diff --git a/TODO b/TODO
index 426fa24f8cefcee88b9694b968e21f2a50d94a60..7888754d828ec1a9861d7066dab881e757c545e2 100644
--- a/TODO
+++ b/TODO
@@ -1,17 +1,17 @@
== Todo at once ==
-allow fit if curve has less slices than data?
-prevent fits for slices with m/ set; allow global fits for the remaining slices
-parallelize global fits
+or+: value does not arrive!
cp: table header placement, correct 1-R^2
store status cg, cx of curve files
+
== To investigate ==
boost::format -> cppformat ?
+
== Current refactoring (everything becomes an object) ==
simplfy tree_ and curve_ calls
@@ -119,6 +119,7 @@ distribution
- include wupscat, wupsbb
- rewrite wupscat in bash instead of ruby
+
== PROJECTS ==
detailed balance
@@ -142,6 +143,8 @@ convolution with function
coord name algebra
+parallelize global fits
+
== WAITING FOR CLUE ==
diff --git a/pub/lib/commands.cpp b/pub/lib/commands.cpp
index 1b0057dbbc850f39d7be6e8a304db807d0a821b6..3679215b7b98db054a9dd9b3e8c5d2f8df11b3e4 100644
--- a/pub/lib/commands.cpp
+++ b/pub/lib/commands.cpp
@@ -275,6 +275,10 @@ bool frida_command( string cmd )
NFileOut::save( "y08" );
} else if (cmd == "fso") {
NFileOut::save( "y08", true );
+ } else if (cmd == "fS") {
+ NFileOut::save( "yda" );
+ } else if (cmd == "fSo") {
+ NFileOut::save( "yda", true );
} else if (cmd == "fe1") {
NFileOut::save( "csv" );
} else if (cmd == "fe2") {
diff --git a/pub/lib/file_out.cpp b/pub/lib/file_out.cpp
index a68dc0510b104befb5a9f61cba244d4d1f3022b7..3d201e31b18710acd9c3c09b4b3f267e536c6e89 100644
--- a/pub/lib/file_out.cpp
+++ b/pub/lib/file_out.cpp
@@ -7,9 +7,12 @@
//! \file file_out.cpp
//! \brief NFileOut: write files.
+#include <iostream> // for debugging
#include <cmath>
#include <string>
#include <vector>
+#include <fstream>
+#include <yaml-cpp/yaml.h>
#include "../trivia/yaml_out.hpp"
#include "../readplus/ask.hpp"
@@ -22,6 +25,7 @@
#include "file_out.hpp"
namespace NFileOut {
+ void save_yda( std::ofstream& ofs, POlo f );
void save_y08( FILE *file, POlo f );
void save_csv( FILE *file, POlo f );
void save_tab( FILE *file, POlo f );
@@ -33,7 +37,6 @@ namespace NFileOut {
void NFileOut::save( string fmt, bool allow_overwrite )
{
string outfnam;
- FILE *file;
NOlm::IterateO iter;
POlo f;
while( (f=iter()) ) {
@@ -47,28 +50,148 @@ void NFileOut::save( string fmt, bool allow_overwrite )
f->lDoc.push_back( "fs " + outfnam + " # " + triv::time2strg( time(0) ) );
// prevent unintended overwriting
if( !allow_overwrite ){
+ FILE *file;
if ( (file = fopen(outfnam.c_str(), "r")) ) {
fclose(file);
throw "file "+outfnam+" exists, use fso to overwrite";
}
}
// save file
- if ( !(file = fopen(outfnam.c_str(), "w")) )
- throw "cannot write to file " + outfnam;
- if( fmt=="y08"){
- save_y08( file, f );
- } else if( fmt=="csv" ) {
- save_csv( file, f );
- } else if( fmt=="tab" ) {
- save_tab( file, f );
- } else
- throw "Unknown format "+fmt;
- fclose(file);
+ if( fmt=="yda"){
+ std::ofstream ofs;
+ ofs.open( outfnam, std::ofstream::out );
+ save_yda( ofs, f );
+ ofs.close();
+ } else {
+ FILE *file;
+ if ( !(file = fopen(outfnam.c_str(), "w")) )
+ throw "cannot write to file " + outfnam;
+ if( fmt=="y08" ) {
+ save_y08( file, f );
+ } else if( fmt=="csv" ) {
+ save_csv( file, f );
+ } else if( fmt=="tab" ) {
+ save_tab( file, f );
+ } else
+ throw "BUG: Unknown format "+fmt;
+ fclose(file);
+ }
f->as_on_disk = true;
}
}
+//! Writes a file in format y15.
+
+void NFileOut::save_yda( std::ofstream& ofs, POlo f )
+{
+ POld fd = P2D( f );
+ POlc fc = P2C( f );
+
+ YAML::Emitter out;
+ out << YAML::BeginMap;
+
+ out << YAML::Key << "Meta" << YAML::Value << YAML::BeginMap;
+ out << YAML::Key << "format" << YAML::Value << "frida/y15 for yaml1.2";
+ out << YAML::Key << "type" << YAML::Value << ( fd ? "generic tabular data" : "frida2 curve" );
+ out << YAML::EndMap;
+
+ out << YAML::Key << "History" << YAML::Value << YAML::BeginSeq;
+ for ( string lin: f->lDoc )
+ out << lin;
+ out << YAML::EndSeq;
+
+ out << YAML::Key << "Coord" << YAML::Value << YAML::BeginMap;
+ out << YAML::Key << "x" << YAML::Value << YAML::Flow << YAML::BeginMap <<
+ YAML::Key << "name" << YAML::Value << f->xco.name <<
+ YAML::Key << "unit" << YAML::Value << f->xco.unit << YAML::EndMap;
+ out << YAML::Key << "y" << YAML::Value << YAML::Flow << YAML::BeginMap <<
+ YAML::Key << "name" << YAML::Value << f->yco.name <<
+ YAML::Key << "unit" << YAML::Value << f->yco.unit << YAML::EndMap;
+ out << YAML::Key << "z" << YAML::Value << YAML::BeginSeq;
+ for ( auto& zco: f->ZCo )
+ out << YAML::Flow << YAML::BeginMap <<
+ YAML::Key << "name" << YAML::Value << zco.name <<
+ YAML::Key << "unit" << YAML::Value << zco.unit << YAML::EndMap;
+ out << YAML::EndSeq;
+ out << YAML::EndMap;
+
+ out << YAML::Key << "RPar" << YAML::Value << YAML::BeginSeq;
+ for ( auto& rpar: f->RPar )
+ out << YAML::BeginMap <<
+ YAML::Key << "name" << YAML::Value << rpar.Co.name <<
+ YAML::Key << "unit" << YAML::Value << rpar.Co.unit <<
+ YAML::Key << "val" << YAML::Value << rpar.val <<
+ YAML::Key << "stdv" << YAML::Value << rpar.dval << YAML::EndMap;
+ out << YAML::EndSeq;
+
+ if( fc ) {
+ out << YAML::Key << "Curve" << YAML::Value << YAML::BeginMap;
+
+ out << YAML::Key << "expr" << YAML::Value << fc->expr;
+ out << YAML::Key << "weighing" << YAML::Value << COlc::wgtNames[fc->weighing];
+ out << YAML::Key << "chi2" << YAML::Value << fc->chi2;
+
+ out << YAML::EndMap;
+ }
+
+ out << YAML::Key << "Slices" << YAML::Value << YAML::BeginSeq;
+ for( size_t j=0; j<f->V.size(); ++j ) {
+ out << YAML::BeginMap;
+ out << YAML::Key << "j" << YAML::Value << j;
+ RSlice s = f->V[j];
+ out << YAML::Key << "z" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( auto& z: s->z ) {
+ out << YAML::BeginMap;
+ if( auto pz = PCAST<const CObjNum>(z) ) {
+ out << YAML::Key << "val" << YAML::Value << pz->to_r();
+ if( auto pdz = PCAST<const CObjEnu>(z) )
+ out << YAML::Key << "stdv" << YAML::Value << pdz->to_dr();
+ } else
+ out << YAML::Key << "string" << YAML::Value << z->to_s();
+ out << YAML::EndMap;
+ }
+ out << YAML::EndSeq;
+ if ( fd ) {
+ RSpec sd = PCAST<const CSpec>(s);
+ out << YAML::Key << "x" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( double v: sd->x )
+ out << v;
+ out << YAML::EndSeq;
+
+ out << YAML::Key << "y" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( double v: sd->y )
+ out << v;
+ out << YAML::EndSeq;
+
+ if( sd->has_dy() ) {
+ out << YAML::Key << "dy" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( double v: sd->dy )
+ out << v;
+ out << YAML::EndSeq;
+ }
+ } else {
+ RCurve sc = PCAST<const CCurve>(s);
+ out << YAML::Key << "p" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( double v: sc->P )
+ out << v;
+ out << YAML::EndSeq;
+
+ out << YAML::Key << "attr" << YAML::Value << YAML::Flow << YAML::BeginSeq;
+ for( char v: sc->ParAttr )
+ out << v;
+ out << YAML::EndSeq;
+
+ out << YAML::Key << "fitOutcome" << YAML::Value << sc->fitOutcome;
+ out << YAML::Key << "fitChi2" << YAML::Value << sc->fitChi2;
+ out << YAML::Key << "fitR2" << YAML::Value << sc->fitR2;
+ }
+ out << YAML::EndMap;
+ }
+ ofs << out.c_str(); // https://github.com/jbeder/yaml-cpp/issues/337
+}
+
+
//! Writes a file in format y08.
void NFileOut::save_y08( FILE *file, POlo f )
diff --git a/pub/lib/olf.cpp b/pub/lib/olf.cpp
index bf52843703252123b17a4e7af815ff58a3ec72a0..0cd8f596bc114ea918215e4cc31c8170aaeeb192 100644
--- a/pub/lib/olf.cpp
+++ b/pub/lib/olf.cpp
@@ -328,6 +328,7 @@ bool COld::has_nonzero_dy() const
//* class COlc - interactive initialization
//**************************************************************************************************
+string COlc::wgtNames[] = { "lin", "log", "var", "varc", "vard" };
//! Prompt for curve description, and initialize things.
diff --git a/pub/lib/olf.hpp b/pub/lib/olf.hpp
index 99b865098aea7fbfca1fa19d3baafbc3316b6377..47e78e557c85ce93e894f559adcb65d69c783364 100644
--- a/pub/lib/olf.hpp
+++ b/pub/lib/olf.hpp
@@ -96,6 +96,7 @@ public:
int kconv; ///< Index of resolution file to convolve with.
enum TWgt { _LIN, _LOG, _VAR, _VARC, _VARD }
weighing; ///< Weight mode for fitting.
+ static string wgtNames[];
bool plot_to_grid; ///< Use grid from file 'kd' ?
string range_expr; ///< Restricts points to be fitted.
RNode range_T; ///< Parsed range_expr.