-
Notifications
You must be signed in to change notification settings - Fork 0
/
SRF_correction.m
421 lines (336 loc) · 13.5 KB
/
SRF_correction.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
%% note
% this script generates the correction for the convolution by the spectral
% response function as in the origional paper of Van der Tol et al. (2023).
% It does not work for the O2B band and it has been improved since. Use
% SRF_correction3.m instead.
% first run the algorithm. Then we have a lot in the workshpace to work
% with.
%master_selecteddays_revision;
%master_Cabauw2;
%% options
experiment1 = 1;
experiment2 = 0;
experiment3 = 0;
%% parameters for plotting of the results
alphabet = {'a','b','c','d'};
colors = [0 0 1;1 0 0];
%% the FWMH values for which the effect of the spectral response function is evaluated
FWHMi = (.01:.01:.7)';
%% parameters for the retrieval algorithm
stoptol = 1E-6;
opt = optimset('MaxIter',30,'TolFun',stoptol);
%% loading SCOPE reflectances and fluorescence
SCOPEoutputfolder = 'OHP_2021-06-25-1444';
rsd = dlmread(['..\output\SCOPE_simulation\', SCOPEoutputfolder, '\rsd.csv'],',',2,0); %#ok<*DLMRD>
rdd = dlmread(['..\output\SCOPE_simulation\', SCOPEoutputfolder, '\rdd.csv'],',',2,0);
fscope = dlmread(['..\output\SCOPE_simulation\', SCOPEoutputfolder, '\fluorescence.csv'],',',2,0);
wlS = load(['..\output\SCOPE_simulation\', SCOPEoutputfolder, '\wlS.txt']);
%% loading (earlier derived, with this script) correction spectra
%load SRCA.mat
%load SRCB.mat
%% loading (earlier derived, with this script) correction spectra
SRCA_SZA = zeros(59,4);
SRCB_SZA = zeros(10,4);
SRCAj = zeros(59,25,4);
SRCBj = zeros(10,25,4);
SRCA = zeros(59,1);
SRCB = zeros(10,1);
%% the wavelength of the FLoX
wl = D(1).wl;
%%
%SZA = [30,45,60,75];
SZA = [75,60,45,30];
cos_sza = cos(SZA/180*pi);
%% load MODTRAN data
%soltir_tp7([ModtranFile{site} '.tp7']);
s1 = importdata('FLEX-S3_SPAIN_SZA75.atm');
s2 = importdata('FLEX-S3_SPAIN_SZA60.atm');
s3 = importdata('FLEX-S3_SPAIN_SZA45.atm');
s4 = importdata('FLEX-S3_SPAIN_SZA30.atm');
%s1 = importdata('FLEX-S3_SPAIN_SZA30.atm');
%s2 = importdata('FLEX-S3_GER1_PC.atm');
%% Experiment 1. For a fixed value of FWMH (of 0.31), error as function of atmospheric path length
% In this piece of code, we also estimate a correction function for the
% effect of the SRF on the spectral shape of the O2A and O2B bands. This
% is estimated as follows:
% We estimate <L> as:
% Second: we estimate L_{approx} as: exp(log(<E>r)*a
% Third: SRC = (<L>-L_{approx}) / (1-a)
ai = (1.000:.004:1.1);
priorweight = 0;
FWHM = 0.31;
sigma = FWHM/2.355; % see https://en.wikipedia.org/wiki/Full_width_at_half_maximum
[piL,E] = deal(NaN*wl);
[ak,Fk,FFLDk,EX]= deal(NaN*ones(length(ai),1));
f = fscope(5,760-639);
for iSZA = 1:length(SZA)
switch iSZA
case 1, s = s1;
case 2, s = s2;
case 3, s = s3;
case 4, s = s4;
end
% interpolations and pre-processing
wl_MODTRAN = transform_wvl_from_vac_to_air(s.data(:,2));
index2 = find(wl_MODTRAN>p.wl_left(1) & wl_MODTRAN<p.wl_right(1));
T = s.data(:,3:20);
atmo.M = [T(:,1) T(:,3) T(:,4) T(:,5) T(:,12) T(:,16)];
atmo.Ta = 25; % influence of air temperature is negligible, but a value
% has to be provided.
%interpolate SCOPE simulated reflectance to MODTRAN wavelengths
SAIL.rsd = interp1(wlS,rsd(5,:),wl_MODTRAN);
SAIL.rdd = interp1(wlS,rdd(5,:),wl_MODTRAN);
% calculate irradiance
[Esun,Esky] = calcIrradiance(atmo,SAIL,wl_MODTRAN);
% Esky(isnan(Esky))=0;
% interpolate SCOPE fluorescence to the MODTRAN wavelengths
F_MODTRAN = interp1((640:850),fscope(5,:),wl_MODTRAN) * sum(Esun)/8.3980e+06; %scale fluorescence
E_MODTRAN = Esun;%+Esky;
SAIL.rsd(isnan(SAIL.rsd)) = 0;
F_MODTRAN(isnan(F_MODTRAN))= 0;
% normalize the band depth by the interpolated values
piL_MODTRAN0 = E_MODTRAN.*SAIL.rsd;
% x = polyfit(wl(I),piL(I)./E(I),2);
% normr = polyval(x,wl(index2));
% normpiL = normE.*normr;
normpiL = interp1([wl_MODTRAN(index2(1)),wl_MODTRAN(index2(end))],[piL_MODTRAN0(index2(1)),piL_MODTRAN0(index2(end))],wl_MODTRAN(index2));
for b = 1:3
% three cases: b=1: no SIF, no correction; b=2: SIF, no correction;
% b=3: SIF+ correction
for j = 1:length(ai)
a = ai(j);
aprior = a;
piL_MODTRAN = piL_MODTRAN0;
piL_MODTRAN(index2) = normpiL.* exp(log(piL_MODTRAN(index2)./normpiL)*a);
if b > 1
piL_MODTRAN = piL_MODTRAN+ F_MODTRAN;
end
% convolution
for k = 1:length(wl)
y = normpdf(wl_MODTRAN,wl(k),sigma);
E(k) = sum(y.*E_MODTRAN)/sum(y);
piL(k) = sum(y.*piL_MODTRAN)/sum(y);
end
[O2A,O2B] = retrievalF(wl,E,piL,opt,aprior,0.7,1,priorweight,p,SRCA/cos_sza((iSZA))*(b==3),SRCB/cos_sza((iSZA))*(b==3));
Fk(j) = O2A.F;
FFLDk(j) = O2A.iFLD;
ak(j) = O2A.a;
EX(j) = O2A.EXITFLAG;
if b==1
SRCAj(:,j,iSZA) = (log(O2A.piL./O2A.normpiL) - aprior* log(O2A.E./O2A.normE));
SRCBj(:,j,iSZA) = (log(O2B.piL./O2B.normpiL) - aprior* log(O2B.E./O2B.normE));
end
%keyboard
if iSZA==4 && j==6 && b<3 % just for one value of atmospheric path length (1.02) and SZA of 30 deg
figure(10), hold on
subplot(1,3,1)
plot(O2A.wl,log(O2A.piL./O2A.normpiL) - aprior*log(O2A.E./O2A.normE),'Color',colors(b,:));
hold on
ylabel('residual = log(L_{norm}) - a log(E_{norm})')
xlabel('wl (nm)')
set(gca, 'FontSize',12)
subplot(1,3,2) % for O3B
plot(O2B.wl,log(O2B.piL./O2B.normpiL) - aprior*log(O2B.E./O2B.normE),'Color',colors(b,:));%*(j+2)/(length(ai)+2))
%set(gca, 'ylim',[0, 0.03])
ylabel('residual = log(L_{norm}) - a log(E_{norm})')
xlabel('wl (nm)')
set(gca, 'FontSize',12)
hold on
end
if iSZA==2 &&j==6 && b==1 %extra fig: for SZA of 60 deg
figure(10)
subplot(1,2,1)
plot(O2A.wl,log(O2A.piL./O2A.normpiL) - aprior*log(O2A.E./O2A.normE),'Color','c');
hold on
subplot(1,2,2)
plot(O2B.wl,log(O2B.piL./O2B.normpiL) - aprior*log(O2B.E./O2B.normE),'Color','c');
hold on
end
end
if b == 1
for k = 1:size(SRCAj,1)
SRCA_SZA(k,iSZA) = (ai-1)' \ SRCAj(k,:,iSZA)';
end
for k = 1:size(SRCBj,1)
SRCB_SZA(k,iSZA) = (ai-1)' \ SRCBj(k,:,iSZA)';
c = polyfit(ai-1,SRCBj(k,:,iSZA),1);
SRCB_slope(k,iSZA) = c(1);
SRCB_offset(k,iSZA) = c(2);
end
end
if b>1 && iSZA==4 % with SIF, and without and with correction for the SRF
figure(8)
subplot(2,1,1), z=plot(ai,ak,'kx');
if b == 2, set(z, 'MarkerEdgeColor','b'), end
hold on
plot([1 1.1],[1,1.1],'k')
ylabel('a_{retrieved}')
subplot(2,1,2), z = plot(ai,Fk,'kx'); hold on
if b == 2, set(z, 'MarkerEdgeColor','b'), end
plot([1 1.1],[f,f],'k')
ylabel('SIF (Wm^{-1}\mum^{-1}sr^{-1})')
xlabel('a_{input}')
end
end
end
SRCA = SRCA_SZA(:,4)./cos(30/180*pi).^4;
SRCA = SRCA_SZA(:,4)./mean(SRCA_SZA(:,4));%mean(SRCA_SZA,2);
%SRCA = SRCAm./mean(SRCAm);
c = polyfit((SZA), mean(SRCA_SZA),2);
save('SRCA_ground.mat','SRCA', 'c')
%SRCB = SRCB_SZA(:,4)*cos(30/180*pi);
SRCB = SRCB_SZA(:,4)./mean(SRCB_SZA(:,4));
c = polyfit((SZA), mean(SRCB_SZA),2);
save('SRCB_ground.mat','SRCB', 'c')
%SRCB = [SRCB_offset(:,4), SRCB_slope(:,4)]./cos(30/180*pi).^4;
%%
figure(10), hold on
subplot(131)
plot(O2A.wl,SRCAj(:,6,2),'c')
legend('\theta_s=30^o','\theta_s=30^o, with F','\theta_s=60^o')
title('a')
subplot(132),
title('b')
subplot(133)
cos_zsa = cos([75,60,45,30]/180*pi);
for k = 1:4, plot(ai,SRCAj(14,:,k)*cos_zsa(k),'x'), hold on, end
ylabel('(log(L_{norm}) - a log(E_{norm}))*cos(\theta_s)')
xlabel('a')
set(gca, 'FontSize',12)
title('c')
legend('\theta_s = 75^o', '\theta_s = 60^o','\theta_s = 45^o','\theta_s = 30^o', 'Location','northwest')
%%
figure(100),
%subplot(1,2,1)
% plot(O2A.wl,log(O2A.piL./O2A.normpiL) - aprior*log(O2A.E./O2A.normE),'Color',colors(b,:));%*(j+2)/(length(ai)+2))
wl = O2A.wl;
hold on
for k = 5:25
for j = 4:4
%plot(wl,SRCA_SZA(:,j)*(1.02-1)/cos_zsa(j));
plot(wl,SRCAj(:,k,j)/(ai(k)-1)/(cos_zsa(j)),'r' );
hold on
% plot(O2A.wl,log(O2A.piL./O2A.normpiL) - aprior*log(O2A.E./O2A.normE),'Color','r');%*(j+2)/(length(ai)+2))
% plot(wl,SRCAj(:,k,j)/(ai(k)-1)/cos_zsa(j));
hold on
end
end
%set(gca, 'ylim',[0,0.1])
ylabel('residual = log(L_{norm}) - a log(E_{norm})')
xlabel('wl (nm)')
set(gca, 'FontSize',12)
%subplot(1,2,2)
%plot(O2B.wl,log(O2B.piL./O2B.normpiL) - aprior*log(O2B.E./O2B.normE),'Color',colors(b,:));%*(j+2)/(length(ai)+2))
%%set(gca, 'ylim',[0, 0.03])
%ylabel('residual = log(L_{norm}) - a log(E_{norm})')
%xlabel('wl (nm)')
%set(gca, 'FontSize',12)
%hold on
%end
%% Experiment 2. Error as function of FWHM for two values of atmospheric path length.
% this is only for O2A!
if experiment2
for c = 1:2 % loop over two cases
switch c
case 1
a = 1; % case 1, TOC with no fluorescence
case 2
a = 1.02; %case 2, tall tower with fluorescence
end
aprior = a;
% we extrapolate the high-res spectrum to ML
piL_MODTRAN = piL_MODTRAN0;
piL_MODTRAN(index2) = normpiL.* exp(log(piL_MODTRAN(index2)./normpiL)*a);
if c>1 % add fluorescence for the second case
piL_MODTRAN = piL_MODTRAN+ F_MODTRAN;
end
% convolution
[piL,E] = deal(NaN*wl);
[ak,Fk,FFLDk,EX]= deal(NaN*ones(length(FWHMi),1));
for j = 1:length(FWHMi)
FWHM = FWHMi(j);
%FWHM = 0.3;
sigma = FWHM/2.355; % see https://en.wikipedia.org/wiki/Full_width_at_half_maximum
for k = 1:length(wl)
y = normpdf(wl_MODTRAN,wl(k),sigma);
E(k) = sum(y.*E_MODTRAN)/sum(y);
piL(k) = sum(y.*piL_MODTRAN)/sum(y);
end
priorweight = 0; % no weights on the prior value (leave the retrieval free)
%[O2A,O2B] = retrievalF(wl,E,piL,opt,aprior,0.7,1,priorweight,p,0*SRC,0*SRCB);
[O2A,O2B] = retrievalF(wl,E,piL,opt,aprior,0.7,1,priorweight,p,0*SRCA,0*SRCB);
Fk(j) = O2A.F;
FFLDk(j) = O2A.iFLD;
ak(j) = O2A.a;
EX(j) = O2A.EXITFLAG;
end
figure (7)
subplot(2,2,c),
z=plot(FWHMi,[ak ones(length(FWHMi),1)*aprior]);
set(z(2), 'Color','k', 'LineWidth',2)
set(gca,'FontSize',11)
set(gca,'ylim',[.995 1.021])
ylabel('a')
title(alphabet{c});
subplot(2,2,c+2),
z = plot(FWHMi,[Fk FFLDk ones(length(FWHMi),1)*fscope(5,760-639)*(c>1)]);
set(z(3), 'Color','k', 'LineWidth',2)
set(gca,'FontSize',11)
set(gca,'ylim',[-.8 0.6])
ylabel('F (Wm^{-2}\mum^{-1}sr^{-1})')
%legend('Retrieved','Input')
xlabel('FWHM (nm)')
title(alphabet{c+2})
end
%subplot(313), plot(FWHMi,EX)
end
%% Experiment 3. Test this for different atmospheric profiles and elevation differences.
if experiment3
files = {'ITALY1', 'SPAIN', 'GER1', 'GER2'};
heights =[7,81.3; 258,324; 111,125; 069,111 ];
for k = 1:4
s1 = importdata(['FLEX-S3_' files{k} '.atm']);
s2 = importdata(['FLEX-S3_' files{k} '_PC.atm']);
for j = 1:2
switch j
case 1, s = s2; if k==4; s = s1; end
case 2, s = s1; if k==4; s = s2; end
end
T = s.data(:,3:20);
atmo.M = [T(:,1) T(:,3) T(:,4) T(:,5) T(:,12) T(:,16)];
atmo.Ta = 25;
[Esun,Esky] = calcIrradiance(atmo,SAIL,wl_MODTRAN);
% figure(12)
% plot(wl_MODTRAN,Esun), hold on
% set(gca, 'xlim', [400 1200])
E_MODTRAN = Esun;
index2 = find(wl_MODTRAN>p.wl_left(1) & wl_MODTRAN<p.wl_right(1));
% normalize the band depth by the interpolated values
normE = interp1([wl_MODTRAN(index2(1)),wl_MODTRAN(index2(end))],[E_MODTRAN(index2(1)),E_MODTRAN(index2(end))],wl_MODTRAN(index2));
E_MODTRANO2A(:,j) = E_MODTRAN(index2)./normE; %#ok<*SAGROW>
%figure(12)
%plot(wl_MODTRAN(index2),E_MODTRANO2A), hold on
end
x=log(E_MODTRANO2A(:,1));
y=log(E_MODTRANO2A(:,2));
slope = x \ y;
ymod = slope*x;
FS = interp1((640:850),fscope(5,:),wl_MODTRAN(index2));
z = log(exp(y)+FS./normE);
figure(12)
subplot(2,2,k)
plot(wl_MODTRAN(index2),[x-y,x-ymod,y-ymod]);%, z-ymod])
xlabel('wl')
ylabel('log(E_{norm})')
title(alphabet{k})
x1(k) = (1-barometric(heights(k,2)-heights(k,1)))/barometric(heights(k,2)-heights(k,1));
slp(k) = slope;
end
%
figure(13), clf
plot(1+x1,slp,'x','MarkerSize',8)
hold on
plot([1, 1.01],[1, 1.01],'k')
xlabel('a_{barometric}')
ylabel('a_{MODTRAN}')
end