##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^Lance Simms, Stanford University 2009 ##PURPOSE: ## To retrieve the values from the LeakyPixel MySQL database ## ## Make sure the database is running with the following commands: ## ## cd /u2/ki/software/mysql-5.0.45-linux-i686-icc-glibc23/ ## sudo ./bin/mysqld_safe -u root & ## ## The tables in the LeakyPix database have the format of ## [DetStr]_[ElecStr] ## where the DetStr, ElecSTr, and WM are defined as inputs. ## ##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') ## NReads - A string with the number of reads in the dark images ## ##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 ## FirstFile: int ## The index of the first read to be plotted (starting at zero) ## LastFile: int ## The index of the last read to be plotted ## UseRef: int ## 0-Don't subtract reference ## 1-Do subtract ## MaxRows: int ## The number of rows to be extracted from the database ## QueryString: string ## The stipulation of the MySQL query. This can be a limit on ## ADU (Single Hit Value) or ADU3 (The sum of all 9 pixels in the box). ## Example: "WHERE ADU < 150" ## FormMaster: int ## 0 - Don't write any new tables to the database ## 1 - Make a new table with the pixels that appear leaky in every ## exposure. This will be the master table ## ##CALLING SEQUENCE: ## run FE55_Create_Database.py [DetStr] [ElecStr] [ ## ##EXAMPLES: ##run LeakyPix_Extract_Database.py 'H2RG-32-147' 'ASIC' '07Dec12' '15.0000' --XStart=200 --XStop=400 --YStart=200 --YStop=400 ## ##run LeakyPix_Extract_Database.py 'H2RG-32-147' 'ASIC' '07Dec12' '15.0000' --XStart=200 --XStop=400 --YStart=200 --YStop=400 --QueryString='WHERE ADU < 150' ## ##///////////////////////////////////////////////////////////////// ##SETUP execfile('/afs/slac/u/ki/lances/python/python_HxRG/HxRG_Setup.py') from HxRG_Class import * #Get the filename and options from command line DetStr = sys.argv[1] ElecStr = sys.argv[2] Date = sys.argv[3] NReads = sys.argv[4] ObjectName = 'Fe55' #Form the class that will contain the necessary info HxRG = HxRG_C(DetStr=DetStr, ElecStr=ElecStr, ObjectName = ObjectName) HxRG.Get_Date(Date) #Now parse the command line keyword arguments keywords = ['XStart=', 'XStop=', 'YStart=', 'YStop=', 'FirstFile=', 'LastFile=', 'UseRef=', 'MaxRows=',\ 'QueryString=','FormMaster='] XStart = 4 XStop = HxRG.FNAxis1-5 YStart = 4 YStop = HxRG.FNAxis2-5 FirstFile = 0 LastFile = 0 UseRef = 0 MaxRows = 0 QueryString = '' FormMaster = 0 opts, extraparams = getopt.getopt(sys.argv[5:],'',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 ['--FirstFile']: FirstFile = int(p) elif o in ['--LastFile']: LastFile = int(p) elif o in ['--UseRef']: UseRef = int(p) elif o in ['--MaxRows']: MaxRows = int(p) elif o in ['--QueryString']: QueryString=p elif o in ['--FormMaster']: FormMaster = int(p) ##CONNECT***************************************************************** ##Open up the connection and include some error handling try: conn=MySQLdb.connect (host="localhost", user="root", passwd="mysql", db="test", unix_socket="/tmp/mysql.sock") except MySQLdb.Error, e: print "Error $d: $s" % (e.args[0],e.args[1]) sys.exit ##OPEN DATABASE************************************************* ##Create the cursor object to handle manipulations cursor=conn.cursor() TableName = HxRG.DetStrMySQL+'_'+HxRG.ElecStr try: cursor.execute("use LeakyPix") except MySQLdb.Error, e: print "Database does not exist" #Get all of the data from the database conn.query("SELECT X, Y, FILTER, DATE, 4RATIO FROM " + \ TableName + " " + QueryString+";") R=conn.store_result() if MaxRows == 0: MaxRows = 0 Rows = R.fetch_row(maxrows=MaxRows, how = 1) NBins = 800 Threshold = 60 MaxThreshold = Threshold+NBins #Extract the data from the tuple of dictionaries if MaxRows == 0: MaxRows = len(Rows) Xs = zeros(MaxRows,dtype=float32) Ys = zeros(MaxRows,dtype=float32) Xs = [] Ys = [] Ratio4 = [] Filters = [] Dates = [] LPTuple = [] for RowNum in arange(MaxRows): #Xs[RowNum] = Rows[RowNum]['X'] #Ys[RowNum] = Rows[RowNum]['Y'] Xs.append(Rows[RowNum]['X']) Ys.append(Rows[RowNum]['Y']) Filters.append(Rows[RowNum]['FILTER']) Dates.append(Rows[RowNum]['DATE']) Ratio4.append(Rows[RowNum]['4RATIO']) LPTuple.append([Xs[RowNum],Ys[RowNum],Filters[RowNum],Dates[RowNum],\ Ratio4[RowNum]]) #Sort the Arrays based upon pixel #Ys.sort() Xs.sort(key=lambda x, p=iter(Ys).next: p()) Dates.sort(key=lambda x, p=iter(Ys).next: p()) Filters.sort(key=lambda x, p=iter(Ys).next: p()) #Sort the tuple by x and y coordinates LPTuple.sort(key=lambda x:x[0]) LPTuple.sort(key=lambda x:x[1]) ThisX = 0 ThisY = 0 ThisRatio = 0 SingX = [] SingY = [] AvgRa = [] NumXY = [] MaxXY = 12 for LPTupleRow in arange(LPTuple.__len__()): if LPTuple[LPTupleRow][0] == ThisX and LPTuple[LPTupleRow][1] == ThisY: ThisRatio.append(LPTuple[LPTupleRow][4]) NumThisXY+=1 else: if ThisX !=0 and ThisY !=0: #A new pixel, append old values if NumThisXY == MaxXY: SingX.append(ThisX) SingY.append(ThisY) AvgRa.append(mean(ThisRatio)) NumXY.append(NumThisXY) #Form a new pixel ratio array NumThisXY = 1 del ThisRatio ThisRatio = [LPTuple[LPTupleRow][4]] else: del ThisRatio ThisRatio = [LPTuple[LPTupleRow][4]] NumThisXY = 1 ThisX = LPTuple[LPTupleRow][0] ; ThisY = LPTuple[LPTupleRow][1] ######################################################################## ##FORM THE MASTER TABLE IF REQUESTED if FormMaster == 1: MasterMask = zeros([HxRG.FNAxis1, HxRG.FNAxis2],dtype=float32) MasterMaskName = HxRG.LeakyDir+'LeakyMask.fits' MasterTableName = HxRG.DetStrMySQL+'_Master' try: cursor.execute('CREATE TABLE '+ MasterTableName +\ '(PIXID MEDIUMINT NOT NULL PRIMARY KEY,'+\ 'X SMALLINT,'+\ 'Y SMALLINT,'+\ 'RATIO FLOAT);') except MySQLdb.Error, e: print "Table exists: Moving On" #Add the values to the master table for LeakyNum in arange(NumXY.__len__()): PixID = SingY[LeakyNum]*HxRG.FNAxis1+SingX[LeakyNum] MasterMask[SingY[LeakyNum], SingX[LeakyNum]] = AvgRa[LeakyNum] cursor.execute("INSERT INTO "+MasterTableName+" VALUES("+\ str(PixID)+","+\ str(SingX[LeakyNum]) +","+\ str(SingY[LeakyNum]) +","+\ str(AvgRa[LeakyNum]) +")") #Write the .fits file HDU = pyfits.PrimaryHDU(MasterMask) HDU.writeto(MasterMaskName) #Now do the histograms N,Bins = histogram(AvgRa, 50)