public void SmoothAndSave(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format, PixelFormat pixelFormat)
{
BSpline bs = new BSpline();
MyCurrentPointSet3D = bs.BSpline3DofPepImage(MyOriginalPointSet3D, BmpRegion);
SaveImage(filename, size, format, pixelFormat);
}
public void SmoothingofSmoothed(float X_min, float X_max, float Y_max, float Y_min)
{
MyCurrentPointSet3D = MyOriginalPointSet3D;
GetSubPointSet(new RegionSize(X_min, X_max, Y_max, Y_min));
ScaleSize = ScaleSize * Math.Min((X_max - X_min) / (MyCurrentPointSet3D.MaxX - MyCurrentPointSet3D.MinX), (Y_max - Y_min) / (MyCurrentPointSet3D.MaxY - MyCurrentPointSet3D.MinY));
BmpRegion = new RegionSize(0, (int)(BmpRegion.RightBound * ScaleSize), (int)(BmpRegion.TopBound * ScaleSize), 0);
MyCurrentPointSet3D = smoothing(MyCurrentPointSet3D);
}
public void initialize()
{
MyCurrentPointSet3D = RawDataPointSet3D;
MyOriginalPointSet3D = RawDataPointSet3D;
NoPoints = MyCurrentPointSet3D.Count;
IsSmoothed = false;
renew_plot = true;
ScaleSize = 1;
BmpRegion = new RegionSize(0, 300, 200, 0);
}
public void GetSubPointSet(RegionSize SR)
{
if (SubPointSetExtract(SR).Count == 0)
{
return;
}
MyCurrentPointSet3D = SubPointSetExtract(SR);
//MyOriginalPointSet3D = MyCurrentPointSet3D;
NoPoints = MyCurrentPointSet3D.Count;
}
public void SaveImage(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format, PixelFormat pixelFormat)
{
Bitmap bmp = new Bitmap(Convert.ToInt32(size.Width), Convert.ToInt32(size.Height), pixelFormat);
Graphics g = Graphics.FromImage(bmp);
g.Clear(Color.White);
this.ImageDraw(g, size);
bmp.Save(filename, format);
bmp.Dispose();
g.Dispose();
}
public MSPointSet3D SubPointSetExtract(RegionSize SR)
{
MSPointSet3D tempPointSet = new MSPointSet3D();
//foreach (MSPoint3D D in MyCurrentPointSet3D.)
for (int i = 0; i < RawDataPointSet3D.Count; i++)
{
if (RawDataPointSet3D._x[i] >= SR.LeftBound && RawDataPointSet3D._x[i] <= SR.RightBound && RawDataPointSet3D._y[i] <= SR.TopBound && RawDataPointSet3D._y[i] >= SR.BottomBound)
{
tempPointSet.Add(RawDataPointSet3D._x[i], RawDataPointSet3D._y[i], RawDataPointSet3D.Z(i));
}
}
return(tempPointSet);
}
private float[,] MSpointSet3DToArray(MSPointSet3D mspointset, RegionSize PaintRegion)
{
RegionSize pointSetRegion = new RegionSize(mspointset.MinX, mspointset.MaxX, mspointset.MaxY, mspointset.MinY);
float[,] Data = new float[(int)PaintRegion.Width + 1, (int)PaintRegion.Height + 1];
int[,] DataCount = new int[(int)PaintRegion.Width + 1, (int)PaintRegion.Height + 1];
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
Data[i, j] = -1;
DataCount[i, j] = 0;
}
}
//foreach (MSPoint3D point3D in mspointset.Points3D)
for (int i = 0; i < mspointset.Count; i++)
{
if (DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] == 0)
{
Data[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] = mspointset.Z(i);
DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))]++;
}
else
{
Data[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] += mspointset.Z(i);
DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))]++;
}
}
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
Data[i, j] = Data[i, j] / DataCount[i, j];
}
}
}
return(Data);
}
public void SmoothingofSmoothed(float X_min, float X_max, float Y_max, float Y_min)
{
MyCurrentPointSet3D = MyOriginalPointSet3D;
GetSubPointSet(new RegionSize(X_min, X_max, Y_max, Y_min));
ScaleSize = ScaleSize * Math.Min((X_max - X_min) / (MyCurrentPointSet3D.MaxX - MyCurrentPointSet3D.MinX), (Y_max - Y_min) / (MyCurrentPointSet3D.MaxY - MyCurrentPointSet3D.MinY));
BmpRegion = new RegionSize(0, (int)(BmpRegion.RightBound * ScaleSize), (int)(BmpRegion.TopBound * ScaleSize), 0);
MyCurrentPointSet3D = smoothing(MyCurrentPointSet3D);
}
public void SmoothAndSave(string filename, RegionSize size)
{
SmoothAndSave(filename, size, System.Drawing.Imaging.ImageFormat.Tiff, PixelFormat.Format4bppIndexed);
}
public static float TimeToX(RegionSize TimeRegion, RegionSize XRegion, float Time)
{
float X = XRegion.LeftBound + ((Time - TimeRegion.LeftBound) * XRegion.Width / TimeRegion.Width);
return X;
}
public MSPointSet3D BSpline3DofPepImage(MSPointSet3D mspointset, RegionSize PaintRegion)
{
MSPointSet3D interpolatedPointSet3D = new MSPointSet3D();
RegionSize pointSetRegion = new RegionSize(mspointset.MinX, mspointset.MaxX, mspointset.MaxY, mspointset.MinY);
if (pointSetRegion.Width * pointSetRegion.Height * PaintRegion.Width * PaintRegion.Height == 0)
{
return mspointset;
}
float[,] Data;
Data = MSpointSet3DToArray(mspointset, PaintRegion);
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
MSPointSet pointset2D = new MSPointSet();
float MaxIntensity = -1;
bool empty = true;
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
empty = false;
if (Data[i, j] > MaxIntensity)
{
MaxIntensity = Data[i, j];
}
}
}
if (empty == false)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] == -1)
{
Data[i, j] = 0;
}
}
}
}
for (int i = 0; i < (int)PaintRegion.Height + 1; i++)
{
MSPointSet pointset2D = new MSPointSet();
float MaxIntensity = 0;
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] > MaxIntensity)
{
MaxIntensity = Data[j, i];
}
}
if (MaxIntensity > 0/*mspointset.MaxZ/1*/)
{
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] != -1)
{
pointset2D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, j), Data[j, i]);
}
}
pointset2D = BSpline2D(pointset2D, pointSetRegion, PaintRegion, "horizontal");
for (int x = 0; x < pointset2D.Count; x++)
{
if (Data[(int)Math.Round((CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, pointset2D.X(x)))), i] == -1)
{
Data[(int)Math.Round((CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, pointset2D.X(x)))), i] = pointset2D.Y(x);
}
}
}
else
{
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] == -1)
{
Data[j, i] = 0;
}
}
}
}
Data = NoiseFiltering(Data, (int)PaintRegion.Height + 1, (int)PaintRegion.Width + 1);
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
interpolatedPointSet3D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, i), CoordinateTrans.YToMass(PaintRegion, pointSetRegion, j), Data[i, j]);
}
else
{
interpolatedPointSet3D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, i), CoordinateTrans.YToMass(PaintRegion, pointSetRegion, j), 0);
}
}
}
return interpolatedPointSet3D;
}
public MSPointSet BSpline2D(MSPointSet pointset2D, RegionSize pointSetRegion, RegionSize targetRegion, string type)
{
MSPointSet interpolatedPointSet = new MSPointSet();
int NoExist = pointset2D.Count;
int NoPoints = 0;
if (type == "horizontal")
{
NoPoints = (int)(targetRegion.Width);
}
if (type == "vertical")
{
NoPoints = (int)(targetRegion.Height);
}
int degree = 2;
float[] Tk = new float[NoExist];
float[,] point_exist = new float[NoExist, 2];
float[] Uk = new float[NoExist + degree + 1];
float[] sum = new float[NoExist];
float[,] Nk = new float[NoExist, NoExist];
float[,] P = new float[NoExist, 2];
float[] P_temp = new float[NoExist];
float[] points = new float[NoPoints + 1];
for (int i = 0; i < NoPoints; i++)
{
points[i] = -1;
}
for (int i = 0; i < pointset2D.Count; i++)
{
if (type == "horizontal")
{
points[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, targetRegion, pointset2D.X(i)))] = pointset2D.Y(i);
}
if (type == "vertical")
{
points[(int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, targetRegion, pointset2D.X(i)))] = pointset2D.Y(i);
}
}
if (NoExist <= 3)
{
for (int i = 0; i < NoPoints; i++)
{
if (points[i] == -1)
{
points[i] = 0;
}
}
}
else
{
int cnt = 0;
for (int i = 0; i < NoPoints; i++)
{
if (points[i] != -1)
{
point_exist[cnt, 0] = i;
point_exist[cnt, 1] = points[i];
cnt++;
}
}
sum[0] = 0;
for (int i = 1; i < NoExist; i++)
{
sum[i] = sum[i - 1] + (float)Math.Pow((Math.Abs(point_exist[i, 0] - point_exist[i - 1, 0]) * Math.Abs(point_exist[i - 1, 0] - point_exist[i, 0]) + Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1]) * Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1])), 0.5);
}
Tk[0] = 0;
for (int i = 1; i < NoExist; i++)
{
Tk[i] = sum[i] / sum[NoExist - 1];
}
for (int i = 0; i < NoExist + degree + 1; i++)
{
if (i <= degree)
{
Uk[i] = 0;
}
if (i > degree && i < NoExist)
{
Uk[i] = 0;
for (int j = i - degree; j < i; j++)
{
Uk[i] += Tk[j];
}
Uk[i] /= degree;
}
if (i >= NoExist)
{
Uk[i] = 1;
}
}
float[,] Temp = new float[NoExist, NoExist + 1];
for (int i = 0; i < NoExist; i++)
{
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, Tk[i], Uk);
for (int j = 0; j < NoExist; j++)
{
Nk[i, j] = Nk_temp[j];
}
}
for (int n = 0; n < 2; n++)
{
for (int i = 0; i < NoExist; i++)
{
for (int j = 0; j < NoExist; j++)
{
Temp[i, j] = Nk[i, j];
}
}
for (int i = 0; i < NoExist; i++)
{
Temp[i, NoExist] = point_exist[i, n];
P_temp[i] = 0;
}
Gaussian_eliminate(Temp, NoExist, ref P_temp);
for (int i = 0; i < NoExist; i++)
{
P[i, n] = P_temp[i];
}
}
int PredictNo = NoPoints * 10;
float[,] points_temp = new float[NoPoints, 2];
for (int i = 0; i < NoPoints; i++)
{
points_temp[i, 0] = 0;
points_temp[i, 1] = 0;
}
for (int i = 0; i < PredictNo; i++)
{
float temp_x = 0;
float temp_y = 0;
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, ((float)1 / PredictNo) * i, Uk);
for (int j = 0; j < NoExist; j++)
{
temp_x += Nk_temp[j] * P[j, 0];
temp_y += Nk_temp[j] * P[j, 1];
}
if (temp_x < 0)
{
temp_x = 0;
}
if (temp_y < 0)
{
temp_y = 0;
}
if ((int)Math.Round(temp_x) <= NoPoints - 1)
{
if (points[(int)Math.Round(temp_x)] == -1)
{
if (temp_y > points_temp[(int)Math.Round(temp_x), 0])
{
points_temp[(int)Math.Round(temp_x), 0] = temp_y;
}
}
}
}
points = linearInterpolation(points);
/*//use linear interpolation to prevent that the value was nonpredicted
bool again = false;
bool first = true;
int pivot_start = 0;
int pivot_end = 0;
float value_start = 0;
float value_end = 0;
do
{
again = false;
first = true;
for (int i = 0; i < NoPoints && again == false; i++)
{
if (points[i] == -1 && first == true)
{
if (i == 0)
{
points[i] = 0;
}
else
{
if (i == NoPoints - 1)
{
points[NoPoints - 1] = points[NoPoints - 2];
}
else
{
first = false;
pivot_start = i - 1;
value_start = points[i - 1];
}
}
}
if (points[i] != -1 && first == false)
{
pivot_end = i;
value_end = points[i];
points[(int)((pivot_start + pivot_end) / 2)] = (value_end + value_start) / 2;
again = true;
}
if (i == (NoPoints - 1) && first == false && again == false)
{
pivot_end = i;
value_end = 0;
points[(int)((pivot_start + pivot_end) / 2)] = (value_end + value_start) / 2;
again = true;
}
}
} while (again);*/
}
for (int i = 0; i < NoPoints; i++)
{
if (type == "horizontal")
{
interpolatedPointSet.Add(CoordinateTrans.XToTime(targetRegion, pointSetRegion, i), points[i]);
}
if (type == "vertical")
{
interpolatedPointSet.Add(CoordinateTrans.YToMass(targetRegion, pointSetRegion, i), points[i]);
}
}
return interpolatedPointSet;
}
public static float XToTime(RegionSize XRegion, RegionSize TimeRegion, float X)
{
float Time = TimeRegion.LeftBound + ((X - XRegion.LeftBound) * TimeRegion.Width / XRegion.Width);
return Time;
}
//public MSPointSet Resize(float width, float height)
//{
// MSPointSet mspoint = new MSPointSet();
// return mspoint;
//}
public void ImageDraw(Graphics g, RegionSize PictureBoxRegion)
{
if (PictureBoxRegion.Width * PictureBoxRegion.Height == 0)
{
//Message = "The data you selected aren't enough for drawing, please reselect again.";
return;
}
//Plot Size
X_start = 60;
Y_start = PictureBoxRegion.TopBound - 40;
X_end = PictureBoxRegion.RightBound - 150;
Y_end = 60;
X_max = MyCurrentPointSet3D.MaxXwWhiteBoarder;
X_min = MyCurrentPointSet3D.MinXwWhiteBoarder;
Y_max = MyCurrentPointSet3D.MaxYwWhiteBoarder;
Y_min = MyCurrentPointSet3D.MinYwWhiteBoarder;
Z_max = MyCurrentPointSet3D.MaxZ;
Z_min = MyCurrentPointSet3D.MinZ;
if (IsScaled)
{
Z_max = ScaleMax;
Z_min = ScaleMin;
}
point_size = Math.Min(PictureBoxRegion.Width / 300, PictureBoxRegion.Height / 300);
SolidBrush RedBrush = new SolidBrush(Color.Red);
SolidBrush BlackBrush = new SolidBrush(Color.Black);
Pen BlackPen = new Pen(Color.Black);
Pen RedPen = new Pen(Color.Red, 3);
Pen PrecursorPen = null;
if (IsGray)
{
PrecursorPen = new Pen(Color.FromArgb(90, 0, 0, 255));
}
if (IsColor)
{
PrecursorPen = new Pen(Color.Black);
}
Font font8Bold = new Font("Time New Roman", 8, FontStyle.Bold);
Font font8Regular = new Font("Time New Roman", 8, FontStyle.Regular);
//PrecursorL = (float)(Y_start - ((MyChargeQuant.MyCharge.LightReagent.MsChart.PrecursorMZ - Y_min) * Math.Abs(Y_end - Y_start) / (Y_max - Y_min)));
//PrecursorH = (float)(Y_start - ((MyChargeQuant.MyCharge.HeavyReagent.MsChart.PrecursorMZ - Y_min) * Math.Abs(Y_end - Y_start) / (Y_max - Y_min)));
int X_tag_number = 10;
int Y_tag_number = 10;
int color_shift = 20;
int Rc, Gc, Bc;
Rc = Bc = Gc = 0;
float[] X_tag = new float[X_tag_number];
float[] Y_tag = new float[Y_tag_number];
float[] X_co = new float[X_tag_number];
float[] Y_co = new float[Y_tag_number];
float[] Z_tag = new float[color_number];
g.DrawLine(BlackPen, X_start, Y_start, X_end, Y_start); //Draw X_axis
g.DrawLine(BlackPen, X_start, Y_start, X_start, Y_end); //Draw Y_axis
g.DrawString("Elution time (Min)", font8Regular, BlackBrush, X_end, (Y_start + 5)); //Draw Text(X_axis)
g.DrawString("m/z (Da)", font8Regular, BlackBrush, (X_start - 30), (Y_end - 20)); //Draw Text(X_axis)
g.DrawString("Intensity", font8Regular, BlackBrush, (X_end + 40), (Y_start - 50)); //Draw Text(X_axis)
g.DrawString(Convert.ToString((int)Z_max), font8Regular, BlackBrush, (X_end + 80), (Y_start - 55 - (color_number * point_size))); // Intensity Max
g.DrawString(Convert.ToString((int)Z_min), font8Regular, BlackBrush, (X_end + 80), (Y_start - 65)); // Intensity Min
// g.DrawString("Spectrum number: " + MyChargeQuant.MyCharge.MyPeptideIdentification.SpecNumber + ", " + MyChargeQuant.MyCharge.MyPeptideIdentification.ModifiedPeptideSequence, font8Regular, BlackBrush, 5, 5);
//g.DrawString("Charge state: +" + MyChargeQuant.MyCharge.ChargeNo, font8Regular, BlackBrush, 5, 20);
//Color Bar
for (int i = 0; i < color_number; i++)
{
if (IsGray)
{
Rc = color_number - 1 - i + color_shift;
Gc = color_number - 1 - i + color_shift;
Bc = color_number - 1 - i + color_shift;
}
if (IsColor)
{
Rc = palette[(color_number - 1 - i), 0];
Gc = palette[(color_number - 1 - i), 1];
Bc = palette[(color_number - 1 - i), 2];
}
SolidBrush peletteBrush = new SolidBrush(Color.FromArgb(Rc, Gc, Bc));
RectangleF Rt = new RectangleF(X_end + 60, (Y_start - 55 - (i * point_size)), 15, point_size);
g.FillRectangle(peletteBrush, Rt);
}
//X_axis number
for (int i = 0; i < X_tag_number; i++)
{
X_tag[i] = (float)Math.Round((X_min + (((X_max - X_min) / X_tag_number) * i)), 2);
X_co[i] = (float)(X_start + ((Math.Abs((X_end - X_start)) / X_tag_number) * i));
g.DrawString(Convert.ToString(X_tag[i]), font8Regular, BlackBrush, X_co[i] - 10, (Y_start + 15));//Draw Text(X_start)
}
//Y_axis number
for (int i = 0; i < Y_tag_number; i++)
{
Y_tag[i] = (float)Math.Round((Y_min + (((Y_max - Y_min) / Y_tag_number) * i)), 2);
Y_co[i] = (float)(Y_start - ((Math.Abs((Y_end - Y_start)) / Y_tag_number) * i));
g.DrawString(Convert.ToString(Y_tag[i]), font8Regular, BlackBrush, (X_start - 45), Y_co[i] - 10);
}
for (int i = 0; i < color_number; i++)
{
Z_tag[i] = (float)(Z_min + (((Z_max - Z_min) / color_number) * i));
}
if (renew_plot)
{
bitmap1 = new Bitmap((int)BmpRegion.RightBound + 1, (int)BmpRegion.TopBound + 1, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
int temp_z = 0;
Graphics bitmapG = Graphics.FromImage(bitmap1);
bitmapG.Clear(Color.White);
float temp_x, temp_y;
temp_x = temp_y = temp_z = 0;
RegionSize DataRegion = new RegionSize(MyCurrentPointSet3D.MinXwWhiteBoarder, MyCurrentPointSet3D.MaxXwWhiteBoarder, MyCurrentPointSet3D.MaxYwWhiteBoarder, MyCurrentPointSet3D.MinYwWhiteBoarder);
if (DataRegion.Width * DataRegion.Height == 0)
{
return;
}
//foreach (MSPoint3D p in MyCurrentPointSet3D.Points3D)
for (int x = 0; x < MyCurrentPointSet3D.Count; x++)
{
if (MyCurrentPointSet3D.Z(x) == -1)
{
Rc = 255;
Gc = 255;
Bc = 255;
}
else
{
for (int i = 0; i < color_number; i++)
{
if (MyCurrentPointSet3D.Z(x) >= Z_tag[i])
{
temp_z = i;
}
else
{
if (i == 0)
{
temp_z = 0;
}
break;
}
}
if (IsGray)
{
IsColor = false;
Rc = color_number - 1 - temp_z + color_shift;
Gc = color_number - 1 - temp_z + color_shift;
Bc = color_number - 1 - temp_z + color_shift;
}
if (IsColor)
{
Rc = palette[color_number - 1 - temp_z, 0];
Gc = palette[color_number - 1 - temp_z, 1];
Bc = palette[color_number - 1 - temp_z, 2];
}
}
bitmap1.SetPixel((int)Math.Round(CoordinateTrans.TimeToX(DataRegion, BmpRegion, MyCurrentPointSet3D.X(x))),
(int)BmpRegion.Height - (int)Math.Round(CoordinateTrans.MassToY(DataRegion, BmpRegion, MyCurrentPointSet3D.Y(x))),
Color.FromArgb(Rc, Gc, Bc));
renew_plot = false;
}
}
g.DrawImage(bitmap1, X_start + 1, Y_end, X_end - X_start, Y_start - Y_end);
for (int i = 0; i < X_tag_number; i++)
{
g.DrawLine(BlackPen, X_co[i], Y_start, X_co[i], Y_start - 5);
}
for (int i = 0; i < Y_tag_number; i++)
{
g.DrawLine(BlackPen, X_start, Y_co[i], X_start + 5, Y_co[i]);
}
//PrecursorPen.DashStyle = System.Drawing.Drawing2D.DashStyle.DashDotDot;
//g.DrawLine(PrecursorPen, X_start, PrecursorL, X_end, PrecursorL);
//g.DrawLine(PrecursorPen, X_start, PrecursorH, X_end, PrecursorH);
//SolidBrush Precursorbrush = new SolidBrush(Color.Red);
//Font font2 = new Font("Time New Roman", 8, FontStyle.Bold);
//g.DrawString("L: " + Math.Round(MyChargeQuant.MyCharge.LightReagent.MsChart.PrecursorMZ, 2)+" Da", font2, Precursorbrush, X_end + 5, PrecursorL - 10);
//g.DrawString("H: " + Math.Round(MyChargeQuant.MyCharge.HeavyReagent.MsChart.PrecursorMZ, 2)+" Da", font2, Precursorbrush, X_end + 5, PrecursorH - 10);
//if (MyChargeQuant.MyCharge.Heavy2Reagent != null)
//{
// g.DrawString("H: " + Math.Round(MyChargeQuant.MyCharge.Heavy2Reagent.MsChart.PrecursorMZ, 2) + " Da", font2, Precursorbrush, X_end + 5, MyChargeQuant.MyCharge.Heavy2Reagent.MsChart.PrecursorMZ - 10);
//}
//Pen TimePen = new Pen(Color.Red);
//SolidBrush brush3 = new SolidBrush(Color.Red);
//TimePen.DashStyle = System.Drawing.Drawing2D.DashStyle.DashDotDot;
//float Time = (float)(X_start + ((MyChargeQuant.MyCharge.MyPeptideIdentification.ElutionTime - X_min) * Math.Abs(X_end - X_start) / (X_max - X_min)));
//g.DrawLine(TimePen, Time, Y_start, Time, Y_end);
//g.DrawString("" + Math.Round(MyChargeQuant.MyCharge.MyPeptideIdentification.ElutionTime, 2), font2, brush3, Time - 5, Y_end-15);
//g.DrawString("Elution Time:", font2, brush3, Time-10, (Y_end - 25));
}
public MSPointSet BSpline2D(MSPointSet argPointset2D, RegionSize argPointSetRegion, RegionSize argTargetRegion)
{
MSPointSet interpolatedPointSet = new MSPointSet();
int NoExist = argPointset2D.Count;
int NoPoints = (int)(argTargetRegion.Width);
int degree = 2;
float[] Tk = new float[NoExist];
float[,] point_exist = new float[NoExist, 2];
float[] Uk = new float[NoExist + degree + 1];
float[] sum = new float[NoExist];
float[,] Nk = new float[NoExist, NoExist];
float[,] P = new float[NoExist, 2];
float[] P_temp = new float[NoExist];
float[] points = new float[NoPoints + 1];
for (int i = 0; i < NoPoints; i++)
{
points[i] = -1;
}
for (int i = 0; i < argPointset2D.Count; i++)
{
points[(int)Math.Round(CoordinateTrans.TimeToX(argPointSetRegion, argTargetRegion, argPointset2D.X(i)))] = argPointset2D.Y(i);
}
if (NoExist <= 3)
{
for (int i = 0; i < NoPoints; i++)
{
if (points[i] == -1)
{
points[i] = 0;
}
}
}
else
{
int cnt = 0;
for (int i = 0; i < NoPoints; i++)
{
if (points[i] != -1)
{
point_exist[cnt, 0] = i;
point_exist[cnt, 1] = points[i];
cnt++;
}
}
sum[0] = 0;
for (int i = 1; i < NoExist; i++)
{
sum[i] = sum[i - 1] + (float)Math.Pow((Math.Abs(point_exist[i, 0] - point_exist[i - 1, 0]) * Math.Abs(point_exist[i - 1, 0] - point_exist[i, 0]) + Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1]) * Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1])), 0.5);
}
Tk[0] = 0;
for (int i = 1; i < NoExist; i++)
{
Tk[i] = sum[i] / sum[NoExist - 1];
}
for (int i = 0; i < NoExist + degree + 1; i++)
{
if (i <= degree)
{
Uk[i] = 0;
}
if (i > degree && i < NoExist)
{
Uk[i] = 0;
for (int j = i - degree; j < i; j++)
{
Uk[i] += Tk[j];
}
Uk[i] /= degree;
}
if (i >= NoExist)
{
Uk[i] = 1;
}
}
float[,] Temp = new float[NoExist, NoExist + 1];
for (int i = 0; i < NoExist; i++)
{
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, Tk[i], Uk);
for (int j = 0; j < NoExist; j++)
{
Nk[i, j] = Nk_temp[j];
}
}
for (int n = 0; n < 2; n++)
{
for (int i = 0; i < NoExist; i++)
{
for (int j = 0; j < NoExist; j++)
{
Temp[i, j] = Nk[i, j];
}
}
for (int i = 0; i < NoExist; i++)
{
Temp[i, NoExist] = point_exist[i, n];
P_temp[i] = 0;
}
Gaussian_eliminate(Temp, NoExist, ref P_temp);
for (int i = 0; i < NoExist; i++)
{
P[i, n] = P_temp[i];
}
}
int PredictNo = NoPoints * 10;
float[,] points_temp = new float[NoPoints, 2];
for (int i = 0; i < NoPoints; i++)
{
points_temp[i, 0] = 0;
points_temp[i, 1] = 0;
}
for (int i = 0; i < PredictNo; i++)
{
float temp_x = 0;
float temp_y = 0;
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, ((float)1 / PredictNo) * i, Uk);
for (int j = 0; j < NoExist; j++)
{
temp_x += Nk_temp[j] * P[j, 0];
temp_y += Nk_temp[j] * P[j, 1];
}
if (temp_x < 0)
{
temp_x = 0;
}
if (temp_y < 0)
{
temp_y = 0;
}
if ((int)Math.Round(temp_x) <= NoPoints - 1)
{
if (points[(int)Math.Round(temp_x)] == -1)
{
if (temp_y > points_temp[(int)Math.Round(temp_x), 0])
{
points_temp[(int)Math.Round(temp_x), 0] = temp_y;
}
}
}
}
points = linearInterpolation(points);
}
for (int i = 0; i < NoPoints; i++)
{
interpolatedPointSet.Add(CoordinateTrans.XToTime(argTargetRegion, argPointSetRegion, i), points[i]);
}
return(interpolatedPointSet);
}
public static float TimeToX(RegionSize TimeRegion, RegionSize XRegion, float Time)
{
float X = XRegion.LeftBound + ((Time - TimeRegion.LeftBound) * XRegion.Width / TimeRegion.Width);
return(X);
}
public void GetSubPointSet(RegionSize SR)
{
if (SubPointSetExtract(SR).Count == 0)
{
return;
}
MyCurrentPointSet3D = SubPointSetExtract(SR);
//MyOriginalPointSet3D = MyCurrentPointSet3D;
NoPoints = MyCurrentPointSet3D.Count;
}
public static float YToMass(RegionSize YRegion, RegionSize MassRegion, float Y)
{
float Mass = MassRegion.BottomBound + ((Y - YRegion.BottomBound) * MassRegion.Height / YRegion.Height);
return(Mass);
}
public static float XToTime(RegionSize XRegion, RegionSize TimeRegion, float X)
{
float Time = TimeRegion.LeftBound + ((X - XRegion.LeftBound) * TimeRegion.Width / XRegion.Width);
return(Time);
}
public static float MassToY(RegionSize MassRegion, RegionSize YRegion, float Mass)
{
float Y = YRegion.BottomBound + ((Mass - MassRegion.BottomBound) * YRegion.Height / MassRegion.Height);
return(Y);
}
public MSPointSet3D SubPointSetExtract(RegionSize SR)
{
MSPointSet3D tempPointSet = new MSPointSet3D();
//foreach (MSPoint3D D in MyCurrentPointSet3D.)
for (int i = 0; i < RawDataPointSet3D.Count; i++)
{
if (RawDataPointSet3D._x[i] >= SR.LeftBound && RawDataPointSet3D._x[i] <= SR.RightBound && RawDataPointSet3D._y[i] <= SR.TopBound && RawDataPointSet3D._y[i] >= SR.BottomBound)
{
tempPointSet.Add(RawDataPointSet3D._x[i], RawDataPointSet3D._y[i], RawDataPointSet3D.Z(i));
}
}
return tempPointSet;
}
public MSPointSet BSpline2D(MSPointSet pointset2D, RegionSize pointSetRegion, RegionSize targetRegion, string type)
{
MSPointSet interpolatedPointSet = new MSPointSet();
int NoExist = pointset2D.Count;
int NoPoints = 0;
if (type == "horizontal")
{
NoPoints = (int)(targetRegion.Width);
}
if (type == "vertical")
{
NoPoints = (int)(targetRegion.Height);
}
int degree = 2;
float[] Tk = new float[NoExist];
float[,] point_exist = new float[NoExist, 2];
float[] Uk = new float[NoExist + degree + 1];
float[] sum = new float[NoExist];
float[,] Nk = new float[NoExist, NoExist];
float[,] P = new float[NoExist, 2];
float[] P_temp = new float[NoExist];
float[] points = new float[NoPoints + 1];
for (int i = 0; i < NoPoints; i++)
{
points[i] = -1;
}
for (int i = 0; i < pointset2D.Count; i++)
{
if (type == "horizontal")
{
points[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, targetRegion, pointset2D.X(i)))] = pointset2D.Y(i);
}
if (type == "vertical")
{
points[(int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, targetRegion, pointset2D.X(i)))] = pointset2D.Y(i);
}
}
if (NoExist <= 3)
{
for (int i = 0; i < NoPoints; i++)
{
if (points[i] == -1)
{
points[i] = 0;
}
}
}
else
{
int cnt = 0;
for (int i = 0; i < NoPoints; i++)
{
if (points[i] != -1)
{
point_exist[cnt, 0] = i;
point_exist[cnt, 1] = points[i];
cnt++;
}
}
sum[0] = 0;
for (int i = 1; i < NoExist; i++)
{
sum[i] = sum[i - 1] + (float)Math.Pow((Math.Abs(point_exist[i, 0] - point_exist[i - 1, 0]) * Math.Abs(point_exist[i - 1, 0] - point_exist[i, 0]) + Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1]) * Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1])), 0.5);
}
Tk[0] = 0;
for (int i = 1; i < NoExist; i++)
{
Tk[i] = sum[i] / sum[NoExist - 1];
}
for (int i = 0; i < NoExist + degree + 1; i++)
{
if (i <= degree)
{
Uk[i] = 0;
}
if (i > degree && i < NoExist)
{
Uk[i] = 0;
for (int j = i - degree; j < i; j++)
{
Uk[i] += Tk[j];
}
Uk[i] /= degree;
}
if (i >= NoExist)
{
Uk[i] = 1;
}
}
float[,] Temp = new float[NoExist, NoExist + 1];
for (int i = 0; i < NoExist; i++)
{
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, Tk[i], Uk);
for (int j = 0; j < NoExist; j++)
{
Nk[i, j] = Nk_temp[j];
}
}
for (int n = 0; n < 2; n++)
{
for (int i = 0; i < NoExist; i++)
{
for (int j = 0; j < NoExist; j++)
{
Temp[i, j] = Nk[i, j];
}
}
for (int i = 0; i < NoExist; i++)
{
Temp[i, NoExist] = point_exist[i, n];
P_temp[i] = 0;
}
Gaussian_eliminate(Temp, NoExist, ref P_temp);
for (int i = 0; i < NoExist; i++)
{
P[i, n] = P_temp[i];
}
}
int PredictNo = NoPoints * 10;
float[,] points_temp = new float[NoPoints, 2];
for (int i = 0; i < NoPoints; i++)
{
points_temp[i, 0] = 0;
points_temp[i, 1] = 0;
}
for (int i = 0; i < PredictNo; i++)
{
float temp_x = 0;
float temp_y = 0;
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, ((float)1 / PredictNo) * i, Uk);
for (int j = 0; j < NoExist; j++)
{
temp_x += Nk_temp[j] * P[j, 0];
temp_y += Nk_temp[j] * P[j, 1];
}
if (temp_x < 0)
{
temp_x = 0;
}
if (temp_y < 0)
{
temp_y = 0;
}
if ((int)Math.Round(temp_x) <= NoPoints - 1)
{
if (points[(int)Math.Round(temp_x)] == -1)
{
if (temp_y > points_temp[(int)Math.Round(temp_x), 0])
{
points_temp[(int)Math.Round(temp_x), 0] = temp_y;
}
}
}
}
points = linearInterpolation(points);
/*//use linear interpolation to prevent that the value was nonpredicted
* bool again = false;
* bool first = true;
* int pivot_start = 0;
* int pivot_end = 0;
* float value_start = 0;
* float value_end = 0;
* do
* {
* again = false;
* first = true;
* for (int i = 0; i < NoPoints && again == false; i++)
* {
* if (points[i] == -1 && first == true)
* {
* if (i == 0)
* {
* points[i] = 0;
* }
* else
* {
* if (i == NoPoints - 1)
* {
* points[NoPoints - 1] = points[NoPoints - 2];
* }
* else
* {
*
* first = false;
* pivot_start = i - 1;
* value_start = points[i - 1];
* }
*
* }
* }
* if (points[i] != -1 && first == false)
* {
* pivot_end = i;
* value_end = points[i];
* points[(int)((pivot_start + pivot_end) / 2)] = (value_end + value_start) / 2;
* again = true;
* }
* if (i == (NoPoints - 1) && first == false && again == false)
* {
* pivot_end = i;
* value_end = 0;
* points[(int)((pivot_start + pivot_end) / 2)] = (value_end + value_start) / 2;
* again = true;
* }
* }
*
* } while (again);*/
}
for (int i = 0; i < NoPoints; i++)
{
if (type == "horizontal")
{
interpolatedPointSet.Add(CoordinateTrans.XToTime(targetRegion, pointSetRegion, i), points[i]);
}
if (type == "vertical")
{
interpolatedPointSet.Add(CoordinateTrans.YToMass(targetRegion, pointSetRegion, i), points[i]);
}
}
return(interpolatedPointSet);
}
public static float YToMass(RegionSize YRegion, RegionSize MassRegion, float Y)
{
float Mass = MassRegion.BottomBound + ((Y - YRegion.BottomBound) * MassRegion.Height / YRegion.Height);
return Mass;
}
public void SaveImageOnlyData(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format)
{
bitmap1.Save(filename, format);
}
//public MSPointSet Resize(float width, float height)
//{
// MSPointSet mspoint = new MSPointSet();
// return mspoint;
//}
public void ImageDraw(Graphics g, RegionSize PictureBoxRegion)
{
if(PictureBoxRegion.Width*PictureBoxRegion.Height==0)
{
//Message = "The data you selected aren't enough for drawing, please reselect again.";
return;
}
//Plot Size
X_start = 60;
Y_start = PictureBoxRegion.TopBound - 40;
X_end = PictureBoxRegion.RightBound - 150;
Y_end = 60;
X_max = MyCurrentPointSet3D.MaxXwWhiteBoarder;
X_min = MyCurrentPointSet3D.MinXwWhiteBoarder;
Y_max = MyCurrentPointSet3D.MaxYwWhiteBoarder;
Y_min = MyCurrentPointSet3D.MinYwWhiteBoarder;
Z_max = MyCurrentPointSet3D.MaxZ;
Z_min = MyCurrentPointSet3D.MinZ;
if (IsScaled)
{
Z_max = ScaleMax;
Z_min = ScaleMin;
}
point_size = Math.Min(PictureBoxRegion.Width / 300, PictureBoxRegion.Height / 300);
SolidBrush RedBrush = new SolidBrush(Color.Red);
SolidBrush BlackBrush = new SolidBrush(Color.Black);
Pen BlackPen = new Pen(Color.Black);
Pen RedPen = new Pen(Color.Red, 3);
Pen PrecursorPen = null;
if(IsGray)
{
PrecursorPen = new Pen(Color.FromArgb(90, 0, 0, 255));
}
if(IsColor)
{
PrecursorPen = new Pen(Color.Black);
}
Font font8Bold = new Font("Time New Roman", 8, FontStyle.Bold);
Font font8Regular = new Font("Time New Roman", 8, FontStyle.Regular);
//PrecursorL = (float)(Y_start - ((MyChargeQuant.MyCharge.LightReagent.MsChart.PrecursorMZ - Y_min) * Math.Abs(Y_end - Y_start) / (Y_max - Y_min)));
//PrecursorH = (float)(Y_start - ((MyChargeQuant.MyCharge.HeavyReagent.MsChart.PrecursorMZ - Y_min) * Math.Abs(Y_end - Y_start) / (Y_max - Y_min)));
int X_tag_number = 10;
int Y_tag_number = 10;
int color_shift = 20;
int Rc, Gc, Bc;
Rc = Bc = Gc = 0;
float[] X_tag = new float[X_tag_number];
float[] Y_tag = new float[Y_tag_number];
float[] X_co = new float[X_tag_number];
float[] Y_co = new float[Y_tag_number];
float[] Z_tag = new float[color_number];
g.DrawLine(BlackPen, X_start, Y_start, X_end, Y_start);//Draw X_axis
g.DrawLine(BlackPen, X_start, Y_start, X_start, Y_end);//Draw Y_axis
g.DrawString("Elution time (Min)", font8Regular, BlackBrush, X_end, (Y_start + 5));//Draw Text(X_axis)
g.DrawString("m/z (Da)", font8Regular, BlackBrush, (X_start - 30), (Y_end - 20));//Draw Text(X_axis)
g.DrawString("Intensity", font8Regular, BlackBrush, (X_end + 40), (Y_start - 50));//Draw Text(X_axis)
g.DrawString(Convert.ToString((int)Z_max), font8Regular, BlackBrush, (X_end + 80), (Y_start - 55 - (color_number * point_size))); // Intensity Max
g.DrawString(Convert.ToString((int)Z_min), font8Regular, BlackBrush, (X_end + 80), (Y_start - 65)); // Intensity Min
// g.DrawString("Spectrum number: " + MyChargeQuant.MyCharge.MyPeptideIdentification.SpecNumber + ", " + MyChargeQuant.MyCharge.MyPeptideIdentification.ModifiedPeptideSequence, font8Regular, BlackBrush, 5, 5);
//g.DrawString("Charge state: +" + MyChargeQuant.MyCharge.ChargeNo, font8Regular, BlackBrush, 5, 20);
//Color Bar
for (int i = 0; i < color_number; i++)
{
if (IsGray)
{
Rc = color_number - 1 - i + color_shift;
Gc = color_number - 1 - i + color_shift;
Bc = color_number - 1 - i + color_shift;
}
if (IsColor)
{
Rc = palette[(color_number - 1 - i), 0];
Gc = palette[(color_number - 1 - i), 1];
Bc = palette[(color_number - 1 - i), 2];
}
SolidBrush peletteBrush = new SolidBrush(Color.FromArgb(Rc, Gc, Bc));
RectangleF Rt = new RectangleF(X_end + 60, (Y_start - 55 - (i * point_size)), 15, point_size);
g.FillRectangle(peletteBrush, Rt);
}
//X_axis number
for (int i = 0; i < X_tag_number; i++)
{
X_tag[i] = (float)Math.Round((X_min + (((X_max - X_min) / X_tag_number) * i)), 2);
X_co[i] = (float)(X_start + ((Math.Abs((X_end - X_start)) / X_tag_number) * i));
g.DrawString(Convert.ToString(X_tag[i]), font8Regular, BlackBrush, X_co[i] - 10, (Y_start + 15));//Draw Text(X_start)
}
//Y_axis number
for (int i = 0; i < Y_tag_number; i++)
{
Y_tag[i] = (float)Math.Round((Y_min + (((Y_max - Y_min) / Y_tag_number) * i)), 2);
Y_co[i] = (float)(Y_start - ((Math.Abs((Y_end - Y_start)) / Y_tag_number) * i));
g.DrawString(Convert.ToString(Y_tag[i]), font8Regular, BlackBrush, (X_start - 45), Y_co[i] - 10);
}
for (int i = 0; i < color_number; i++)
{
Z_tag[i] = (float)(Z_min + (((Z_max - Z_min) / color_number) * i));
}
if (renew_plot)
{
bitmap1 = new Bitmap((int)BmpRegion.RightBound + 1, (int)BmpRegion.TopBound + 1, System.Drawing.Imaging.PixelFormat.Format24bppRgb);
int temp_z = 0;
Graphics bitmapG = Graphics.FromImage(bitmap1);
bitmapG.Clear(Color.White);
float temp_x, temp_y;
temp_x = temp_y = temp_z = 0;
RegionSize DataRegion = new RegionSize(MyCurrentPointSet3D.MinXwWhiteBoarder, MyCurrentPointSet3D.MaxXwWhiteBoarder, MyCurrentPointSet3D.MaxYwWhiteBoarder, MyCurrentPointSet3D.MinYwWhiteBoarder);
if (DataRegion.Width * DataRegion.Height == 0)
{
return;
}
//foreach (MSPoint3D p in MyCurrentPointSet3D.Points3D)
for (int x = 0; x < MyCurrentPointSet3D.Count; x++)
{
if (MyCurrentPointSet3D.Z(x) == -1)
{
Rc = 255;
Gc = 255;
Bc = 255;
}
else
{
for (int i = 0; i < color_number; i++)
{
if (MyCurrentPointSet3D.Z(x) >= Z_tag[i])
{
temp_z = i;
}
else
{
if (i == 0)
{
temp_z = 0;
}
break;
}
}
if (IsGray)
{
IsColor = false;
Rc = color_number - 1 - temp_z + color_shift;
Gc = color_number - 1 - temp_z + color_shift;
Bc = color_number - 1 - temp_z + color_shift;
}
if (IsColor)
{
Rc = palette[color_number - 1 - temp_z, 0];
Gc = palette[color_number - 1 - temp_z, 1];
Bc = palette[color_number - 1 - temp_z, 2];
}
}
bitmap1.SetPixel((int)Math.Round(CoordinateTrans.TimeToX(DataRegion, BmpRegion, MyCurrentPointSet3D.X(x))),
(int)BmpRegion.Height - (int)Math.Round(CoordinateTrans.MassToY(DataRegion, BmpRegion, MyCurrentPointSet3D.Y(x))),
Color.FromArgb(Rc, Gc, Bc));
renew_plot = false;
}
}
g.DrawImage(bitmap1, X_start+1, Y_end, X_end - X_start, Y_start - Y_end);
for (int i = 0; i < X_tag_number; i++)
{
g.DrawLine(BlackPen, X_co[i], Y_start, X_co[i], Y_start - 5);
}
for (int i = 0; i < Y_tag_number; i++)
{
g.DrawLine(BlackPen, X_start, Y_co[i], X_start + 5, Y_co[i]);
}
//PrecursorPen.DashStyle = System.Drawing.Drawing2D.DashStyle.DashDotDot;
//g.DrawLine(PrecursorPen, X_start, PrecursorL, X_end, PrecursorL);
//g.DrawLine(PrecursorPen, X_start, PrecursorH, X_end, PrecursorH);
//SolidBrush Precursorbrush = new SolidBrush(Color.Red);
//Font font2 = new Font("Time New Roman", 8, FontStyle.Bold);
//g.DrawString("L: " + Math.Round(MyChargeQuant.MyCharge.LightReagent.MsChart.PrecursorMZ, 2)+" Da", font2, Precursorbrush, X_end + 5, PrecursorL - 10);
//g.DrawString("H: " + Math.Round(MyChargeQuant.MyCharge.HeavyReagent.MsChart.PrecursorMZ, 2)+" Da", font2, Precursorbrush, X_end + 5, PrecursorH - 10);
//if (MyChargeQuant.MyCharge.Heavy2Reagent != null)
//{
// g.DrawString("H: " + Math.Round(MyChargeQuant.MyCharge.Heavy2Reagent.MsChart.PrecursorMZ, 2) + " Da", font2, Precursorbrush, X_end + 5, MyChargeQuant.MyCharge.Heavy2Reagent.MsChart.PrecursorMZ - 10);
//}
//Pen TimePen = new Pen(Color.Red);
//SolidBrush brush3 = new SolidBrush(Color.Red);
//TimePen.DashStyle = System.Drawing.Drawing2D.DashStyle.DashDotDot;
//float Time = (float)(X_start + ((MyChargeQuant.MyCharge.MyPeptideIdentification.ElutionTime - X_min) * Math.Abs(X_end - X_start) / (X_max - X_min)));
//g.DrawLine(TimePen, Time, Y_start, Time, Y_end);
//g.DrawString("" + Math.Round(MyChargeQuant.MyCharge.MyPeptideIdentification.ElutionTime, 2), font2, brush3, Time - 5, Y_end-15);
//g.DrawString("Elution Time:", font2, brush3, Time-10, (Y_end - 25));
}
public MSPointSet3D BSpline3DofPepImage(MSPointSet3D mspointset, RegionSize PaintRegion)
{
MSPointSet3D interpolatedPointSet3D = new MSPointSet3D();
RegionSize pointSetRegion = new RegionSize(mspointset.MinX, mspointset.MaxX, mspointset.MaxY, mspointset.MinY);
if (pointSetRegion.Width * pointSetRegion.Height * PaintRegion.Width * PaintRegion.Height == 0)
{
return(mspointset);
}
float[,] Data;
Data = MSpointSet3DToArray(mspointset, PaintRegion);
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
MSPointSet pointset2D = new MSPointSet();
float MaxIntensity = -1;
bool empty = true;
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
empty = false;
if (Data[i, j] > MaxIntensity)
{
MaxIntensity = Data[i, j];
}
}
}
if (empty == false)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] == -1)
{
Data[i, j] = 0;
}
}
}
}
for (int i = 0; i < (int)PaintRegion.Height + 1; i++)
{
MSPointSet pointset2D = new MSPointSet();
float MaxIntensity = 0;
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] > MaxIntensity)
{
MaxIntensity = Data[j, i];
}
}
if (MaxIntensity > 0 /*mspointset.MaxZ/1*/)
{
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] != -1)
{
pointset2D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, j), Data[j, i]);
}
}
pointset2D = BSpline2D(pointset2D, pointSetRegion, PaintRegion, "horizontal");
for (int x = 0; x < pointset2D.Count; x++)
{
if (Data[(int)Math.Round((CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, pointset2D.X(x)))), i] == -1)
{
Data[(int)Math.Round((CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, pointset2D.X(x)))), i] = pointset2D.Y(x);
}
}
}
else
{
for (int j = 0; j < (int)PaintRegion.Width + 1; j++)
{
if (Data[j, i] == -1)
{
Data[j, i] = 0;
}
}
}
}
Data = NoiseFiltering(Data, (int)PaintRegion.Height + 1, (int)PaintRegion.Width + 1);
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
interpolatedPointSet3D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, i), CoordinateTrans.YToMass(PaintRegion, pointSetRegion, j), Data[i, j]);
}
else
{
interpolatedPointSet3D.Add(CoordinateTrans.XToTime(PaintRegion, pointSetRegion, i), CoordinateTrans.YToMass(PaintRegion, pointSetRegion, j), 0);
}
}
}
return(interpolatedPointSet3D);
}
public void initialize()
{
MyCurrentPointSet3D = RawDataPointSet3D;
MyOriginalPointSet3D = RawDataPointSet3D;
NoPoints = MyCurrentPointSet3D.Count;
IsSmoothed = false;
renew_plot = true;
ScaleSize = 1;
BmpRegion = new RegionSize(0, 300, 200, 0);
}
public void SaveImage(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format, PixelFormat pixelFormat)
{
Bitmap bmp = new Bitmap(Convert.ToInt32(size.Width), Convert.ToInt32(size.Height), pixelFormat);
Graphics g = Graphics.FromImage(bmp);
g.Clear(Color.White);
this.ImageDraw(g, size);
bmp.Save(filename, format);
bmp.Dispose();
g.Dispose();
}
public void SmoothAndSave(string filename, RegionSize size)
{
SmoothAndSave(filename, size, System.Drawing.Imaging.ImageFormat.Tiff, PixelFormat.Format4bppIndexed);
}
public void SaveImage(string filename, RegionSize size)
{
SaveImage(filename, size, System.Drawing.Imaging.ImageFormat.Tiff, PixelFormat.Format16bppRgb555);
}
public void SaveImage(string filename, RegionSize size)
{
SaveImage(filename, size, System.Drawing.Imaging.ImageFormat.Tiff, PixelFormat.Format16bppRgb555);
}
public void SaveImageOnlyData(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format)
{
bitmap1.Save(filename, format);
}
public void SaveImageOnlyData(string filename, RegionSize size)
{
SaveImageOnlyData(filename, size, System.Drawing.Imaging.ImageFormat.Tiff);
}
public void SaveImageOnlyData(string filename, RegionSize size)
{
SaveImageOnlyData(filename, size, System.Drawing.Imaging.ImageFormat.Tiff);
}
public MSPointSet BSpline2D(MSPointSet argPointset2D, RegionSize argPointSetRegion, RegionSize argTargetRegion)
{
MSPointSet interpolatedPointSet = new MSPointSet();
int NoExist = argPointset2D.Count;
int NoPoints = (int)(argTargetRegion.Width);
int degree = 2;
float[] Tk = new float[NoExist];
float[,] point_exist = new float[NoExist, 2];
float[] Uk = new float[NoExist + degree + 1];
float[] sum = new float[NoExist];
float[,] Nk = new float[NoExist, NoExist];
float[,] P = new float[NoExist, 2];
float[] P_temp = new float[NoExist];
float[] points = new float[NoPoints + 1];
for (int i = 0; i < NoPoints; i++)
{
points[i] = -1;
}
for (int i = 0; i < argPointset2D.Count; i++)
{
points[(int)Math.Round(CoordinateTrans.TimeToX(argPointSetRegion, argTargetRegion, argPointset2D.X(i)))] = argPointset2D.Y(i);
}
if (NoExist <= 3)
{
for (int i = 0; i < NoPoints; i++)
{
if (points[i] == -1)
{
points[i] = 0;
}
}
}
else
{
int cnt = 0;
for (int i = 0; i < NoPoints; i++)
{
if (points[i] != -1)
{
point_exist[cnt, 0] = i;
point_exist[cnt, 1] = points[i];
cnt++;
}
}
sum[0] = 0;
for (int i = 1; i < NoExist; i++)
{
sum[i] = sum[i - 1] + (float)Math.Pow((Math.Abs(point_exist[i, 0] - point_exist[i - 1, 0]) * Math.Abs(point_exist[i - 1, 0] - point_exist[i, 0]) + Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1]) * Math.Abs(point_exist[i - 1, 1] - point_exist[i, 1])), 0.5);
}
Tk[0] = 0;
for (int i = 1; i < NoExist; i++)
{
Tk[i] = sum[i] / sum[NoExist - 1];
}
for (int i = 0; i < NoExist + degree + 1; i++)
{
if (i <= degree)
{
Uk[i] = 0;
}
if (i > degree && i < NoExist)
{
Uk[i] = 0;
for (int j = i - degree; j < i; j++)
{
Uk[i] += Tk[j];
}
Uk[i] /= degree;
}
if (i >= NoExist)
{
Uk[i] = 1;
}
}
float[,] Temp = new float[NoExist, NoExist + 1];
for (int i = 0; i < NoExist; i++)
{
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, Tk[i], Uk);
for (int j = 0; j < NoExist; j++)
{
Nk[i, j] = Nk_temp[j];
}
}
for (int n = 0; n < 2; n++)
{
for (int i = 0; i < NoExist; i++)
{
for (int j = 0; j < NoExist; j++)
{
Temp[i, j] = Nk[i, j];
}
}
for (int i = 0; i < NoExist; i++)
{
Temp[i, NoExist] = point_exist[i, n];
P_temp[i] = 0;
}
Gaussian_eliminate(Temp, NoExist, ref P_temp);
for (int i = 0; i < NoExist; i++)
{
P[i, n] = P_temp[i];
}
}
int PredictNo = NoPoints * 10;
float[,] points_temp = new float[NoPoints, 2];
for (int i = 0; i < NoPoints; i++)
{
points_temp[i, 0] = 0;
points_temp[i, 1] = 0;
}
for (int i = 0; i < PredictNo; i++)
{
float temp_x = 0;
float temp_y = 0;
float[] Nk_temp = new float[NoExist];
for (int j = 0; j < NoExist; j++)
{
Nk_temp[j] = 0;
}
Compute_Nk_fast(Nk_temp, NoExist, degree, ((float)1 / PredictNo) * i, Uk);
for (int j = 0; j < NoExist; j++)
{
temp_x += Nk_temp[j] * P[j, 0];
temp_y += Nk_temp[j] * P[j, 1];
}
if (temp_x < 0)
{
temp_x = 0;
}
if (temp_y < 0)
{
temp_y = 0;
}
if ((int)Math.Round(temp_x) <= NoPoints - 1)
{
if (points[(int)Math.Round(temp_x)] == -1)
{
if (temp_y > points_temp[(int)Math.Round(temp_x), 0])
{
points_temp[(int)Math.Round(temp_x), 0] = temp_y;
}
}
}
}
points = linearInterpolation(points);
}
for (int i = 0; i < NoPoints; i++)
{
interpolatedPointSet.Add(CoordinateTrans.XToTime(argTargetRegion, argPointSetRegion, i), points[i]);
}
return interpolatedPointSet;
}
public void SmoothAndSave(string filename, RegionSize size, System.Drawing.Imaging.ImageFormat format, PixelFormat pixelFormat)
{
BSpline bs=new BSpline();
MyCurrentPointSet3D = bs.BSpline3DofPepImage(MyOriginalPointSet3D, BmpRegion);
SaveImage(filename, size, format, pixelFormat);
}
private float[,] MSpointSet3DToArray(MSPointSet3D mspointset, RegionSize PaintRegion)
{
RegionSize pointSetRegion = new RegionSize(mspointset.MinX, mspointset.MaxX, mspointset.MaxY, mspointset.MinY);
float[,] Data = new float[(int)PaintRegion.Width + 1, (int)PaintRegion.Height + 1];
int[,] DataCount = new int[(int)PaintRegion.Width + 1, (int)PaintRegion.Height + 1];
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
Data[i, j] = -1;
DataCount[i, j] = 0;
}
}
//foreach (MSPoint3D point3D in mspointset.Points3D)
for (int i = 0; i < mspointset.Count; i++)
{
if (DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] == 0)
{
Data[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] = mspointset.Z(i);
DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))]++;
}
else
{
Data[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))] += mspointset.Z(i);
DataCount[(int)Math.Round(CoordinateTrans.TimeToX(pointSetRegion, PaintRegion, mspointset.X(i))), (int)Math.Round(CoordinateTrans.MassToY(pointSetRegion, PaintRegion, mspointset.Y(i)))]++;
}
}
for (int i = 0; i < (int)PaintRegion.Width + 1; i++)
{
for (int j = 0; j < (int)PaintRegion.Height + 1; j++)
{
if (Data[i, j] != -1)
{
Data[i, j] = Data[i, j] / DataCount[i, j];
}
}
}
return Data;
}
public static float MassToY(RegionSize MassRegion, RegionSize YRegion, float Mass)
{
float Y = YRegion.BottomBound + ((Mass - MassRegion.BottomBound) * YRegion.Height / MassRegion.Height);
return Y;
}
