[med-svn] [Git][med-team/simrisc][upstream] New upstream version 15.02.00
Frank B. Brokken (@fbb-guest)
gitlab at salsa.debian.org
Fri Jun 16 09:17:00 BST 2023
Frank B. Brokken pushed to branch upstream at Debian Med / simrisc
Commits:
9b114cd9 by Frank B. Brokken at 2023-06-16T10:16:15+02:00
New upstream version 15.02.00
- - - - -
13 changed files:
- VERSION
- c++std
- changelog
- + costs.txt
- costs/cost.cc
- costs/costs.f
- costs/costs.h
- costs/setlungcancer.cc
- dot.config/simrisc
- loop/headerdata.cc
- modbase/modbase.f
- modbase/modbase.h
- simulator/simulator.h
Changes:
=====================================
VERSION
=====================================
@@ -1,3 +1,3 @@
#define AUTHOR "Frank B. Brokken (f.b.brokken at rug.nl)";
-#define VERSION "15.01.00"
+#define VERSION "15.02.00"
#define YEARS "2020-2023"
=====================================
c++std
=====================================
@@ -1 +1 @@
-#define CPPSTD "--std=c++20"
+#define CPPSTD "--std=c++23"
=====================================
changelog
=====================================
@@ -1,3 +1,9 @@
+simrisc (15.02.00)
+
+ * Costs values are now stored in size_t instead of in uint16_t variables
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Wed, 14 Jun 2023 16:22:36 +0200
+
simrisc (15.01.00)
* Added a column TNM to the data file containing the TNM categories per
=====================================
costs.txt
=====================================
@@ -0,0 +1,26 @@
+simulator/simulator.h
+costs/costs.h
+probgroup/probgroup.h
+round/round.h
+typedefs/typedefs.h
+configlines/configlines.h
+enums/enums.h
+parser/parser.h
+ct/ct.h
+densities/densities.h
+modbase/modbase.h
+mammo/mammo.h
+modalities/modalities.h
+tumor/tumor.h
+analysis/analysis.h
+agegroupvsd/agegroupvsd.h
+screening/screening.h
+group/group.h
+tomo/tomo.h
+incidence/incidence.h
+loop/loop.h
+globals/globals.h
+growth/growth.h
+tumorinfo/tumorinfo.h
+local/local/includes:9:simulator/simulator.ih:13://#include "../costs/costs.h"
+loop/loop.h:15:#include "../costs/costs.h"
=====================================
costs/cost.cc
=====================================
@@ -1,7 +1,7 @@
//#define XERR
#include "costs.ih"
-uint16_t Costs::cost(double diameter) const
+size_t Costs::cost(double diameter) const
{
// reversed search: start at the max. diameter
return find_if(d_treatmntPair.rbegin(), d_treatmntPair.rend(),
=====================================
costs/costs.f
=====================================
@@ -3,7 +3,7 @@ inline double Costs::usingAt(double age) const
return discount(age, d_usingCosts);
}
-inline double Costs::screening(double age, uint16_t cost) const
+inline double Costs::screening(double age, size_t cost) const
{
return discount(age, cost);
}
=====================================
costs/costs.h
=====================================
@@ -23,7 +23,7 @@
class Costs
{
// lower diam., cost
- typedef std::pair<double, uint16_t> CostPair;
+ typedef std::pair<double, size_t> CostPair;
StringVect d_base;
@@ -33,10 +33,10 @@ class Costs
double d_referenceAge; // discount reference age
double d_discountProportion;
- uint16_t d_usingCosts; // for lungCancer: diagnosis,
+ size_t d_usingCosts; // for lungCancer: diagnosis,
// otherwise biopsy cost
- std::vector<uint16_t> d_treatmentCosts; // for lungCancer: M0/M1 states
+ std::vector<size_t> d_treatmentCosts; // for lungCancer: M0/M1 states
// lcTreatment or otherTreatment
double (Costs::*d_treatment)(double age, double diameter,
@@ -48,7 +48,7 @@ class Costs
double usingAt(double age) const; // .f
- double screening(double age, uint16_t cost) const; // .f
+ double screening(double age, size_t cost) const; // .f
double treatment(double age, double diameter,
bool metastasis) const; // .f
@@ -65,7 +65,7 @@ class Costs
void setProportion(bool lungCancer);
void setVariables(bool lungCancer);
- uint16_t cost(double diameter) const;
+ size_t cost(double diameter) const;
// for LungCancer
double lcTreatment(double age, double diameter, // @ treatment
@@ -79,18 +79,4 @@ class Costs
#include "costs.f"
-// // lcUsing or otherUsing
-// double (Costs::*d_using)(double age, size_t cost) const;
-// // lcScreening or otherScreening
-// double (Costs::*d_screening)(double age, size_t cost) const;
-
-
-// double lcUsing(double age, size_t cost) const; // @ using
-// double lcScreening(double age, size_t cost) const; // @ screening
-// double otherUsing(double age, size_t cost) const; // @ using
-// double otherScreening(double age, size_t cost) const; // @ screening
-
- // double biopsy(double age) const; // .f
-
-
#endif
=====================================
costs/setlungcancer.cc
=====================================
@@ -3,7 +3,7 @@
void Costs::setLungCancer()
{
- uint16_t unused; // = modbase->cost(), extracted by ModBase
+ size_t unused; // = modbase->cost(), extracted by ModBase
if (not Parser::extract(Parser::one(d_base), unused,
d_usingCosts,
=====================================
dot.config/simrisc
=====================================
@@ -54,6 +54,7 @@ Modalities:
# screening diagnosis M0 M1 (M0, M1: Table S3)
costs: 176 1908 37909 56556
+
dose: 1
# diam. value (must be integral 0..100 or -1)
=====================================
loop/headerdata.cc
=====================================
@@ -16,6 +16,8 @@ CSVTable Loop::headerData(size_t iter) const
labels(tab.stream());
+ // the fmt() insertions define the widths of the columns,
+ // not their header labels. Blanks are ignored, hence 'costs67890'
tab.fmt() << right(7) << // 1
"Natural" << right("100.12", 2) << // 2 - 3
"natural" << "status" << // 4 - 5
@@ -24,7 +26,7 @@ CSVTable Loop::headerData(size_t iter) const
// death:
"onset" << "self-detect" << "100.00" << // 12 - 14
- "costs" << "self" << "round" << // 15 - 17
+ "costs67890" << "self" << "round" << // 15 - 17
right(d_nRounds > 10 ? d_nRounds : 10) << // 18
right(5); // 19
=====================================
modbase/modbase.f
=====================================
@@ -3,7 +3,7 @@ inline StringVect &ModBase::base()
return d_base;
}
-inline uint16_t ModBase::cost() const
+inline size_t ModBase::cost() const
{
return d_cost;
}
@@ -28,11 +28,6 @@ inline std::string const &ModBase::id() const
return d_id;
}
-//inline VSDvect const *ModBase::dose() const
-//{
-// return vDose();
-//}
-
inline double ModBase::dose(uint16_t idx) const
{
return vDose(idx);
@@ -58,12 +53,3 @@ inline void ModBase::vary(std::ostream &out)
return vVary(out);
}
-//inline void ModBase::count(std::ostream &out, size_t round) const
-//{
-// out << ',' << std::setw(7) << d_count[round];
-//}
-
-//inline void ModBase::roundHeader(std::ostream &out) const
-//{
-// out << ", #" << d_id;
-//}
=====================================
modbase/modbase.h
=====================================
@@ -22,7 +22,7 @@ class ModBase
bool d_defined;
- uint16_t d_cost = 0; // cost of using th modality
+ size_t d_cost = 0; // cost of using th modality
SizeVect d_count;
uint16_t d_falsePositives;
@@ -31,9 +31,8 @@ class ModBase
virtual ~ModBase();
- uint16_t cost() const; // .f
+ size_t cost() const; // .f
void count(size_t round); // .f
-// VSDvect const *dose() const; // .f
bool defined() const; // .f
double dose(uint16_t idx) const; // .f
void falsePositive(); // .f
=====================================
simulator/simulator.h
=====================================
@@ -2,6 +2,7 @@
#define INCLUDED_SIMULATOR_
#include <fstream>
+#include <cstdint>
// analyses specfy different parameters, like screeningRound, iterations,
// nWomen
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/commit/9b114cd92e8488b3157a4dfafe35b5e891b15591
--
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/commit/9b114cd92e8488b3157a4dfafe35b5e891b15591
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