#include "step2.h"

/*---------------------------------------------------------------*/

/* Step2: calculate local minimum

* Input: data from step1

*

* **/

void cumsum(vector<vector<double> > const &x, vector<vector<double> > &sx) //cumsum the value vertically and horizontally, then the value of each cell (i,j) represent the sum of matrix[0:i,0:j]

{ int i, j, l = (int)x.size();

sx = x;

for(i = 0; i < l; i++)

{ printProgress((double)(i + 1) / (double)l);

for(j = 1; j < l; j++) sx[i][j] += sx[i][j - 1];

if(i > 0)

{ for(j = 0; j < l; j++)

sx[i][j] += sx[i - 1][j];

}

}

}

void getScore(vector<vector<double> > const &sx, int maxsz, vector<vector<double> > &score) //use matrix[0:i,0:(i+j)] minus matrix[0:i,0:i] and minus (matrix[0:i-j,0:i+j]-matrix[0:i-j,0:i])

{ int i, j, k, l = (int)sx.size();

score.clear();

score.resize(l, vector<double>(maxsz, 0));

for(i = 1; i < l; i++)

{ printProgress((double)(i + 1) / (double)l);

for(j = 0; j < maxsz; j++)

{ score[i][j] = sx[i - 1][min(l - 1, i + j + 1)] - sx[i - 1][i];

if(i - j - 2 >= 0) score[i][j] += - sx[i - j - 2][min(l - 1, i + j + 1)] + sx[i - j - 2][i];

k = min(l - i, j + 1) * min(i, j + 1);

score[i][j] /= (double)k;

}

}

}

void calMins(vector<vector<double> > const &score, vector<vector<bool> > &lm, int hsz, double ldiff) //compare score for each bin with adjacent bins and determine local minimum

{ int l = (int)score.size(), n = (int)score[0].size();

//int hsz =5;

int i, j, k;

lm.clear();

lm.resize(l, vector<bool>(n, false));

vector<int> map;

for(i = 0; i < l; i++)

{ double m = 0, s = 0;

for(j = 0; j < n; j++)

{ m += score[i][j];

s += score[i][j] * score[i][j];

}

if(s > m * m / (double)n) map.push_back(i);

}

if((int)map.size() < 2) return;

for(i = 0; i < n; i++)

{ printProgress((double)(i+1) / (double)n);

double m = 0, s = 0;

for(j = 1; j < (int)map.size(); j++)

{ m += score[map[j]][i] - score[map[j - 1]][i];

s += pow(score[map[j]][i] - score[map[j - 1]][i], 2.);

}

m /= (double)((int)map.size() - 1);

s = sqrt(s / (double)((int)map.size() - 1) - m * m);

double cut = s * ldiff;/// sqrt((double)hsz) * 3.89; ///1,96std from mean

for(j = 0; j < (int)map.size(); j++)

{ double mins = score[map[j]][i], maxs = mins;

for(k = max(0, j - hsz); k < min((int)map.size(), j + hsz + 1); k++)

{ if(mins >= score[map[k]][i] && k != j) break;

maxs = max(maxs, score[map[k]][i]);

}

if(k >= min(l, j + hsz + 1) && maxs - mins > cut)

lm[map[j]][i] = 1;

}

lm[0][i] = lm[l - 1][i] = 1;

}

}

void setPair(vector<vector<bool> > const &lm, vector<vector<bool> > &sel) //create a sel matrix that mark local minimum bins on diag and edges.

{ int i, j, k, l = (int)lm.size(), n = (int)lm[0].size();

sel.clear();

sel.resize(l, vector<bool>(l, false));

for(i = 0; i < n; i++)

{ vector<int> map;

for(j = 0; j < l; j++)

{ if(lm[j][i]) map.push_back(j);

}

for(j = 0; j < (int)map.size(); j++)

{ for(k = 1; k <= 5; k++)

{ if(j + k >= (int)map.size()) break;

sel[0][map[j]] = sel[0][map[j+k]] = sel[map[j]][l-1] = sel[map[j+k]][l-1] = sel[map[j]][map[j+k]] = 1;

}

}

}

}