##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^Lance Simms, Stanford University 2009 ##PlotRamps.py ## ##PURPOSE: ##To plot ramps for a pixel with (Row, Col) for a series of consecutive exposures ##in order to see the effects of persistence. ## ##There are two modes of operation ## 1) Make radial plots around a center spot and show the corresponding ## images ## For this mode, Col, Row, and BoxSize must be defined ## ## 2) Plot the ramps for a set of pixels. ## For this mode, Row and Col must be input as a set of arrays ## ##INPUTS: ## DetStr - 'H1RG-022','H2RG-32-147', or 'H4RG-10-007' ## ElecSt - 'ASIC' or 'LEACH' ## Date - A string containing the date in the path (ex. '07Nov16') ## ObjectName - A string containing the name of the object under study ## Filter - A string designating the filter used: 'G,I,Y' ## NReads - A string with the number of reads in the dark images ## ##KEYWORDS: ## FirstFile - The index of the first read to be plotted ## LastFile - The index of the last read to be plotted ## UseRef - A Boolean; 0-Don't subtract reference 1-Do subtract ## PlotMode - 0 - Plot ramps individually, clearing plot each time ## 1 - Plot all the ramps over each other ## DarkSub - 0 - Don't subtract a dark ## 1 - Subtract a median dark with the same NReads ## FileList - Optionally, all of the files to be examined can ## be specified in this file, one per line ## DoCentroid - 0 - Don't center image around intenisty peak ## 1 - Center the image around intensity ## PlotMode - 0 - Plot The ramps, along with reference pixels below ## 1 - Only plot ramps after ref pixs have been subtracted ## 2 - Only plot the bias read ## PlotTitle - The title to write on the plot ## SaveImg - 0 - Don't save plot ## 1 - Save the plot ## Row - The row(s) of the pixels (either a single int or an array) ## Col - The col(s) of the pixels (either a single int or an array) ## IncLeg - 0 - Don't put a legend on the plot ## - 1 - Put a legend on the plot ##CALLING SEQUENCE: ## run PlotRamps.py [DetStr] [ElecSt] [Date] [ObjectName] [NReads] [Filter] ## ##EXAMPLES: ##________ ##H2RG ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec12' 'NGC2683' 30 'G' --UseRef=1 --LastFile=2 --Col=1530 --Row=1290 ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec12' 'NGC2683' 30 'I' --UseRef=1 --LastFile=2 --Col=1556 --Row=1326 ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec14' 'HorseHead' 30 'G' --UseRef=1 --LastFile=5 Col=272 --Row=325 ## ##H4RG ##run PlotRamps.py 'H4RG-10-007' 'ASIC' '07Apr29' 'M16' 15 'I' --UseRef=0 --LastFile=8 --Col=2875 --Row=2890 --DarkSub=1 ##run PlotRamps.py 'H4RG-10-007' 'ASIC' '07Apr29' 'M16' 20 'G' --UseRef=0 --LastFile=8 --Col=1312 --Row=2100 --DarkSub=1 ##run PlotRamps.py 'H4RG-10-007' 'ASIC' '07Apr26' 'M13' 30 'G' --UseRef=0 --LastFile=8 --Col=2605 --Row=3790 --DarkSub=1 ## ##H2RG_Mars ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec17' 15 'I' 'Mars' --FileList='/nfs/slac/g/ki/ki03/lances/H2RG-32-147/ASIC/MarsBurnedIn/MarsYBandExposures.lst' --Col=1182 --Row=1102 --UseRef=1 ## ##FORWARD BIASED DIODES ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec17' 15 'I' 'ForwardBiasedDiodes' --FileList='/nfs/slac/g/ki/ki03/lances/H2RG-32-147/ForwardBiasedDiodes/NegPersistenceForwardBiasedDiodes1.lst' --Col=912 --Row=1010 --UseRef=1 ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec17' 15 'I' 'ForwardBiasedDiodes' --FileList='/nfs/slac/g/ki/ki03/lances/H2RG-32-147/NegPersistence/NegPersistenceForwardBiasedDiodes2.lst' --Col=882 --Row=1017 --UseRef=1 ##run PlotRamps.py 'H2RG-32-147' 'ASIC' '07Dec17' 15 'I' 'ForwardBiasedDiodes' --FileList='/nfs/slac/g/ki/ki03/lances/H2RG-32-147/ForwardBiasedDiodes/DarksAndForwardBiasedDiodes.lst' --Col=882 --Row=1017 --UseRef=1 ## ##COSMIC RAYS IN SUCCESSIVE DARKS: ##run PlotRamps.py 'H2RG-001' 'ASIC' '08Dec13' 'Dark' '100' 'Blank' --FileList='/nfs/slac/g/ki/ki04/lances/H2RG-001/ASIC/08Dec13/Dark/DarkFiles_160K_5V.txt' --Row=1230 --Col=176 ## ##VSUB EXPERIMENTS ##run PlotRamps.py 'H1RG-022' 'ASIC' '07Nov16' 'VSUB' '100' 'All' --FileList='/nfs/slac/g/ki/ki04/lances/H1RG-022/ASIC/07Nov16/1.5V.txt' --Row=100 --Col=100 ##//////////////////////////////////////////////////////////////////////// ##SETUP execfile('/afs/slac/u/ki/lances/python/python_HxRG/HxRG_Setup.py') execfile('/afs/slac/u/ki/lances/python/SPIEPlotSettings.py') from HxRG_Class import * from ReturnCentroid import * from ReturnRadialAvg import * import TableIO import csv import pdb #Get the filename and options from command line DetStr = sys.argv[1] ElecStr = sys.argv[2] Date = sys.argv[3] ObjectName = sys.argv[4] NReads = sys.argv[5] Filter = sys.argv[6] ##INITIAL SETUP HxRG = HxRG_C(DetStr=DetStr, ElecStr=ElecStr, ObjectName=ObjectName) ##PARSE KEYWORDS keywords = ['FirstFile=','LastFile=','UseRef=','DarkSub=','PlotMode=',\ 'SaveImg=','PlotTitle=','FileList=','Col=', 'Row=', 'IncLeg='] FirstFile = 0 LastFile = 0 UseRef = 0 DarkSub = 0 PlotMode = 0 PlotTitle = '' FileList = '' SaveImg = 0 Col = 100 Row = 100 IncLeg = 0 opts, extraparams = getopt.getopt(sys.argv[7:],'',keywords) for o,p in opts: if o in ['--FirstFile']: FirstFile = int(p) elif o in ['--LastFile']: LastFile = int(p) elif o in ['--UseRef']: UseRef = int(p) elif o in ['--DarkSub']: DarkSub = int(p) elif o in ['--PlotMode']: PlotMode= int(p) elif o in ['--PlotTitle']: PlotTitle = p elif o in ['--FileList']: FileList=p elif o in ['--Col']: Col =int(p) elif o in ['--Row']: Row =int(p) elif o in ['--SaveImg']: SaveImg=int(p) elif o in ['--IncLeg']: IncLeg =int(p) #Form the class that will contain the necessary info HxRG = HxRG_C(DetStr=DetStr, ElecStr=ElecStr, ObjectName=ObjectName, \ Filter=Filter, Date=Date, UseRef=UseRef, NReads=NReads) HxRG.Get_Date(Date) PlotDir = HxRG.DataDir+HxRG.DetStr+'/Plots/NegPersistence/' ##FIND THE MATCHING DARK if DarkSub == 1: HxRG.Get_Median_Dark(HxRG.NReads) DarkHDU = pyfits.open(HxRG.DarkName) if FileList=='': ##FIND THE FILES THAT MATCH THE SEQUENCE IN MIND AND ORDER THEM BY TIME if HxRG.DetStr != 'H4RG-10-007': FitsFiles = sort_files_by_date(HxRG.RawObjectDir+HxRG.ObjectName+'*_'\ +HxRG.Filter+'_*'+NReads+'_Reads_*.fits') else: FitsFiles = sort_files_by_date(HxRG.RawObjectDir+HxRG.ObjectName+'*_'\ +NReads+'_Reads_*.fits') ##SELECT ONLY THE ONES NEEDED if LastFile == 0 : LastFile = len(FitsFiles) FitsFiles = SortFilesByTime(FitsFiles) NumFitsFiles = LastFile-FirstFile FitsFiles = FitsFiles[FirstFile:LastFile] else: ##READ THE FILES IN FROM FILELIST FitsFiles=ReadFileList(FileList) if LastFile == 0 : LastFile = len(FitsFiles) NumFitsFiles = LastFile-FirstFile FitsFiles = FitsFiles[FirstFile:LastFile] #GO THROUGH THE FILES AND PLOT THE PERSISTENCE mplot.close('all') RadFig = mplot.figure(0) RadFig.add_axes([0.05,0.05,0.95,0.7]) ##USE THESE SYMBOLS AND COLORS PSyms = ['r','b','g','m','c','orange'] PlotHandles = [] LegendLabs = [r'\textbf{Time\ \ \ \ \ \ \ \ \ \ \ Slope'+\ '\ \ \ \ Error}'] LegendSyms = [''] FiltersArr = [] FiltersStr = '' ##GO THROUGH THE FILES IN SEQUENCE for FileNum, FitsFileName in zip(arange(NumFitsFiles), FitsFiles): print 'FileNum: '+str(FileNum) FitsHDU = pyfits.open(FitsFileName) HxRG = HxRG_C(FitsFileName=FitsFileName, ObjectName=ObjectName) HxRG.Get_Raw_Header(FitsFileName) ThisRamp = zeros(HxRG.NAxis3, dtype=float64) print 'Analysing File :' + FitsFileName if UseRef: ThisRefRamp = ReturnRSRamp(FitsHDU, Row, Col, HxRG=HxRG) else: ThisRefRamp = zeros(HxRG.NAxis3, dtype=float64) for ReadNum in arange(HxRG.NAxis3): ThisRead = FitsHDU[0].section[ReadNum,Row,Col]+float(HxRG.BZero) ThisRamp[ReadNum] = ThisRead[0] ##Now try to determine C_Fac by finding the straightest line HxRG.CFac = 1.0 ThisRamp = ThisRamp-HxRG.CFac*ThisRefRamp ##Clear the plot on the first file if FileNum == 0: mplot.clf() Fig = mplot.figure(0) Fig.add_axes([0.100,0.100,0.875,0.750]) ##Plot the ramp if PlotMode == 0 : m,b,Error,CosE = Linefit(arange(len(ThisRamp)),ThisRamp, RejectCos=0) if NumFitsFiles < 6: mplot.plot(ThisRamp, PSyms[FileNum]) ThisP=mplot.plot(arange(len(ThisRamp))*m+b, PSyms[FileNum]+'--') else: mplot.plot(ThisRamp) ThisP=mplot.plot(arange(len(ThisRamp))*m+b, '--') mplot.xlabel('Read Number') mplot.ylabel('ADU (Raw)') mStr = "%.2f" % m ErrStr = "%.2f" % Error[0] LegendLabs.append(HxRG.Time+'\ \ \ \ \ '+mStr+'\ \ \ \ \ '+ErrStr) LegendSyms.append(ThisP[0]) if FileNum==NumFitsFiles-1: if IncLeg == 1: mplot.legend(LegendSyms,LegendLabs,loc=2) mplot.xlabel('Read Number') mplot.ylabel('ADU (Raw)') thisylim=ylim() ax2=twiny() xlim(0, HxRG.ITime) ylim(thisylim[0],thisylim[1]) mplot.xlabel('Time (Seconds)') mplot.figtext(.7,.2, 'Row : ' +str(Row)) mplot.figtext(.7,.15,'Col : ' +str(Col)) gca().yaxis.set_major_formatter(ScalarFormatter(useOffset=False)) if PlotTitle != '': mplot.figtext(0.55,0.95,PlotTitle, \ horizontalalignment='center',fontsize=14) else : mplot.clf() mplot.subplot(211) mplot.plot(ThisRamp, 'k') mplot.figtext(.5,.95,strip_sc(BaseName), fontsize=10, horizontalalignment='center') mplot.figtext(.7,.4, 'Row : ' +str(Row)) mplot.figtext(.7,.35,'Col : ' +str(Col)) mplot.ylabel('Sci. Pixel ADU', horizontalalignment='right') mplot.subplot(212) mplot.plot(ThisRefRamp, 'k') mplot.ylabel('Ref. Pixel ADU') mplot.xlabel('Read Number') #Save the file if requested if SaveImg==1: PlotDir=HxRG.DataDir+HxRG.DetStr+'/'+'Plots/Ramps/' mplot.savefig(PlotDir+HxRG.RawObjectKey+'_'+str(Row)+'_'+str(Col)+'.png')