def centroidObs(obsPath,centroidPath,centroidRa,centroidDec,haOffset,xGuess,yGuess,hotPath,flatPath):
obs = ObsFile(obsPath)
print obsPath,obs.getFromHeader('exptime'),obs
if not os.path.exists(hotPath):
hp.findHotPixels(obsFile=obs,outputFileName=hotPath)
obs.loadHotPixCalFile(hotPath,switchOnMask=False)
obs.loadBestWvlCalFile()
obs.loadFlatCalFile(flatPath)
obs.setWvlCutoffs(3000,8000)
cc.centroidCalc(obs,centroidRa,centroidDec,guessTime=300,integrationTime=30,secondMaxCountsForDisplay=2000,HA_offset=haOffset,xyapprox=[xGuess,yGuess],outputFileName=centroidPath)
print 'done centroid',centroidPath
del obs
def centroidObs(obsPath,centroidPath,centroidRa,centroidDec,haOffset,xGuess,yGuess):
obs = ObsFile(obsPath)
print obsPath,obs.getFromHeader('exptime'),obs
obs.loadAllCals()
# obs.loadBestWvlCalFile()
# obs.loadFlatCalFile(flatPath)
obs.setWvlCutoffs(3000,11000)
# if not os.path.exists(hotPath):
# hp.findHotPixels(obsFile=obs,outputFileName=hotPath,display=True,fwhm=2.,boxSize=5, nSigmaHot=4.0,)
# obs.loadHotPixCalFile(hotPath,switchOnMask=True)
cc.centroidCalc(obs,centroidRa,centroidDec,guessTime=300,integrationTime=30,secondMaxCountsForDisplay=2000,HA_offset=haOffset,xyapprox=[xGuess,yGuess],outputFileName=centroidPath,usePsfFit=True,radiusOfSearch=8)
print 'done centroid',centroidPath
del obs
obsFN = FileName(run=run,date=date,tstamp=tstamp)
obsPath = obsFN.obs()
flatPath = FileName(run=run,date=date).flatSoln()
hotPath = obsFN.timeMask()
centroidPath = obsFN.centroidList()
obs = ObsFile(obsPath)
if not os.path.exists(hotPath):
hp.findHotPixels(obsPath,hotPath)
obs.loadHotPixCalFile(hotPath,switchOnMask=False)
obs.loadBestWvlCalFile()
obs.loadFlatCalFile(flatPath)
obs.setWvlCutoffs(3000,8000)
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
def main(testRun=False):
#INPUTS:
# - testRun : If True, run only a single exposure.
#Try remapping the pixels - set to None to not do this....
pixRemapFileName = FileName(run='PAL2012').pixRemap()
obsSequence0="""
051516
052018
052520
"""
obsSequence1="""
033323
033825
034327
034830
035332
035834
040336
040838
041341
041843
042346
042848
043351
043853
044355
044857
045359
045902
"""
obsSequence2="""
050404
050907
051409
051912
052414
052917
053419
053922
"""
# 054424 - repointed mid-exposure, leave out for now.
obsSequence3="""
054926
055428
055930
060432
060934
061436
061938
062440
062942
"""
run = 'PAL2012'
obsSequences = [obsSequence0,obsSequence1,obsSequence2,obsSequence3]
#If test run is requested, override and just run one test exposure.
if testRun is True:
obsSequences = ['9999999',
'''
033323
''',
'9999999',
'9999999']
wvlCals = ['051341','063518','063518','063518']
flatCals = ['20121211','20121211','20121211','20121211']
#fluxCalDates = ['20121206','20121206','20121206','20121206']
#fluxCals = ['20121207-072055','20121207-072055','20121207-072055','20121207-072055']
fluxCalDates = ['20121211','20121211','20121211','20121211']
fluxCals = ['absolute_021727','absolute_021727','absolute_021727','absolute_021727']
#Row coordinate of center of crab pulsar for each obsSequence
centersRow = [9,30,29,10]
#Col coordinate of center of crab pulsar for each obsSequence
centersCol = [13,30,30,14]
centerRA = '05:34:31.93830'
centerDec = '+22:00:52.1758'
obsUtcDate = '20121212'
obsUtcDates = ['20121206','20121212','20121212','20121212']
obsFileNames = []
obsFileNameTimestamps = []
wvlFileNames = []
flatFileNames = []
fluxFileNames = []
timeMaskFileNames = []
centroidFileNames = []
for iSeq in range(len(obsSequences)):
obsSequence = obsSequences[iSeq]
obsSequence = obsSequence.strip().split()
obsFileNameTimestamps.append(obsSequence)
obsUtcDate = obsUtcDates[iSeq]
sunsetDate = str(int(obsUtcDate)-1)
obsSequence = [obsUtcDates[iSeq]+'-'+ts for ts in obsSequence]
obsFileNames.append([FileName(run=run,date=sunsetDate,tstamp=ts).obs() for ts in obsSequence])
timeMaskFileNames.append([FileName(run=run,date=sunsetDate,tstamp=ts).timeMask() for ts in obsSequence])
centroidFileNames.append([FileName(run=run,date=sunsetDate,tstamp=ts).centroidList() for ts in obsSequence])
wvlCalTstamp = obsUtcDate+'-'+wvlCals[iSeq]
wvlFileNames.append(FileName(run=run,date=sunsetDate,tstamp=wvlCalTstamp).calSoln())
fluxFileNames.append(FileName(run=run,date=fluxCalDates[iSeq],tstamp=fluxCals[iSeq]).fluxSoln())
flatFileNames.append(FileName(run=run,date=flatCals[iSeq]).illumSoln()) # *** CURRENTLY USES ILLUMINATION SOLUTION! ***
centroidFileNames.append(FileName(run=run,date=sunsetDate,tstamp=ts).centroidList())
# #Make hot pixel masks if needed
# for iSeq,obsSequence in enumerate(obsSequences):
# obsSequence = obsSequence.strip().split()
# print obsSequence
# for iOb,obs in enumerate(obsSequence):
# timeMaskFileName = timeMaskFileNames[iSeq][iOb]
# if os.path.exists(obsFileNames[iSeq][iOb]) and not os.path.exists(timeMaskFileName):
# print 'Running hotpix for ',obs
# hp.findHotPixels(obsFileNames[iSeq][iOb],timeMaskFileName)
# print "Flux file pixel mask saved to %s"%(timeMaskFileName)
# else:
# print 'Skipping hot pixel mask creation for file '+obsFileNames[iSeq][iOb]
#apertureRadius = 4
obLists = [[ObsFile(fn)for fn in seq if os.path.exists(fn)] for seq in obsFileNames]
tstampFormat = '%H:%M:%S'
#print 'fileName','headerUnix','headerUTC','logUnix','packetReceivedUnixTime'
print '---------Making hot pixel masks/getting centroids-----------'
for iSeq,obList in enumerate(obLists):
for iOb,ob in enumerate(obList):
timeAdjFileName = FileName(run='PAL2012').timeAdjustments()
wvlCalFileName = wvlFileNames[iSeq]
flatCalFileName = flatFileNames[iSeq]
fluxCalFileName = fluxFileNames[iSeq]
timeMaskFileName = FileName(obsFile=ob).timeMask() #timeMaskFileNames[iSeq][iOb]
centroidFileName = FileName(obsFile=ob).centroidList()
if not os.path.exists(centroidFileName) or not os.path.exists(timeMaskFileName):
print 'Loading calibration files:'
print [os.path.basename(x) for x in [timeAdjFileName,wvlCalFileName,flatCalFileName, \
fluxCalFileName,timeMaskFileName, centroidFileName]]
ob.loadTimeAdjustmentFile(timeAdjFileName)
ob.loadWvlCalFile(wvlCalFileName)
ob.loadFlatCalFile(flatCalFileName)
ob.loadFluxCalFile(fluxCalFileName)
ob.setWvlCutoffs(3000.,12000.) #Keep most of the wavelength range for the purposes of centroiding/hot pixel detection.
if not os.path.exists(timeMaskFileName):
print 'Running hotpix for ',ob.fileName
#Run hot pixel detection on *calibrated* file.
#But don't use flux weighting, as this scales by a large amount, and throws
#the poisson statistics way too much. (i.e., we really need to use
#counts *detected* for shot noise statistics, rather than
#estimated counts above the atmosphere....)
hp.findHotPixels(obsFile=ob,outputFileName=timeMaskFileName,
useRawCounts=False,weighted=True,fluxWeighted=False)
print "Flux file pixel mask saved to %s"%(timeMaskFileName)
else:
print 'Skipping hot pixel mask creation for file '+obsFileNames[iSeq][iOb]
if not os.path.exists(centroidFileName):
ob.loadHotPixCalFile(timeMaskFileName)
print 'Running CentroidCalc for ',ob.fileName
cc.centroidCalc(ob, centerRA, centerDec, outputFileName=centroidFileName,
guessTime=300, integrationTime=30, secondMaxCountsForDisplay=500,
xyapprox=[centersCol[iSeq],centersRow[iSeq]])
print "Centroiding calculations saved to %s"%(centroidFileName)
else:
print "Centroid file already exists - skipping: "+centroidFileName