// Partial Match Algorithm
// From Line 368-438
public static Match partialMatch(List <Phi> DNAseq1, List <Phi> DNAseq2)
{
bool flag = true; // ToDo: Compare the control points in contours between two parts
Match segment; // create an empty match segment
segment.t11 = 0;
segment.t12 = 0;
segment.t21 = 0;
segment.t22 = 0;
List <Phi> seq1, seq2; // two empty List of edge maps
int best = 0, max_match;
int offset = 0, length = 0;
// sticking
// .While comparing a pair of DNA pattern, the smaller one is reversed while the longer one is copied and placed at its tail,
//such that now the angle accumulated over the string is 4π
if (DNAseq1.Count > DNAseq2.Count) // if the contour in first part has more control points than the second part
{
seq1 = replicateDNA(DNAseq1); //replicate the larger DNA
seq2 = DNAseq2.ToList(); //reverse the smaller one
seq2.Reverse();
}
else
{
flag = false;
seq1 = replicateDNA(DNAseq2); // if the first one has less control point, attach all the control points of the second part
seq2 = DNAseq1.ToList(); //reverse the smaller one
seq2.Reverse();
}
// sliding
//The shorter sequence is slided through the longer one and for every shift ‘d’, the difference Δφabd = φbd – φa is stored
for (int shift = 0; shift < seq1.Count - seq2.Count; shift += Constants.STEP)
{
List <int> diff = new List <int>();
int start = 0, end = 0;
for (int i = 0; i < seq2.Count; ++i)
{
int difference = (int)(seq1[i + shift].theta - seq2[i].theta);
diff.Add(difference);
}
max_match = histogram(diff, seq2, ref start, ref end, Constants.DELTA_THETA);
if (best < max_match)
{
offset = shift;
best = max_match;
int t_start = start + shift;
int t_end = end + shift;
if (start + shift >= seq1.Count / 2)
{
t_start = start + shift - seq1.Count / 2;
}
if (end + shift >= seq1.Count / 2)
{
t_end = end + shift - seq1.Count / 2;
}
length = t_start - t_end;
if (flag)
{
segment.t21 = seq2.Count - end - 1;
segment.t22 = seq2.Count - start - 1;
segment.t11 = t_start;
segment.t12 = t_end;
}
else
{
segment.t11 = seq2.Count - end - 1;
segment.t12 = seq2.Count - start - 1;
segment.t21 = t_start;
segment.t22 = t_end;
}
}
}
segment.x11 = (int)DNAseq1[segment.t11].x;
segment.y11 = (int)DNAseq1[segment.t11].y;
segment.x12 = (int)DNAseq1[segment.t12].x;
segment.y12 = (int)DNAseq1[segment.t12].y;
segment.x21 = (int)DNAseq2[segment.t21].x;
segment.y21 = (int)DNAseq2[segment.t21].y;
segment.x22 = (int)DNAseq2[segment.t22].x;
segment.y22 = (int)DNAseq2[segment.t22].y;
// consider the color feature for rejection
// Step 1: extract the color on the edge into a list (done)
List <Bgr> colors1 = new List <Bgr>();
List <Bgr> colors2 = new List <Bgr>();
if (segment.t12 > segment.t11)
{
for (int i = segment.t11; i <= segment.t12; i++)
{
colors1.Add(DNAseq1[i].color);
}
}
else
{
for (int i = segment.t11; i <= DNAseq1.Count - 1; i++)
{
colors1.Add(DNAseq1[i].color);
}
for (int i = 0; i <= segment.t12; i++)
{
colors1.Add(DNAseq1[i].color);
}
}
if (segment.t22 > segment.t21)
{
for (int i = segment.t21; i <= segment.t22; i++)
{
colors2.Add(DNAseq2[i].color);
}
}
else
{
for (int i = segment.t21; i <= DNAseq2.Count - 1; i++)
{
colors2.Add(DNAseq2[i].color);
}
for (int i = 0; i <= segment.t22; i++)
{
colors2.Add(DNAseq2[i].color);
}
}
// Step 2: Calculate the total color difference
int totalColorDifference = 0;
for (int i = 0; i < Math.Min(colors1.Count, colors2.Count); i++)
{
totalColorDifference += Metrics.colorDifference(colors1[i], colors2[i]);
}
// Step 3: if the color difference is too great, reject
double avgColorDifference = totalColorDifference / (Math.Min(colors1.Count, colors2.Count));
if (avgColorDifference > Constants.EDGE_COLOR_DIFFERENCE)
{
segment.confidence = 0; // reject
}
// rejections for final inconsistent matches
else if (best == 0)
{
segment.confidence = 0;
}
else if (segment.t11 > segment.t12)
{
segment.confidence = 0; // if the first segment run over the origin, reject the match
}
else if (segment.t21 > segment.t22)
{
segment.confidence = 0; // if the second segment run over the origin, reject the match
}
else
{
segment.confidence = Math.Sqrt((double)(length * length) / best);
}
return(segment);
}
// Partial Match Algorithm using color feature
// I used the framework for the partial matching algorithm using turning angle
// but using the differences of the color on the edge
public static Match partialColorMatch(List <Phi> DNAseq1, List <Phi> DNAseq2)
{
bool flag = true; // ToDo: Compare the control points in contours between two parts
Match segment; // create an empty match segment
segment.t11 = 0;
segment.t12 = 0;
segment.t21 = 0;
segment.t22 = 0;
List <Phi> seq1, seq2; // two empty List of edge maps
int best = 0, max_match;
int offset = 0, length = 0;
if (DNAseq1.Count > DNAseq2.Count) // if the contour in first part has more control points than the second part
{
seq1 = replicateDNA(DNAseq1); //replicate the larger DNA
seq2 = DNAseq2.ToList(); //reverse the smaller one
seq2.Reverse();
}
else
{
flag = false;
seq1 = replicateDNA(DNAseq2); // if the first one has less control point, attach all the control points of the second part
seq2 = DNAseq1.ToList(); //reverse the smaller one
seq2.Reverse();
}
List <int> zc = new List <int>();
List <int> starts = new List <int>();
int iteration = 0;
for (int shift = 0; shift < seq1.Count - seq2.Count; shift += Constants.STEP)
{
List <int> diff = new List <int>();
bool flag1 = false;
int start = 0, end = 0;
// TODO: change the differences into color difference (done)
List <int> zeroCounts = new List <int>();
int zeroCount = 0;
List <int> starts2 = new List <int>();
// TODO: need to add a tolerance level for some random non 0 differences
int tolerCount = 0; // tolerance count for random non 0s.
for (int i = 0; i < seq2.Count; ++i)
{
int difference = Metrics.colorDifference(seq1[i + shift].color, seq2[i].color);
// if difference==0, flag
// if difference!=0, unflag
if (difference <= 0)
{
// if it is in unflag state, mark the point as starting point
if (!flag1)
{
flag1 = true;
start = i;
//starts.Add(start);
starts2.Add(start);
}
// count the number of zero difference points in this section
zeroCount++;
tolerCount = 0;
}
else
{
if (tolerCount <= Constants.COLOR_TOLERANCE)
{
if (flag1)
{
zeroCount++;
tolerCount++;
}
}
else
{
if (flag1)
{
zeroCounts.Add(zeroCount); // add to a upper level storage
zeroCount = 0; // reset the counter
flag1 = false; // unflag
tolerCount = 0;
}
}
}
diff.Add(difference);
}
if (iteration == 33)
{
Console.WriteLine("33");
}
if (zeroCounts.Count == 0)
{
starts.Add(-1);
}
else
{
starts.Add(starts2[zeroCounts.IndexOf(zeroCounts.Max())]);
}
if (zeroCounts.Count == 0)
{
zc.Add(0);
}
else
{
zc.Add(zeroCounts.Max());
}
// TTODO: implement a histogram algorithm for color match
//max_match = colorHistogram(diff, seq2, ref start, ref end, Util.DELTA_THETA);
max_match = 0;
/*if (end < start)
* {
* Console.WriteLine("22");
* }*/
/* if (best < max_match)
* {
* offset = shift;
* best = max_match;
* int t_start = start + shift;
* int t_end = end + shift;
* if (start + shift >= seq1.Count / 2)
* t_start = start + shift - seq1.Count / 2;
* if (end + shift >= seq1.Count / 2)
* t_end = end + shift - seq1.Count / 2;
* length = t_start - t_end; // problematic
*
*
* if (flag)
* {
* segment.t21 = seq2.Count - end - 1;
* segment.t22 = seq2.Count - start - 1;
* segment.t11 = t_start;
* segment.t12 = t_end;
* }
* else
* {
* segment.t11 = seq2.Count - end - 1;
* segment.t12 = seq2.Count - start - 1;
* segment.t21 = t_start;
* segment.t22 = t_end;
* }
* } */
iteration++;
}
Console.WriteLine("Max:" + zc.Max());
if (zc.Max() == 0)
{
goto a;
}
int t_shift = 0;
int s_start = 0;
for (int i = 0; i < zc.Count; i++)
{
if (zc[i] == zc.Max())
{
t_shift = Constants.STEP * i;
s_start = starts[i];
}
}
int startPos1 = t_shift + s_start;
int endPos1 = startPos1 + zc.Max();
int startPos2 = s_start;
int endPos2 = startPos2 + zc.Max();
length = zc.Max();
// check if the algorithm get the correct position of the matching color
Console.WriteLine("Flag:" + flag);
Console.WriteLine("Shiftreq:" + startPos1);
Console.WriteLine("Count:" + DNAseq1.Count);
Console.WriteLine("P1_start_x" + seq1[startPos1].x);
Console.WriteLine("P1_start_y" + seq1[startPos1].y);
Console.WriteLine("P1_end_x" + seq1[endPos1].x);
Console.WriteLine("P1_end_y" + seq1[endPos1].y);
Console.WriteLine("P2_start_x" + seq2[startPos2].x);
Console.WriteLine("P2_start_y" + seq2[startPos2].y);
Console.WriteLine("P2_end_x" + seq2[endPos2].x);
Console.WriteLine("P2_end_y" + seq2[endPos2].y);
// correct for all the code above
// regression analysis for the relationship between seq and DNA
// flag=true for 3*3 frag5 and frag6
if (flag)
{
for (int j = 0; j < DNAseq1.Count; j++)
{
if ((seq1[startPos1].x == DNAseq1[j].x) && (seq1[startPos1].y == DNAseq1[j].y))
{
segment.t11 = j;
//segment.x11 = (int)DNAseq1[j].x;
// segment.y11 = (int)DNAseq1[j].y;
segment.t12 = j + zc.Max();
if (segment.t12 >= DNAseq1.Count)
{
segment.t12 -= DNAseq1.Count;
}
//segment.x12 = (int)DNAseq1[j + zc.Max()].x;
//segment.y12 = (int)DNAseq1[j + zc.Max()].y;
}
}
for (int j = 0; j < DNAseq2.Count; j++)
{
if ((seq2[startPos2].x == DNAseq2[j].x) && (seq2[startPos2].y == DNAseq2[j].y))
{
segment.t21 = j;
//segment.x21 = (int)DNAseq2[j].x;
//segment.y21 = (int)DNAseq2[j].y;
segment.t22 = j - zc.Max();
if (segment.t22 < 0)
{
segment.t22 += DNAseq2.Count;
}
//segment.x22 = (int)DNAseq2[j - zc.Max()].x;
//segment.y22 = (int)DNAseq2[j - zc.Max()].y;
}
}
}
else
{
for (int j = 0; j < DNAseq2.Count; j++)
{
if ((seq1[startPos1].x == DNAseq2[j].x) && (seq1[startPos1].y == DNAseq2[j].y))
{
segment.t21 = j;
//segment.x11 = (int)DNAseq2[j].x;
//segment.y11 = (int)DNAseq2[j].y;
segment.t22 = j + zc.Max();
if (segment.t22 >= DNAseq2.Count)
{
segment.t22 -= DNAseq2.Count;
}
// segment.x12 = (int)DNAseq2[j - zc.Max()].x;
//segment.y12 = (int)DNAseq2[j - zc.Max()].y;
}
}
for (int j = 0; j < DNAseq1.Count; j++)
{
if ((seq2[startPos2].x == DNAseq1[j].x) && (seq2[startPos2].y == DNAseq1[j].y))
{
segment.t11 = j;
// segment.x21 = (int)DNAseq1[j].x;
// segment.y21 = (int)DNAseq1[j].y;
segment.t12 = j - zc.Max();
if (segment.t12 < 0)
{
segment.t12 += DNAseq1.Count;
}
//segment.x22 = (int)DNAseq1[j + zc.Max()].x;
//segment.y22 = (int)DNAseq1[j + zc.Max()].y;
}
}
}
/*int t_start = t_shift;
* int t_end = t_shift;
* if (t_shift >= seq1.Count / 2)
* t_start = t_shift - seq1.Count / 2;
* if (t_shift >= seq1.Count / 2)
* t_end = t_shift - seq1.Count / 2;
* length = zc.Max(); // problematic
*
*
* /*if (flag)
* {
* segment.t21 = seq2.Count - -1;
* segment.t22 = seq2.Count - t_start - 1;
* segment.t11 = t_start;
* segment.t12 = t_end;
* }
* else
* {
* segment.t11 = seq2.Count - t_end - 1;
* segment.t12 = seq2.Count - t_start - 1;
* segment.t21 = t_start;
* segment.t22 = t_end;
* }*/
// fine code below
a : segment.x11 = (int)DNAseq1[segment.t11].x;
segment.y11 = (int)DNAseq1[segment.t11].y;
segment.x12 = (int)DNAseq1[segment.t12].x;
segment.y12 = (int)DNAseq1[segment.t12].y;
segment.x21 = (int)DNAseq2[segment.t21].x;
segment.y21 = (int)DNAseq2[segment.t21].y;
segment.x22 = (int)DNAseq2[segment.t22].x;
segment.y22 = (int)DNAseq2[segment.t22].y;
// correct at this point
/*if (best == 0)
* segment.confidence = 0;
* else
* segment.confidence = Math.Sqrt((double)(length * length) / best); */
segment.confidence = length;
Console.WriteLine(segment.ToString());
// all the code above is the matching segment without considering edge feature
// we need to consider edge feature at this point
// and cull out the matching edge that does not match
// consider the most simple case: straight line without rotating
// then to edges with turning angles but still without rotating
// then to general case
// Step 1: extract the portion of DNA that forms the matching edge (done)
List <Phi> edge1 = new List <Phi>(); // valid edge in image 1
List <Phi> edge2 = new List <Phi>(); // valid edge in image 2
for (int i = Math.Min(segment.t11, segment.t12); i < Math.Max(segment.t11, segment.t12); i++)
{
edge1.Add(DNAseq1[i]);
}
for (int i = Math.Min(segment.t21, segment.t22); i < Math.Max(segment.t21, segment.t22); i++)
{
edge2.Add(DNAseq2[i]);
}
if (edge1.Count == 0 || edge2.Count == 0)
{
goto r; // if there is no matching edge, it is not nessesary for culling
}
// Step 2: Analyze the edge feature
// convert edge into contour
Contour <Point> c1;
Contour <Point> c2;
List <Point> pedge1;
List <Point> pedge2;
c1 = new Contour <Point>(Form1.mem);
foreach (Phi p in edge1)
{
c1.Push(new Point((int)p.x, (int)p.y));
}
if (c1.Total == 0)
{
}
// stor.Dispose();
c1 = c1.ApproxPoly(2.0, Form1.mem);
pedge1 = c1.ToList();
c2 = new Contour <Point>(Form1.mem);
foreach (Phi p in edge2)
{
c2.Push(new Point((int)p.x, (int)p.y));
}
c2 = c2.ApproxPoly(2.0);
pedge2 = c2.ToList();
// Step 3: Cull the edge
// calculate the turning angle for each edge
// if the cumulative turning angle change is greater than 90, restart
// use a brute force longest straight line approach first, this solves a lot of cases
int maxDistance = -99999;
int pos1 = 0, pos2 = 0;
for (int i = 0; i < pedge1.Count - 1; i++)
{
if (pedge1[i + 1].X == pedge1[i].X)
{
if (Math.Abs(pedge1[i + 1].Y - pedge1[i].Y) > maxDistance)
{
maxDistance = Math.Abs(pedge1[i + 1].Y - pedge1[i].Y);
pos1 = i;
}
}
else if (pedge1[i + 1].Y == pedge1[i].Y)
{
if (Math.Abs(pedge1[i + 1].X - pedge1[i].X) > maxDistance)
{
maxDistance = Math.Abs(pedge1[i + 1].X - pedge1[i].X);
pos1 = i;
}
}
}
maxDistance = -99999;
for (int i = 0; i < pedge2.Count - 1; i++)
{
if (pedge2[i + 1].X == pedge2[i].X)
{
if (Math.Abs(pedge2[i + 1].Y - pedge2[i].Y) > maxDistance)
{
maxDistance = Math.Abs(pedge2[i + 1].Y - pedge2[i].Y);
pos2 = i;
}
}
else if (pedge2[i + 1].Y == pedge2[i].Y)
{
if (Math.Abs(pedge2[i + 1].X - pedge2[i].X) > maxDistance)
{
maxDistance = Math.Abs(pedge2[i + 1].X - pedge2[i].X);
pos2 = i;
}
}
}
// now the new matching edge is calculated, send the result to output
for (int j = 0; j < DNAseq1.Count; j++)
{
if ((pedge1[pos1].X == DNAseq1[j].x) && (pedge1[pos1].Y == DNAseq1[j].y))
{
segment.t11 = j;
}
}
for (int j = 0; j < DNAseq2.Count; j++)
{
if ((pedge2[pos2].X == DNAseq2[j].x) && (pedge2[pos2].Y == DNAseq2[j].y))
{
segment.t21 = j;
}
}
for (int j = 0; j < DNAseq1.Count; j++)
{
if ((pedge1[pos1 + 1].X == DNAseq1[j].x) && (pedge1[pos1 + 1].Y == DNAseq1[j].y))
{
segment.t12 = j;
}
}
for (int j = 0; j < DNAseq2.Count; j++)
{
if ((pedge2[pos2 + 1].X == DNAseq2[j].x) && (pedge2[pos2 + 1].Y == DNAseq2[j].y))
{
segment.t22 = j;
}
}
segment.x11 = (int)DNAseq1[segment.t11].x;
segment.y11 = (int)DNAseq1[segment.t11].y;
segment.x12 = (int)DNAseq1[segment.t12].x;
segment.y12 = (int)DNAseq1[segment.t12].y;
segment.x21 = (int)DNAseq2[segment.t21].x;
segment.y21 = (int)DNAseq2[segment.t21].y;
segment.x22 = (int)DNAseq2[segment.t22].x;
segment.y22 = (int)DNAseq2[segment.t22].y;
r : return(segment);
}
