matlab_class/ecco_v4/cost_altimeter.m

function []=cost_altimeter(dirModel,dirMat);
%object:       compute or plot the various sea level statistics
%              (std model-obs, model, obs, leading to cost function terms)
%inputs:       dirModel is the model run directory
%              dirMat is the directory where diagnozed .mat files will be saved
%                     -> set it to '' to use the default [dirModel 'mat/']
%              doComp is the switch from computation to plot

doComp=1;
if doComp==1;
    doSave=1;
    doPlot=0;
else;
    doSave=0;
    doPlot=1;
end;
doPrint=0;

%%%%%%%%%%%
%load grid:
%%%%%%%%%%%
    
gcmfaces_global;
if ~isfield(mygrid,'XC'); grid_load('./GRID/',5,'compact'); end;
if ~isfield(mygrid,'LATS_MASKS'); gcmfaces_lines_zonal; end;
    
%%%%%%%%%%%%%%%
%define pathes:
%%%%%%%%%%%%%%%

nameSigma='sigma_MDT_glob_eccollc.bin';
if ~isempty(dir([dirModel nameSigma]));
  dirSigma=dirModel;
elseif ~isempty(dir([dirModel 'inputfiles/' nameSigma]));
  dirSigma=[dirModel 'inputfiles/'];
else;
  error(['could not find ' nameSigma]);
end;

if isempty(dir([dirModel 'barfiles']));
  dirEcco=dirModel;
else;
  dirEcco=[dirModel 'barfiles' filesep];
end;

%nameSigma={'sigma_MDT_glob_eccollc.bin','sigma_SLA_smooth_eccollc.bin','sigma_SLA_PWS07r2_glob_eccollc.bin'}; maxLatObs=66
nameSigma={'sigma_MDT_glob_eccollc.bin','slaerr_largescale_r5.err','slaerr_gridscale_r5.err'}; maxLatObs=90

if isempty(dirMat); dirMat=[dirModel 'mat/']; else; dirMat=[dirMat '/']; end;
if isempty(dir(dirMat));     mkdir([dirMat]); end;
if ~isdir([dirMat 'cost/']); mkdir([dirMat 'cost/']); end;
runName=pwd; tmp1=strfind(runName,filesep); runName=runName(tmp1(end)+1:end);


%%%%%%%%%%%%%%%%%
%global means:
%%%%%%%%%%%%%%%%%

tmpName=dir([dirEcco 'm_eta_day*data']);
avisoName=which('MSL_aviso.bin');
if length(tmpName)==1&~isempty(avisoName);
  m_eta_day=rdmds2gcmfaces([dirEcco tmpName.name(1:end-5)]);
  avisoName=which('MSL_aviso.bin');
  etaglo_aviso=read2memory(avisoName)';
  %global mean
  nt=size(m_eta_day{1},3); etaglo=NaN*zeros(1,nt);
  area=mygrid.mskC(:,:,1).*mygrid.RAC; areatot=nansum(area);
  for tt=1:nt;
    etaglo(tt)=nansum(area.*m_eta_day(:,:,tt))/areatot;
  end;
  %monthly mean
  etaglo_mon=NaN*zeros(1,240);
  etaglo_aviso_mon=NaN*zeros(1,240);
  etadate=datenum([1992 1 1 12 0 0])+[1:nt]-1;
  for mm=1:240;
    t0=datenum([1992 1+(mm-1) 1 0 0 0]);
    t1=datenum([1992 1+mm 1 0 0 0]);
    tt=find(etadate>t0&etadate<t1);
    etaglo_mon(mm)=mean(etaglo(tt));
    etaglo_aviso_mon(mm)=mean(etaglo_aviso(tt));
  end;
  %
  if doSave; eval(['save ' dirMat 'cost/cost_altimeter_etaglo.mat etaglo*;']); end;
end;

%%%%%%%%%%%%%%%%%
%do computations:
%%%%%%%%%%%%%%%%%

for doDifObsOrMod=1:3;

    if doDifObsOrMod==1; suf='modMobs'; elseif doDifObsOrMod==2; suf='obs'; else; suf='mod'; end;
    
    if doComp==0;
        eval(['load ' dirMat 'cost/cost_altimeter_' suf '.mat myflds;']);
    else;
        
        tic;
        %mdt cost function term (misfit plot)
        dif_mdt=rdmds2gcmfaces([dirEcco 'mdtdiff_smooth']);
        sig_mdt=read_bin([dirSigma nameSigma{1}],1,0);
        sig_mdt(find(sig_mdt==0))=NaN;
        %store:
        myflds.dif_mdt=dif_mdt;
        myflds.sig_mdt=sig_mdt;
        
        %skip blanks:
        tmp1=dir([dirEcco 'sladiff_smooth*data']);
        nrec=tmp1.bytes/90/1170/4;
        ttShift=17;
        %skip 1992
        listRecs=[1+365-ttShift:17+365*18-ttShift];
        nRecs=length(listRecs); TT=1993+[0:nRecs-1]/365.25;
        
        toc; tic;
        %pointwise/1day terms:
        sladiff_point=repmat(0*mygrid.RAC,[1 1 nRecs]); count_point=sladiff_point;
        for ii=1:3;
            if ii==1; myset='tp'; elseif ii==2; myset='gfo'; else; myset='ers'; end;
            %topex pointwise misfits:
            if doDifObsOrMod==1;
                sladiff_tmp=cost_altimeter_read([dirEcco 'sladiff_' myset '_raw'],ttShift+listRecs);
            elseif doDifObsOrMod==2;
                sladiff_tmp=cost_altimeter_read([dirEcco 'slaobs_' myset '_raw'],ttShift+listRecs);
            else;
                sladiff_tmp=cost_altimeter_read([dirEcco 'sladiff_' myset '_raw'],ttShift+listRecs);
                sladiff_tmp=sladiff_tmp+cost_altimeter_read([dirEcco 'slaobs_' myset '_raw'],ttShift+listRecs);
            end;
            %add to overall data set:
            sladiff_point=sladiff_point+sladiff_tmp; count_point=count_point+(sladiff_tmp~=0);
            %finalize data set:
            sladiff_tmp(sladiff_tmp==0)=NaN;
            %compute rms:
            count_tmp=sum(~isnan(sladiff_tmp),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
            eval(['myflds.rms_' myset '=sqrt(nansum(sladiff_tmp.^2,3)./count_tmp);']);
            eval(['myflds.std_' myset '=nanstd(sladiff_tmp,0,3).*msk_tmp;']);
        end;
        %finalize overall data set:
        count_point(count_point==0)=NaN;
        sladiff_point=sladiff_point./count_point;
        %compute overall rms,std:
        count_tmp=sum(~isnan(sladiff_point),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
        myflds.rms_sladiff_point=sqrt(nansum(sladiff_point.^2,3)./count_tmp);
        myflds.std_sladiff_point=nanstd(sladiff_point,0,3).*msk_tmp;
        %
        msk_point=1*(count_point>0);
        %fill blanks:
        warning('off','MATLAB:divideByZero');
        msk=mygrid.mskC(:,:,1); msk(find(abs(mygrid.YC)>maxLatObs))=NaN;
        myflds.xtrp_rms_sladiff_point=diffsmooth2D_extrap_inv(myflds.rms_sladiff_point,msk);
        myflds.xtrp_std_sladiff_point=diffsmooth2D_extrap_inv(myflds.std_sladiff_point,msk);
        warning('on','MATLAB:divideByZero');
        %get weight:
        sig_sladiff_point=read_bin([dirSigma nameSigma{3}],1,0);
        sig_sladiff_point(find(sig_sladiff_point==0))=NaN;
        myflds.sig_sladiff_point=sig_sladiff_point;
        
        %computational mask : only points that were actually observed, and in 35d average
        msk_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
        msk_point35d=1*(msk_point35d~=0);
        tmp1=sum(msk_point35d==0&msk_point~=0);
        tmp2=sum(msk_point35d~=0&msk_point~=0);
        fprintf('after masking : %d omitted, %d retained \n',tmp1,tmp2);
        msk_point=msk_point.*msk_point35d;
        msk_point(msk_point==0)=NaN;
        %plotting mask : regions of less than 100 observations are omitted
        msk_100pts=1*(nansum(msk_point,3)>=100);
        msk_100pts(msk_100pts==0)=NaN;
        %store
        myflds.msk_100pts=msk_100pts;
        
        toc; tic;
        %lsc cost function term:
        if doDifObsOrMod==1;
            sladiff_smooth=cost_altimeter_read([dirEcco 'sladiff_smooth'],listRecs);
        elseif doDifObsOrMod==2;
            sladiff_smooth=cost_altimeter_read([dirEcco 'slaobs_smooth'],listRecs);
        else;
            sladiff_smooth=cost_altimeter_read([dirEcco 'sladiff_smooth'],listRecs);
            sladiff_smooth=sladiff_smooth+cost_altimeter_read([dirEcco 'slaobs_smooth'],listRecs);
        end;
        %mask missing points:
        sladiff_smooth(sladiff_smooth==0)=NaN;
        sladiff_smooth=sladiff_smooth.*msk_point;
        count_tmp=sum(~isnan(sladiff_smooth),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
        %compute rms:
        rms_sladiff_smooth=msk_tmp.*sqrt(nanmean(sladiff_smooth.^2,3));
        std_sladiff_smooth=msk_tmp.*nanstd(sladiff_smooth,0,3);
        %get weight:
        sig_sladiff_smooth=read_bin([dirSigma nameSigma{2}],1,0);
        sig_sladiff_smooth(find(sig_sladiff_smooth==0))=NaN;
        %store:
        myflds.rms_sladiff_smooth=rms_sladiff_smooth;
        myflds.std_sladiff_smooth=std_sladiff_smooth;
        myflds.sig_sladiff_smooth=sig_sladiff_smooth;
        
        toc; tic;
        %pointwise/point35days cost function term:
        if doDifObsOrMod==1;
            sladiff_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
        elseif doDifObsOrMod==2;
            sladiff_point35d=cost_altimeter_read([dirEcco 'slaobs_raw'],listRecs);
        else;
            sladiff_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
            sladiff_point35d=sladiff_point35d+cost_altimeter_read([dirEcco 'slaobs_raw'],listRecs);
        end;
        %mask missing points:
        sladiff_point35d(sladiff_point35d==0)=NaN;
        sladiff_point35d=sladiff_point35d.*msk_point;
        count_tmp=sum(~isnan(sladiff_point35d),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
        %compute rms:
        rms_sladiff_point35d=msk_tmp.*sqrt(nanmean(sladiff_point35d.^2,3));
        std_sladiff_point35d=msk_tmp.*nanstd(sladiff_point35d,0,3);
        %store:
        myflds.rms_sladiff_point35d=rms_sladiff_point35d;
        myflds.std_sladiff_point35d=std_sladiff_point35d;
        
        if 0;
            %difference between scales
            rms_sladiff_35dMsmooth=msk_tmp.*sqrt(nanmean((sladiff_point35d-sladiff_smooth).^2,3));
            std_sladiff_35dMsmooth=msk_tmp.*nanstd((sladiff_point35d-sladiff_smooth),0,3);
            %store:
            myflds.rms_sladiff_35dMsmooth=rms_sladiff_35dMsmooth;
            myflds.std_sladiff_35dMsmooth=std_sladiff_35dMsmooth;

            %difference between scales
            rms_sladiff_pointMpoint35d=msk_tmp.*sqrt(nanmean((sladiff_point-sladiff_point35d).^2,3));
            std_sladiff_pointMpoint35d=msk_tmp.*nanstd((sladiff_point-sladiff_point35d),0,3);
            %store:
            myflds.rms_sladiff_pointMpoint35d=rms_sladiff_pointMpoint35d;
            myflds.std_sladiff_pointMpoint35d=std_sladiff_pointMpoint35d;
        end;
        
        %compute zonal mean/median:
        for ii=1:4;
            switch ii;
                case 1; tmp1='mdt'; cost_fld=(mygrid.mskC(:,:,1).*myflds.dif_mdt./myflds.sig_mdt).^2;
                case 2; tmp1='lsc'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_smooth./myflds.sig_sladiff_smooth).^2;
                case 3; tmp1='point35d'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_point35d./myflds.sig_sladiff_point).^2;
                case 4; tmp1='point'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_point./myflds.sig_sladiff_point).^2;
            end;
            cost_zmean=calc_zonmean_T(cost_fld); eval(['mycosts_mean.' tmp1 '=cost_zmean;']);
            cost_zmedian=calc_zonmedian_T(cost_fld); eval(['mycosts_median.' tmp1 '=cost_zmedian;']);
        end;
        
        toc; %write to disk:
        if doSave; eval(['save ' dirMat 'cost/cost_altimeter_' suf '.mat myflds mycosts_mean mycosts_median;']); end;
        
    end;%if doComp
    
    if doPlot;
        cc=[-0.4:0.05:-0.25 -0.2:0.03:-0.05 -0.03:0.01:0.03 0.05:0.03:0.2 0.25:0.05:0.4];
        figure; m_map_gcmfaces(myflds.dif_mdt,0,{'myCaxis',cc}); drawnow;
        cc=[0:0.005:0.02 0.03:0.01:0.05 0.06:0.02:0.1 0.14:0.03:0.2 0.25:0.05:0.4];
        figure; m_map_gcmfaces(myflds.rms_sladiff_smooth,0,{'myCaxis',cc}); drawnow;
        figure; m_map_gcmfaces(myflds.rms_sladiff_point35d,0,{'myCaxis',cc}); drawnow;
        figure; m_map_gcmfaces(myflds.rms_sladiff_point,0,{'myCaxis',cc}); drawnow;
    end;
    
    if doPlot&doPrint;
        dirFig='../figs/altimeter/'; ff0=gcf-4;
        for ff=1:4;
            figure(ff+ff0); saveas(gcf,[dirFig runName '_' suf num2str(ff)],'fig');
            eval(['print -depsc ' dirFig runName '_' suf num2str(ff) '.eps;']);
            eval(['print -djpeg90 ' dirFig runName '_' suf num2str(ff) '.jpg;']);
        end;
    end;
    
end;%for doDifObsOrMod=1:3;


function [fldOut]=cost_altimeter_read(fileIn,recIn);

nrec=length(recIn);
global mygrid; siz=[size(convert2gcmfaces(mygrid.XC)) nrec];
lrec=siz(1)*siz(2)*4;
myprec='float32';

fldOut=zeros(siz);
fid=fopen([fileIn '.data'],'r','b');
for irec=1:nrec;
    status=fseek(fid,(recIn(irec)-1)*lrec,'bof');
    fldOut(:,:,irec)=fread(fid,siz(1:2),myprec);
end;

fldOut=convert2gcmfaces(fldOut);


1	gforget	1.7	function []=cost_altimeter(dirModel,dirMat);
2			%object: compute or plot the various sea level statistics
3			% (std model-obs, model, obs, leading to cost function terms)
4			%inputs: dirModel is the model run directory
5			% dirMat is the directory where diagnozed .mat files will be saved
6			% -> set it to '' to use the default [dirModel 'mat/']
7			% doComp is the switch from computation to plot
8	gforget	1.13
9	gforget	1.4	doComp=1;
10			if doComp==1;
11	gforget	1.11	doSave=1;
12			doPlot=0;
13	gforget	1.4	else;
14	gforget	1.11	doSave=0;
15			doPlot=1;
16	gforget	1.4	end;
17			doPrint=0;
18
19	gforget	1.14	%%%%%%%%%%%
20			%load grid:
21			%%%%%%%%%%%
22
23			gcmfaces_global;
24			if ~isfield(mygrid,'XC'); grid_load('./GRID/',5,'compact'); end;
25			if ~isfield(mygrid,'LATS_MASKS'); gcmfaces_lines_zonal; end;
26
27			%%%%%%%%%%%%%%%
28			%define pathes:
29			%%%%%%%%%%%%%%%
30
31	gforget	1.16	nameSigma='sigma_MDT_glob_eccollc.bin';
32			if ~isempty(dir([dirModel nameSigma]));
33	gforget	1.14	dirSigma=dirModel;
34	gforget	1.17	elseif ~isempty(dir([dirModel 'inputfiles/' nameSigma]));
35			dirSigma=[dirModel 'inputfiles/'];
36	gforget	1.14	else;
37	gforget	1.16	error(['could not find ' nameSigma]);
38	gforget	1.14	end;
39
40			if isempty(dir([dirModel 'barfiles']));
41			dirEcco=dirModel;
42			else;
43			dirEcco=[dirModel 'barfiles' filesep];
44			end;
45
46			%nameSigma={'sigma_MDT_glob_eccollc.bin','sigma_SLA_smooth_eccollc.bin','sigma_SLA_PWS07r2_glob_eccollc.bin'}; maxLatObs=66
47	gforget	1.17	nameSigma={'sigma_MDT_glob_eccollc.bin','slaerr_largescale_r5.err','slaerr_gridscale_r5.err'}; maxLatObs=90
48	gforget	1.14
49			if isempty(dirMat); dirMat=[dirModel 'mat/']; else; dirMat=[dirMat '/']; end;
50			if isempty(dir(dirMat)); mkdir([dirMat]); end;
51			if ~isdir([dirMat 'cost/']); mkdir([dirMat 'cost/']); end;
52			runName=pwd; tmp1=strfind(runName,filesep); runName=runName(tmp1(end)+1:end);
53
54	gforget	1.15
55			%%%%%%%%%%%%%%%%%
56			%global means:
57			%%%%%%%%%%%%%%%%%
58
59			tmpName=dir([dirEcco 'm_eta_day*data']);
60			avisoName=which('MSL_aviso.bin');
61			if length(tmpName)==1&~isempty(avisoName);
62			m_eta_day=rdmds2gcmfaces([dirEcco tmpName.name(1:end-5)]);
63			avisoName=which('MSL_aviso.bin');
64			etaglo_aviso=read2memory(avisoName)';
65			%global mean
66			nt=size(m_eta_day{1},3); etaglo=NaN*zeros(1,nt);
67			area=mygrid.mskC(:,:,1).*mygrid.RAC; areatot=nansum(area);
68			for tt=1:nt;
69			etaglo(tt)=nansum(area.*m_eta_day(:,:,tt))/areatot;
70			end;
71			%monthly mean
72			etaglo_mon=NaN*zeros(1,240);
73			etaglo_aviso_mon=NaN*zeros(1,240);
74			etadate=datenum([1992 1 1 12 0 0])+[1:nt]-1;
75			for mm=1:240;
76			t0=datenum([1992 1+(mm-1) 1 0 0 0]);
77			t1=datenum([1992 1+mm 1 0 0 0]);
78			tt=find(etadate>t0&etadate<t1);
79			etaglo_mon(mm)=mean(etaglo(tt));
80			etaglo_aviso_mon(mm)=mean(etaglo_aviso(tt));
81			end;
82			%
83			if doSave; eval(['save ' dirMat 'cost/cost_altimeter_etaglo.mat etaglo*;']); end;
84			end;
85
86	gforget	1.14	%%%%%%%%%%%%%%%%%
87			%do computations:
88			%%%%%%%%%%%%%%%%%
89
90	gforget	1.4	for doDifObsOrMod=1:3;
91	gforget	1.14
92	gforget	1.11	if doDifObsOrMod==1; suf='modMobs'; elseif doDifObsOrMod==2; suf='obs'; else; suf='mod'; end;
93
94			if doComp==0;
95			eval(['load ' dirMat 'cost/cost_altimeter_' suf '.mat myflds;']);
96			else;
97
98			tic;
99			%mdt cost function term (misfit plot)
100	gforget	1.14	dif_mdt=rdmds2gcmfaces([dirEcco 'mdtdiff_smooth']);
101	gforget	1.12	sig_mdt=read_bin([dirSigma nameSigma{1}],1,0);
102	gforget	1.11	sig_mdt(find(sig_mdt==0))=NaN;
103			%store:
104			myflds.dif_mdt=dif_mdt;
105			myflds.sig_mdt=sig_mdt;
106
107			%skip blanks:
108	gforget	1.14	tmp1=dir([dirEcco 'sladiff_smooth*data']);
109	gforget	1.11	nrec=tmp1.bytes/90/1170/4;
110			ttShift=17;
111			%skip 1992
112			listRecs=[1+365-ttShift:17+365*18-ttShift];
113			nRecs=length(listRecs); TT=1993+[0:nRecs-1]/365.25;
114
115			toc; tic;
116			%pointwise/1day terms:
117			sladiff_point=repmat(0*mygrid.RAC,[1 1 nRecs]); count_point=sladiff_point;
118			for ii=1:3;
119			if ii==1; myset='tp'; elseif ii==2; myset='gfo'; else; myset='ers'; end;
120			%topex pointwise misfits:
121			if doDifObsOrMod==1;
122	gforget	1.14	sladiff_tmp=cost_altimeter_read([dirEcco 'sladiff_' myset '_raw'],ttShift+listRecs);
123	gforget	1.11	elseif doDifObsOrMod==2;
124	gforget	1.14	sladiff_tmp=cost_altimeter_read([dirEcco 'slaobs_' myset '_raw'],ttShift+listRecs);
125	gforget	1.11	else;
126	gforget	1.14	sladiff_tmp=cost_altimeter_read([dirEcco 'sladiff_' myset '_raw'],ttShift+listRecs);
127			sladiff_tmp=sladiff_tmp+cost_altimeter_read([dirEcco 'slaobs_' myset '_raw'],ttShift+listRecs);
128	gforget	1.11	end;
129			%add to overall data set:
130			sladiff_point=sladiff_point+sladiff_tmp; count_point=count_point+(sladiff_tmp~=0);
131			%finalize data set:
132			sladiff_tmp(sladiff_tmp==0)=NaN;
133			%compute rms:
134			count_tmp=sum(~isnan(sladiff_tmp),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
135			eval(['myflds.rms_' myset '=sqrt(nansum(sladiff_tmp.^2,3)./count_tmp);']);
136			eval(['myflds.std_' myset '=nanstd(sladiff_tmp,0,3).*msk_tmp;']);
137			end;
138			%finalize overall data set:
139			count_point(count_point==0)=NaN;
140			sladiff_point=sladiff_point./count_point;
141			%compute overall rms,std:
142			count_tmp=sum(~isnan(sladiff_point),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
143			myflds.rms_sladiff_point=sqrt(nansum(sladiff_point.^2,3)./count_tmp);
144			myflds.std_sladiff_point=nanstd(sladiff_point,0,3).*msk_tmp;
145			%
146			msk_point=1*(count_point>0);
147			%fill blanks:
148			warning('off','MATLAB:divideByZero');
149			msk=mygrid.mskC(:,:,1); msk(find(abs(mygrid.YC)>maxLatObs))=NaN;
150			myflds.xtrp_rms_sladiff_point=diffsmooth2D_extrap_inv(myflds.rms_sladiff_point,msk);
151			myflds.xtrp_std_sladiff_point=diffsmooth2D_extrap_inv(myflds.std_sladiff_point,msk);
152			warning('on','MATLAB:divideByZero');
153			%get weight:
154	gforget	1.12	sig_sladiff_point=read_bin([dirSigma nameSigma{3}],1,0);
155	gforget	1.11	sig_sladiff_point(find(sig_sladiff_point==0))=NaN;
156			myflds.sig_sladiff_point=sig_sladiff_point;
157
158			%computational mask : only points that were actually observed, and in 35d average
159	gforget	1.14	msk_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
160	gforget	1.11	msk_point35d=1*(msk_point35d~=0);
161			tmp1=sum(msk_point35d==0&msk_point~=0);
162			tmp2=sum(msk_point35d~=0&msk_point~=0);
163			fprintf('after masking : %d omitted, %d retained \n',tmp1,tmp2);
164			msk_point=msk_point.*msk_point35d;
165			msk_point(msk_point==0)=NaN;
166			%plotting mask : regions of less than 100 observations are omitted
167			msk_100pts=1*(nansum(msk_point,3)>=100);
168			msk_100pts(msk_100pts==0)=NaN;
169			%store
170			myflds.msk_100pts=msk_100pts;
171
172			toc; tic;
173			%lsc cost function term:
174			if doDifObsOrMod==1;
175	gforget	1.14	sladiff_smooth=cost_altimeter_read([dirEcco 'sladiff_smooth'],listRecs);
176	gforget	1.11	elseif doDifObsOrMod==2;
177	gforget	1.14	sladiff_smooth=cost_altimeter_read([dirEcco 'slaobs_smooth'],listRecs);
178	gforget	1.11	else;
179	gforget	1.14	sladiff_smooth=cost_altimeter_read([dirEcco 'sladiff_smooth'],listRecs);
180			sladiff_smooth=sladiff_smooth+cost_altimeter_read([dirEcco 'slaobs_smooth'],listRecs);
181	gforget	1.11	end;
182			%mask missing points:
183			sladiff_smooth(sladiff_smooth==0)=NaN;
184			sladiff_smooth=sladiff_smooth.*msk_point;
185			count_tmp=sum(~isnan(sladiff_smooth),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
186			%compute rms:
187			rms_sladiff_smooth=msk_tmp.*sqrt(nanmean(sladiff_smooth.^2,3));
188			std_sladiff_smooth=msk_tmp.*nanstd(sladiff_smooth,0,3);
189			%get weight:
190	gforget	1.12	sig_sladiff_smooth=read_bin([dirSigma nameSigma{2}],1,0);
191	gforget	1.11	sig_sladiff_smooth(find(sig_sladiff_smooth==0))=NaN;
192			%store:
193			myflds.rms_sladiff_smooth=rms_sladiff_smooth;
194			myflds.std_sladiff_smooth=std_sladiff_smooth;
195			myflds.sig_sladiff_smooth=sig_sladiff_smooth;
196
197			toc; tic;
198			%pointwise/point35days cost function term:
199			if doDifObsOrMod==1;
200	gforget	1.14	sladiff_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
201	gforget	1.11	elseif doDifObsOrMod==2;
202	gforget	1.14	sladiff_point35d=cost_altimeter_read([dirEcco 'slaobs_raw'],listRecs);
203	gforget	1.11	else;
204	gforget	1.14	sladiff_point35d=cost_altimeter_read([dirEcco 'sladiff_raw'],listRecs);
205			sladiff_point35d=sladiff_point35d+cost_altimeter_read([dirEcco 'slaobs_raw'],listRecs);
206	gforget	1.11	end;
207			%mask missing points:
208			sladiff_point35d(sladiff_point35d==0)=NaN;
209			sladiff_point35d=sladiff_point35d.*msk_point;
210			count_tmp=sum(~isnan(sladiff_point35d),3); count_tmp(find(count_tmp<10))=NaN; msk_tmp=1+0*count_tmp;
211			%compute rms:
212			rms_sladiff_point35d=msk_tmp.*sqrt(nanmean(sladiff_point35d.^2,3));
213			std_sladiff_point35d=msk_tmp.*nanstd(sladiff_point35d,0,3);
214			%store:
215			myflds.rms_sladiff_point35d=rms_sladiff_point35d;
216			myflds.std_sladiff_point35d=std_sladiff_point35d;
217
218			if 0;
219			%difference between scales
220			rms_sladiff_35dMsmooth=msk_tmp.*sqrt(nanmean((sladiff_point35d-sladiff_smooth).^2,3));
221			std_sladiff_35dMsmooth=msk_tmp.*nanstd((sladiff_point35d-sladiff_smooth),0,3);
222			%store:
223			myflds.rms_sladiff_35dMsmooth=rms_sladiff_35dMsmooth;
224			myflds.std_sladiff_35dMsmooth=std_sladiff_35dMsmooth;
225
226			%difference between scales
227			rms_sladiff_pointMpoint35d=msk_tmp.*sqrt(nanmean((sladiff_point-sladiff_point35d).^2,3));
228			std_sladiff_pointMpoint35d=msk_tmp.*nanstd((sladiff_point-sladiff_point35d),0,3);
229			%store:
230			myflds.rms_sladiff_pointMpoint35d=rms_sladiff_pointMpoint35d;
231			myflds.std_sladiff_pointMpoint35d=std_sladiff_pointMpoint35d;
232			end;
233
234			%compute zonal mean/median:
235			for ii=1:4;
236			switch ii;
237			case 1; tmp1='mdt'; cost_fld=(mygrid.mskC(:,:,1).*myflds.dif_mdt./myflds.sig_mdt).^2;
238			case 2; tmp1='lsc'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_smooth./myflds.sig_sladiff_smooth).^2;
239			case 3; tmp1='point35d'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_point35d./myflds.sig_sladiff_point).^2;
240			case 4; tmp1='point'; cost_fld=(mygrid.mskC(:,:,1).*myflds.rms_sladiff_point./myflds.sig_sladiff_point).^2;
241			end;
242			cost_zmean=calc_zonmean_T(cost_fld); eval(['mycosts_mean.' tmp1 '=cost_zmean;']);
243			cost_zmedian=calc_zonmedian_T(cost_fld); eval(['mycosts_median.' tmp1 '=cost_zmedian;']);
244			end;
245
246			toc; %write to disk:
247			if doSave; eval(['save ' dirMat 'cost/cost_altimeter_' suf '.mat myflds mycosts_mean mycosts_median;']); end;
248
249			end;%if doComp
250
251			if doPlot;
252			cc=[-0.4:0.05:-0.25 -0.2:0.03:-0.05 -0.03:0.01:0.03 0.05:0.03:0.2 0.25:0.05:0.4];
253			figure; m_map_gcmfaces(myflds.dif_mdt,0,{'myCaxis',cc}); drawnow;
254			cc=[0:0.005:0.02 0.03:0.01:0.05 0.06:0.02:0.1 0.14:0.03:0.2 0.25:0.05:0.4];
255			figure; m_map_gcmfaces(myflds.rms_sladiff_smooth,0,{'myCaxis',cc}); drawnow;
256			figure; m_map_gcmfaces(myflds.rms_sladiff_point35d,0,{'myCaxis',cc}); drawnow;
257			figure; m_map_gcmfaces(myflds.rms_sladiff_point,0,{'myCaxis',cc}); drawnow;
258			end;
259
260			if doPlot&doPrint;
261			dirFig='../figs/altimeter/'; ff0=gcf-4;
262			for ff=1:4;
263			figure(ff+ff0); saveas(gcf,[dirFig runName '_' suf num2str(ff)],'fig');
264			eval(['print -depsc ' dirFig runName '_' suf num2str(ff) '.eps;']);
265			eval(['print -djpeg90 ' dirFig runName '_' suf num2str(ff) '.jpg;']);
266			end;
267			end;
268
269	gforget	1.4	end;%for doDifObsOrMod=1:3;
270
271
272
273			function [fldOut]=cost_altimeter_read(fileIn,recIn);
274
275			nrec=length(recIn);
276			global mygrid; siz=[size(convert2gcmfaces(mygrid.XC)) nrec];
277			lrec=siz(1)siz(2)4;
278			myprec='float32';
279
280			fldOut=zeros(siz);
281			fid=fopen([fileIn '.data'],'r','b');
282			for irec=1:nrec;
283	gforget	1.11	status=fseek(fid,(recIn(irec)-1)*lrec,'bof');
284			fldOut(:,:,irec)=fread(fid,siz(1:2),myprec);
285	gforget	1.4	end;
286
287			fldOut=convert2gcmfaces(fldOut);
288
289
290