From 41f654a317afba7f4dba3fcd0a6557773528845a Mon Sep 17 00:00:00 2001 From: westcott Date: Wed, 19 Jan 2011 18:41:56 +0000 Subject: [PATCH] working on nmds command --- nmdscommand.cpp | 265 +----------------------------------------------- nmdscommand.h | 11 +- 2 files changed, 7 insertions(+), 269 deletions(-) diff --git a/nmdscommand.cpp b/nmdscommand.cpp index 9984247..cfd70c2 100644 --- a/nmdscommand.cpp +++ b/nmdscommand.cpp @@ -13,7 +13,7 @@ //********************************************************************************************************************** vector NMDSCommand::getValidParameters(){ try { - string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","trace","epsilon","outputdir","inputdir"}; + string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); return myArray; } @@ -70,7 +70,7 @@ NMDSCommand::NMDSCommand(string option) { else { //valid paramters for this command - string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","trace","epsilon","outputdir", "inputdir"}; + string Array[] = {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir", "inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -140,9 +140,6 @@ NMDSCommand::NMDSCommand(string option) { temp = validParameter.validFile(parameters, "epsilon", false); if (temp == "not found") { temp = "0.000000000001"; } convert(temp, epsilon); - temp = validParameter.validFile(parameters, "trace", false); if (temp == "not found") { temp = "F"; } - trace = m->isTrue(temp); - if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; } if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; } } @@ -157,7 +154,7 @@ NMDSCommand::NMDSCommand(string option) { void NMDSCommand::help(){ try { m->mothurOut("The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling."); m->mothurOutEndLine(); - m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters, epsilon and trace."); m->mothurOutEndLine(); + m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine(); m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine(); m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine(); m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine(); @@ -165,7 +162,6 @@ void NMDSCommand::help(){ m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine(); m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine(); m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine(); - m->mothurOut("The trace parameter allows you to see the output after each iter. Default=F"); m->mothurOutEndLine(); m->mothurOut("Example nmds(phylip=yourDistanceFile).\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n"); } @@ -217,7 +213,7 @@ int NMDSCommand::execute(){ out2 << "Iter\tStress\tCorr" << endl; for (int j = 0; j < iters; j++) { - if (trace) { m->mothurOut(toString(j+1)); m->mothurOutEndLine(); } + m->mothurOut(toString(j+1)); m->mothurOutEndLine(); //get configuration - either randomly generate or resize to this dimension vector< vector > thisConfig; @@ -281,8 +277,6 @@ vector< vector > NMDSCommand::nmdsCalc(vector< vector >& matrix, double stress2 = calculateStress(matrix, euclid); stress1 = stress2 + 1.0 + epsilon; - if (trace) { m->mothurOutEndLine(); m->mothurOut("Iter\tStress"); m->mothurOutEndLine(); } - int count = 0; while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) { count++; @@ -323,9 +317,6 @@ vector< vector > NMDSCommand::nmdsCalc(vector< vector >& matrix, euclid = linearCalc.calculateEuclidianDistance(newConfig); stress2 = calculateStress(matrix, euclid); - - if (trace) { m->mothurOut(count + "\t" + toString(stress1)); m->mothurOutEndLine(); } - } return newConfig; @@ -558,253 +549,7 @@ vector< vector > NMDSCommand::readAxes(vector names){ exit(1); } } -/********************************************************************************************************************** - vector< vector > NMDSCommand::calculateStressGradientVector(vector& eDists, vector& D, double rawStress, double stress, vector< vector >& axes) { - try { - vector< vector > gradient; gradient.resize(dimension); - for (int i = 0; i < gradient.size(); i++) { gradient[i].resize(axes[0].size(), 0.0); } - - double sumDij = 0.0; - for (int i = 0; i < eDists.size(); i++) { sumDij += (eDists[i].dist * eDists[i].dist); } - - for (int i = 0; i < eDists.size(); i++) { - - for (int j = 0; j < dimension; j++) { - - if (m->control_pressed) { return gradient; } - - double firstTerm1 = (stress / rawStress) * (eDists[i].dist - D[i].dist); - double firstTerm2 = (stress / sumDij) * eDists[i].dist; - double firstTerm = firstTerm1 - firstTerm2; - - float r = (dimension-1.0); - double temp = 1.0 / (pow(eDists[i].dist, r)); - float absTemp = abs(axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]); - double secondTerm = pow(absTemp, r) * temp; - - double sigNum = 1.0; - if ((axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) == 0) { sigNum = 0.0; } - else if ((axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) < 0) { sigNum = -1.0; } - - double results = (firstTerm * secondTerm * sigNum); - cout << i << '\t' << j << '\t' << "results = " << results << endl; - gradient[j][eDists[i].seq1] += results; - gradient[j][eDists[i].seq2] -= results; - } - } - - return gradient; - } - catch(exception& e) { - m->errorOut(e, "NMDSCommand", "calculateStressGradientVector"); - exit(1); - } - } - //********************************************************************************************************************** - double NMDSCommand::calculateMagnitude(vector< vector >& gradient) { - try { - double magnitude = 0.0; - - double sum = 0.0; - for (int i = 0; i < gradient.size(); i++) { - for (int j = 0; j < gradient[i].size(); j++) { - sum += (gradient[i][j] * gradient[i][j]); - } - } - - magnitude = sqrt(((1.0/(float)gradient[0].size()) * sum)); - - return magnitude; - } - catch(exception& e) { - m->errorOut(e, "NMDSCommand", "calculateMagnitude"); - exit(1); - } - } - //********************************************************************************************************************** - //described in Kruskal paper page 121 + 122 - double NMDSCommand::calculateStep(vector< vector >& prevGrad, vector< vector >& grad, vector& prevStress) { - try { - double newStep = step; - - //calc the cos theta - double sumNum = 0.0; - double sumDenom1 = 0.0; - double sumDenom2 = 0.0; - for (int i = 0; i < prevGrad.size(); i++) { - for (int j = 0; j < prevGrad[i].size(); j++) { - sumDenom1 += (grad[i][j] * grad[i][j]); - sumDenom2 += (prevGrad[i][j] * prevGrad[i][j]); - sumNum += (grad[i][j] * prevGrad[i][j]); - } - } - - double cosTheta = sumNum / (sqrt(sumDenom1) * sqrt(sumDenom2)); - cosTheta *= cosTheta; - - //calc angle factor - double angle = pow(4.0, cosTheta); - - //calc 5 step ratio - double currentStress = prevStress[prevStress.size()-1]; - double lastStress = prevStress[0]; - if (prevStress.size() > 1) { lastStress = prevStress[prevStress.size()-2]; } - double fivePrevStress = prevStress[0]; - if (prevStress.size() > 5) { fivePrevStress = prevStress[prevStress.size()-6]; } - - double fiveStepRatio = min(1.0, (currentStress / fivePrevStress)); - - //calc relaxation factor - double relaxation = 1.3 / (1.0 + pow(fiveStepRatio, 5.0)); - - //calc good luck factor - double goodLuck = min(1.0, (currentStress / lastStress)); - - //calc newStep - //cout << "\ncos = " << cosTheta << " step = " << step << " angle = " << angle << " relaxation = " << relaxation << " goodluck = " << goodLuck << endl; - newStep = step * angle * relaxation * goodLuck; - - return newStep; - } - catch(exception& e) { - m->errorOut(e, "NMDSCommand", "calculateStep"); - exit(1); - } - } - //********************************************************************************************************************** - vector< vector > NMDSCommand::calculateNewConfiguration(double magnitude, vector< vector >& axes, vector< vector >& gradient) { - try { - - vector< vector > newAxes = axes; - - for (int i = 0; i < newAxes.size(); i++) { - - if (m->control_pressed) { return newAxes; } - - for (int j = 0; j < newAxes[i].size(); j++) { - newAxes[i][j] = axes[i][j] + ((step / magnitude) * gradient[i][j]); - } - } - - return newAxes; - } - catch(exception& e) { - m->errorOut(e, "NMDSCommand", "calculateNewConfiguration"); - exit(1); - } - }*/ -/********************************************************************************************************************** - //adjust eDists so that it creates monotonically increasing series of succesive values that increase or stay the same, but never decrease - vector NMDSCommand::satisfyMonotonicity(vector eDists, vector partitions) { - try { - - //find averages of each partitions - vector sums; sums.resize(partitions.size(), 0.0); - vector sizes; sizes.resize(partitions.size(), 0); - - for (int i = 0; i < partitions.size(); i++) { - //i is not the last one - int start = partitions[i]; - int end; - if (i != (partitions.size()-1)) { end = partitions[i+1]; } - else{ end = eDists.size(); } - - for (int j = start; j < end; j++) { sums[i] += eDists[j].dist; } - - sizes[i] = (end - start); - } - - - vector D = eDists; - - //i represents the "active block" - int i = 0; - while (i < partitions.size()) { - - if (m->control_pressed) { return D; } - - bool upActive = true; - bool upSatisfied = false; - bool downSatisfied = false; - - //while we are not done with this block - while ((!upSatisfied) || (!downSatisfied)) { - - if (upActive) { - - //are we are upSatisfied? - is the average of the next block greater than mine? - if (i != (partitions.size()-1)) { //if we are the last guy then we are upsatisfied - if ((sums[i+1]/(float)sizes[i+1]) >= (sums[i]/(float)sizes[i])) { - upSatisfied = true; - upActive = false; - }else { - //find new weighted average - double newSum = sums[i] + sums[i+1]; - - //merge blocks - putting everything in i - sums[i] = newSum; - sizes[i] += sizes[i+1]; - partitions[i] = partitions[i+1]; - - sums.erase(sums.begin()+(i+1)); - sizes.erase(sizes.begin()+(i+1)); - partitions.erase(partitions.begin()+(i+1)); - - upActive = false; - } - }else { upSatisfied = true; upActive = false; } - - }else { //downActive - - //are we are DownSatisfied? - is the average of the previous block less than mine? - if (i != 0) { //if we are the first guy then we are downSatisfied - if ((sums[i-1]/(float)sizes[i-1]) <= (sums[i]/(float)sizes[i])) { - downSatisfied = true; - upActive = true; - }else { - //find new weighted average - double newSum = sums[i] + sums[i-1];; - - //merge blocks - putting everything in i-1 - sums[i-1] = newSum; - sizes[i-1] += sizes[i]; - - sums.erase(sums.begin()+i); - sizes.erase(sizes.begin()+i); - partitions.erase(partitions.begin()+i); - i--; - - upActive = true; - } - }else { downSatisfied = true; upActive = true; } - } - } - - i++; // go to next block - } - - //sanity check - for rounding errors - vector averages; averages.resize(sums.size(), 0.0); - for (int i = 0; i < sums.size(); i++) { averages[i] = sums[i] / (float) sizes[i]; } - for (int i = 0; i < averages.size(); i++) { if (averages[i+1] < averages[i]) { averages[i+1] = averages[i]; } } - - //fill D - int placeHolder = 0; - for (int i = 0; i < averages.size(); i++) { - for (int j = 0; j < sizes[i]; j++) { - D[placeHolder].dist = averages[i]; - placeHolder++; - } - } - - return D; - } - catch(exception& e) { - m->errorOut(e, "NMDSCommand", "satisfyMonotonicity"); - exit(1); - } - }*/ +/**********************************************************************************************************************/ -//********************************************************************************************************************** diff --git a/nmdscommand.h b/nmdscommand.h index d7bedcf..7979c67 100644 --- a/nmdscommand.h +++ b/nmdscommand.h @@ -42,7 +42,7 @@ public: private: - bool abort, trace; + bool abort; string phylipfile, outputDir, axesfile; int maxdim, mindim, maxIters, iters; double epsilon; @@ -56,14 +56,7 @@ private: int normalizeConfiguration(vector< vector >&, int, int); double calculateStress(vector< vector >&, vector< vector >&); vector< vector > readAxes(vector); - int output(vector< vector >&, vector&, ofstream&); - - //vector satisfyMonotonicity(vector, vector); - //vector< vector > calculateStressGradientVector(vector&, vector&, double, double, vector< vector >&); - //double calculateMagnitude(vector< vector >&); - //double calculateStep(vector< vector >&, vector< vector >&, vector&); - //vector< vector > calculateNewConfiguration(double, vector< vector >&, vector< vector >&); - + int output(vector< vector >&, vector&, ofstream&); }; /*****************************************************************/ -- 2.39.2