def main():
"""
params = []
paramfile = sys.argv[1]
f = open(paramfile,'r')
for line in f:
params.append(line)
f.close()
datadir = params[0].split('=')[1].strip()
flatdir = params[1].split('=')[1].strip()
fluxdir = params[2].split('=')[1].strip()
wvldir = params[3].split('=')[1].strip()
obsfile = params[4].split('=')[1].strip()
skyfile = params[5].split('=')[1].strip()
flatfile = params[6].split('=')[1].strip()
fluxfile = params[7].split('=')[1].strip()
wvlfile = params[8].split('=')[1].strip()
objectName = params[9].split('=')[1].strip()
fluxCalObject = params[10].split('=')[1].strip()
obsFileName = os.path.join(datadir, obsfile)
skyFileName = os.path.join(datadir, skyfile)
wvlCalFileName = os.path.join(wvldir, wvlfile)
flatCalFileName = os.path.join(flatdir, flatfile)
fluxCalFileName = os.path.join(fluxdir, fluxfile)
"""
if len(sys.argv) >3:
filenum = str('_'+sys.argv[3])
else:
filenum = '_0'
#science object parameter file
params = []
paramfile = sys.argv[1]
f = open(paramfile,'r')
for line in f:
params.append(line)
f.close()
datadir = params[0].split('=')[1].strip()
flatdir = params[1].split('=')[1].strip()
wvldir = params[2].split('=')[1].strip()
obsfile = params[3].split('=')[1].strip()
skyfile = params[4].split('=')[1].strip()
flatfile = params[5].split('=')[1].strip()
wvlfile = params[6].split('=')[1].strip()
objectName = params[9].split('=')[1].strip()
if len(params)>10:
xpix = int(params[10].split('=')[1].strip())
ypix = int(params[11].split('=')[1].strip())
apertureRadius = int(params[12].split('=')[1].strip())
#flux cal object parameter file
params2 = []
param2file = sys.argv[2]
f = open(param2file,'r')
for line in f:
params2.append(line)
f.close()
fluxdir = params2[7].split('=')[1].strip()
fluxfile = params2[8].split('=')[1].strip()
fluxCalObject = params2[9].split('=')[1].strip()
obsFileName = os.path.join(datadir, obsfile)
skyFileName = os.path.join(datadir, skyfile)
wvlCalFileName = os.path.join(wvldir, wvlfile)
flatCalFileName = os.path.join(flatdir, flatfile)
fluxCalFileName = os.path.join(fluxdir, fluxfile)
print "obsfile = ",obsFileName
print "skyfile = ",skyFileName
print "wvlcal = ", wvlCalFileName
print "flatcal = ", flatCalFileName
print "fluxcal = ", fluxCalFileName
print "object = ", objectName
print "flux cal object = ", fluxCalObject
print "\n---------------------\n"
obs = ObsFile(obsFileName)
obs.loadWvlCalFile(wvlCalFileName)
obs.loadFlatCalFile(flatCalFileName)
obs.loadFluxCalFile(fluxCalFileName)
print "loaded data file and calibrations\n---------------------\n"
nRow = obs.nRow
nCol = obs.nCol
obsTime = obs.getFromHeader("exptime")
#wvlBinEdges,obsSpectra = loadSpectra(obs,nCol,nRow)
#nWvlBins=len(wvlBinEdges)-1
#print np.shape(obsSpectra)
#print nRow
#print nCol
#print nWvlBins
"""
medianObsSpectrum = calculateMedian(obsSpectra,nCol,nRow,nWvlBins)
print "target spectrum loaded\n---------------------\n"
if skyfile != "None":
sky = ObsFile(skyFileName)
sky.loadWvlCalFile(wvlCalFileName)
sky.loadFlatCalFile(flatCalFileName)
sky.loadFluxCalFile(fluxCalFileName)
skyTime = sky.getFromHeader("exptime")
wvlBinEdges,skySpectra = loadSpectra(sky,nCol,nRow)
skySpectrum = calculateMedian(skySpectra, nCol, nRow, nWvlBins)
skySpectrum = skySpectrum*float(obsTime)/float(skyTime) #scale sky spectrum to target observation time
print "sky spectrum loaded\n---------------------\n"
else:
#if no sky file given, estimate sky spectrum as median spectrum of obs file, assuming object is tiny
skySpectrum = calculateMedian(obsSpectra, nCol, nRow, nWvlBins)
print "sky spectrum estimated as median of target file spectrum\n---------------------\n"
#subtract sky spectrum from every pixel
allSkySpectrum = obsSpectra-skySpectrum
#set any negative values to 0 after sky subtraction
allSkySpectrum[allSkySpectrum<0]=0
#take median of remaining sky subtracted spectra to get median object spectrum
finalSpectrum = calculateMedian(allSkySpectrum,nCol,nRow,nWvlBins)
"""
#load/generate hot pixel mask file
HotPixFile = getTimeMaskFileName(obsFileName)
if not os.path.exists(HotPixFile):
hp.findHotPixels(obsFileName,HotPixFile)
print "Flux file pixel mask saved to %s"%(HotPixFile)
obs.loadHotPixCalFile(HotPixFile)
print "Hot pixel mask loaded %s"%(HotPixFile)
print "Making spectrum with Aperture Spectrum in ObsFile"
#use Aperture Spectrum from obsfile
medianObsSpectrum, wvlBinEdges = obs.getApertureSpectrum(pixelCol=ypix,pixelRow=xpix,radius1=apertureRadius, radius2 = apertureRadius*2.0,weighted=True, fluxWeighted=True, lowCut=3000, highCut=7000)
nWvlBins=len(wvlBinEdges)-1
#load std spectrum for comparison
try:
realSpectra = loadStd(objectName,wvlBinEdges)
print "real std spectrum loaded for reference\n---------------------\n"
stdTitle = "Rebinned Std Spectrum of %s"%(objectName)
except KeyError:
print "Key Error loading MKIDStd"
realSpectra = np.ones(nWvlBins)
stdTitle = "No MKIDStd spectrum available for %s"%(objectName)
#create plots
plotDir = "/home/srmeeker/ARCONS-pipeline/fluxcal/test/plots"
plotFileName = "%s_from_%s%s.pdf"%(objectName,fluxCalObject,filenum)
fullFluxPlotFileName = os.path.join(plotDir,plotFileName)
pp = PdfPages(fullFluxPlotFileName)
matplotlib.rcParams['font.size']=6
#calculate midpoints of wvl bins for plotting
wvls = np.empty((nWvlBins),dtype=float)
for n in xrange(nWvlBins):
binsize=wvlBinEdges[n+1]-wvlBinEdges[n]
wvls[n] = (wvlBinEdges[n]+(binsize/2.0))
plt.figure()
ax1 = plt.subplot(221)
ax1.set_title('ARCONS median flat/flux cal\'d obs in counts')
ax1.set_xlim((4000,11000))
ax1.set_ylim((min(medianObsSpectrum[(wvls>4000) & (wvls<11000)]),max(medianObsSpectrum[(wvls>4000) & (wvls<8000)])))
plt.plot(wvls,medianObsSpectrum)
#plt.show()
#ax2 = plt.subplot(232)
#ax2.set_title('ARCONS median flat/flux cal\'d sky in counts')
#plt.plot(wvls,skySpectrum)
#plt.show()
ax5 = plt.subplot(223)
ax5.set_title('Sensitivity Spectrum')
ax5.set_xlim((3000,13000))
ax5.set_ylim((0,5))
plt.plot(wvls,obs.fluxWeights)
#ax3 = plt.subplot(234)
#ax3.set_title('MKID data minus sky in counts')
#plt.plot(wvls,finalSpectrum/max(finalSpectrum))
ax4 = plt.subplot(222)
ax4.set_title(stdTitle)
plt.plot(wvls,realSpectra)
#ax7 = plt.subplot(337)
#ax7.set_title('Flux Cal\'d ARCONS Spectrum of Std')
#plt.plot(wvls,fluxFactors*subtractedSpectra)
pp.savefig()
pp.close()
#del obs
#del sky
print "output plots to %s\n---------------------\n"%(fullFluxPlotFileName)
txtDir = "/home/srmeeker/ARCONS-pipeline/fluxcal/test/txt"
txtFileName = "%s_from_%s%s.txt"%(objectName,fluxCalObject,filenum)
fullFluxTxtFileName = os.path.join(txtDir,txtFileName)
outarr = np.empty((len(medianObsSpectrum),2),dtype=float)
outarr[:,0]=wvls
outarr[:,1]=medianObsSpectrum
#save sensitivity spectrum to file
np.savetxt(fullFluxTxtFileName, outarr)
print "output txt file to %s\n---------------------\n"%(fullFluxPlotFileName)
