/// <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());
}
/// <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>
/// 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 = cGlobalInfo.CurrentScreening.GetNumberOfActiveDescriptor();
double[,] DataForKMeans = new double[NumWell, Numdesc];
int IdxDesc = 0;
for (int desc = 0; desc < cGlobalInfo.CurrentScreening.ListDescriptors.Count; desc++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[desc].IsActive() == false) continue;
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) 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 < 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
{
richTextBoxInfoClustering.AppendText("\nPlate: " + PlateToProcess.GetName() + " 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 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);
}
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();
}
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);
}
public cWell(cListSignature ListDesc, int Col, int Row, cScreening screenParent, cPlate CurrentPlate)
{
// Parent = screenParent;
this.AssociatedPlate = CurrentPlate;
this.ListSignatures = new cListSignature();
this.ListSignatures = ListDesc;
this.PosX = Col;
this.PosY = Row;
// this.CurrentColor = this.cGlobalInfo.ListClasses[ClassForClassif].ColourForDisplay;
foreach (var item in this.ListSignatures)
item.AssociatedWell = this;
//this.ListClass.Add(this.InitialClass);
this.ListProperties = new cListWellProperty(this);
this.ListProperties.UpdateValueByName("Well Class", 2);
this.ListProperties.UpdateValueByName("Plate Name", CurrentPlate.GetName());
}
public FormToDisplayPlate(cPlate PlateToDisplay)
{
//this.BorderStyle = System.Windows.Forms.BorderStyle.Fixed3D;
// this.WindowToDisplayEntireScreening = WindowToDisplayEntireScreening;
this.PlateToDisplay = PlateToDisplay;
// this.CompleteScreening = CompleteScreening;
// this.CurrentScreening = CompleteScreening;
this.LUT = cGlobalInfo.CurrentPlateLUT;
this.AssociatedPlate = PlateToDisplay;
base.Tag = PlateToDisplay;
bool ResMiss = false;
this.MouseDoubleClick += new MouseEventHandler(this.FormToDisplayPlate_MouseDoubleClick);
this.MouseClick += new MouseEventHandler(this.FormToDisplayPlate_MouseClick);
ValuesMatrix = PlateToDisplay.GetAverageValueDescTable1(cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx, out ResMiss);
System.Windows.Forms.ToolTip ToolTip = new System.Windows.Forms.ToolTip();
ToolTip.SetToolTip(this, PlateToDisplay.GetName() /*+ ". Replicate " + PlateToDisplay.AssociatedReplicateType.Name*/);
ToolTip.Tag = PlateToDisplay;
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();
}
