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Added support for netcdf output for the uv action

interpolate
Michael Uleysky 1 year ago
parent
1d9268b32d
commit
ed1282413f
2 changed files with 302 additions and 63 deletions
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  1. 88
      actions/actionuv.cpp
  2. 277
      actions/actionuv.h

88
actions/actionuv.cpp
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@ -0,0 +1,88 @@
#define MICHLIB_NOSOURCE
#include "actionuv.h"
void UVMethods::StPoints::WriteBinBile(const MString& name) const
{
BFileW stp;
stp.Create(name, 3);
stp.SetColumnName(1, lonlat ? "Longitude" : "x");
stp.SetColumnName(2, lonlat ? "Latitude" : "x");
stp.SetColumnName(3, "Stability (0 - saddle, 1 - st. anticicl. focus, 2 - st. knot, 3 - unst. anticicl. focus, 4 - unst. knot, 5 - st. cicl. focus, 6 - unst. cicl. focus)");
for(size_t i = 0; i < N(); i++)
{
stp.Write(x[i]);
stp.Write(y[i]);
stp.Write(michlib::int_cast<size_t>(t[i]));
}
stp.Finalize();
stp.Close();
}
MString UVMethods::StPoints::WriteNcFile(const MString& name, const MString& history, int comp) const
{
int ret;
int ncid;
int dimid;
int xid, yid, tid;
MString text;
ret = nc_create(name.Buf(), NC_CLOBBER | NC_NETCDF4, &ncid);
if(ret != NC_NOERR) return "Can't create netcdf file: " + name;
ret = nc_put_att_text(ncid, NC_GLOBAL, "history", history.Len() + 1, history.Buf());
if(ret != NC_NOERR) return "Can't write history attribute in the netcdf file";
ret = nc_def_dim(ncid, "i", N(), &dimid);
if(ret != NC_NOERR) return "Can't create dimension in the netcdf file";
ret = nc_def_var(ncid, lonlat ? "longitude" : "x", NC_FLOAT, 1, &dimid, &xid);
if(ret != NC_NOERR) return "Can't create x variable in the netcdf file";
ret = nc_def_var(ncid, lonlat ? "latitude" : "y", NC_FLOAT, 1, &dimid, &yid);
if(ret != NC_NOERR) return "Can't create y variable in the netcdf file";
if(lonlat)
{
text = "longitude";
ret = nc_put_att_text(ncid, xid, "standard_name", text.Len() + 1, text.Buf());
if(ret != NC_NOERR) return "Can't write standard_name attribute of longitude variable in the netcdf file";
text = "latitude";
ret = nc_put_att_text(ncid, yid, "standard_name", text.Len() + 1, text.Buf());
if(ret != NC_NOERR) return "Can't write standard_name attribute of latitude variable in the netcdf file";
}
ret = nc_def_var_deflate(ncid, xid, 1, 1, comp);
if(ret != NC_NOERR) return "Can't set deflate parameters for x variable in the netcdf file";
ret = nc_def_var_deflate(ncid, yid, 1, 1, comp);
if(ret != NC_NOERR) return "Can't set deflate parameters for y variable in the netcdf file";
ret = nc_def_var(ncid, "type", NC_UBYTE, 1, &dimid, &tid);
if(ret != NC_NOERR) return "Can't create type variable in the netcdf file";
ret = nc_def_var_deflate(ncid, tid, 1, 1, comp);
if(ret != NC_NOERR) return "Can't set deflate parameters for type variable in the netcdf file";
text = "Stationary point type, 0 - saddle, 1 - st. anticicl. focus, 2 - st. knot, 3 - unst. anticicl. focus, 4 - unst. knot, 5 - st. cicl. focus, 6 - unst. cicl. focus";
ret = nc_put_att_text(ncid, tid, "long_name", text.Len() + 1, text.Buf());
if(ret != NC_NOERR) return "Can't write long_name attribute of type variable in the netcdf file";
ret = nc_enddef(ncid);
if(ret != NC_NOERR) return "Can't finish definition of the netcdf file";
const size_t i = 0, c = N();
float buf[c];
for(size_t ix = 0; ix < c; ix++) buf[ix] = x[ix];
ret = nc_put_vara_float(ncid, xid, &i, &c, buf);
if(ret != NC_NOERR) return "Can't write x variable in the netcdf file";
for(size_t ix = 0; ix < c; ix++) buf[ix] = y[ix];
ret = nc_put_vara_float(ncid, yid, &i, &c, buf);
if(ret != NC_NOERR) return "Can't write y variable in the netcdf file";
ret = nc_put_vara_ubyte(ncid, tid, &i, &c, t.data());
if(ret != NC_NOERR) return "Can't write type variable in the netcdf file";
ret = nc_close(ncid);
if(ret != NC_NOERR) return "Can't close netcdf file";
return "";
}

277
actions/actionuv.h
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@ -1,11 +1,98 @@
#pragma once #pragma once
#include "BFileW.h" #include "BFileW.h"
#include "actiondep.h" #include "actiondep.h"
#include <memory> #include "ncfilew.h"
#include <utility>
using michlib::BFileW; using michlib::BFileW;
ADD_ACTION(UV, uv, ReadPSupported<Source> || ReadSupported<Source>); class UVMethods
{
protected:
template<class D> class SparserHolder
{
protected:
const D& data;
size_t shiftx, shifty, skipx, skipy;
SparserHolder(const D& d, size_t shx, size_t shy, size_t sx, size_t sy): data(d), shiftx(shx), shifty(shy), skipx(sx), skipy(sy) {}
size_t I2Ix(size_t i) const { return i * skipx + shiftx; }
size_t I2Iy(size_t i) const { return i * skipy + shifty; }
public:
size_t Nx() const
{
size_t n = data.Nx() - shiftx;
return n / skipx + ((n % skipx > 0) ? 1 : 0);
}
size_t Ny() const
{
size_t n = data.Ny() - shifty;
return n / skipy + ((n % skipy > 0) ? 1 : 0);
}
static constexpr auto Fillval() { return D::Fillval(); }
real Lon(size_t ix, size_t iy) const { return data.Lon(I2Ix(ix), I2Iy(iy)); }
real Lat(size_t ix, size_t iy) const { return data.Lat(I2Ix(ix), I2Iy(iy)); }
real U(size_t ix, size_t iy) const { return data.U(I2Ix(ix), I2Iy(iy)); }
real V(size_t ix, size_t iy) const { return data.V(I2Ix(ix), I2Iy(iy)); }
bool IsFill(size_t ix, size_t iy) const { return data.IsFill(I2Ix(ix), I2Iy(iy)); }
};
template<class D, bool b> class Sparser2DGeoRectArray: public SparserHolder<D>
{
protected:
Sparser2DGeoRectArray(const D& d, size_t shx, size_t shy, size_t sx, size_t sy): SparserHolder<D>(d, shx, shy, sx, sy) {}
};
template<class D> class Sparser2DGeoRectArray<D, true>: public SparserHolder<D>
{
protected:
using SparserHolder<D>::data;
using SparserHolder<D>::I2Ix;
using SparserHolder<D>::I2Iy;
Sparser2DGeoRectArray(const D& d, size_t shx, size_t shy, size_t sx, size_t sy): SparserHolder<D>(d, shx, shy, sx, sy) {}
public:
real Ix2Lon(size_t ix) const { return data.Ix2Lon(I2Ix(ix)); }
real Iy2Lat(size_t iy) const { return data.Iy2Lat(I2Iy(iy)); }
};
template<class D> class Sparser: public Sparser2DGeoRectArray<D, ReadIs2DGeoRectArray<D>>
{
public:
Sparser(const D& d, size_t shx, size_t shy, size_t sx, size_t sy): Sparser2DGeoRectArray<D, ReadIs2DGeoRectArray<D>>(d, shx, shy, sx, sy) {}
};
class StPoints
{
std::vector<real> x, y;
std::vector<michlib::uint1> t;
bool lonlat;
size_t N() const { return t.size(); }
public:
StPoints(bool ll): lonlat(ll) {}
void Add(const std::vector<UVDataStorage::StPoint>& points)
{
for(const auto& p: points)
{
x.push_back(p.x);
y.push_back(p.y);
t.push_back(michlib::int_cast<michlib::uint1>(p.type));
}
}
void WriteBinBile(const MString& name) const;
MString WriteNcFile(const MString& name, const MString& history, int comp) const;
};
};
ADD_ACTION(UV, uv, ReadPSupported<Source> || ReadSupported<Source>, UVMethods);
template<class D> MString ActionUV::DoAction(const CLArgs& args, D& ds) template<class D> MString ActionUV::DoAction(const CLArgs& args, D& ds)
{ {
@ -44,39 +131,81 @@ template<class D> MString ActionUV::DoAction(const CLArgs& args, D& ds)
if(!data) return "Can't read data"; if(!data) return "Can't read data";
// Main file // Main file
MString name = args.contains("out") ? args.at("out") : ""; MString name = args.contains("out") ? args.at("out") : "";
MString outfmt = args.contains("outformat") ? args.at("outformat") : (GetExt(name) == "nc" ? "nc" : "bin");
MString u = data.Unit().Exist() ? data.Unit() : "unknown", d = data.DUnit().Exist() ? data.DUnit() : "unknown";
if(name.Exist()) if(name.Exist())
{ {
BFileW fw; if(outfmt == "bin")
fw.Create(name, 9);
fw.SetColumnName(1, "Longitude");
fw.SetColumnName(2, "Latitude");
fw.SetColumnName(3, "u, cm/s");
fw.SetColumnName(4, "v, cm/s");
fw.SetColumnName(5, "Div, (cm/s)/km");
fw.SetColumnName(6, "Rot, (cm/s)/km");
fw.SetColumnName(7, "Okubo-Weiss parameter, (cm^2/s^2)/km^2");
fw.SetColumnName(8, "Kinetic energy, cm^2/s^2");
fw.SetColumnName(9, "Eddy kinetic energy, cm^2/s^2");
fw.SetParameters(pars);
for(size_t i = 0; i < data.N(); i++)
{ {
fw.Write(data.Lon(i)); BFileW fw;
fw.Write(data.Lat(i)); fw.Create(name, 9);
fw.Write(data.U(i) == data.Fillval() ? NAN : data.U(i)); fw.SetColumnName(1, "Longitude");
fw.Write(data.V(i) == data.Fillval() ? NAN : data.V(i)); fw.SetColumnName(2, "Latitude");
fw.Write(data.Div(i) == data.Fillval() ? NAN : data.Div(i)); fw.SetColumnName(3, "u, " + u);
fw.Write(data.Rot(i) == data.Fillval() ? NAN : data.Rot(i)); fw.SetColumnName(4, "v, " + u);
fw.Write(data.OW(i) == data.Fillval() ? NAN : data.OW(i)); fw.SetColumnName(5, "Div, (" + u + ")/" + d);
fw.Write(data.U2(i) == data.Fillval() ? NAN : data.U2(i)); fw.SetColumnName(6, "Rot, (" + u + ")/" + d);
fw.Write((data.U(i) == data.Fillval() || data.V(i) == data.Fillval()) ? NAN : (data.U2(i) - (data.U(i) * data.U(i) + data.V(i) * data.V(i)))); fw.SetColumnName(7, "Okubo-Weiss parameter, (" + u + ")2/" + d + "2");
fw.SetColumnName(8, "Kinetic energy, (" + u + ")2");
fw.SetColumnName(9, "Eddy kinetic energy, (" + u + ")2");
fw.SetParameters(pars);
for(size_t i = 0; i < data.N(); i++)
{
fw.Write(data.Lon(i));
fw.Write(data.Lat(i));
fw.Write(data.U(i) == data.Fillval() ? NAN : data.U(i));
fw.Write(data.V(i) == data.Fillval() ? NAN : data.V(i));
fw.Write(data.Div(i) == data.Fillval() ? NAN : data.Div(i));
fw.Write(data.Rot(i) == data.Fillval() ? NAN : data.Rot(i));
fw.Write(data.OW(i) == data.Fillval() ? NAN : data.OW(i));
fw.Write(data.U2(i) == data.Fillval() ? NAN : data.U2(i));
fw.Write((data.U(i) == data.Fillval() || data.V(i) == data.Fillval()) ? NAN : (data.U2(i) - (data.U(i) * data.U(i) + data.V(i) * data.V(i))));
}
fw.Finalize();
fw.Close();
} }
fw.Finalize(); else if(outfmt == "nc" || outfmt == "netcdf")
fw.Close(); {
int compress = 3;
NCFileW fw;
MString err;
if(args.contains("compress")) compress = args.at("compress").ToInt();
if(!err.Exist()) err = fw.Create(data, name, args.at("_cmdline"), compress);
if(!err.Exist()) err = fw.AddVariable("u", "", "Eastward velocity", u);
if(!err.Exist()) err = fw.AddVariable("v", "", "Northward velocity", u);
if(!err.Exist()) err = fw.AddVariable("div", "", "Velocity divergence", "(" + u + ")/" + d);
if(!err.Exist()) err = fw.AddVariable("rot", "", "Velocity rotor", "(" + u + ")/" + d);
if(!err.Exist()) err = fw.AddVariable("ow", "", "Okubo-Weiss parameter", "(" + u + ")2/" + d + "2");
if(!err.Exist()) err = fw.AddVariable("ke", "", "Squared velocity module, u^2+v^2", "(" + u + ")2");
if(!err.Exist()) err = fw.AddVariable("eke", "", "Squared velocity dispersion aka eddy kinetic energy, <u^2+v^2>-<u>^2-<v>^2", "(" + u + ")2");
if(!err.Exist()) err = fw.WriteGrid(data);
if(!err.Exist()) err = fw.WriteVariable(data, "u", [&data = std::as_const(data)](size_t i, size_t j) { return data.U(i, j); });
if(!err.Exist()) err = fw.WriteVariable(data, "v", [&data = std::as_const(data)](size_t i, size_t j) { return data.V(i, j); });
if(!err.Exist()) err = fw.WriteVariable(data, "div", [&data = std::as_const(data)](size_t i, size_t j) { return data.Div(i, j); });
if(!err.Exist()) err = fw.WriteVariable(data, "rot", [&data = std::as_const(data)](size_t i, size_t j) { return data.Rot(i, j); });
if(!err.Exist()) err = fw.WriteVariable(data, "ow", [&data = std::as_const(data)](size_t i, size_t j) { return data.OW(i, j); });
if(!err.Exist()) err = fw.WriteVariable(data, "ke", [&data = std::as_const(data)](size_t i, size_t j) { return data.U2(i, j); });
if(!err.Exist())
err = fw.WriteVariable(data, "eke", [&data = std::as_const(data)](size_t i, size_t j) { return data.U2(i, j) - (data.U(i, j) * data.U(i, j) + data.V(i, j) * data.V(i, j)); });
if(err.Exist()) return err;
fw.Close();
}
else
return "Unknown format: " + outfmt;
} }
// Filtered vectors file // Filtered vectors file
name = args.contains("velout") ? args.at("velout") : ""; name = args.contains("velout") ? args.at("velout") : "";
outfmt = args.contains("veloutformat") ? args.at("veloutformat") : (GetExt(name) == "nc" ? "nc" : "bin");
if(name.Exist()) if(name.Exist())
{ {
size_t shiftx = args.contains("shiftx") ? args.at("shiftx").ToInteger<size_t>() : 0; size_t shiftx = args.contains("shiftx") ? args.at("shiftx").ToInteger<size_t>() : 0;
@ -84,48 +213,70 @@ template<class D> MString ActionUV::DoAction(const CLArgs& args, D& ds)
size_t skipx = args.contains("skipx") ? args.at("skipx").ToInteger<size_t>() : 1; size_t skipx = args.contains("skipx") ? args.at("skipx").ToInteger<size_t>() : 1;
size_t skipy = args.contains("skipy") ? args.at("skipy").ToInteger<size_t>() : 1; size_t skipy = args.contains("skipy") ? args.at("skipy").ToInteger<size_t>() : 1;
BFileW vel; Sparser<decltype(data)> sdata(data, shiftx, shifty, skipx, skipy);
vel.Create(name, 4); if(outfmt == "bin")
vel.SetColumnName(1, "Longitude"); {
vel.SetColumnName(2, "Latitude"); BFileW vel;
vel.SetColumnName(3, "u, cm/s"); vel.Create(name, 4);
vel.SetColumnName(4, "v, cm/s"); vel.SetColumnName(1, "Longitude");
vel.SetColumnName(2, "Latitude");
vel.SetColumnName(3, "u, " + u);
vel.SetColumnName(4, "v, " + u);
for(size_t ix = shiftx; ix < data.Nx(); ix += skipx) for(size_t ix = 0; ix < sdata.Nx(); ix++)
for(size_t iy = shifty; iy < data.Ny(); iy += skipy) for(size_t iy = 0; iy < sdata.Ny(); iy++)
{ {
vel.Write(data.Lon(ix, iy)); vel.Write(sdata.Lon(ix, iy));
vel.Write(data.Lat(ix, iy)); vel.Write(sdata.Lat(ix, iy));
vel.Write(data.U(ix, iy) == data.Fillval() ? NAN : data.U(ix, iy)); vel.Write(sdata.U(ix, iy) == sdata.Fillval() ? NAN : sdata.U(ix, iy));
vel.Write(data.V(ix, iy) == data.Fillval() ? NAN : data.V(ix, iy)); vel.Write(sdata.V(ix, iy) == sdata.Fillval() ? NAN : sdata.V(ix, iy));
} }
vel.Finalize(); vel.Finalize();
vel.Close(); vel.Close();
}
else if(outfmt == "nc" || outfmt == "netcdf")
{
int compress = 3;
NCFileW fw;
MString err;
if(args.contains("compress")) compress = args.at("compress").ToInt();
if(!err.Exist()) err = fw.Create(sdata, name, args.at("_cmdline"), compress);
if(!err.Exist()) err = fw.AddVariable("u", "", "Eastward velocity", u);
if(!err.Exist()) err = fw.AddVariable("v", "", "Northward velocity", u);
if(!err.Exist()) err = fw.WriteGrid(sdata);
if(!err.Exist()) err = fw.WriteVariable(sdata, "u", [&data = std::as_const(sdata)](size_t i, size_t j) { return data.U(i, j); });
if(!err.Exist()) err = fw.WriteVariable(sdata, "v", [&data = std::as_const(sdata)](size_t i, size_t j) { return data.V(i, j); });
if(err.Exist()) return err;
fw.Close();
}
else
return "Unknown format: " + outfmt;
} }
// Stationary points // Stationary points
name = args.contains("stpout") ? args.at("stpout") : ""; name = args.contains("stpout") ? args.at("stpout") : "";
outfmt = args.contains("stpoutformat") ? args.at("stpoutformat") : (GetExt(name) == "nc" ? "nc" : "bin");
if(name.Exist()) if(name.Exist())
{ {
BFileW stp; StPoints p(true);
stp.Create(name, 3);
stp.SetColumnName(1, "Longitude");
stp.SetColumnName(2, "Latitude");
stp.SetColumnName(3, "Stability (0 - saddle, 1 - st. anticicl. focus, 2 - st. knot, 3 - unst. anticicl. focus, 4 - unst. knot, 5 - st. cicl. focus, 6 - unst. cicl. focus)");
for(size_t ix = 0; ix < data.Nx() - 1; ix++) for(size_t ix = 0; ix < data.Nx() - 1; ix++)
for(size_t iy = 0; iy < data.Ny() - 1; iy++) for(size_t iy = 0; iy < data.Ny() - 1; iy++) p.Add(data.StablePoints(ix, iy));
{
auto points = data.StablePoints(ix, iy); if(outfmt == "bin")
for(size_t i = 0; i < points.size(); i++) p.WriteBinBile(name);
{ else if(outfmt == "nc" || outfmt == "netcdf")
stp.Write(points[i].x); {
stp.Write(points[i].y); int compress = args.contains("compress") ? args.at("compress").ToInt() : 3;
stp.Write(michlib::int_cast<size_t>(points[i].type)); MString err = p.WriteNcFile(name, args.at("_cmdline"), compress);
} if(err.Exist()) return err;
} }
stp.Finalize(); else
stp.Close(); return "Unknown format: " + outfmt;
} }
return ""; return "";

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