; Name: ; refsub_h4rg.pro ; ; PURPOSE: ; This program performs a reference pixel correction ; on Rockwell HAWAII-4RG detector data when read out using 32 ; outputs. ; ; CALLING SEQUENCE: ; refsub_h4rg, input_data, output_data, scaName ; ; INPUTS: ; input_data - A 4096x4096 array containing the image data. ; output_data - A 4096x4096 fltarr for the result ; scaName - The name of the device that generated the input data ; ; KEYWORD PARAMETERS: ; fwindow - The size of the filter window. ; order - Filter order, see the SAVGOL help page ; degree - Filter degree, see the SAVGOL help page ; plot - Set this =1 to plot the fits ; simple - Set this =1 for Maximal Spatial Averaging ; (subtract a median reference pixel) ; ; verbose - Set this =1 for verbose mode. ; ; ; EXAMPLE ; IDL> fits_read, 'theImage.fits', myData, myHeader ; IDL> myNewDate = fltarr(4096, 4096) ; IDL> refsub_h4rg, myData, myNewData ; ; ; REFERENCE: ; ; ; MODIFICATION HISTORY: ; Written by: ; Modified: B.J. Rauscher, IDTL, January 20, 2002 ; Initial release based on most recent ; version of refsub_h1rg ; ; B.J. Rauscher, IDTL, February 12, 2003 1/f ; noise correlates across all 4 outputs. ; Use row reference pixels to make DC ; corrections to each output. Use columns to ; remove 1/f ; ; Ernie Morse, IDTL, April 11, 2003 (v2.1) ; added scaName as input parameter ; added code block specific to device H2RG-003-4.8mu ; performed general code cleanup ; ; Don Figer, RIDL, April 28, 2007 ; modified for H4RG device; ; ; Define a function to return the mean of pixels in reference rows of ; one output. The output number ranges from 0-3. function Get_RefRow_Mean, Data, Output X_size = 4096./32. ; Number of pixels in x-dimension of an output _Data = fltarr(X_size, 8); Create an array to hold the reference pixel data X_start = Output * X_size; First column to extract X_stop = (Output + 1) * X_size - 1; Last column to extract _Data[0:X_size-1,0:3] = Data[X_start:X_stop,0:3]; Get bottom rows of reference pixels _Data[0:X_size-1,4:7] = Data[X_start:X_stop,4092:4095]; Get top rows of refernce pixels DJS_Iterstat, _Data, mean = The_Mean return, The_Mean end pro RefSub_H4rg, Input_Data, Output_Data, SCAName, Fwindow=Fwindow, $ Order=Order, Degree=Degree, Plot=Plot, Simple=Simple, $ Verbose=Verbose, Help=Help ; The reference pixels on the Rockwell HAWAII-4RG SCA are the ; outermost 4 pixels all around the chip. ; create variables to hold the dimensions of the H2RG SCA (in pixels) Xsize = long(4096) Ysize = long(4096) NumOutputs = 32 ; Set defaults if (not keyword_set(plot)) then plot = 0 ; Default is no plots if (not keyword_set(verbose)) then verbose = 0; Default is quiet mode if (not keyword_set(help)) then help = 0; Default does not print help message if (not keyword_set(simple)) then simple = 0 ; Print a help message and exit if requested if (help) then $ stop, 'Usage: refsub_h4rg, input_data, output_data [, fwindow=fwindow, order=order, degree=degree, /plot, /simple, /verbose, /help]' ; Adjust all NumOutputs outputs to have the same mean as output #0 in ; the reference rows. for Output = 1, 31 do begin ; Get first and last columns of output to correct X_Start = Output * Xsize/NumOutputs ; First column of output X_Stop = (Output + 1) * (Xsize/NumOutputs) - 1 ; Last column of output ; Offset the output Input_Data[X_start:X_stop,*] = Input_Data[X_start:X_stop,*] $ + Get_RefRow_Mean(Input_Data, Output - 1) $ - Get_RefRow_Mean(Input_Data, Output) endfor ; We will use a Savitzky-Golay filter to smooth the reference pixel data. ; See the SAVGOL procedure's help page for more information on ; the following. ; Default uses 64 pixels on either side of current pixel for smoothing If (not(keyword_set(fwindow))) then fwindow = 64 ; Default uses 64 pixels If (not(keyword_set(order))) then order = 0; Use zero to smooth If (not(keyword_set(degree))) then degree=3; Three seems reasonable ; Extract and average reference pixels If (verbose) then $ print, 'Extracting averaged reference columns on left and right hand sides of SCA' Row = intarr(Ysize) ; Y values vector. Undersize Mean_RefCol_L = fltarr(Ysize) ; Signals vector on left Mean_RefCol_R = fltarr(ysize) ; Signals vector on right For y=0, ysize-1 do begin Row[y] = y ; Do not use the first reference pixel on each ; output. Rockwell's HAWAII-1RG worked best like this. For ; now, assume that HAWAII-2RG will do the same. Mean_RefCol_L[y] = mean(Input_Data[1:3,y]) ; Average left side reference pixels Mean_RefCol_R[y] = mean(Input_Data[Xsize-4:Xsize-2,y]) ; Average right side reference pixels Endfor ; Sigma clip to get rid of outliers If (verbose) then $ print, 'Sigma clipping reference columns to remove outliers' Sigclip, Mean_RefCol_L, threshold=3.0, maxiter=5 Sigclip, Mean_RefCol_R, threshold=3.0, maxiter=5 If (verbose) then begin print, 'Mean reference pixel on left = ', mean(input_data[0:3,*]) print, 'Mean reference pixel on right = ', mean(input_data[xsize-4:xsize-2,*]) Endif ; Apply reference pixel correction ; Create arrays to hold columns of values to be subtracted from the science pixels RefPixCol_Left = Mean_RefCol_L RefPixCol_Right = Mean_RefCol_R If (not Simple) then begin ; Apply Spatial Averaging reference pixel correction using ; Savitzky-Golay filter. See the SAVGOL help page for ; more information. ; ; Exclude the first and last 4 rows from convolution with the kernel. ; These are reference rows and they need to be handled differently ; for unknown physical reasons. savgol_filter = savgol(fwindow, fwindow, order, degree) refpixcol_left[4:ysize-5] = convol(mean_refcol_l[4:ysize-5], $ savgol_filter, /EDGE_TRUNCATE) refpixcol_right[4:ysize-5] = convol(mean_refcol_r[4:ysize-5], $ savgol_filter, /EDGE_TRUNCATE) stop Endif else begin ; Apply Maximal Spatial Averaging reference pixel correction. As before, ; exclude outtermost reference pixels in columns. ; ; The approach will be to create a 1D array containing ; reference pixel values. Loop over all pixels and load ; the reference pixel array refrows_bottom = reform(input_data[4:xsize-5, 0:3], $ n_elements(input_data[4:xsize-5, 0:3])) refrows_top = reform(input_data[4:xsize-5, ysize-4:ysize-1], $ n_elements(input_data[4:xsize-5, ysize-4:ysize-1])) refcols_left = reform(input_data[1:3, 4:ysize-5], $ n_elements(input_data[1:3, 4:ysize-5])) refcols_right = reform(input_data[xsize-4:xsize-2, 4:ysize-5], $ n_elements(input_data[xsize-4:xsize-2, 4:ysize-5])) ; add all the reference pixels into one array ; allrefpix = [refrows_bottom, refrows_top, refcols_left, refcols_right] ; as a test, exclude the bottom row this seems to be bad for the first read allrefpix = [refrows_top, refcols_left, refcols_right] ; Calculate mean of all reference pixels using ; djs_iterstat and 3 sigma clipping (the default) djs_iterstat, allrefpix, mean=mean_refpix ; Both reference columns are the same for Maximal Spatial Averaging RefPixcol_Left[*] = Mean_Refpix RefPixcol_Right = RefPixCol_Left endelse ; Make plots if requested if (plot) then begin set_device = 'WIN' ; window, retain=2; Necessary on some x displays !P.MULTI = [0,1,2] ; Plot 1 plot over the other ; First plot left hand reference pixels plot, row, mean_refcol_l, $ title = 'Mean Reference Column [1:3,*]', $ xtitle = 'Row Number', $ ytitle = 'Signal (ADU)', $ xrange = [0,xsize-1], $ xstyle = 1 ; Draw a smooth curve through pixels oplot, row, refpixcol_left, thick=3 ; Now plot right hand reference pixels plot, row, mean_refcol_r, $ title = 'Mean Reference Column [2044:2046,*]', $ xtitle = 'Row Number', $ ytitle = 'Signal (ADU)', $ xrange = [0,xsize-1], $ xstyle = 1 ; Draw a smooth curve through points. oplot, row, refpixcol_right, thick=3 !P.MULTI = 0 ; Return to default plotting mode endif ; print, "avg of left ref pixels ",avg(refpixcol_left) ;Perform reference pixel correction ; if (not simple) then begin for x=0, (xsize/2)-1 do begin output_data[x,*] = input_data[x,*] - refpixcol_left output_data[(xsize-1)-x,*] = input_data[(xsize-1)-x,*] - refpixcol_right endfor ; endif else begin ; output_data = input_data - mean_refpix ; endelse end