void Process()
{
// here is the core of the meta component ...
// just a list of Component steps
cViewertext VT = new cViewertext();
VT.SetInputData(this.Input);
VT.Run();
cDesignerSinglePanel MyDesigner = new cDesignerSinglePanel();
MyDesigner.SetInputData(VT.GetOutPut());
MyDesigner.Run();
cDisplayToWindow MyDisplay = new cDisplayToWindow();
MyDisplay.SetInputData(MyDesigner.GetOutPut());
MyDisplay.Title = this.Title;
MyDisplay.Run();
MyDisplay.Display();
}
private void PerformTestType(eTestType TestType)
{
#region extract classes of interest
cGUI_ListClasses GUI_ListClasses = new cGUI_ListClasses();
GUI_ListClasses.IsCheckBoxes = !_DescEvolCellByCellItem.Checked;
GUI_ListClasses.IsSelectAll = true;
if (GUI_ListClasses.Run().IsSucceed == false) return;
cExtendedTable ListClassSelected = GUI_ListClasses.GetOutPut();
if (ListClassSelected.Sum() < 1)
{
MessageBox.Show("At least one classe has to be selected.", "Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
#endregion
cDesignerTab DT = new cDesignerTab();
for (int i = 0; i < cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[i].IsActive() == false) continue;
cDesignerSplitter DS = new cDesignerSplitter();
DS.Orientation = Orientation.Vertical;
cViewerTable VTable = new cViewerTable();
cViewertext VT = new cViewertext();
cExtendedTable FinalTable = new cExtendedTable(cGlobalInfo.ListWellClasses.Count, 0, 0);
for (int j = 0; j < cGlobalInfo.ListWellClasses.Count; j++)
{
FinalTable[j].Tag = cGlobalInfo.ListWellClasses[j];
FinalTable[j].Name = cGlobalInfo.ListWellClasses[j].Name;
}
cListWells ListWellsToProcess = new cListWells(null);
cDescriptorType CurrentDesc = cGlobalInfo.CurrentScreening.ListDescriptors[i];
// build the table
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell CurrentWell in CurrentPlate.ListActiveWells)
{
if ((CurrentWell.GetCurrentClassIdx() < 0) || (ListClassSelected[0][CurrentWell.GetCurrentClassIdx()] == 0)) continue;
{
FinalTable[CurrentWell.GetCurrentClassIdx()].Add(CurrentWell.GetAverageValue(CurrentDesc));
ListWellsToProcess.Add(CurrentWell);
}
}
}
cClean C = new cClean();
C.SetInputData(FinalTable);
C.Run();
cExtendedTable NewTable = C.GetOutPut();
cTwoSampleFTest TSFTest = null;
cANOVA Anova = null;
cTwoSampleUnpooledTTest TwoSampleTTest = null;
cStudent_tTest StudentTTest = null;
if (TestType == eTestType.F_TEST)
{
TSFTest = new cTwoSampleFTest();
TSFTest.SetInputData(NewTable);
TSFTest.Run();
VTable.SetInputData(TSFTest.GetOutPut());
VT.SetInputData(TSFTest.GetInfo());
}
else if (TestType == eTestType.ANOVA)
{
Anova = new cANOVA();
Anova.SetInputData(NewTable);
Anova.Run();
VTable.SetInputData(Anova.GetOutPut());
VT.SetInputData(Anova.GetInfo());
}
else if (TestType == eTestType.TWO_SAMPLES_T_TEST)
{
TwoSampleTTest = new cTwoSampleUnpooledTTest();
TwoSampleTTest.SetInputData(NewTable);
TwoSampleTTest.Run();
VTable.SetInputData(TwoSampleTTest.GetOutPut());
VT.SetInputData(TwoSampleTTest.GetInfo());
}
else if (TestType == eTestType.STUDENT_T_TEST)
{
StudentTTest = new cStudent_tTest();
StudentTTest.SetInputData(NewTable);
StudentTTest.Run();
VTable.SetInputData(StudentTTest.GetOutPut());
VT.SetInputData(StudentTTest.GetInfo());
}
VTable.DigitNumber = -1;
VTable.Run();
DS.SetInputData(VTable.GetOutPut());
VT.Run();
DS.SetInputData(VT.GetOutPut());
DS.Run();
DS.Title = cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName();
cDesignerSplitter DSMain = new cDesignerSplitter();
DSMain.Orientation = Orientation.Horizontal;
DSMain.SetInputData(DS.GetOutPut());
// Compute and display associated Stacked histogram
//CDW1.Title = CompleteScreening.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptorIdx].GetName() + " - Stacked Histogram - " + PlateList.Count + " plates";
cExtendedTable TableForHisto = ListWellsToProcess.GetAverageDescriptorValues(i);
TableForHisto.Name = "";
cViewerStackedHistogram CV1 = new cViewerStackedHistogram();
CV1.SetInputData(TableForHisto);
CV1.Chart.LabelAxisX = cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName();
CV1.Chart.IsLegend = true;
CV1.Run();
DSMain.SetInputData(CV1.GetOutPut());
DSMain.Title = cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName();
DSMain.Run();
DT.SetInputData(DSMain.GetOutPut());
}
DT.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(DT.GetOutPut());
DTW.Title = "Classification Significance - " + TestType.ToString();
DTW.Run();
DTW.Display();
}
private void backgroundWorkerForCSVtoDB_RunWorkerCompleted(object sender, RunWorkerCompletedEventArgs e)
{
if (e.Error != null)
{
System.Windows.Forms.MessageBox.Show("Error while processing the data", "Error!", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
else
{
// //FormForPlateDimensions PlateDim = new FormForPlateDimensions();
// //PlateDim.Text = "Load generated screening";
// //PlateDim.checkBoxAddCellNumber.Visible = true;
// //PlateDim.checkBoxIsOmitFirstColumn.Visible = true;
// //PlateDim.labelHisto.Visible = true;
// //PlateDim.numericUpDownHistoSize.Visible = true;
// //if (PlateDim.ShowDialog() != System.Windows.Forms.DialogResult.OK)
// // return;
// // LoadCellByCellDB(PlateDim, this.SelectedPath);
cDesignerSplitter DS = new cDesignerSplitter();
DS.Orientation = Orientation.Vertical;
cViewertext VT = new cViewertext();
VT.SetInputData(this.CompleteReportString);
VT.Run();
cViewerGraph1D VG1 = new cViewerGraph1D();
VG1.Chart.LabelAxisX = "Well Index";
VG1.Chart.LabelAxisY = "Number of objects";
VG1.Chart.IsLine = true;
VG1.Chart.IsZoomableX = true;
VG1.Chart.IsXGrid = true;
VG1.SetInputData(ReportTable);
VG1.Run();
DS.SetInputData(VT.GetOutPut());
DS.SetInputData(VG1.GetOutPut());
DS.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.Title = "CSV->DB report";
DTW.IsModal = false;
DTW.SetInputData(DS.GetOutPut());
DTW.Run();
DTW.Display();
if (MessageBox.Show("Database successfully created.\nDo you want load it?", "Question !", MessageBoxButtons.YesNo, MessageBoxIcon.Question) == System.Windows.Forms.DialogResult.No)
return;
else
cGlobalInfo.WindowHCSAnalyzer.LoadDB(this.SelectedPath, false);
}
}
public cExtendedControl GetOutPut()
{
if ((IsDisplayInfo) && (Sender != null))
{
cDesignerSplitter SplitterForInfo = new cDesignerSplitter();
SplitterForInfo.Orientation = Orientation.Horizontal;
SplitterForInfo.SetInputData(CurrentPanel);
cViewertext VT = new cViewertext();
VT.SetInputData(Sender.GetInfo());
VT.Run();
SplitterForInfo.SetInputData(VT.GetOutPut());
SplitterForInfo.Run();
return SplitterForInfo.GetOutPut();
}
return CurrentPanel;
}
public void PerformClassification()
{
FormForSingleCellClassifOptions FFSC = new FormForSingleCellClassifOptions();
//cGUI_ListClasses GLC = new cGUI_ListClasses();
//GLC.ClassType = eClassType.PHENOTYPE;
//GLC.IsCheckBoxes = true;
//GLC.IsSelectAll = true;
//GLC.Run(GlobalInfo);
PanelForClassSelection PhenotypeSelectionPanel = new PanelForClassSelection( true, eClassType.PHENOTYPE);
PhenotypeSelectionPanel.Height = FFSC.panelPhenoToBeClassified.Height;
FFSC.panelPhenoToBeClassified.Controls.Add(PhenotypeSelectionPanel);
PanelForClassSelection WellClassSelectionPanel = new PanelForClassSelection( true, eClassType.WELL);
WellClassSelectionPanel.Height = FFSC.panelWellToBeClassified.Height;
FFSC.panelWellToBeClassified.Controls.Add(WellClassSelectionPanel);
PanelForPlatesSelection PlatesSelectionPanel = new PanelForPlatesSelection( true, null, true);
PlatesSelectionPanel.Height = FFSC.panelWellToBeClassified.Height;
FFSC.tabPagePlates.Controls.Add(PlatesSelectionPanel);
if (FFSC.ShowDialog() != DialogResult.OK) return;
// ----------------------- Classification ------------------------------
int DescrCount = cGlobalInfo.CurrentScreening.ListDescriptors.Count;
this.UpDateNumberOfCluster();
if (NumberOfClusters == 0)
{
System.Windows.Forms.MessageBox.Show("Number of cluster is null", "Error !", MessageBoxButtons.OK, MessageBoxIcon.Hand);
return;
}
//if (FFSC.checkBoxGenerationRatio.Checked)
//{
// // first we update the descriptor
// for (int i = 0; i < this.NumberOfClusters; i++)
// GlobalInfo.CurrentScreening.ListDescriptors.AddNew(new cDescriptorType("Ratio_" + GlobalInfo.ListCellularPhenotypes[i].Name, true, 1, GlobalInfo));
//}
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
#region Confusion Matrix init
cListExtendedTable LT = new cListExtendedTable();
cExtendedTable ConfusionMatrix = new cExtendedTable(cGlobalInfo.ListCellularPhenotypes.Count, cGlobalInfo.ListCellularPhenotypes.Count, 0);
ConfusionMatrix.Name = "Confusion Matrix (global)";
ConfusionMatrix.ListRowNames = new List<string>();
for (int i = 0; i < cGlobalInfo.ListCellularPhenotypes.Count; i++)
{
ConfusionMatrix.ListRowNames.Add(cGlobalInfo.ListCellularPhenotypes[i].Name + "*");
ConfusionMatrix[i].Name = cGlobalInfo.ListCellularPhenotypes[i].Name;
}
LT.Add(ConfusionMatrix);
for (int i = 0; i < cGlobalInfo.ListWellClasses.Count; i++)
{
cExtendedTable ConfusionMatrixTmp = new cExtendedTable(cGlobalInfo.ListCellularPhenotypes.Count, cGlobalInfo.ListCellularPhenotypes.Count, 0);
ConfusionMatrixTmp.Name = "Confusion Matrix - " + cGlobalInfo.ListWellClasses[i].Name;
ConfusionMatrixTmp.ListRowNames = new List<string>();
for (int j = 0; j < cGlobalInfo.ListCellularPhenotypes.Count; j++)
{
ConfusionMatrixTmp.ListRowNames.Add(cGlobalInfo.ListCellularPhenotypes[j].Name + "*");
ConfusionMatrixTmp[j].Name =cGlobalInfo.ListCellularPhenotypes[j].Name;
}
LT.Add(ConfusionMatrixTmp);
}
#endregion
cListPlates LP = PlatesSelectionPanel.GetListSelectedPlates();
foreach (cPlate CurrentPlateToProcess in LP /*GlobalInfo.CurrentScreening.ListPlatesAvailable*/)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
FastVector attVals = new FastVector();
for (int i = 0; i < this.NumberOfClusters; i++)
attVals.addElement(i.ToString());
cPlate CurrentDispPlate = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate();
foreach (cPlate CurrentPlateToProcess in LP/* GlobalInfo.CurrentScreening.ListPlatesAvailable*/)
{
foreach (cWell TmpWell in CurrentPlateToProcess.ListActiveWells)
{
ProgressWindow.progressBar.Value = IdxProgress++;
if (TmpWell.GetCurrentClassIdx() == -1) continue;
if (WellClassSelectionPanel.ListCheckBoxes[TmpWell.GetCurrentClassIdx()].Checked == false) continue;
DataTable FinalDataTable = new DataTable();
TmpWell.AssociatedPlate.DBConnection = new cDBConnection(TmpWell.AssociatedPlate, TmpWell.SQLTableName);
TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, this.GlobalInfo);
cListSingleBiologicalObjects LSBO = TmpWell.AssociatedPlate.DBConnection.GetBiologicalPhenotypes(TmpWell);
//TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, checkBoxIncludeWellClassAsDesc.Checked, GlobalInfo);
Instances ListInstancesTOClassify = this.CreateInstancesWithoutClass(FinalDataTable);
ListInstancesTOClassify.insertAttributeAt(new weka.core.Attribute("Class", attVals), ListInstancesTOClassify.numAttributes());
ListInstancesTOClassify.setClassIndex(ListInstancesTOClassify.numAttributes() - 1);
cExtendedList ListNewClasses = new cExtendedList();
int NumInstances = ListInstancesTOClassify.numInstances();
for (int i = 0; i < NumInstances; i++)
{
// ClassId contains the new class
Instance CurrentInst = ListInstancesTOClassify.instance(i);
double classId = this.CurrentClassifier.classifyInstance(CurrentInst);
double[] ClassConfidence = this.CurrentClassifier.distributionForInstance(CurrentInst);
LSBO[i].ClassificationConfidence = ClassConfidence[(int)classId];
ListNewClasses.Add(classId);
if (CurrentPlateToProcess == CurrentDispPlate)
{
LT[0][LSBO[i].GetAssociatedPhenotype().Idx][(int)classId]++;
if (TmpWell.GetCurrentClassIdx() >= 0)
LT[TmpWell.GetCurrentClassIdx() + 1][LSBO[i].GetAssociatedPhenotype().Idx][(int)classId]++;
}
}
ProgressWindow.richTextBoxForComment.AppendText(TmpWell.GetShortInfo().Remove(TmpWell.GetShortInfo().Length - 2) + " : " + NumInstances + " objects\n");
ProgressWindow.Refresh();
// ------------- update class within the database -----------------------------
TmpWell.AssociatedPlate.DBConnection.ChangePhenotypeClass(TmpWell, ListNewClasses);
//if (FFSC.checkBoxGenerationRatio.Checked)
//{
// List<double[]> Histo = ListNewClasses.CreateHistogram(0, ListInstancesTOClassify.numClasses(), ListInstancesTOClassify.numClasses());
// cListSignature LDesc = new cListSignature();
// for (int IdxHisto = 0; IdxHisto < Histo[1].Length - 1; IdxHisto++)
// {
// Histo[1][IdxHisto] = (100.0 * Histo[1][IdxHisto]) / (double)ListInstancesTOClassify.numInstances();
// cSignature NewDesc = new cSignature(Histo[1][IdxHisto], GlobalInfo.CurrentScreening.ListDescriptors[IdxHisto + DescrCount], GlobalInfo.CurrentScreening);
// LDesc.Add(NewDesc);
// }
// TmpWell.AddSignatures(LDesc);
//}
TmpWell.AssociatedPlate.DBConnection.CloseConnection();
}
}
#region Display Report
cDesignerSplitter DS = new cDesignerSplitter();
DS.Orientation = Orientation.Vertical;
cViewertext VTEXT = new cViewertext();
VTEXT.SetInputData(ProgressWindow.richTextBoxForComment.Text);
VTEXT.Run();
cDesignerTab DT = new cDesignerTab();
DT.IsMultiline = false;
foreach (var item in LT)
{
cViewerTable VT = new cViewerTable();
VT.SetInputData(item);
VT.DigitNumber = 0;
VT.Run();
DT.SetInputData(VT.GetOutPut());
}
DT.Run();
cExtendedControl TextEC = DT.GetOutPut();
TextEC.Width = 0;
TextEC.Height = 0;
TextEC.Anchor = (System.Windows.Forms.AnchorStyles)(System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom
| System.Windows.Forms.AnchorStyles.Left
| System.Windows.Forms.AnchorStyles.Right);
DS.SetInputData(VTEXT.GetOutPut());
DS.SetInputData(TextEC);
DS.Run();
ProgressWindow.Close();
cDisplayToWindow CDT = new cDisplayToWindow();
CDT.SetInputData(DS.GetOutPut());
CDT.IsModal = true;
CDT.Title = "Phenotypic Classificaton Report";
CDT.Run();
CDT.Display();
#endregion
//if (IsKeepOriginalDesc == System.Windows.Forms.DialogResult.No)
//{
// // int DescNumToRemove = GlobalInfo.CurrentScreen.ListDescriptors.Count -
// for (int IdxDesc = 0; IdxDesc < DescrCount; IdxDesc++)
// GlobalInfo.CurrentScreening.ListDescriptors.RemoveDesc(GlobalInfo.CurrentScreening.ListDescriptors[0], GlobalInfo.CurrentScreening);
//}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
//WindowFormForCellbyCellClassif.Close();
//WindowClusteringInfo.Close();
}
private void ToolStripMenuItem_PlateInfo(object sender, EventArgs e)
{
cDesignerSplitter DSV = new cDesignerSplitter();
DSV.Orientation = Orientation.Vertical;
cViewertext VT = new cViewertext();
string InfoPlate = "NAME: " + this.Name + "\n\n";
InfoPlate += "DIMENSIONS: " + ParentScreening.Columns + " x " + ParentScreening.Rows + " (" + ParentScreening.Rows * ParentScreening.Columns + ")\n\n";
InfoPlate += "WELLS: " + this.ListWells.Count + " (" + this.ListActiveWells.Count + " actives)\n\n";
InfoPlate += "PROPERTIES:\n\n";
foreach (var item in this.ListProperties)
{
InfoPlate += " NAME: " + item.PropertyType.Name + "\n TYPE: " + item.PropertyType.Type + "\n VALUE: ";
object ValueProp = item.GetValue();
if (ValueProp == null)
InfoPlate += "NULL\n";
else
{
//if(ValueProp.GetType()==typeof(double))
InfoPlate += ValueProp.ToString() + "\n";
//else if(ValueProp.GetType()==typeof(string))
}
InfoPlate += " INFO: " + item.Info + "\n\n";
}
VT.SetInputData(InfoPlate);
VT.Run();
DSV.SetInputData(VT.GetOutPut());
DSV.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(VT.GetOutPut());
DTW.Title = this.Name + " (Info)";
DTW.Run();
DTW.Display();
}
private void AssociatedChart_DragDrop(object sender, DragEventArgs e)
{
cListWells List_Wells = (cListWells)e.Data.GetData(typeof(cListWells));
cExtendedTable ET = new cExtendedTable();
ET.Name = "Distance to " + this.GetShortInfo().Remove(this.GetShortInfo().Length - 1);
ET.ListRowNames = new List<string>();
ET.ListTags = new List<object>();
ET.Add(new cExtendedList("Euclidean"));
ET.Add(new cExtendedList("Manhattan"));
ET.Add(new cExtendedList("Vector Cosine"));
ET[0].ListTags = new List<object>();
ET[1].ListTags = new List<object>();
ET[2].ListTags = new List<object>();
string Info = "Distance from:\n" + this.GetShortInfo() + "\nto:\n";
foreach (cWell item in List_Wells)
{
ET.ListRowNames.Add(item.GetShortInfo().Remove(item.GetShortInfo().Length - 1));
ET.ListTags.Add(item);
ET[0].Add(item.DistanceTo(this, eDistances.EUCLIDEAN));
ET[0].ListTags.Add(item);
ET[1].Add(item.DistanceTo(this, eDistances.MANHATTAN));
ET[1].ListTags.Add(item);
ET[2].Add(item.DistanceTo(this, eDistances.VECTOR_COS));
ET[2].ListTags.Add(item);
Info += item.GetShortInfo();
}
cViewerTable VT = new cViewerTable();
VT.SetInputData(ET);
VT.Run();
cDesignerSplitter DS = new cDesignerSplitter();
DS.Orientation = Orientation.Vertical;
cViewertext VText = new cViewertext();
Info += "\nDescriptors:\n\n";
int Idx = 0;
for (int i = 0; i < cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[i].IsActive())
{
Info += (Idx++) + " - " + cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName() + "\n";
}
}
VText.SetInputData(Info);
VText.Run();
DS.SetInputData(VText.GetOutPut());
DS.SetInputData(VT.GetOutPut());
DS.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(DS.GetOutPut());
DTW.Title = ET.Name;
DTW.Run();
DTW.Display();
}