How to set level values of a variable in a nc file

Hi Friends

With the below code

ncfile_1 = 'A20150322015059.L3m_MO_CHL_chlor_a_4km.nc';
lat_1 = ncread(ncfile_1,'lat') ;
lon_1 = ncread(ncfile_1,'lon') ;
chlor_a_1 = ncread(ncfile_1,'chlor_a');
[X_1,Y_1] = meshgrid(lon_1,lat_1) ;
xi_1 = linspace(30,100,1000) ;
yi_1 = linspace(0,30,1000) ;
[Xi_1,Yi_1] = meshgrid(xi_1,yi_1);
iwant_1 = interp2(X_1,Y_1,chlor_a_1',Xi_1,Yi_1)' ;
pcolor(xi_1,yi_1,iwant_1'); shading interp;
c = colorbar;
cmap = jet(255);
cmap(:,3) = 0;
colormap(cmap)
caxis([-5, 5])

I could able to interpolate and plot chlor_a conc. with respective x ,y need to display the minimum and maximum level of chlorophyll value for example min value <=10 and max value >= 0.

I have tried with this code but shows error

if chlor_a_1>=0 && chlor_a_1<=10
disp(chlor_a_1);
[Xi_1,Yi_1,chlor_a_1] = peaks;
plot(Xi_1,Yi_1,chlor_a_1,49)

kindly help

regards

[Mathieu NOE]

hello

maybe you should share the data as well

[Karthik M]

data link https://drive.google.com/file/d/1hAeVz54bKLA1dDyk5uxMyjJIppG-XS77/view?usp=sharing

[Karthik M]

Dear @Mathieu NOE

Thank you for the response

Answer 1

[Mathieu NOE]

hello again3

so I tried to a few things to get the min and max points of the data and display them (the big crosses)

I am still unsure about what was the intention : this is not clear to me : min value <=10 and max value >= 0.

your "raw" data has min value = 0.0593 and max value = 84.0117 but at the end you plot C axis is limited to 5 , so I guessed that the intention to find the max point is for the data after i's being truncated to scale 0 to 5 , so I decided to remove the data outside that range otherwise the max point will not be located at value = 5 . Now when you say min value <=10 and max value >= 0., I don't know what this 10 means

Code is :

ncfile_1 = 'A20150322015059.L3m_MO_CHL_chlor_a_4km.nc';
lat_1 = ncread(ncfile_1,'lat') ;
lon_1 = ncread(ncfile_1,'lon') ;
chlor_a_1 = ncread(ncfile_1,'chlor_a');
[X_1,Y_1] = meshgrid(lon_1,lat_1) ;
nn = 1000;
xi_1 = linspace(30,100,nn) ;
yi_1 = linspace(0,30,nn) ;
[Xi_1,Yi_1] = meshgrid(xi_1,yi_1);
iwant_1 = interp2(X_1,Y_1,chlor_a_1',Xi_1,Yi_1)' ;

% I could able to interpolate and plot chlor_a conc. with respective x ,y 
% need to display the minimum and maximum level of chlorophyll value for example min value <=10 and max value >= 0.
% I have tried with this code but shows error

% rescale data between 0 and 10 (or 5 ?)
ind = find(iwant_1<0 | iwant_1>5);
iwant_1(ind) = NaN; % remove data out of range

% find min and max points
[min_val,min_ind] = min(iwant_1',[],'all','linear');
[r1,c1]=ind2sub(nn,min_ind);
x_min = xi_1(c1);
y_min = yi_1(r1);

[max_val,max_ind] = max(iwant_1',[],'all','linear');
[r2,c2]=ind2sub(nn,max_ind);
x_max = xi_1(c2);
y_max = yi_1(r2);

% plot 
figure(1)
pcolor(xi_1,yi_1,iwant_1'); shading interp;
c = colorbar;
cmap = jet(255);
cmap(:,3) = 0;
colormap(cmap)
caxis([-5, 5])
hold on
plot(x_min,y_min,'k +', 'MarkerSize', 40);
plot(x_max,y_max,'m +', 'MarkerSize', 40);
hold off
legend('','min','max');


% if chlor_a_1>=0 && chlor_a_1<=10
% disp(chlor_a_1);
% [Xi_1,Yi_1,chlor_a_1] = peaks;
% plot(Xi_1,Yi_1,chlor_a_1,49)

[Karthik M]

Dear @Mathieu NOE

Thank you for your code

while evaluating your script I have found this error

Error using min

Invalid option. Option must be 'omitnan' or 'includenan'.

I was trying my level best but still couldn't arrive what I need

you ar right need to find the min and max value of data along x and y

see the max conc. of chlro_a was with in the range value 0 and 10

After review took 10 as the reference chlor conc. value with red as its colorbar

scaling to that value colormap (cmap); c-axis [0, 5 ]

.....

Working on prediction of HAB hotspot along North Indian Ocean

Using chlorophyll as primary indicator trying to find hotspot and variation among seasons

With remote sensing data am trying to predict its seasonal trends

Need to plot spatial distribution of chlor_a within desired level

At present working on last 10 years data

Took reference to write codes to read the .nc file

Extracted 1000 points of chlor_a values for lat [0 30] lon [30 100]

Found min and max value of the chlor_a data points

Plot shows thick chlor_a conc. from 0 to 5 colorbar range

Need to plot histogram of the data points for min and max value

....

By means of subtraction (present to past year) comparing 2 years same month of extracted chlor_a data

[+ve] value means max chlor_a conc. [-ve] value means less conc.

This comparison will identify max persistence of chlor_a

objective to find particular month chlor conc. hotspot for successive years

similary need to compare for weekly data to find the hotspot variation

Similarly need to perform for other variables as that of to chlor_a

Waitng for your suggestion and your valuable inputs

data link

https://drive.google.com/file/d/1hAeVz54bKLA1dDyk5uxMyjJIppG-XS77/view?usp=sharing

https://drive.google.com/file/d/1XIcbaEbqLQOPgi0Ooq72J2elvZwfQnoO/view?usp=sharing

regards

[Walter Roberson]

Use

[min_val,min_ind] = min(reshape(iwant_1',[],1));

[max_val,max_ind] = max(reshape(iwant_1',[],1));

[Karthik M]

Dear @Walter Roberson

Thank you for the response

Your code worked fine

while including this line iwant_2(ind) = NaN; I don't find plot

while excluding this line I find plot...

Hope you understood my requirement

want to save file in nc format for 1st file before plot and same for next ...

To follow below steps need your suggestion, kindly help

Need to subtract (present to past year) compare 2 years same month of extracted chlor_a data

[+ve] value means max chlor_a conc. [-ve] value means less conc.

This comparison will identify max persistence of chlor_a

objective to find particular month chlor conc. hotspot for successive years

similary need to compare for weekly data to find the hotspot variation

Similarly need to perform for other variables as that of to chlor_a

Waitng for your suggestion and your valuable inputs

regards

[Walter Roberson]

I do not see an iwant_2 in your code, so I do not know how it is being computed

Is ind still the result of ind = find(iwant_1<0 | iwant_1>5); ?

[Karthik M]

Hi @Walter Roberson

Thank you for the response

yes, ind value was defined with that code shared by Mathieu NOE

Evaluate with this code to get iwant_2

ncfile_2 = 'A20160322016060.L3m_MO_CHL_chlor_a_4km.nc';
lat_2 = ncread(ncfile_2,'lat') ;
lon_2 = ncread(ncfile_2,'lon') ;
chlor_a_2 = ncread(ncfile_2,'chlor_a');
[X_2,Y_2] = meshgrid(lon_2,lat_2) ;
nn = 1000;
xi_2 = linspace(30,100,nn) ;
yi_2 = linspace(0,30,nn) ;
[Xi_2,Yi_2] = meshgrid(xi_2,yi_2);
iwant_2 = interp2(X_2,Y_2,chlor_a_2',Xi_2,Yi_2)' ;

ind = find(iwant_2<10 | iwant_2>0);
%iwant_2(ind) = NaN;

[min_val,min_ind] = min(reshape(iwant_2',[],1));
[r1,c1]=ind2sub(nn,min_ind);
x_min = xi_2(c1);
y_min = yi_2(r1);

[max_val,max_ind] = max(reshape(iwant_2',[],1));
[r2,c2]=ind2sub(nn,max_ind);
x_max = xi_2(c2);
y_max = yi_2(r2);

 figure(2)
pcolor(xi_2,yi_2,iwant_2'); shading interp;
c = colorbar;
cmap = jet(255);
cmap(:,2) = 0;
colormap(cmap)
caxis([0, 5])
hold on
plot(x_min,y_min,'k +', 'MarkerSize', 10);
plot(x_max,y_max,'m +', 'MarkerSize', 10);
hold off
legend('','min','max');

kidly help, waiting for your valuable suggestion

[Mathieu NOE]

hello

I simply run the same exact code with the second nc file and got no issue. It works as well

% ncfile_1 = 'A20150322015059.L3m_MO_CHL_chlor_a_4km.nc';
ncfile_1 = 'A20160322016060.L3m_MO_CHL_chlor_a_4km.nc';
lat_1 = ncread(ncfile_1,'lat') ;
lon_1 = ncread(ncfile_1,'lon') ;
chlor_a_1 = ncread(ncfile_1,'chlor_a');
[X_1,Y_1] = meshgrid(lon_1,lat_1) ;
nn = 1000;
xi_1 = linspace(30,100,nn) ;
yi_1 = linspace(0,30,nn) ;
[Xi_1,Yi_1] = meshgrid(xi_1,yi_1);
iwant_1 = interp2(X_1,Y_1,chlor_a_1',Xi_1,Yi_1)' ;

% I could able to interpolate and plot chlor_a conc. with respective x ,y 
% need to display the minimum and maximum level of chlorophyll value for example min value <=10 and max value >= 0.
% I have tried with this code but shows error

% rescale data between 0 and 10 (or 5 ?)
ind = find(iwant_1<0 | iwant_1>5);
iwant_1(ind) = NaN; % remove data out of range

% find min and max points
% [min_val,min_ind] = min(iwant_1',[],'all','linear');
[min_val,min_ind] = min(reshape(iwant_1',[],1));
[r1,c1]=ind2sub(nn,min_ind);
x_min = xi_1(c1);
y_min = yi_1(r1);

% [max_val,max_ind] = max(iwant_1',[],'all','linear');
[max_val,max_ind] = max(reshape(iwant_1',[],1));

[r2,c2]=ind2sub(nn,max_ind);
x_max = xi_1(c2);
y_max = yi_1(r2);

% plot 
figure(1)
pcolor(xi_1,yi_1,iwant_1'); shading interp;
c = colorbar;
cmap = jet(255);
cmap(:,3) = 0;
colormap(cmap)
caxis([-5, 5])
hold on
plot(x_min,y_min,'k +', 'MarkerSize', 40);
plot(x_max,y_max,'m +', 'MarkerSize', 40);
hold off
legend('','min','max');


% if chlor_a_1>=0 && chlor_a_1<=10
% disp(chlor_a_1);
% [Xi_1,Yi_1,chlor_a_1] = peaks;
% plot(Xi_1,Yi_1,chlor_a_1,49)

[Karthik M]

Dear @Mathieu NOE

Thank you for the response

Your code worked fine

while including this line iwant_2(ind) = NaN; I didn't find plot

while excluding this line I find plot...

Hope you understood my requirement

want to save file in nc format for 1st file before plot and same for next ...

To follow below steps need your suggestion, kindly help

Need to subtract (present to past year) compare 2 years same month of extracted chlor_a data

[+ve] value means max chlor_a conc. [-ve] value means less conc.

This comparison will identify max persistence of chlor_a

objective to find particular month chlor conc. hotspot for successive years

similary need to compare for weekly data to find the hotspot variation

Similarly need to perform for other variables as that of to chlor_a

Waitng for your suggestion and your valuable inputs

regards

[Walter Roberson]

ind = find(iwant_2<10 | iwant_2>0);

Consider the values -1, 0, 1, 9, 10, 11

-1 < 10 so it matches the first part of the condition but not the second part of the condition. But you use "or" and one result is enough for "or"

0 < 10 so it matches the first part of the condition and the second part of the condition

1 < 10 so it matches the first part of the condtion and the second part of the condition

9 < 10 so it matches the first part of the condition and the second part of the condition

10 < 10 fails so the first part of the condition fails, but 10 > 0 so the second part of the condition matches, and you are using "or"

11 < 10 fails so the first part of the condition fails, but 10 > 0 so the second part of the condition matches, and you are using "or"

So... all of the values would be selected. And then you change all of them to nan.

If you want to set values that are outside the range 0 to 10 (exclusive) to nan, then you need

ind = find(iwant_2>10 | iwant_2<0);

if you want to set values that are inside the range 0 to 10 (exclusive) to nan, then you need

ind = find(iwant_2 > 0 & iwant_2<10);

[Karthik M]

Thanks @Walter Roberson for your deatiled eplaination

kindly help for the below steps using 2 nc files

want to save file in nc format for 1st file before plot and same for next ...

Need to subtract (present to past year) compare 2 years same month of extracted chlor_a data

[+ve] value means max chlor_a conc. [-ve] value means less conc.

This comparison will identify max persistence of chlor_a

objective to find particular month chlor conc. hotspot for successive years

I couldn't able to arrive what I want

regards

[Karthik M]

Dear @Walter Roberson

kindly help for the below steps using 2 nc files

want to save file in nc format for 1st file before plot and same for next ...

Need to subtract (present to past year) compare 2 years same month of extracted chlor_a data

[+ve] value means max chlor_a conc. [-ve] value means less conc.

This comparison will identify max persistence of chlor_a

objective to find particular month chlor conc. hotspot for successive years

I couldn't able to arrive what I want

regards