;pro Bad_Pixel_Mask ; ;PURPOSE: ; To take a series of dark images and extract from them the pixels that ; appear to have no dark current. These pixels are ; ;INPUTS: ; ;OUTPUTS: ; ;KEYWORDS: ; ROOTDIR: ; The Directory holding the directories of Raw files ; DATE: ; The Date during which they were taken. Also the subdirectory that ; the files are in. ; REDUCEDDIR: ; The directory where the processed images and plots will be placed in. ; BLOCKLENGTH: ; An offset for files that were written improperly. The readu ; function reads the values with this offset in place. ; OBJECTNAME: ; The string that indicates what files are being sought. The filenames ; should begin with this string ('Dark', 'Flat', etc.). ; NREADS: ; The number of reads (NAXIS3) that are present in the file. This ; is also a string in the filename that will be used as a regular ; expression in searching for matched files. ; FIRSTREAD: ; The first read to be used in the difference ; Diff = LastRead - FirstRead ; LASTREAD: ; The last read to be used in the difference ; THISFILTER: ; The filter through which the files were taken. ('I', 'G', or 'Y') ; OVERRIDE: ; Do the processing even if the output file already exists ; ALLFILES: ; 1 - Process all files matching the #Reads, Filter, and Object ; 0 - Only process one file (the first by default) ;************************************************************************** pro Bad_Pixel_Mask, RootDir=RootDir, Date=Date, $ ReducedDir = ReducedDir, BlockLength = BlockLength, $ ObjectName=ObjectName, NReads = NReads, ThisFilter = ThisFilter,$ OverRide = OverRide, FirstRead = FirstRead, LastRead = LastRead, $ Threshold = Threshold ; set directory path delimiter pathdelim=path_sep() ;Directory and FileName Keywords If Not keyword_set(RootDir) then RootDir = '/nfs/slac/g/ki/ki09/lances/' If Not keyword_set(Date) then Date='07Apr30' If Not keyword_set(ReducedDir) then ReducedDir= RootDir+$ PathDelim+'Reduced'+PathDelim+Date+PathDelim If Not keyword_set(BlockLength) then BlockLength = 0 If Not keyword_set(ObjectName) then ObjectName = 'Flat' If Not keyword_set(NReads) then NReads = 2 If Not keyword_set(FirstRead) then FirstRead = 0 If Not keyword_set(LastRead) then LastRead = NReads - 1 If Not keyword_set(ThisFilter) then ThisFilter = 'Blank' If Not keyword_set(OverRide) then OverRide = 0 If Not keyword_set(AllFiles) then AllFiles = 1 BadPixDir = ReducedDir+'BadPix'+PathDelim ;Parameters If Not keyword_set(Threshold) then Threshold = 100 ;Start in the RootDir/Date directory cd, Rootdir+Date ;Get all of the Dark Files for this Number of Reads RawFiles = File_Search(ObjectName+'*'+strtrim(NReads,2)+'_Reads*.fits') If RawFiles(0) eq '' then stop NumFiles = 1 if AllFiles then NumFiles = N_elements(RawFiles) ;Get a Few Kewyords Fits_Read, RawFiles(0), NoData, FitsHeader, /header_only Naxis1 = long(sxpar(FitsHeader, 'NAXIS1')) Naxis2 = long(sxpar(FitsHeader, 'NAXIS2')) TotalReads = long(sxpar(FitsHeader,'NAXIS3')) ArrSize = long(Naxis1*Naxis2) ;Form a Bad Pixel Mask Array BadPix = UIntArr(Naxis1,Naxis2) ;How many files to go through For FileNum = 0, NumFiles - 1 do begin print, 'Finding bad pixels in ' + RawFiles(FileNum) + ' : ' + $ strtrim(FileNum,2) + ' out of ' + strtrim(NumFiles, 2) ;Go through all of the reads, take differences and sort out dead pixels For ReadNum=0, TotalReads-2 do begin ;Get difference of ReadNum and ReadNum+1 DiffIm = Return_Cube_Diff(RawFiles(FileNum), ArrSize, Naxis1, Naxis2, $ ReadNum, ReadNum+1) ;Look for pixels that aren't building signal BadPixTemp=UIntArr(Naxis1,Naxis2) BadPixInd = where(DiffIm lt Threshold) If BadPixInd(0) ne -1 then BadPixTemp(BadPixInd) = 1 ;Add them to the map so that really dead ones build up BadPix = BadPix + BadPixTemp EndFor EndFor ;*******************************************************************OUTPUT ;Form a string designating what type of Bad Pixel test was run ;and what date it's from, etc. BadPixStr = 'DeadPixelMap_'+strtrim(NumFiles,2)+$+ ObjectName+'s_Threshold_'+strtrim(Threshold,2)+$ '_'+Date ;Make a Histogram of the Number of times that the pixel did not meet the ;threshold ;Write a .txt file that shows the pixel number and how many times it was ;flagged, sorted from highest to least TextFile = 1 If TextFile then begin BadPixNoCh0NoRef = BadPix(128:Naxis2-5,4:Naxis2-5) ;Skip Ch0 and ref pixels XSize = long((size(BadPixNoCh0NoRef))[1]) YSize = long((size(BadPixNoCh0NoRef))[2]) DeadPixInd = where(BadPixNoCh0NoRef eq NumFiles*(TotalReads-1)) DeadPixInd = DeadPixInd(reverse(sort(DeadPixInd))) DeadPix = BadPixNoCh0NoRef(DeadPixInd) RowNum = DeadPixInd/XSize+4 ColNum = (DeadPixInd mod XSize)+128 get_lun, BadPixTxtFile openw, BadPixTxtFile, BadPixDir+BadPixStr+'.txt' printf, BadPixTxtFile, FORMAT = '(%"%s\t%s\t%s\t%s")',$ 'Row', 'Column', 'Pixel Number', 'Times Flagged' for PixInd = 0L, N_Elements(DeadPix)-1 do begin printf, BadPixTxtFile, FORMAT = '(%"%I\t%I\t%I\t%I")', $ RowNum(PixInd), ColNum(PixInd), $ DeadPixInd(PixInd), DeadPix(PixInd) endfor close, BadPixTxtFile free_lun, BadPixTxtFile EndIf ;Write a .fits file showing the pixels with value dependent on how many ;times they were flagged through the stack of images MkHdr, FitsHeader, BadPix FxAddPar, FitsHeader, 'THRESHOL', Threshold, $ 'Difference value below which pixel is flagged' FxAddPar, FitsHeader, 'FILETYPE', ObjectName, $ 'Type of File used for flagging bad pixels' FxAddPar, FitsHeader, 'DATADATE', Date, $ 'Directory from which data was taken' FxAddPar, FitsHeader, 'NUMREADS', TotalReads, $ 'Total Number of reads used in subtraction from each file' FxAddPar, FitsHeader, 'NUMFILES', NumFiles, $ 'Total Number of files used to create mask' FxAddPar, FitsHeader, 'MAXPIXVL', NumFiles*TotalReads, $ 'Maximum value a pixel will have (dead sh pixels)' Fits_Write, BadPixDir+'DeadPixelMap_'+strtrim(NumFiles,2)+$+ ObjectName+'s_Threshold_'+strtrim(Threshold,2)+$ '_'+Date+'.fits', BadPix, FitsHeader stop end