public cWindowToDisplayHisto(cScreening CompleteScreening0, cExtendedList RawValues0)
{
this.CompleteScreening = CompleteScreening0;
this.parametersToolStripMenuItem.Click += new System.EventHandler(this.parametersToolStripMenuItem_Click);
RequestWindow.label3.Text = "Bin Number";
this.RawValues = RawValues0;
CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
this.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
if(CompleteScreening!=null)
CurrentChartArea.Axes[0].Title = CompleteScreening.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptorIdx].GetName();
CurrentChartArea.Axes[1].Title = "Sum";
CurrentChartArea.AxisX.LabelStyle.Format = "N2";
this.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
if (CompleteScreening != null)
CurrentChartArea.BackColor = Color.White;
this.chartForSimpleForm.ChartAreas[0].CursorX.IsUserEnabled = true;
this.chartForSimpleForm.ChartAreas[0].CursorX.IsUserSelectionEnabled = true;
this.chartForSimpleForm.ChartAreas[0].AxisX.ScaleView.Zoomable = true;
this.chartForSimpleForm.ChartAreas[0].AxisX.ScrollBar.IsPositionedInside = true;
if ((CompleteScreening != null) && (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHistoDisplayStats.Checked))
{
StripLine AverageLine = new StripLine();
AverageLine.BackColor = Color.Black;
AverageLine.IntervalOffset = RawValues.Mean();
AverageLine.StripWidth = double.Epsilon;
CurrentChartArea.AxisX.StripLines.Add(AverageLine);
AverageLine.Text = String.Format("{0:0.###}", AverageLine.IntervalOffset);
StripLine StdLine = new StripLine();
StdLine.BackColor = Color.FromArgb(64, Color.Black);
double Std = RawValues.Std();
StdLine.IntervalOffset = AverageLine.IntervalOffset - 0.5 * Std;
StdLine.StripWidth = Std;
CurrentChartArea.AxisX.StripLines.Add(StdLine);
AverageLine.StripWidth = 0.0001;
}
SerieForHisto = new Series();
SerieForHisto.ShadowOffset = 1;
SerieForHisto.ChartType = SeriesChartType.Column;
if (CompleteScreening != null)
SerieForHisto.Color = cGlobalInfo.ListWellClasses[1].ColourForDisplay;
List<double[]> HistoPos = RawValues.CreateHistogram(this.BinNumber, false);
if (HistoPos.Count == 0) return;
for (int IdxValue = 0; IdxValue < HistoPos[0].Length; IdxValue++)
{
SerieForHisto.Points.AddXY(HistoPos[0][IdxValue], HistoPos[1][IdxValue]);
SerieForHisto.Points[IdxValue].ToolTip = HistoPos[1][IdxValue].ToString();
if (CompleteScreening != null)
{
if (CompleteScreening.SelectedClass == -1)
SerieForHisto.Points[IdxValue].Color = Color.Black;
else
SerieForHisto.Points[IdxValue].Color = cGlobalInfo.ListWellClasses[CompleteScreening.SelectedClass].ColourForDisplay;
}
}
this.chartForSimpleForm.Series.Add(SerieForHisto);
}
public cHisto(cExtendedList OriginalValues, int NumBin)
{
List<double[]> Res= OriginalValues.CreateHistogram(NumBin, false);
ListValuesX = Res[0];
ListValuesY = Res[1];
}
private void DisplayHisto(object sender, EventArgs e)
{
if ((Parent.ListDescriptors == null) || (Parent.ListDescriptors.Count == 0)) return;
cExtendedList Pos = new cExtendedList();
cWell TempWell;
int NumberOfPlates = Parent.GlobalInfo.PlateListWindow.listBoxPlateNameToProcess.Items.Count;
// loop on all the plate
for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
{
cPlate CurrentPlateToProcess = Parent.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());
}
}
}
if (Pos.Count == 0)
{
MessageBox.Show("No well of class " + Parent.SelectedClass + " selected !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
List<double[]> HistoPos = Pos.CreateHistogram((int)Parent.GlobalInfo.OptionsWindow.numericUpDownHistoBin.Value);
if (HistoPos == null) return;
SimpleForm NewWindow = new SimpleForm();
Series SeriesPos = new Series();
SeriesPos.ShadowOffset = 1;
if (HistoPos.Count == 0) return;
for (int IdxValue = 0; IdxValue < HistoPos[0].Length; IdxValue++)
{
SeriesPos.Points.AddXY(HistoPos[0][IdxValue], HistoPos[1][IdxValue]);
SeriesPos.Points[IdxValue].ToolTip = HistoPos[1][IdxValue].ToString();
if (this.ClassForClassif == -1)
SeriesPos.Points[IdxValue].Color = Color.Black;
else
SeriesPos.Points[IdxValue].Color = Parent.GlobalInfo.GetColor(this.ClassForClassif);
}
ChartArea CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
NewWindow.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
CurrentChartArea.Axes[0].Title = Parent.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetName();
CurrentChartArea.Axes[1].Title = "Sum";
CurrentChartArea.AxisX.LabelStyle.Format = "N2";
NewWindow.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
CurrentChartArea.BackGradientStyle = GradientStyle.TopBottom;
CurrentChartArea.BackColor = Parent.GlobalInfo.OptionsWindow.panel1.BackColor;
CurrentChartArea.BackSecondaryColor = Color.White;
SeriesPos.ChartType = SeriesChartType.Column;
// SeriesPos.Color = Parent.GetColor(1);
NewWindow.chartForSimpleForm.Series.Add(SeriesPos);
NewWindow.chartForSimpleForm.ChartAreas[0].CursorX.IsUserEnabled = true;
NewWindow.chartForSimpleForm.ChartAreas[0].CursorX.IsUserSelectionEnabled = true;
NewWindow.chartForSimpleForm.ChartAreas[0].AxisX.ScaleView.Zoomable = true;
NewWindow.chartForSimpleForm.ChartAreas[0].AxisX.ScrollBar.IsPositionedInside = true;
StripLine AverageLine = new StripLine();
AverageLine.BackColor = Color.Red;
AverageLine.IntervalOffset = this.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetValue();
AverageLine.StripWidth = 0.0001;
AverageLine.Text = String.Format("{0:0.###}", this.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetValue());
CurrentChartArea.AxisX.StripLines.Add(AverageLine);
if (Parent.GlobalInfo.OptionsWindow.checkBoxDisplayHistoStats.Checked)
{
StripLine NAverageLine = new StripLine();
NAverageLine.BackColor = Color.Black;
NAverageLine.IntervalOffset = Pos.Mean();
NAverageLine.StripWidth = 0.0001;// double.Epsilon;
CurrentChartArea.AxisX.StripLines.Add(NAverageLine);
NAverageLine.Text = String.Format("{0:0.###}", NAverageLine.IntervalOffset);
StripLine StdLine = new StripLine();
StdLine.BackColor = Color.FromArgb(64, Color.Black);
double Std = Pos.Std();
StdLine.IntervalOffset = NAverageLine.IntervalOffset - 0.5 * Std;
StdLine.StripWidth = Std;
CurrentChartArea.AxisX.StripLines.Add(StdLine);
//NAverageLine.StripWidth = 0.01;
}
Title CurrentTitle = new Title(this.StateForClassif + " - " + Parent.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetName() + " histogram.");
CurrentTitle.Font = new System.Drawing.Font("Arial", 11, FontStyle.Bold);
NewWindow.chartForSimpleForm.Titles.Add(CurrentTitle);
NewWindow.Text = CurrentTitle.Text;
NewWindow.Show();
NewWindow.chartForSimpleForm.Update();
NewWindow.chartForSimpleForm.Show();
NewWindow.Controls.AddRange(new System.Windows.Forms.Control[] { NewWindow.chartForSimpleForm });
return;
}
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();
}
