oceanography-visualizations/Aug6_chl_cal.m at master · evb123/oceanography-visualizations · GitHub

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
%% Aug 6 - correcting eco to ctd Aug 2 - ctd correctedregressing...%% July 25, 2018 - this script is a modification of model II regression script sent by Filipa
% the corrected ecopuck chlorophyll is still really off, never approaches
% zero - actually because ctd corrected look a bit high?

%CTD chl correction
cor_chl=combdat.ctd.raw.ctd_chl*1.4905+0.246;

ctd_chl=cor_chl(:);
eco_chl=combdat.ctd.raw.eco_chl(:);

close all
xx=ctd_chl;
y=eco_chl;

%can't have nans
aa=~isnan(xx) & ~isnan(y);

[a,b,sa,sb,r,pv] = rma(xx(aa),y(aa),size(eco_chl,2));
[b,bint,l,ang,~] = rmaregress(xx,y,[2 2]);
P(1)=b(2);
P(2)=b(1);
L(1)=bint(4);
L(2)=bint(3);
U(1)=bint(2);
U(2)=bint(1);
x=[nanmin(xx);nanmax(xx)];
yz=x*L(1)+L(2);
f=fill([x; flipud(x); x(1)], [x*L(1)+L(2); flipud(x*U(1)+U(2)); yz(1)], 'r');
set(f, 'linestyle', 'none', 'facecolor', [1.0000    0.7500    0.7930]);

hold on
t=plot(eco_chl,ctd_chl,'.');
set(t, 'markersize', 7)
xlabel('Ecopuck chl(ug/L)')
ylabel('CTD chl (ug/L)')

hold on;
% Create variable name p1-p3
p=plot(x,x*P(1)+P(2), '--','Color', 'r');
l=plot(x,x*L(1)+L(2), '-','Color', 'r');
u=plot(x,x*U(1)+U(2), '-','Color', 'r');

legend([p, l],{['y=' num2str(P(1)) 'x+' num2str(P(2)) 10 'r^2=' num2str(r) 10 'p=' num2str(pv(2))], [ 10 '95% CI' 10 '.']}, 'location', 'northwest')
title('Model II Regression - ctd chl calibration')

combdat.ctd.raw.ctd_chl_corr=cor_chl;


%% calibrating chla ctd

eco_chl_cal=(0.8805*combdat.ctd.raw.eco_chl)+0.34788;

close all

clf

for i=1:7
    figure(i)
plot(combdat.ctd.raw.eco_chl(:,i),combdat.ctd.zdepth(:,i),'o','markersize',3)
hold on
plot(combdat.ctd.raw.ctd_chl_corr(:,i),combdat.ctd.zdepth(:,i),'o','markersize',3)
hold on
plot(eco_chl_cal(:,i),combdat.ctd.zdepth(:,i))
title('Ecopuck - calibration')
xlabel('Chlorophyll (ug/l)')
ylabel('Depth (m)')
legend({'raw eco chl','raw ctd chl','calibrated eco chl'},'location','south')
end

%% saving ctd ecopuck cal

combdat.ctd.raw.eco_chl_cal=eco_chl_cal;

%% looking at corrected CTD values, do they appear strange? look okay actually

for i=1:7
    figure(i)
plot(combdat.ctd.raw.ctd_chl_corr(:,i),combdat.ctd.zdepth(:,i))
end

%% next, apply correction to RCF eco puck, then calibrate RCF RBR

rcf_eco_chl_cal=(0.8805*combdat.rcf.raw.eco_chl)+0.34788;
close all
for i=10:21
    figure(i)
plot(rcf_eco_chl_cal(:,i),combdat.rcf.zdepth(:,i))
end

aa=rcf_eco_chl_cal<0;
rcf_eco_chl_cal(aa)=nan;

%% linear regression for rcf after calibrating ecopuck rcf

ctd_chl=combdat.rcf.raw.rbr_chl(:);
eco_chl=rcf_eco_chl_cal(:);

close all
xx=ctd_chl;
y=eco_chl;

%can't have nans
aa=~isnan(xx) & ~isnan(y);

[a,b,sa,sb,r,pv] = rma(xx(aa),y(aa),size(eco_chl,2));
[b,bint,l,ang,~] = rmaregress(xx,y,[2 2]);
P(1)=b(2);
P(2)=b(1);
L(1)=bint(4);
L(2)=bint(3);
U(1)=bint(2);
U(2)=bint(1);
x=[nanmin(xx);nanmax(xx)];
yz=x*L(1)+L(2);
f=fill([x; flipud(x); x(1)], [x*L(1)+L(2); flipud(x*U(1)+U(2)); yz(1)], 'r');
set(f, 'linestyle', 'none', 'facecolor', [1.0000    0.7500    0.7930]);

hold on
t=plot(xx(aa),y(aa),'.');
set(t, 'markersize', 7)
ylabel('RCF Ecopuck chl(ug/L)')
xlabel('RBR chl (ug/L)')

hold on;

p=plot(x,x*P(1)+P(2), '--','Color', 'r');
l=plot(x,x*L(1)+L(2), '-','Color', 'r');
u=plot(x,x*U(1)+U(2), '-','Color', 'r');

legend([p, l],{['y=' num2str(P(1)) 'x+' num2str(P(2)) 10 'r^2=' num2str(r) 10 'p=' num2str(pv(2))], [ 10 '95% CI' 10 '.']}, 'location', 'northwest')
title('Model II Regression - RCF CHL calibration')


%% calibrating chla rcf - this looks fantastic

rbr_chl_cal=(combdat.rcf.raw.rbr_chl*0.3327)+0.177;

close all

clf

for i=1
    figure(i)
plot(rcf_eco_chl_cal(:,i),combdat.rcf.zdepth(:,i),'o','markersize',3)
hold on
plot(combdat.rcf.raw.rbr_chl(:,i),combdat.rcf.zdepth(:,i),'o','markersize',3)
hold on
plot(rbr_chl_cal(:,i),combdat.rcf.zdepth(:,i))
title('RBR - calibration')
xlabel('Chlorophyll (ug/l)')
ylabel('Depth (m)')
legend({'rcf eco chl-cal','raw rbr chl','cal rbr chl'},'location','south')
end

%% saving calibrated files

combdat.rcf.raw.eco_chl_cal=rcf_eco_chl_cal;
combdat.rcf.raw.rbr_chl_cal=rbr_chl_cal;