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slicedespike.pro
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slicedespike.pro
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; -------------------------------------------------------------
; NAME:
; -------------------------------------------------------------
; SLICEDESPIKE
;
; ver 4.0 - after despike.pro
; author: Lu Pan (Caltech) and John Carter (IAS)
;
; -------------------------------------------------------------
; VERSION HISTORY:
; -------------------------------------------------------------
; - v 4.0 (dec 2014)
; Deleted the n-blocks part for clarifications in dimension.
; Now despiking only in the spectral dimention
; [Added for-loops may slow down the process.]
;
; - v 3.0 (nov 2011)
; Removed reduced lambda dimension option
; Improved spike re-construction
; Added block processing for memory limitations
;
; - v 2.2 (jul 2010)
; Improved efficiency > +300%
; Added customizable parameters
;
; - v 2.1 (apr 2010)
; Does not overwrite input if 1D array
; For memory considerations, 3D array is replaced by its despiked
; version
;
; - v 2.0 (feb 2010)
; Revamped
;
; - Original version - 2009
;
; ISSUE ! with N_blocks!!!! final output has wrong dimensions (SINFONI)
;
; -------------------------------------------------------------
FUNCTION slicedespike, input, threshold, pass, step, bad_spectel,ratio
if n_elements(input) le 1 then return,0
input=reform(input)
input_size=size(input,/dimensions)
output=0
if n_elements(input_size) eq 1 then begin
size_x=1
size_y=1
size_l=n_elements(input)
input=reform(input,1,size_l,1)
endif
if n_elements(input_size) eq 2 then return,0
if n_elements(input_size) eq 3 then begin
size_x=input_size(0)
size_y=input_size(2)
size_l=input_size(1)
endif
; threshold settings
if n_elements(threshold) eq 0 then threshold = 0.02 ; 1 = 100%
threshold0=threshold
threshold=float(threshold)
;if threshold lt 0. then threshold=0.
if threshold gt 1. then threshold=1.
; pass settings
if n_elements(pass) eq 0 then pass=2
pass0=pass
pass=fix(pass)
if pass lt 1 then pass=1
; step settings
if n_elements(step) eq 0 then step=0
step0=step
step=float(step)
if step lt 0 then step=0
;if step gt threshold then step=threshold
;if pass eq 1 then step=0
threshold1=threshold
output = input
; -----------------------------------
; FIND GOOD DATA
; Only perform despike on valid data
; if skipped may have problem when replace with smoothed spectral data
; -----------------------------------
min_x=0 & min_y=0 & max_x=0 & max_y=0
if size_x gt 1 then begin
;Find CRISM no data values on the edge of file.
for i=0,size_x/4,1 do begin
check_min=where(finite(input(i,size_l/2,*)) eq 0 or input(i,size_l/2,*) le 0. or input(i,size_l/2,*) gt 2.,count_min)
if count_min lt size_y/4 then break
endfor
min_x=i
for i=size_x-1,3*size_x/4,-1 do begin
check_max=where(finite(input(i,size_l/2,*)) eq 0 or input(i,size_l/2,*) le 0. or input(i,size_l/2,*) gt 2.,count_max)
if count_max lt size_y/4 then break
endfor
max_x=i
for i=0,size_y/4,1 do begin
check_min=where(finite(input(*,size_l/2,i)) eq 0 or input(*,size_l/2,i) le 0. or input(*,size_l/2,i) gt 2.,count_min)
if count_min lt size_x/4 then break
endfor
min_y=i
for i=size_y-1,3*size_y/4,-1 do begin
check_max=where(finite(input(*,size_l/2,i)) eq 0 or input(*,size_l/2,i) le 0. or input(*,size_l/2,i) gt 2.,count_max)
if count_max lt size_x/4 then break
endfor
max_y=i
check_min=0b & check_max=0b & count_min=0b & count_max=0b
endif
;Check off-channels for original image before ratio
;Skip if it's a ratioed cube.
for i=min_y,max_y do begin
threshold=threshold1
slice_xl=input(min_x:max_x,0:size_l-1,i)
slice_xl=reform(temporary(slice_xl))
; count_bad=0l
; check_bad=where(finite(slice_xl) eq 0,count_bad)
; if count_bad gt 0 then slice_xl(check_bad)=0.
medderivdat=fltarr(max_x-min_x+1,size_l)
derivdat3=medderivdat
derivdat=medderivdat
for loop=0,pass-1 do begin
for j=0,max_x-min_x do begin
;medderivdat=fltarr(max_x-min_x+1,size_l)
;derivdat=medderivdat
medderivdat(j,*)=smooth(slice_xl(j,*),10,/edge_truncate,/NAN)
derivdat(j,*)=deriv(slice_xl(j,*))
endfor
;derivdat3=medderivdat
derivdat3=abs(slice_xl-medderivdat)/abs(medderivdat)
w1=where(derivdat gt 0.,c1)
w2=where(derivdat le 0.,c2)
if c1 gt 0. then derivdat(w1)=2.
if c2 gt 0. then derivdat(w2)=1.
derivdat=byte(derivdat)
derivdat2 = fltarr(max_x-min_x+1,size_l)
for j=0,max_x-min_x do begin
derivdat2(j,*)=shift(derivdat(j,*),-1)+shift(derivdat(j,*),+1)
test=where(derivdat3(j,*) gt threshold and derivdat2(j,*) eq 3, c3)
if c3 gt 0 then begin
medderivdat(j,*)=smooth(slice_xl(j,*),30,/edge_truncate,/NAN)
slice_xl(j,test)=medderivdat(j,test)
endif
endfor
medderivdat=0b & test=0b & derivdat2=0b & derivdat3=0b & derivdat = 0b
threshold=(threshold-step)>0.
endfor
output(min_x:max_x,0:size_l-1,i)=slice_xl
slice_xl=0
endfor
if n_elements(input_size) eq 3 then begin
output(*,0:3,*)=input(*,0:3,*)
output(*,size_l-10:size_l-1,*)=input(*,size_l-10:size_l-1,*)
endif
if n_elements(input_size) eq 1 then begin
output(0:3)=input(0:3)
output(size_l-10:size_l-1)=input(size_l-10:size_l-1)
endif
threshold=threshold0
pass=pass0
step=step0
return,output
end