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co2usa_los_angeles_to_netCDF.m
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% clear all
% close all
set(0,'DefaultFigureWindowStyle','docked')
%% netCDF creation documentation
% Following the Climate Forecasting conventions for netCDF files documented here:
% http://cfconventions.org/
% http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html
%
% Also following the Attribute Convention for Data Discovery version 1.3
% https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3
%
% Variables must have a standard_name, a long_name, or both.
% A standard_name is the name used to identify the physical quantity. A standard name contains no whitespace and is case sensitive.
% A long_name has an ad hoc, human readable format.
% A comment can be used to add further detail, but is not required.
%
% Time and date formating follow this convention:
% https://www.edf.org/health/data-standards-date-and-timestamp-guidelines
%
% Data will be archived at the ORNL DAAC:
% https://daac.ornl.gov/PI/
%
%% Creation date
% date_created: The date on which this version of the data was created. Recommended.
date_created_now = datetime(now,'ConvertFrom','datenum','TimeZone','America/Denver'); date_created_now.TimeZone = 'UTC';
date_created_str = datestr(date_created_now,'yyyy-mm-ddThh:MM:ssZ');
% date_issued: The date on which this data (including all modifications) was formally issued (i.e., made available to a wider audience). Suggested.
date_issued_now = datestr(now,'yyyy-mm-dd');
date_issued = datetime(2021,05,03);
date_issued_str = datestr(date_issued,'yyyy-mm-ddThh:MM:ssZ');
% Working folders
if ~exist('currentFolder','var'); currentFolder = pwd; end
if ~exist('readFolder','var'); readFolder = fullfile(currentFolder(1:regexp(currentFolder,'gcloud.utah.edu')+14),'data','co2-usa','data_input'); end
if ~exist('writeFolder','var'); writeFolder = fullfile(currentFolder(1:regexp(currentFolder,'gcloud.utah.edu')+14),'data','co2-usa','synthesis_output'); end
%% City & provider information:
city = 'los_angeles';
city_long_name = 'Los Angeles';
city_url = 'https://megacities.jpl.nasa.gov/';
i=1;
provider(i).name = 'Jooil Kim';
provider(i).address1 = 'Scripps Institution of Oceanography';
provider(i).address2 = '9500 Gilman Dr #0244';
provider(i).address3 = 'La Jolla, CA 92093-0244';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Scripps Institution of Oceanography';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0002-2610-4882';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=i+1;
provider(i).name = 'Kristal R. Verhulst';
provider(i).address1 = 'Jet Propulsion Laboratory M/S 233-300';
provider(i).address2 = '4800 Oak Grove Drive';
provider(i).address3 = 'Pasadena, CA 91109';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Jet Propulsion Laboratory, California Institute of Technology';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0001-5678-9678';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=i+1;
provider(i).name = 'Charles E. Miller';
provider(i).address1 = 'Jet Propulsion Laboratory M/S 183-501';
provider(i).address2 = '4800 Oak Grove Drive';
provider(i).address3 = 'Pasadena, CA 91109';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Jet Propulsion Laboratory, California Institute of Technology';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0002-9380-4838';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=i+1;
provider(i).name = 'Ray F. Weiss';
provider(i).address1 = 'Scripps Institution of Oceanography';
provider(i).address2 = '9500 Gilman Dr #0244';
provider(i).address3 = 'La Jolla, CA 92093-0244';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Scripps Institution of Oceanography';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0001-9551-7739';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=i+1;
provider(i).name = 'Ralph F. Keeling';
provider(i).address1 = 'Scripps Institution of Oceanography';
provider(i).address2 = '9500 Gilman Dr #0244';
provider(i).address3 = 'La Jolla, CA 92093-0244';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Scripps Institution of Oceanography';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0002-9749-2253';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=i+1;
provider(i).name = 'Steve Prinzivalli';
provider(i).address1 = 'Earth Networks Inc.';
provider(i).address2 = '12410 Milestone Center Dr., Suite 300';
provider(i).address3 = 'Germantown, MD 20876';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Earth Networks Inc.';
provider(i).email = '[email protected]';
provider(i).orcid = '';
provider(i).parameter = 'Provider has contributed measurements for: ';
%% Site meta data
clear site % start fresh
site.reference = 'Verhulst, Kristal R., Anna Karion, Jooil Kim, Peter K. Salameh, Ralph F. Keeling, Sally Newman, John Miller, et al. Carbon Dioxide and Methane Measurements from the Los Angeles Megacity Carbon Project – Part 1: Calibration, Urban Enhancements, and Uncertainty Estimates. Atmospheric Chemistry and Physics 17, no. 13 (July 7, 2017): 8313–41. https://doi.org/10.5194/acp-17-8313-2017.';
site.groups = {}; % List of the site "code_species_inletHt"
site.species = {}; % List of the "species"
site.date_issued = date_issued;
site.date_issued_str = date_issued_str;
site.date_created_str = date_created_str;
version_folder = 'v20210503';
fn = dir(fullfile(readFolder,city,version_folder,'LAM_sites.csv'));
fid = fopen(fullfile(fn.folder,fn.name));
read_dat = textscan(fid,'%s%s%f%s%s%f%f%f%f%f','HeaderLines',1,'Delimiter',',','CollectOutput',true,'TreatAsEmpty','NaN');
fclose(fid);
for i = 1:size(read_dat{1},1)
site.codes{1,i} = read_dat{1}{i,1};
site.(site.codes{i}).name = replace(read_dat{1}{i,2},' ','_');
site.(site.codes{i}).long_name = read_dat{1}{i,2};
site.(site.codes{i}).code = site.codes{1,i};
site.(site.codes{i}).country = 'United States';
site.(site.codes{i}).time_zone = 'America/Los_Angeles'; % use timezones to find out the available time zone designations.
site.(site.codes{i}).inlet_height = num2cell(unique(read_dat{4}(i,[4,5])));
for j = 1:length(site.(site.codes{i}).inlet_height); site.(site.codes{i}).inlet_height_long_name{1,j} = [num2str(site.(site.codes{i}).inlet_height{1,j}),'m']; end
site.(site.codes{i}).files = dir(fullfile(readFolder,city,version_folder,[site.codes{1,i},'*.csv']));
site.(site.codes{i}).species = {};
for k = 1:length(site.(site.codes{i}).files)
idx = strfind(site.(site.codes{i}).files(k).name,'-');
site.(site.codes{i}).species = unique([site.(site.codes{i}).species,{site.(site.codes{i}).files(k).name(idx(2)+1:idx(3)-1)}]);
end
for j = 1:length(site.(site.codes{i}).species)
if strcmp(site.(site.codes{i}).species{1,j},'co2')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CO2 X2007';
site.(site.codes{i}).species_standard_name{1,j} = 'carbon_dioxide';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppm';
site.(site.codes{i}).species_units{1,j} = 'micromol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
elseif strcmp(site.(site.codes{i}).species{1,j},'ch4')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CH4 X2004A';
site.(site.codes{i}).species_standard_name{1,j} = 'methane';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppb';
site.(site.codes{i}).species_units{1,j} = 'nanomol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
elseif strcmp(site.(site.codes{i}).species{1,j},'co')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CO X2014A';
site.(site.codes{i}).species_standard_name{1,j} = 'carbon_monoxide';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppb';
site.(site.codes{i}).species_units{1,j} = 'nanomol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
end
end
site.(site.codes{i}).date_issued = date_issued;
site.(site.codes{i}).date_issued_str = datestr(site.(site.codes{i}).date_issued,'yyyy-mm-ddThh:MM:ssZ');
site.date_issued = max([site.date_issued,site.(site.codes{i}).date_issued]);
end
%% Loading the data
for i = 1:length(site.codes)
for sp = 1:length(site.(site.codes{i}).species)
sptxt = site.(site.codes{i}).species{sp};
for inlet = 1:length(site.(site.codes{i}).inlet_height_long_name)
intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
site.(site.codes{i}).([sptxt,'_',intxt]) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_lat']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_lon']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_files']) = dir(fullfile(readFolder,city,version_folder,[site.codes{i},'*',sptxt,'*',intxt,'*.csv']));
if isempty(site.(site.codes{i}).([sptxt,'_',intxt,'_files'])) % The 'rooftop' sites don't include the intxt in the file name.
site.(site.codes{i}).([sptxt,'_',intxt,'_files']) = dir(fullfile(readFolder,city,version_folder,[site.codes{i},'*',sptxt,'-all-','*.csv']));
end
if isempty(site.(site.codes{i}).([sptxt,'_',intxt,'_files']))
fprintf('*** No file for %s %s. Continuing onto the next file.\n',site.codes{i},sptxt)
%keyboard
continue
end
for fni = 1:length(site.(site.codes{i}).([sptxt,'_',intxt,'_files']))
fn = fullfile(site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).folder,site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).name);
if isempty(fn); fprintf('No file %s.\nContinuing onto the next file.\n',fn); keyboard; end
%in_format = '%{yyyy-MM-dd HH:mm:ss}D%f%f%f%f%f%s%s%f%f%f%f%f%f%f%f%f%f%f%f%s';
in_format = '%{yyyy-MM-dd''T''HH''Z}D%f%f%f%f%s%s%s%f%f%f%f%f%f%f%f%f%f%f%f%s';
fid = fopen(fn);
read_dat = textscan(fid,in_format,'HeaderLines',1,'Delimiter',',','CollectOutput',true,'TreatAsEmpty','NaN');
fclose(fid);
site.(site.codes{i}).([sptxt,'_',intxt]) = [site.(site.codes{i}).([sptxt,'_',intxt]); read_dat{4}(:,5)]; % CO2
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_std']); read_dat{4}(:,7)]; % CO2 std
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_n']); read_dat{4}(:,8)]; % CO2 n
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_unc']); read_dat{4}(:,6)]; % CO2 uncertainty
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_time']); read_dat{1}]; % time
site.(site.codes{i}).([sptxt,'_',intxt,'_lat']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_lat']); read_dat{4}(:,1)];
site.(site.codes{i}).([sptxt,'_',intxt,'_lon']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_lon']); read_dat{4}(:,2)];
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']); read_dat{4}(:,3)];
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']); read_dat{4}(:,4)];
fprintf('File read: %s\n',site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).name)
end
fields = {'','_std','_n','_unc','_time','_lat','_lon','_elevation','_inlet_height'};
% Removes the leading and trailing NaNs
data_range_ind = find(~isnan(site.(site.codes{i}).([sptxt,'_',intxt])),1,'first'):find(~isnan(site.(site.codes{i}).([sptxt,'_',intxt])),1,'last');
for j = 1:length(fields)
site.(site.codes{i}).([sptxt,'_',intxt,fields{j}]) = site.(site.codes{i}).([sptxt,'_',intxt,fields{j}])(data_range_ind);
end
clear data_range_ind
% If there is no data (ie if there is no CH4 data but there is CO2 & CO data), remove the site/inlet/species.
if isempty(site.(site.codes{i}).([sptxt,'_',intxt]))
fprintf('***No data found for %s: %s_%s. Removing that species-inlet from the site.\n',site.codes{i},sptxt,intxt)
for j = 1:length(fields)
site.(site.codes{i}) = rmfield(site.(site.codes{i}),[sptxt,'_',intxt,fields{j}]);
end
continue
end
% Set fill values:
for j = 1:length(fields)
if ~strcmp(fields{j},'_time') % don't fill the time
site.(site.codes{i}).([sptxt,'_',intxt,fields{j}])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,fields{j}]))) = -9999.0;
end
end
site.groups = [site.groups; {[sptxt,'_',site.(site.codes{i}).code,'_',intxt]}];
site.species = [site.species; {sptxt}];
end
end
end
%% Custom QAQC based on discussion with ??? on MMMM YYYY
%
% fprintf('*** Custom QAQC implemented in Aug 2020***\n')
%
% % CO2 QC
% i = find(strcmp(site.codes,'LJO')); %site.(site.codes{i})
% inlet = find(strcmp(site.(site.codes{i}).inlet_height_long_name,'13m')); intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
% sp = find(strcmp(site.(site.codes{i}).species,'co2')); sptxt = site.(site.codes{i}).species{sp};
% mask = false(size(site.(site.codes{i}).([sptxt,'_',intxt])));
% fprintf('Remove short spike of low CO2 at LJO 13m on Oct 30, 2019\n')
% t1 = datetime(2019,10,30,15,00,00); t2 = datetime(2019,11,04,19,00,00);
% mask(and(site.(site.codes{i}).([sptxt,'_',intxt,'_time'])>t1,site.(site.codes{i}).([sptxt,'_',intxt,'_time'])<t2)) = true;
% site.(site.codes{i}).([sptxt,'_',intxt])(mask) = -9999.0;
%
% % CO QC:
% i = find(strcmp(site.codes,'CIT')); %site.(site.codes{i})
% inlet = find(strcmp(site.(site.codes{i}).inlet_height_long_name,'48m')); intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
% sp = find(strcmp(site.(site.codes{i}).species,'co')); sptxt = site.(site.codes{i}).species{sp};
% mask = false(size(site.(site.codes{i}).([sptxt,'_',intxt])));
% fprintf('Remove short spike of CO at CIT 48m on Jun 13, 2020\n')
% t1 = datetime(2020,06,13,01,00,00); t2 = datetime(2020,06,13,04,00,00);
% mask(and(site.(site.codes{i}).([sptxt,'_',intxt,'_time'])>t1,site.(site.codes{i}).([sptxt,'_',intxt,'_time'])<t2)) = true;
% fprintf('Remove short spike of CO at CIT on Jun 17, 2020\n')
% t1 = datetime(2020,06,17,02,00,00); t2 = datetime(2020,06,17,04,00,00);
% mask(and(site.(site.codes{i}).([sptxt,'_',intxt,'_time'])>t1,site.(site.codes{i}).([sptxt,'_',intxt,'_time'])<t2)) = true;
% site.(site.codes{i}).([sptxt,'_',intxt])(mask) = -9999.0;
%% Temporary code to truncate all sites to Dec 31, 2019 for the 4/21 ORNL DAAC archive
for i = 1:length(site.codes)
for sp = 1:length(site.(site.codes{i}).species) % only doing CO2 for now.
sptxt = site.(site.codes{i}).species{sp};
for inlet = 1:length(site.(site.codes{i}).inlet_height_long_name)
intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
mask = site.(site.codes{i}).([sptxt,'_',intxt,'_time'])<datetime(2020,1,1); % Mask for data before 2020-01-01
fields = {'','_std','_n','_unc','_time','_lat','_lon','_elevation','_inlet_height'};
for j = 1:length(fields)
site.(site.codes{i}).([sptxt,'_',intxt,fields{j}]) = site.(site.codes{i}).([sptxt,'_',intxt,fields{j}])(mask); % Apply the mask
end
end
end
end
%% Optional plots to spot check the data.
%i = 4;
%site.(site.codes{i}).species
clear('ax')
for i = 1:length(site.codes)
intxt = site.(site.codes{i}).inlet_height_long_name{1};
figure(i); clf;
for j = 1:length(site.(site.codes{i}).species)
sptxt = site.(site.codes{i}).species{j};
pltxt = [sptxt,'_',intxt];
mask = true(size(site.(site.codes{i}).(pltxt))); mask(site.(site.codes{i}).(pltxt)==-9999) = false;
if sum(mask)==0; mask(mask==false) = true; end % if they're all false, make them true so the plotting works. Will show up as -9999 line.
ax(i,j) = subplot(length(site.(site.codes{i}).species),1,j);
plot(site.(site.codes{i}).([sptxt,'_',intxt,'_time'])(mask),site.(site.codes{i}).(pltxt)(mask))
grid on; ylabel(replace(pltxt,'_',' ')); title(site.codes{i})
end
linkaxes(ax(i,:),'x')
end
%% Identify the netCDF files to create based on species.
site.unique_species = unique(site.species);
site.species_list = [];
for species_ind = 1:length(site.unique_species)
site.species_list = [site.species_list, site.unique_species{species_ind},' '];
end
site.species_list = strip(site.species_list); % Removes the last space
for j = 1:length(site.species)
if strcmp(site.species{j,1},'co2')
site.species_standard_name{j,1} = 'carbon dioxide';
elseif strcmp(site.species{j,1},'ch4')
site.species_standard_name{j,1} = 'methane';
elseif strcmp(site.species{j,1},'co')
site.species_standard_name{j,1} = 'carbon monoxide';
end
end
%% Creating the netCDF file
fprintf('Now creating the netCDF files.\n')
eval('co2usa_create_netCDF')