsci(1)
ppgplot.pgask(False)
phases = observedData.getColumn('phase')
flux = observedData.getColumn('flux')
flux_err = observedData.getColumn('flux_err')
flux_err = [f/10 for f in flux_err]
flux = [f * 3631E3 for f in flux]
flux_err = [f * 3631E3 for f in flux_err]
mag = observedData.getColumn('mag')
err = observedData.getColumn('err')
maxFlux = 0
for f, fe in zip(flux, flux_err):
if f + fe > maxFlux: maxFlux = f + fe
# Duplicate data out to phase 2.0
extendedPhases = copy.deepcopy(phases)
for p in phases:
extendedPhases.append(p + 1.0)
phases = extendedPhases
flux.extend(flux)
flux_err.extend(flux_err)
mag.extend(mag)
err.extend(err)
"""
ppgplot.pgsch(1.6)
ppgplot.pgenv(0, 2, numpy.max(mag), numpy.min(mag), 0, 0)
ppgplot.pglab("Phase", "PTF magnitude", "%s"%(arg.name))
ppgplot.pgsch(1.0)
ppgplot.pgpt(phases, mag)
ppgplot.pgerrb(2, phases, mag, err, 0)
ppgplot.pgerrb(4, phases, mag, err, 0)
ppgplot.pgsci(2)
model = modelledData.getColumn('mag')
model.extend(model)
ppgplot.pgsls(2)
ppgplot.pgslw(7)
ppgplot.pgline(phases, model)
"""
ppgplot.pgsch(1.6)
ppgplot.pgenv(0, 2, 0, maxFlux, 0, 0)
ppgplot.pglab("Phase", "PTF flux (mJy)", "%s"%(arg.name))
ppgplot.pgsch(1.0)
ppgplot.pgpt(phases, flux)
ppgplot.pgerrb(2, phases, flux, flux_err, 0)
ppgplot.pgerrb(4, phases, flux, flux_err, 0)
ppgplot.pgsci(2)
ppgplot.pgsls(2)
ppgplot.pgslw(7)
modelPhases = modelledData.getColumn('phase')
temp = copy.deepcopy(modelPhases)
for p in modelPhases: temp.append(p + 1.0)
modelPhases = temp
model = modelledData.getColumn('flux')
model = [m * 3631E3 for m in model]
model.extend(model)
ppgplot.pgline(modelPhases, model)
ppgplot.pgsci(1)
ppgplot.pgsls(1)
ppgplot.pgslw(1)
# Plot the inset subplot showing the eclipse
subFlux = []
subFluxErr = []
subPhases = []
subModelPhases = []
subModel = []
startPhase = 0.96
endPhase = 1.04
print "maxFlux:", maxFlux
for index, phase in enumerate(phases):
if phase > startPhase and phase < endPhase:
subFlux.append(flux[index])
subPhases.append(phase)
subFluxErr.append(flux_err[index])
for index, phase in enumerate(modelPhases):
if phase > startPhase and phase < endPhase:
subModel.append(model[index])
subModelPhases.append(phase)
print ppgplot.pgqvp(0)
(x1, x2, y1, y2) = ppgplot.pgqvp(0)
print ppgplot.pgqwin(0)
xlower = (x1 + x2) / 2 + 0.05
xupper = x2 - 0.05
yupper = (y1 + y2) / 2
ylower = 0.22
ppgplot.pgsvp(xlower, xupper, ylower, yupper)
ppgplot.pgswin(startPhase, endPhase, 0, numpy.max(subFlux))
print ppgplot.pgqvp(0)
print ppgplot.pgqwin(0)
# ppgplot.pgsubp(4, 3)
# ppgplot.pgpanl(2, 2)
# ppgplot.pgenv(startPhase, endPhase, 0, numpy.max(flux), 0, -1)
# ppgplot.pglab("Phase", "PTF flux", "%s"%(arg.name))
ppgplot.pgbox("BCN", 0, 0, "BC", 0, 0)
ppgplot.pgpt(subPhases, subFlux)
ppgplot.pgerrb(2, subPhases, subFlux, subFluxErr, 0)
ppgplot.pgerrb(4, subPhases, subFlux, subFluxErr, 0)
ppgplot.pgsls(2)
ppgplot.pgline(subModelPhases, subModel)
ppgplot.pgsls(4)
ppgplot.pgline([1, 1], [0, numpy.max(subFlux)])
ppgplot.pgclos()
sys.exit()