##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^Lance Simms, Stanford University 2009 ##ExaminePhotonTransfer.py ## ##PURPOSE: ## To examine the shot noise and fixed pattern noise as a function ## of signal. ## ##INPUTS: ## FitsFileName1, FitsFileName2 : string ## The full path to the two fits files that contains the ## uniform illumination ##KEYWORDS: ## XStart: int ## X start coordinate for region of interest ## XStop: int ## X stop coordinate for region of interest ## YStart: int ## Y start coordinate for region of interest ## YStop: int ## Y stop coordinate for region of interest ## UseRef: int ## A Boolean; 0-Don't subtract reference 1-Do subtract ## CFac: float ## The multiplicative factor for reference pix subtraction ## ReadNoise: float ## The readnoise value to subtract from the shot noise curve ## Mode: int ## 0 - Examine region of pixels ## DarkSub: int ## 0 - Don't subtract a dark ## 1 - Subtract a median dark with the same NReads ## TvFlag: int ## 0 - Don't plot ## 1 - Plot ## 2 - Plot Ramps and Deltas ## AllReads: int ## 0 - Collect data only for read specified by ReadNum ## 1 - Collect data for all reads in all exposures ## ##CALLING SEQUENCE: ## run ExaminePhotonTransfer.py [FitsFileName1] [FitsFileName2] ## ##EXAMPLES: ## ##Extremely good linearity: ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec19/Flat/Flat_Y_H2RG_SIPIN_30_Reads_Dec19_2007_18_50_12.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec19/Flat/Flat_Y_H2RG_SIPIN_30_Reads_Dec19_2007_18_51_07.fits' --YStart=1000 --YStop=1450 --XStart=1470 --XStop=1700 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ## ##ASIC: ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_Y_H2RG_SIPIN_30_Reads_Dec15_2007_21_22_17.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_Y_H2RG_SIPIN_30_Reads_Dec15_2007_21_23_10.fits' --YStart=1000 --YStop=1100 --XStart=1500 --XStop=1600 --TvFlag=0 --Mode=0 --UseRef=0 ## ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec15_2007_20_59_53.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec15_2007_21_00_45.fits' --YStart=1400 --YStop=2000 --XStart=1100 --XStop=1500 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec19/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec19_2007_18_43_47.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec19/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec19_2007_18_44_39.fits' --YStart=1000 --YStop=1450 --XStart=1470 --XStop=1700 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec15_2007_21_01_39.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec15/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec15_2007_21_02_31.fits' --YStart=1000 --YStop=1450 --XStart=1470 --XStop=1700 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec12/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec13_2007_00_46_17.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec12/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec13_2007_00_47_10.fits' --YStart=100 --YStop=500 --XStart=100 --XStop=500 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec12/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec13_2007_00_46_17.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/ASIC/07Dec12/Flat/Flat_G_H2RG_SIPIN_30_Reads_Dec13_2007_00_47_10.fits' --YStart=1600 --YStop=2000 --XStart=1600 --XStop=2000 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ## ## ##LEACH ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/LEACH/2007Dec15/Flat/Flat_G_Filter_2.fits' '/nfs/slac/g/ki/ki04/lances/H2RG-32-147/LEACH/2007Dec15/Flat/Flat_G_Filter_3.fits' --YStart=100 --YStop=500 --XStart=100 --XStop=500 --TvFlag=0 --Mode=0 --UseRef=0 --CFac=1.45 ##H1RG====================================== ##LEACH ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_Y_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_Y_7.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_I_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_I_7.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_G_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov14/Flat/Flat_G_7.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_Y_Filter_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_Y_Filter_7.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_I_Filter_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_I_Filter_7.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_G_Filter_6.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/LEACH/2007Nov18/Flat/Flats_G_Filter_7.fits' --YStart=600 --YStop=800 --XStart=600 --XStop=800 ##ASIC ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_Y_H1RG_SIPIN_15_Reads_Nov17_2007_06_01_44.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_Y_H1RG_SIPIN_15_Reads_Nov17_2007_06_02_01.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_G_H1RG_SIPIN_15_Reads_Nov17_2007_05_54_49.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_G_H1RG_SIPIN_15_Reads_Nov17_2007_05_55_06.fits' --YStart=300 --YStop=700 --XStart=512 --XStop=970 --UseRef=1 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_G_H1RG_SIPIN_15_Reads_Nov17_2007_05_56_32.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_G_H1RG_SIPIN_15_Reads_Nov17_2007_05_56_50.fits' --YStart=300 --YStop=700 --XStart=512 --XStop=970 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_I_H1RG_SIPIN_15_Reads_Nov17_2007_05_49_13.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/Flat_I_H1RG_SIPIN_15_Reads_Nov17_2007_05_49_30.fits' --YStart=300 --YStop=700 --XStart=512 --XStop=970 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov19/Flat_Y_H1RG_SIPIN_15_Reads_Nov19_2007_19_52_08.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov19/Flat_Y_H1RG_SIPIN_15_Reads_Nov19_2007_19_52_27.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##run ExaminePhotonTransfer.py '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov19/Flat_G_H1RG_SIPIN_15_Reads_Nov19_2007_19_46_22.fits' '/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov19/Flat_G_H1RG_SIPIN_15_Reads_Nov19_2007_19_46_41.fits' --YStart=500 --YStop=800 --XStart=500 --XStop=800 ##THESIS PLOTS: ## ## ##SETUP execfile('/afs/slac/u/ki/lances/python/python_HxRG/HxRG_Setup.py') execfile('/afs/slac/u/ki/lances/python/SPIEPlotSettings.py') PlotDir = '/nfs/slac/g/ki/ki04/lances/LSST/KPNO/Latex/Thesis/NoiseVsSignal/Figures/' from HxRG_Class import * from ReturnCentroid import * from ReturnRadialAvg import * from Djs_Iterstat import * from ReadNoise import * import TableIO import csv import pdb import asciidata #Get the filename and options from command line FitsFileName1 = sys.argv[1] FitsFileName2 = sys.argv[2] ##INITIAL SETUP HxRG1 = HxRG_C(FitsFileName=FitsFileName1) HxRG2 = HxRG_C(FitsFileName=FitsFileName2) ##PARSE KEYWORDS keywords = ['XStart=', 'XStop=', 'YStart=', 'YStop=',\ 'UseRef=','DarkSub=','Mode=',\ 'TvFlag=', 'Verbose=', \ 'CFac=', 'ReadNoise='] XStart = 4 XStop = HxRG1.FNAxis1-5 YStart = 4 YStop = HxRG1.FNAxis2-5 UseRef = 0 DarkSub = 0 Mode = 0 TvFlag = 0 Verbose = 1 CFac = -1 ReadNoise = 8.0 opts, extraparams = getopt.getopt(sys.argv[3:],'',keywords) for o,p in opts: if o in ['--XStart']: XStart =int(p) elif o in ['--XStop']: XStop =int(p) elif o in ['--YStart']: YStart = int(p) elif o in ['--YStop']: YStop = int(p) elif o in ['--UseRef']: UseRef = int(p) elif o in ['--DarkSub']: DarkSub = int(p) elif o in ['--Mode']: Mode= int(p) elif o in ['--CenSize']: CenSize = int(p) elif o in ['--TvFlag']: TvFlag = int(p) elif o in ['--Verbose']: TrackStar = int(p) elif o in ['--CFac']: CFac = float(p) elif o in ['--ReadNoise']: ReadNoise = float(p) ##FIND THE MATCHING DARK if DarkSub == 1: HxRG.Get_Median_Dark(HxRG.NReads) DarkHDU = pyfits.open(HxRG.DarkName) ##GO THROUGH THE FILES AND PLOT THE PERSISTENCE if TvFlag > 0: mplot.close('all') Fig = mplot.figure(0) ##GET THE FIRST DATACUBE.......................................... ##Get the slope and the slope header FitsHDU = pyfits.open(FitsFileName1) HxRG1.Get_Raw_Header(FitsFileName1) #Get the Bias Read and allow for dark subtraction Im1 = FitsHDU[0].section[:,:,:] if UseRef == 1: if CFac == -1: HxRG1.CFac = 3.1 HxRG1.CFac = 1.5 HxRG1.CFac = 1.45 if HxRG1.DetStr == 'H2RG-001': HxRG1.CFac = 2.0 else: HxRG1.CFac = CFac Im1 = ReturnRSCube(Im1, HxRG1.CFac, BadCols=HxRG1.BadCols) if DarkSub == 1: Dark = DarkHDU[0].section[0:,:,:] Im1 = Im1 -Dark ##GET THE VARIANCE DATACUBE========== ##Get the slope and the slope header HxRG2.Get_Raw_Header(FitsFileName2) FitsHDU = pyfits.open(FitsFileName2) Im2 = FitsHDU[0].section[:,:,:] Header2 = FitsHDU[0].header if UseRef == 1: Im2 = ReturnRSCube(Im2, HxRG1.CFac, BadCols=HxRG1.BadCols) if DarkSub == 1: Dark = DarkHDU[0].section[0:,:,:] Im2 = Im2 -Dark ##Find the full range of pixels being considered XRange = XStop - XStart YRange = YStop - YStart if Mode == 0: MeanADUArr1 = zeros(HxRG1.NAxis3-1, dtype=float32) MeanADUArr2 = zeros(HxRG1.NAxis3-1, dtype=float32) SigADUArr1 = zeros(HxRG1.NAxis3-1, dtype=float32) #Total Noise SigADUArr2 = zeros(HxRG1.NAxis3-1, dtype=float32) #Total Noise SigADUArrD = zeros(HxRG1.NAxis3-1, dtype=float32) #Read Noise + ShotNoise SNRNADUArr = zeros(HxRG1.NAxis3-1, dtype=float32) #Read Noise + ShotNoise SNADUArr = zeros(HxRG1.NAxis3-1, dtype=float32) #ShotNoise Alone FPADUArr = zeros(HxRG1.NAxis3-1, dtype=float32) #Fixed Pattern Noise for ReadNum in arange(HxRG1.NAxis3-1)+1: ThisIm1 = Im1[ReadNum, YStart:YStop, XStart:XStop]-\ Im1[0, YStart:YStop, XStart:XStop] ThisIm2 = Im2[ReadNum, YStart:YStop, XStart:XStop]-\ Im2[0, YStart:YStop, XStart:XStop] ThisDiff = ThisIm2-ThisIm1 if TvFlag > 0 : #Histogram and find FWHM NBins = int(ThisVar.max()-ThisVar.min()) MinNoise = ThisVar.min() Bins = arange(NBins)+MinNoise Bins, N = histOutline.histOutline(ThisVar, binsIn=Bins) mplot.figure(2) mplot.clf() ThisP = mplot.plot(Bins,N, 'o') print 'Read Number : ' + str(ReadNum) pdb.set_trace() Mean1, Sig1, Med1, Mode1, Mask1 = \ Djs_Iterstat(ThisIm1, RejVal=-100000., SigRej=3.5) Mean2, Sig2, Med2, Mode2, Mask2 = \ Djs_Iterstat(ThisIm2, RejVal=-100000., SigRej=3.5) MeanD, SigD, MedD, ModeD, MaskD = \ Djs_Iterstat(ThisDiff, RejVal=-100000., SigRej=3.5) Mean1 = ThisIm1.mean() Mean2 = ThisIm2.mean() MeanD = ThisDiff.mean() Sig1 = ThisIm1.std() Sig2 = ThisIm2.std() SigD = ThisDiff.std() MeanADUArr1[ReadNum-1] = Mean1 MeanADUArr2[ReadNum-1] = Mean2 SigADUArr1[ReadNum-1] = Sig1 SigADUArr2[ReadNum-1] = Sig2 SigADUArrD[ReadNum-1] = SigD/sqrt(2) SNRNADUArr[ReadNum-1] = SigD/sqrt(2) SNADUArr[ReadNum-1] = sqrt((SigD/sqrt(2))**2-ReadNoise**2) FPADUArr[ReadNum-1] = sqrt(Sig1**2-(SigD/sqrt(2))**2) mplot.figure(0) mplot.clf() mplot.plot(MeanADUArr1, SigADUArr1**2, 'b') mplot.plot(MeanADUArr1, SigADUArr1**2, 'bo') mplot.plot(MeanADUArr2, SigADUArr2**2, 'r') mplot.plot(MeanADUArr2, SigADUArr2**2, 'ro') mplot.figure(1) mplot.clf() mplot.plot(MeanADUArr1, SigADUArrD**2, 'b') mplot.plot(MeanADUArr1, SigADUArrD**2, 'bo') m, b, E, CosE = Linefit(MeanADUArr1, SigADUArrD**2, RejectCos=0) mplot.plot(MeanADUArr1, m*MeanADUArr1+b, 'r--') Fig=mplot.figure(2) mplot.clf() Ax1=Fig.add_axes([0.08,0.12,0.90,0.85]) mplot.loglog(MeanADUArr1, SNADUArr, 'b', linewidth=2) mplot.loglog(MeanADUArr1, SNADUArr, 'bo', label=r'\textbf{Shot Noise}', \ markersize=6, markeredgewidth=1) mplot.loglog(MeanADUArr1, FPADUArr, 'r', linewidth=2) mplot.loglog(MeanADUArr1, FPADUArr, 'ro', label=r'\textbf{Fixed Pattern Noise}', \ markersize=6, markeredgewidth=1) mplot.loglog(MeanADUArr1, SigADUArr1, 'g', linewidth=2) mplot.loglog(MeanADUArr1, SigADUArr1, 'go', label=r'\textbf{Total Noise}', \ markersize=6, markeredgewidth=1) xvals = arange(100000)+1 mplot.loglog(xvals, .0095*xvals,'k--', label=r'\textbf{Slope =\ 1}', linewidth=3) mplot.loglog(xvals, (.26*xvals**.5), 'k-.', label=r'\textbf{Slope = 1/2}', linewidth=3) ylim(4, 300) xlim(500, 2.5e4) xlabel(r'\textbf{Signal (ADU)}') ylabel(r'\textbf{RMS Noise (ADU)}') mplot.legend(loc=2, numpoints=1) mplot.grid(True, which='minor') SaveImg = 0 if SaveImg == 1: if UseRef == 0: mplot.savefig(PlotDir+'NoiseVsSignal_'+HxRG.DetStr+\ '_X_'+str(XStart)+'_'+str(XStop)+\ '_Y_'+str(YStart)+'_'+str(YStop)+\ '_CFAC_'+str(HxRG.CFac)+'.png') mplot.savefig(PlotDir+'NoiseVsSignal_'+HxRG.DetStr+\ '_X_'+str(XStart)+'_'+str(XStop)+\ '_Y_'+str(YStart)+'_'+str(YStop)+\ '_CFAC_'+str(HxRG.CFac)+'.eps') else: mplot.savefig(PlotDir+'NoiseVsSignal_RPS_'+HxRG.DetStr+\ '_X_'+str(XStart)+'_'+str(XStop)+\ '_Y_'+str(YStart)+'_'+str(YStop)+\ '_CFAC_'+str(HxRG.CFac)+'.png') mplot.savefig(PlotDir+'NoiseVsSignal_RPS_'+HxRG.DetStr+\ '_X_'+str(XStart)+'_'+str(XStop)+\ '_Y_'+str(YStart)+'_'+str(YStop)+\ '_CFAC_'+str(HxRG.CFac)+'.eps')