pro radar_mask_mmcr

	common mask_variables, dif_sig, count_pro, levels_t, mask

	; assume the mask comes in already scanned for obvious positives (1) and negatives (-1)

	;mask=intarr(count_pro,levels_t)
	prob=dblarr(count_pro,levels_t)
	noise_k=fltarr(count_pro)

	;mask(where(alog10(dif_sig) lt -1.))=-1
	;;print, min(alog10(dif_sig))
	;mask(where(alog10(dif_sig) gt 0))=1

	;print, 'total elements ', n_elements(mask)
	;print, 'elements eq to 0 ', n_elements(mask(where(mask eq 0)))
	;print, 'elements eq to 1 ', n_elements(mask(where(mask eq 1)))
	if min(mask) eq -1 then print, 'elements eq to -1 ', n_elements(mask(where(mask eq -1)))
	print, 'minimum signal value is ',min(dif_sig)

	lower_thresh=1.d11	; origial 700.
	upper_thresh=1.d9 	; original 100.


	num_t=2
	num_z=2

	iter=1
	factor=1.

	for j=num_t+1,count_pro-num_t-1 do begin


			min_noise=1.e9
			sdv_top=0.
			min_sdv=1.


;c	need to find the min noise in the profile

		if max(mask(j,*)) ge 0 then begin

	noise_flag=-1
	k=levels_t-5
	while noise_flag eq -1 and k gt 5 do begin

	;for k=6,levels_t-5,5 do begin

			if max(mask[j-num_t:j+num_t,k-num_z:k+num_z]) le 0 then begin

		x=moment(dif_sig[j-num_t:j+num_t,k-num_z:k+num_z])
		mean_noise=x[0]

		if mean_noise lt min_noise then begin

			min_noise=mean_noise
			min_sdv=sqrt(x[1])
			noise_k[j]=k

		endif
			noise_flag=1

			endif ; max(dif_sig[j-num_t:j+num_t,k-num_z:k+num_z]) lt 0

		;endif	; flag check

	;endfor	; k=6,levels_t-5 do begin
	k=k-1
	endwhile

		mean_noise=min_noise
		sdv_top=min_sdv
		sigma=sdv_top

		low_signal=where(dif_sig[j,0:levels_t-num_z] lt min_noise-(2.*min_sdv))
		high_signal=where(dif_sig[j,0:levels_t-num_z] gt min_noise+(2.*min_sdv))
			if n_elements(low_signal) gt 1 then begin
		for lll=0,(n_elements(low_signal))-1 do begin
			mask[j,low_signal[lll]]=-1
		endfor
			endif
			if n_elements(high_signal) gt 1 then begin
		for lll=0,(n_elements(high_signal))-1 do begin
			mask[j,high_signal[lll]]=1
		endfor
			endif

;ccccccccccccccccccccccccc
		if min_noise lt 1.e9 and noise_flag eq 1 then begin

		start_index=1

		for k=start_index+num_z,levels_t-num_z-1 do begin

		;cur_gate=hts(k)

;c	now go through each point in 3 by 5 boxes. estimate significance.

			if mask[j,k] eq 0 then begin

			sum=0.
			count2=0
			for jj=j-num_t,j+num_t do begin
				for kk=k-num_z,k+num_z do begin
						if mask[jj,kk] ne 1 then begin
					sum=sum+(dif_sig[jj,kk])
					count2=count2+1
						endif
				endfor
			endfor
			;z=((double(sum)/double(count2))-double(mean_noise)))/double(sigma)
			z=((double(sum)/double(count2))-double(mean_noise))/double(sigma)
			z=z/100.

			prob[j,k]=((2.d/sqrt(2.d*3.14159d)))*exp(-(abs(z))^2)
				;if prob[j,k] eq 0. then begin
				;	print, z
				;endif
			;if prob[j,k] lt prob_temp then prob[j,k]=prob_temp
		;prob[j,k]=prob[j,k]+((2./sqrt(2.*3.14159)))*exp(-(abs(z))^2)



			endif
		endfor	;k=start_index+num_z,levels_t-num_z do begin

		endif else begin
			prob[j,*]=1.e9
		endelse

		endif ; if max(mask(j,*)) ge 0 then begin


	endfor ;j=num_t+1,count_pro-num_t do begin



	for j=num_t+1,count_pro-num_t-1 do begin

		if min(mask(j,*)) le 0 and noise_k[j] gt 0 then begin

					num_thresh=0 & thresh=0.
			for k=noise_k[j]-num_z,noise_k[j]+num_z do begin
					thresh=thresh+prob[j,k] & num_thresh=num_thresh+1
			endfor
					thresh=thresh/double(num_thresh)

		for k=1,levels_t-3 do begin
					if mask[j,k] eq 0 then begin
				if k lt 50 then param=lower_thresh
				if k ge 100 then param=upper_thresh
				if k ge 50 and k lt 100 then begin
						param=lower_thresh+(((upper_thresh-lower_thresh)/((100.d)-(50.d)))*(double(k)-(50.d)))

				endif
			if prob[j,k] lt thresh/param then begin
				mask[j,k]=1
			endif else begin
				mask[j,k]=0
			endelse
					endif else begin	; mask eq 0
						if mask[j,k] eq -1 then mask[j,k]=0
					endelse
		endfor

		endif ; if max(mask(j,*)) ge 0 then begin

	endfor

	if min(mask) lt 0 then mask[where(mask lt 0)]=0

	for j=0,num_t do begin
	for k=0,levels_t-1 do begin
	if mask[j,k] ne 1 then begin
		mask[j,k]=0
	endif
	endfor
	endfor
	for j=count_pro-num_t-1,count_pro-1 do begin
	for k=0,levels_t-1 do begin
	if mask[j,k] ne 1 then begin
		mask[j,k]=0
	endif
	endfor
	endfor
	for j=0,count_pro-1 do begin
	for k=0,5 do begin
	if mask[j,k] ne 1 then begin
		mask[j,k]=0
	endif
	if mask[j,k] eq 1 and alog10(dif_sig[j,k]) lt -1.0 then begin
		mask[j,k]=0
	endif

	endfor
	endfor
	for j=0,count_pro-1 do begin
	for k=levels_t-num_z-1,levels_t-1 do begin
	if mask[j,k] ne 1 then begin
		mask[j,k]=0
	endif
	endfor
	endfor

	return
	end