-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathnetcdf_create.m
211 lines (175 loc) · 11.2 KB
/
netcdf_create.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
function [ ncid, nc_obj,nc_params] = netcdf_create( current_run, NPrint,nodes_N,gsd_MG,LstrMat,nc_params )
%SAVE_ASNETC Summary of this function goes here
% Detailed explanation goes here
nc_filename = strcat(current_run,'_store.nc');
%% SET NETCDF MODE
storenc_mode = netcdf.getConstant('NETCDF4'); % 4096 - 1000000000000 % Create a NetCDF-4/HDF5 file
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('CLOBBER')); % 0 - 0000000000000 % Overwrite any existing file with the same name.
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('NOCLOBBER')); % 4 - 0000000000100 % Prevent overwriting of existing file with the same name.
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('CLASSIC_MODEL')); % 256 - 0000100000000 % Enforce the classic model; has no effect unless used in a bitwise-or with NETCDF4
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('64BIT_OFFSET')); % 512 - 0001000000000 % Allow easier creation of files and variables which are larger than two gigabytes.
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('SHARE')); % 2048 - 0100000000000 % Allow synchronous file updates.
%storenc_mode = netcdf.getConstant('64BIT_OFFSET');
%storenc_mode = bitor(storenc_mode,netcdf.getConstant('NETCDF4'));
% CREATE FILE
if exist(nc_filename,'file')
try
ncid = netcdf.open(nc_filename,'WRITE');
netcdf.close(ncid);
delete(nc_filename);
catch err
fprintf('Could not delete previous netcdf file....')
end
end
try
[ncid,nc_params.chunksize] = netcdf.create(nc_filename,storenc_mode);
catch err
disp('NETCDF mode problem!')
%keyboard
end
%%
disp(strcat('Creating netcdf as: ',nc_filename));
nc_params.filename = nc_filename;
% testing....
% close netcdf
netcdf.close(ncid);
% open in write mode (so sync works??)
netcdf.open(nc_filename,'NC_WRITE')
% \testing!
if(nc_params.premp >= 1)
message = sprintf('WARNING: nc_params.premp is >=1. I had problems with runs crashing while saving if nc_params.premp == 1. I set it to 1 for now... Expect crash...');
fprintf(fdev,message);
disp(message)
warning(s'')
nc_params.premp = min(1,nc_params.premp);
end
netcdf.setChunkCache(nc_params.csize, nc_params.nelems, nc_params.premp)
netcdf.setFill(ncid,nc_params.setFill);
%% SAVE DIMENSIONS
%ncid = netcdf.open('OAWC135000kg18000hGsigp50_7_store.nc','NC_WRITE');
netcdf.reDef(ncid)
nc_obj.dim_NPrint = netcdf.defDim(ncid,'prints',NPrint+3);
nc_obj.dim_nodes = netcdf.defDim(ncid,'nodes',nodes_N);
nc_obj.dim_gsd = netcdf.defDim(ncid,'gsd',gsd_MG);
nc_obj.dim_gsdp1 = netcdf.defDim(ncid,'gsdp1',gsd_MG+1);
nc_obj.dim_const = netcdf.defDim(ncid,'const',1);
nc_obj.dim_string = netcdf.defDim(ncid,'string',200);
nc_obj.dim_LstrMat = netcdf.defDim(ncid,'LstrMat',LstrMat);
% dimension vars (best practices)
nc_obj.var_NPrint = netcdf.defVar(ncid,'prints','int',nc_obj.dim_NPrint);
nc_obj.var_nodes = netcdf.defVar(ncid,'nodes','int',nc_obj.dim_nodes);
nc_obj.var_gsd = netcdf.defVar(ncid,'gsd','int',nc_obj.dim_gsd);
nc_obj.var_gsdp1 = netcdf.defVar(ncid,'gsdp1','int',nc_obj.dim_gsdp1);
nc_obj.var_const = netcdf.defVar(ncid,'const','int',nc_obj.dim_const);
nc_obj.var_string = netcdf.defVar(ncid,'string','int',nc_obj.dim_string);
nc_obj.var_LstrMat = netcdf.defVar(ncid,'LstrMat','int',nc_obj.dim_LstrMat);
%% CREATE VARIABLES
% zero dimensional var
nc_obj.var_t = netcdf.defVar(ncid,'store_t','int',nc_obj.dim_NPrint);
netcdf.putAtt(ncid,nc_obj.var_t,'unit','steps');
netcdf.putAtt(ncid,nc_obj.var_t,'description','model steps')
netcdf.defVarFill(ncid,nc_obj.var_t,false,NaN);
netcdf.defVarDeflate(ncid,nc_obj.var_t,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
nc_obj.var_time = netcdf.defVar(ncid,'store_time','double',nc_obj.dim_NPrint);
netcdf.putAtt(ncid,nc_obj.var_time,'unit','hours');
netcdf.putAtt(ncid,nc_obj.var_time,'description','time in hours')
netcdf.defVarFill(ncid,nc_obj.var_time,false,NaN);
netcdf.defVarDeflate(ncid,nc_obj.var_time,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
% one dimensional var (nodesN)
nc_obj.var_etab = netcdf.defVar(ncid,'store_etab','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_etab,'unit','m');
netcdf.defVarDeflate(ncid,nc_obj.var_etab,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_etab,false,NaN);
nc_obj.var_Dsg = netcdf.defVar(ncid,'store_Dsg','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_Dsg,'unit','mm');
netcdf.defVarDeflate(ncid,nc_obj.var_Dsg,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_Dsg,false,NaN);
nc_obj.var_Ds90 = netcdf.defVar(ncid,'store_Ds90','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_Ds90,'unit','mm');
netcdf.defVarDeflate(ncid,nc_obj.var_Ds90,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_Ds90,false,NaN);
nc_obj.var_SDg = netcdf.defVar(ncid,'store_SDg','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_SDg,'unit','stdev');
netcdf.defVarDeflate(ncid,nc_obj.var_SDg,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_SDg,false,NaN);
nc_obj.var_qbx = netcdf.defVar(ncid,'store_qbx','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_qbx,'unit','mps');
netcdf.defVarDeflate(ncid,nc_obj.var_qbx,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_qbx,false,NaN);
nc_obj.var_Msj = netcdf.defVar(ncid,'store_Msj','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_Msj,'unit','none');
netcdf.defVarDeflate(ncid,nc_obj.var_Msj,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_Msj,false,NaN);
nc_obj.var_slope = netcdf.defVar(ncid,'store_slope','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_slope,'unit','mpm');
netcdf.defVarDeflate(ncid,nc_obj.var_slope,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_slope,false,NaN);
nc_obj.var_ustar = netcdf.defVar(ncid,'store_ustar','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_ustar,'unit','none');
netcdf.defVarDeflate(ncid,nc_obj.var_ustar,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_ustar,false,NaN);
nc_obj.var_waterSurf = netcdf.defVar(ncid,'store_waterSurf','double',[nc_obj.dim_nodes nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_waterSurf,'unit','m');
netcdf.defVarDeflate(ncid,nc_obj.var_waterSurf,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_waterSurf,false,NaN);
% two dimensional var (nodesN, GSD)
nc_obj.var_TranspPbi = netcdf.defVar(ncid,'store_TranspPbi','double',[nc_obj.dim_nodes nc_obj.dim_gsd nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_TranspPbi,'unit','perc');
netcdf.defVarDeflate(ncid,nc_obj.var_TranspPbi,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_TranspPbi,false,NaN);
nc_obj.var_SurfFsi = netcdf.defVar(ncid,'store_SurfFsi','double',[nc_obj.dim_nodes nc_obj.dim_gsdp1 nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_SurfFsi,'unit','freq');
netcdf.defVarDeflate(ncid,nc_obj.var_SurfFsi,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_SurfFsi,false,NaN);
nc_obj.var_SurfPbi = netcdf.defVar(ncid,'store_SurfPbi','double',[nc_obj.dim_nodes nc_obj.dim_gsd nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_SurfPbi,'unit','perc');
netcdf.defVarDeflate(ncid,nc_obj.var_SurfPbi,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_SurfPbi,false,NaN);
% METADATA / DESCRIPTION OF NETCDF FILE
nc_obj.var_current_run = netcdf.defVar(ncid,'current_run','char',[nc_obj.dim_string]);
nc_obj.var_run_name = netcdf.defVar(ncid,'run_name','char',[nc_obj.dim_string]);
nc_obj.var_creation_date = netcdf.defVar(ncid,'creation_date','char',[nc_obj.dim_string]);
nc_obj.var_dx_array = netcdf.defVar(ncid,'dx_array','double',[nc_obj.dim_nodes]);
nc_obj.var_reach_width = netcdf.defVar(ncid,'reach_width','double',[nc_obj.dim_nodes]);
nc_obj.var_param_dt = netcdf.defVar(ncid,'param_dt','double',[nc_obj.dim_const]);
nc_obj.var_reach_length = netcdf.defVar(ncid,'reach_length','double',[nc_obj.dim_const]);
nc_obj.var_delta_s = netcdf.defVar(ncid,'param_delta_s','double',[nc_obj.dim_const]);
nc_obj.var_zbase = netcdf.defVar(ncid,'zbase','double',[nc_obj.dim_const]);
% inital values
nc_obj.var_gsd_initDsi = netcdf.defVar(ncid,'gsd_initDsi','double',[nc_obj.dim_gsdp1]);
%% save subsurface if configured
if nc_params.saveNC_subs
% subsurface (takes long time to store):
% two dimensional var (nodesN, LStrMat)
nc_obj.var_eta_subs = netcdf.defVar(ncid,'store_eta_subs','double',[nc_obj.dim_nodes nc_obj.dim_LstrMat nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_eta_subs,'unit','m');
netcdf.defVarDeflate(ncid,nc_obj.var_eta_subs,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_eta_subs,false,NaN);
% three dimensional var (nodesN, LstrMat, GSD)
% nc_obj.var_Dssg_subsurface = netcdf.defVar(ncid,'store_Dssg_subsurface','double',[nc_obj.dim_LstrMat nc_obj.dim_nodes nc_obj.dim_NPrint]);
% netcdf.putAtt(ncid,nc_obj.var_Dssg_subsurface,'unit','mm');
% netcdf.defVarDeflate(ncid,nc_obj.var_Dssg_subsurface,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
% netcdf.defVarFill(ncid,nc_obj.var_Dssg_subsurface,false,NaN);
%
% nc_obj.var_Dss90_subsurface = netcdf.defVar(ncid,'store_Dss90_subsurface','double',[nc_obj.dim_LstrMat nc_obj.dim_nodes nc_obj.dim_NPrint]);
% netcdf.putAtt(ncid,nc_obj.var_Dss90_subsurface,'unit','mm');
% netcdf.defVarDeflate(ncid,nc_obj.var_Dss90_subsurface,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
% netcdf.defVarFill(ncid,nc_obj.var_Dss90_subsurface,false,NaN);
nc_obj.var_pssi_subs = netcdf.defVar(ncid,'store_pssi_subs','double',[nc_obj.dim_nodes nc_obj.dim_LstrMat nc_obj.dim_gsd nc_obj.dim_NPrint]);
netcdf.putAtt(ncid,nc_obj.var_pssi_subs,'unit','perc');
netcdf.defVarDeflate(ncid,nc_obj.var_pssi_subs,nc_params.shufflefilter,nc_params.deflate,nc_params.deflate_level);
netcdf.defVarFill(ncid,nc_obj.var_pssi_subs,false,NaN);
end
% DISPLAY CONTENT OF NETCDF FILE
%ncdisp(storenc_filename)
% Take file out of define mode.
netcdf.endDef(ncid);
%% SAVE DIMENSIONS (as per best practices)
netcdf.putVar(ncid,nc_obj.var_NPrint ,0, NPrint+3 ,[1:NPrint+3])
netcdf.putVar(ncid,nc_obj.var_nodes ,0, nodes_N ,[1:nodes_N])
netcdf.putVar(ncid,nc_obj.var_gsd ,0, gsd_MG ,[1:gsd_MG])
netcdf.putVar(ncid,nc_obj.var_gsdp1 ,0, gsd_MG+1 ,[1:gsd_MG+1])
netcdf.putVar(ncid,nc_obj.var_const ,0, 1 ,1)
netcdf.putVar(ncid,nc_obj.var_string ,0, 200 ,[1:200])
netcdf.putVar(ncid,nc_obj.var_LstrMat ,0, LstrMat ,[1:LstrMat])
end