// protected Size SizeHisto = new System.Drawing.Size(10, 5);
public cWell(cWell NewWell)
{
this.PosX = NewWell.PosX;
this.PosY = NewWell.PosY;
this.ListDescriptors = NewWell.ListDescriptors;
this.Parent = NewWell.Parent;
this.AssociatedChart = NewWell.AssociatedChart;
this.AssociatedPlate = NewWell.AssociatedPlate;
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
}
public void DrawSignature()
{
if (ListWells == null) return;
g = this.panelForDesignDisplay.CreateGraphics();
g.SmoothingMode = System.Drawing.Drawing2D.SmoothingMode.HighQuality;
g.Clear(Color.White);
int SizeWell = 8;
CurrBrush = new SolidBrush(Color.Fuchsia);
PosXMin = int.MaxValue;
PosYMin = int.MaxValue;
PosXMax = int.MinValue;
PosYMax = int.MinValue;
foreach (cWell TmpWell in ListWells)
{
if (TmpWell == null) continue;
AssociatedPlate = TmpWell.AssociatedPlate;
if (TmpWell.GetPosX() > PosXMax) PosXMax = TmpWell.GetPosX();
if (TmpWell.GetPosY() > PosYMax) PosYMax = TmpWell.GetPosY();
if (TmpWell.GetPosX() < PosXMin) PosXMin = TmpWell.GetPosX();
if (TmpWell.GetPosY() < PosYMin) PosYMin = TmpWell.GetPosY();
}
if (AssociatedPlate == null) return;
int SizeX = PosXMax - PosXMin + 1;
int SizeY = PosYMax - PosYMin + 1;
if (this.radioButtonOrientationLine.Checked)
{
this.numericUpDownConcentrationNumber.Value = (decimal)SizeX;
this.numericUpDownReplication.Value = (decimal)SizeY;
if (PosXMin > PosXMax) return;
TemplateRegion = new cDRC_Region(AssociatedPlate, (int)this.numericUpDownConcentrationNumber.Value, (int)this.numericUpDownReplication.Value, PosXMin, PosYMin, true);
}
else
{
this.numericUpDownConcentrationNumber.Value = (decimal)SizeY;
this.numericUpDownReplication.Value = (decimal)SizeX;
if (PosXMin > PosXMax) return;
TemplateRegion = new cDRC_Region(AssociatedPlate, (int)this.numericUpDownConcentrationNumber.Value, (int)this.numericUpDownReplication.Value, PosXMin, PosYMin, false);
}
DrawSingleRegion(0, 0, 0);
for (int j = 1; j <= AssociatedPlate.ParentScreening.Columns + 1; j++)
g.DrawLine(new Pen(Color.Black), new Point(j * SizeWell, SizeWell), new Point(j * SizeWell, (AssociatedPlate.ParentScreening.Rows + 1) * SizeWell));
for (int i = 1; i <= AssociatedPlate.ParentScreening.Rows + 1; i++)
g.DrawLine(new Pen(Color.Black), new Point(SizeWell, i * SizeWell), new Point((AssociatedPlate.ParentScreening.Columns + 1) * SizeWell, i * SizeWell));
}
public cDBConnection(cPlate Plate, string SQLFileDBName)
{
AssociatedPlate = Plate;
if (Plate.DBConnection == null)
this.SQLFileDBName = SQLFileDBName;
else
this.SQLFileDBName = Plate.DBConnection.SQLFileDBName;
if (this.OpenConnection() == false) this.IsSucceed = false;
}
public cWell(List<cDescriptor> ListDesc, int Col, int Row, cScreening screenParent, cPlate CurrentPlate)
{
this.Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
this.ListDescriptors = new List<cDescriptor>();
this.ListDescriptors = ListDesc;
this.PosX = Col;
this.PosY = Row;
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
}
//public cWell(cWell NewWell)
//{
// this.PosX = NewWell.PosX;
// this.PosY = NewWell.PosY;
// this.ListDescriptors = NewWell.ListDescriptors;
// this.Parent = NewWell.Parent;
// this.AssociatedChart = NewWell.AssociatedChart;
// this.AssociatedPlate = NewWell.AssociatedPlate;
// this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
//}
public cWell(cDescriptor Desc, int Col, int Row, cScreening screenParent, cPlate CurrentPlate)
{
this.CellNumber = -1;
this.Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
this.ListDescriptors = new List<cDescriptor>();
List<cDescriptor> TmpListDescriptors = new List<cDescriptor>();
TmpListDescriptors.Add(Desc);
this.AddDescriptors(TmpListDescriptors);
this.PosX = Col;
this.PosY = Row;
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
}
public cWell(cSignature Desc, int Col, int Row, cScreening screenParent, cPlate CurrentPlate)
{
//Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
this.ListSignatures = new cListSignature();
this.ListSignatures.Add(Desc);
this.PosX = Col;
this.PosY = Row;
// this.CurrentColor = this.cGlobalInfo.ListClasses[ClassForClassif].ColourForDisplay;
Desc.AssociatedWell = this;
// this.ListClass.Add(this.InitialClass);
this.ListProperties = new cListWellProperty(this);
this.ListProperties.UpdateValueByName("Well Class", 2);
}
private void hitsDistributionMapToolStripMenuItem_Click(object sender, EventArgs e)
{
if (cGlobalInfo.CurrentScreening == null) return;
List<cPanelForDisplayArray> ListPlates = new List<cPanelForDisplayArray>();
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
ListPlates.Add(new FormToDisplayPlate(CurrentPlate));
}
cWindowToDisplayEntireScreening WindowToDisplayArray = new cWindowToDisplayEntireScreening(ListPlates, cGlobalInfo.CurrentScreening.ListDescriptors[cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx].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 (cGlobalInfo.CurrentScreening != null) cGlobalInfo.CurrentScreening.Close3DView();
// CompleteScreening.ListDescriptors.RemoveDesc(CompleteScreening.ListDescriptors[IntToTransfer], CompleteScreening);
cScreening MergedScreening = new cScreening("Class Screen");
MergedScreening.PanelForPlate = this.panelForPlate;
MergedScreening.Rows = cGlobalInfo.CurrentScreening.Rows;
MergedScreening.Columns = cGlobalInfo.CurrentScreening.Columns;
MergedScreening.ListPlatesAvailable = new cListPlates();
// create the descriptor
MergedScreening.ListDescriptors.Clean();
List<cDescriptorType> ListDescType = new List<cDescriptorType>();
List<int[][]> Values = new List<int[][]>();
for (int i = 0; i < cGlobalInfo.ListWellClasses.Count; i++)
{
cDescriptorType DescClass = new cDescriptorType("Class_" + i, true, 1);
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.CurrentSelectedDescriptorIdx = 0;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in CurrentPlate.ListActiveWells)
{
int Class = TmpWell.GetCurrentClassIdx();
if (Class >= 0)
Values[Class][TmpWell.GetPosX() - 1][TmpWell.GetPosY() - 1]++;
}
}
cPlate NewPlate = new cPlate(cGlobalInfo.CurrentScreening.GetName(), MergedScreening);
for (int X = 0; X < cGlobalInfo.CurrentScreening.Columns; X++)
for (int Y = 0; Y < cGlobalInfo.CurrentScreening.Rows; Y++)
{
cListSignature LDesc = new cListSignature();
for (int i = 0; i < cGlobalInfo.ListWellClasses.Count; i++)
{
cSignature Desc = new cSignature(Values[i][X][Y], ListDescType[i], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc);
}
cWell NewWell = new cWell(LDesc, X + 1, Y + 1, MergedScreening, NewPlate);
// NewWell.SetCpdName("Well [" + (X + 1) + ":" + (Y + 1) + "]");
NewPlate.AddWell(NewWell);
}
// check if the plate exist already
MergedScreening.AddPlate(NewPlate);
MergedScreening.ListPlatesActive = new cListPlates();
cGlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Clear();
for (int i = 0; i < MergedScreening.ListPlatesAvailable.Count; i++)
{
MergedScreening.ListPlatesActive.Add(MergedScreening.ListPlatesAvailable[i]);
cGlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Add(NewPlate.GetName());
}
cGlobalInfo.CurrentScreening.ListDescriptors = MergedScreening.ListDescriptors;
cGlobalInfo.CurrentScreening.ListPlatesAvailable = MergedScreening.ListPlatesAvailable;
cGlobalInfo.CurrentScreening.ListPlatesActive = MergedScreening.ListPlatesActive;
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), true);
ListPlates = new List<cPanelForDisplayArray>();
for (int DescIdx = 0; DescIdx < cGlobalInfo.CurrentScreening.ListDescriptors.Count; DescIdx++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[DescIdx].IsActive())
ListPlates.Add(new FormToDisplayDescriptorPlate(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate(), cGlobalInfo.CurrentScreening, DescIdx));
}
cWindowToDisplayEntireDescriptors WindowToDisplayDesc = new cWindowToDisplayEntireDescriptors(ListPlates, cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().GetName(), cGlobalInfo.ListWellClasses.Count);
WindowToDisplayDesc.checkBoxGlobalNormalization.Checked = true;
WindowToDisplayDesc.Show();
}
/// <summary>
/// K - Mean clustering procedure
/// </summary>
/// <param name="Classes"></param>
/// <param name="PlateToProcess"></param>
/// <returns></returns>
private bool KMeans(int Classes, cPlate PlateToProcess)
{
int NumWell = PlateToProcess.GetNumberOfActiveWells();
int Numdesc = CompleteScreening.GetNumberOfActiveDescriptor();
double[,] DataForKMeans = new double[NumWell, Numdesc];
int IdxDesc = 0;
for (int desc = 0; desc < CompleteScreening.ListDescriptors.Count; desc++)
{
if (CompleteScreening.ListDescriptors[desc].IsActive() == false) continue;
List<double> CurrentDesc = new List<double>();
double[] NormDesc = null;
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = PlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
CurrentDesc.Add(TmpWell.ListDescriptors[desc].GetValue());
}
if (CurrentDesc.Count == 0) continue;
NormDesc = MeanCenteringStdStandarization(CurrentDesc.ToArray());
for (int row = 0; row < NumWell; row++)
DataForKMeans[row, IdxDesc] = NormDesc[row];
IdxDesc++;
}
int Info;
double[,] CenterPos;
int[] ClusterIndx;
try
{
alglib.kmeansgenerate(DataForKMeans, NumWell, Numdesc, Classes, 10, out Info, out CenterPos, out ClusterIndx);
int Idx = 0;
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = PlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
{
if (ClusterIndx[Idx] == -1)
TmpWell.SetAsNoneSelected();
else
TmpWell.SetClass(ClusterIndx[Idx]);
Idx++;
}
}
}
catch
{
richTextBoxInfoClustering.AppendText("\nPlate: " + PlateToProcess.Name + " skipped: data corrupted (check your descriptor data validity).");
//MessageBox.Show("Check the data validity", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return false;
}
return true;
}
private void buttonGenerate_Click(object sender, EventArgs e)
{
if (MessageBox.Show("This process will generate a new screening and delete the current one. Are you sure?", "Warning", MessageBoxButtons.OKCancel, MessageBoxIcon.Warning) != System.Windows.Forms.DialogResult.OK)
return;
// Now Let's write the CSV file
//string FilePath = "c:\\test.csv";
//System.IO.StreamWriter file = new System.IO.StreamWriter(FilePath);
//file.WriteLine("PlateName,WellPosition,ImageNumbers");
//foreach (var itemPlate in MainScreenDico)
//{
// foreach (var itemWell in itemPlate.Value)
// {
// string Line = itemPlate.Key.ToString()+","+itemWell.Key.ToString()+","+itemWell.Value;
// file.WriteLine(Line);
// }
//}
//file.Close();
// return;
// if (this.CurrentScreening == null)
string[] ForNames = this.textBoxImageRoot.Text.Split('\\');
cGlobalInfo.CurrentScreening = new cScreening(ForNames[ForNames.Length - 1]);
cGlobalInfo.CurrentScreening.Columns = 24;
cGlobalInfo.CurrentScreening.Rows = 16;
cGlobalInfo.CurrentScreening.ListDescriptors.Clean();
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(new cDescriptorType("ImageNumbers", true, 1));
foreach (var itemPlate in MainScreenDico)
{
cPlate CurrentPlate = cGlobalInfo.CurrentScreening.GetPlateIfNameIsContainIn(itemPlate.Key);
if (CurrentPlate == null)
{
CurrentPlate = new cPlate(itemPlate.Key, cGlobalInfo.CurrentScreening);
cGlobalInfo.CurrentScreening.AddPlate(CurrentPlate);
}
else
{
this.richTextBoxReport.AppendText("----------- Error ----------\nPlate " + itemPlate.Key + " has already been processed. Plate skipped !\n");
continue;
}
foreach (var itemWell in itemPlate.Value)
{
cListSignature LDesc = new cListSignature();
cSignature CurrentDescriptor = new cSignature((double)(int)itemWell.Value, cGlobalInfo.CurrentScreening.ListDescriptors[0/* + ShiftIdx*/], cGlobalInfo.CurrentScreening);
LDesc.Add(CurrentDescriptor);
int[] Pos = new int[2];
Pos = cGlobalInfo.WindowHCSAnalyzer.ConvertPosition(itemWell.Key.ToString());
cWell CurrentWell = new cWell(LDesc, Pos[0], Pos[1], cGlobalInfo.CurrentScreening, CurrentPlate);
CurrentPlate.AddWell(CurrentWell);
}
}
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
foreach (var item in cGlobalInfo.CurrentScreening.ListPlatesActive)
item.UpDataMinMax();
cGlobalInfo.WindowHCSAnalyzer.StartingUpDateUI();
cGlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
cGlobalInfo.WindowHCSAnalyzer.toolStripcomboBoxPlateList.Items.Add(Name);
cGlobalInfo.WindowHCSAnalyzer.PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
cGlobalInfo.WindowHCSAnalyzer.PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).UpDataMinMax();
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(cGlobalInfo.WindowHCSAnalyzer.comboBoxClass.SelectedIndex - 1);
cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx = 0;
cGlobalInfo.WindowHCSAnalyzer.UpdateUIAfterLoading();
// now Image Analysis
// first create a descriptor for each readout
cDescriptorType TmpDescType = new cDescriptorType("Total_Intensity_0", true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(TmpDescType);
//FormForPlateDimensions PlateDim = new FormForPlateDimensions();
//PlateDim.checkBoxAddCellNumber.Visible = true;
//PlateDim.checkBoxIsOmitFirstColumn.Visible = true;
//PlateDim.labelHisto.Visible = true;
//PlateDim.numericUpDownHistoSize.Visible = true;
FormForDoubleProgress WindowProgress = new FormForDoubleProgress();
WindowProgress.Show();
WindowProgress.progressBarPlate.Maximum = cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
WindowProgress.progressBarPlate.Value = 0;
WindowProgress.progressBarPlate.Refresh();
int IdxPlateProg = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
WindowProgress.progressBarPlate.Value++;
WindowProgress.progressBarPlate.Refresh();
WindowProgress.labelPlateIdx.Text = (IdxPlateProg + 1) + " / " + cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
WindowProgress.progressBarWell.Value = 0;
WindowProgress.progressBarWell.Maximum = TmpPlate.ListWells.Count;
#region modif
//List<cImageMetaInfo> ListImageMetaInfo = new List<cImageMetaInfo>();
//string Pathds = this.textBoxImageRoot.Text;
//string XMLFile = Pathds+"\\"+ TmpPlate.GetName()+"\\MeasurementDetail.mrf";
//int NumberOfChannels = (int)this.numericUpDownChannelNumber.Value;
//List<string> ListFiles = Directory.GetFiles(Pathds + "\\" + TmpPlate.GetName(), "*C0*.tif", SearchOption.AllDirectories).ToList();
//ListFiles.Sort(); //OrderBy(q=>q).ToList();
//if (File.Exists(XMLFile))
//{
// XmlDocument xmlDoc = new XmlDocument();
// xmlDoc.Load(XMLFile);
// for (int Channel = 0; Channel < NumberOfChannels; Channel++)
// {
// //string FinalName = ListChannels[Channel];
// cImageMetaInfo TmpMetaInfo = new cImageMetaInfo();
// //TmpMetaInfo.FileName = FinalName;
// TmpMetaInfo.Name = xmlDoc.ChildNodes[1].ChildNodes[1].Attributes["bts:Ch"].Value;//ListChannelNames[Channel];
// TmpMetaInfo.ResolutionX = double.Parse(xmlDoc.ChildNodes[1].ChildNodes[1].Attributes["bts:HorizontalPixelDimension"].Value);//1;
// TmpMetaInfo.ResolutionY = double.Parse(xmlDoc.ChildNodes[1].ChildNodes[1].Attributes["bts:VerticalPixelDimension"].Value);//1;
// TmpMetaInfo.ResolutionZ = 1;
// ListImageMetaInfo.Add(TmpMetaInfo);
// }
//}
//else
//{
// for (int Channel = 0; Channel < NumberOfChannels; Channel++)
// {
// //string FinalName = ListChannels[Channel];
// cImageMetaInfo TmpMetaInfo = new cImageMetaInfo();
// //TmpMetaInfo.FileName = FinalName;
// // TmpMetaInfo.Name = ListChannelNames[Channel];
// TmpMetaInfo.ResolutionX = 1;
// TmpMetaInfo.ResolutionY = 1;
// TmpMetaInfo.ResolutionZ = 1;
// ListImageMetaInfo.Add(TmpMetaInfo);
// }
//}
#endregion
int IdxWell = 0;
foreach (cWell TmpWell in TmpPlate.ListWells)
{
WindowProgress.labelWellIdx.Text = (IdxWell + 1) + " / " + TmpPlate.ListWells.Count;
WindowProgress.progressBarWell.Value = IdxWell + 1;
WindowProgress.progressBarWell.Refresh();
WindowProgress.Refresh();
int NumberOfFieldProcessed = 0;
double AverageValue = 0;
for (int IdxField = 0; IdxField < this.numericUpDownFieldNumber.Value; IdxField++)
{
//var watch = Stopwatch.StartNew();
cGetImageFromWells IFW = new cGetImageFromWells();
IFW.SetInputData(new cListWells(TmpWell));
IFW.ListProperties.FindByName("Field").SetNewValue(IdxField);
IFW.Run();
cImage TmpImage = IFW.GetOutPut();
//watch.Stop();
//cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText("IFW = "+watch.ElapsedMilliseconds + "\n");
if ((TmpImage == null) || (TmpImage.GetNumChannels() == 0))
{
cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText("Error while loading [Plate] " + TmpPlate.GetName() + " [Well] " + TmpWell.GetPos() + " [Field] " + IdxField + "\n");
continue;
}
else
{
AverageValue = 25; //TmpImage.SingleChannelImage[0].Data.Sum();
}
IFW.GetOutPut().Dispose();
//GC.Collect();
NumberOfFieldProcessed++;
}
if (NumberOfFieldProcessed != 0)
AverageValue /= (double)NumberOfFieldProcessed;
else
AverageValue = 0;
cListSignature LDesc = new cListSignature();
cSignature NewDesc = new cSignature(AverageValue, TmpDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
TmpWell.AddSignatures(LDesc);
IdxWell++;
}
IdxPlateProg++;
}
WindowProgress.Dispose();
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
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();
}
/// <summary>
/// Perform an EM clustering on each plate independantely
/// </summary>
/// <param name="CurrentPlateToProcess">the plate to process</param>
/// <param name="ClassNumber">Number of class</param>
private void ClusteringEMSinglePlate(cPlate CurrentPlateToProcess, int ClassNumber, FormForEMInfo WindowEMinfo)
{
weka.core.Instances Ninsts = CurrentPlateToProcess.CreateInstancesWithoutClass();// CreateInstanceWithoutClass(CurrentTable);
if (Ninsts.numInstances() == 0)
{
MessageBox.Show("No active wells !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
weka.clusterers.EM EMCluster = new EM();
EMCluster.setNumClusters(ClassNumber);
EMCluster.setMaxIterations((int)WindowEMinfo.numericUpDownMaxIterations.Value);
EMCluster.setMinStdDev((double)WindowEMinfo.numericUpDownMinStdev.Value);
EMCluster.setSeed((int)WindowEMinfo.numericUpDownSeedNumber.Value);
EMCluster.buildClusterer(Ninsts);
EMCluster.getClusterModelsNumericAtts();
if (EMCluster.numberOfClusters() > GlobalInfo.GetNumberofDefinedClass())
{
richTextBoxInfoClustering.AppendText("\n Plate " + CurrentPlateToProcess.Name + ", cluster Number: more than " + GlobalInfo.GetNumberofDefinedClass() + ", clustering not operated.\n");
return;
}
else
richTextBoxInfoClustering.AppendText("\n" + CurrentPlateToProcess.Name + ": " + EMCluster.numberOfClusters() + " cluster(s)");
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(EMCluster);
eval.evaluateClusterer(Ninsts);
CurrentPlateToProcess.AssignClass(eval.getClusterAssignments());
}
public void SetInputData(cPlate Input)
{
this.Input = Input;
}
/// <summary>
/// K-Mean for Systematic error Identification
/// </summary>
/// <param name="Classes"></param>
/// <param name="PlateToProcess"></param>
/// <param name="Desc"></param>
/// <returns></returns>
private bool KMeans(int Classes, cPlate PlateToProcess, int Desc)
{
int NumWell = PlateToProcess.GetNumberOfActiveWells();
int Numdesc = cGlobalInfo.CurrentScreening.GetNumberOfActiveDescriptor();
double[,] DataForKMeans = new double[NumWell, Numdesc];
List<double> CurrentDesc = new List<double>();
double[] NormDesc = null;
for (int IdxValue = 0; IdxValue < cGlobalInfo.CurrentScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < cGlobalInfo.CurrentScreening.Rows; IdxValue0++)
{
cWell TmpWell = PlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
CurrentDesc.Add(TmpWell.ListSignatures[Desc].GetValue());
}
if (CurrentDesc.Count == 0) return false;
NormDesc = MeanCenteringStdStandarization(CurrentDesc.ToArray());
for (int row = 0; row < NumWell; row++)
DataForKMeans[row, 0] = NormDesc[row];
int Info;
double[,] CenterPos;
int[] ClusterIndx;
try
{
alglib.kmeansgenerate(DataForKMeans, NumWell, Numdesc, Classes, 10, out Info, out CenterPos, out ClusterIndx);
int Idx = 0;
for (int IdxValue = 0; IdxValue < cGlobalInfo.CurrentScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < cGlobalInfo.CurrentScreening.Rows; IdxValue0++)
{
cWell TmpWell = PlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
{
if (ClusterIndx[Idx] == -1)
TmpWell.SetAsNoneSelected();
else
TmpWell.SetClass(ClusterIndx[Idx]);
Idx++;
}
}
}
catch
{
MessageBox.Show("Check the data validity", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return false;
}
return true;
}
public FormToDisplayDistanceMap(cPlate CurrentPlate, cScreening CompleteScreening)
{
this.CurrentScreening = CompleteScreening;
this.LUT = this.CurrentScreening.GlobalInfo.LUTs.LUT_FIRE;
this.AssociatedPlate = CurrentPlate;
bool ResMiss = false;
//this.MouseDoubleClick += new MouseEventHandler(this.FormToDisplayPlate_MouseDoubleClick);
this.MouseClick += new MouseEventHandler(this.FormToDisplayDistanceMap_MouseClick);
ValuesMatrix = new double[CurrentPlate.ListActiveWells.Count][];
for (int i = 0; i < ValuesMatrix.Length; i++)
ValuesMatrix[i] = new double[CurrentPlate.ListActiveWells.Count];
RecomputeDistances(eDistances.EUCLIDEAN);
this.SetNewCellSize(2);
}
public FormToDisplayPlate(cPlate PlateToDisplay, cScreening CompleteScreening)
{
//this.BorderStyle = System.Windows.Forms.BorderStyle.Fixed3D;
// this.WindowToDisplayEntireScreening = WindowToDisplayEntireScreening;
this.PlateToDisplay = PlateToDisplay;
this.CompleteScreening = CompleteScreening;
this.CurrentScreening = CompleteScreening;
this.LUT = this.CurrentScreening.GlobalInfo.LUT;
this.AssociatedPlate = PlateToDisplay;
bool ResMiss = false;
this.MouseDoubleClick += new MouseEventHandler(this.FormToDisplayPlate_MouseDoubleClick);
this.MouseClick += new MouseEventHandler(this.FormToDisplayPlate_MouseClick);
ValuesMatrix = PlateToDisplay.GetAverageValueDescTable1(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, out ResMiss);
System.Windows.Forms.ToolTip ToolTip = new System.Windows.Forms.ToolTip();
ToolTip.SetToolTip(this, PlateToDisplay.Name);
for (int j = 0; j < ValuesMatrix.Length; j++)
for (int i = 0; i < ValuesMatrix[0].Length; i++)
{
if(double.IsNaN(ValuesMatrix[j][i])) continue;
if (ValuesMatrix[j][i] > Max)
Max = ValuesMatrix[j][i];
if (ValuesMatrix[j][i] < Min)
Min = ValuesMatrix[j][i];
}
this.SetNewCellSize(5);
//DisplayMatrix();
// this.Update();
}
public void RemovePlate(cPlate PlateToRemove)
{
for (int i = 0; i < PanelList.Count; i++)
{
if (PanelList[i].AssociatedPlate == PlateToRemove)
{
PanelList.RemoveAt(i);
RefreshDisplay(false);
break;
}
}
}
private Microsoft.Msagl.Drawing.Graph DisplayTheGraph(cPlate PlateForTree)
{
FormForClassificationTree WindowForTree = new FormForClassificationTree();
WindowForTree.Text = PlateForTree.GetName();
string StringForTree = PlateForTree.GetInfoClassif().StringForTree;
if ((StringForTree == null) || (StringForTree.Length == 0))
return null;
WindowForTree.richTextBoxConsoleForClassification.Clear();
WindowForTree.richTextBoxConsoleForClassification.AppendText(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().GetInfoClassif().StringForQuality);
WindowForTree.richTextBoxConsoleForClassification.AppendText(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().GetInfoClassif().ConfusionMatrix);
return ComputeAndDisplayGraph(StringForTree.Remove(StringForTree.Length - 3, 3), false);
}
private cExtendedTable GenerateArtifactMessage(cExtendedTable TmpTable, cPlate PlateToProcess)
{
cLinearize Lin = new cLinearize();
Lin.SetInputData(TmpTable);
Lin.Run();
cExtendedTable LINTable = Lin.GetOutPut();
cClustering Cluster = new cClustering();
Cluster.SetInputData(LINTable);
Cluster.ParamAlgoForClustering = this.ParamAlgoForClustering;
if (Cluster.Run().IsSucceed == false) return null;
this.ClusteredTable = Cluster.GetOutPut();
// now clustering
//if (!KMeans((int)cGlobalInfo.OptionsWindow.numericUpDownSystErrorIdentKMeansClasses.Value, PlateToProcess, CurrentDescSel))
//{
// List<string> ListMessageError = new List<string>();
// ListMessageError.Add("K-Means Error");
// return ListMessageError;
//}
//// and finally classification
// return this.ComputePlateBasedClassification(MinObjectsNumber);
//}
cExtendedTable ET = PlateToProcess.ListWells.GetPositionRelatedSignatures();
ET.Add(this.ClusteredTable[this.ClusteredTable.Count - 1]);
weka.core.Instances insts = ET.CreateWekaInstancesWithClasses(); //CurrentPlateToProcess.CreateInstancesWithClassesWithPlateBasedDescriptor(Classes);
weka.classifiers.trees.J48 ClassificationModel = new weka.classifiers.trees.J48();
ClassificationModel.setMinNumObj(MinObjectsNumber);
weka.core.Instances train = new weka.core.Instances(insts, 0, insts.numInstances());
ClassificationModel.buildClassifier(train);
string DotString = ClassificationModel.graph().Remove(0, ClassificationModel.graph().IndexOf("{") + 2);
int DotLenght = DotString.Length;
string NewDotString = DotString.Remove(DotLenght - 3, 3);
// display the tree is requested
//cDisplayTree DT = new cDisplayTree();
//DT.SetInputData(NewDotString);
//DT.Run();
cExtendedTable ToReturn = new cExtendedTable(4, 1, 0);
ToReturn.ListRowNames = new List<string>();
ToReturn.ListTags = new List<object>();
int CurrentPos = 0;
int NextReturnPos = CurrentPos;
List<int> ListNodeId = new List<int>();
string TmpDotString = NewDotString;
int TmpClass = 0;
string ErrorString = "";
int ErrorMessage = 0;
ToReturn[0].Name = "Edge artifact"; // edge
ToReturn[1].Name = "Column artifact"; // col
ToReturn[2].Name = "Row artifact"; // row
ToReturn[3].Name = "Bowl artifact"; // bowl
#region build message
while (NextReturnPos != -1)
{
int NextBracket = NewDotString.IndexOf("[");
string StringToProcess = NewDotString.Remove(NextBracket - 1);
string StringToProcess1 = StringToProcess.Remove(0, 1);
if (StringToProcess1.Contains("N") == false)
{
int Id = Convert.ToInt32(StringToProcess1);
int LabelPos = NewDotString.IndexOf("label=\"");
string LabelString = NewDotString.Remove(0, LabelPos + 7);
LabelPos = LabelString.IndexOf("\"");
string FinalLabel = LabelString.Remove(LabelPos);
// if (TmpClass < Classes)
{
if ((FinalLabel == "Dist_To_Border") || (FinalLabel == "Col_Pos") || (FinalLabel == "Row_Pos") || (FinalLabel == "Dist_To_Center"))
{
if ((FinalLabel == "Dist_To_Border") && (!ErrorString.Contains(" an edge effect")) && (!ErrorString.Contains(" a bowl effect")) && (ErrorMessage < 2))
{
if (TmpClass > 0) ErrorString += " combined with";
ErrorString += " an " + cGlobalInfo.ListArtifacts[0];
ErrorMessage++;
ToReturn[0][0] = 1;
}
else if ((FinalLabel == "Col_Pos") && (!ErrorString.Contains(" a column artifact")) && (ErrorMessage < 2))
{
if (TmpClass > 0) ErrorString += " combined with";
ErrorString += " a " + cGlobalInfo.ListArtifacts[1];
ErrorMessage++;
ToReturn[1][0] = 1;
}
else if ((FinalLabel == "Row_Pos") && (!ErrorString.Contains(" a row artifact")) && (ErrorMessage < 2))
{
if (TmpClass > 0) ErrorString += " combined with";
ErrorString += " a " + cGlobalInfo.ListArtifacts[2];
ErrorMessage++;
ToReturn[2][0] = 1;
}
else if ((FinalLabel == "Dist_To_Center") && (!ErrorString.Contains(" a bowl effect")) && (!ErrorString.Contains(" an edge effect")) && (ErrorMessage < 2))
{
if (TmpClass > 0) ErrorString += " combined with";
ErrorString += " a " + cGlobalInfo.ListArtifacts[3];
ErrorMessage++;
ToReturn[3][0] = 1;
}
TmpClass++;
}
}
}
NextReturnPos = NewDotString.IndexOf("\n");
if (NextReturnPos != -1)
{
string TmpString = NewDotString.Remove(0, NextReturnPos + 1);
NewDotString = TmpString;
}
}
if (TmpClass == 0)
{
string NoError = "No systematic error detected !";
ToReturn.ListTags.Add(NoError);
//ToReturn.Add(NoError);
return ToReturn;
}
string FinalString = "You have a systematic error !\nThis is " + ErrorString;
NewDotString = TmpDotString;
NextReturnPos = 0;
while (NextReturnPos != -1)
{
int NextBracket = NewDotString.IndexOf("[");
string StringToProcess = NewDotString.Remove(NextBracket - 1);
string StringToProcess1 = StringToProcess.Remove(0, 1);
if (StringToProcess1.Contains("N"))
{
//// this is an edge
string stringNodeIdxStart = StringToProcess1.Remove(StringToProcess1.IndexOf("-"));
int NodeIdxStart = Convert.ToInt32(stringNodeIdxStart);
string stringNodeIdxEnd = StringToProcess1.Remove(0, StringToProcess1.IndexOf("N") + 1);
int NodeIdxSEnd = Convert.ToInt32(stringNodeIdxEnd);
int LabelPos = NewDotString.IndexOf("label=");
LabelPos += 7;
string CurrLabelString = NewDotString.Remove(0, LabelPos);
}
NextReturnPos = NewDotString.IndexOf("\n");
if (NextReturnPos != -1)
{
string TmpString = NewDotString.Remove(0, NextReturnPos + 1);
NewDotString = TmpString;
}
}
ToReturn.ListTags.Add(FinalString + ".");
#endregion
return ToReturn;
}
private void createAveragePlateToolStripMenuItem_Click(object sender, EventArgs e)
{
FormForPlateAveraging FFPA = new FormForPlateAveraging();
PanelForPlatesSelection PlatesSelectionPanel = new PanelForPlatesSelection(true, null, true);
PlatesSelectionPanel.Height = FFPA.panelForPlateList.Height;
FFPA.panelForPlateList.Controls.Add(PlatesSelectionPanel);
if (FFPA.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
cListPlates LP = PlatesSelectionPanel.GetListSelectedPlates();
cPlate NewPlate = new cPlate("Average Plate", cGlobalInfo.CurrentScreening);
cWell TmpWell;
#region QC report
cExtendedList TmpReportForQuality = new cExtendedList("Weight");
TmpReportForQuality.ListTags = new List<object>();
cExtendedTable TableForQCReport = new cExtendedTable(TmpReportForQuality);
TableForQCReport.ListRowNames = new List<string>();
TableForQCReport.ListTags = new List<object>();
foreach (cPlate TmpPlate in LP)
{
object QualityValue = TmpPlate.ListProperties.FindValueByName("Quality");
if ((QualityValue != null) && (FFPA.checkBoxWeightedSum.Checked))
TableForQCReport[0].Add((double)QualityValue);
else
{
this.richTextBoxConsole.AppendText(TmpPlate.GetName() + " - Quality is NULL. Weight set to 1.\n");
TableForQCReport[0].Add(1);
}
TableForQCReport.ListRowNames.Add(TmpPlate.GetName());
TableForQCReport.ListTags.Add(TmpPlate);
TableForQCReport[0].ListTags.Add(TmpPlate);
}
cDisplayExtendedTable DET = new cDisplayExtendedTable();
DET.SetInputData(TableForQCReport);
DET.Title = "QC report";
TableForQCReport.Name = "QC report";
DET.Run();
#endregion
for (int X = 0; X < cGlobalInfo.CurrentScreening.Columns; X++)
for (int Y = 0; Y < cGlobalInfo.CurrentScreening.Rows; Y++)
{
cListSignature LDesc = new cListSignature();
for (int i = 0; i < cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
double Value = 0;
double NormFactor = 0;
foreach (cPlate TmpPlate in LP)
{
double Weight = 1;
object QualityValue = TmpPlate.ListProperties.FindValueByName("Quality");
if ((QualityValue != null) && (FFPA.checkBoxWeightedSum.Checked))
Weight = (double)QualityValue;
NormFactor += Weight;
TmpWell = TmpPlate.GetWell(X, Y, false);
if (TmpWell != null)
{
Value += Weight * TmpWell.ListSignatures[i].GetValue();
}
}
if (NormFactor > 0)
{
cSignature Desc = new cSignature(Value / NormFactor, cGlobalInfo.CurrentScreening.ListDescriptors[i], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc);
}
}
cWell NewWell = new cWell(LDesc, X + 1, Y + 1, cGlobalInfo.CurrentScreening, NewPlate);
NewWell.SetCpdName("Average Well [" + (X + 1) + ":" + (Y + 1) + "]");
NewPlate.AddWell(NewWell);
}
cGlobalInfo.CurrentScreening.AddPlate(NewPlate);
cGlobalInfo.CurrentScreening.ListPlatesActive.Add(NewPlate);
toolStripcomboBoxPlateList.Items.Add(NewPlate.GetName());
cGlobalInfo.CurrentScreening.ListPlatesActive[cGlobalInfo.CurrentScreening.ListPlatesActive.Count - 1].UpDataMinMax();
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), true);
}
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;
}
/// <summary>
/// Perform an Hierarchical clustering on each plate independantely
/// </summary>
/// <param name="CurrentPlateToProcess">the plate to process</param>
/// <param name="ClassNumber">Number of class</param>
private void ClusteringHierarchicalSinglePlate(cPlate CurrentPlateToProcess, int ClassNumber)
{
weka.core.Instances Ninsts = CurrentPlateToProcess.CreateInstancesWithoutClass();
weka.clusterers.HierarchicalClusterer HClusterer = new HierarchicalClusterer();
//string OptionDistance = " -A \"weka.core.";
string OptionDistance = " -A \"";
switch (cGlobalInfo.OptionsWindow.comboBoxHierarchicalDistance.SelectedIndex)
{
case 0:
OptionDistance += "EuclideanDistance";
break;
case 1:
OptionDistance += "ManhattanDistance";
break;
case 2:
OptionDistance += "ChebyshevDistance";
break;
default:
break;
}
OptionDistance += " -R first-last\"";
string[] TAGS_LINK_TYPE = { "SINGLE", "COMPLETE", "AVERAGE", "MEAN", "CENTROID", "WARD", "ADJCOMPLETE" };
string WekaOption = "-L " + TAGS_LINK_TYPE[cGlobalInfo.OptionsWindow.comboBoxHierarchicalLinkType.SelectedIndex];// + OptionDistance;
HClusterer.setOptions(weka.core.Utils.splitOptions(WekaOption));
//EuclideanDistance2 Dist2 = new EuclideanDistance2();
//HClusterer.setDistanceFunction(Dist2);
HClusterer.setNumClusters(ClassNumber);
HClusterer.buildClusterer(Ninsts);
richTextBoxInfoClustering.AppendText("\n" + CurrentPlateToProcess.GetName() + ": " + HClusterer.numberOfClusters() + " cluster(s)");
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(HClusterer);
eval.evaluateClusterer(Ninsts);
CurrentPlateToProcess.AssignClass(eval.getClusterAssignments());
}
/// <summary>
/// Perform an EM clustering on each plate independantely
/// </summary>
/// <param name="CurrentPlateToProcess">the plate to process</param>
/// <param name="ClassNumber">Number of class</param>
private void ClusteringEMSinglePlate(cPlate CurrentPlateToProcess, int ClassNumber)
{
weka.core.Instances Ninsts = CurrentPlateToProcess.CreateInstancesWithoutClass();// CreateInstanceWithoutClass(CurrentTable);
weka.clusterers.EM EMCluster = new EM();
EMCluster.setNumClusters(ClassNumber);
EMCluster.buildClusterer(Ninsts);
EMCluster.getClusterModelsNumericAtts();
if (EMCluster.numberOfClusters() > GlobalInfo.GetNumberofDefinedClass())
{
richTextBoxInfoClustering.AppendText("\n Plate " + CurrentPlateToProcess.Name + ", cluster Number: more than " + GlobalInfo.GetNumberofDefinedClass() + ", clustering not operated.\n");
return;
}
else
richTextBoxInfoClustering.AppendText("\n" + CurrentPlateToProcess.Name + ": " + EMCluster.numberOfClusters() + " cluster(s)");
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(EMCluster);
eval.evaluateClusterer(Ninsts);
CurrentPlateToProcess.AssignClass(eval.getClusterAssignments());
}
/// <summary>
/// Perform an EM clustering on each plate independantely
/// </summary>
/// <param name="CurrentPlateToProcess">the plate to process</param>
/// <param name="ClassNumber">Number of class</param>
private void ClusteringEMSinglePlate(cPlate CurrentPlateToProcess, int ClassNumber, FormForEMInfo WindowEMinfo)
{
weka.core.Instances Ninsts = CurrentPlateToProcess.CreateInstancesWithoutClass();// CreateInstanceWithoutClass(CurrentTable);
weka.clusterers.EM EMCluster = new EM();
EMCluster.setNumClusters(ClassNumber);
EMCluster.setMaxIterations((int)WindowEMinfo.numericUpDownMaxIterations.Value);
EMCluster.setMinStdDev((double)WindowEMinfo.numericUpDownMinStdev.Value);
EMCluster.setSeed((int)WindowEMinfo.numericUpDownSeedNumber.Value);
EMCluster.buildClusterer(Ninsts);
EMCluster.getClusterModelsNumericAtts();
if (EMCluster.numberOfClusters() > cGlobalInfo.ListWellClasses.Count)
{
richTextBoxInfoClustering.AppendText("\n Plate " + CurrentPlateToProcess.GetName() + ", cluster Number: more than " + cGlobalInfo.ListWellClasses.Count + ", clustering not operated.\n");
return;
}
else
richTextBoxInfoClustering.AppendText("\n" + CurrentPlateToProcess.GetName() + ": " + EMCluster.numberOfClusters() + " cluster(s)");
ClusterEvaluation eval = new ClusterEvaluation();
eval.setClusterer(EMCluster);
eval.evaluateClusterer(Ninsts);
CurrentPlateToProcess.AssignClass(eval.getClusterAssignments());
}
private List<string> GenerateArtifactMessage(cPlate PlateToProcess, int CurrentDescSel)
{
int NumWell = PlateToProcess.GetNumberOfActiveWells();
List<string> Messages = new List<string>();
// Normality Test
List<double> CurrentDesc = new List<double>();
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = PlateToProcess.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
CurrentDesc.Add(TmpWell.ListDescriptors[CurrentDescSel].GetValue());
}
CurrentDesc.Sort();
if ((std(CurrentDesc.ToArray()) == 0))
{
//Messages.Add(/*PlateToProcess.Name + "\n \n*/"No systematic error detected !");
return null;
}
double Anderson_DarlingValue = Anderson_Darling(CurrentDesc.ToArray());
Messages.Add(string.Format("{0:0.###}", Anderson_DarlingValue));
// now clustering
if (!KMeans((int)GlobalInfo.OptionsWindow.numericUpDownSystErrorIdentKMeansClasses.Value, PlateToProcess, CurrentDescSel))
{
List<string> ListMessageError = new List<string>();
ListMessageError.Add("K-Means Error");
return ListMessageError;
}
// and finally classification
int MinObjectsNumber = (NumWell * (int)GlobalInfo.OptionsWindow.numericUpDownSystemMinWellRatio.Value) / 100;
List<string> ListMessage = ComputePlateBasedClassification((int)GlobalInfo.OptionsWindow.numericUpDownSystErrorIdentKMeansClasses.Value, MinObjectsNumber, PlateToProcess);
for (int i = 0; i < ListMessage.Count; i++)
Messages.Add(ListMessage[i]);
return Messages;
}
private List<string> ComputePlateBasedClassification(int Classes, int MinObjectsNumber, cPlate CurrentPlateToProcess)
{
CurrentPlateToProcess.ComputePlateBasedDescriptors();
weka.core.Instances insts = CurrentPlateToProcess.CreateInstancesWithClassesWithPlateBasedDescriptor(Classes);
weka.classifiers.trees.J48 ClassificationModel = new weka.classifiers.trees.J48();
ClassificationModel.setMinNumObj(MinObjectsNumber);
weka.core.Instances train = new weka.core.Instances(insts, 0, insts.numInstances());
ClassificationModel.buildClassifier(train);
// display the tree
string DotString = ClassificationModel.graph().Remove(0, ClassificationModel.graph().IndexOf("{") + 2);
int DotLenght = DotString.Length;
string NewDotString = DotString.Remove(DotLenght - 3, 3);
ComputeAndDisplayGraph(NewDotString);
return ComputeGraph(NewDotString, Classes);
}
public cWell(string FileName, cScreening screenParent, cPlate CurrentPlate)
{
// 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 (cGlobalInfo.CurrentScreening.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
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(new cDescriptorType(DescName, true, NumValue));
}
line = sr.ReadLine();
}
sr.Close();
}
this.ListSignatures = new cListSignature();
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);
cExtendedList readData = new cExtendedList();
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);
}
cSignature CurrentDesc = new cSignature(readData, cGlobalInfo.CurrentScreening.ListDescriptors[IDxLine].GetBinNumber() - 1, cGlobalInfo.CurrentScreening.ListDescriptors[IDxLine], cGlobalInfo.CurrentScreening);
this.ListSignatures.Add(CurrentDesc);
}
line = sr.ReadLine();
IDxLine++;
}
sr.Close();
// this.ListClass.Add(this.InitialClass);
this.ListProperties = new cListWellProperty(this);
this.ListProperties.UpdateValueByName("Well Class", 2);
// this.CurrentColor = this.cGlobalInfo.ListClasses[ClassForClassif].ColourForDisplay;
return;
}
public cPlateLUTManager(cPlate Sender)
{
this.AssociatedPlate = Sender;
}
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);
}
