public cWell(cDescriptor Desc, int Col, int Row, cScreening screenParent, cPlate CurrentPlate)
{
this.Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
this.ListDescriptors = new List<cDescriptor>();
this.ListDescriptors.Add(Desc);
this.PosX = Col;
this.PosY = Row;
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
}
public cWell(string FileName, cScreening screenParent, cPlate CurrentPlate)
{
this.Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
StreamReader sr = new StreamReader(FileName);
int Idx;
string NewLine;
string TmpLine;
string line;
// we have to build the descriptor list
if (screenParent.ListDescriptors.Count == 0)
{
Idx = FileName.LastIndexOf("\\");
NewLine = FileName.Remove(0, Idx + 1);
TmpLine = NewLine;
Idx = TmpLine.IndexOf("x");
NewLine = TmpLine.Remove(Idx);
if (!int.TryParse(NewLine, out this.PosX))
{
MessageBox.Show("Error in load the current file.\n", "Loading error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
sr.Close();
return;
}
NewLine = TmpLine.Remove(0, Idx + 1);
Idx = NewLine.IndexOf(".");
TmpLine = NewLine.Remove(Idx);
this.PosY = Convert.ToInt16(TmpLine);
line = sr.ReadLine();
while (line != null)
{
if (line != null)
{
Idx = line.IndexOf("\t");
string DescName = line.Remove(Idx);
List<double> readData = new List<double>();
NewLine = line.Remove(0, Idx + 1);
line = NewLine;
Idx = line.IndexOf("\t");
int NumValue = 0;
while (Idx > 0)
{
string DescValue = line.Remove(Idx);
double CurrentValue = Convert.ToDouble(DescValue);
readData.Add(CurrentValue);
NewLine = line.Remove(0, Idx + 1);
line = NewLine;
Idx = line.IndexOf("\t");
NumValue++;
}
if (line.Length > 0)
{
double Value = Convert.ToDouble(line);
readData.Add(Value);
}
// first check if the descriptor exist
screenParent.ListDescriptors.AddNew(new cDescriptorsType(DescName, true, NumValue));
}
line = sr.ReadLine();
}
sr.Close();
}
this.ListDescriptors = new List<cDescriptor>();
sr = new StreamReader(FileName);
Idx = FileName.LastIndexOf("\\");
NewLine = FileName.Remove(0, Idx + 1);
TmpLine = NewLine;
Idx = TmpLine.IndexOf("x");
NewLine = TmpLine.Remove(Idx);
this.PosX = Convert.ToInt16(NewLine);
NewLine = TmpLine.Remove(0, Idx + 1);
Idx = NewLine.IndexOf(".");
TmpLine = NewLine.Remove(Idx);
this.PosY = Convert.ToInt16(TmpLine);
line = sr.ReadLine();
int IDxLine = 0;
while (line != null)
{
if (line != null)
{
Idx = line.IndexOf("\t");
string DescName = line.Remove(Idx);
List<double> readData = new List<double>();
NewLine = line.Remove(0, Idx + 1);
line = NewLine;
Idx = line.IndexOf("\t");
while (Idx > 0)
{
string DescValue = line.Remove(Idx);
double CurrentValue = Convert.ToDouble(DescValue);
readData.Add(CurrentValue);
NewLine = line.Remove(0, Idx + 1);
line = NewLine;
Idx = line.IndexOf("\t");
}
if (line.Length > 0)
{
double Value = Convert.ToDouble(line);
readData.Add(Value);
}
cDescriptor CurrentDesc = new cDescriptor(readData.ToArray(), 0, screenParent.ListDescriptors[IDxLine].GetBinNumber() - 1, screenParent.ListDescriptors[IDxLine], this.Parent/* DescName*/);
this.ListDescriptors.Add(CurrentDesc);
}
line = sr.ReadLine();
IDxLine++;
}
sr.Close();
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
return;
}
private void AddCorrelatedSquareDescItem(object sender, EventArgs e)
{
cDescriptorsType ColumnType = new cDescriptorsType("Square(" + CompleteScreening.ListDescriptors[IntToTransfer].GetName() + ")", true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
cDescriptor NewDesc = new cDescriptor(Math.Pow(Tmpwell.ListDescriptors[IntToTransfer].GetValue(), 2), ColumnType, CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void AverageDescItem(object sender, EventArgs e)
{
//int NumBin = CompleteScreening.ListDescriptors[IntToTransfer].GetBinNumber();
// first we update the descriptor
cDescriptorsType NewAverageType = new cDescriptorsType("Average(" + CompleteScreening.ListDescriptors[IntToTransfer].GetName() + ")", true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(NewAverageType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
cDescriptor NewDesc = new cDescriptor(Tmpwell.ListDescriptors[IntToTransfer].Histogram.GetAverageValue(), NewAverageType, CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void SplitDescItem(object sender, EventArgs e)
{
int NumBin = CompleteScreening.ListDescriptors[IntToTransfer].GetBinNumber();
// first we update the descriptor
for (int i = 0; i < NumBin; i++)
CompleteScreening.ListDescriptors.AddNew(new cDescriptorsType(CompleteScreening.ListDescriptors[IntToTransfer].GetName() + "_" + i, true, 1, GlobalInfo));
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int i = 0; i < NumBin; i++)
{
cDescriptor NewDesc = new cDescriptor(Tmpwell.ListDescriptors[IntToTransfer].GetHistovalue(i), CompleteScreening.ListDescriptors[i + IntToTransfer + 1], CompleteScreening);
LDesc.Add(NewDesc);
}
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void SumCheckedDescToDescriptorItem(object sender, EventArgs e)
{
string NewName = "";
for (int Idx = 0; Idx < CompleteScreening.GlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count; Idx++)
{
if (CompleteScreening.ListDescriptors[Idx].IsActive())
if (CompleteScreening.ListDescriptors[Idx].GetBinNumber() == 1)
{
NewName += CompleteScreening.ListDescriptors[Idx].GetName() + "+";
}
else
{
MessageBox.Show("Descriptor length not consistent (" + CompleteScreening.ListDescriptors[Idx].GetName() + " : " + CompleteScreening.ListDescriptors[Idx].GetBinNumber() + " bins", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
}
cDescriptorsType ColumnType = new cDescriptorsType(NewName.Remove(NewName.Length - 1), true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
double NewValue = 0;
for (int IdxActiveDesc = 0; IdxActiveDesc < CompleteScreening.ListDescriptors.Count - 1; IdxActiveDesc++)
{
if (CompleteScreening.ListDescriptors[IdxActiveDesc].IsActive())
NewValue += Tmpwell.ListDescriptors[IdxActiveDesc].GetValue();
}
cDescriptor NewDesc = new cDescriptor(NewValue, ColumnType, CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void RowToDescriptorItem(object sender, EventArgs e)
{
cDescriptorsType RowType = new cDescriptorsType("Row", true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(RowType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
cDescriptor NewDesc = new cDescriptor(Tmpwell.GetPosY(), RowType, CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
}
public string GeneratePCADescriptor(cExtendPlateList PlatesToProcess, int NumberOfAxis, int NeutralClass)
{
int NumWell = 0;
int NumWellForLearning = 0;
foreach (cPlate CurrentPlate in PlatesToProcess)
{
NumWellForLearning += CurrentPlate.GetNumberOfWellOfClass(NeutralClass);
NumWell += CompleteScreening.GetCurrentDisplayPlate().GetNumberOfActiveWells();
}
if (NumWellForLearning == 0)
{
MessageBox.Show("No well identified !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return null;
}
int NumDesc = CompleteScreening.GetNumberOfActiveDescriptor();
if (NumDesc <= 1)
{
MessageBox.Show("More than one descriptor are required for this operation", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return null;
}
double[,] DataForLDA = new double[NumWellForLearning, CompleteScreening.GetNumberOfActiveDescriptor() + 1];
// return;
Matrix EigenVectors = PCAComputation(DataForLDA, NumWellForLearning, NumWell, NumDesc, NeutralClass, PlatesToProcess);
string AxeName = "";
int IDxDesc = 0;
//for (int Desc = 0; Desc < CompleteScreening.ListDescriptors.Count; Desc++)
//{
// if (CompleteScreening.ListDescriptors[Desc].IsActive() == false) continue;
// // AxeName += String.Format("{0:0.##}", EigenVectors.getElement(CompleteScreening.ListDescriptors.Count - 1, 0)) + "x" + CompleteScreening.ListDescriptorName[CompleteScreening.ListDescriptors.Count - 1];
//}
int OriginalDescNumber = CompleteScreening.GlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count;
for (int AxesIdx = 0; AxesIdx < NumberOfAxis; AxesIdx++)
{
//for (int Idx = 0; Idx < CompleteScreening.GlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count; Idx++)
//{
// if (CompleteScreening.ListDescriptors[Idx].IsActive())
// if (CompleteScreening.ListDescriptors[Idx].GetBinNumber() == 1)
// {
// AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc++, AxesIdx)) + "x" + CompleteScreening.ListDescriptors[Idx].GetName() + " + ";
// }
// else
// {
// MessageBox.Show("Descriptor length not consistent (" + CompleteScreening.ListDescriptors[Idx].GetName() + " : " + CompleteScreening.ListDescriptors[Idx].GetBinNumber() + " bins", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
// return;
// }
// }
//cDescriptorsType ColumnType = new cDescriptorsType(AxeName.Remove(AxeName.Length - 3), true, 1);
cDescriptorsType ColumnType = new cDescriptorsType("PCA_" + (AxesIdx + 1), true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
double NewValue = 0;
IDxDesc = 0;
// AxeName += "\nPCA_" + (AxesIdx + 1);
for (int Idx = 0; Idx < OriginalDescNumber - 1; Idx++)
{
if (CompleteScreening.ListDescriptors[Idx].IsActive())
// AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc, AxesIdx)) + "x" + CompleteScreening.ListDescriptors[Idx].GetName() + " + ";
NewValue += EigenVectors.getElement(IDxDesc++, AxesIdx) * Tmpwell.ListDescriptors[Idx].GetValue();
}
cDescriptor NewDesc = new cDescriptor(NewValue, ColumnType, CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
return AxeName;
}
private void generateHitsDistributionMapToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
List<cPanelForDisplayArray> ListPlates = new List<cPanelForDisplayArray>();
foreach (cPlate CurrentPlate in CompleteScreening.ListPlatesActive)
{
ListPlates.Add(new FormToDisplayPlate(CurrentPlate, CompleteScreening));
}
cWindowToDisplayEntireScreening WindowToDisplayArray = new cWindowToDisplayEntireScreening(ListPlates, CompleteScreening.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptor].GetName(), 6);
WindowToDisplayArray.checkBoxDisplayClasses.Checked = true;
WindowToDisplayArray.Text = "Generate Hits Distribution Maps";
WindowToDisplayArray.Show();
System.Windows.Forms.DialogResult ResWin = MessageBox.Show("By applying this process, the current screening will be entirely updated ! Proceed ?", "Warning", MessageBoxButtons.YesNo, MessageBoxIcon.Warning);
if (ResWin == System.Windows.Forms.DialogResult.No)
{
WindowToDisplayArray.Close();
return;
}
WindowToDisplayArray.Close();
if (CompleteScreening != null) CompleteScreening.Close3DView();
// CompleteScreening.ListDescriptors.RemoveDesc(CompleteScreening.ListDescriptors[IntToTransfer], CompleteScreening);
cScreening MergedScreening = new cScreening("Class Screen", GlobalInfo);
MergedScreening.PanelForPlate = this.panelForPlate;
MergedScreening.Rows = CompleteScreening.Rows;
MergedScreening.Columns = CompleteScreening.Columns;
MergedScreening.ListPlatesAvailable = new cExtendPlateList();
// create the descriptor
MergedScreening.ListDescriptors.Clean();
List<cDescriptorsType> ListDescType = new List<cDescriptorsType>();
List<int[][]> Values = new List<int[][]>();
for (int i = 0; i < GlobalInfo.GetNumberofDefinedClass(); i++)
{
cDescriptorsType DescClass = new cDescriptorsType("Class_" + i, true, 1, GlobalInfo);
ListDescType.Add(DescClass);
MergedScreening.ListDescriptors.AddNew(DescClass);
int[][] TMpVal = new int[MergedScreening.Columns][];
for (int ii = 0; ii < MergedScreening.Columns; ii++)
TMpVal[ii] = new int[MergedScreening.Rows];
Values.Add(TMpVal);
}
MergedScreening.ListDescriptors.CurrentSelectedDescriptor = 0;
foreach (cPlate CurrentPlate in CompleteScreening.ListPlatesActive)
{
foreach (cWell TmpWell in CurrentPlate.ListActiveWells)
{
int Class = TmpWell.GetClass();
if (Class >= 0)
Values[Class][TmpWell.GetPosX() - 1][TmpWell.GetPosY() - 1]++;
}
}
cPlate NewPlate = new cPlate("Cpds", CompleteScreening.Name, MergedScreening);
for (int X = 0; X < CompleteScreening.Columns; X++)
for (int Y = 0; Y < CompleteScreening.Rows; Y++)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int i = 0; i < GlobalInfo.GetNumberofDefinedClass(); i++)
{
cDescriptor Desc = new cDescriptor(Values[i][X][Y], ListDescType[i], CompleteScreening);
LDesc.Add(Desc);
}
cWell NewWell = new cWell(LDesc, X + 1, Y + 1, MergedScreening, NewPlate);
NewWell.Name = "Well [" + (X + 1) + ":" + (Y + 1) + "]";
NewPlate.AddWell(NewWell);
}
// check if the plate exist already
MergedScreening.AddPlate(NewPlate);
MergedScreening.ListPlatesActive = new cExtendPlateList();
MergedScreening.GlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Clear();
for (int i = 0; i < MergedScreening.ListPlatesAvailable.Count; i++)
{
MergedScreening.ListPlatesActive.Add(MergedScreening.ListPlatesAvailable[i]);
MergedScreening.GlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Add(NewPlate.Name);
}
CompleteScreening.ListDescriptors = MergedScreening.ListDescriptors;
CompleteScreening.ListPlatesAvailable = MergedScreening.ListPlatesAvailable;
CompleteScreening.ListPlatesActive = MergedScreening.ListPlatesActive;
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
CompleteScreening.CurrentDisplayPlateIdx = 0;
CompleteScreening.GetCurrentDisplayPlate().DisplayDistribution(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, true);
ListPlates = new List<cPanelForDisplayArray>();
for (int DescIdx = 0; DescIdx < CompleteScreening.ListDescriptors.Count; DescIdx++)
{
if (CompleteScreening.ListDescriptors[DescIdx].IsActive())
ListPlates.Add(new FormToDisplayDescriptorPlate(CompleteScreening.GetCurrentDisplayPlate(), CompleteScreening, DescIdx));
}
cWindowToDisplayEntireDescriptors WindowToDisplayDesc = new cWindowToDisplayEntireDescriptors(ListPlates, CompleteScreening.GetCurrentDisplayPlate().Name, GlobalInfo.GetNumberofDefinedClass());
WindowToDisplayDesc.checkBoxGlobalNormalization.Checked = true;
WindowToDisplayDesc.Show();
}
private void generateDRCsToolStripMenuItem_Click(object sender, EventArgs e)
{
int nbrofdrugs = 6;
int nbrofconcentrations = 10;
int nbrofdesc = 3;
double[, ,] DRC = new double[nbrofconcentrations, nbrofdrugs, nbrofdesc];
float[] X1 = new float[nbrofconcentrations];
X1[0] = 1000;
for (int i = 1; i < X1.Length; i++)
{
X1[i] = X1[i - 1] / 3;
}
Random Bot = new Random();
Random To = new Random();
Random Ec5 = new Random();
Random Slop = new Random();
CompleteScreening = new cScreening("Current Screen", this.GlobalInfo);
CompleteScreening.Columns = nbrofconcentrations;
CompleteScreening.Rows = nbrofdrugs;
for (int j = 0; j < nbrofdrugs; j++)
{
for (int k = 0; k < nbrofdesc; k++)
{
float Bottom = Bot.Next(10);
float Top = To.Next(80, 100);
float Ec50 = Ec5.Next(40, 60);
float Slope = Slop.Next(1, 5);
for (int i = 0; i < X1.Length; i++)
{
//DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow(((Math.Pow(10, Ec50) / Math.Pow(10, X1[0]))), Slope));
DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow((X1[i] / Ec50), -Slope));
}
}
}
cPlate NewPlate = new cPlate("Cpds", "Plate0", CompleteScreening);
CompleteScreening.AddPlate(NewPlate);
CompleteScreening.ListDescriptors.Clean();
for (int k = 0; k < nbrofdesc; k++)
{
cDescriptorsType DescType = new cDescriptorsType("Desc" + k, true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(DescType);
}
for (int j = 0; j < nbrofdrugs; j++)
{
for (int i = 0; i < nbrofconcentrations; i++)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int k = 0; k < nbrofdesc; k++)
{
//DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow(((Math.Pow(10, Ec50) / Math.Pow(10, X1[0]))), Slope));
cDescriptor CurrentDesc = new cDescriptor(DRC[i, j, k], CompleteScreening.ListDescriptors[k], CompleteScreening);
LDesc.Add(CurrentDesc);
}
cWell NewWell = new cWell(LDesc, i+1, j+1, CompleteScreening, NewPlate);
NewWell.Concentration = X1[i];
NewPlate.AddWell(NewWell);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < CompleteScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = CompleteScreening.ListPlatesActive.GetPlate(IdxPlate).Name;
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
CompleteScreening.CurrentDisplayPlateIdx = 0;
CompleteScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
}
private void convertDRCToWellToolStripMenuItem1_Click(object sender, EventArgs e)
{
System.Windows.Forms.DialogResult ResWin = MessageBox.Show("By applying this process, the current screening will be entirely updated ! Proceed ?", "Warning", MessageBoxButtons.YesNo, MessageBoxIcon.Warning);
if (ResWin == System.Windows.Forms.DialogResult.No) return;
//foreach (cDescriptorsType DescType in CompleteScreening.ListDescriptors)
//{
// CompleteScreening.ListDescriptors.RemoveDescUnSafe(DescType, CompleteScreening);
//}
if (CompleteScreening != null) CompleteScreening.Close3DView();
// CompleteScreening.ListDescriptors.RemoveDesc(CompleteScreening.ListDescriptors[IntToTransfer], CompleteScreening);
cScreening MergedScreening = new cScreening("Merged Screen", GlobalInfo);
MergedScreening.PanelForPlate = this.panelForPlate;
MergedScreening.Rows = CompleteScreening.Rows;
MergedScreening.Columns = CompleteScreening.Columns;
MergedScreening.ListPlatesAvailable = new cExtendPlateList();
// create the descriptor
MergedScreening.ListDescriptors.Clean();
int Idesc = 0;
List<cDescriptorsType> ListDescType = new List<cDescriptorsType>();
for (int i = 0; i < CompleteScreening.ListDescriptors.Count; i++)
{
if (!CompleteScreening.ListDescriptors[i].IsActive()) continue;
cDescriptorsType DescEC50 = new cDescriptorsType("EC50_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescEC50);
MergedScreening.ListDescriptors.AddNew(DescEC50);
cDescriptorsType DescTop = new cDescriptorsType("Top_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescTop);
MergedScreening.ListDescriptors.AddNew(DescTop);
cDescriptorsType DescBottom = new cDescriptorsType("Bottom_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescBottom);
MergedScreening.ListDescriptors.AddNew(DescBottom);
cDescriptorsType DescSlope = new cDescriptorsType("Slope_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescSlope);
MergedScreening.ListDescriptors.AddNew(DescSlope);
Idesc++;
}
MergedScreening.ListDescriptors.CurrentSelectedDescriptor = 0;
foreach (cPlate CurrentPlate in CompleteScreening.ListPlatesAvailable)
{
cPlate NewPlate = new cPlate("Cpds", CurrentPlate.Name + " Merged", MergedScreening);
// check if the plate exist already
MergedScreening.AddPlate(NewPlate);
foreach (cDRC_Region CurrentRegion in CurrentPlate.ListDRCRegions)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
Idesc = 0;
int IDESCBase = 0;
for (int i = 0; i < CompleteScreening.ListDescriptors.Count; i++)
{
if (!CompleteScreening.ListDescriptors[i].IsActive()) continue;
cDRC CurrentDRC = CurrentRegion.GetDRC(CompleteScreening.ListDescriptors[IDESCBase++]);
cDescriptor Desc_EC50 = new cDescriptor(CurrentDRC.EC50, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_EC50);
cDescriptor Desc_Top = new cDescriptor(CurrentDRC.Top, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Top);
cDescriptor Desc_Bottom = new cDescriptor(CurrentDRC.Bottom, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Bottom);
cDescriptor Desc_Slope = new cDescriptor(CurrentDRC.Slope, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Slope);
}
cWell NewWell = new cWell(LDesc, CurrentRegion.PosXMin + 1, CurrentRegion.PosYMin + 1, MergedScreening, NewPlate);
NewWell.Name = "DRC [" + CurrentRegion.PosXMin + ":" + CurrentRegion.PosYMin + "]";
NewPlate.AddWell(NewWell);
}
}
// PanelList[0].CurrentScreening.ListPlatesActive.Clear();
// PanelList[0].CurrentScreening.GlobalInfo.WindowHCSAnalyzer.RefreshInfoScreeningRichBox();
MergedScreening.ListPlatesActive = new cExtendPlateList();
for (int i = 0; i < MergedScreening.ListPlatesAvailable.Count; i++)
{
MergedScreening.ListPlatesActive.Add(MergedScreening.ListPlatesAvailable[i]);
// MergedScreening.GlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Add(PanelList[0].CurrentScreening.ListPlatesActive[i].Name);
}
//PanelList[0].CurrentScreening.CurrentDisplayPlateIdx = 0;
//PanelList[0].CurrentScreening.GlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.SelectedIndex = 0;
//PanelList[0].CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(PanelList[0].CurrentScreening.ListDescriptors.CurrentSelectedDescriptor, false);
CompleteScreening.ListDescriptors = MergedScreening.ListDescriptors;
CompleteScreening.ListPlatesAvailable = MergedScreening.ListPlatesAvailable;
CompleteScreening.ListPlatesActive = MergedScreening.ListPlatesActive;
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
CompleteScreening.GetCurrentDisplayPlate().DisplayDistribution(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, true);
}
private void ConcentrationToDescriptorItem(object sender, EventArgs e)
{
cDescriptorsType ConcentrationType = new cDescriptorsType("Concentration", true, 1);
CompleteScreening.ListDescriptors.AddNew(ConcentrationType);
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
cDescriptor NewDesc = new cDescriptor(Tmpwell.Concentration, ConcentrationType,CompleteScreening);
LDesc.Add(NewDesc);
Tmpwell.AddDescriptors(LDesc);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
}
private void buttonStartCluster_Click(object sender, EventArgs e)
{
FormSingleCellClusteringInfo WindowClusteringInfo = new FormSingleCellClusteringInfo(GlobalInfo);
if (WindowClusteringInfo.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
Instances ListInstances = GlobalInfo.CurrentScreen.CellBasedClassification.CreateInstancesWithoutClass(dt);
if ((WindowClusteringInfo.radioButtonAutomated.Checked) && (WindowClusteringInfo.radioButtonEM.Checked))
{
ClusterEvaluation eval;
Classes = new cExtendedList();
weka.clusterers.EM EMCluster = new EM();
if(WindowClusteringInfo.checkBoxEMAutomated.Checked)
EMCluster.setNumClusters(-1);
else
EMCluster.setNumClusters((int)WindowClusteringInfo.numericUpDownClassNumber.Value);
EMCluster.buildClusterer(ListInstances);
EMCluster.getClusterModelsNumericAtts();
eval = new ClusterEvaluation();
eval.setClusterer(EMCluster);
eval.evaluateClusterer(ListInstances);
Classes.AddRange(eval.getClusterAssignments());
NumClusters= eval.getNumClusters();
ReDraw();
FormForCellByCellClusteringResults WindowFormForCellByCellClusteringResults = new FormForCellByCellClusteringResults();
WindowFormForCellByCellClusteringResults.richTextBoxResults.Clear();
WindowFormForCellByCellClusteringResults.richTextBoxResults.AppendText(eval.clusterResultsToString());
if (WindowFormForCellByCellClusteringResults.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
}
else if (WindowClusteringInfo.radioButtonDescriptorBased.Checked)
{
Classes = new cExtendedList();
DataTable FinalDataTable = new DataTable();
int IdxDescForClassSelect = WindowClusteringInfo.comboBoxDescriptorForClass.SelectedIndex;
for (int IdxWell = 0; IdxWell < GlobalInfo.ListSelectedWell.Count; IdxWell++)
{
cWell TmpWell = GlobalInfo.ListSelectedWell[IdxWell];
// if (IdxWell == 0)
if (TmpWell.ListDescriptors[IdxDescForClassSelect].GetAssociatedType().DataType == eDataType.HISTOGRAM)
{
Classes.AddRange(TmpWell.ListDescriptors[IdxDescForClassSelect].GetOriginalValues());
}
else
{
double ClasseValue = TmpWell.ListDescriptors[IdxDescForClassSelect].GetValue();
for (int IdxCell = 0; IdxCell < TmpWell.CellNumber; IdxCell++)
Classes.Add(ClasseValue);
//TmpWell.AddDescriptors
}
}
List<double> ListClassValues = new List<double>();
foreach (var item in Classes.Distinct())
{
ListClassValues.Add(item);
}
//(List<double>)Classes.Distinct();
NumClusters = ListClassValues.Count();
//Classes = new cExtendedList();
for (int IdxClust = 0; IdxClust < Classes.Count; IdxClust++)
{
for (int IdxCl = 0; IdxCl < ListClassValues.Count; IdxCl++)
{
if (ListClassValues[IdxCl] == Classes[IdxClust])
{
Classes[IdxClust] = IdxCl;
break;
}
}
//Classes[IdxClust] = ListClassValues.Find(Classes[IdxClust]);
}
//int NumClusters =
ReDraw();
}
// ReDraw();
//if (MessageBox.Show("Do you want perform a j48 training process ?", "Question", MessageBoxButtons.YesNo, MessageBoxIcon.Question) != System.Windows.Forms.DialogResult.Yes) return;
weka.core.FastVector attVals = new FastVector();
for (int i = 0; i < NumClusters; i++)
attVals.addElement("Class__" + (i).ToString());
ListInstances.insertAttributeAt(new weka.core.Attribute("Class__", attVals), ListInstances.numAttributes());
for (int i = 0; i < Classes.Count; i++)
{
ListInstances.get(i).setValue(ListInstances.numAttributes() - 1, Classes[i]);
}
ListInstances.setClassIndex(ListInstances.numAttributes() - 1);
GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased = new weka.classifiers.trees.J48();
GlobalInfo.CurrentScreen.CellBasedClassification.SetJ48Tree((weka.classifiers.trees.J48)GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased,Classes.Count);
GlobalInfo.CurrentScreen.CellBasedClassification.J48Model.setMinNumObj((int)GlobalInfo.OptionsWindow.numericUpDownJ48MinNumObjects.Value);
weka.core.Instances train = new weka.core.Instances(ListInstances, 0, ListInstances.numInstances());
GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.buildClassifier(train);
GlobalInfo.ConsoleWriteLine(GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.ToString());
GlobalInfo.CurrentScreen.CellBasedClassification.evaluation = new weka.classifiers.Evaluation(ListInstances);
GlobalInfo.CurrentScreen.CellBasedClassification.evaluation.crossValidateModel(GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased, ListInstances, 2, new java.util.Random(1));
GlobalInfo.CurrentScreen.CellBasedClassification.DisplayTree(GlobalInfo).Show();
FormForCellbyCellClassif WindowFormForCellbyCellClassif = new FormForCellbyCellClassif();
if (WindowFormForCellbyCellClassif.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int DescrCount = GlobalInfo.CurrentScreen.ListDescriptors.Count;
// first we update the descriptor
for (int i = 0; i < ListInstances.numClasses(); i++)
GlobalInfo.CurrentScreen.ListDescriptors.AddNew(new cDescriptorsType("Ratio_Class " + i, true, 1, GlobalInfo));
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in GlobalInfo.CurrentScreen.ListPlatesAvailable)
MaxProgress += CurrentPlateToProcess.ParentScreening.Columns * CurrentPlateToProcess.ParentScreening.Rows;
ProgressWindow.progressBar.Maximum = MaxProgress;
attVals = new FastVector();
for (int i = 0; i < NumClusters; i++)
attVals.addElement(i.ToString());
//ParallelOptions options = new ParallelOptions();
//options.MaxDegreeOfParallelism = -1; // -1 is for unlimited. 1 is for sequential.
//Stopwatch stopwatch = new Stopwatch();
//stopwatch.Start();
//////for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
//int NumberOfPlates = CompleteScreening.ListPlatesAvailable.Count;
//Parallel.For(0, NumberOfPlates, options, (PlateIdx) =>
//{
// cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate((string)Parent.GlobalInfo.PlateListWindow.listBoxPlateNameToProcess.Items[PlateIdx]);
// for (int row = 0; row < Parent.Rows; row++)
// for (int col = 0; col < Parent.Columns; col++)
// {
// TempWell = CurrentPlateToProcess.GetWell(col, row, false);
// if (TempWell == null) continue;
// else
// {
// if (TempWell.GetClass() == this.ClassForClassif)
// Pos.Add(TempWell.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetValue());
// }
// }
//}
//);
foreach (cPlate CurrentPlateToProcess in GlobalInfo.CurrentScreen.ListPlatesAvailable)
//Parallel.ForEach(GlobalInfo.CurrentScreen.ListPlatesActive, options, CurrentPlateToProcess =>
{
//Parallel.ForEach(CurrentPlateToProcess.ListActiveWells, options, TmpWell =>
for(int j=0;j<CurrentPlateToProcess.ParentScreening.Rows;j++)
for (int k = 0; k < CurrentPlateToProcess.ParentScreening.Columns; k++)
{
cWell TmpWell = CurrentPlateToProcess.GetWell(k, j, false);
if (TmpWell == null) continue;
ProgressWindow.progressBar.Value = IdxProgress++;
//DataTable FinalDataTable = new DataTable();
//TmpWell.AssociatedPlate.DBConnection = new cDBConnection(TmpWell.AssociatedPlate, TmpWell.SQLTableName);
//TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, false);
DataTable FinalDataTable = TmpWell.GetDescDataTable(true);
Instances ListInstancesTOClassify = GlobalInfo.CurrentScreen.CellBasedClassification.CreateInstancesWithoutClass(FinalDataTable);
ListInstancesTOClassify.insertAttributeAt(new weka.core.Attribute("Class", attVals), ListInstancesTOClassify.numAttributes());
ListInstancesTOClassify.setClassIndex(ListInstancesTOClassify.numAttributes() - 1);
cExtendedList ListClasses = new cExtendedList();
for (int i = 0; i < ListInstancesTOClassify.numInstances(); i++)
{
double classId = GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.classifyInstance(ListInstancesTOClassify.instance(i));
ListClasses.Add(classId);
}
List<double[]> Histo = ListClasses.CreateHistogram(0, ListInstances.numClasses() - 1, ListInstances.numClasses() - 1);
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int IdxHisto = 0; IdxHisto < Histo[1].Length; IdxHisto++)
{
double Value = (100.0 * Histo[1][IdxHisto]) / (double)ListInstancesTOClassify.numInstances();
cDescriptor NewDesc = new cDescriptor(Value, GlobalInfo.CurrentScreen.ListDescriptors[IdxHisto + DescrCount], GlobalInfo.CurrentScreen);
LDesc.Add(NewDesc);
}
TmpWell.AddDescriptors(LDesc);
//TmpWell.AssociatedPlate.DBConnection.DB_CloseConnection();
}//);
}
ProgressWindow.Close();
if (WindowFormForCellbyCellClassif.checkBoxKeepOriginalDesc.Checked == false)
{
// int DescNumToRemove = GlobalInfo.CurrentScreen.ListDescriptors.Count -
for (int IdxDesc = 0; IdxDesc < DescrCount; IdxDesc++)
GlobalInfo.CurrentScreen.ListDescriptors.RemoveDesc(GlobalInfo.CurrentScreen.ListDescriptors[0], GlobalInfo.CurrentScreen);
}
GlobalInfo.CurrentScreen.ListDescriptors.UpDateDisplay();
GlobalInfo.CurrentScreen.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < GlobalInfo.CurrentScreen.ListPlatesActive.Count; idxP++)
GlobalInfo.CurrentScreen.ListPlatesActive[idxP].UpDataMinMax();
if (WindowFormForCellbyCellClassif.checkBoxKeepOriginalDesc.Checked == false)
GlobalInfo.CurrentScreen.GetCurrentDisplayPlate().DisplayDistribution(0, false);
//WindowFormForCellbyCellClassif.Close();
//WindowClusteringInfo.Close();
}
