java - Unable to get Fuzzy C means working -

i need find out why centroid positions close each other?

i found fuzzy c means code here http://msugvnua000.web710.discountasp.net/posts/details/3347 , tried hard convert java code (below) there missing.

i tried looking @ implementation http://www.codeproject.com/articles/91675/computer-vision-applications-with-c-fuzzy-c-means code looks similar it's different because instead of updating cluster indexes membership values updates - i'm not sure why change implemented?

public class cmeansalgorithm3 {     private static int fuzzyness = 2;      private final map<double, species> integerclusterhashmap = new hashmap<double, species>();      /// array containing points used algorithm     private list<job> points;      /// gets or sets membership matrix     public double[][] u;      /// algorithm precision     private double eps = math.pow(10, -5);      /// gets or sets objective function     private double j;      /// gets or sets log message     public string log;      private list<species> clusterlist;      public cmeansalgorithm3(list<job> points, int clustersize){         this.points = points;         clusterlist = initialisecentroids(points, clustersize);         u = new double[points.size()][clusterlist.size()];         calculateclustermembershipvalues();         recalculateclusterindexes();     }      private void calculateclustermembershipvalues() {         // iterate through points create initial u matrix         (int = 0; < points.size(); i++) {             job p = points.get(i);             double sum = 0.0;              (int j = 0; j < clusterlist.size(); j++) {                 cluster c = clusterlist.get(j);                 double diff = math.sqrt(math.pow(p.getmidpointx() - c.getcentroid().getx(), 2.0) + math.pow(p.getmidpointy() - c.getcentroid().gety(), 2.0));                 u[i][j] = (diff == 0) ? eps : diff;                 sum += u[i][j];              }               double sum2 = 0.0;              (int j = 0; j < clusterlist.size(); j++) {                  u[i][j] = 1.0 / math.pow(u[i][j] / sum, 2.0 / (fuzzyness - 1.0));                 sum2 += u[i][j];              }               (int j = 0; j < clusterlist.size(); j++) {                 u[i][j] = u[i][j] / sum2;              }             }    }     /// recalculates cluster indexes    private void recalculateclusterindexes() {         (int = 0; < points.size(); i++) {             double max = -1.0;             job p = points.get(i);              (int j = 0; j < clusterlist.size(); j++) {                 max = u[i][j] > max ? u[i][j] : max; //              if (max < u[i][j]) { //                    max = u[i][j]; //                    p.setclusterindex((max == 0.5) ? 0.5 : j); //              }             }             p.setclusterindex(max);         }     }      /// perform complete run of algorithm until desired accuracy achieved.     /// demonstration issues, maximum iteration counter set 20.     /// algorithm accuracy     /// number of steps algorithm needed complete     public list<species> run(double accuracy) {         int k = 0;         int maxiterations = 100;          {             k++;             j = calculateobjectivefunction();             calculateclustercentroids();             step();             double jnew = calculateobjectivefunction();              if (math.abs(j - jnew) < accuracy) break;         }         while (maxiterations > k);          assignjobstoclusters();         return clusterlist;     }      /// calculate objective function     /// objective function double value     private double calculateobjectivefunction() {         double jk = 0;          (int = 0; < this.points.size();i++) {             (int j = 0; j < clusterlist.size(); j++) {                 jk += math.pow(u[i][j], this.fuzzyness) * math.pow(this.calculateeucliddistance(points.get(i), clusterlist.get(j)), 2);             }         }         return jk;     }      private list<species> initialisecentroids(final list<job> dataset, final int speciessize) {         final list<species> clusterlist = new arraylist<species>();         final list<integer> uniqueindexes = toolbox.uniqueindexes(dataset.size(), speciessize);          (int i=0; i< uniqueindexes.size(); i++){             final int randomindex = uniqueindexes.get(i);             final species species = new species(i);             final centroid centroid = new centroid(dataset.get(randomindex).getmidpointx(), dataset.get(randomindex).getmidpointy(), i);             species.setcentroid(centroid);             specieslist.add(species);         }         return clusterlist;     }      /// perform 1 step of algorithm     public void step() {         (int c = 0; c < clusterlist.size(); c++) {             (int h = 0; h < points.size(); h++) {                 double top;                 top = calculateeucliddistance(points.get(h), clusterlist.get(c));                 if (top < 1.0) top = eps;                  // sumterms sum of distances data point clusters.                 double sumterms = 0.0;                  (int ck = 0; ck < clusterlist.size(); ck++) {                     double thisdistance = calculateeucliddistance(points.get(h), clusterlist.get(ck));                     if (thisdistance < 1.0) thisdistance = eps;                     sumterms += math.pow(top / thisdistance, 2.0 / (fuzzyness - 1.0));                  }                 // membership value can calculated as...                 u[h][c] = (1.0 / sumterms);             }         }          recalculateclusterindexes();     }      /// calculates euclid distance between point , centroid     /// point     /// centroid     /// calculated distance     private double calculateeucliddistance(job p, species c) {         return toolbox.calculatedistance(p.getmidpointx(), p.getmidpointy(), c.getcentroid().getx(), c.getcentroid().gety());     }      /// calculates centroids of clusters     private void calculateclustercentroids() {         (int j = 0; j < clusterlist.size(); j++) {             species c = clusterlist.get(j);             double ux = 0.0;             double uy = 0.0;             double membershipsum = 0.0;              (int = 0; < points.size(); i++) {                 job p = points.get(i);                  double uu = math.pow(u[i][j], this.fuzzyness);                 ux += uu * p.getmidpointx();                 uy += uu * p.getmidpointy();                 membershipsum += uu;             }              c.setmembershipsum(membershipsum);             c.getcentroid().setx(((ux / membershipsum)));             c.getcentroid().sety(((uy / membershipsum)));              log += string.format("cluster centroid: (" + c.getcentroid().getx() + "; " + c.getcentroid().gety() + ")");         }     }      private void assignjobstoclusters(){         (final cluster cluster : clusterlist){             if (!integerclusterhashmap.containskey(cluster.getmembershipsum()))                 integerclusterhashmap.put(cluster.getmembershipsum(), cluster);         }          (job job : points){             final double clusterindex = job.getclusterindex();             species c = integerspecieshashmap.get(clusterindex);              if (c != null) {                 c.add(job);             }         }     } 

fuzzy c means code in java

package f; import java.io.file; import java.io.filenotfoundexception; import java.util.scanner;  /**  *  * @author anooj.k.varghese  */ public class f{   static double data_set[][]=new double[20000][100];     static double diff[][]=new double[20000][100];         static double eud[][]=new double[20000][1000];     static double intial_centroid[][]=new double[300][400];      static double new_center[][]=new double[300][400];     static int num = 0;     static int row=4;//rows in dataset here use iris dataset       static int cnum;     static int itc=0;     static int checker=1;        private static void readfile() throws filenotfoundexception         {         scanner scanner = new scanner(new file("e:/aa.txt"));//dataset path         scanner.usedelimiter(system.getproperty("line.separator"));         //scanner.usedelimiter(",");         int lineno = 0;             while (scanner.hasnext())              {                 parseline(scanner.next(),lineno);                 lineno++;                 system.out.println();              }              // system.out.println("total"+num); print total      scanner.close();         }     //read file copey data_set     public static void parseline(string line,int lineno)       { itc=0;         scanner linescanner = new scanner(line);         linescanner.usedelimiter(",");           for(int col=0;col<row;col++)               {                   double arry=linescanner.nextdouble();                   data_set[num][col]=arry;                          ///here read  data set assign variable data_set                }          num++;          }     public static void init()     {         for(int i=0;i<num;i++)         {           data_set[i][row]=0.0;          data_set[i][row+1]=0.0;         }     }     public static void print()     {         double re=0;         double a=0;          if(itc==0)        {               system.out.println("enter k");          scanner sc=new scanner(system.in);                cnum=sc.nextint();   //enter number of cenroid        system.out.println("centroid");          for(int i=0;i<cnum;i++)          {             for(int j=0;j<row;j++)                 {                      intial_centroid[i][j]=data_set[i][j];                  //// centroid stored in intial_centroid variable                     system.out.print(intial_centroid[i][j]);                       }             system.out.println();          }         }        else        {              for(int i=0;i<cnum;i++)          {             for(int j=0;j<row;j++)                 {                     intial_centroid[i][j]=new_center[i][j];                  //// centroid stored in intial_centroid variable                     system.out.print(intial_centroid[i][j]);                       }             system.out.println();          }          }            for(int i=0;i<num;i++)         {                 for(int j=0;j<cnum;j++)                        {                     re=0;                      for(int k=0;k<row;k++)                      {                             a= (intial_centroid[j][k]-data_set[i][k]);                             //system.out.println(a);                              a=a*a;                              re=re+a;                                                 // store row sum                          }                           diff[i][j]= math.sqrt(re);// find squre root                          system.out.println(diff[i][j]);          }         }      }     public static void s()     {          double b,c;         for(int i=0;i<num;i++)         {             for(int j=0;j<cnum;j++)             {                 c=0.0;                 b=0.0;                 for(int k=0;k<cnum;k++)                 {                     if(diff[i][k]==0)                    {                         b=0;                     }                  if(diff[i][k]!=0)                    {                     b=diff[i][j]/diff[i][k];                     }                     c=c+b;                 }                 if(c==0)                 {                     eud[i][j]=0.0;                 }                 else                 {                      eud[i][j]=1/c;                 }             }           }         double a=0;           for(int i=0;i<num;i++)         {             a=0;             for(int j=0;j<cnum;j++)             {                 a=a+eud[i][j];              system.out.print(eud[i][j]+"    ");             }             system.out.print("total  "+a);             system.out.println();             }           double aaa;           int counter=0;                for(int i=0;i<num;i++)         {counter=0;             aaa=eud[i][0];             for(int j=0;j<cnum;j++)                         {                             if(aaa<=eud[i][j])                             {                                 aaa=eud[i][j];                                 counter=j;                             }                         }           if(itc%2==0)           {                 data_set[i][row]=(double)counter;           }             if(itc%2==1)           {                data_set[i][row+1]=(double)counter;           }         }            for(int i=0;i<num;i++)            {                for(int j=0;j<=row+1;j++)                {                 system.out.print(data_set[i][j]+",  ");                 }                system.out.println();            }     }       public static void newcenter()           {               itc++;               double a=0.0;               double c=0.0;               double d=0.0;               double f=0.0;               for(int k=0;k<cnum;k++)               {                    for(int j=0;j<row;j++)                   {                       a=0.0;                       d=0.0;                   c=0.0;                  f=0.0;                       for(int i=0;i<num;i++)                       {                           //system.out.print("edu"+eud[i][k]);                           a=eud[i][k];                           a=a*a;                           c=c+a;                           //system.out.println("data"+data_set[i][j]);                           d=a*data_set[i][j];                           f=f+d;                       }                       new_center[k][j]=f/c;                          system.out.println("centroid new "+new_center[k][j]);                      // j=row+5;                     //  k=cnum+5;                    }               }           }        public static void print11()     {         system.out.println();          system.out.println();           system.out.println();         system.out.println("----output----");         int c=0;         int a=0;         for(int i=0;i<cnum;i++)         {             system.out.println("---------cluster-"+i+"-----");          a=0;             for(int j=0;j<num;j++)             {                  if(data_set[j][row]==i)                  {a++;                 for(int k=0;k<row;k++)                 {                      system.out.print(data_set[j][k]+"  ");                 }                 c++;                 system.out.println();                 }                  //system.out.println(num);              }                system.out.println("cluster instances="+a);           }         system.out.println("total instance"+c);     }       public static void check() {      checker=0;     for(int i=0;i<num;i++)     {          //system.out.println("hii");         if(double.compare(data_set[i][row],data_set[i][row+1]) != 0)          {             checker=1;             //system.out.println("hii " +  + " " + data_set[i][4]+ " "+data_set[i][4]);             break;         }         system.out.println();     }  }      public static void main(string[] args) throws filenotfoundexception {   readfile();    //   init(); while(checker!=0)  //for(int i=0;i<5;i++)    {    print();  s();  newcenter();  check();      } print11(); } }