from util.FileName import FileName
from util.popup import plotArray
import astrometry.CentroidCalc as cc
from photonlist.photlist import writePhotonList
from headers.ArconsHeaders import PulsarPhotonList
if __name__=='__main__':
run = 'PAL2014'
date = '20140924'
tstamp = '20140925-112538'
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'
def main():
#open the sky file for hr9087
run = 'PAL2012'
date = '20121210'
wvlCal = '20121211-052230'
obsTimestamp = '20121211-051650'
flatCalDate = '20121211'
flatCalTstamp = '20121212-074700'
obsFN = FileName(run=run,date=date,tstamp=obsTimestamp)
obsFileName = obsFN.obs()
timeMaskFileName = obsFN.timeMask()
wvlFileName = FileName(run=run,date=date,tstamp=wvlCal).calSoln()
flatFileName = FileName(run=run,date=flatCalDate,tstamp=flatCalTstamp).flatSoln()
if not os.path.exists(timeMaskFileName):
print 'Running hotpix for ',obsFileName
hp.findHotPixels(obsFileName,timeMaskFileName)
print "Flux file pixel mask saved to %s"%(timeMaskFileName)
obs = ObsFile(obsFileName)
obs.loadTimeAdjustmentFile(FileName(run='PAL2012').timeAdjustments())
obs.loadWvlCalFile(wvlFileName)
obs.loadFlatCalFile(flatFileName)
obs.loadHotPixCalFile(timeMaskFileName)
#obs.setWvlCutoffs(4000,8000)
#get image before and after flat cal
print 'getting images'
beforeImgDict = obs.getPixelCountImage(weighted=False,fluxWeighted=False,scaleByEffInt=True)
rawCubeDict = obs.getSpectralCube(weighted=False)
rawCube = np.array(rawCubeDict['cube'],dtype=np.double)
effIntTime = rawCubeDict['effIntTime']
maxIntTime = np.max(effIntTime)
#add third dimension for broadcasting
effIntTime3d = np.reshape(effIntTime,np.shape(effIntTime)+(1,))
rawCube *= maxIntTime / effIntTime3d
rawCube[np.isnan(rawCube)] = 0
rawCube[rawCube == np.inf] = 0
beforeImg = np.sum(rawCube,axis=-1)
print 'finished first cube'
flatCubeDict = obs.getSpectralCube(weighted=True)
flatCube = np.array(flatCubeDict['cube'],dtype=np.double)
effIntTime = flatCubeDict['effIntTime']
maxIntTime = np.max(effIntTime)
#add third dimension for broadcasting
effIntTime3d = np.reshape(effIntTime,np.shape(effIntTime)+(1,))
flatCube *= maxIntTime / effIntTime3d
flatCube[np.isnan(flatCube)] = 0
flatCube[flatCube == np.inf] = 0
afterImg = np.sum(flatCube,axis=-1)
plotArray(title='before flatcal',image=beforeImg)
plotArray(title='after flatcal',image=afterImg)
print 'before sdev',np.std(beforeImg[afterImg!=0])
print 'after sdev',np.std(afterImg[afterImg!=0])
np.savez('flatCubeGem.npz',beforeImg=beforeImg,afterImg=afterImg,rawCube=rawCube,flatCube=flatCube)
# test the theory that that extra photons show up 23 clock ticks
# after the beginning of each second. Plot properties of the photons
offsets = [23, 100, 1234, 54321]
#offsets = [23]
beginTime = 0
expTime = 300
pickleFile = open("csb2.pkl","wb")
fn = FileName(run, sundownDate, obsDate+"-"+seq)
pickle.dump(fn,pickleFile)
obsFile = ObsFile(fn.obs())
obsFile.loadTimeAdjustmentFile(FileName(run=run).timeAdjustments()) # Matt's time fix
timeMaskFile = fn.timeMask()
if os.path.exists(timeMaskFile):
obsFile.loadHotPixCalFile(timeMaskfile, switchOnMask=True)
if False:
iRow0 = 25
iRow1 = iRow0+1
iCol0 = 40
iCol1 = iCol0+1
else:
iRow0 = 0
iRow1 = obsFile.nRow
iCol0 = 0
iCol1 = obsFile.nCol
#obsTimestamp ='20140925-124809' #early twilight
#obsTimestamp ='20140925-124912' #early twilight
#obsTimestamp ='20140925-125015' #late twilight
#obsTimestamp ='20140925-125118' #late twilight
#obsTimestamp ='20140925-125221' #late twilight
#obsTimestamp ='20140925-125324' #late twilight
#obsTimestamp ='20140925-125427' #late twilight
#date = '20140925'
#obsTimestamp ='20140926-104528' #psr J0337
obsFN = FileName(run=run,date=date,tstamp=obsTimestamp)
obsFileName = obsFN.obs()
print obsFileName
timeMaskFileName = obsFN.timeMask()
if wvlCal != '':
wvlFileName = FileName(run=run,date=date,tstamp=wvlCal).calSoln()
flatFileName = FileName(run=run,date=flatCalDate,tstamp=flatCalTstamp).flatSoln()
illumFileName = FileName(run=run,date=flatCalDate,tstamp=flatCalTstamp).illumSoln()
if not os.path.exists(timeMaskFileName):
print 'Running hotpix for ',obsFileName
hp.findHotPixels(inputFileName=obsFileName,outputFileName=timeMaskFileName)
print "Flux file pixel mask saved to %s"%(timeMaskFileName)
obs = ObsFile(obsFileName)
exptime = obs.getFromHeader('exptime')
#obs.loadTimeAdjustmentFile(FileName(run='PAL2012').timeAdjustments())
if wvlCal != '':
