public FormForManualClustering(cGlobalInfo GlobalInfo)
{
InitializeComponent();
this.GlobalInfo = GlobalInfo;
WellClassSelectionPanel = new PanelForClassSelection(true, eClassType.WELL);
WellClassSelectionPanel.SelectAll();
WellClassSelectionPanel.Height = tabPageWellClasses.Height;
tabPageWellClasses.Controls.Add(WellClassSelectionPanel);
HitClassPanel = new PanelForClassSelection(false, eClassType.WELL);
HitClassPanel.Height = panelForHitClass.Height;
HitClassPanel.UnSelectAll();
HitClassPanel.Select(1);
panelForHitClass.Controls.Add(HitClassPanel);
NonHitClassPanel = new PanelForClassSelection( false, eClassType.WELL);
NonHitClassPanel.Height = panelForNonHitClass.Height;
NonHitClassPanel.UnSelectAll();
NonHitClassPanel.Select(0);
panelForNonHitClass.Controls.Add(NonHitClassPanel);
PlatesSelectionPanel = new PanelForPlatesSelection(true, null, true);
PlatesSelectionPanel.Height = tabPageWellClasses.Height;
PlatesSelectionPanel.Width = tabPageWellClasses.Width;
TabPagePlates.Controls.Add(PlatesSelectionPanel);
}
public cFeedBackMessage Run()
{
FormForDisplay WindowToDisplay = new FormForDisplay();
WindowToDisplay.Text = "Plates Selection";
WindowToDisplay.FormBorderStyle = FormBorderStyle.Sizable;
PanelForPlatesSelection PlateSelectionPanel = new PanelForPlatesSelection(this.IsCheckBoxes, ListInitialPlates, IsCheckOnlyActive);
PlateSelectionPanel.Height = WindowToDisplay.Height - 70;
PlateSelectionPanel.Width = WindowToDisplay.Width - 30;
// PlateSelectionPanel.SelectAll();
//ClassSelectionPanel.Select(0);
//ClassSelectionPanel.Select(1);
PlateSelectionPanel.Location = new System.Drawing.Point(5, 5);
//PlateSelectionPanel.Width = 300;
//PlateSelectionPanel.Height = PlateSelectionPanel.ListCheckBoxes.Count * 25;
PlateSelectionPanel.BorderStyle = BorderStyle.Fixed3D;
PlateSelectionPanel.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);
// MyPanel.Controls.Add(ClassSelectionPanel);
Button ReturnButton = new Button();
ReturnButton.Text = "Ok";
ReturnButton.Anchor = (System.Windows.Forms.AnchorStyles)(System.Windows.Forms.AnchorStyles.Bottom | System.Windows.Forms.AnchorStyles.Left);
ReturnButton.DialogResult = DialogResult.OK;
ReturnButton.Location = new System.Drawing.Point(PlateSelectionPanel.Location.X, PlateSelectionPanel.Location.Y + PlateSelectionPanel.Height );
WindowToDisplay.Controls.Add(ReturnButton);
WindowToDisplay.Controls.Add(PlateSelectionPanel);
WindowToDisplay.Width = PlateSelectionPanel.Width + 28;
WindowToDisplay.Height = PlateSelectionPanel.Height + ReturnButton.Height + 48;
if (WindowToDisplay.ShowDialog() != System.Windows.Forms.DialogResult.OK)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "Selection aborded !";
return FeedBackMessage;
}
this.ListSelectedPlates = PlateSelectionPanel.GetListSelectedPlates();
if (this.ListSelectedPlates.Count == 0)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No class selected !";
return FeedBackMessage;
}
return FeedBackMessage;
}
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 buttonApply_Click(object sender, EventArgs e)
{
FormForDRCDesignValidation FFDRCVal = new FormForDRCDesignValidation();
PanelForPlatesSelection PanelForPlates = new PanelForPlatesSelection(true, null, false);
PanelForPlates.Width = FFDRCVal.panelForPlatesName.Width;
PanelForPlates.Height = FFDRCVal.panelForPlatesName.Height;
FFDRCVal.panelForPlatesName.Controls.Add(PanelForPlates);
if (!this.radioButtonConcentrationsManual.Checked) FFDRCVal.label.Text = "";
if (FFDRCVal.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
this.Visible = false;
//cScreening CurrentScreen = cGlobalInfo.CurrentScreening;
int IdxGroup = 0;
foreach (cPlate TmpPlate in PanelForPlates.GetListSelectedPlates())
{
TmpPlate.ListDRCRegions = new cListDRCRegion();
int SizeX, SizeY;
if (TemplateRegion.IsConcentrationHorizontal)
{
SizeX = TemplateRegion.NumConcentrations;
SizeY = TemplateRegion.NumReplicate;
}
else
{
SizeX = TemplateRegion.NumReplicate;
SizeY = TemplateRegion.NumConcentrations;
}
int NumRepeatX = (AssociatedPlate.ParentScreening.Columns - (TemplateRegion.PosXMin - 1)) / SizeX;
int NumRepeatY = (AssociatedPlate.ParentScreening.Rows - (TemplateRegion.PosYMin - 1)) / SizeY;
if (!this.radioButtonOrientationColumn.Checked)
{
for (int j = 0; j < NumRepeatY; j++)
for (int i = 0; i < NumRepeatX; i++)
{
cDRC_Region TempRegion = new cDRC_Region(TmpPlate, (int)this.numericUpDownConcentrationNumber.Value, (int)this.numericUpDownReplication.Value, i * SizeX + (TemplateRegion.PosXMin - 1), j * SizeY + (TemplateRegion.PosYMin - 1), true);
TmpPlate.ListDRCRegions.AddNewRegion(TempRegion);
// Update the concentration from the manual entry
for (int Replicate = 0; Replicate < TempRegion.NumReplicate; Replicate++)
{
cWell[] TmpList = TempRegion.GetlistReplicate(Replicate);
for (int IdxConc = 0; IdxConc < TmpList.Length; IdxConc++)
{
if ((this.radioButtonConcentrationsManual.Checked) && (TmpList[IdxConc] != null))
TmpList[IdxConc].ListProperties.UpdateValueByName("Concentration", (double)Convert.ToDouble(dataGridViewForConcentration.Rows[IdxConc].Cells[1].Value.ToString(), CultureInfo.CreateSpecificCulture("en-US")));
if ((FFDRCVal.checkBoxUpdateGroupID.Checked) && (TmpList[IdxConc] != null))
TmpList[IdxConc].ListProperties.UpdateValueByName("Group", (int)IdxGroup);
}
}
IdxGroup++;
}
}
else
{
for (int j = 0; j < NumRepeatY; j++)
for (int i = 0; i < NumRepeatX; i++)
{
cDRC_Region TempRegion = new cDRC_Region(TmpPlate, (int)this.numericUpDownConcentrationNumber.Value, (int)this.numericUpDownReplication.Value, i * SizeX + (TemplateRegion.PosXMin - 1), j * SizeY + (TemplateRegion.PosYMin - 1), false);
TmpPlate.ListDRCRegions.AddNewRegion(TempRegion);
// Update the concentration from the manual entry
// if (this.radioButtonConcentrationsManual.Checked)
{
for (int Replicate = 0; Replicate < TempRegion.NumReplicate; Replicate++)
{
cWell[] TmpList = TempRegion.GetlistReplicate(Replicate);
for (int IdxConc = 0; IdxConc < TmpList.Length; IdxConc++)
{
if ((this.radioButtonConcentrationsManual.Checked) && (TmpList[IdxConc] != null))
TmpList[IdxConc].ListProperties.UpdateValueByName("Concentration", Convert.ToDouble(dataGridViewForConcentration.Rows[IdxConc].Cells[1].Value.ToString()));
if ((FFDRCVal.checkBoxUpdateGroupID.Checked) && (TmpList[IdxConc] != null))
TmpList[IdxConc].ListProperties.UpdateValueByName("Group", (int)IdxGroup);
}
}
}
IdxGroup++;
}
}
}
//cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().Refresh3D(cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx);
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
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();
}