def timePL(tstamp,obsPath,centroidPath):
obs = ObsFile(obsPath)
obs.loadAllCals()
obs.setWvlCutoffs(3000,11000)
obs.loadCentroidListFile(centroidPath)
writePhotonList(obs,photListDescription=PulsarPhotonList,checkForExisting=False)
del obs
def centroidObs(obsPath,centroidPath,centroidRa,centroidDec,haOffset,xGuess,yGuess,savePath,tstamp):
obs = ObsFile(obsPath)
# if not os.path.exists(hotPath):
# hp.findHotPixels(obsFile=obs,outputFileName=hotPath)
obs.loadAllCals()
# obs.loadHotPixCalFile(hotPath,switchOnMask=True)
# obs.loadBestWvlCalFile()
# obs.loadFlatCalFile(flatPath)
obs.setWvlCutoffs(3000,11000)
obs.loadCentroidListFile(centroidPath)
ctrdFile = obs.centroidListFile
sliceTimes = ctrdFile.root.centroidlist.times.read()
xPositions = ctrdFile.root.centroidlist.xPositions.read()
yPositions = ctrdFile.root.centroidlist.yPositions.read()
intTime = sliceTimes[1]-sliceTimes[0]
for iTime,time in enumerate(sliceTimes):
x = xPositions[iTime]
y = yPositions[iTime]
title='centroid_{}_{}s'.format(tstamp,time)
imgDict = obs.getPixelCountImage(firstSec=time,integrationTime=intTime,weighted=True)
imgPath=os.path.join(savePath,title+'.png')
pop = PopUp(showMe=False)
pop.plotArray(imgDict['image'],title=title)
pop.axes.plot(x,y,color='g',marker='d')
pop.fig.savefig(imgPath)
print 'saved to',imgPath
del obs
def testWritePhotonList(outputFileName=None,firstSec=0,integrationTime=-1,doPixRemap=True):
'''
Test run of obsFile.writePhotonList. fileName can be used
to specify the output file name. If not specified, default
name/location is used.
Now includes test for pixel remapping....
'''
#Details of example obs file to run test on.
# run = 'PAL2012'
# date = '20121207'
# tstamp = '20121208-074649'
# calTstamp='20121208-070505'
# fluxTstamp='20121208-133002'
run = 'PAL2012'
date = '20121208'
tstamp = '20121209-120530'
centroidTstamp = '20121209-120530'
calTstamp='20121209-131132'
fluxTstamp='20121209-020416'
flatTstamp='20121209-021036'
if doPixRemap==True:
pixRemapFileName = FileName(run=run).pixRemap()
else:
pixRemapFileName = None
#Load up the obs file
obsFileName = FileName(run=run, date=date, tstamp=tstamp)
obsFile = ObsFile(obsFileName.obs())
#Load up associated calibrations
obsFile.loadWvlCalFile(FileName(run=run,date=date,tstamp=calTstamp).calSoln())
obsFile.loadFlatCalFile(FileName(run=run,date=date,tstamp=flatTstamp).flatSoln())
obsFile.loadFluxCalFile(FileName(run=run,date=date,tstamp=fluxTstamp).fluxSoln())
obsFile.loadTimeAdjustmentFile(FileName(run=run,date=date,tstamp=tstamp).timeAdjustments())
obsFile.loadHotPixCalFile(FileName(run=run,date=date,tstamp=tstamp).timeMask())
obsFile.loadCentroidListFile(FileName(run=run,date=date,tstamp=tstamp).centroidList())
#And write out the results....
obsFile.writePhotonList(outputFileName,firstSec,integrationTime,
pixRemapFileName=pixRemapFileName)
obsFN = FileName(run=run,date=date,tstamp=tstamp)
obsPath = obsFN.obs()
flatPath = FileName(run=run,date=date).flatSoln()
hotPath = obsFN.timeMask()
centroidPath = obsFN.centroidList()
fluxPath = FileName(run='PAL2012',date='20121211',tstamp='absolute_021727').fluxSoln()
obs = ObsFile(obsPath)
if not os.path.exists(hotPath):
hp.findHotPixels(obsPath,hotPath)
obs.loadHotPixCalFile(hotPath,switchOnMask=False)
obs.loadBestWvlCalFile()
obs.loadFlatCalFile(flatPath)
obs.loadFluxCalFile(fluxPath)
obs.loadCentroidListFile(centroidPath)
obs.setWvlCutoffs(3000,11000)
centroidRa = '03:37:43.826'
centroidDec = '14:15:14.828'
haOffset = 150.
# imgDict = obs.getPixelCountImage(integrationTime=60,scaleByEffInt=True)
# plotArray(imgDict['image'])
xGuess = 18 #col
yGuess = 15 #row
#cc.centroidCalc(obs,centroidRa,centroidDec,guessTime=300,integrationTime=30,secondMaxCountsForDisplay=2000,HA_offset=haOffset,xyapprox=[xGuess,yGuess],outputFileName=centroidPath)
def testWritePhotonList(outputFileName=None,firstSec=0,integrationTime=-1,doPixRemap=False):
'''
Test run of obsFile.writePhotonList. fileName can be used
to specify the output file name. If not specified, default
name/location is used.
Now includes test for pixel remapping....
'''
#Details of example obs file to run test on.
# run = 'PAL2012'
# date = '20121207'
# tstamp = '20121208-074649'
# calTstamp='20121208-070505'
# fluxTstamp='20121208-133002'
run = 'PAL2013'
date = '20131209'
tstamp = '20131209-115553'
centroidTstamp = tstamp
calTstamp='20131209-132225'
fluxTstamp='ones'
flatTstamp='20131209'
if doPixRemap==True:
pixRemapFileName = FileName(run=run).pixRemap()
else:
pixRemapFileName = None
#Load up the obs file
obsFileName = FileName(run=run, date=date, tstamp=tstamp)
obsFile = ObsFile(obsFileName.obs())
obsFile.loadWvlCalFile(FileName(run=run,date=date,tstamp=calTstamp).calSoln())
obsFile.loadFlatCalFile(FileName(run=run,date=date,tstamp=flatTstamp).flatSoln())
obsFile.loadFluxCalFile(FileName(run=run,date=date,tstamp=fluxTstamp).fluxSoln())
HotPixFile = FileName(run=run,date=date,tstamp=tstamp).timeMask()
if not os.path.exists(HotPixFile): #check if hot pix file already exists
hp.findHotPixels(obsFileName.obs(),HotPixFile)
print "Flux file pixel mask saved to %s"%(HotPixFile)
obsFile.loadHotPixCalFile(HotPixFile)
print "Hot pixel mask loaded %s"%(HotPixFile)
#hz21 location alpha(2000) = 12h 13m 56.42s , delta(2000) = +32d 56' 30.8''
centroid_RA = '12:13:56.42'
centroid_DEC = '32:56:30.8'
CentFile = FileName(run=run,date=date,tstamp=tstamp).centroidList()
#print "checking centroid file", CentFile
#if not os.path.exists(CentFile): #check if cent pix file already exists
cent.centroidCalc(obsFile, centroid_RA, centroid_DEC, outputFileName = CentFile, guessTime=10, integrationTime=10)
# print "Flux file centroid cal saved to %s"%(CentFile)
obsFile.loadCentroidListFile(CentFile)
print "Centroid File loaded %s"%(CentFile)
#Load up associated calibrations
#obsFile.loadTimeAdjustmentFile(FileName(run=run,date=date,tstamp=tstamp).timeAdjustments())
#obsFile.loadHotPixCalFile(FileName(run=run,date=date,tstamp=tstamp).timeMask())
#obsFile.loadCentroidListFile(FileName(run=run,date=date,tstamp=tstamp).centroidList())
#And write out the results....
obsFile.writePhotonList(outputFileName,firstSec,integrationTime,
pixRemapFileName=pixRemapFileName)
#Read the results back in....
#photFile = photList.PhotFile(outputFilename)
print "Wrote photon list file: ", outputFileName
flatTstamp='20131209'
obsFileName = FileName(run=run, date=date, tstamp=tstamp)
obsFile = ObsFile(obsFileName.obs())
frames = []
print '-----------------------'
print tstamp
for i in xrange(30):
print "making frame ", i
frame = obsFile.getFrame(10*i,10)
#plt.matshow(frame,vmin=10000,vmax=40000,cmap=plt.cm.gray)
#plt.show()
frames.append(frame)
makeMovie(frames,frameTitles=np.arange(30)*10,cbar=True,outName='%s.gif'%(tstamp), normMin=400, normMax=4000)
CentFile = FileName(run=run,date=date,tstamp=tstamp).centroidList()
obsFile.loadCentroidListFile(CentFile)
xs = obsFile.centroidListFile.getNode('/centroidlist/xPositions').read()
ys = obsFile.centroidListFile.getNode('/centroidlist/yPositions').read()
plt.figure()
ax1 = plt.subplot(111)
plt.plot(np.arange(len(xs)),xs,label="xs")
plt.plot(np.arange(len(ys)),ys,label='ys')
plt.legend()
plt.title(tstamp)
#plt.show()
plt.savefig(tstamp)
