forked from uataq/co2usa_data_synthesis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathco2usa_portland_to_netCDF.m
259 lines (217 loc) · 14 KB
/
co2usa_portland_to_netCDF.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
% clear all
% close all
set(0,'DefaultFigureWindowStyle','docked')
%% Outstanding questions:
fprintf('No outstanding questions as of 2019/07/30:\n')
%% 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(2019,07,30);
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 = 'portland';
city_long_name = 'Portland';
city_url = 'http://web.pdx.edu/~arice/CO2_PDX.html';
provider(1).name = 'Andrew Rice';
provider(1).address1 = 'Department of Physics';
provider(1).address2 = '472 Science Research & Teaching Center';
provider(1).address3 = 'Portland, OR 97207';
provider(1).country = 'United States';
provider(1).city = city_long_name;
provider(1).affiliation = 'Portland State University';
provider(1).email = '[email protected]';
provider(1).orcid = '';
provider(1).parameter = 'Provider has contributed measurements for: ';
%% Site meta data
clear site % start fresh
site.reference = 'Rice, Andrew, and Gregory Bostrom. Measurements of Carbon Dioxide in an Oregon Metropolitan Region. Atmospheric Environment 45, no. 5 (February 2011): 1138–44. https://doi.org/10.1016/j.atmosenv.2010.11.026.';
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;
i = 1;
site.codes{1,i} = 'PSU';
site.(site.codes{i}).name = 'PSU';
site.(site.codes{i}).long_name = 'Portland State University';
site.(site.codes{i}).code = 'PSU';
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 = {21};
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}).species = {'co2'};
site.(site.codes{i}).species_standard_name = {'carbon_dioxide'};
site.(site.codes{i}).species_units = {'micromol mol-1'};
site.(site.codes{i}).species_units_long_name = {'ppm'};
site.(site.codes{i}).instrument = {'LiCor 840'};
site.(site.codes{i}).calibration_scale = {'WMO CO2 X2007'};
site.(site.codes{i}).in_lat = 45.5132;
site.(site.codes{i}).in_lon = -122.6864;
site.(site.codes{i}).in_elevation = 63;
site.(site.codes{i}).date_issued = datetime(2018,10,01);
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]);
i = i+1;
site.codes{1,i} = 'SEL';
site.(site.codes{i}).name = 'SEL';
site.(site.codes{i}).long_name = 'SE Lafayette';
site.(site.codes{i}).code = 'SEL';
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 = {9};
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}).species = {'co2'};
site.(site.codes{i}).species_standard_name = {'carbon_dioxide'};
site.(site.codes{i}).species_units = {'micromol mol-1'};
site.(site.codes{i}).species_units_long_name = {'ppm'};
site.(site.codes{i}).instrument = {'LiCor 840'};
site.(site.codes{i}).calibration_scale = {'WMO CO2 X2007'};
site.(site.codes{i}).in_lat = 45.4966;
site.(site.codes{i}).in_lon = -122.6029;
site.(site.codes{i}).in_elevation = 75;
site.(site.codes{i}).date_issued = datetime(2018,10,01);
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]);
i = i+1;
site.codes{1,i} = 'SIS';
site.(site.codes{i}).name = 'SIS';
site.(site.codes{i}).long_name = 'Sauvie Island';
site.(site.codes{i}).code = 'SIS';
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 = {7};
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}).species = {'co2'};
site.(site.codes{i}).species_standard_name = {'carbon_dioxide'};
site.(site.codes{i}).species_units = {'micromol mol-1'};
site.(site.codes{i}).species_units_long_name = {'ppm'};
site.(site.codes{i}).instrument = {'LiCor 840'};
site.(site.codes{i}).calibration_scale = {'WMO CO2 X2007'};
site.(site.codes{i}).in_lat = 45.7685;
site.(site.codes{i}).in_lon = -122.7721;
site.(site.codes{i}).in_elevation = 6;
site.(site.codes{i}).date_issued = datetime(2018,10,01);
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]);
site.date_issued_str = datestr(site.date_issued,'yyyy-mm-ddThh:MM:ssZ');
%% Loading the data
for i = 1:length(site.codes)
for inlet = 1:length(site.(site.codes{i}).inlet_height_long_name)
intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
for sp = 1:length(site.(site.codes{i}).species)
sptxt = site.(site.codes{i}).species{sp};
if ~exist(fullfile(readFolder,city,['hourly_avg_',site.codes{i},'_',sptxt,'_',intxt,'.mat']),'file')
fprintf('Computing %s hourly %s averaged data...\n',site.codes{i},sptxt)
site.(site.codes{i}).files = dir(fullfile(readFolder,city,[site.(site.codes{i}).name,'.csv']));
site.(site.codes{i}).(['min_',sptxt,'_',intxt]) = [];
site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']) = [];
for fn = 1:length(site.(site.codes{i}).files)
formatSpec = '%f%f%f%f%f%f%f%f';
% Read the data file
fid = fopen(fullfile(site.(site.codes{i}).files(fn).folder,site.(site.codes{i}).files(fn).name));
read_dat = textscan(fid,formatSpec,'HeaderLines',0,'Delimiter',',','CollectOutput',true,'TreatAsEmpty','NaN');
fclose(fid);
site.(site.codes{i}).(['min_',sptxt,'_',intxt]) = [site.(site.codes{i}).(['min_',sptxt,'_',intxt]); read_dat{1,1}(:,8)]; % species
site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']) = [site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']); datetime(read_dat{1,1}(:,2:7))]; % time
fprintf('%-3s read from file: %s\n',sptxt,site.(site.codes{i}).files(fn).name)
end
% Sort the data in chronological order since it wasn't necessarily loaded that way.
[site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']),sort_index] = sortrows(site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']));
site.(site.codes{i}).(['min_',sptxt,'_',intxt]) = site.(site.codes{i}).(['min_',sptxt,'_',intxt])(sort_index,1);
% Removes the leading and trailing NaNs
data_range_ind = find(~isnan(site.(site.codes{i}).(['min_',sptxt,'_',intxt])),1,'first'):find(~isnan(site.(site.codes{i}).(['min_',sptxt,'_',intxt])),1,'last');
site.(site.codes{i}).(['min_',sptxt,'_',intxt]) = site.(site.codes{i}).(['min_',sptxt,'_',intxt])(data_range_ind);
site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']) = site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time'])(data_range_ind);
clear sort_index data_range_ind
% Creating an hourly averaged data set from the minute data.
qht = (dateshift(site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time'])(1),'start','hour'):1/24:dateshift(site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time'])(end),'start','hour'))'; % Date numbers of the floored hours.
qhdata = nan(size(qht,1),1);
qhdataStd = nan(size(qht,1),1);
qhdataCount = nan(size(qht,1),1);
qtFloorHour = dateshift(site.(site.codes{i}).(['min_',sptxt,'_',intxt,'_time']),'start','hour');
tic
for j = 1:size(qht,1)
qhdataTemp = site.(site.codes{i}).(['min_',sptxt,'_',intxt])(qtFloorHour==qht(j,1),:);
if size(qhdataTemp,1)>=2 % Must be at least two data points in order to save an "hourly average"
qhdata(j,:) = nanmean(qhdataTemp,1);
qhdataStd(j,:) = nanstd(qhdataTemp,1);
qhdataCount(j,:) = sum(~isnan(qhdataTemp));
end
end
toc
save(fullfile(readFolder,city,['hourly_avg_',site.codes{i},'_',sptxt,'_',intxt,'.mat']),'qht','qhdata','qhdataStd','qhdataCount')
else
fprintf('Loading previously computed %s hourly %s averaged data.\n',site.codes{i},sptxt)
load(fullfile(readFolder,city,['hourly_avg_',site.codes{i},'_',sptxt,'_',intxt,'.mat']))
end
site.(site.codes{i}).([sptxt,'_',intxt]) = qhdata;
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = qhdataStd;
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = qhdataCount;
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = qht;
% No uncertainty data yet.
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = nan(length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
% Lat, Lon, Elevation, and Inlet heights do not change, so they are all entered as a constant through the data set.
site.(site.codes{i}).([sptxt,'_',intxt,'_lat']) = repmat(site.(site.codes{i}).in_lat,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_lon']) = repmat(site.(site.codes{i}).in_lon,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']) = repmat(site.(site.codes{i}).in_elevation,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']) = repmat(site.(site.codes{i}).inlet_height{inlet},length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
% Set fill values:
site.(site.codes{i}).([sptxt,'_',intxt])(isnan(site.(site.codes{i}).([sptxt,'_',intxt]))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_std'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_std']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_n'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_n']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_unc'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_unc']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_lat'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_lat']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_lon'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_lon']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']))) = -9999.0;
site.groups = [site.groups; {[sptxt,'_',site.(site.codes{i}).code,'_',intxt]}];
site.species = [site.species; {sptxt}];
end
end
fprintf('---- %-6s complete ----\n\n',site.codes{i})
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')