cv::Mat process(int newSize) {
image = Thresholding(image).transform();
// cut egdes:
for (int i = 0; i < image.rows; i ++) {
if (!processRow(i)) {
break;
}
}
for (int i = image.rows - 1; i >= 0; i --) {
if (!processRow(i)) {
break;
}
}
for (int i = 0; i < image.cols; i ++) {
if (!processCol(i)) {
break;
}
}
for (int i = image.cols - 1; i >= 0; i --) {
if (!processCol(i)) {
break;
}
}
for (int i = 0; i < used.size(); i ++)
for (int j = 0; j < used[i].size(); j ++)
used[i][j] = 0;
int L = 1;
for (int i = 0; i < image.rows; i ++)
for (int j = 0; j < image.cols; j ++)
if (image.at<uchar>(i, j) == BLACK && used[i][j] == 0) {
dfs(i, j, L);
L ++;
}
std::map<int,int> cnt;
for (int i = 0; i < image.rows; i ++)
for (int j = 0; j < image.cols; j ++)
if (used[i][j] != 0)
cnt[used[i][j]] ++;
int max_value = 0;
int best_comp;
for (std::map<int,int>::iterator it = cnt.begin(); it != cnt.end(); it ++)
if (it->second > max_value) {
max_value = it->second;
best_comp = it->first;
}
for (int i = 0; i < image.rows; i ++)
for (int j = 0; j < image.cols; j ++)
if (used[i][j] != best_comp) {
image.at<uchar>(i,j) = WHITE;
}
int minRow = image.rows;
int maxRow = -1;
int minCol = image.cols;
int maxCol = -1;
for (int i = 0; i < image.rows; i ++)
for (int j = 0; j < image.cols; j ++)
if (image.at<uchar>(i,j) == BLACK) {
minRow = std::min(minRow, i);
maxRow = std::max(maxRow, i);
minCol = std::min(minCol, j);
maxCol = std::max(maxCol, j);
}
int X = minCol;
int Y = minRow;
int W = maxCol - minCol + 1;
int H = maxRow - minRow + 1;
int X0 = X - std::max(0, H - W) / 2;
int Y0 = Y - std::max(0, W - H) / 2;
try {
image = Image::getSubMatrix(image, X0, Y0, std::max(W, H), std::max(W,H));
} catch (...) {
}
cv::Mat newImage;
cv::resize(image, newImage, cv::Size(newSize, newSize));
newImage = Thresholding(newImage).transform();
return newImage;
}
static crosspoint_t ort_split_2(Sequence *seq0, Sequence *seq1, int i0, int j0, int i1, int j1,
int type_s, int type_e, int score_s, int score_e,
int *h0, int *h1, int *e0, int *e1, cell_t *r0, cell_t *r1, cell_t *c0, cell_t *c1) {
if (DEBUG) printf("%d %d %d %d %d %d %d %d\n", i0, j0, i1, j1, type_s, type_e, score_s, score_e);
int seq0_len = i1-i0;
int seq1_len = j1-j0;
if (seq1_len >= H_MAX) {
fprintf(stderr, "Partition size is too large (%d > %d). You need to store more special rows in stages 1-3.\n", seq1_len, H_MAX);
exit(1);
}
int diff = (score_e + (type_e == TYPE_MATCH ? 0 : dna_gap_open)*0) - score_s;
int imid = seq0_len/2;
int imid0 = imid;
int imid1 = seq0_len - imid; // (imid1 >= imid0) is always true
int jmid = seq1_len/2;
int jmid0 = jmid;
int jmid1 = seq1_len - jmid; // (jmid1 >= jmid0) is always true
/* Forward */
const char* s0 = seq0->getData(false)+(i0);
const char* s1 = seq1->getData(false)+(j0);
const char* s0r = seq0->getData(true)+(seq0->getInfo()->getSize()-i1);
const char* s1r = seq1->getData(true)+(seq1->getInfo()->getSize()-j1);
// for (int i=0; i<seq0_len; i++) {
// printf("%d: %c%c\n", i, s0[i], s0r[i]);
// }
for (int i=0; i<imid0; i++) {
c0[i].h = -(i+1)*dna_gap_ext - dna_gap_open*(type_s!=TYPE_GAP_2);
c0[i].e = -INF;
}
for (int i=0; i<imid1; i++) {
c1[i].h = -(i+1)*dna_gap_ext - dna_gap_open;//*(type_e!=TYPE_GAP_2);
c1[i].e = -INF;
}
r0[0].h = r0[0].f = c0[imid0-1].h;
r1[0].h = r1[0].f = c1[imid1-1].h;
crosspoint_t cross;
int d0 = (type_s!=TYPE_MATCH)?-INF:0;
int d1 = (type_e!=TYPE_MATCH)?-INF:0;
for (int j=0; j<seq1_len; j++) {
int h0 = -(j+1)*dna_gap_ext - dna_gap_open*(type_s!=TYPE_GAP_1);
cell_t rr0 = processCol(s0, s1[j], d0, h0, c0, imid0);
d0 = h0;
int h1 = -(j+1)*dna_gap_ext - dna_gap_open;//*(type_e!=TYPE_GAP_1);
cell_t rr1 = processCol(s0r, s1r[j], d1, h1, c1, imid1);
d1 = h1;
if (j+1<=jmid1) {
r0[j+1] = rr0;
r1[j+1] = rr1;
}
if (DEBUG) printf("%d: %d %d (%d %d) (%d %d)\n", j, rr0.h, rr1.h, imid0, imid1, jmid0, jmid1);
if (j+1>=jmid1) {
if (match(rr0, r1[seq1_len-(j+1)], diff, &cross)) {
cross.j = j0+(j+1);
cross.i = imid0+i0;
cross.score += score_s;
return cross;
}
if (match(r0[seq1_len-(j+1)], rr1, diff, &cross)) {
cross.j = j0+(seq1_len-(j+1));
cross.i = imid0+i0;
cross.score += score_s;
return cross;
}
}
}
if (DEBUG) printf("NOT FOUND %d\n", diff);
fprintf(stderr, "NOT FOUND %d (%d %d %d %d - %d %d %d %d)\n", diff, type_s, i0, j0, score_s, type_e, i1, j1, score_e);
exit(1);
}