Changeset 1048 for cpp/frams/model/similarity

Timestamp:

12/11/20 21:36:41 (4 years ago)

Author:

Maciej Komosinski

Message:

SimilMeasure? -> SimilMeasureBase?; introduced a new class (SimilMeasure?) that allows scripts to access all similarity measures; a number of minor fixes and improvements

Location:

cpp/frams/model/similarity

Files:

• measure-distribution.h (modified) (1 diff)
• measure-greedy.cpp (modified) (2 diffs)
• measure-greedy.h (modified) (1 diff)
• measure-hungarian.cpp (modified) (2 diffs)
• measure-mds-based.cpp (modified) (1 diff)
• measure-mds-based.h (modified) (1 diff)
• simil-measure-base.cpp (added)
• simil-measure-base.h (added)
• simil-measure.cpp (modified) (4 diffs)
• simil-measure.h (modified) (1 diff)

cpp/frams/model/similarity/measure-distribution.h

@@ -6 +6 @@
 #define DISTRIBUTION_MEASURE_H
 
-#include "simil-measure.h"
+#include "simil-measure-base.h"
 #include "EMD/emd.h"
 
-class SimilMeasureDistribution : public SimilMeasure
+class SimilMeasureDistribution : public SimilMeasureBase
 {
 public:

cpp/frams/model/similarity/measure-greedy.cpp

@@ -4 +4 @@
 
 #include "measure-greedy.h"
+#include <assert.h>
 
 #define DB(x)  //define as x if you want to print debug information
 
 const int SimilMeasureGreedy::iNOFactors = 4;
-int fuzzDepth = 0; //TODO make local, but "fuzzy vertex degree" is not activated by default
+int fuzzDepth = 0; //TODO make local, but not crucial because currently "fuzzy vertex degree" is not activated by default
 
 #define FIELDSTRUCT SimilMeasureGreedy
@@ -20 +21 @@
                 { "simil_fixedZaxis", 0, 0, "Fix 'z' (vertical) axis?", "d 0 1 0", FIELD(fixedZaxis), "", },
                 { "simil_weightedMDS", 0, 0, "Should weighted MDS be used?", "d 0 1 0", FIELD(wMDS), "If activated, weighted MDS with vertex (i.e., Part) degrees as weights is used for 3D alignment of body structure.", },
-                { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
+                { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
                 { 0, },
 };

cpp/frams/model/similarity/measure-greedy.h

@@ -10 +10 @@
 #include "frams/model/model.h"
 #include "simil-match.h"
-#include "measure-greedy.h"
 
 #define TDN_SIZE 5

cpp/frams/model/similarity/measure-hungarian.cpp

@@ -10 +10 @@
 
 static ParamEntry simil_hungarian_paramtab[] = {
-                { "Similarity: hungarian", 1, 7, "similHungarianMeasure", "Evaluates morphological dissimilarity using hungarian measure. More information:\nhttp://www.framsticks.com/bib/Komosinski-et-al-2001\nhttp://www.framsticks.com/bib/Komosinski-and-Kubiak-2011\nhttp://www.framsticks.com/bib/Komosinski-2016\nhttps://doi.org/10.1007/978-3-030-16692-2_8", },
+                { "Similarity: hungarian", 1, 7, "SimilMeasureHungarian", "Evaluates morphological dissimilarity using hungarian measure. More information:\nhttp://www.framsticks.com/bib/Komosinski-et-al-2001\nhttp://www.framsticks.com/bib/Komosinski-and-Kubiak-2011\nhttp://www.framsticks.com/bib/Komosinski-2016\nhttps://doi.org/10.1007/978-3-030-16692-2_8", },
                 { "simil_parts", 0, 0, "Weight of parts count", "f 0 100 0", FIELD(m_adFactors[0]), "Differing number of parts is also handled by the 'part degree' similarity component.", },
                 { "simil_partdeg", 0, 0, "Weight of parts' degree", "f 0 100 1", FIELD(m_adFactors[1]), "", },
@@ -17 +17 @@
                 { "simil_fixedZaxis", 0, 0, "Fix 'z' (vertical) axis?", "d 0 1 0", FIELD(fixedZaxis), "", },
                 { "simil_weightedMDS", 0, 0, "Should weighted MDS be used?", "d 0 1 0", FIELD(wMDS), "If activated, weighted MDS with vertex (i.e., Part) degrees as weights is used for 3D alignment of body structure.", },
-                { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
+                { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
                 { 0, },
 };

cpp/frams/model/similarity/measure-mds-based.cpp

@@ -5 +5 @@
 #include "measure-mds-based.h"
 #include "SVD/matrix_tools.h"
+#include <assert.h>
 
 SimilMeasureMDSBased::SimilMeasureMDSBased()

cpp/frams/model/similarity/measure-mds-based.h

@@ -6 +6 @@
 #define _SIMIL_MEASURE_MDS_BASED_H
 
-#include "simil-measure.h"
+#include "simil-measure-base.h"
 
-class SimilMeasureMDSBased : public SimilMeasure
+class SimilMeasureMDSBased : public SimilMeasureBase
 {
 public:

cpp/frams/model/similarity/simil-measure.cpp

@@ -5 +5 @@
 #include "simil-measure.h"
 #include <frams/vm/classes/genoobj.h>
-#include <frams/model/geometry/geometryutils.h>
 #include <frams/model/geometry/meshbuilder.h>
+#include <frams/_demos/geometry/geometrytestutils.h>
 
 #define FIELDSTRUCT SimilMeasure
 
 static ParamEntry simil_measure_paramtab[] = {
-        { "Similarity", 1, 2, "SimilMeasure", "Evaluates morphological dissimilarity.", },
-        { "measure_type", 0, 0, "Type of similarity measure", "d 1 3 1", FIELD(measure_type), "", },
-        { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
+        { "Similarity", 1, 2, "SimilMeasure", "Evaluates morphological dissimilarity. More information:\nhttp://www.framsticks.com/bib/Komosinski-et-al-2001\nhttp://www.framsticks.com/bib/Komosinski-and-Kubiak-2011\nhttp://www.framsticks.com/bib/Komosinski-2016\nhttps://doi.org/10.1007/978-3-030-16692-2_8", },
+        { "measure_type", 0, 0, "Type of similarity measure", "d 0 2 0 ~Greedy (flexible criteria order and optimal matching)~Hungarian (vertex degree order and greedy matching)~Distribution (EMD on a histogram of descriptor values)", FIELD(measure_type), "", },
+        { "evaluateDistance", 0, PARAM_DONTSAVE | PARAM_USERHIDDEN, "Evaluate model dissimilarity", "p f(oGeno,oGeno)", PROCEDURE(p_evaldistance), "Calculates dissimilarity between two models created from Geno objects.", },
         { 0, },
 };
@@ -21 +21 @@
 SimilMeasure::SimilMeasure() : localpar(simil_measure_paramtab, this)
 {
-        for (int i = 0; i < 2; i++)
-        {
-                genos[i] = nullptr;
-                models[i] = nullptr;
-        }
         localpar.setDefault();
 }
@@ -31 +26 @@
 double SimilMeasure::evaluateDistance(const Geno* G0, const Geno* G1)
 {
-        genos[0] = G0;
-        genos[1] = G1;
-
-        // create models of objects to compare
-        models[0] = newModel(genos[0]);
-        models[1] = newModel(genos[1]);
-
-        if (models[0] == NULL || models[1] == NULL)
-        {
-                logPrintf("SimilarityMeasure", "EvaluateDistance", LOG_ERROR, "Unable to create model from one of the genotypes.");
-                return -1;
-        }
-        
-        double distance = getDistance();
-        SAFEDELETE(models[0]);
-        SAFEDELETE(models[1]);
-        return distance;
-}
-
-Model* SimilMeasure::newModel(const Geno *g)
-{
-        if (g == NULL)
-        {
-                logPrintf("SimilarityMeasure", "newModel", LOG_ERROR, "NULL genotype pointer");
-                return NULL;
-        }
-        Model *m = new Model(*g, ModelEnum::SHAPETYPE_UNKNOWN);
-        if (!m->isValid())
-        {
-                logPrintf("SimilarityMeasure", "newModel", LOG_ERROR, "Invalid model for the genotype of '%s'", g->getName().c_str());
-                delete m;
-                return NULL;
-        }
-        return m;
+        SimilMeasureBase *measures[] = { &simil_measure_greedy,&simil_measure_hungarian,&simil_measure_distribution };
+        if (measure_type >= 0 && measure_type <= 2)
+                return measures[measure_type]->evaluateDistance(G0, G1);
+        logPrintf("SimilarityMeasure", "evaluateDistance", LOG_ERROR, "Measure type '%d' not supported", measure_type);
+        return -1;
 }
 
@@ -77 +43 @@
 }
 
-Model SimilMeasure::sampleSurface(Model* M, double density)
-{
-    Model resultModel;
-    resultModel.open();
-    GeometryUtils::addAnchorToModel(resultModel);
-
-    MeshBuilder::ModelSurface iterator(density);
-    iterator.initialize(M);
-
-    Pt3D point;
-    while (iterator.tryGetNext(point))
-    {
-        GeometryUtils::addPointToModel(point, resultModel);
-    }
-
-    resultModel.close();
-    return resultModel;
-}

cpp/frams/model/similarity/simil-measure.h

@@ -6 +6 @@
 #define _SIMIL_MEASURE_H
 
-#include "frams/genetics/geno.h"
-#include "frams/model/model.h"
-#include <assert.h>
+#include "frams/model/similarity/measure-greedy.h"
+#include "frams/model/similarity/measure-hungarian.h"
+#include "frams/model/similarity/measure-distribution.h"
 
 class SimilMeasure
 {
 public:
-        SimilMeasure();
         int measure_type;
+
+        SimilMeasureGreedy simil_measure_greedy;
+        SimilMeasureHungarian simil_measure_hungarian;
+        SimilMeasureDistribution simil_measure_distribution;
+
         /// Interface to local parameters
         Param localpar;
 
-        virtual ~SimilMeasure(){};
-        virtual double getDistance() = 0;
+        SimilMeasure();
+        virtual ~SimilMeasure() {};
         double evaluateDistance(const Geno *G0, const Geno *G1);
-        virtual int setParams(std::vector<double> params) = 0;
-    Model sampleSurface(Model *M, double density);
 
         #define STATRICKCLASS SimilMeasure
         PARAMPROCDEF(p_evaldistance);
         #undef STATRICKCLASS
-
-protected:
-        /// Genotypes between which distance is evaluated.
-        const Geno *genos[2];
-        /// Models created from the genotypes array
-        Model *models[2];
-        Model* newModel(const Geno *g);
 };
 
 #endif
-