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
|
/***********************************************/
/**
* @file griddedData2NetCdf.cpp
*
* @brief Convert gridded data to a netCDF file.
*
* @author Andreas Kvas
* @author Torsten Mayer-Guerr
* @date 2018-06-17
*/
/***********************************************/
// Latex documentation
#define DOCSTRING docstring
static const char *docstring = R"(
This program converts a \configFile{inputfileGriddedData}{griddedData}
to a COARDS compliant NetCDF file. The output data can be defined with \config{dataVariable}.
You should add at least the attributes \verb|units|, \verb|long_name|, and maybe \verb|_FillValue|
to the variables. For the \config{dataVariable:value} the standard \reference{dataVariables}{general.parser:dataVariables}
are available to select the data columns of \configFile{inputfileGriddedData}{griddedData}.
See also \program{NetCdfInfo}, \program{GriddedDataTimeSeries2NetCdf}, \program{NetCdf2GriddedData}.
)";
/***********************************************/
#include "programs/program.h"
#include "parser/dataVariables.h"
#include "inputOutput/fileNetCdf.h"
#include "files/fileGriddedData.h"
/***** CLASS ***********************************/
/** @brief Convert gridded data to a netCDF file.
* @ingroup programsConversionGroup */
class GriddedData2NetCdf
{
public:
class Attribute
{
public:
std::string name;
std::string text;
std::vector<Double> values;
NetCdf::DataType dataType;
};
class DataVariable
{
public:
std::string name;
ExpressionVariablePtr valueExpr;
Vector values;
NetCdf::DataType dataType;
std::vector<Attribute> attributes;
NetCdf::Variable variable;
};
void run(Config &config, Parallel::CommunicatorPtr comm);
};
GROOPS_REGISTER_PROGRAM(GriddedData2NetCdf, SINGLEPROCESS, "Convert gridded data to a netCDF file", Conversion, Grid)
/***********************************************/
template<> Bool readConfig(Config &config, const std::string &name, GriddedData2NetCdf::Attribute &var, Config::Appearance mustSet, const std::string &defaultValue, const std::string &annotation)
{
std::string choice;
if(!readConfigChoice(config, name, choice, mustSet, defaultValue, annotation))
return FALSE;
if(readConfigChoiceElement(config, "text", choice, ""))
{
readConfig(config, "name", var.name, Config::MUSTSET, "", "");
readConfig(config, "value", var.text, Config::MUSTSET, "", "");
}
if(readConfigChoiceElement(config, "value", choice, ""))
{
std::string choice;
readConfig(config, "name", var.name, Config::MUSTSET, "", "");
readConfig(config, "value", var.values, Config::MUSTSET, "", "");
if(readConfigChoice(config, "dataType", choice, Config::MUSTSET, "", ""))
{
if(readConfigChoiceElement(config, "double", choice, "")) var.dataType = NetCdf::DOUBLE;
if(readConfigChoiceElement(config, "float", choice, "")) var.dataType = NetCdf::FLOAT;
if(readConfigChoiceElement(config, "int", choice, "")) var.dataType = NetCdf::INT;
endChoice(config);
}
}
endChoice(config);
return TRUE;
}
/***********************************************/
template<> Bool readConfig(Config &config, const std::string &name, GriddedData2NetCdf::DataVariable &var, Config::Appearance mustSet, const std::string &defaultValue, const std::string &annotation)
{
if(!readConfigSequence(config, name, mustSet, defaultValue, annotation))
return FALSE;
readConfig(config, "name", var.name, Config::MUSTSET, "data0", "netCDF variable name");
readConfig(config, "value", var.valueExpr, Config::DEFAULT, "data0", "expression (variables 'height', 'data', 'longitude', 'latitude' and, 'area' are taken from the gridded data");
std::string choice;
if(readConfigChoice(config, "dataType", choice, Config::MUSTSET, "", ""))
{
if(readConfigChoiceElement(config, "double", choice, "")) var.dataType = NetCdf::DOUBLE;
if(readConfigChoiceElement(config, "float", choice, "")) var.dataType = NetCdf::FLOAT;
if(readConfigChoiceElement(config, "int", choice, "")) var.dataType = NetCdf::INT;
endChoice(config);
}
readConfig(config, "attribute", var.attributes, Config::OPTIONAL, "", "netCDF attributes");
endSequence(config);
return TRUE;
}
/***********************************************/
void GriddedData2NetCdf::run(Config &config, Parallel::CommunicatorPtr /*comm*/)
{
try
{
FileName fileNameOut, fileNameIn;
std::vector<DataVariable> dataVariables;
std::vector<Attribute> globalAttributes;
readConfig(config, "outputfileNetCdf", fileNameOut, Config::MUSTSET, "", "file name of NetCDF output");
readConfig(config, "inputfileGriddedData", fileNameIn, Config::MUSTSET, "", "input grid sequence");
readConfig(config, "dataVariable", dataVariables, Config::MUSTSET, "", "metadata for data variables");
readConfig(config, "globalAttribute", globalAttributes, Config::OPTIONAL, "", "additional meta data");
if(isCreateSchema(config)) return;
#ifdef GROOPS_DISABLE_NETCDF
throw(Exception("Compiled without NetCDF library"));
#else
// read grid
// ---------
logStatus<<"read gridded data <"<<fileNameIn<<">"<<Log::endl;
GriddedDataRectangular grid;
readFileGriddedData(fileNameIn, grid);
// create data variables
// ---------------------
VariableList varList;
addDataVariables(grid, varList);
for(auto &data : dataVariables)
data.valueExpr->simplify(varList);
for(auto &data : dataVariables)
data.values = Vector(grid.longitudes.size() * grid.latitudes.size());
UInt idx = 0;
for(UInt i=0; i<grid.latitudes.size(); i++)
for(UInt k=0; k<grid.longitudes.size(); k++)
{
evaluateDataVariables(grid, i, k, varList);
for(auto &data : dataVariables)
data.values(idx) = data.valueExpr->evaluate(varList);
idx++;
}
// write attributes
// ----------------
logStatus<<"write NETCDF file <"<<fileNameOut<<">"<<Log::endl;
NetCdf::OutFile file(fileNameOut);
for(const auto &attr : globalAttributes)
{
if(attr.text.empty())
file.addAttribute(attr.name, attr.dataType, attr.values);
else
file.addAttribute(attr.name, attr.text);
}
{
auto dim = file.addDimension("lat", grid.latitudes.size());
auto var = file.addVariable("lat", NetCdf::DOUBLE, {dim});
var.addAttribute("units", "degrees_north");
Vector lats(grid.latitudes.size());
for(UInt i=0; i<grid.latitudes.size(); i++)
lats(i) = RAD2DEG * grid.latitudes.at(i);
var.setValues(lats);
}
{
auto dim = file.addDimension("lon", grid.longitudes.size());
auto var = file.addVariable("lon", NetCdf::DOUBLE, {dim});
var.addAttribute("units", "degrees_east");
Vector lons(grid.longitudes.size());
for(UInt i=0; i<grid.longitudes.size(); i++)
lons(i) = RAD2DEG * grid.longitudes.at(i);
var.setValues(lons);
}
for(auto &data : dataVariables)
{
data.variable = file.addVariable(data.name, data.dataType, file.dimensions());
for(auto &attr : data.attributes)
{
if(attr.text.empty())
data.variable.addAttribute(attr.name, attr.dataType, attr.values);
else
data.variable.addAttribute(attr.name, attr.text);
}
data.variable.setValues({0, 0}, {grid.latitudes.size(), grid.longitudes.size()}, data.values);
}
#endif
}
catch(std::exception &e)
{
GROOPS_RETHROW(e)
}
}
/***********************************************/
|
