[1044] | 1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
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| 2 | // Copyright (C) 1999-2020 Maciej Komosinski and Szymon Ulatowski. |
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| 3 | // See LICENSE.txt for details. |
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| 4 | |
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| 5 | #include "measure-mds-based.h" |
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| 6 | #include "SVD/matrix_tools.h" |
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| 7 | |
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| 8 | SimilMeasureMDSBased::SimilMeasureMDSBased() |
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| 9 | { |
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| 10 | coordinates[0] = nullptr; |
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| 11 | coordinates[1] = nullptr; |
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| 12 | |
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| 13 | with_alignment = true; |
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| 14 | save_matching = false; |
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| 15 | fixedZaxis = 0; |
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| 16 | wMDS = 1; |
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| 17 | } |
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| 18 | |
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| 19 | double SimilMeasureMDSBased::getDistance() |
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| 20 | { |
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| 21 | double dResult = -1; |
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| 22 | m_iSmaller = models[0]->getPartCount() <= models[1]->getPartCount() ? 0 : 1; |
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| 23 | |
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| 24 | prepareData(); |
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| 25 | |
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| 26 | if (with_alignment) |
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| 27 | { |
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| 28 | if (!getPartPositions()) |
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| 29 | { |
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| 30 | logPrintf("SimilMDSBasedMeasure", "getDistance", LOG_ERROR, "Cannot compute part positions"); |
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| 31 | return -1; |
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| 32 | } |
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| 33 | |
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| 34 | if (!computePartsPositionsByMDS()) |
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| 35 | { |
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| 36 | logPrintf("SimilMDSBasedMeasure", "getDistance", LOG_ERROR, "Cannot perform MDS"); |
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| 37 | return -1; |
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| 38 | } |
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| 39 | |
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| 40 | // tutaj zacznij pętlę po przekształceniach geometrycznych |
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| 41 | const int NO_OF_TRANSFORM = 8; // liczba transformacji geometrycznych (na razie tylko ID i O_YZ) |
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| 42 | // tablice transformacji współrzędnych; nie są to dokładnie tablice tranformacji, ale raczej tablice PRZEJŚĆ |
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| 43 | // pomiędzy transformacjami; |
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| 44 | const int dMulX[NO_OF_TRANSFORM] = { 1, -1, -1, 1, -1, 1, -1, -1 }; |
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| 45 | const int dMulY[NO_OF_TRANSFORM] = { 1, 1, -1, -1, -1, -1, -1, 1 }; |
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| 46 | const int dMulZ[NO_OF_TRANSFORM] = { 1, 1, 1, -1, -1, -1, 1, 1 }; |
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| 47 | |
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| 48 | #ifdef max |
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| 49 | #undef max //this macro would conflict with line below |
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| 50 | #endif |
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| 51 | double dMinSimValue = std::numeric_limits<double>::max(); // minimum value of similarity |
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| 52 | |
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| 53 | int iTransform; // a counter of geometric transformations |
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| 54 | for (iTransform = 0; iTransform < NO_OF_TRANSFORM; iTransform++) |
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| 55 | { |
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| 56 | beforeTransformation(); |
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| 57 | |
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| 58 | for (int iPart = 0; iPart < models[m_iSmaller]->getPartCount(); iPart++) |
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| 59 | { |
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| 60 | // for each iPart, a part of the model iMod |
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| 61 | coordinates[m_iSmaller][iPart].x *= dMulX[iTransform]; |
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| 62 | coordinates[m_iSmaller][iPart].y *= dMulY[iTransform]; |
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| 63 | coordinates[m_iSmaller][iPart].z *= dMulZ[iTransform]; |
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| 64 | } |
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| 65 | // now the positions are recomputed |
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| 66 | double dCurrentSim = distanceForTransformation(); |
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| 67 | |
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| 68 | // załóż poprawną wartość podobieństwa |
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| 69 | assert(dCurrentSim >= 0.0); |
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| 70 | |
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| 71 | // porównaj wartość obliczoną z dotychczasowym minimum |
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| 72 | if (dCurrentSim < dMinSimValue) |
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| 73 | { |
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| 74 | //printf("lesser sim\n"); |
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| 75 | dMinSimValue = dCurrentSim; |
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| 76 | if (save_matching) |
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| 77 | copyMatching(); |
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| 78 | } |
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| 79 | } |
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| 80 | |
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| 81 | dResult = dMinSimValue; |
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| 82 | |
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| 83 | SAFEDELETEARRAY(coordinates[0]); |
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| 84 | SAFEDELETEARRAY(coordinates[1]); |
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| 85 | } |
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| 86 | else |
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| 87 | { |
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| 88 | dResult = distanceWithoutAlignment(); |
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| 89 | } |
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| 90 | |
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| 91 | cleanData(); |
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| 92 | |
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| 93 | return dResult; |
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| 94 | } |
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| 95 | |
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| 96 | |
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| 97 | /** Gets information about Parts' positions in 3D from models into the arrays |
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| 98 | coordinates. |
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| 99 | Assumptions: |
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| 100 | - Models (models) are created and available. |
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| 101 | - Arrays coordinates are created. |
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| 102 | @return 1 if success, otherwise 0. |
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| 103 | */ |
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| 104 | int SimilMeasureMDSBased::getPartPositions() |
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| 105 | { |
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| 106 | // for each model copy its part coordinates |
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| 107 | Part *pPart; |
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| 108 | for (int iMod = 0; iMod < 2; iMod++) |
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| 109 | { |
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| 110 | // utworz tablice dla pozycji 3D Parts (wielkosc tablicy: liczba Parts organizmu) |
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| 111 | coordinates[iMod] = new Pt3D[models[iMod]->getPartCount()]; |
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| 112 | assert(coordinates[iMod] != NULL); |
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| 113 | // dla każdego z modeli iMod |
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| 114 | for (int iPart = 0; iPart < models[iMod]->getPartCount(); iPart++) |
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| 115 | { |
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| 116 | // dla każdego iPart organizmu iMod |
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| 117 | // pobierz tego Part |
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| 118 | pPart = models[iMod]->getPart(iPart); |
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| 119 | // zapamietaj jego pozycje 3D w tablicy coordinates |
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| 120 | coordinates[iMod][iPart].x = pPart->p.x; |
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| 121 | coordinates[iMod][iPart].y = pPart->p.y; |
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| 122 | coordinates[iMod][iPart].z = pPart->p.z; |
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| 123 | } |
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| 124 | } |
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| 125 | |
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| 126 | return 1; |
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| 127 | } |
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| 128 | |
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| 129 | bool SimilMeasureMDSBased::computePartsPositionsByMDS() |
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| 130 | { |
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| 131 | bool bResult = true; |
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| 132 | |
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| 133 | // use MDS to obtain different point of view on organisms |
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| 134 | // and store the new positions (currently the original ones are still stored) |
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| 135 | for (int iMod = 0; iMod < 2; iMod++) |
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| 136 | { |
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| 137 | // prepare the vector of errors of approximation for the SVD |
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| 138 | std::vector<double> vEigenvalues; |
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| 139 | int nSize = models[iMod]->getPartCount(); |
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| 140 | |
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| 141 | double *pDistances = new double[nSize * nSize]; |
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| 142 | |
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| 143 | for (int i = 0; i < nSize; i++) |
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| 144 | { |
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| 145 | pDistances[i] = 0; |
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| 146 | } |
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| 147 | |
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| 148 | Model *pModel = models[iMod]; // use the model of the iMod (current) organism |
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| 149 | int iP1, iP2; // indices of Parts in the model |
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| 150 | Part *P1, *P2; // pointers to Parts |
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| 151 | Pt3D P1Pos, P2Pos; // positions of parts |
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| 152 | double dDistance; // the distance between Parts |
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| 153 | |
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| 154 | double *weights = new double[nSize]; |
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| 155 | for (int i = 0; i < nSize; i++) |
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| 156 | { |
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| 157 | if (wMDS == 1) |
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| 158 | weights[i] = 0; |
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| 159 | else |
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| 160 | weights[i] = 1; |
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| 161 | } |
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| 162 | |
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| 163 | if (wMDS == 1) |
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| 164 | for (int i = 0; i < pModel->getJointCount(); i++) |
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| 165 | { |
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| 166 | weights[pModel->getJoint(i)->p1_refno]++; |
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| 167 | weights[pModel->getJoint(i)->p2_refno]++; |
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| 168 | } |
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| 169 | |
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| 170 | for (iP1 = 0; iP1 < pModel->getPartCount(); iP1++) |
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| 171 | { |
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| 172 | // for each iP1, a Part index in the model of organism iMod |
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| 173 | P1 = pModel->getPart(iP1); |
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| 174 | // get the position of the Part |
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| 175 | P1Pos = P1->p; |
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| 176 | if (fixedZaxis == 1) |
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| 177 | { |
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| 178 | P1Pos.z = 0; //fixed vertical axis, so pretend all points are on the xy plane |
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| 179 | } |
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| 180 | for (iP2 = 0; iP2 < pModel->getPartCount(); iP2++) |
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| 181 | { |
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| 182 | // for each (iP1, iP2), a pair of Parts index in the model |
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| 183 | P2 = pModel->getPart(iP2); |
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| 184 | // get the position of the Part |
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| 185 | P2Pos = P2->p; |
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| 186 | if (fixedZaxis == 1) |
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| 187 | { |
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| 188 | P2Pos.z = 0; //fixed vertical axis, so pretend all points are on the xy plane |
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| 189 | } |
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| 190 | // compute the geometric (Euclidean) distance between the Parts |
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| 191 | dDistance = P1Pos.distanceTo(P2Pos); |
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| 192 | // store the distance |
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| 193 | pDistances[iP1 * nSize + iP2] = dDistance; |
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| 194 | } // for (iP2) |
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| 195 | } // for (iP1) |
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| 196 | |
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| 197 | MatrixTools::weightedMDS(vEigenvalues, nSize, pDistances, coordinates[iMod], weights); |
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| 198 | |
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| 199 | if (fixedZaxis == 1) //restore the original vertical coordinate of each Part |
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| 200 | { |
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| 201 | for (int part = 0; part < pModel->getPartCount(); part++) |
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| 202 | { |
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| 203 | coordinates[iMod][part].z = pModel->getPart(part)->p.z; |
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| 204 | } |
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| 205 | } |
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| 206 | |
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| 207 | delete[] pDistances; |
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| 208 | delete[] weights; |
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| 209 | } |
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| 210 | |
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| 211 | return bResult; |
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| 212 | } |
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| 213 | |
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