diff --git a/TODO b/TODO
index 7888754d828ec1a9861d7066dab881e757c545e2..a5dfd3fe963df67392d6ab4f52949778c40b669f 100644
--- a/TODO
+++ b/TODO
@@ -148,6 +148,8 @@ parallelize global fits
== WAITING FOR CLUE ==
+parallel execution: upon first exception kill all threads
+
rework dy, dp
How to treat blanks in user input:
diff --git a/pub/lib/file_in.cpp b/pub/lib/file_in.cpp
index 96c6dd0caae75bf3a24ab545338a1b42fb4c26dc..a1f1b9f12290f5c377fcc0d5957c30f1ff4cbd61 100644
--- a/pub/lib/file_in.cpp
+++ b/pub/lib/file_in.cpp
@@ -33,7 +33,7 @@
using namespace std;
namespace NFileIn {
- void Load_08( ifstream& F_in, string fnam );
+ void Load_yda( ifstream& F_in, string fnam );
}
@@ -53,12 +53,7 @@ void NFileIn::load(void)
if( FS.fail() )
throw string("cannot open file");
cout << ".. loading file " << fnam << "\n";
- if ( fext=="y08" )
- Load_08( FS, fshort );
- else if ( fext=="yda" )
- cout << "TODO\n";
- else
- throw "BUG: unforeseen extension " + fext;
+ Load_yda( FS, fshort );
FS.close();
}
catch(string& ex) {
@@ -70,9 +65,9 @@ void NFileIn::load(void)
}
}
-//! Load a YAML file in y08 format.
+//! Load a YAML file in yda format.
-void NFileIn::Load_08(ifstream& FS, string fnam)
+void NFileIn::Load_yda(ifstream& FS, string fnam)
{
const YAML::Node doc = YAML::Load(FS);
if( doc.Type() != YAML::NodeType::Map )
@@ -81,14 +76,19 @@ void NFileIn::Load_08(ifstream& FS, string fnam)
//read meta
if(!doc["Meta"])
throw S("no Meta");
- if ( doc["Meta"].Type() != YAML::NodeType::Map && doc["Meta"].size() > 0 )
- throw S("Meta is not a MAP type");
+ if ( doc["Meta"].Type() != YAML::NodeType::Map )
+ throw S("Meta is not of MAP type");
if(!doc["Meta"]["format"])
throw S("no format in Meta");
string s = doc["Meta"]["format"].as<string>();
- if ( s != "frida/y08 for yaml1" )
- throw S("format is not frida/y08 for yaml1");
+ int version;
+ if ( s == "frida/y08 for yaml1" )
+ version = 1;
+ else if ( s == "frida/y15 for yaml1.2" )
+ version = 2;
+ else
+ throw "unknown data format '" + s + "'";
if(!doc["Meta"]["type"])
throw S("no type in Meta");
@@ -108,13 +108,14 @@ void NFileIn::Load_08(ifstream& FS, string fnam)
fc = POlc( new COlc );
fout = fc;
} else
- throw "Meta section has invalid type "+type;
+ throw "Invalid file type "+type;
// read history
if(!doc["History"])
throw S("no History");
- if ( doc["History"].Type() != YAML::NodeType::Sequence && doc["History"].size() > 0 )
- throw S("History is not a SEQUENCE type");
+ if ( doc["History"].Type() != YAML::NodeType::Sequence &&
+ (version>1 || doc["History"].size()>0 ) )
+ throw S("History is not of SEQUENCE type");
for (int i = 0; i < doc["History"].size(); i++) {
string s = doc["History"][i].as<string>();
fout->lDoc.push_back(s);
@@ -123,113 +124,225 @@ void NFileIn::Load_08(ifstream& FS, string fnam)
// read coord
if(!doc["Coord"])
throw S("no Coord");
- if ( doc["Coord"].Type() != YAML::NodeType::Map && doc["Coord"].size() > 0 )
- throw S("Coord is not a MAP type");
- if( const YAML::Node& pName = doc["Coord"]["x"] ){
- fout->xco.name = pName["name"].as<string>();
- fout->xco.unit =pName["unit"].as<string>();
+ if ( doc["Coord"].Type() != YAML::NodeType::Map )
+ throw S("Coord is not of MAP type");
+ if( const YAML::Node& dCo = doc["Coord"]["x"] ){
+ fout->xco.name = dCo["name"].as<string>();
+ fout->xco.unit =dCo["unit"].as<string>();
} else
throw S("no x coord");
- if( const YAML::Node& pName = doc["Coord"]["y"] ){
- fout->yco.name = pName["name"].as<string>();
- fout->yco.unit = pName["unit"].as<string>();
+ if( const YAML::Node& dCo = doc["Coord"]["y"] ){
+ fout->yco.name = dCo["name"].as<string>();
+ fout->yco.unit = dCo["unit"].as<string>();
} else
throw S("no y coord");
-
- int iz = 0;
- while(const YAML::Node& pName = doc["Coord"]["z"+S(iz)]){
- CCoord co(pName["name"].as<string>(), pName["unit"].as<string>());
- fout->ZCo.push_back( co );
- ++iz;
+ if ( version==1 ) {
+ int iz = 0;
+ while(const YAML::Node& dCo = doc["Coord"]["z"+S(iz)]){
+ CCoord co(dCo["name"].as<string>(), dCo["unit"].as<string>());
+ fout->ZCo.push_back( co );
+ ++iz;
+ }
+ } else {
+ if ( doc["Coord"]["z"].Type() != YAML::NodeType::Sequence )
+ throw S("Coord[z] is not of SEQUENCE type");
+ for ( auto dCo: doc["Coord"]["z"] ) {
+ CCoord co(dCo["name"].as<string>(), dCo["unit"].as<string>());
+ fout->ZCo.push_back( co );
+ }
}
- // read Param
- if(!doc["Param"])
- throw S("no Param");
- if ( doc["Param"].Type() != YAML::NodeType::Sequence && doc["Param"].size() > 0)
- throw S("Param is not a SEQUENCE type");
- for( int iParam = 0; iParam < (doc["Param"].size()); iParam++ ){
- if ( doc["Param"][iParam].Type() != YAML::NodeType::Map )
- throw "Param " + S(iParam) + " is not a MAP type";
- CCoord co(doc["Param"][iParam]["name"].as<string>(),
- doc["Param"][iParam]["unit"].as<string>());
- string s = doc["Param"][iParam]["value"].as<string>();
- double num;
- if( !triv::any2dbl( s, &num ) )
- throw "param(" + co.name + "): invalid value " + s;
- fout->RPar.push_back( CParam( co, num ) );
+ // read r-pars
+ if ( version==1 ) {
+ if(!doc["Param"])
+ throw S("no Param");
+ if ( doc["Param"].Type() != YAML::NodeType::Sequence && doc["Param"].size() > 0)
+ throw S("Param is not of SEQUENCE type");
+ for( int iParam = 0; iParam < (doc["Param"].size()); iParam++ ){
+ if ( doc["Param"][iParam].Type() != YAML::NodeType::Map )
+ throw "Param " + S(iParam) + " is not of MAP type";
+ CCoord co(doc["Param"][iParam]["name"].as<string>(),
+ doc["Param"][iParam]["unit"].as<string>());
+ string s = doc["Param"][iParam]["value"].as<string>();
+ double num;
+ if( !triv::any2dbl( s, &num ) )
+ throw "param(" + co.name + "): invalid value " + s;
+ fout->RPar.push_back( CParam( co, num ) );
+ }
+ } else {
+ if(!doc["RPar"])
+ throw S("no RPar");
+ if ( doc["RPar"].Type() != YAML::NodeType::Sequence )
+ throw S("RPar is not of SEQUENCE type");
+ for ( auto dCo: doc["RPar"] ) {
+ if ( dCo.Type() != YAML::NodeType::Map )
+ throw S("an r-par is not of MAP type");
+ CCoord co(dCo["name"].as<string>(), dCo["unit"].as<string>());
+ double val = dCo["val"].as<double>();
+ fout->RPar.push_back( CParam( co, val ) );
+ }
}
// for curve, read formula
if( !isdata ) {
- const YAML::Node& pName = doc["Formula"];
- if( !pName )
- throw S("DEFICIENT FILE: no formula");
- string s = pName.as<string>();
- fc->parse_function( s );
+ string expr;
+ if ( version==1 ) {
+ const YAML::Node& nod = doc["Formula"];
+ if( !nod )
+ throw S("DEFICIENT FILE: no formula");
+ expr = nod.as<string>();
+ fc->parse_function( s );
+ fc->curve_set_defaults();
+ } else {
+ const YAML::Node& nod = doc["Curve"];
+ if( !nod )
+ throw S("DEFICIENT FILE: no Curve section");
+ expr = nod["expr"].as<string>();
+ fc->nP = nod["nPar"].as<int>();
+ fc->weighing = COlc::name2wgt( nod["weighing"].as<string>() );
+ fc->chi2 = nod["chi2"].as<double>();
+ }
+ fc->parse_function( expr );
fc->curve_set_defaults();
}
- //start to read Tables
- if(!doc["Tables"])
- throw S("no Tables");
- if ( doc["Tables"].Type() != YAML::NodeType::Sequence && doc["Tables"].size() > 0 )
- throw S("Tables is not a SEQUENCE type");
- for (int iTable = 0; iTable < (doc["Tables"].size()); iTable++) {
- if ( doc["Tables"][iTable].Type() != YAML::NodeType::Map )
- throw "Tables " + S(iTable) + " is not a MAP type";
- vector<RObj> z;
- for(int iz=0; iz<fout->ZCo.size(); ++iz ){
- string s = doc["Tables"][iTable]["z" + S(iz)].as<string>() ;
- double num;
- if( !triv::any2dbl( s, &num ) )
- throw "z" + S(iz) + ": invalid value " + s;
- z.push_back( RObjDbl( new CObjDbl( num ) ) );
+ // start to read slices
+ if ( version==1 ) {
+ if(!doc["Tables"])
+ throw S("no Tables");
+ if ( doc["Tables"].Type() != YAML::NodeType::Sequence && doc["Tables"].size() > 0 )
+ throw S("Tables is not of SEQUENCE type");
+ for (int iTable = 0; iTable < (doc["Tables"].size()); iTable++) {
+ if ( doc["Tables"][iTable].Type() != YAML::NodeType::Map )
+ throw "Tables " + S(iTable) + " is not of MAP type";
+ vector<RObj> z;
+ for(int iz=0; iz<fout->ZCo.size(); ++iz ){
+ string s = doc["Tables"][iTable]["z" + S(iz)].as<string>() ;
+ double num;
+ if( !triv::any2dbl( s, &num ) )
+ throw "z" + S(iz) + ": invalid value " + s;
+ z.push_back( RObjDbl( new CObjDbl( num ) ) );
+ }
+
+ if( isdata ) {
+ PSpec sout( new CSpec );
+ sout->z = z;
+ string xytag;
+ if ( doc["Tables"][iTable]["xy"] ) {
+ string res, lin;
+ string val = doc["Tables"][iTable]["xy"].as<string>();
+ while( val != "" ) {
+ triv::string_extract_line( val, &lin, &res );
+ double vx, vy;
+ if( sscanf( lin.c_str(), "%lg %lg\n", &vx, &vy )!=2 )
+ throw "xy: bad data line: " + lin;
+ sout->push_xy( vx, vy );
+ val = res;
+ };
+ } else if ( doc["Tables"][iTable]["xyd"] ) {
+ //itxy.second() >> val;
+ string res, lin;
+ string val = doc["Tables"][iTable]["xyd"].as<string>();
+ while( val != "" ) {
+ triv::string_extract_line( val, &lin, &res );
+ double vx, vy, dy;
+ if( sscanf( lin.c_str(), "%lg %lg %lg\n",&vx, &vy, &dy )!=3 )
+ throw "xyd: bad data line: " + lin;
+ sout->push_xyd( vx, vy, dy );
+ val = res;
+ };
+ } else
+ throw "invalid xytag " + xytag;
+ fout->V.push_back( sout );
+ } else {
+ PCurve cout( new CCurve );
+ cout->z = z;
+ for( int ip=0; ip<fc->nP; ++ip ){
+ string res;
+ string val = doc["Tables"][iTable]["p" + S(ip)].as<string>();
+ double num;
+ if( !triv::any2dbl( val, &num ) )
+ throw "p" + S(ip) + ": invalid value " + val;
+ cout->P.push_back( num );
+ cout->ParAttr.push_back( 'u' );
+ }
+ fout->V.push_back( cout );
+ }
}
+ } else {
+ if(!doc["Slices"])
+ throw S("no Slices");
+ if ( doc["Slices"].Type() != YAML::NodeType::Sequence )
+ throw S("section Slices is not of SEQUENCE type");
+ for ( const YAML::Node& nodeSlic: doc["Slices"] ) {
+ if ( nodeSlic.Type() != YAML::NodeType::Map )
+ throw S("a slice is not of MAP type");
+ const YAML::Node& nodeZ = nodeSlic["z"];
+ if(!nodeZ)
+ throw S("a slice has no z entry");
+ if ( nodeZ.Type() != YAML::NodeType::Sequence )
+ throw S("a z entry is not of SEQUENCE type");
+ vector<RObj> z;
+ for ( const YAML::Node& nodeZi: nodeZ ) {
+ if ( nodeSlic.Type() != YAML::NodeType::Map )
+ throw S("a z entry is not of MAP type");
+ z.push_back( RObjDbl( new CObjDbl( nodeZi["val"].as<double>() ) ) );
+ }
+ if( isdata ) {
+ PSpec sout( new CSpec );
+ sout->z = z;
+ if(!nodeSlic["x"])
+ throw S("a slice has no x entry");
+ if ( nodeSlic["x"].Type() != YAML::NodeType::Sequence )
+ throw S("an x entry is not of SEQUENCE type");
+ for ( const YAML::Node& nodeEle: nodeSlic["x"] )
+ sout->x.push_back( nodeEle.as<double>() );
- if( isdata ) {
- PSpec sout( new CSpec );
- sout->z = z;
- string xytag;
- if ( doc["Tables"][iTable]["xy"] ) {
- string res, lin;
- string val = doc["Tables"][iTable]["xy"].as<string>();
- while( val != "" ) {
- triv::string_extract_line( val, &lin, &res );
- double vx, vy;
- if( sscanf( lin.c_str(), "%lg %lg\n", &vx, &vy )!=2 )
- throw "xy: bad data line: " + lin;
- sout->push_xy( vx, vy );
- val = res;
- };
- } else if ( doc["Tables"][iTable]["xyd"] ) {
- //itxy.second() >> val;
- string res, lin;
- string val = doc["Tables"][iTable]["xyd"].as<string>();
- while( val != "" ) {
- triv::string_extract_line( val, &lin, &res );
- double vx, vy, dy;
- if( sscanf( lin.c_str(), "%lg %lg %lg\n",&vx, &vy, &dy )!=3 )
- throw "xyd: bad data line: " + lin;
- sout->push_xyd( vx, vy, dy );
- val = res;
- };
- } else
- throw "invalid xytag " + xytag;
- fout->V.push_back( sout );
- } else {
- PCurve cout( new CCurve );
- cout->z = z;
- for( int ip=0; ip<fc->nP; ++ip ){
- string res;
- string val = doc["Tables"][iTable]["p" + S(ip)].as<string>();
- double num;
- if( !triv::any2dbl( val, &num ) )
- throw "p" + S(ip) + ": invalid value " + val;
- cout->P.push_back( num );
- cout->ParAttr.push_back( 'u' );
+ if(!nodeSlic["y"])
+ throw S("a slice has no y entry");
+ if ( nodeSlic["y"].Type() != YAML::NodeType::Sequence )
+ throw S("a y entry is not of SEQUENCE type");
+ for ( const YAML::Node& nodeEle: nodeSlic["y"] )
+ sout->y.push_back( nodeEle.as<double>() );
+ if( sout->y.size() != sout->x.size() )
+ throw S("a y entry differs in length from x");
+
+ if( nodeSlic["dy"] ) {
+ if ( nodeSlic["dy"].Type() != YAML::NodeType::Sequence )
+ throw S("a dy entry is not of SEQUENCE type");
+ for ( const YAML::Node& nodeEle: nodeSlic["dy"] )
+ sout->dy.push_back( nodeEle.as<double>() );
+ if( sout->dy.size() != sout->x.size() )
+ throw S("a dy entry differs in length from x");
+ }
+ fout->V.push_back( sout );
+ } else {
+ PCurve cout( new CCurve );
+ cout->z = z;
+ if(!nodeSlic["p"])
+ throw S("a slice has no p entry");
+ if ( nodeSlic["p"].Type() != YAML::NodeType::Sequence )
+ throw S("a p entry is not of SEQUENCE type");
+ for ( const YAML::Node& nodeEle: nodeSlic["p"] )
+ cout->P.push_back( nodeEle.as<double>() );
+ if ( cout->P.size()!=fc->nP )
+ throw S("number of p entries conflicts with nPar");
+
+ if(!nodeSlic["attr"])
+ throw S("a slice has no attr entry");
+ if ( nodeSlic["attr"].Type() != YAML::NodeType::Sequence )
+ throw S("an attr entry is not of SEQUENCE type");
+ for ( const YAML::Node& nodeEle: nodeSlic["attr"] )
+ cout->ParAttr.push_back( nodeEle.as<char>() );
+ if ( cout->ParAttr.size()!=fc->nP )
+ throw S("number of attr entries conflicts with nPar");
+
+ cout->fitOutcome = nodeSlic["fitOutcome"].as<double>();
+ cout->fitChi2 = nodeSlic["fitChi2"].as<double>();
+ cout->fitR2 = nodeSlic["fitR2"].as<double>();
+
+ fout->V.push_back( cout );
}
- fout->V.push_back( cout );
}
}
diff --git a/pub/lib/file_out.cpp b/pub/lib/file_out.cpp
index b9ed944547d2e1055aca2d7591ff35514dcf3c8a..0864aac23f2013c712f9affebb974a180fee28ee 100644
--- a/pub/lib/file_out.cpp
+++ b/pub/lib/file_out.cpp
@@ -95,7 +95,7 @@ void NFileOut::save_yda( std::ofstream& ofs, POlo f )
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;
@@ -108,7 +108,7 @@ void NFileOut::save_yda( std::ofstream& ofs, POlo f )
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::Flow << YAML::BeginSeq;
+ out << YAML::Key << "z" << YAML::Value << YAML::Flow << YAML::BeginSeq;
for ( auto& zco: f->ZCo )
out << YAML::BeginMap <<
YAML::Key << "name" << YAML::Value << zco.name <<
@@ -129,12 +129,13 @@ void NFileOut::save_yda( std::ofstream& ofs, POlo f )
out << YAML::Key << "Curve" << YAML::Value << YAML::BeginMap;
out << YAML::Key << "expr" << YAML::Value << fc->expr;
+ out << YAML::Key << "nPar" << YAML::Value << fc->nP;
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;
diff --git a/pub/lib/olf.cpp b/pub/lib/olf.cpp
index 0cd8f596bc114ea918215e4cc31c8170aaeeb192..bed8246427733ca86ef2f2279d0b4fe95368fa07 100644
--- a/pub/lib/olf.cpp
+++ b/pub/lib/olf.cpp
@@ -330,6 +330,16 @@ bool COld::has_nonzero_dy() const
string COlc::wgtNames[] = { "lin", "log", "var", "varc", "vard" };
+//! Converts weight from string to enum
+
+COlc::TWgt COlc::name2wgt( string name )
+{
+ for ( int i=0; i<=_LAST_TWGT; ++i )
+ if( name==COlc::wgtNames[i] )
+ return (TWgt)i;
+ throw "undefined weighing key '" + name + "'";
+}
+
//! Prompt for curve description, and initialize things.
void COlc::curve_query( const string& quest )
diff --git a/pub/lib/olf.hpp b/pub/lib/olf.hpp
index 47e78e557c85ce93e894f559adcb65d69c783364..3a5812e77f90e205779edd930f0a3b119bac253c 100644
--- a/pub/lib/olf.hpp
+++ b/pub/lib/olf.hpp
@@ -94,9 +94,10 @@ public:
// Fitting:
int kd; ///< Index of data file to be fitted.
int kconv; ///< Index of resolution file to convolve with.
- enum TWgt { _LIN, _LOG, _VAR, _VARC, _VARD }
+ enum TWgt { _LIN, _LOG, _VAR, _VARC, _VARD, _LAST_TWGT=_VARD }
weighing; ///< Weight mode for fitting.
static string wgtNames[];
+ static TWgt name2wgt( string name );
bool plot_to_grid; ///< Use grid from file 'kd' ?
string range_expr; ///< Restricts points to be fitted.
RNode range_T; ///< Parsed range_expr.