reads CbPM from web

get_cbpm.m

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get CbPM carbon mg / m**3: 
% This script reads CbPM data from web and saves to file. 
%
% Source: http://www.science.oregonstate.edu/ocean.productivity/custom.php
%
% L. Gloege 2016 (Augmented a script from A.Fay)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear; clc

% Which satellite do you want to read?
% s = SEAWIFS 
% m = MODIS
satellite = 'm';  

% defines year range for seawifs and modis satellite
if strcmp(satellite,'s')==1
    yearRange = [1997 2010];
elseif strcmp(satellite,'m')==1
    yearRange = [2010 2011];
else
    error([satellite ' is not an option. choose s for seawif or m for modis']);
end

% day of year for nonleap year (mo) and leapyears (mol)
mo  = ['001';'032';'060';'091';'121';'152';'182';'213';'244';'274';'305';'335'];
mol = ['001';'032';'061';'092';'122';'153';'183';'214';'245';'275';'306';'336'];

% initialize time vector
time_CbPM_carbon = [];
iter = 1;

for yr = yearRange(1):yearRange(2)
    disp(yr)
    for m = 1:12
        % Controls Leap Years
        if yr == 2000 || yr == 2004 || yr == 2008 || yr == 2012 %leap years
            mon = mol;
        else
            mon = mo;
        end
        % Defines data URL
        fl1 = 'http://orca.science.oregonstate.edu/data/1x2/monthly/';    
        fl2 = ['carbon.' satellite '.r2014.gsm.v8/hdf/'];
        filename = ['carbon.' num2str(yr) num2str(mon(m,:)) '.hdf'];
        url=[fl1 fl2 filename '.gz'];
        try
            outfilename = websave([filename '.gz'],url);
            system(['gunzip ' outfilename])  

            %load in hdf file
            file_info = hdfinfo(filename);
            sds_info = file_info.SDS;
            x = hdfread(sds_info);
            [nrow,ncol]=size(x);
            x(x==-9999.)=NaN;
            x = double(x);  % Loaded as single, needs be double
            x2 = flipud(x); % orients globe to correct direction

            if exist('lat_Cbpm_carbon','var')==0
                lat_Cbpm_carbon=linspace(-90,90,nrow);
                lon_Cbpm_carbon=linspace(-180,180,ncol);
                [X_Cbpm_carbon,Y_Cbpm_carbon]=meshgrid(lon_Cbpm_carbon,lat_Cbpm_carbon);
            end

            % Allocate space for this
            CbPM_carbon(iter,:,:) = x2;
            
            % update time vector in [year month day] format
            time_CbPM_carbon = [time_CbPM_carbon; yr m 1];
            
            % clear variables you do not need anymore
            clear x x2 filename file* sds_info
            
            %update Iteration
            iter = iter+1;
        catch
            continue
        end
    end
end

% put data into structure
disp('Storing data as structure...')
out.time = time_CbPM_carbon;
out.biomass = CbPM_carbon;
out.lat = lat_Cbpm_carbon;
out.lon = lon_Cbpm_carbon;
out.X = X_Cbpm_carbon;
out.Y = Y_Cbpm_carbon;
out.UNITS = {'biomass units are mg m**3'; 'time units YYYY MM DD'};
out.SOURCE = {'http://www.science.oregonstate.edu/ocean.productivity/custom.php'};
out.ACCESSDATE = [date];

% save data
disp('Saving data...')
if strcmp(satellite,'s')==1
    outFile = 'cbpm_seawifs.mat';
    cbpm_seawifs=out; clear out;
    save(outFile,'cbpm_seawifs','-v7.3');
elseif strcmp(satellite,'m')==1
    outFile = 'cbpm_modis.mat';
    cbpm_modis=out; clear out;
    save(outFile,'cbpm_modis','-v7.3');
else
    error('Satellite needs to be s or m')
end

% completetion statement
disp('Complete!')